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Sample records for efficient catalytic rna

  1. Small catalytic RNA: Structure, function and application

    Energy Technology Data Exchange (ETDEWEB)

    Monforte, Joseph Albert [Univ. of California, Berkeley, CA (United States)

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the ``paperclip`` and ``hammerhead`` RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a ``hammerhead,`` to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 121±s are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus_minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  2. Small catalytic RNA: Structure, function and application

    Energy Technology Data Exchange (ETDEWEB)

    Monforte, J.A.

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the paperclip'' and hammerhead'' RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a hammerhead,'' to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  3. Efficient RNA structure comparison algorithms.

    Science.gov (United States)

    Arslan, Abdullah N; Anandan, Jithendar; Fry, Eric; Monschke, Keith; Ganneboina, Nitin; Bowerman, Jason

    2017-12-01

    Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonoverlapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan ). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.

  4. Efficient catalytic combustion in integrated micropellistors

    International Nuclear Information System (INIS)

    Bársony, I; Ádám, M; Fürjes, P; Dücső, Cs; Lucklum, R; Hirschfelder, M; Kulinyi, S

    2009-01-01

    This paper analyses two of the key issues of the development of catalytic combustion-type sensors: the selection and production of active catalytic particles on the micropellistor surface as well as the realization of a reliable thermal conduction between heater element and catalytic surface, for the sensing of temperature increase produced by the combustion. The report also demonstrates that chemical sensor product development by a MEMS process is a continuous struggle for elimination of all uncertainties influencing reliability and sensitivity of the final product

  5. Highly efficient catalytic systems based on Pd-coated microbeads

    Science.gov (United States)

    Lim, Jin Hyun; Cho, Ahyoung; Lee, Seung Hwan; Park, Bumkyo; Kang, Dong Woo; Koo, Chong Min; Yu, Taekyung; Park, Bum Jun

    2018-01-01

    The efficiency of two prototype catalysis systems using palladium (Pd)-coated microparticles was investigated with regard to the recovery and recyclability of the catalytic particles. One such system was the interface-adsorption method, in which polymer particles coated with Pd nanoparticles strongly and irreversibly attach to the oil-water interface. Due to the irreversible adsorption of the catalytic particles to the interface, particle loss was completely prevented while mixing the aqueous solution and while collecting the products. The other system was based on the magnetic field-associated particle recovery method. The use of polymeric microparticles containing Pd nanoparticles and magnetite nanoparticles accelerated the sedimentation of the particles in the aqueous phase by applying a strong magnetic field, consequently suppressing drainage of the particles from the reactor along the product stream. Upon multiple runs of the catalytic reactions, it was found that conversion does not change significantly, demonstrating the excellent recyclability and performance efficiency in the catalytic processes.

  6. Domain motions of Argonaute, the catalytic engine of RNA interference

    Directory of Open Access Journals (Sweden)

    Wall Michael E

    2007-11-01

    Full Text Available Abstract Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. Results The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes – an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different. Conclusion Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

  7. Highly Efficient Catalytic Cyclic Carbonate Formation by Pyridyl Salicylimines.

    Science.gov (United States)

    Subramanian, Saravanan; Park, Joonho; Byun, Jeehye; Jung, Yousung; Yavuz, Cafer T

    2018-03-21

    Cyclic carbonates as industrial commodities offer a viable nonredox carbon dioxide fixation, and suitable heterogeneous catalysts are vital for their widespread implementation. Here, we report a highly efficient heterogeneous catalyst for CO 2 addition to epoxides based on a newly identified active catalytic pocket consisting of pyridine, imine, and phenol moieties. The polymeric, metal-free catalyst derived from this active site converts less-reactive styrene oxide under atmospheric pressure in quantitative yield and selectivity to the corresponding carbonate. The catalyst does not need additives, solvents, metals, or co-catalysts, can be reused at least 10 cycles without the loss of activity, and scaled up easily to a kilogram scale. Density functional theory calculations reveal that the nucleophilicity of pyridine base gets stronger due to the conjugated imines and H-bonding from phenol accelerates the reaction forward by stabilizing the intermediate.

  8. Natural RNA circles function as efficient microRNA sponges

    DEFF Research Database (Denmark)

    Hansen, Thomas Birkballe; Jensen, Trine I; Clausen, Bettina Hjelm

    2013-01-01

    MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called comp......MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so......-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more...... sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA....

  9. DNA/RNA hybrid substrates modulate the catalytic activity of purified AID.

    Science.gov (United States)

    Abdouni, Hala S; King, Justin J; Ghorbani, Atefeh; Fifield, Heather; Berghuis, Lesley; Larijani, Mani

    2018-01-01

    Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids. Here, we examined the binding and catalytic behavior of purified AID on DNA/RNA hybrid substrates bearing either random sequences or GC-rich sequences simulating Ig S regions. If substrates were made up of a random sequence, AID preferred substrates composed entirely of DNA over DNA/RNA hybrids. In contrast, if substrates were composed of S region sequences, AID preferred to mutate DNA/RNA hybrids over substrates composed entirely of DNA. Accordingly, AID exhibited a significantly higher affinity for binding DNA/RNA hybrid substrates composed specifically of S region sequences, than any other substrates composed of DNA. Thus, in the absence of any other cellular processes or factors, AID itself favors binding and mutating DNA/RNA hybrids composed of S region sequences. AID:DNA/RNA complex formation and supporting mutational analyses suggest that recognition of DNA/RNA hybrids is an inherent structural property of AID. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Highly efficient catalytic reductive degradation of various organic ...

    Indian Academy of Sciences (India)

    aDepartment of Applied Sciences (Chemical Science Division), GUIST, Gauhati University, ... Highly improved catalytic reductive degradation of different organic dyes, in the ... was prepared by a facile co-precipitation method using ultra-high dilute aqueous solutions. ...... face chemical-modification for engineering the intrin-.

  11. Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube.

    Science.gov (United States)

    Díaz Arenas, Carolina; Lehman, Niles

    2010-03-23

    During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous. Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen with a catalytic RNA. Extensive genotypic sampling from two replicate lineages was gathered and phylogenetic networks were constructed to elucidate the structure of the evolving RNA populations. A common distribution was found in which a mutant sequence was present at high frequency, surrounded by a cloud of mutant with lower frequencies. This is a typical distribution of quasispecies. Most of the mutants in these clouds were connected by short Hamming distance values, indicating their close relatedness. The quasispecies nature of mutant RNA clouds facilitates the recovery of genotypes under pressure of being removed from the population by random drift. The empirical populations therefore evolved a genotypic resiliency despite a high mutation rate by adopting the characteristics of quasispecies, implying that primordial RNA pools could have used this strategy to avoid extinction.

  12. Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube

    Directory of Open Access Journals (Sweden)

    Lehman Niles

    2010-03-01

    Full Text Available Abstract Background During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous. Results Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen with a catalytic RNA. Extensive genotypic sampling from two replicate lineages was gathered and phylogenetic networks were constructed to elucidate the structure of the evolving RNA populations. A common distribution was found in which a mutant sequence was present at high frequency, surrounded by a cloud of mutant with lower frequencies. This is a typical distribution of quasispecies. Most of the mutants in these clouds were connected by short Hamming distance values, indicating their close relatedness. Conclusions The quasispecies nature of mutant RNA clouds facilitates the recovery of genotypes under pressure of being removed from the population by random drift. The empirical populations therefore evolved a genotypic resiliency despite a high mutation rate by adopting the characteristics of quasispecies, implying that primordial RNA pools could have used this strategy to avoid extinction.

  13. Significant Improvement of Catalytic Efficiencies in Ionic Liquids

    International Nuclear Information System (INIS)

    Song, Choong Eui; Yoon, Mi Young; Choi, Doo Seong

    2005-01-01

    The use of ionic liquids as reaction media can confer many advantages upon catalytic reactions over reactions in organic solvents. In ionic liquids, catalysts having polar or ionic character can easily be immobilized without additional structural modification and thus the ionic solutions containing the catalyst can easily be separated from the reagents and reaction products, and then, be reused. More interestingly, switching from an organic solvent to an ionic liquid often results in a significant improvement in catalytic performance (e.g., rate acceleration, (enantio)selectivity improvement and an increase in catalyst stability). In this review, some recent interesting results which can nicely demonstrate these positive 'ionic liquid effect' on catalysis are discussed

  14. Strategies for Improving siRNA-Induced Gene Silencing Efficiency.

    Science.gov (United States)

    Safari, Fatemeh; Rahmani Barouji, Solmaz; Tamaddon, Ali Mohammad

    2017-12-01

    Purpose: Human telomerase reverse transcriptase (hTERT) plays a crucial role in tumorigenesis and progression of cancers. Gene silencing of hTERT by short interfering RNA (siRNA) is considered as a promising strategy for cancer gene therapy. Various algorithms have been devised for designing a high efficient siRNA which is a significant issue in the clinical usage. Thereby, in the present study, the relation of siRNA designing criteria and the gene silencing efficiency was evaluated. Methods: The siRNA sequences were designed and characterized by using on line soft wares. Cationic co-polymer (polyethylene glycol-g-polyethylene imine (PEG-g-PEI)) was used for the construction of polyelectrolyte complexes (PECs) containing siRNAs. The cellular uptake of the PECs was evaluated. The gene silencing efficiency of different siRNA sequences was investigated and the effect of observing the rational designing on the functionality of siRNAs was assessed. Results: The size of PEG-g-PEI siRNA with N/P (Nitrogen/Phosphate) ratio of 2.5 was 114 ± 0.645 nm. The transfection efficiency of PECs was desirable (95.5% ± 2.4%.). The results of Real-Time PCR showed that main sequence (MS) reduced the hTERT expression up to 90% and control positive sequence (CPS) up to 63%. These findings demonstrated that the accessibility to the target site has priority than the other criteria such as sequence preferences and thermodynamic features. Conclusion: siRNA opens a hopeful window in cancer therapy which provides a convenient and tolerable therapeutic approach. Thereby, using the set of criteria and rational algorithms in the designing of siRNA remarkably affect the gene silencing efficiency.

  15. Surface Catalytic Efficiency of Advanced Carbon Carbon Candidate Thermal Protection Materials for SSTO Vehicles

    Science.gov (United States)

    Stewart, David A.

    1996-01-01

    The catalytic efficiency (atom recombination coefficients) for advanced ceramic thermal protection systems was calculated using arc-jet data. Coefficients for both oxygen and nitrogen atom recombination on the surfaces of these systems were obtained to temperatures of 1650 K. Optical and chemical stability of the candidate systems to the high energy hypersonic flow was also demonstrated during these tests.

  16. An efficient catalytic reductive amination: A facile one-pot access to ...

    Indian Academy of Sciences (India)

    An efficient catalytic reductive amination: A facile one-pot access to ... itors and in the manufacture of detergents and plastics.1 ... ammoniaborane/Ti(OiPr)4,5e ... demonstrated the first method for synthesis of 1,2- ... and column chromatography (Silica gel, n-hexane/ethyl .... supporting information at www.ias.ac.in/chemsci.

  17. Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer.

    Science.gov (United States)

    Mohamed, Mark F; Hollfelder, Florian

    2013-01-01

    The observation that one enzyme can accelerate several chemically distinct reactions was at one time surprising because the enormous efficiency of catalysis was often seen as inextricably linked to specialization for one reaction. Originally underreported, and considered a quirk rather than a fundamental property, enzyme promiscuity is now understood to be important as a springboard for adaptive evolution. Owing to the large number of promiscuous enzymes that have been identified over the last decade, and the increased appreciation for promiscuity's evolutionary importance, the focus of research has shifted to developing a better understanding of the mechanistic basis for promiscuity and the origins of tolerant or restrictive specificity. We review the evidence for widespread crosswise promiscuity amongst enzymes that catalyze phosphoryl transfer, including several members of the alkaline phosphatase superfamily, where large rate accelerations between 10(6) and 10(17) are observed for both native and multiple promiscuous reactions. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Efficient and gentle siRNA delivery by magnetofection

    Science.gov (United States)

    Ensenauer, R; Hartl, D; Vockley, J; Roscher, AA; Fuchs, U

    2015-01-01

    Magnetic force combined with magnetic nanoparticles recently has shown potential for enhancing nucleic acid delivery. Achieving effective siRNA delivery into primary cultured cells is challenging. We compared the utility of magnetofection with lipofection procedures for siRNA delivery to primary and immortalized mammalian fibroblasts. Transfection efficiency and cell viability were analyzed by flow cytometry and effects of gene knockdown were quantified by real-time PCR. Lipofectamine 2000 and magnetofection achieved high transfection efficiencies comparable to similar gene silencing effects of about 80%; the cytotoxic effect of magnetofection, however, was significantly less. Magnetofection is a reliable and gentle alternative method with low cytotoxicity for siRNA delivery into difficult to transfect cells such as mammalian fibroblasts. These features are especially advantageous for functional end point analyses of gene silencing, e.g., on the metabolite level. PMID:20297946

  19. Effect of apolipoprotein B mRNA-editing catalytic polypeptide-like protein-3G in cervical cancer.

    Science.gov (United States)

    Xu, Yanhua; Leng, Junhong; Xue, Fang; Dong, Ruiqian

    2015-01-01

    Cervical cancer is one of the most common gynecologic cancers. The role of apolipoprotein B mRNA-editing catalytic polypeptide-like protein-3G (APCBEC-3G) in cervical cancer has yet to be elucidated. This study intends to explore the effect of APCBEC-3G on cervical cancer cell proliferation and invasion. In vitro, the cervical cancer cell line Hela was transfected by APCBEC-3G plasmid. The mRNA and protein expression levels of APCBEC-3G were detected by Real-time PCR and Western blot, respectively. Cervical cancer cell proliferation was determined by MTT. Transwell assay was applied to measure the effect of APCBEC-3G on cell invasion. APCBEC-3G mRNA and protein increased significantly after transfection (P3G serves as a suppressor of cervical cancer cell proliferation and invasion. Our research provides theoretical basis for further investigation APOBEC-3G effect in cervical cancer occurrence and development.

  20. Iron doped fibrous-structured silica nanospheres as efficient catalyst for catalytic ozonation of sulfamethazine.

    Science.gov (United States)

    Bai, Zhiyong; Wang, Jianlong; Yang, Qi

    2018-04-01

    Sulfonamide antibiotics are ubiquitous pollutants in aquatic environments due to their large production and extensive application. In this paper, the iron doped fibrous-structured silica (KCC-1) nanospheres (Fe-KCC-1) was prepared, characterized, and applied as a catalyst for catalytic ozonation of sulfamethazine (SMT). The effects of ozone dosage, catalyst dosage, and initial concentration of SMT were examined. The experimental results showed that Fe-KCC-1 had large surface area (464.56 m2 g -1 ) and iron particles were well dispersed on the catalyst. The catalyst had high catalytic performance especially for the mineralization of SMT, with mineralization ratio of about 40% in a wide pH range. With addition of Fe-KCC-1, the ozone utilization increased nearly two times than single ozonation. The enhancement of SMT degradation was mainly due to the surface reaction, and the increased mineralization of SMT was due to radical mechanism. Fe-KCC-1 was an efficient catalyst for SMT degradation in catalytic ozonation system.

  1. Catalytic efficiency is a better predictor of arsenic toxicity to soil alkaline phosphatase.

    Science.gov (United States)

    Wang, Ziquan; Tian, Haixia; Lu, Guannan; Zhao, Yiming; Yang, Rui; Megharaj, Mallavarapu; He, Wenxiang

    2018-02-01

    Arsenic (As) is an inhibitor of phosphatase, however, in the complex soil system, the substrate concentration effect and the mechanism of As inhibition of soil alkaline phosphatase (ALP) and its kinetics has not been adequately studied. In this work, we investigated soil ALP activity in response to As pollution at different substrate concentrations in various types of soils and explored the inhibition mechanism using the enzyme kinetics. The results showed that As inhibition of soil ALP activity was substrate concentration-dependent. Increasing substrate concentration decreased inhibition rate, suggesting reduced toxicity. This dependency was due to the competitive inhibition mechanism of As to soil ALP. The kinetic parameters, maximum reaction velocity (V max ) and Michaelis constant (K m ) in unpolluted soils were 0.012-0.267mMh -1 and 1.34-3.79mM respectively. The competitive inhibition constant (K ic ) was 0.17-0.70mM, which was lower than K m , suggesting higher enzyme affinity for As than for substrate. The ecological doses, ED 10 and ED 50 (concentration of As that results in 10% and 50% inhibition on enzyme parameter) for inhibition of catalytic efficiency (V max /K m ) were lower than those for inhibition of enzyme activity at different substrate concentrations. This suggests that the integrated kinetic parameter, catalytic efficiency is substrate concentration independent and more sensitive to As than ALP activity. Thus, catalytic efficiency was proposed as a more reliable indicator than ALP activity for risk assessment of As pollution. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Cache and energy efficient algorithms for Nussinov's RNA Folding.

    Science.gov (United States)

    Zhao, Chunchun; Sahni, Sartaj

    2017-12-06

    An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.

  3. Catalytic mechanism of Sep-tRNA:Cys-tRNA synthase: sulfur transfer is mediated by disulfide and persulfide.

    Science.gov (United States)

    Liu, Yuchen; Dos Santos, Patricia C; Zhu, Xiang; Orlando, Ron; Dean, Dennis R; Söll, Dieter; Yuan, Jing

    2012-02-17

    Sep-tRNA:Cys-tRNA synthase (SepCysS) catalyzes the sulfhydrylation of tRNA-bound O-phosphoserine (Sep) to form cysteinyl-tRNA(Cys) (Cys-tRNA(Cys)) in methanogens that lack the canonical cysteinyl-tRNA synthetase (CysRS). A crystal structure of the Archaeoglobus fulgidus SepCysS apoenzyme provides information on the binding of the pyridoxal phosphate cofactor as well as on amino acid residues that may be involved in substrate binding. However, the mechanism of sulfur transfer to form cysteine was not known. Using an in vivo Escherichia coli complementation assay, we showed that all three highly conserved Cys residues in SepCysS (Cys(64), Cys(67), and Cys(272) in the Methanocaldococcus jannaschii enzyme) are essential for the sulfhydrylation reaction in vivo. Biochemical and mass spectrometric analysis demonstrated that Cys(64) and Cys(67) form a disulfide linkage and carry a sulfane sulfur in a portion of the enzyme. These results suggest that a persulfide group (containing a sulfane sulfur) is the proximal sulfur donor for cysteine biosynthesis. The presence of Cys(272) increased the amount of sulfane sulfur in SepCysS by 3-fold, suggesting that this Cys residue facilitates the generation of the persulfide group. Based upon these findings, we propose for SepCysS a sulfur relay mechanism that recruits both disulfide and persulfide intermediates.

  4. Upward Trend in Catalytic Efficiency of Rare-Earth Triflate Catalysts in Friedel-Crafts Aromatic Sulfonylation Reactions

    DEFF Research Database (Denmark)

    Duus, Fritz; Le, Thach Ngoc; Nguyen, Vo Thu An

    2014-01-01

    A series of 14 lanthanide (Ln) triflates were investigated as sustainable catalysts for aromatic sulfonylation reactions under microwave irradiation. The catalytic efficiency of the early triflates La(OTf)3–Eu(OTf)3 is good for long irradiation times. For the later lanthanides, yields reaching over...... 90 % were achieved for short irradiation periods. This was the case especially for Tm(OTf)3, Yb(OTf)3, and Lu(OTf)3, of which Yb(OTf)3 was the most efficient. The upward trend in catalytic efficiency therefore correlates with the lanthanide sequence in the periodic table. The results can be explained...

  5. Catalytic mechanism and inhibition of tRNA (Uracil-5-)methyltransferase: evidence for covalent catalysis

    International Nuclear Information System (INIS)

    Santi, D.V.; Hardy, L.W.

    1987-01-01

    tRNA (Ura-5-) methyltransferase catalyzes the transfer of a methyl group from S-adenosylmethionine (AdoMet) to the 5-carbon of a specific Urd residue in tRNA. This results in stoichiometric release of tritium from [5- 3 H] Urd-labeled substrate tRNA isolated from methyltransferase-deficient Escherichia coli. The enzyme also catalyzes an AdoMet-independent exchange reaction between [5- 3 H]-Urd-labeled substrate tRNA and protons of water at a rate that is about 1% that of the normal methylation reaction, but with identical stoichiometry. S-Adenosylhomocysteine inhibits the rate of the exchange reaction by 2-3-fold, whereas an analog having the sulfur of AdoMet replaced by nitrogen accelerates the exchange reaction 9-fold. In the presence (but not absence) of AdoMet, 5-fluorouracil-substituted tRNA (FUra-tRNA) leads to the first-order inactivation of the enzyme. This is accompanied by the formation of a stable covalent complex containing the enzyme, FUra-tRNA, and the methyl group AdoMet. A mechanism for catalysis is proposed that explains both the 5-H exchange reaction and the inhibition by FUra-tRNA: the enzyme forms a covalent Michael adduct with substrate or inhibitor tRNA by attack of a nucleophilic group of the enzyme at carbon 6 of the pyrimidine residue to be modified. As a result, an anion equivalent is generated at carbon 5 that is sufficiently reactive to be methylated by AdoMet. Preliminary experiments and precedents suggest that the nucleophilic catalyst of the enzyme is a thiol group of cysteine. The potent irreversible inhibition by FUra-tRNA suggest that a mechanism for the RNA effects of FUra may also involve irreversible inhibition of RNA-modifying enzymes

  6. Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination.

    Science.gov (United States)

    Marasco, Michelle; Li, Weiyi; Lynch, Michael; Pikaard, Craig S

    2017-11-02

    All eukaryotes have three essential nuclear multisubunit RNA polymerases, abbreviated as Pol I, Pol II and Pol III. Plants are remarkable in having two additional multisubunit RNA polymerases, Pol IV and Pol V, which synthesize noncoding RNAs that coordinate RNA-directed DNA methylation for silencing of transposons and a subset of genes. Based on their subunit compositions, Pols IV and V clearly evolved as specialized forms of Pol II, but their catalytic properties remain undefined. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is considerably more error-prone than Pols II or V, which may be tolerable in its synthesis of short RNAs that serve as precursors for siRNAs targeting non-identical members of transposon families. By contrast, Pol V exhibits high fidelity transcription, similar to Pol II, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci to which siRNA-Argonaute silencing complexes are recruited. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Efficient catalytic cycloalkane oxidation employing a "helmet" phthalocyaninato iron(III) complex.

    Science.gov (United States)

    Brown, Elizabeth S; Robinson, Jerome R; McCoy, Aaron M; McGaff, Robert W

    2011-06-14

    We have examined the catalytic activity of an iron(III) complex bearing the 14,28-[1,3-diiminoisoindolinato]phthalocyaninato (diiPc) ligand in oxidation reactions with three substrates (cyclohexane, cyclooctane, and indan). This modified metallophthalocyaninato complex serves as an efficient and selective catalyst for the oxidation of cyclohexane and cyclooctane, and to a far lesser extent indan. In the oxidations of cyclohexane and cyclooctane, in which hydrogen peroxide is employed as the oxidant under inert atmosphere, we have observed turnover numbers of 100.9 and 122.2 for cyclohexanol and cyclooctanol, respectively. The catalyst shows strong selectivity for alcohol (vs. ketone) formation, with alcohol to ketone (A/K) ratios of 6.7 and 21.0 for the cyclohexane and cyclooctane oxidations, respectively. Overall yields (alcohol + ketone) were 73% for cyclohexane and 92% for cyclooctane, based upon the total hydrogen peroxide added. In the catalytic oxidation of indan under similar conditions, the TON for 1-indanol was 10.1, with a yield of 12% based upon hydrogen peroxide. No 1-indanone was observed in the product mixture.

  8. Theranostic Niosomes for Efficient siRNA/microRNA Delivery and Activatable Near-Infrared Fluorescent Tracking of Stem Cells

    DEFF Research Database (Denmark)

    Yang, Chuanxu; Shan, Gao; Song, Ping

    2018-01-01

    RNA interference (RNAi) mediated gene regulation in stem cells offers great potential in regenerative medicine. In this study, we developed a theranostic platform for efficient delivery of small RNAs (siRNA/miRNA) to human mesenchymal stem cells (hMSCs) to promote differentiation, and meanwhile...... OFF/ON activatable fluorescence upon cellular internalization, resulting in efficient NIR labeling and the capability to dynamically monitor stem cells in mice. In addition, iSPN/siRNA achieved simultaneous long-term cell tracking and in vivo gene silencing after implantation in mice. These results...

  9. Redox status affects the catalytic activity of glutamyl-tRNA synthetase

    DEFF Research Database (Denmark)

    Katz, Assaf; Banerjee, Rajat; de Armas, Merly

    2010-01-01

    Glutamyl-tRNA synthetases (GluRS) provide Glu-tRNA for different processes including protein synthesis, glutamine transamidation and tetrapyrrole biosynthesis. Many organisms contain multiple GluRSs, but whether these duplications solely broaden tRNA specificity or also play additional roles in t...... inactivation by hemin plus hydrogen peroxide. The sensitivity to oxidation of A. ferrooxidans GluRS1 might provide a means to regulate tetrapyrrole and protein biosynthesis in response to extreme changes in both the redox and heme status of the cell via a single enzyme....

  10. Improvement of the catalytic efficiency of a hyperthermophilic xylanase from Bispora sp. MEY-1.

    Directory of Open Access Journals (Sweden)

    Xiaoyu Wang

    Full Text Available Extremophilic xylanases have attracted great scientific and industrial interest. In this study, a GH10 xylanase-encoding gene, Xyl10E, was cloned from Bispora sp. MEY-1 and expressed in Pichia pastoris GS115. Deduced Xyl10E shares the highest identities of 62% and 57% with characterized family GH10 xylanases from Talaromyces leycettanus and Penicillium canescens (structure 4F8X, respectively. Xyl10E was most active at 93 to 95°C and pH 4.0, retained more than 75% or 48% of the initial activity when heated at 80°C or 90°C for 30 min, respectively, and hardly lost activity at pH 1.0 to 7.0, but was completely inhibited by SDS. Two residues, A160 and A161, located on loop 4, were identified to play roles in catalysis. Mutants A160D/E demonstrated higher affinity to substrate with lower Km values, while mutants A161D/E mainly displayed elevated Vmax values. All of these mutants had significantly improved catalytic efficiency. According to the molecular dynamics simulation, the mutation of A160E was able to affect the important substrate binding site Y204 and then improve the substrate affinity, and the mutation of A161D was capable of forming a hydrogen bond with the substrate to promote the substrate binding or accelerate the product release. This study introduces a highly thermophilic fungal xylanase and reveals the importance of loop 4 for catalytic efficiency.

  11. Involvement of the catalytic subunit of protein kinase A and of HA95 in pre-mRNA splicing

    International Nuclear Information System (INIS)

    Kvissel, Anne-Katrine; Orstavik, Sigurd; Eikvar, Sissel; Brede, Gaute; Jahnsen, Tore; Collas, Philippe; Akusjaervi, Goeran; Skalhegg, Bjorn Steen

    2007-01-01

    Protein kinase A (PKA) is a holoenzyme consisting of two catalytic (C) subunits bound to a regulatory (R) subunit dimer. Stimulation by cAMP dissociates the holoenzyme and causes translocation to the nucleus of a fraction of the C subunit. Apart from transcription regulation, little is known about the function of the C subunit in the nucleus. In the present report, we show that both Cα and Cβ are localized to spots in the mammalian nucleus. Double immunofluorescence analysis of splicing factor SC35 with the C subunit indicated that these spots are splicing factor compartments (SFCs). Using the E1A in vivo splicing assay, we found that catalytically active C subunits regulate alternative splicing and phosphorylate several members of the SR-protein family of splicing factors in vitro. Furthermore, nuclear C subunits co-localize with the C subunit-binding protein homologous to AKAP95, HA95. HA95 also regulates E1A alternative splicing in vivo, apparently through its N-terminal domain. Localization of the C subunit to SFCs and the E1A splicing pattern were unaffected by cAMP stimulation. Our findings demonstrate that the nuclear PKA C subunit co-locates with HA95 in SFCs and regulates pre-mRNA splicing, possibly through a cAMP-independent mechanism

  12. Palladium Nanoparticle-Loaded Cellulose Paper: A Highly Efficient, Robust, and Recyclable Self-Assembled Composite Catalytic System.

    Science.gov (United States)

    Zheng, Guangchao; Kaefer, Katharina; Mourdikoudis, Stefanos; Polavarapu, Lakshminarayana; Vaz, Belén; Cartmell, Samantha E; Bouleghlimat, Azzedine; Buurma, Niklaas J; Yate, Luis; de Lera, Ángel R; Liz-Marzán, Luis M; Pastoriza-Santos, Isabel; Pérez-Juste, Jorge

    2015-01-15

    We present a novel strategy based on the immobilization of palladium nanoparticles (Pd NPs) on filter paper for development of a catalytic system with high efficiency and recyclability. Oleylamine-capped Pd nanoparticles, dispersed in an organic solvent, strongly adsorb on cellulose filter paper, which shows a great ability to wick fluids due to its microfiber structure. Strong van der Waals forces and hydrophobic interactions between the particles and the substrate lead to nanoparticle immobilization, with no desorption upon further immersion in any solvent. The prepared Pd NP-loaded paper substrates were tested for several model reactions such as the oxidative homocoupling of arylboronic acids, the Suzuki cross-coupling reaction, and nitro-to-amine reduction, and they display efficient catalytic activity and excellent recyclability and reusability. This approach of using NP-loaded paper substrates as reusable catalysts is expected to open doors for new types of catalytic support for practical applications.

  13. Experimental demonstration of the reverse flow catalytic membrane reactor concept for energy efficient syngas production. Part 2: Model development

    NARCIS (Netherlands)

    Smit, J.; Bekink, G.J.; Sint Annaland, van M.; Kuipers, J.A.M.

    2007-01-01

    In this contribution the technical feasibility of the reverse flow catalytic membrane reactor (RFCMR) concept with porous membranes for energy efficient syngas production is investigated. In earlier work an experimental proof of principle was already provided [Smit, J., Bekink, G.J., van Sint

  14. MysiRNA-designer: a workflow for efficient siRNA design.

    Directory of Open Access Journals (Sweden)

    Mohamed Mysara

    Full Text Available The design of small interfering RNA (siRNA is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.

  15. Enhancement of single guide RNA transcription for efficient CRISPR/Cas-based genomic engineering.

    Science.gov (United States)

    Ui-Tei, Kumiko; Maruyama, Shohei; Nakano, Yuko

    2017-06-01

    Genomic engineering using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein is a promising approach for targeting the genomic DNA of virtually any organism in a sequence-specific manner. Recent remarkable advances in CRISPR/Cas technology have made it a feasible system for use in therapeutic applications and biotechnology. In the CRISPR/Cas system, a guide RNA (gRNA), interacting with the Cas protein, recognizes a genomic region with sequence complementarity, and the double-stranded DNA at the target site is cleaved by the Cas protein. A widely used gRNA is an RNA polymerase III (pol III)-driven single gRNA (sgRNA), which is produced by artificial fusion of CRISPR RNA (crRNA) and trans-activation crRNA (tracrRNA). However, we identified a TTTT stretch, known as a termination signal of RNA pol III, in the scaffold region of the sgRNA. Here, we revealed that sgRNA carrying a TTTT stretch reduces the efficiency of sgRNA transcription due to premature transcriptional termination, and decreases the efficiency of genome editing. Unexpectedly, it was also shown that the premature terminated sgRNA may have an adverse effect of inducing RNA interference. Such disadvantageous effects were avoided by substituting one base in the TTTT stretch.

  16. UV-LEDs Efficiently Inactivate DNA and RNA Coliphages

    Directory of Open Access Journals (Sweden)

    Alyaa M. Zyara

    2017-01-01

    Full Text Available UV-LEDs are a new method of disinfecting drinking water. Some viruses are very resistant to UV and the efficiency of UV-LEDs to disinfect them needs to be studied. Drinking water was disinfected with UV-LEDs after spiking the water with MS2 and four UV- and/or Cl-resistant coliphages belonging to RNA or DNA coliphages isolated from municipal wastewater. UV-LEDs operating at a wavelength of 270 nm for 2 min with 120 mW of irradiation caused 0.93–2.73 Log10-reductions of coliphages tested in a reactor of a 5.2 L volume. Irradiation time of 10 min in the same system increased the Log10-reductions to 4.30–5.16. Traditional mercury UV (Hg-UV lamp at a 254 nm wavelength caused 0.67–4.08 Log10-reductions in 2 min and 4.56–7.21 Log10-reductions in 10 min in 10 mL of water. All coliphages tested except MS2 achieved 4 Log10-reductions with UV-LEDs at a dose that corresponded to 70 mWs/cm2 using Hg-UV. Thus, UV-LEDs are a promising method of disinfecting UV- and/or Cl-resistant viruses.

  17. New Metamaterials with Combined Subnano - and Mesoscale Topology for High-efficiency Catalytic Combustion Chambers of Innovative Gas Turbine Engines

    Science.gov (United States)

    Knysh, Yu A.; Xanthopoulou, G. G.

    2018-01-01

    The object of the study is a catalytic combustion chamber that provides a highly efficient combustion process through the use of effects: heat recovery from combustion, microvortex heat transfer, catalytic reaction and acoustic resonance. High efficiency is provided by a complex of related technologies: technologies for combustion products heat transfer (recuperation) to initial mixture, catalytic processes technology, technology for calculating effective combustion processes based on microvortex matrices, technology for designing metamaterials structures and technology for obtaining the required topology product by laser fusion of metal powder compositions. The mesoscale level structure provides combustion process with the use of a microvortex effect with a high intensity of heat and mass transfer. High surface area (extremely high area-to-volume ratio) created due to nanoscale periodic structure and ensures catalytic reactions efficiency. Produced metamaterial is the first multiscale product of new concept which due to combination of different scale level periodic topologies provides qualitatively new set of product properties. This research is aimed at solving simultaneously two global problems of the present: ensure environmental safety of transport systems and power industry, as well as the economy and rational use of energy resources, providing humanity with energy now and in the foreseeable future.

  18. Fluorine-doped carbon nanotubes as an efficient metal-free catalyst for destruction of organic pollutants in catalytic ozonation.

    Science.gov (United States)

    Wang, Jing; Chen, Shuo; Quan, Xie; Yu, Hongtao

    2018-01-01

    Metal-free carbon materials have been presented to be potential alternatives to metal-based catalysts for heterogeneous catalytic ozonation, yet the catalytic performance still needs to be enhanced. Doping carbon with non-metallic heteroatoms (e.g., N, B, and F) could alter the electronic structure and electrochemical properties of original carbon materials, has been considered to be an effective method for improving the catalytic activity of carbon materials. Herein, fluorine-doped carbon nanotubes (F-CNTs) were synthesized via a facile method and characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Raman spectroscopy. The as-synthesized F-CNTs exhibited notably enhanced catalytic activity towards catalytic ozonation for the degradation of organic pollutants. The oxalic acid removal efficiency of optimized F-CNTs was approximately two times as much as that of pristine CNTs, and even exceeded those of four conventional metal-based catalysts (ZnO, Al 2 O 3 , Fe 2 O 3 , and MnO 2 ). The XPS and Raman studies confirmed that the covalent CF bonds were formed at the sp 3 C sites instead of sp 2 C sites on CNTs, not only resulting in high positive charge density of C atoms adjacent to F atoms, but remaining the delocalized π-system with intact carbon structure of F-CNTs, which then favored the conversion of ozone molecules (O 3 ) into reactive oxygen species (ROS) and contributed to the high oxalic acid removal efficiency. Furthermore, electron spin resonance (ESR) studies revealed that superoxide radicals (O 2 - ) and singlet oxygen ( 1 O 2 ) might be the dominant ROS that responsible for the degradation of oxalic acid in these catalytic systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Small Molecules that Enhance the Catalytic Efficiency of HLA-DM

    International Nuclear Information System (INIS)

    Nicholson, M.; Moradi, B.; Seth, N.; Xing, X.; Cuny, G.; Stein, R.; Wucherpfenning, K.

    2006-01-01

    HLA-DM (DM) plays a critical role in Ag presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Large lateral surfaces involved in the DM:HLA-DR (DR) interaction have been defined, but the mechanism of catalysis is not understood. In this study, we describe four small molecules that accelerate DM-catalyzed peptide exchange. Mechanistic studies demonstrate that these small molecules substantially enhance the catalytic efficiency of DM, indicating that they make the transition state of the DM:DR/peptide complex energetically more favorable. These compounds fall into two functional classes: two compounds are active only in the presence of DM, and binding data for one show a direct interaction with DM. The remaining two compounds have partial activity in the absence of DM, suggesting that they may act at the interface between DM and DR/peptide. A hydrophobic ridge in the DMβ1 domain was implicated in the catalysis of peptide exchange because the activity of three of these enhancers was substantially reduced by point mutations in this area

  20. Malbranchea cinnamomea: A thermophilic fungal source of catalytically efficient lignocellulolytic glycosyl hydrolases and metal dependent enzymes.

    Science.gov (United States)

    Mahajan, Chhavi; Basotra, Neha; Singh, Surender; Di Falco, Marcos; Tsang, Adrian; Chadha, B S

    2016-01-01

    This study reports thermophilic fungus Malbranchea cinnamomea as an important source of lignocellulolytic enzymes. The secretome analysis using LC-MS/MS orbitrap showed that fungus produced a spectrum of glycosyl hydrolases (cellulase/hemicellulase), polysaccharide lyases (PL) and carbohydrate esterases (CE) in addition to cellobiose dehydrogenase (CDH) indicating the presence of functional classical and oxidative cellulolytic mechanisms. The protein fractions in the secretome resolved by ion exchange chromatography were analyzed for ability to hydrolyze alkali treated carrot grass (ATCG) in the presence of Mn(2+)/Cu(2+). This strategy in tandem with peptide mass fingerprinting led to identification of metal dependent protein hydrolases with no apparent hydrolytic activity, however, showed 5.7 folds higher saccharification in presence of Mn(2+). Furthermore, adding different protein fractions to commercial cellulase (Novozymes: Cellic CTec2) resulted in enhanced hydrolysis of ATCG ranging between 1.57 and 3.43 folds indicating the enzymes from M. cinnamomea as catalytically efficient. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Catalytic Efficiency of Basidiomycete Laccases: Redox Potential versus Substrate-Binding Pocket Structure

    Directory of Open Access Journals (Sweden)

    Olga A. Glazunova

    2018-04-01

    Full Text Available Laccases are copper-containing oxidases that catalyze a one-electron abstraction from various phenolic and non-phenolic compounds with concomitant reduction of molecular oxygen to water. It is well-known that laccases from various sources have different substrate specificities, but it is not completely clear what exactly provides these differences. The purpose of this work was to study the features of the substrate specificity of four laccases from basidiomycete fungi Trametes hirsuta, Coriolopsis caperata, Antrodiella faginea, and Steccherinum murashkinskyi, which have different redox potentials of the T1 copper center and a different structure of substrate-binding pockets. Enzyme activity toward 20 monophenolic substances and 4 phenolic dyes was measured spectrophotometrically. The kinetic parameters of oxidation of four lignans and lignan-like substrates were determined by monitoring of the oxygen consumption. For the oxidation of the high redox potential (>700 mV monophenolic substrates and almost all large substrates, such as phenolic dyes and lignans, the redox potential difference between the enzyme and the substrate (ΔE played the defining role. For the low redox potential monophenolic substrates, ΔE did not directly influence the laccase activity. Also, in the special cases, the structure of the large substrates, such as dyes and lignans, as well as some structural features of the laccases (flexibility of the substrate-binding pocket loops and some amino acid residues in the key positions affected the resulting catalytic efficiency.

  2. Characterization of catalytic efficiency parameters of brain cholinesterases in tropical fish.

    Science.gov (United States)

    de Assis, Caio Rodrigo Dias; Linhares, Amanda Guedes; Oliveira, Vagne Melo; França, Renata Cristina Penha; Santos, Juliana Ferreira; Marcuschi, Marina; Carvalho, Elba Verônica Matoso Maciel; Bezerra, Ranilson Souza; Carvalho, Luiz Bezerra

    2014-12-01

    Brain cholinesterases from four fish (Arapaima gigas, Colossoma macropomum, Rachycentron canadum and Oreochromis niloticus) were characterized using specific substrates and selective inhibitors. Parameters of catalytic efficiency such as activation energy (AE), k(cat) and k(cat)/k(m) as well as rate enhancements produced by these enzymes were estimated by a method using crude extracts described here. Despite the BChE-like activity, specific substrate kinetic analysis pointed to the existence of only acetylcholinesterase (AChE) in brain of the species studied. Selective inhibition suggests that C. macropomum brain AChE presents atypical activity regarding its behavior in the presence of selective inhibitors. AE data showed that the enzymes increased the rate of reactions up to 10(12) in relation to the uncatalyzed reactions. Zymograms showed the presence of AChE isoforms with molecular weights ranging from 202 to 299 kDa. Values of k(cat) and k(cat)/k(m) were similar to those found in the literature.

  3. Alterations in Lipoxygenase and Cyclooxygenase-2 Catalytic Activity and mRNA Expression in Prostate Carcinoma

    Directory of Open Access Journals (Sweden)

    Scott B. Shappell

    2001-01-01

    Full Text Available Recent studies in prostate tissues and especially cell lines have suggested roles for arachidonic acid (AA metabolizing enzymes in prostate adenocarcinoma (Pca development or progression. The goal of this study was to more fully characterize lipoxygenase (LOX and cyclooxygenase-2 (COX-2 gene expression and AA metabolism in benign and malignant prostate using snap-frozen tissues obtained intraoperatively and mRNA analyses and enzyme assays. Formation of 15-hydroxyeicosatetraenoic acid (15-HETE was detected in 23/29 benign samples and 15-LOX-2 mRNA was detected in 21/25 benign samples. In pairs of pure benign and Pca from the same patients, 15-HETE production and 15-LOX-2 mRNA were reduced in Pca versus benign in 9/14 (P=.04 and 14/17 (P=.002, respectively. Under the same conditions, neither 5HETE nor 12-HETE formation was detectable in 29 benign and 24 tumor samples; with a more sensitive assay, traces were detected in some samples, but there was no clear association with tumor tissue. COX-2 mRNA was detected by nuclease protection assay in 7/16 benign samples and 5/16 tumors. In benign and tumor pairs from 10 patients, COX-2 was higher in tumor versus benign in only 2, with similar results by in situ hybridization. Paraffin immunoperoxidase for COX2 was performed in whole mount sections from 87 additional radical prostatectomy specimens, with strong expression in ejaculatory duct as a positive control and corroboration with in situ hybridization. No immunostaining was detected in benign prostate or tumor in 45% of cases. Greater immunostaining in tumor versus benign was present in only 17% of cases, and correlated with high tumor grade (Gleason score 8 and 9 vs. 5 to 7. In conclusion, reduced 15-LOX-2 expression and 15-HETE formation is the most characteristic alteration of AA metabolism in Pca. Increased 12-HETE and 5-HETE formation in Pca were not discernible. Increased COX-2 expression is not a typical abnormality in Pca in general, but

  4. Efficient ex vivo delivery of chemically modified messenger RNA using lipofection and magnetofection.

    Science.gov (United States)

    Badieyan, Zohreh Sadat; Pasewald, Tamara; Mykhaylyk, Olga; Rudolph, Carsten; Plank, Christian

    2017-01-22

    Recently, chemically modified mRNA (cmRNA) therapeutics have been the subject of extensive application-oriented research in both academia and industry as a safer alternative for gene and recombinant protein therapies. However, the lack of an efficient delivery system hinders widespread application. Here we used ∼100-nm lipoplexes and magnetic lipoplexes that can protect cmRNA from RNases and efficiently deliver it into muscle and fat tissues as well as to the endothelium of the carotid artery. Establishing magnetofection for ex vivo cmRNA delivery for the first time, we suggest this method for potential enhanced and targeted delivery of cmRNA. This study introduces optimal cmRNA complexes with high ex vivo efficiency as good candidates for further in vivo cmRNA delivery. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Energy Efficient Microlith-Based Catalytic Reactor and Recuperator for Air Quality Control Applications

    Science.gov (United States)

    Vilekar, Saurabh A.; Hawley, Kyle; Junaedi, Christian; Crowder, Bruce; Prada, Julian; Mastanduno, Richard; Perry, Jay L.; Kayatin, Matthew J.

    2017-01-01

    Precision Combustion, Inc. (PCI) and NASA’s Marshall Space Flight Center (MSFC) have been developing, characterizing, and optimizing high temperature catalytic oxidizers (HTCO) based on PCI’s patented Microlith technology to meet the requirements of future extended human spaceflight explorations. Previous efforts focused on integrating PCI’s HTCO unit with a compact, simple recuperative heat exchanger to reduce the overall system size and weight. Significant improvement was demonstrated over traditional approaches of integrating the HTCO with an external recuperative heat exchanger. While the critical target performance metrics were achieved, the thermal effectiveness of PCI’s recuperator remained a potential area of improvement to further reduce the energy requirements of the integrated system. Using the same material combinations and an improved recuperator design, the redesigned prototype has experimentally demonstrated 20 – 30% reduction (flow dependent) in steady state power consumption compared to the earlier prototype without compromising the destruction efficiency of methane and volatile organic compounds (VOCs). Moreover, design modifications and improvements allow our redesigned prototype to be more easily manufactured compared to traditional brazed plate-fin recuperator designs. The redesigned prototype was delivered to MSFC for validation testing. Here, we report and discuss the performance of the improved prototype HTCO unit with a high efficiency recuperative heat exchanger based on testing at PCI and MSFC. The device is expected to provide a reliable and robust means of disposing of trace levels of methane and VOCs by oxidizing them into carbon dioxide and water in order to maintain clean air in enclosed spaces, such as crewed spacecraft cabins.

  6. Iron Phthalocyanine as New Efficient Catalyst for Catalytic Transfer Hydrogenation of Simple Aldehydes and Ketones

    Czech Academy of Sciences Publication Activity Database

    Bata, P.; Notheisz, F.; Klusoň, Petr; Zsigmond, A.

    2015-01-01

    Roč. 29, JAN 2015 (2015), s. 45-49 ISSN 0268-2605 Institutional support: RVO:67985858 Keywords : heterogenized complexes * catalytic transfer hydrogenation * reusable catalyst Subject RIV: CC - Organic Chemistry Impact factor: 2.452, year: 2015

  7. Efficient computation of optimal oligo-RNA binding.

    Science.gov (United States)

    Hodas, Nathan O; Aalberts, Daniel P

    2004-01-01

    We present an algorithm that calculates the optimal binding conformation and free energy of two RNA molecules, one or both oligomeric. This algorithm has applications to modeling DNA microarrays, RNA splice-site recognitions and other antisense problems. Although other recent algorithms perform the same calculation in time proportional to the sum of the lengths cubed, O((N1 + N2)3), our oligomer binding algorithm, called bindigo, scales as the product of the sequence lengths, O(N1*N2). The algorithm performs well in practice with the aid of a heuristic for large asymmetric loops. To demonstrate its speed and utility, we use bindigo to investigate the binding proclivities of U1 snRNA to mRNA donor splice sites.

  8. Kinetic analysis of the effects of target structure on siRNA efficiency

    Science.gov (United States)

    Chen, Jiawen; Zhang, Wenbing

    2012-12-01

    RNAi efficiency for target cleavage and protein expression is related to the target structure. Considering the RNA-induced silencing complex (RISC) as a multiple turnover enzyme, we investigated the effect of target mRNA structure on siRNA efficiency with kinetic analysis. The 4-step model was used to study the target cleavage kinetic process: hybridization nucleation at an accessible target site, RISC-mRNA hybrid elongation along with mRNA target structure melting, target cleavage, and enzyme reactivation. At this model, the terms accounting for the target accessibility, stability, and the seed and the nucleation site effects are all included. The results are in good agreement with that of experiments which show different arguments about the structure effects on siRNA efficiency. It shows that the siRNA efficiency is influenced by the integrated factors of target's accessibility, stability, and the seed effects. To study the off-target effects, a simple model of one siRNA binding to two mRNA targets was designed. By using this model, the possibility for diminishing the off-target effects by the concentration of siRNA was discussed.

  9. Energy Efficient Catalytic Activation of Hydrogen peroxide for Green Chemical Processes: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Terrence J.; Horwitz, Colin

    2004-11-12

    A new, highly energy efficient approach for using catalytic oxidation chemistry in multiple fields of technology has been pursued. The new catalysts, called TAML® activators, catalyze the reactions of hydrogen peroxide and other oxidants for the exceptionally rapid decontamination of noninfectious simulants (B. atrophaeus) of anthrax spores, for the energy efficient decontamination of thiophosphate pesticides, for the facile, low temperature removal of color and organochlorines from pulp and paper mill effluent, for the bleaching of dyes from textile mill effluents, and for the removal of recalcitrant dibenzothiophene compounds from diesel and gasoline fuels. Highlights include the following: 1) A 7-log kill of Bacillus atrophaeus spores has been achieved unambiguously in water under ambient conditions within 15 minutes. 2) The rapid total degradation under ambient conditions of four thiophosphate pesticides and phosphonate degradation intermediates has been achieved on treatment with TAML/peroxide, opening up potential applications of the decontamination system for phosphonate structured chemical warfare agents, for inexpensive, easy to perform degradation of stored and aged pesticide stocks (especially in Africa and Asia), for remediation of polluted sites and water bodies, and for the destruction of chemical warfare agent stockpiles. 3) A mill trial conducted in a Pennsylvanian bleached kraft pulp mill has established that TAML catalyst injected into an alkaline peroxide bleach tower can significantly lower color from the effluent stream promising a new, more cost effective, energy-saving approach for color remediation adding further evidence of the value and diverse engineering capacity of the approach to other field trials conducted on effluent streams as they exit the bleach plant. 4) Dibenzothiophenes (DBTs), including 4,6-dimethyldibenzothiophene, the most recalcitrant sulfur compounds in diesel and gasoline, can be completely removed from model gasoline

  10. Catalytic ozonation of oxalate with a cerium supported palladium oxide: An efficient degradation not relying on hydroxyl radical oxidation

    KAUST Repository

    Zhang, Tao; Li, Weiwei; Croue, Jean-Philippe

    2011-01-01

    The cerium supported palladium oxide (PdO/CeO 2) at a low palladium loading was found very effective in catalytic ozonation of oxalate, a probe compound that is difficult to be efficiently degraded in water with hydroxyl radical oxidation and one of the major byproducts in ozonation of organic matter. The oxalate was degraded into CO 2 during the catalytic ozonation. The molar ratio of oxalate degraded to ozone consumption increased with increasing catalyst dose and decreasing ozone dosage and pH under the conditions of this study. The maximum molar ratio reached around 1, meaning that the catalyst was highly active and selective for oxalate degradation in water. The catalytic ozonation, which showed relatively stable activity, does not promote hydroxyl radical generation from ozone. Analysis with ATR-FTIR and in situ Raman spectroscopy revealed that 1) oxalate was adsorbed on CeO 2 of the catalyst forming surface complexes, and 2) O 3 was adsorbed on PdO of the catalyst and further decomposed to surface atomic oxygen (*O), surface peroxide (*O 2), and O 2 gas in sequence. The results indicate that the high activity of the catalyst is related to the synergetic function of PdO and CeO 2 in that the surface atomic oxygen readily reacts with the surface cerium-oxalate complex. This kind of catalytic ozonation would be potentially effective for the degradation of polar refractory organic pollutants and hydrophilic natural organic matter. © 2011 American Chemical Society.

  11. Catalytic ozonation of oxalate with a cerium supported palladium oxide: An efficient degradation not relying on hydroxyl radical oxidation

    KAUST Repository

    Zhang, Tao

    2011-11-01

    The cerium supported palladium oxide (PdO/CeO 2) at a low palladium loading was found very effective in catalytic ozonation of oxalate, a probe compound that is difficult to be efficiently degraded in water with hydroxyl radical oxidation and one of the major byproducts in ozonation of organic matter. The oxalate was degraded into CO 2 during the catalytic ozonation. The molar ratio of oxalate degraded to ozone consumption increased with increasing catalyst dose and decreasing ozone dosage and pH under the conditions of this study. The maximum molar ratio reached around 1, meaning that the catalyst was highly active and selective for oxalate degradation in water. The catalytic ozonation, which showed relatively stable activity, does not promote hydroxyl radical generation from ozone. Analysis with ATR-FTIR and in situ Raman spectroscopy revealed that 1) oxalate was adsorbed on CeO 2 of the catalyst forming surface complexes, and 2) O 3 was adsorbed on PdO of the catalyst and further decomposed to surface atomic oxygen (*O), surface peroxide (*O 2), and O 2 gas in sequence. The results indicate that the high activity of the catalyst is related to the synergetic function of PdO and CeO 2 in that the surface atomic oxygen readily reacts with the surface cerium-oxalate complex. This kind of catalytic ozonation would be potentially effective for the degradation of polar refractory organic pollutants and hydrophilic natural organic matter. © 2011 American Chemical Society.

  12. Efficient fully controlled up-to-date equipment for catalytic treatment of waste gases

    International Nuclear Information System (INIS)

    Dvorak, Radek; Stulir, Roman; Cagas, Pavel

    2007-01-01

    This paper describes research and development of a new unit for catalytic destruction of waste gases polluted mainly by volatile organic compounds (VOC), halogenated organic compounds (HOC) or carbon monoxide. Novel equipment has considerable advantages compared with commonly used arrangement (combustion chamber (catalytic reactor)-pipeline-heat exchanger). It is very compact and light and has the combustion chamber, catalytic reactor and heat exchanger integrated into one unit. Maximum utilizing heat losses in the combustion chamber and catalytic reactor is achieved. During the development of this unit experience from tests of previously developed equipment used for thermal treatment of waste gases was used, as well as from experimental studies of catalytic disposal of various VOC carried out in the newly built experimental unit. During the development calculation methods were created allowing design modifications of this unit for real industrial applications. The newly developed unit can be used in various branches of industry such as paint shops, refining plants, sewage treatment plants, food processing industry, pharmaceutical industry, but also in companies processing and transporting crude-oil or natural gas, etc

  13. Defect-meditated efficient catalytic activity toward p-nitrophenol reduction: A case study of nitrogen doped calcium niobate system

    International Nuclear Information System (INIS)

    Su, Yiguo; Huang, Shushu; Wang, Tingting; Peng, Liman; Wang, Xiaojing

    2015-01-01

    Graphical abstract: A series of nitrogen doped Ca 2 Nb 2 O 7 was successfully prepared via ion-exchange method, which was found to be an efficient and green noble-metal-free catalyst toward catalytic reduction of p-nitrophenol. - Highlights: • Nitrogen doped Ca 2 Nb 2 O 7 was found to be an efficient and green noble-metal-free catalyst toward catalytic reduction of p-nitrophenol. • Defective nitrogen and oxygen species were found to play synergetic roles in the reduction of p-nitrophenol. • Nitrogen doped Ca 2 Nb 2 O 7 showed photo-synergistic promotion effects toward p-nitrophenol reduction under UV light irradiation. - Abstract: This work reported on the synthesis of a series of nitrogen doped Ca 2 Nb 2 O 7 with tunable nitrogen content that were found to be efficient and green noble-metal-free catalysts toward catalytic reduction of p-nitrophenol. XPS and ESR results indicated that the introduction of nitrogen in Ca 2 Nb 2 O 7 gave rise to a large number of defective nitrogen and oxygen species. Defective nitrogen and oxygen species were found to play synergetic roles in the reduction of p-nitrophenol. The underlying mechanism is completely different from those reported for metallic nanoparticles. Moreover, the more negative conduction band edge potential enabled nitrogen doped Ca 2 Nb 2 O 7 to show photo-synergistic effects that could accelerate the reduction rate toward p-nitrophenol under UV light irradiation. This work may provide a strategy for tuning the catalytic performance by modulating the chemical composition, electronic structure as well as surface defect chemistry

  14. An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

    Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

  15. Efficient siRNA delivery system using carboxilated single-wall carbon nanotubes in cancer treatment.

    Science.gov (United States)

    Neagoe, Ioana Berindan; Braicu, Cornelia; Matea, Cristian; Bele, Constantin; Florin, Graur; Gabriel, Katona; Veronica, Chedea; Irimie, Alexandru

    2012-08-01

    Several functionalized carbon nanotubes have been designed and tested for the purpose of nucleic acid delivery. In this study, the capacity of SWNTC-COOH for siRNA deliverey were investigated delivery in parallel with an efficient commercial system. Hep2G cells were reverse-transfected with 50 nM siRNA (p53 siRNA, TNF-alphasiRNA, VEGFsiRNA) using the siPORT NeoFX (Ambion) transfection agent in paralel with SWNTC-COOH, functionalised with siRNA. The highest level of gene inhibition was observed in the cases treated with p53 siRNA gene; in the case of transfection with siPort, the NeoFX value was 33.8%, while in the case of SWNTC-COOH as delivery system for p53 siRNA was 37.5%. The gene silencing capacity for VEGF was 53.7%, respectively for TNF-alpha 56.7% for siPORT NeoFX delivery systems versus 47.7% (VEGF) and 46.5% (TNF-alpha) for SWNTC-COOH delivery system. SWNTC-COOH we have been showed to have to be an efficient carrier system. The results from the inhibition of gene expresion for both transfection systems were confirmed at protein level. Overall, the lowest mRNA expression was confirmed at protein level, especially in the case of p53 siRNA and TNF-alpha siRNA transfection. Less efficient reduction protein expressions were observed in the case of VEGF siRNA, for both transfection systems at 24 h; only at 48 h, there was a statistically significant reduction of VEGF protein expression. SWCNT-COOH determined an efficient delivery of siRNA. SWNTC-COOH, combined with suitable tumor markers like p53 siRNA, TNFalpha siRNA or VEGF siRNA can be used for the efficient delivery of siRNA.

  16. Highly efficient conversion of terpenoid biomass to jet-fuel range cycloalkanes in a biphasic tandem catalytic process

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaokun [Univ. of Nevada, Reno, NV (United States); Li, Teng [Washington State Univ., Pullman, WA (United States); Tang, Kan [Washington State Univ., Pullman, WA (United States); Zhou, Xinpei [Univ. of Nevada, Reno, NV (United States); Lu, Mi [Univ. of Nevada, Reno, NV (United States); Ounkham, Whalmany L. [Univ. of Nevada, Reno, NV (United States); Spain, Stephen M. [Univ. of Nevada, Reno, NV (United States); Frost, Brian J. [Univ. of Nevada, Reno, NV (United States); Lin, Hongfei [Washington State Univ., Pullman, WA (United States)

    2017-06-12

    The demand for bio-jet fuels to reduce carbon emissions is increasing substantially in the aviation sector, while the scarcity of high-density jet fuel components limits the use of bio-jet fuels in high-performance aircrafts compared with conventional jet fuels. In this paper, we report a novel biphasic tandem catalytic process (biTCP) for synthesizing cycloalkanes from renewable terpenoid biomass, such as 1,8-cineole. Multistep tandem reactions, including C–O ring opening by hydrolysis, dehydration, and hydrogenation, were carried out in the “one-pot” biTCP. 1,8-Cineole was efficiently converted to p-menthane at high yields (>99%) in the biTCP under mild reaction conditions. Finally, the catalytic reaction mechanism is discussed.

  17. High-efficiency plasma catalytic removal of dilute benzene from air

    International Nuclear Information System (INIS)

    Fan, Hong-Yu; Shi, Chuan; Li, Xiao-Song; Zhao, De-Zhi; Xu, Yong; Zhu, Ai-Min

    2009-01-01

    Achieving complete oxidation, good humidity tolerance and low energy cost is the key issue that needs to be addressed in plasma catalytic volatile organic compounds removal from air. For this purpose, Ag/HZSM-5 catalyst-packed dielectric barrier discharge using a cycled system composed of a storage stage and a discharge stage was studied. For dilute benzene removal from simulated air, Ag/HZSM-5 catalysts exhibit not only preferential adsorption of benzene in humid air at the storage stage but also almost complete oxidation of adsorbed benzene at the discharge stage. Five 'storage-discharge' cycles were examined, which suggests that Ag/HZSM-5 catalysts are very stable during the cycled 'storage-discharge' (CSD) plasma catalytic process. High oxidation rate of absorbed benzene as well as low energy cost can be achieved at a moderate discharge power. In an example of the CSD plasma catalytic remedy of simulated air containing 4.7 ppm benzene with 50% RH and 600 ml min -1 flow rate, the energy cost was as low as 3.7 x 10 -3 kWh m -3 air. This extremely low energy cost to remove low-concentration pollutants from air undoubtedly makes the environmental applications of the plasma catalytic technique practical.

  18. Silica Sulphuric Acid as an Efficient Catalyst for the Catalytic and ...

    African Journals Online (AJOL)

    NJD

    presence of a catalytic amount of silica sulphuric acid under micellar media in moderate to good yields. KEYWORDS. Sodium ... Production of aromatic nitro compounds is an important industrial process and involves the unsolved problems of ... V7 and Re9) and titanium and chromium silicates.10 Some of the procedures ...

  19. Influence and efficiency of catalytic stripper in organic carbon removal from laboratory generated soot aerosols

    Science.gov (United States)

    A catalytic stripper (CS) is a device used to remove the semi-volatile, typically organic carbon, fraction by passing raw or diluted exhaust over an oxidation catalyst heated to 300˚C. The oxidation catalyst used in this study is a commercially available diesel oxidation ca...

  20. Efficient algorithms for probing the RNA mutation landscape.

    Directory of Open Access Journals (Sweden)

    Jérôme Waldispühl

    Full Text Available The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented. This broad range of functions is achieved through specific structures that have been (presumably optimized through evolution. State-of-the-art methods, such as McCaskill's algorithm, use a statistical mechanics framework based on the computation of the partition function over the canonical ensemble of all possible secondary structures on a given sequence. Although secondary structure predictions from thermodynamics-based algorithms are not as accurate as methods employing comparative genomics, the former methods are the only available tools to investigate novel RNAs, such as the many RNAs of unknown function recently reported by the ENCODE consortium. In this paper, we generalize the McCaskill partition function algorithm to sum over the grand canonical ensemble of all secondary structures of all mutants of the given sequence. Specifically, our new program, RNAmutants, simultaneously computes for each integer k the minimum free energy structure MFE(k and the partition function Z(k over all secondary structures of all k-point mutants, even allowing the user to specify certain positions required not to mutate and certain positions required to base-pair or remain unpaired. This technically important extension allows us to study the resilience of an RNA molecule to pointwise mutations. By computing the mutation profile of a sequence, a novel graphical representation of the mutational tendency of nucleotide positions, we analyze the deleterious nature of mutating specific nucleotide positions or groups of positions. We have successfully applied RNAmutants to investigate deleterious mutations (mutations that radically modify the secondary structure in the Hepatitis C virus cis-acting replication element and to evaluate the evolutionary pressure applied on different regions of the HIV trans-activation response

  1. Efficient reverse transcription using locked nucleic acid nucleotides towards the evolution of nuclease resistant RNA aptamers

    DEFF Research Database (Denmark)

    Crouzier, Lucile; Dubois, Camille; Edwards, Stacey L

    2012-01-01

    We found that SuperScript® III Reverse Transcriptase is an efficient enzyme for the recognition of LNA nucleotides, making it a prime candidate to be used in de novo selection of LNA containing RNA aptamers....

  2. Nonreplicative RNA Recombination of an Animal Plus-Strand RNA Virus in the Absence of Efficient Translation of Viral Proteins.

    Science.gov (United States)

    Kleine Büning, Maximiliane; Meyer, Denise; Austermann-Busch, Sophia; Roman-Sosa, Gleyder; Rümenapf, Tillmann; Becher, Paul

    2017-04-01

    RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a nonreplicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family Flaviviridae) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region. The emergence of a number of recombinant viruses demonstrated that IRES-mediated translation of viral proteins is dispensable for efficient recombination and suggests that RNA recombination can occur in the absence of viral proteins. Analyses of 58 independently emerged viruses led to the detection of recombinant genomes with duplications, deletions and insertions in the 5' terminal region of the open reading frame, leading to enlarged core fusion proteins detectable by Western blot analysis. This demonstrates a remarkable flexibility of the pestivirus core protein. Further experiments with capped and uncapped genome fragments containing a luciferase gene for monitoring the level of protein translation revealed that even a ∼1,000-fold enhancement of translation of viral proteins did not increase the frequency of RNA recombination. Taken together, this study highlights that nonreplicative RNA recombination does not require translation of viral proteins. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Nonreplicative RNA Recombination of an Animal Plus-Strand RNA Virus in the Absence of Efficient Translation of Viral Proteins

    Science.gov (United States)

    Kleine Büning, Maximiliane; Meyer, Denise; Austermann-Busch, Sophia; Roman-Sosa, Gleyder; Rümenapf, Tillmann

    2017-01-01

    RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a nonreplicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family Flaviviridae) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region. The emergence of a number of recombinant viruses demonstrated that IRES-mediated translation of viral proteins is dispensable for efficient recombination and suggests that RNA recombination can occur in the absence of viral proteins. Analyses of 58 independently emerged viruses led to the detection of recombinant genomes with duplications, deletions and insertions in the 5′ terminal region of the open reading frame, leading to enlarged core fusion proteins detectable by Western blot analysis. This demonstrates a remarkable flexibility of the pestivirus core protein. Further experiments with capped and uncapped genome fragments containing a luciferase gene for monitoring the level of protein translation revealed that even a ∼1,000-fold enhancement of translation of viral proteins did not increase the frequency of RNA recombination. Taken together, this study highlights that nonreplicative RNA recombination does not require translation of viral proteins. PMID:28338950

  4. Efficient catalytic system for the direct transformation of lignocellulosic biomass to furfural and 5-hydroxymethylfurfural.

    Science.gov (United States)

    Zhang, Luxin; Xi, Guoyun; Zhang, Jiaxin; Yu, Hongbing; Wang, Xiaochang

    2017-01-01

    A feasible approach was developed for the co-production of 5-hydroxymethylfurfural (5-HMF) and furfural from corncob via a new porous polytriphenylamine-SO 3 H (SPTPA) solid acid catalyst in lactone solvents. XRD, SEM, XPS, N 2 adsorption-desorption, elemental analysis, TG-DTA, acid-base titration and FTIR spectroscopy techniques were used to characterize the catalyst. This study demonstrates and optimizes the catalytic performance of SPTPA and solvent selection. SPTPA was found to exhibit superior catalytic ability in γ-valerolactone (GVL). Under the optimum reaction conditions, simultaneously encouraging yields of furfural (73.9%) and 5-HMF (32.3%) were achieved at 448K. The main advantages of this process include reasonable yields of both 5-HMF and furfural in the same reaction system, practical simplicity for the raw biomass utilization, and the use of a safe and environmentally benign solvent. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Synthesis of ternary oxide for efficient photo catalytic conversion of CO2

    Science.gov (United States)

    Wan, Lijuan

    2018-01-01

    Zn2GeO4 Nan rods were prepared by solution phase route. The morphology and structure of the as-prepared products were characterized by scanning electron microscopy (SEM) and Bruner-Emmett-Teller (BET) surface area measurements. The results revealed that Zn2GeO4 Nan rods with higher surface area have higher photo catalytic activity in photo reduction of CO2 than Zn2GeO4 prepared through solid-state reaction.

  6. Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.

    Science.gov (United States)

    Will, Sebastian; Jabbari, Hosna

    2016-01-01

    RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by [Formula: see text], but are typically much smaller. The time complexity of RNA folding is reduced from [Formula: see text] to [Formula: see text]; the space complexity, from [Formula: see text] to [Formula: see text]. Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA-RNA-interaction prediction are expected to profit even stronger than "standard" MFE folding. SparseMFEFold is free

  7. Upgrading of bio-oil to boiler fuel by catalytic hydrotreatment and esterification in an efficient process

    International Nuclear Information System (INIS)

    Zhang, Xinghua; Chen, Lungang; Kong, Wei; Wang, Tiejun; Zhang, Qi; Long, Jinxing; Xu, Ying; Ma, Longlong

    2015-01-01

    Bio-oil can't be directly used as fuel due to its deteriorate properties. Here, an efficient catalytic upgrading process for the bio-oil, including esterification, hydrogenation, hydrodeoxygenation and depolymerization, is proposed with multifunctional catalyst Ni/SiO 2 –ZrO 2 and biomass-derived solvent ethanol. Results showed that esters, alcohols, phenolics, and cyclo-ketones were the main components in the upgraded bio-oil while aldehydes were removed completely via catalytic hydrogenation and acids were removed by catalytic esterification with supercritical ethanol. The pH value of upgraded bio-oil rose drastically from 2.38 to 5.24, and the high heating value increased to 24.4 MJ kg −1 . Comparison characterization on the upgraded and crude bio-oil using FT-IR, GPC (Gel permeation chromatography) and 13 C NMR (Nuclear Magnetic Resonance) demonstrated that lignin-derived oligomers contained in crude bio-oil were further depolymerized over Ni/SiO 2 –ZrO 2 catalyst. The improved properties suggest that the upgraded bio-oil is more suitable to be used as boiler fuel. Furthermore, the loss of carbon is negligible because formation of coke is suppressed during the upgrading process. - Highlights: • Acid can be converted via catalytic esterification in supercritical ethanol. • Aldehydes can be removed completely during the upgrading process. • Lignin-derived oligomers were further depolymerized during the upgrading process. • Formation of coke is effectively inhibited during the upgrading process

  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. Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study.

    Science.gov (United States)

    Gredell, Joseph A; Berger, Angela K; Walton, S Patrick

    2008-07-01

    The selection of active siRNAs is generally based on identifying siRNAs with certain sequence and structural properties. However, the efficiency of RNA interference has also been shown to depend on the structure of the target mRNA, primarily through studies using exogenous transcripts with well-defined secondary structures in the vicinity of the target sequence. While these studies provide a means for examining the impact of target sequence and structure independently, the predicted secondary structures for these transcripts are often not reflective of structures that form in full-length, native mRNAs where interactions can occur between relatively remote segments of the mRNAs. Here, using a combination of experimental results and analysis of a large dataset, we demonstrate that the accessibility of certain local target structures on the mRNA is an important determinant in the gene silencing ability of siRNAs. siRNAs targeting the enhanced green fluorescent protein were chosen using a minimal siRNA selection algorithm followed by classification based on the predicted minimum free energy structures of the target transcripts. Transfection into HeLa and HepG2 cells revealed that siRNAs targeting regions of the mRNA predicted to have unpaired 5'- and 3'-ends resulted in greater gene silencing than regions predicted to have other types of secondary structure. These results were confirmed by analysis of gene silencing data from previously published siRNAs, which showed that mRNA target regions unpaired at either the 5'-end or 3'-end were silenced, on average, approximately 10% more strongly than target regions unpaired in the center or primarily paired throughout. We found this effect to be independent of the structure of the siRNA guide strand. Taken together, these results suggest minimal requirements for nucleation of hybridization between the siRNA guide strand and mRNA and that both mRNA and guide strand structure should be considered when choosing candidate si

  10. Polycistronic tRNA and CRISPR guide-RNA enables highly efficient multiplexed genome engineering in human cells.

    Science.gov (United States)

    Dong, Fengping; Xie, Kabin; Chen, Yueying; Yang, Yinong; Mao, Yingwei

    2017-01-22

    CRISPR/Cas9 has been widely used for genomic editing in many organisms. Many human diseases are caused by multiple mutations. The CRISPR/Cas9 system provides a potential tool to introduce multiple mutations in a genome. To mimic complicated genomic variants in human diseases, such as multiple gene deletions or mutations, two or more small guide RNAs (sgRNAs) need to be introduced all together. This can be achieved by separate Pol III promoters in a construct. However, limited enzyme sites and increased insertion size lower the efficiency to make a construct. Here, we report a strategy to quickly assembly multiple sgRNAs in one construct using a polycistronic-tRNA-gRNA (PTG) strategy. Taking advantage of the endogenous tRNA processing system in mammalian cells, we efficiently express multiple sgRNAs driven using only one Pol III promoter. Using an all-in-one construct carrying PTG, we disrupt the deacetylase domain in multiple histone deacetylases (HDACs) in human cells simultaneously. We demonstrate that multiple HDAC deletions significantly affect the activation of the Wnt-signaling pathway. Thus, this method enables to efficiently target multiple genes and provide a useful tool to establish mutated cells mimicking human diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Layer-by-layer nanoparticles as an efficient siRNA delivery vehicle for SPARC silencing.

    Science.gov (United States)

    Tan, Yang Fei; Mundargi, Raghavendra C; Chen, Min Hui Averil; Lessig, Jacqueline; Neu, Björn; Venkatraman, Subbu S; Wong, Tina T

    2014-05-14

    Efficient and safe delivery systems for siRNA therapeutics remain a challenge. Elevated secreted protein, acidic, and rich in cysteine (SPARC) protein expression is associated with tissue scarring and fibrosis. Here we investigate the feasibility of encapsulating SPARC-siRNA in the bilayers of layer-by-layer (LbL) nanoparticles (NPs) with poly(L-arginine) (ARG) and dextran (DXS) as polyelectrolytes. Cellular binding and uptake of LbL NPs as well as siRNA delivery were studied in FibroGRO cells. siGLO-siRNA and SPARC-siRNA were efficiently coated onto hydroxyapatite nanoparticles. The multilayered NPs were characterized with regard to particle size, zeta potential and surface morphology using dynamic light scattering and transmission electron microscopy. The SPARC-gene silencing and mRNA levels were analyzed using ChemiDOC western blot technique and RT-PCR. The multilayer SPARC-siRNA incorporated nanoparticles are about 200 nm in diameter and are efficiently internalized into FibroGRO cells. Their intracellular fate was also followed by tagging with suitable reporter siRNA as well as with lysotracker dye; confocal microscopy clearly indicates endosomal escape of the particles. Significant (60%) SPARC-gene knock down was achieved by using 0.4 pmole siRNA/μg of LbL NPs in FibroGRO cells and the relative expression of SPARC mRNA reduced significantly (60%) against untreated cells. The cytotoxicity as evaluated by xCelligence real-time cell proliferation and MTT cell assay, indicated that the SPARC-siRNA-loaded LbL NPs are non-toxic. In conclusion, the LbL NP system described provides a promising, safe and efficient delivery platform as a non-viral vector for siRNA delivery that uses biopolymers to enhance the gene knock down efficiency for the development of siRNA therapeutics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. SS-mPEG chemical modification of recombinant phospholipase C for enhanced thermal stability and catalytic efficiency.

    Science.gov (United States)

    Fang, Xian; Wang, Xueting; Li, Guiling; Zeng, Jun; Li, Jian; Liu, Jingwen

    2018-05-01

    PEGylation is one of the most promising and extensively studied strategies for improving the properties of proteins as well as enzymic physical and thermal stability. Phospholipase C, hydrolyzing the phospholipids offers tremendous applications in diverse fields. However, the poor thermal stability and higher cost of production have restricted its industrial application. This study focused on improving the stabilization of recombinant PLC by chemical modification with methoxypolyethylene glycol-Succinimidyl Succinate (SS-mPEG, MW 5000). PLC gene from isolate Bacillus cereus HSL3 was fused with SUMO, a novel small ubiquitin-related modifier expression vector and over expressed in Escherichia coli. The soluble fraction of SUMO-PLC reached 80% of the total recombinant protein. The enzyme exhibited maximum catalytic activity at 80 °C and was relatively thermostable at 40-70 °C. It showed extensive substrate specificity pattern and marked activity toward phosphatidylcholine, which made it a typical non-specific PLC for industrial purpose. SS-mPEG-PLC complex exhibited an enhanced thermal stability at 70-80 °C and the catalytic efficiency (K cat /K m ) had increased by 3.03 folds compared with free PLC. CD spectrum of SS-mPEG-PLC indicated a possible enzyme aggregation after chemical modification, which contributed to the higher thermostability of SS-mPEG-PLC. The increase of antiparallel β sheets in secondary structure also made it more stable than parallel β sheets. The presence of SS-mPEG chains on the enzyme molecule surface somewhat changed the binding rate of the substrates, leading to a significant improvement in catalytic efficiency. This study provided an insight into the addition of SS-mPEG for enhancing the industrial applications of phospholipase C at higher temperature. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Lysosome-controlled efficient ROS overproduction against cancer cells with a high pH-responsive catalytic nanosystem

    Science.gov (United States)

    Fu, Jingke; Shao, Yiran; Wang, Liyao; Zhu, Yingchun

    2015-04-01

    Excess reactive oxygen species (ROS) have been proved to damage cancer cells efficiently. ROS overproduction is thus greatly desirable for cancer therapy. To date, ROS production is generally uncontrollable and outside cells, which always bring severe side-effects in the vasculature. Since most ROS share a very short half-life and primarily react close to their site of formation, it would be more efficient if excess ROS are controllably produced inside cancer cells. Herein, we report an efficient lysosome-controlled ROS overproduction via a pH-responsive catalytic nanosystem (FeOx-MSNs), which catalyze the decomposition of H2O2 to produce considerable ROS selectively inside the acidic lysosomes (pH 5.0) of cancer cells. After a further incorporation of ROS-sensitive TMB into the nanosystem (FeOx-MSNs-TMB), both a distinct cell labeling and an efficient death of breast carcinoma cells are obtained. This lysosome-controlled efficient ROS overproduction suggests promising applications in cancer treatments.Excess reactive oxygen species (ROS) have been proved to damage cancer cells efficiently. ROS overproduction is thus greatly desirable for cancer therapy. To date, ROS production is generally uncontrollable and outside cells, which always bring severe side-effects in the vasculature. Since most ROS share a very short half-life and primarily react close to their site of formation, it would be more efficient if excess ROS are controllably produced inside cancer cells. Herein, we report an efficient lysosome-controlled ROS overproduction via a pH-responsive catalytic nanosystem (FeOx-MSNs), which catalyze the decomposition of H2O2 to produce considerable ROS selectively inside the acidic lysosomes (pH 5.0) of cancer cells. After a further incorporation of ROS-sensitive TMB into the nanosystem (FeOx-MSNs-TMB), both a distinct cell labeling and an efficient death of breast carcinoma cells are obtained. This lysosome-controlled efficient ROS overproduction suggests

  14. An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type.

    Science.gov (United States)

    Byun, Yanga; Han, Kyungsook

    2016-06-01

    An RNA pseudoknot is a tertiary structural element in which bases of a loop pair with complementary bases are outside the loop. A drawing of RNA secondary structures is a tree, but a drawing of RNA pseudoknots is a graph that has an inner cycle within a pseudoknot and possibly outer cycles formed between the pseudoknot and other structural elements. Visualizing a large-scale RNA structure with pseudoknots as a planar drawing is challenging because a planar drawing of an RNA structure requires both pseudoknots and an entire structure enclosing the pseudoknots to be embedded into a plane without overlapping or crossing. This paper presents an efficient heuristic algorithm for visualizing a pseudoknotted RNA structure as a planar drawing. The algorithm consists of several parts for finding crossing stems and page mapping the stems, for the layout of stem-loops and pseudoknots, and for overlap detection between structural elements and resolving it. Unlike previous algorithms, our algorithm generates a planar drawing for a large RNA structure with pseudoknots of any type and provides a bracket view of the structure. It generates a compact and aesthetic structure graph for a large pseudoknotted RNA structure in O([Formula: see text]) time, where n is the number of stems of the RNA structure.

  15. Gold Decorated Graphene for Rapid Dye Reduction and Efficient Electro Catalytic Oxidation of Ethanol

    Science.gov (United States)

    Siddhardha, R. S.; Kumar v, Lakshman; Kaniyoor, A.; Podila, R.; Kumar, V. S.; Venkataramaniah, K.; Ramaprabhu, S.; Rao, A.; Ramamurthy, S. S.; Clemson University Team; Sri Sathya Sai Institute of Higher Learning Team; IITMadras Team

    2013-03-01

    A well known disadvantage in fabrication of metal-graphene composite is the use of surfactants that strongly adsorb on the surface and reduce the performance of the catalyst. Here, we demonstrate a novel one pot synthesis of gold nanoparticles (AuNPs) by laser ablation of gold strip and simultaneous decoration of these on functionalized graphene derivatives. Not only the impregnation of AuNPs was linker free, but also the synthesis by itself was surfactant free. This resulted in in-situ decoration of pristine AuNPs on functionalized graphene derivatives. These materials were well characterized and tested for catalytic applications pertaining to dye reduction and electrooxidation. The catalytic reduction rates are 1.4 x 102 and 9.4x102 times faster for Rhodamine B and Methylene Blue dyes respectively, compared to earlier reports. The enhanced rate involves synergistic interplay of electronic relay between AuNPs and the dye, also charge transfer between the graphene system and dye. In addition, the onset potential for ethanol oxidation was found to be more negative ~ 100 mV, an indication of its promising application in direct ethanol fuel cells.

  16. Evaluation of the conversion efficiency of ceramic and metallic three way catalytic converters

    International Nuclear Information System (INIS)

    Santos, H.; Costa, M.

    2008-01-01

    Ceramic and metallic three way catalytic converters have been compared to assess the influence of the substrate geometrical and physical parameters on the exhaust gas conversions for several vehicle operating conditions. Both catalysts were placed on a vehicle equipped with a 2.8 l DOHC V6 spark ignition engine that was tested on a chassis dynamometer under steady state conditions for several engine speeds and loads. The data obtained include exhaust gas species concentrations and temperature taken both upstream and downstream of the catalytic converter, as well as temperatures in various locations within the substrate of the catalysts. The experimental data revealed that: (i) at low space velocities, the ceramic substrate presents better conversions, particularly for HC and CO, as compared to the metallic substrate, possibly because of its lower thermal conductivity which facilitates local ignition; (ii) at high space velocities, the metallic substrate presents better conversions, as compared to the ceramic substrate, mainly because of its larger geometric surface area and lower transverse Peclet number; and (iii) in general, the HC conversion for small space velocities is kinetically controlled while for high space velocities it is mass transfer limited; both limitations are less pronounced for the CO conversion and insignificant for the NO x conversion

  17. Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication.

    Directory of Open Access Journals (Sweden)

    Eveline Kindler

    2017-02-01

    Full Text Available Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I. This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU activity is key to prevent early induction of double-stranded RNA (dsRNA host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis-within the replicase complex-suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses.

  18. Catalytic oxidation efficiencies for tritium and tritiated methane in a mature, industrial-scale decontamination system

    International Nuclear Information System (INIS)

    Mintz, J.M.; Gildea, P.D.

    1981-01-01

    Almost all tritium decontamination systems proposed for fusion facilities employ catalytic oxidation to water, followed by drying, to remove tritium and tritiated hydrocarbons from gas streams. One such large-scale system, the gas purification system (GPS), has been operating in the Tritium Research Laboratory (TRL) at Sandia National Laboratories, Livermore, CA, since October 1977. A series of experiments have recently been conducted there to assesss the current operating characteristics of the GPS catalyst. The experiments used tritium and tritiated methane and covered a range of temperatures, flow rates, and concentration levels. When contrasted with 1977 data, the results indicate that no measurable degradation of catalyst function had occurred. However, some reduction in active metal surface area, as indicated by B.E.T. surface area measurements (approx. 100 → 90m 2 /g) and AES scans (approx. 1.4 → 0.9 at. % Pt), had occurred. Kinetic rate coefficients were also derived and a rough temperature dependence obtained

  19. Catalytic oxidation efficiencies for tritium and tritiated methane in a mature, industrial-scale decontamination system

    International Nuclear Information System (INIS)

    Mintz, J.M.; Gildea, P.D.

    1980-10-01

    Almost all tritium decontamination systems proposed for fusion facilities employ catalytic oxidation to water, followed by drying, to remove tritium and tritiated hydrocarbons from gas streams. One such large-scale system, the gas purification system (GPS), has been operating in the Tritium Research Laboratory (TRL) at Sandia National Laboratories, Livermore, CA, since October 1977. A series of experiments have recently been conducted there to assess the current operating characteristics of the GPS catalyst. The experiments used tritium and tritiated methane and covered a range of temperatures, flow rates, and concentration levels. When contrasted with 1977 data, the results indicate that no measurable degradation of catalyst function had occurred. However, some reduction in active metal surface area, as indicated by B.E.T. surface area measurements (approx. 100 → 90 m 2 /g) and AES scans (approx. 1.4 → 0.9 at% Pt), had occurred. Kinetic rate coefficients were also derived and a rough temperature dependence obtained

  20. Efficient construction of an inverted minimal H1 promoter driven siRNA expression cassette: facilitation of promoter and siRNA sequence exchange.

    Directory of Open Access Journals (Sweden)

    Hoorig Nassanian

    2007-08-01

    Full Text Available RNA interference (RNAi, mediated by small interfering RNA (siRNA, is an effective method used to silence gene expression at the post-transcriptional level. Upon introduction into target cells, siRNAs incorporate into the RNA-induced silencing complex (RISC. The antisense strand of the siRNA duplex then "guides" the RISC to the homologous mRNA, leading to target degradation and gene silencing. In recent years, various vector-based siRNA expression systems have been developed which utilize opposing polymerase III promoters to independently drive expression of the sense and antisense strands of the siRNA duplex from the same template.We show here the use of a ligase chain reaction (LCR to develop a new vector system called pInv-H1 in which a DNA sequence encoding a specific siRNA is placed between two inverted minimal human H1 promoters (approximately 100 bp each. Expression of functional siRNAs from this construct has led to efficient silencing of both reporter and endogenous genes. Furthermore, the inverted H1 promoter-siRNA expression cassette was used to generate a retrovirus vector capable of transducing and silencing expression of the targeted protein by>80% in target cells.The unique design of this construct allows for the efficient exchange of siRNA sequences by the directional cloning of short oligonucleotides via asymmetric restriction sites. This provides a convenient way to test the functionality of different siRNA sequences. Delivery of the siRNA cassette by retroviral transduction suggests that a single copy of the siRNA expression cassette efficiently knocks down gene expression at the protein level. We note that this vector system can potentially be used to generate a random siRNA library. The flexibility of the ligase chain reaction suggests that additional control elements can easily be introduced into this siRNA expression cassette.

  1. MicroRNA-triggered, cascaded and catalytic self-assembly of functional ``DNAzyme ferris wheel'' nanostructures for highly sensitive colorimetric detection of cancer cells

    Science.gov (United States)

    Zhou, Wenjiao; Liang, Wenbin; Li, Xin; Chai, Yaqin; Yuan, Ruo; Xiang, Yun

    2015-05-01

    The construction of DNA nanostructures with various sizes and shapes has significantly advanced during the past three decades, yet the application of these DNA nanostructures for solving real problems is still in the early stage. On the basis of microRNA-triggered, catalytic self-assembly formation of the functional ``DNAzyme ferris wheel'' nanostructures, we show here a new signal amplification platform for highly sensitive, label-free and non-enzyme colorimetric detection of a small number of human prostate cancer cells. The microRNA (miR-141), which is catalytically recycled and reused, triggers isothermal self-assembly of a pre-designed, G-quadruplex sequence containing hairpin DNAs into ``DNAzyme ferris wheel''-like nanostructures (in association with hemin) with horseradish peroxidase mimicking activity. These DNAzyme nanostructures catalyze an intensified color transition of the probe solution for highly sensitive detection of miR-141 down to 0.5 pM with the naked eye, and the monitoring of as low as 283 human prostate cancer cells can also, theoretically, be achieved in a colorimetric approach. The work demonstrated here thus offers new opportunities for the construction of functional DNA nanostructures and for the application of these DNA nanostructures as an effective signal amplification means in the sensitive detection of nucleic acid biomarkers.

  2. Effect of process parameters and injector position on the efficiency of NOx reduction by selective non catalytic reduction technique

    International Nuclear Information System (INIS)

    Hamid, A.; Mehmood, M.A.; Irfan, N.; Javed, M.T.; Waheed, K.

    2009-01-01

    An experimental investigation has been performed to study the effect of atomizer pressure dilution of the reducing reagent and the injector position on the efficiency or the NOx reduction by a selective non-catalytic reduction technique using urea as a reducing agent. Experiments were performed with a flow reactor in which flue gas was generated by the combustion of methane in air at stoichiometric amount of oxygen and the desired levels of initial NOx (400-450 ppm) were achieved by doping the flame with ammonia. The work was directed to investigate the effect of atomizer pressure, dilution of urea reagent and the injector position. The atomizer pressure was varied from 1 to 3bar and 20-25% increase in efficiency was observed by decreasing the pressure. Effect of dilution of urea solution was investigated by varying the strength of the solution from the 8 to 32% and 40-45% increase in the efficiency was observed. Effects of injector position was investigated by injecting the urea solution both in co current and counter current direction of the flue gases and 20-25% increase in the efficiency was observed in counter current direction. (author)

  3. Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses

    Directory of Open Access Journals (Sweden)

    Hironobu Yanagisawa

    2016-03-01

    Full Text Available The presence of high molecular weight double-stranded RNA (dsRNA within plant cells is an indicator of infection with RNA viruses as these possess genomic or replicative dsRNA. DECS (dsRNA isolation, exhaustive amplification, cloning, and sequencing analysis has been shown to be capable of detecting unknown viruses. We postulated that a combination of DECS analysis and next-generation sequencing (NGS would improve detection efficiency and usability of the technique. Here, we describe a model case in which we efficiently detected the presumed genome sequence of Blueberry shoestring virus (BSSV, a member of the genus Sobemovirus, which has not so far been reported. dsRNAs were isolated from BSSV-infected blueberry plants using the dsRNA-binding protein, reverse-transcribed, amplified, and sequenced using NGS. A contig of 4,020 nucleotides (nt that shared similarities with sequences from other Sobemovirus species was obtained as a candidate of the BSSV genomic sequence. Reverse transcription (RT-PCR primer sets based on sequences from this contig enabled the detection of BSSV in all BSSV-infected plants tested but not in healthy controls. A recombinant protein encoded by the putative coat protein gene was bound by the BSSV-antibody, indicating that the candidate sequence was that of BSSV itself. Our results suggest that a combination of DECS analysis and NGS, designated here as “DECS-C,” is a powerful method for detecting novel plant viruses.

  4. Efficient Catalytic Reduction of Hexavalent Chromium With Pd-decorated Carbon Nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ji Dang; Choi, Hyun Chul [Chonnam National University, Gwangju (Korea, Republic of)

    2016-05-15

    Heavy metal pollution is currently a serious environmental issue. Chromium (Cr) and chromium compounds are commonly found in wastewater discharged by various industries such as wood preservation, leather tanning, electroplating, metal finishing, and the production of chemicals. Pd nanoparticles can easily be introduced into CNTs by performing DCC-activated amidation. Our TEM and XRD results indicate that well-dispersed metallic Pd nanoparticles are anchored on the surface of the amidated CNTs. The XPS results suggest that the Pd content of the sample is approximately 9.8 atomic %. In comparison with the commercial Pd catalyst, the prepared Pd-CNTs were demonstrated to exhibit good catalytic activity in the reduction of 4-NP by NaBH4. Moreover, the Pd-CNT catalyst can easily be separated by performing a simple filtration and reused over at least 10 cycles. This Pd-CNT catalyst is therefore believed to have significant potential for use as a reusable catalyst in the reduction of Cr(Vi)

  5. Efficient photo-catalytic degradation of malachite green using nickel tungstate material as photo-catalyst.

    Science.gov (United States)

    Helaïli, N; Boudjamaa, A; Kebir, M; Bachari, K

    2017-03-01

    The present study focused on the evaluation of photo-catalytic and photo-electrochemical properties of the photo-catalyst based on nickel tungstate material prepared by a nitrate method through the degradation of malachite green (MG) dye's. The effect of catalyst loading and dye concentration was examined. Physico-chemical, optical, electrical, electrochemical, and photo-electrochemical properties of the prepared material were analyzed by X-ray diffraction (XRD), fourier transform-infrared spectroscopy (FTIR), BET analysis, optical reflectance diffuse (DR), scanning electron microscopy (SEM/EDX), electrical conductivity, cyclic voltammetry (CV), current intensity, mott-shottky, and nyquist. XRD revealed the formation of monoclinic structure with a small particle size. BET surface area of the sample was around 10 m 2 /g. The results show that the degradation of MG was more than 80%, achieved after 3 h of irradiation at pH 4.6 and with a catalyst loading of 75 mg. Also, it was found that the dye photo-degradation obeyed the pseudo-first order kinetic via Langmuir Hinshelwood model.

  6. Efficient Multiple Genome Modifications Induced by the crRNAs, tracrRNA and Cas9 Protein Complex in Zebrafish

    Science.gov (United States)

    Ohga, Rie; Ota, Satoshi; Kawahara, Atsuo

    2015-01-01

    The type II clustered regularly interspaced short palindromic repeats (CRISPR) associated with Cas9 endonuclease (CRISPR/Cas9) has become a powerful genetic tool for understanding the function of a gene of interest. In zebrafish, the injection of Cas9 mRNA and guide-RNA (gRNA), which are prepared using an in vitro transcription system, efficiently induce DNA double-strand breaks (DSBs) at the targeted genomic locus. Because gRNA was originally constructed by fusing two short RNAs CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA), we examined the effect of synthetic crRNAs and tracrRNA with Cas9 mRNA or Cas9 protein on the genome editing activity. We previously reported that the disruption of tyrosinase (tyr) by tyr-gRNA/Cas9 mRNA causes a retinal pigment defect, whereas the disruption of spns2 by spns2-gRNA1/Cas9 mRNA leads to a cardiac progenitor migration defect in zebrafish. Here, we found that the injection of spns2-crRNA1, tyr-crRNA and tracrRNA with Cas9 mRNA or Cas9 protein simultaneously caused a migration defect in cardiac progenitors and a pigment defect in retinal epithelial cells. A time course analysis demonstrated that the injection of crRNAs and tracrRNA with Cas9 protein rapidly induced genome modifications compared with the injection of crRNAs and tracrRNA with Cas9 mRNA. We further show that the crRNA-tracrRNA-Cas9 protein complex is functional for the visualization of endogenous gene expression; therefore, this is a very powerful, ready-to-use system in zebrafish. PMID:26010089

  7. RNA.

    Science.gov (United States)

    Darnell, James E., Jr.

    1985-01-01

    Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…

  8. Zinc oxide nanostructures and its nano-compounds for efficient visible light photo-catalytic processes

    Science.gov (United States)

    Adam, Rania E.; Alnoor, Hatim; Elhag, Sami; Nur, Omer; Willander, Magnus

    2017-02-01

    Zinc oxide (ZnO) in its nanostructure form is a promising material for visible light emission/absorption and utilization in different energy efficient photocatalytic processes. We will first present our recent results on the effect of varying the molar ratio of the synthesis nutrients on visible light emission. Further we will use the optimized conditions from the molar ration experiments to vary the synthesis processing parameters like stirring time etc. and the effect of all these parameters in order to optimize the efficiency and control the emission spectrum are investigated using different complementary techniques. Cathodoluminescence (CL) is combined with photoluminescence (PL) and electroluminescence (EL) as the techniques to investigate and optimizes visible light emission from ZnO/GaN light emitting diodes. We will then show and discuss our recent finding of the use of high quality ZnO nanoparticles (NPs) for efficient photo-degradation of toxic dyes using the visible spectra, namely with a wavelength up to 800 nm. In the end, we show how ZnO nanorods (NRs) are used as the first template to be transferred to bismuth zinc vanadate (BiZn2VO6). The BiZn2VO6 is then used to demonstrate efficient and cost effective hydrogen production through photoelectrochemical water splitting using solar radiation.

  9. Insight into the recognition, binding, and reactivity of catalytic metallodrugs targeting stem loop IIb of hepatitis C IRES RNA.

    Science.gov (United States)

    Bradford, Seth S; Ross, Martin James; Fidai, Insiya; Cowan, James A

    2014-06-01

    The complex Cu-GGHYrFK-amide (1-Cu) was previously reported as a novel metallotherapeutic that catalytically inactivates stem loop IIb (SLIIb) of the hepatitis C virus (HCV) internal ribosomal entry site (IRES) RNA and demonstrates significant antiviral activity in a cellular HCV replicon assay. Herein we describe additional studies focused on understanding the cleavage mechanism as well as the relationship of catalyst configuration to structural recognition and site-selective cleavage of the structured RNA motif. These are advanced by use of a combination of MALDI-TOF mass spectrometry, melting temperature determinations, and computational analysis to develop a structural model for binding and reactivity toward SLIIb of the IRES RNA. In addition, the binding, reactivity, and structural chemistry of the all-D-amino acid form of this metallopeptide, complex 2-Cu, are reported and compared with those of complex 1-Cu. In vitro RNA binding and cleavage assays for complex 2-Cu show a KD value of 76 ± 3 nM, and Michaelis-Menten parameters of kcat =0.14 ± 0.01 min(-1) and KM =7.9 ± 1.2 μM, with a turnover number exceeding 40. In a luciferase-based cellular replicon assay Cu-GGhyrfk-amide shows activity similar to that of the 1-Cu parent peptide, with an IC50 value of 1.9 ± 0.4 μM and cytotoxicity exceeding 100 μM. RT-PCR experiments confirm a significant decrease in HCV RNA levels in replicon assays for up to nine days when treated with complex 1-Cu in three-day dosing increments. This study shows the influence that the α-carbon stereocenter has for this new class of compounds, while detailed mass spectrometry and computational analyses provide new insight into the mechanisms of recognition, binding, and reactivity. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Catalytic asymmetric epoxidation of alpha,beta-unsaturated amides: efficient synthesis of beta-aryl alpha-hydroxy amides using a one-pot tandem catalytic asymmetric epoxidation-Pd-catalyzed epoxide opening process.

    Science.gov (United States)

    Nemoto, Tetsuhiro; Kakei, Hiroyuki; Gnanadesikan, Vijay; Tosaki, Shin-Ya; Ohshima, Takashi; Shibasaki, Masakatsu

    2002-12-11

    The catalytic asymmetric epoxidation of alpha,beta-unsaturated amides using Sm-BINOL-Ph3As=O complex was succeeded. Using 5-10 mol % of the asymmetric catalyst, a variety of amides were epoxidized efficiently, yielding the corresponding alpha,beta-epoxy amides in up to 99% yield and in more than 99% ee. Moreover, the novel one-pot tandem process, one-pot tandem catalytic asymmetric epoxidation-Pd-catalyzed epoxide opening process, was developed. This method was successfully utilized for the efficient synthesis of beta-aryl alpha-hydroxy amides, including beta-aryllactyl-leucine methyl esters. Interestingly, it was found that beneficial modifications on the Pd catalyst were achieved by the constituents of the first epoxidation, producing a more suitable catalyst for the Pd-catalyzed epoxide opening reaction in terms of chemoselectivity.

  11. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.

    Science.gov (United States)

    Song, Li; Florea, Liliana

    2015-01-01

    Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing. We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read. Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.

  12. Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp

    Science.gov (United States)

    Gotic, Ivana; Omidi, Saeed; Fleury-Olela, Fabienne; Molina, Nacho; Naef, Felix; Schibler, Ueli

    2016-01-01

    In mammals, body temperature fluctuates diurnally around a mean value of 36°C–37°C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, likely, animals. Here we studied the mechanisms responsible for the temperature-dependent expression of cold-inducible RNA-binding protein (CIRBP). In NIH3T3 fibroblasts exposed to simulated mouse body temperature cycles, Cirbp mRNA oscillates about threefold in abundance, as it does in mouse livers. This daily mRNA accumulation cycle is directly controlled by temperature oscillations and does not depend on the cells’ circadian clocks. Here we show that the temperature-dependent accumulation of Cirbp mRNA is controlled primarily by the regulation of splicing efficiency, defined as the fraction of Cirbp pre-mRNA processed into mature mRNA. As revealed by genome-wide “approach to steady-state” kinetics, this post-transcriptional mechanism is widespread in the temperature-dependent control of gene expression. PMID:27633015

  13. Efficient nanoparticle mediated sustained RNA interference in human primary endothelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Mukerjee, Anindita; Shankardas, Jwalitha; Ranjan, Amalendu P; Vishwanatha, Jamboor K, E-mail: Jamboor.vishwanatha@unthsc.edu [Department of Molecular Biology and Immunology and Institute for Cancer Research, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States)

    2011-11-04

    Endothelium forms an important target for drug and/or gene therapy since endothelial cells play critical roles in angiogenesis and vascular functions and are associated with various pathophysiological conditions. RNA mediated gene silencing presents a new therapeutic approach to overcome many such diseases, but the major challenge of such an approach is to ensure minimal toxicity and effective transfection efficiency of short hairpin RNA (shRNA) to primary endothelial cells. In the present study, we formulated shAnnexin A2 loaded poly(D,L-lactide-co-glycolide) (PLGA) nanoparticles which produced intracellular small interfering RNA (siRNA) against Annexin A2 and brought about the downregulation of Annexin A2. The per cent encapsulation of the plasmid within the nanoparticle was found to be 57.65%. We compared our nanoparticle based transfections with Lipofectamine mediated transfection, and our studies show that nanoparticle based transfection efficiency is very high ({approx}97%) and is more sustained compared to conventional Lipofectamine mediated transfections in primary retinal microvascular endothelial cells and human cancer cell lines. Our findings also show that the shAnnexin A2 loaded PLGA nanoparticles had minimal toxicity with almost 95% of cells being viable 24 h post-transfection while Lipofectamine based transfections resulted in only 30% viable cells. Therefore, PLGA nanoparticle based transfection may be used for efficient siRNA transfection to human primary endothelial and cancer cells. This may serve as a potential adjuvant treatment option for diseases such as diabetic retinopathy, retinopathy of prematurity and age related macular degeneration besides various cancers.

  14. Efficient nanoparticle mediated sustained RNA interference in human primary endothelial cells

    Science.gov (United States)

    Mukerjee, Anindita; Shankardas, Jwalitha; Ranjan, Amalendu P.; Vishwanatha, Jamboor K.

    2011-11-01

    Endothelium forms an important target for drug and/or gene therapy since endothelial cells play critical roles in angiogenesis and vascular functions and are associated with various pathophysiological conditions. RNA mediated gene silencing presents a new therapeutic approach to overcome many such diseases, but the major challenge of such an approach is to ensure minimal toxicity and effective transfection efficiency of short hairpin RNA (shRNA) to primary endothelial cells. In the present study, we formulated shAnnexin A2 loaded poly(D,L-lactide-co-glycolide) (PLGA) nanoparticles which produced intracellular small interfering RNA (siRNA) against Annexin A2 and brought about the downregulation of Annexin A2. The per cent encapsulation of the plasmid within the nanoparticle was found to be 57.65%. We compared our nanoparticle based transfections with Lipofectamine mediated transfection, and our studies show that nanoparticle based transfection efficiency is very high (~97%) and is more sustained compared to conventional Lipofectamine mediated transfections in primary retinal microvascular endothelial cells and human cancer cell lines. Our findings also show that the shAnnexin A2 loaded PLGA nanoparticles had minimal toxicity with almost 95% of cells being viable 24 h post-transfection while Lipofectamine based transfections resulted in only 30% viable cells. Therefore, PLGA nanoparticle based transfection may be used for efficient siRNA transfection to human primary endothelial and cancer cells. This may serve as a potential adjuvant treatment option for diseases such as diabetic retinopathy, retinopathy of prematurity and age related macular degeneration besides various cancers.

  15. Efficient nanoparticle mediated sustained RNA interference in human primary endothelial cells

    International Nuclear Information System (INIS)

    Mukerjee, Anindita; Shankardas, Jwalitha; Ranjan, Amalendu P; Vishwanatha, Jamboor K

    2011-01-01

    Endothelium forms an important target for drug and/or gene therapy since endothelial cells play critical roles in angiogenesis and vascular functions and are associated with various pathophysiological conditions. RNA mediated gene silencing presents a new therapeutic approach to overcome many such diseases, but the major challenge of such an approach is to ensure minimal toxicity and effective transfection efficiency of short hairpin RNA (shRNA) to primary endothelial cells. In the present study, we formulated shAnnexin A2 loaded poly(D,L-lactide-co-glycolide) (PLGA) nanoparticles which produced intracellular small interfering RNA (siRNA) against Annexin A2 and brought about the downregulation of Annexin A2. The per cent encapsulation of the plasmid within the nanoparticle was found to be 57.65%. We compared our nanoparticle based transfections with Lipofectamine mediated transfection, and our studies show that nanoparticle based transfection efficiency is very high (∼97%) and is more sustained compared to conventional Lipofectamine mediated transfections in primary retinal microvascular endothelial cells and human cancer cell lines. Our findings also show that the shAnnexin A2 loaded PLGA nanoparticles had minimal toxicity with almost 95% of cells being viable 24 h post-transfection while Lipofectamine based transfections resulted in only 30% viable cells. Therefore, PLGA nanoparticle based transfection may be used for efficient siRNA transfection to human primary endothelial and cancer cells. This may serve as a potential adjuvant treatment option for diseases such as diabetic retinopathy, retinopathy of prematurity and age related macular degeneration besides various cancers.

  16. High Efficiency Solar-based Catalytic Structure for CO2 Reforming

    Energy Technology Data Exchange (ETDEWEB)

    Menkara, Hisham [PhosphorTech Corporation, Kennesaw, GA (United States)

    2013-09-30

    Throughout this project, we developed and optimized various photocatalyst structures for CO2 reforming into hydrocarbon fuels and various commodity chemical products. We also built several closed-loop and continuous fixed-bed photocatalytic reactor system prototypes for a larger-scale demonstration of CO2 reforming into hydrocarbons, mainly methane and formic acid. The results achieved have indicated that with each type of reactor and structure, high reforming yields can be obtained by refining the structural and operational conditions of the reactor, as well as by using various sacrificial agents (hole scavengers). We have also demonstrated, for the first time, that an aqueous solution containing acid whey (a common bio waste) is a highly effective hole scavenger for a solar-based photocatalytic reactor system and can help reform CO2 into several products at once. The optimization tasks performed throughout the project have resulted in efficiency increase in our conventional reactors from an initial 0.02% to about 0.25%, which is 10X higher than our original project goal. When acid whey was used as a sacrificial agent, the achieved energy efficiency for formic acid alone was ~0.4%, which is 16X that of our original project goal and higher than anything ever reported for a solar-based photocatalytic reactor. Therefore, by carefully selecting sacrificial agents, it should be possible to reach energy efficiency in the range of the photosynthetic efficiency of typical crop and biofuel plants (1-3%).

  17. Experimental demonstration of the reverse flow catalytic membrane reactor concept for energy efficient syngas production. Part 1: Influence of operating conditions

    NARCIS (Netherlands)

    Smit, J.; Bekink, G.J.; Sint Annaland, van M.; Kuipers, J.A.M.

    2007-01-01

    In this contribution the technical feasibility of the reverse flow catalytic membrane reactor (RFCMR) concept with porous membranes for energy efficient syngas production is investigated. In earlier work an experimental proof of principle was already provided [Smit, J., Bekink, G.J., van Sint

  18. A General Catalytic Method for Highly Cost- and Atom-Efficient Nucleophilic Substitutions.

    Science.gov (United States)

    Huy, Peter H; Filbrich, Isabel

    2018-05-23

    A general formamide-catalyzed protocol for the efficient transformation of alcohols into alkyl chlorides, which is promoted by substoichiometric amounts (down to 34 mol %) of inexpensive trichlorotriazine (TCT), is introduced. This is the first example of a TCT-mediated dihydroxychlorination of an OH-containing substrate (e.g., alcohols and carboxylic acids) in which all three chlorine atoms of TCT are transferred to the starting material. The consequently enhanced atom economy facilitates a significantly improved waste balance (E-factors down to 4), cost efficiency, and scalability (>50 g). Furthermore, the current procedure is distinguished by high levels of functional-group compatibility and stereoselectivity, as only weakly acidic cyanuric acid is released as exclusive byproduct. Finally, a one-pot protocol for the preparation of amines, azides, ethers, and sulfides enabled the synthesis of the drug rivastigmine with twofold S N 2 inversion, which demonstrates the high practical value of the presented method. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Efficiency and fidelity of cell-free protein synthesis by transfer RNA from aged mice

    Energy Technology Data Exchange (ETDEWEB)

    Foote, R.S.; Stulberg, M.P.

    1980-01-01

    Transfer RNAs (tRNAs) from heart, kidney, liver, and spleen of mature (10 to 12 months old) and aged (29 months old) C57BL/6 mice were tested for their ability to translate encephalomyocarditis viral RNA in a tRNA-dependent cell-free system derived from mouse ascites tumor cells. The rates of in vitro protein synthesis were compared as a function of tRNA concentration, and the fidelity of translation was examined by sodium dodecyl sulfate gel electrophoresis and isoelectric focusing of the viral polypeptides synthesized in vitro. No significant age-related differences in either the efficiency or fidelity of synthesis were discovered, indicating that alternations in tRNAs are probably not involved in the cellular aging of these tissues.

  20. Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency.

    Science.gov (United States)

    Sindhu, Raveendran; Binod, Parameswaran; Madhavan, Aravind; Beevi, Ummalyma Sabeela; Mathew, Anil Kuruvilla; Abraham, Amith; Pandey, Ashok; Kumar, Vinod

    2017-12-01

    α-Amylases is one of the most important industrial enzyme which contributes to 25% of the industrial enzyme market. Though it is produced by plant, animals and microbial source, those from microbial source seems to have potential applications due to their stability and economic viability. However a large number of α-amylases from different sources have been detailed in the literature, only few numbers of them could withstand the harsh industrial conditions. Thermo-stability, pH tolerance, calcium independency and oxidant stability and starch hydrolyzing efficiency are the crucial qualities for α-amylase in starch based industries. Microbes can be genetically modified and fine tuning can be done for the production of enzymes with desired characteristics for specific applications. This review focuses on the native and recombinant α-amylases from microorganisms, their heterologous production and the recent molecular strategies which help to improve the properties of this industrial enzyme. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Selection of mRNA 5'-untranslated region sequence with high translation efficiency through ribosome display

    International Nuclear Information System (INIS)

    Mie, Masayasu; Shimizu, Shun; Takahashi, Fumio; Kobatake, Eiry

    2008-01-01

    The 5'-untranslated region (5'-UTR) of mRNAs functions as a translation enhancer, promoting translation efficiency. Many in vitro translation systems exhibit a reduced efficiency in protein translation due to decreased translation initiation. The use of a 5'-UTR sequence with high translation efficiency greatly enhances protein production in these systems. In this study, we have developed an in vitro selection system that favors 5'-UTRs with high translation efficiency using a ribosome display technique. A 5'-UTR random library, comprised of 5'-UTRs tagged with a His-tag and Renilla luciferase (R-luc) fusion, were in vitro translated in rabbit reticulocytes. By limiting the translation period, only mRNAs with high translation efficiency were translated. During translation, mRNA, ribosome and translated R-luc with His-tag formed ternary complexes. They were collected with translated His-tag using Ni-particles. Extracted mRNA from ternary complex was amplified using RT-PCR and sequenced. Finally, 5'-UTR with high translation efficiency was obtained from random 5'-UTR library

  2. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

    KAUST Repository

    Butt, Haroon

    2017-08-24

    The CRISPR/Cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. However, targeted gene editing is inefficient and requires the simultaneous delivery of a DNA template for homology-directed repair (HDR). Here, we used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by regions of homology to the target. Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand. We applied this cgRNA repair method to generate herbicide resistance in rice, which showed that this cgRNA repair method can be used for targeted gene editing in plants. Our findings will facilitate applications in functional genomics and targeted improvement of crop traits.

  3. Comparison of Efficiencies and Mechanisms of Catalytic Ozonation of Recalcitrant Petroleum Refinery Wastewater by Ce, Mg, and Ce-Mg Oxides Loaded Al2O3

    Directory of Open Access Journals (Sweden)

    Chunmao Chen

    2017-02-01

    Full Text Available The use of catalytic ozonation processes (COPs for the advanced treatment of recalcitrant petroleum refinery wastewater (RPRW is rapidly expanding. In this study, magnesium (Mg, cerium (Ce, and Mg-Ce oxide-loaded alumina (Al2O3 were developed as cost efficient catalysts for ozonation treatment of RPRW, having performance metrics that meet new discharge standards. Interactions between the metal oxides and the Al2O3 support influence the catalytic properties, as well as the efficiency and mechanism. Mg-Ce/Al2O3 (Mg-Ce/Al2O3-COP reduced the chemical oxygen demand by 4.7%, 4.1%, 6.0%, and 17.5% relative to Mg/Al2O3-COP, Ce/Al2O3-COP, Al2O3-COP, and single ozonation, respectively. The loaded composite metal oxides significantly increased the hydroxyl radical-mediated oxidation. Surface hydroxyl groups (–OHs are the dominant catalytic active sites on Al2O3. These active surface –OHs along with the deposited metal oxides (Mg2+ and/or Ce4+ increased the catalytic activity. The Mg-Ce/Al2O3 catalyst can be economically produced, has high efficiency, and is stable under acidic and alkaline conditions.

  4. Efficient cellular release of Rift Valley fever virus requires genomic RNA.

    Directory of Open Access Journals (Sweden)

    Mary E Piper

    2011-03-01

    Full Text Available The Rift Valley fever virus is responsible for periodic, explosive epizootics throughout sub-Saharan Africa. The development of therapeutics targeting this virus is difficult due to a limited understanding of the viral replicative cycle. Utilizing a virus-like particle system, we have established roles for each of the viral structural components in assembly, release, and virus infectivity. The envelope glycoprotein, Gn, was discovered to be necessary and sufficient for packaging of the genome, nucleocapsid protein and the RNA-dependent RNA polymerase into virus particles. Additionally, packaging of the genome was found to be necessary for the efficient release of particles, revealing a novel mechanism for the efficient generation of infectious virus. Our results identify possible conserved targets for development of anti-phlebovirus therapies.

  5. Seedless synthesis and efficient recyclable catalytic activity of Ag@Fe nanocomposites towards methyl orange

    Science.gov (United States)

    Alzahrani, Salma Ahmed; Malik, Maqsood Ahmad; Al-Thabaiti, Shaeel Ahmed; Khan, Zaheer

    2018-03-01

    This work demonstrates a competitive reduction method of synthesis of nanomaterials. In this method along cetyltrimethylammonium bromide (CTAB), the reduction of Ag+ and Fe3+ ions is achieved by ascorbic acid-to-bimetallic Ag@Fe yellow-colored nanomaterials. The shape of UV-visible spectra and wavelengths absorbed of Ag@Fe can be tuned from ca. 290-600 nm by controlling [CTAB] and [Ag+]. The apparent first-order rate constants were calculated within the approximation of 6.1 × 10-3 s-1. The as-prepared Ag@Fe NPs have been found to be very important catalyst in terms of depredate methyl orange in vicinity of sodium borohydride (NaBH4), which exhibits excellent efficiency and re-usability in the prototypical reaction. The cmc of cationic surfactant CTAB has been determined by conductivity method under different experimental conditions. In the presence of CTAB, Ag+ and Fe3+ ions reduce to Ag@Fe core/shell nanoparticles, comprehend a change in wavelength and intensity of SRP band. The apparent first-order rate constant, activation energy, and turnover frequency for the methyl orange reduction catalyzed by Ag@Fe NPs were found to be 1.6 × 10-3 s-1, 58.2 kJ mol-1, and 1.1 × 10-3 s-1, respectively.

  6. Indium triflate in 1-isobutyl-3-methylimidazolium dihydrogenphosphate: an efficient and green catalytic system for Friedel-Crafts acylation

    DEFF Research Database (Denmark)

    Tran, Phuong Hoang; Hoang, Huy Manh; Chau, Duy-Khiem Nguyen

    2015-01-01

    Indium triflate in the ionic liquid, 1-isobutyl-3-methylimidazolium dihydrogen phosphate ([i-BMIM]H2PO4), was found to show enhanced catalytic activity in the Friedel–Crafts acylation of various aromatic compounds with acid anhydrides. The catalytic system was easily recovered and reused without...

  7. Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics.

    Science.gov (United States)

    Stark, Lucy; Giersch, Tina; Wünschiers, Röbbe

    2014-10-01

    Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Deuterohemin-Peptide Enzyme Mimic-Embedded Metal-Organic Frameworks through Biomimetic Mineralization with Efficient ATRP Catalytic Activity.

    Science.gov (United States)

    Jiang, Wei; Wang, Xinghuo; Chen, Jiawen; Liu, Ying; Han, Haobo; Ding, Yi; Li, Quanshun; Tang, Jun

    2017-08-16

    An enzyme mimic harboring iron porphyrin (DhHP-6) embedded in zeolite imidazolate framework-8 (ZIF-8) was constructed through a biomimetic mineralization approach to obtain composite DhHP-6@ZIF-8. The composite was then used as a catalyst in the atom transfer radical polymerization (ATRP) of poly(ethylene glycol) methyl ether methacrylate (PEGMA 500 ) in which poly(PEGMA 500 ) could be synthesized with monomer conversion of 76.1% and M n of 45 900 g/mol, stronger than that obtained when using free DhHP-6 as a catalyst. More importantly, it could efficiently overcome the drawbacks of free DhHP-6 and achieve the easy separation of DhHP-6 from the catalytic system and the elimination of iron residues in the synthesized polymer. In addition, it exhibited an enhanced recyclability with monomer conversion of 75.7% after five cycles and favorable stability during the ATRP reaction with mimic-ZIF-8 composite developed through biomimetic mineralization can be potentially used as an effective catalyst for preparing well-defined polymers with biomedical applications.

  9. Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligase

    Science.gov (United States)

    Lohman, Gregory J. S.; Zhang, Yinhua; Zhelkovsky, Alexander M.; Cantor, Eric J.; Evans, Thomas C.

    2014-01-01

    Single-stranded DNA molecules (ssDNA) annealed to an RNA splint are notoriously poor substrates for DNA ligases. Herein we report the unexpectedly efficient ligation of RNA-splinted DNA by Chlorella virus DNA ligase (PBCV-1 DNA ligase). PBCV-1 DNA ligase ligated ssDNA splinted by RNA with kcat ≈ 8 x 10−3 s−1 and KM DNA ligase produced only 5′-adenylylated DNA with a 20-fold lower kcat and a KM ≈ 300 nM. The rate of ligation increased with addition of Mn2+, but was strongly inhibited by concentrations of NaCl >100 mM. Abortive adenylylation was suppressed at low ATP concentrations (8, leading to increased product yields. The ligation reaction was rapid for a broad range of substrate sequences, but was relatively slower for substrates with a 5′-phosphorylated dC or dG residue on the 3′ side of the ligation junction. Nevertheless, PBCV-1 DNA ligase ligated all sequences tested with 10-fold less enzyme and 15-fold shorter incubation times than required when using T4 DNA ligase. Furthermore, this ligase was used in a ligation-based detection assay system to show increased sensitivity over T4 DNA ligase in the specific detection of a target mRNA. PMID:24203707

  10. The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during MicroRNA biogenesis

    KAUST Repository

    Liu, Chenggang

    2012-04-03

    Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 mutants accumulate low levels of miRNAs and display pleiotropic developmental phenotypes. We report the identification of five new hyl1 suppressor mutants, all of which are alleles of DCL1. These new alleles affect either the helicase or the RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. Biochemical analysis of the DCL1 suppressor variants reveals that they process the primary transcript (pri-miRNA) more efficiently than wild-type DCL1, with both higher Kcat and lower Km values. The DCL1 variants largely rescue wild-type miRNA accumulation levels in vivo, but do not rescue the MIRNA processing precision defects of the hyl1 mutant. In vitro, the helicase domain confers ATP dependence on DCL1-catalyzed MIRNA processing, attenuates DCL1 cleavage activity, and is required for precise MIRNA processing of some substrates. © 2012 American Society of Plant Biologists.

  11. Relationship between RNA polymerase II and efficiency of vaccinia virus replication

    International Nuclear Information System (INIS)

    Wilton, S.; Dales, S.

    1989-01-01

    It is clear from previous studies that host transcriptase or RNA polymerase II (pol II) has a role in poxvirus replication. To elucidate the participation of this enzyme further, in this study the authors examined several parameters related to pol II during the cycle of vaccinia virus infection in L-strain fibroblasts, HeLa cells, and L 6 H 9 rat myoblasts. Nucleocytoplasmic transposition of pol II into virus factories and virions was assessed by immunofluorescence and immunoblotting by using anti-pol II immunoglobulin G. RNA polymerase activities were compared in nuclear extracts containing cured enzyme preparations. Rates of translation into cellular or viral polypeptides were ascertained by labeling with [ 35 S]methionine. In L and HeLa cells, which produced vaccinia virus more abundantly, the rate of RNA polymerase and translation in controls and following infection were higher than in myoblasts. The data on synthesis and virus formation could be correlated with observations on transmigration of pol II, which was more efficient and complete in L and HeLa cells. The stimulus for pol II to leave the nucleus required the expression of both early and late viral functions. On the basis of current and past information, the authors suggest that mobilization of pol II depends on the efficiency of vaccinia virus replication and furthermore that control over vaccinia virus production by the host is related to the content or availability (or both) of pol II in different cell types

  12. Polyphosphonium polymers for siRNA delivery: An efficient and nontoxic alternative to polyammonium carriers

    KAUST Repository

    Ornelas-Megiatto, Cá tia; Wich, Peter R.; Frechet, Jean

    2012-01-01

    A water-soluble polyphosphonium polymer was synthesized and directly compared with its ammonium analog in terms of siRNA delivery. The triethylphosphonium polymer shows transfection efficiency up to 65% with 100% cell viability, whereas the best result obtained for the ammonium analog reaches only 25% transfection with 85% cell viability. Moreover, the nature of the alkyl substituents on the phosphonium cations is shown to have an important influence on the transfection efficiency and toxicity of the polyplexes. The present results show that the use of positively charged phosphonium groups is a worthy choice to achieve a good balance between toxicity and transfection efficiency in gene delivery systems. © 2012 American Chemical Society.

  13. Polyphosphonium polymers for siRNA delivery: An efficient and nontoxic alternative to polyammonium carriers

    KAUST Repository

    Ornelas-Megiatto, Cátia

    2012-02-01

    A water-soluble polyphosphonium polymer was synthesized and directly compared with its ammonium analog in terms of siRNA delivery. The triethylphosphonium polymer shows transfection efficiency up to 65% with 100% cell viability, whereas the best result obtained for the ammonium analog reaches only 25% transfection with 85% cell viability. Moreover, the nature of the alkyl substituents on the phosphonium cations is shown to have an important influence on the transfection efficiency and toxicity of the polyplexes. The present results show that the use of positively charged phosphonium groups is a worthy choice to achieve a good balance between toxicity and transfection efficiency in gene delivery systems. © 2012 American Chemical Society.

  14. Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

    Science.gov (United States)

    Wolfinger, Michael T; Flamm, Christoph; Hofacker, Ivo L

    2018-05-04

    Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2 ' -deoxyguanosine (2 ' dG)-sensing riboswitch from Mesoplasma florum. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics

    Directory of Open Access Journals (Sweden)

    Vladimir Reinharz

    2017-10-01

    Full Text Available The multiscale model of hepatitis C virus (HCV dynamics, which includes intracellular viral RNA (vRNA replication, has been formulated in recent years in order to provide a new conceptual framework for understanding the mechanism of action of a variety of agents for the treatment of HCV. We present a robust and efficient numerical method that belongs to the family of adaptive stepsize methods and is implicit, a Rosenbrock type method that is highly suited to solve this problem. We provide a Graphical User Interface that applies this method and is useful for simulating viral dynamics during treatment with anti-HCV agents that act against HCV on the molecular level.

  16. Thermoresponsive pegylated bubble liposome nanovectors for efficient siRNA delivery via endosomal escape

    KAUST Repository

    Alamoudi, Kholod; Martins, Patricia; Croissant, Jonas G.; Patil, Sachin; Omar, Haneen; Khashab, Niveen M.

    2017-01-01

    Improving the delivery of siRNA into cancer cells via bubble liposomes. Designing a thermoresponsive pegylated liposome through the introduction of ammonium bicarbonate salt into liposomes so as to control their endosomal escape for gene therapy.A sub-200 nm nanovector was fully characterized and examined for cellular uptake, cytotoxicity, endosomal escape and gene silencing.The siRNA-liposomes were internalized into cancer cells within 5 min and then released siRNAs in the cytosol prior to lysosomal degradation upon external temperature elevation. This was confirmed by confocal bioimaging and gene silencing reaching up to 90% and further demonstrated by the protein inhibition of both target genes.The thermoresponsiveness of ammonium bicarbonate containing liposomes enabled the rapid endosomal escape of the particles and resulted in an efficient gene silencing.

  17. Thermoresponsive pegylated bubble liposome nanovectors for efficient siRNA delivery via endosomal escape

    KAUST Repository

    Alamoudi, Kholod

    2017-05-19

    Improving the delivery of siRNA into cancer cells via bubble liposomes. Designing a thermoresponsive pegylated liposome through the introduction of ammonium bicarbonate salt into liposomes so as to control their endosomal escape for gene therapy.A sub-200 nm nanovector was fully characterized and examined for cellular uptake, cytotoxicity, endosomal escape and gene silencing.The siRNA-liposomes were internalized into cancer cells within 5 min and then released siRNAs in the cytosol prior to lysosomal degradation upon external temperature elevation. This was confirmed by confocal bioimaging and gene silencing reaching up to 90% and further demonstrated by the protein inhibition of both target genes.The thermoresponsiveness of ammonium bicarbonate containing liposomes enabled the rapid endosomal escape of the particles and resulted in an efficient gene silencing.

  18. A Rapid and Efficient Method for Purifying High Quality Total RNA from Peaches (Prunus persica for Functional Genomics Analyses

    Directory of Open Access Journals (Sweden)

    LEE MEISEL

    2005-01-01

    Full Text Available Prunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica. Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.

  19. Receptor-targeted liposome-peptide-siRNA nanoparticles represent an efficient delivery system for MRTF silencing in conjunctival fibrosis.

    Science.gov (United States)

    Yu-Wai-Man, Cynthia; Tagalakis, Aristides D; Manunta, Maria D; Hart, Stephen L; Khaw, Peng T

    2016-02-24

    There is increasing evidence that the Myocardin-related transcription factor/Serum response factor (MRTF/SRF) pathway plays a key role in fibroblast activation and that knocking down MRTF can lead to reduced scarring and fibrosis. Here, we have developed a receptor-targeted liposome-peptide-siRNA nanoparticle as a non-viral delivery system for MRTF-B siRNA in conjunctival fibrosis. Using 50 nM siRNA, the MRTF-B gene was efficiently silenced by 76% and 72% with LYR and LER nanoparticles, respectively. The silencing efficiency was low when non-targeting peptides or siRNA alone or liposome-siRNA alone were used. LYR and LER nanoparticles also showed higher silencing efficiency than PEGylated LYR-P and LER-P nanoparticles. The nanoparticles were not cytotoxic using different liposomes, targeting peptides, and 50 nM siRNA. Three-dimensional fibroblast-populated collagen matrices were also used as a functional assay to measure contraction in vitro, and showed that MRTF-B LYR nanoparticles completely blocked matrix contraction after a single transfection treatment. In conclusion, this is the first study to develop and show that receptor-targeted liposome-peptide-siRNA nanoparticles represent an efficient and safe non-viral siRNA delivery system that could be used to prevent fibrosis after glaucoma filtration surgery and other contractile scarring conditions in the eye.

  20. Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression

    DEFF Research Database (Denmark)

    Radzisheuskaya, Aliaksandra; Shlyueva, Daria; Müller, Iris

    2016-01-01

    CRISPR interference (CRISPRi) represents a newly developed tool for targeted gene repression. It has great application potential for studying gene function and mapping gene regulatory elements. However, the optimal parameters for efficient single guide RNA (sgRNA) design for CRISPRi are not fully...

  1. Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain.

    Science.gov (United States)

    Fang, Zhen; Zhang, Juan; Du, Guocheng; Chen, Jian

    2016-06-14

    The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s(-1) mM(-1). The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD.

  2. Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm.

    Science.gov (United States)

    Zhou, Hong; Zhou, Michael; Li, Daisy; Manthey, Joseph; Lioutikova, Ekaterina; Wang, Hong; Zeng, Xiao

    2017-11-17

    The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection. A highly efficient computationl algorithm was developed for whole genome sgRNA design and off-target homology searches. By means of a dynamically constructed sequence-indexed database and a simplified sequence alignment method, this algorithm achieves very high efficiency while guaranteeing the identification of all existing potential off-target homologies. Via this algorithm, 1,876,775 sgRNAs were designed for the 19,153 human mRNA genes and only two sgRNAs were found to be free of off-target homology. By means of the novel and efficient sgRNA homology search algorithm introduced in this article, genome wide sgRNA design and off-target analysis were conducted and the results confirmed the mathematical analysis that for a sgRNA sequence, it is almost impossible to escape potential off-target homologies. Future innovations on the CRISPR Cas9 gene editing technology need to focus on how to eliminate the Cas9 off-target activity.

  3. Host apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3G is an innate defensive factor and drug target against hepatitis C virus.

    Science.gov (United States)

    Peng, Zong-Gen; Zhao, Zhi-Yun; Li, Yan-Ping; Wang, Yu-Ping; Hao, Lan-Hu; Fan, Bo; Li, Yu-Huan; Wang, Yue-Ming; Shan, Yong-Qiang; Han, Yan-Xing; Zhu, Yan-Ping; Li, Jian-Rui; You, Xue-Fu; Li, Zhuo-Rong; Jiang, Jian-Dong

    2011-04-01

    Host cellular factor apolipoprotein B messenger RNA (mRNA)-editing enzyme catalytic polypeptide-like 3G (hA3G) is a cytidine deaminase that inhibits a group of viruses including human immunodeficiency virus-1 (HIV-1). In the continuation of our research on hA3G, we found that hA3G stabilizing compounds significantly inhibited hepatitis C virus (HCV) replication. Therefore, this study investigated the role of hA3G in HCV replication. Introduction of external hA3G into HCV-infected Huh7.5 human hepatocytes inhibited HCV replication; knockdown of endogenous hA3G enhanced HCV replication. Exogenous HIV-1 virion infectivity factor (Vif) decreased intracellular hA3G and therefore enhanced HCV proliferation, suggesting that the presence of Vif might be an explanation for the HIV-1/HCV coinfection often observed in HIV-1(+) individuals. Treatment of the HCV-infected Huh7.5 cells with RN-5 or IMB-26, two known hA3G stabilizing compounds, increased intracellular hA3G and accordingly inhibited HCV replication. The compounds inhibit HCV through increasing the level of hA3G incorporated into HCV particles, but not through inhibiting HCV enzymes. However, G/A hypermutation in the HCV genome were not detected, suggesting a new antiviral mechanism of hA3G in HCV, different from that in HIV-1. Stabilization of hA3G by RN-5 was safe in vivo. hA3G appears to be a cellular restrict factor against HCV and could be a potential target for drug discovery. 2011 American Association for the Study of Liver Diseases.

  4. Specific and Efficient Regression of Cancers Harboring KRAS Mutation by Targeted RNA Replacement.

    Science.gov (United States)

    Kim, Sung Jin; Kim, Ju Hyun; Yang, Bitna; Jeong, Jin-Sook; Lee, Seong-Wook

    2017-02-01

    Mutations in the KRAS gene, which persistently activate RAS function, are most frequently found in many types of human cancers. Here, we proposed and verified a new approach against cancers harboring the KRAS mutation with high cancer selectivity and efficient anti-cancer effects based on targeted RNA replacement. To this end, trans-splicing ribozymes from Tetrahymena group I intron were developed, which can specifically target and reprogram the mutant KRAS G12V transcript to induce therapeutic gene activity in cells. Adenoviral vectors containing the specific ribozymes with downstream suicide gene were constructed and then infection with the adenoviruses specifically downregulated KRAS G12V expression and killed KRAS G12V-harboring cancer cells additively upon pro-drug treatment, but it did not affect the growth of wild-type KRAS-expressing cells. Minimal liver toxicity was noted when the adenoviruses were administered systemically in vivo. Importantly, intratumoral injection of the adenoviruses with pro-drug treatment specifically and significantly impeded the growth of xenografted tumors harboring KRAS G12V through a trans-splicing reaction with the target RNA. In contrast, xenografted tumors harboring wild-type KRAS were not affected by the adenoviruses. Therefore, RNA replacement with a mutant KRAS-targeting trans-splicing ribozyme is a potentially useful therapeutic strategy to combat tumors harboring KRAS mutation. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

  5. Efficient transformation and artificial miRNA gene silencing in Lemna minor.

    Science.gov (United States)

    Cantó-Pastor, A; Mollá-Morales, A; Ernst, E; Dahl, W; Zhai, J; Yan, Y; Meyers, B C; Shanklin, J; Martienssen, R

    2015-01-01

    Despite rapid doubling time, simple architecture and ease of metabolic labelling, a lack of genetic tools in the Lemnaceae (duckweed) has impeded the full implementation of this organism as a model for biological research. Here, we present technologies to facilitate high-throughput genetic studies in duckweed. We developed a fast and efficient method for producing Lemna minor stable transgenic fronds via Agrobacterium-mediated transformation and regeneration from tissue culture. Additionally, we engineered an artificial microRNA (amiRNA) gene silencing system. We identified a Lemna gibba endogenous miR166 precursor and used it as a backbone to produce amiRNAs. As a proof of concept we induced the silencing of CH42, a magnesium chelatase subunit, using our amiRNA platform. Expression of CH42 in transgenic L. minor fronds was significantly reduced, which resulted in reduction of chlorophyll pigmentation. The techniques presented here will enable tackling future challenges in the biology and biotechnology of Lemnaceae. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  6. An anti-HIV-1 compound that increases steady-state expression of apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G.

    Science.gov (United States)

    Ejima, Tomohiko; Hirota, Mayuko; Mizukami, Tamio; Otsuka, Masami; Fujita, Mikako

    2011-10-01

    Human apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) 3G (A3G) is an antiviral protein that blocks HIV-1 replication. However, the antiviral activity of A3G is overcome by the HIV-1 protein Vif. This inhibitory function of Vif is related to its ability to degrade A3G in the proteasome. This finding prompted us to examine the activities of 4-(dimethylamino)-2,6-bis[(N-(2-[(2-nitrophenyl)dithio]ethyl)amino)methyl]pyridine (SN-2) and SN-3. We found that 5 µM SN-2 increases the expression of A3G to a level much higher than that observed in the absence of Vif, without affecting the level of Vif expression. The proteasome inhibitor MG-132 increased the level of both A3G and Vif expression. These results demonstrate that A3G is ubiquitinated and degraded in the proteasome by a factor other than Vif, and that SN-2 selectively inhibits these processes. Furthermore, 5 µM SN-2 significantly inhibited the MAGI cell infectivity of wild-type HIV-1. These findings may contribute to the development of a novel anti-HIV-1 drug.

  7. Preparation and characterization of LTA-type zeolite framework dispersed ruthenium nanoparticles and their catalytic application in the hydrolytic dehydrogenation of ammonia–borane for efficient hydrogen generation

    International Nuclear Information System (INIS)

    Zahmakiran, Mehmet

    2012-01-01

    Highlights: ► Ru(0)NPs-ZK-4 were prepared and characterized by advanced analytical techniques. ► They achieve the hydrolysis of ammonia-borane with TOF = 5410 h −1 and TTO = 36700. ► They maintain 85% of their activity even at the fifth catalytic run. - Abstract: The safe and efficient hydrogen storage and production are major obstacles to use hydrogen as an energy carrier. Therefore, significant efforts have been focused on the development of new materials for the chemical hydrogen storage and production. Of particular importance, ammonia–borane (NH 3 BH 3 ) is emerging as one of the most promising solid hydrogen carrier due to its high gravimetric hydrogen storage capacity (19.6 wt.%) and low molecular weight (30.8 g/mol). ammonia–borane can release hydrogen gas upon catalytic hydrolysis under mild conditions. Herein, the discovery of a new catalytic material, ruthenium nanoparticles stabilized by ZK-4 zeolite framework, for this important reaction has been reported. This new catalyst system was prepared by borohydride reduction of ruthenium(III)-exchanged ZK-4 zeolite in water at room temperature. The characterization of the resulting material by advanced analytical tools shows the formation of ZK-4 zeolite dispersed ruthenium nanoparticles (2.9 ± 0.9 nm). The catalytic performance of the resulting supported ruthenium nanoparticles depending on activity, lifetime and reusability was demonstrated in the hydrolytic dehydrogenation of ammonia–borane. They were found to be highly active (initial TOF = 5410 h −1 ), long-lived (TTO = 36,700) and reusable catalyst (retaining of >85% of initial activity in the 5th reuse) in this important catalytic reaction at room temperature under air.

  8. Heritability in the efficiency of nonsense-mediated mRNA decay in humans.

    LENUS (Irish Health Repository)

    Seoighe, Cathal

    2010-01-01

    BACKGROUND: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. PRINCIPAL FINDINGS: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. CONCLUSIONS: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3.

  9. Heritability in the efficiency of nonsense-mediated mRNA decay in humans

    KAUST Repository

    Seoighe, Cathal

    2010-07-21

    Background: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. Principal Findings: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. Conclusions: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3. © 2010 Seoighe, Gehring.

  10. Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70

    Directory of Open Access Journals (Sweden)

    Noireaux Vincent

    2010-06-01

    Full Text Available Abstract Background Escherichia coli cell-free expression systems use bacteriophage RNA polymerases, such as T7, to synthesize large amounts of recombinant proteins. These systems are used for many applications in biotechnology, such as proteomics. Recently, informational processes have been reconstituted in vitro with cell-free systems. These synthetic approaches, however, have been seriously limited by a lack of transcription modularity. The current available cell-free systems have been optimized to work with bacteriophage RNA polymerases, which put significant restrictions to engineer processes related to biological information. The development of efficient cell-free systems with broader transcription capabilities is required to study complex informational processes in vitro. Results In this work, an efficient cell-free expression system that uses the endogenous E. coli RNA polymerase only and sigma factor 70 for transcription was prepared. Approximately 0.75 mg/ml of Firefly luciferase and enhanced green fluorescent protein were produced in batch mode. A plasmid was optimized with different regulatory parts to increase the expression. In addition, a new eGFP was engineered that is more translatable in cell-free systems than the original eGFP. The protein production was characterized with three different adenosine triphosphate (ATP regeneration systems: creatine phosphate (CP, phosphoenolpyruvate (PEP, and 3-phosphoglyceric acid (3-PGA. The maximum protein production was obtained with 3-PGA. Preparation of the crude extract was streamlined to a simple routine procedure that takes 12 hours including cell culture. Conclusions Although it uses the endogenous E. coli transcription machinery, this cell-free system can produce active proteins in quantities comparable to bacteriophage systems. The E. coli transcription provides much more possibilities to engineer informational processes in vitro. Many E. coli promoters/operators specific to sigma

  11. The inhibitory effect of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) and its family members on the activity of cellular microRNAs.

    Science.gov (United States)

    Zhang, Hui

    2010-01-01

    The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G or APOBEC3G) and its fellow cytidine deaminase family members are potent restrictive factors for human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. However, the cellular function of APOBEC3G remains to be further clarified. It has been reported that APOBEC3s can restrict the mobility of endogenous retroviruses and LTR-retrotransposons, suggesting that they can maintain stability in host genomes. However, APOBEC3G is normally cytoplasmic. Further studies have demonstrated that it is associated with an RNase-sensitive high molecular mass (HMM) and located in processing bodies (P-bodies) of replicating T-cells, indicating that the major cellular function of APOBEC3G seems to be related to P-body-related RNA processing and metabolism. As the function of P-body is closely related to miRNA activity, APOBEC3G could affect the miRNA function. Recent studies have demonstrated that APOBEC3G and its family members counteract miRNA-mediated repression of protein translation. Further, APOBEC3G enhances the association of miRNA-targeted mRNA with polysomes, and facilitates the dissociation of miRNA-targeted mRNA from P-bodies. As such, APOBEC3G regulate the activity of cellular miRNAs. Whether this function is related to its potent antiviral activity remains to be further determined.

  12. Catalytic Ammonia Decomposition over High-Performance Ru/Graphene Nanocomposites for Efficient COx-Free Hydrogen Production

    Directory of Open Access Journals (Sweden)

    Gang Li

    2017-01-01

    Full Text Available Highly-dispersed Ru nanoparticles were grown on graphene nanosheets by simultaneously reducing graphene oxide and Ru ions using ethylene glycol (EG, and the resultant Ru/graphene nanocomposites were applied as a catalyst to ammonia decomposition for COx-free hydrogen production. Tuning the microstructures of Ru/graphene nanocomposites was easily accomplished in terms of Ru particle size, morphology, and loading by adjusting the preparation conditions. This was the key to excellent catalytic activity, because ammonia decomposition over Ru catalysts is structure-sensitive. Our results demonstrated that Ru/graphene prepared using water as a co-solvent greatly enhanced the catalytic performance for ammonia decomposition, due to the significantly improved nano architectures of the composites. The long-term stability of Ru/graphene catalysts was evaluated for COx-free hydrogen production from ammonia at high temperatures, and the structural evolution of the catalysts was investigated during the catalytic reactions. Although there were no obvious changes in the catalytic activities at 450 °C over a duration of 80 h, an aggregation of the Ru nanoparticles was still observed in the nanocomposites, which was ascribed mainly to a sintering effect. However, the performance of the Ru/graphene catalyst was decreased gradually at 500 °C within 20 h, which was ascribed mainly to both the effect of the methanation of the graphene nanosheet under a H2 atmosphere and to enhanced sintering under high temperatures.

  13. Efficient Catalytic Conversion of Ethanol to 1-Butanol via the Guerbet Reaction over Copper- and Nickel-Doped Porous

    NARCIS (Netherlands)

    Sun, Zhuohua; Vasconcelos, Anais Couto; Bottari, Giovanni; Stuart, Marc C. A.; Bonura, Giuseppe; Cannilla, Catia; Frusteri, Francesco; Barta, Katalin

    The direct conversion of ethanol to higher value 1-butanol is a catalytic transformation of great interest in light of the expected wide availability of bioethanol originating from the fermentation of renewable resources. In this contribution we describe several novel compositions of porous metal

  14. Gold nanoparticle mediated laser transfection for efficient siRNA mediated gene knock down.

    Directory of Open Access Journals (Sweden)

    Dag Heinemann

    Full Text Available Laser based transfection methods have proven to be an efficient and gentle alternative to established molecule delivery methods like lipofection or electroporation. Among the laser based methods, gold nanoparticle mediated laser transfection bears the major advantage of high throughput and easy usability. This approach uses plasmon resonances on gold nanoparticles unspecifically attached to the cell membrane to evoke transient and spatially defined cell membrane permeabilization. In this study, we explore the parameter regime for gold nanoparticle mediated laser transfection for the delivery of molecules into cell lines and prove its suitability for siRNA mediated gene knock down. The developed setup allows easy usage and safe laser operation in a normal lab environment. We applied a 532 nm Nd:YAG microchip laser emitting 850 ps pulses at a repetition rate of 20.25 kHz. Scanning velocities of the laser spot over the sample of up to 200 mm/s were tested without a decline in perforation efficiency. This velocity leads to a process speed of ∼8 s per well of a 96 well plate. The optimal particle density was determined to be ∼6 particles per cell using environmental scanning electron microscopy. Applying the optimized parameters transfection efficiencies of 88% were achieved in canine pleomorphic adenoma ZMTH3 cells using a fluorescent labeled siRNA while maintaining a high cell viability of >90%. Gene knock down of d2-EGFP was demonstrated and validated by fluorescence repression and western blot analysis. On basis of our findings and established mathematical models we suppose a mixed transfection mechanism consisting of thermal and multiphoton near field effects. Our findings emphasize that gold nanoparticle mediated laser transfection provides an excellent tool for molecular delivery for both, high throughput purposes and the transfection of sensitive cells types.

  15. Gold nanoparticle mediated laser transfection for efficient siRNA mediated gene knock down.

    Science.gov (United States)

    Heinemann, Dag; Schomaker, Markus; Kalies, Stefan; Schieck, Maximilian; Carlson, Regina; Murua Escobar, Hugo; Ripken, Tammo; Meyer, Heiko; Heisterkamp, Alexander

    2013-01-01

    Laser based transfection methods have proven to be an efficient and gentle alternative to established molecule delivery methods like lipofection or electroporation. Among the laser based methods, gold nanoparticle mediated laser transfection bears the major advantage of high throughput and easy usability. This approach uses plasmon resonances on gold nanoparticles unspecifically attached to the cell membrane to evoke transient and spatially defined cell membrane permeabilization. In this study, we explore the parameter regime for gold nanoparticle mediated laser transfection for the delivery of molecules into cell lines and prove its suitability for siRNA mediated gene knock down. The developed setup allows easy usage and safe laser operation in a normal lab environment. We applied a 532 nm Nd:YAG microchip laser emitting 850 ps pulses at a repetition rate of 20.25 kHz. Scanning velocities of the laser spot over the sample of up to 200 mm/s were tested without a decline in perforation efficiency. This velocity leads to a process speed of ∼8 s per well of a 96 well plate. The optimal particle density was determined to be ∼6 particles per cell using environmental scanning electron microscopy. Applying the optimized parameters transfection efficiencies of 88% were achieved in canine pleomorphic adenoma ZMTH3 cells using a fluorescent labeled siRNA while maintaining a high cell viability of >90%. Gene knock down of d2-EGFP was demonstrated and validated by fluorescence repression and western blot analysis. On basis of our findings and established mathematical models we suppose a mixed transfection mechanism consisting of thermal and multiphoton near field effects. Our findings emphasize that gold nanoparticle mediated laser transfection provides an excellent tool for molecular delivery for both, high throughput purposes and the transfection of sensitive cells types.

  16. Gold Nanoparticle Mediated Laser Transfection for Efficient siRNA Mediated Gene Knock Down

    Science.gov (United States)

    Heinemann, Dag; Schomaker, Markus; Kalies, Stefan; Schieck, Maximilian; Carlson, Regina; Escobar, Hugo Murua; Ripken, Tammo; Meyer, Heiko; Heisterkamp, Alexander

    2013-01-01

    Laser based transfection methods have proven to be an efficient and gentle alternative to established molecule delivery methods like lipofection or electroporation. Among the laser based methods, gold nanoparticle mediated laser transfection bears the major advantage of high throughput and easy usability. This approach uses plasmon resonances on gold nanoparticles unspecifically attached to the cell membrane to evoke transient and spatially defined cell membrane permeabilization. In this study, we explore the parameter regime for gold nanoparticle mediated laser transfection for the delivery of molecules into cell lines and prove its suitability for siRNA mediated gene knock down. The developed setup allows easy usage and safe laser operation in a normal lab environment. We applied a 532 nm Nd:YAG microchip laser emitting 850 ps pulses at a repetition rate of 20.25 kHz. Scanning velocities of the laser spot over the sample of up to 200 mm/s were tested without a decline in perforation efficiency. This velocity leads to a process speed of ∼8 s per well of a 96 well plate. The optimal particle density was determined to be ∼6 particles per cell using environmental scanning electron microscopy. Applying the optimized parameters transfection efficiencies of 88% were achieved in canine pleomorphic adenoma ZMTH3 cells using a fluorescent labeled siRNA while maintaining a high cell viability of >90%. Gene knock down of d2-EGFP was demonstrated and validated by fluorescence repression and western blot analysis. On basis of our findings and established mathematical models we suppose a mixed transfection mechanism consisting of thermal and multiphoton near field effects. Our findings emphasize that gold nanoparticle mediated laser transfection provides an excellent tool for molecular delivery for both, high throughput purposes and the transfection of sensitive cells types. PMID:23536802

  17. 5S rRNA Promoter for Guide RNA Expression Enabled Highly Efficient CRISPR/Cas9 Genome Editing in Aspergillus niger.

    Science.gov (United States)

    Zheng, Xiaomei; Zheng, Ping; Zhang, Kun; Cairns, Timothy C; Meyer, Vera; Sun, Jibin; Ma, Yanhe

    2018-04-30

    The CRISPR/Cas9 system is a revolutionary genome editing tool. However, in eukaryotes, search and optimization of a suitable promoter for guide RNA expression is a significant technical challenge. Here we used the industrially important fungus, Aspergillus niger, to demonstrate that the 5S rRNA gene, which is both highly conserved and efficiently expressed in eukaryotes, can be used as a guide RNA promoter. The gene editing system was established with 100% rates of precision gene modifications among dozens of transformants using short (40-bp) homologous donor DNA. This system was also applicable for generation of designer chromosomes, as evidenced by deletion of a 48 kb gene cluster required for biosynthesis of the mycotoxin fumonisin B1. Moreover, this system also facilitated simultaneous mutagenesis of multiple genes in A. niger. We anticipate that the use of the 5S rRNA gene as guide RNA promoter can broadly be applied for engineering highly efficient eukaryotic CRISPR/Cas9 toolkits. Additionally, the system reported here will enable development of designer chromosomes in model and industrially important fungi.

  18. Efficient RNA extraction protocol for the wood mangrove species Laguncularia racemosa suited for next-generation RNA sequencing

    International Nuclear Information System (INIS)

    Wilwerth, M. W.; Rossetto, P.

    2016-01-01

    Mangrove flora and habitat have immeasurable importance in marine and coastal ecology as well as in the economy. Despite their importance, they are constantly threatened by oil spill accidents and environmental contamination; therefore, it is crucial to understand the changes in gene expression to better predict toxicity in these plants. Among the species of Atlantic coast mangrove (Americas and Africa), Laguncularia racemosa, or white mangrove, is a conspicuous species. The wide distribution of L. racemosa in areas where marine oil exploration is rapidly increasing make it a candidate mangrove species model to uncover the impact of oil spills at the molecular level with the use of massive transcriptome sequencing. However, for this purpose, the RNA extraction protocol should ensure low levels of contaminants and structure integrity. In this study, eight RNA extraction methods were tested and analysed using downstream applications. The InviTrap Spin Plant RNA Mini Kit performed best with regard to purity and integrity. Moreover, the obtained RNA was submitted to cDNA synthesis and RT-PCR, successfully generating amplification products of the expected size. These Results show the applicability of the RNA obtained here for downstream methodologies, such as the construction of cDNA libraries for the Illumina Hi-seq platform. (author)

  19. Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

    Science.gov (United States)

    Liphardt, J; Napthine, S; Kontos, H; Brierley, I

    1999-05-07

    RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those

  20. Efficient recovery of whole blood RNA - a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species

    Directory of Open Access Journals (Sweden)

    Schwochow Doreen

    2012-06-01

    Full Text Available Abstract Background Since the emergence of next generation sequencing platforms, unprecedented opportunities have arisen in the study of natural vertebrate populations. In particular, insights into the genetic and epigenetic mechanisms of adaptation can be revealed through study of the expression profiles of genes. However, as a pre-requisite to expression profiling, care must be taken in RNA preparation as factors like DNA contamination, RNA integrity or transcript abundance can affect downstream applications. Here, we evaluated five commonly used RNA extraction methods using whole blood sampled under varying conditions from 20 wild carnivores. Results Despite the use of minute starting volumes, all methods produced quantifiable RNA extracts (1.4 – 18.4 μg with varying integrity (RIN 4.6 - 7.7, the latter being significantly affected by the storage and extraction method used. We observed a significant overall effect of the extraction method on DNA contamination. One particular extraction method, the LeukoLOCK™ filter system, yielded high RNA integrity along with low DNA contamination and efficient depletion of hemoglobin transcripts highly abundant in whole blood. In a proof of concept sequencing experiment, we found globin RNA transcripts to occupy up to ¼ of all sequencing reads if libraries were not depleted of hemoglobin prior to sequencing. Conclusion By carefully choosing the appropriate RNA extraction method, whole blood can become a valuable source for high-throughput applications like expression arrays or transcriptome sequencing from natural populations. Additionally, candidate genes showing signs of selection could subsequently be genotyped in large population samples using whole blood as a source for RNA without harming individuals from rare or endangered species.

  1. Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease

    Science.gov (United States)

    Flowers, G. Parker; Timberlake, Andrew T.; Mclean, Kaitlin C.; Monaghan, James R.; Crews, Craig M.

    2014-01-01

    Among tetrapods, only urodele salamanders, such as the axolotl Ambystoma mexicanum, can completely regenerate limbs as adults. The mystery of why salamanders, but not other animals, possess this ability has for generations captivated scientists seeking to induce this phenomenon in other vertebrates. Although many recent advances in molecular biology have allowed limb regeneration and tissue repair in the axolotl to be investigated in increasing detail, the molecular toolkit for the study of this process has been limited. Here, we report that the CRISPR-Cas9 RNA-guided nuclease system can efficiently create mutations at targeted sites within the axolotl genome. We identify individual animals treated with RNA-guided nucleases that have mutation frequencies close to 100% at targeted sites. We employ this technique to completely functionally ablate EGFP expression in transgenic animals and recapitulate developmental phenotypes produced by loss of the conserved gene brachyury. Thus, this advance allows a reverse genetic approach in the axolotl and will undoubtedly provide invaluable insight into the mechanisms of salamanders' unique regenerative ability. PMID:24764077

  2. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases.

    Science.gov (United States)

    Citorik, Robert J; Mimee, Mark; Lu, Timothy K

    2014-11-01

    Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.

  3. Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B.

    Directory of Open Access Journals (Sweden)

    Zhu Li

    Full Text Available The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.

  4. Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B.

    Science.gov (United States)

    Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

    2017-01-01

    The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.

  5. Efficient selective catalytic reduction of NO by novel carbon-doped metal catalysts made from electroplating sludge.

    Science.gov (United States)

    Zhang, Jia; Zhang, Jingyi; Xu, Yunfeng; Su, Huimin; Li, Xiaoman; Zhou, Ji Zhi; Qian, Guangren; Li, Li; Xu, Zhi Ping

    2014-10-07

    Electroplating sludges, once regarded as industrial wastes, are precious resources of various transition metals. This research has thus investigated the recycling of an electroplating sludge as a novel carbon-doped metal (Fe, Ni, Mg, Cu, and Zn) catalyst, which was different from a traditional carbon-supported metal catalyst, for effective NO selective catalytic reduction (SCR). This catalyst removed >99.7% NO at a temperature as low as 300 °C. It also removed NO steadily (>99%) with a maximum specific accumulative reduced amount (MSARA) of 3.4 mmol/g. Gas species analyses showed that NO removal was accompanied by evolving N2 and CO2. Moreover, in a wide temperature window, the sludge catalyst showed a higher CO2 selectivity (>99%) than an activated carbon-supported metal catalyst. Structure characterizations revealed that carbon-doped metal was transformed to metal oxide in the sludge catalyst after the catalytic test, with most carbon (2.33 wt %) being consumed. These observations suggest that NO removal over the sludge catalyst is a typical SCR where metals/metal oxides act as the catalytic center and carbon as the reducing reagent. Therefore, our report probably provides an opportunity for high value-added utilizations of heavy-metal wastes in mitigating atmospheric pollutions.

  6. A Simple and Efficient RNA Extraction Method from Deep-Sea Hydrothermal Vent Chimney Structures.

    Science.gov (United States)

    Muto, Hisashi; Takaki, Yoshihiro; Hirai, Miho; Mino, Sayaka; Sawayama, Shigeki; Takai, Ken; Nakagawa, Satoshi

    2017-12-27

    RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals. This decrease in RNA was prevented by the addition of sodium tripolyphosphate (STPP), deoxynucleotide triphosphates (dNTPs), salmon sperm DNA, and NaOH. The addition of STPP was also effective for RNA extraction from the mixture of E. coli cells and mock chimney minerals when TRIzol reagent and the RNeasy column were used, but not when the RNeasy PowerSoil total RNA kit was used. A combination of STPP, TRIzol reagent, the RNeasy column, and sonication resulted in the highest RNA yield from a natural chimney. This indirect extraction procedure is simple, rapid, inexpensive, and may be used for large-scale RNA extraction.

  7. Calcium-microRNA Complexes Functionalized Nanotubular Implant Surface for Highly Efficient Transfection and Enhanced Osteogenesis of Mesenchymal Stem Cells

    DEFF Research Database (Denmark)

    Song, Wen; Yang, Chuanxu; Svend Le, Dang Quang

    2018-01-01

    Controlling mesenchymal stem cells (MSCs) differentiation by RNA interference (RNAi) is a promising approach for next-generation regenerative medicine. However, efficient delivery of RNAi therapeutics is still a limiting factor. In this study, we have developed a simple, biocompatible and highly...... effective delivery method of small RNA therapeutics into hMSCs from an implant surface by calcium ions. First, we demonstrated that simple Ca/siGFP nanocomplexes were able to efficiently silence GFP in GFP-expressing hMSCs with adequate Ca2+ concentration (>5 mM). In addition, a single transfection could...

  8. High loading efficiency and sustained release of siRNA encapsulated in PLGA nanoparticles: quality by design optimization and characterization.

    Science.gov (United States)

    Cun, Dongmei; Jensen, Ditte Krohn; Maltesen, Morten Jonas; Bunker, Matthew; Whiteside, Paul; Scurr, David; Foged, Camilla; Nielsen, Hanne Mørck

    2011-01-01

    Poly(DL-lactide-co-glycolide acid) (PLGA) is an attractive polymer for delivery of biopharmaceuticals owing to its biocompatibility, biodegradability and outstanding controlled release characteristics. The purpose of this study was to understand and define optimal parameters for preparation of small interfering RNA (siRNA)-loaded PLGA nanoparticles by the double emulsion solvent evaporation method and characterize their properties. The experiments were performed according to a 2(5-1) fractional factorial design based on five independent variables: The volume ratio between the inner water phase and the oil phase, the PLGA concentration, the sonication time, the siRNA load and the amount of acetylated bovine serum albumin (Ac-BSA) in the inner water phase added to stabilize the primary emulsion. The effects on the siRNA encapsulation efficiency and the particle size were investigated. The most important factors for obtaining an encapsulation efficiency as high as 70% were the PLGA concentration and the volume ratio whereas the size was mainly affected by the PLGA concentration. The viscosity of the oil phase was increased at high PLGA concentration, which explains the improved encapsulation by stabilization of the primary emulsion and reduction of siRNA leakage to the outer water phase. Addition of Ac-BSA increased the encapsulation efficiency at low PLGA concentrations. The PLGA matrix protected siRNA against nuclease degradation, provided a burst release of surface-localized siRNA followed by a triphasic sustained release for two months. These results enable careful understanding and definition of optimal process parameters for preparation of PLGA nanoparticles encapsulating high amounts of siRNA with immediate and long-term sustained release properties. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Zinc-mediated binding of a low-molecular-weight stabilizer of the host anti-viral factor apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G.

    Science.gov (United States)

    Radwan, Mohamed O; Sonoda, Sachiko; Ejima, Tomohiko; Tanaka, Ayumi; Koga, Ryoko; Okamoto, Yoshinari; Fujita, Mikako; Otsuka, Masami

    2016-09-15

    Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G, A3G), is a human anti-virus restriction protein which works deaminase-dependently and -independently. A3G is known to be ubiquitinated by HIV-1 viral infectivity factor (Vif) protein, leading to proteasomal degradation. A3G contains two zinc ions at the N-terminal domain and the C-terminal domain. Four lysine residues, K(297), K(301), K(303), and K(334), are known to be required for Vif-mediated A3G ubiquitination and degradation. Previously, we reported compound SN-1, a zinc chelator that increases steady-state expression level of A3G in the presence of Vif. In this study, we prepared Biotin-SN-1, a biotinylated derivative of SN-1, to study the SN-1-A3G interaction. A pull-down assay revealed that Biotin-SN-1 bound A3G. A zinc-abstraction experiment indicated that SN-1 binds to the zinc site of A3G. We carried out a SN-1-A3G docking study using molecular operating environment. The calculations revealed that SN-1 binds to the C-terminal domain through Zn(2+), H(216), P(247), C(288), and Y(315). Notably, SN-1-binding covers the H(257), E(259), C(288), and C(291) residues that participate in zinc-mediated deamination, and the ubiquitination regions of A3G. The binding of SN-1 presumably perturbs the secondary structure between C(288) and Y(315), leading to less efficient ubiquitination. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Optimized paired-sgRNA/Cas9 cloning and expression cassette triggers high-efficiency multiplex genome editing in kiwifruit.

    Science.gov (United States)

    Wang, Zupeng; Wang, Shuaibin; Li, Dawei; Zhang, Qiong; Li, Li; Zhong, Caihong; Liu, Yifei; Huang, Hongwen

    2018-01-13

    Kiwifruit is an important fruit crop; however, technologies for its functional genomic and molecular improvement are limited. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability is variable depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Optimizing conditions for its use within a particular species is therefore needed to achieve highly efficient genome editing. In this study, we developed a new cloning strategy for generating paired-sgRNA/Cas9 vectors containing four sgRNAs targeting the kiwifruit phytoene desaturase gene (AcPDS). Comparing to the previous method of paired-sgRNA cloning, our strategy only requires the synthesis of two gRNA-containing primers which largely reduces the cost. We further compared efficiencies of paired-sgRNA/Cas9 vectors containing different sgRNA expression devices, including both the polycistronic tRNA-sgRNA cassette (PTG) and the traditional CRISPR expression cassette. We found the mutagenesis frequency of the PTG/Cas9 system was 10-fold higher than that of the CRISPR/Cas9 system, coinciding with the relative expressions of sgRNAs in two different expression cassettes. In particular, we identified large chromosomal fragment deletions induced by the paired-sgRNAs of the PTG/Cas9 system. Finally, as expected, we found both systems can successfully induce the albino phenotype of kiwifruit plantlets regenerated from the G418-resistance callus lines. We conclude that the PTG/Cas9 system is a more powerful system than the traditional CRISPR/Cas9 system for kiwifruit genome editing, which provides valuable clues for optimizing CRISPR/Cas9 editing system in other plants. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons

  11. Efficient delivery of Notch1 siRNA to SKOV3 cells by cationic cholesterol derivative-based liposome

    Directory of Open Access Journals (Sweden)

    Zhao Y

    2016-10-01

    Full Text Available Yun-Chun Zhao,1 Li Zhang,2 Shi-Sen Feng,3 Lu Hong,3 Hai-Li Zheng,3 Li-Li Chen,4 Xiao-Ling Zheng,1 Yi-Qing Ye,1 Meng-Dan Zhao,1 Wen-Xi Wang,3 Cai-Hong Zheng1 1Pharmacy Department, Women’s Hospital, 2Pharmacy Department, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China; 3Department of Pharmaceutic Preparation, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 4Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China Abstract: A novel cationic cholesterol derivative-based small interfering RNA (siRNA interference strategy was suggested to inhibit Notch1 activation in SKOV3 cells for the gene therapy of ovarian cancer. The cationic cholesterol derivative, N-(cholesterylhemisuccinoyl-amino-3-propyl-N, N-dimethylamine (DMAPA-chems liposome, was incubated with siRNA at different nitrogen-to-phosphate ratios to form stabilized, near-spherical siRNA/DMAPA-chems nanoparticles with sizes of 100–200 nm and zeta potentials of 40–50 mV. The siRNA/DMAPA-chems nanoparticles protected siRNA from nuclease degradation in 25% fetal bovine serum. The nanoparticles exhibited high cell uptake and Notch1 gene knockdown efficiency in SKOV3 cells at an nitrogen-to-phosphate ratio of 100 and an siRNA concentration of 50 nM. They also inhibited the growth and promoted the apoptosis of SKOV3 cells. These results may provide the potential for using cationic cholesterol derivatives as efficient nonviral siRNA carriers for the suppression of Notch1 activation in ovarian cancer cells. Keywords: siRNA, cationic cholesterol derivative, Notch1, ovarian cancer cells

  12. Directed modification of L-LcLDH1, an L-lactate dehydrogenase from Lactobacillus casei, to improve its specific activity and catalytic efficiency towards phenylpyruvic acid.

    Science.gov (United States)

    Li, Jian-Fang; Li, Xue-Qing; Liu, Yan; Yuan, Feng-Jiao; Zhang, Ting; Wu, Min-Chen; Zhang, Ji-Ru

    2018-05-22

    To improve the specific activity and catalytic efficiency of L-LcLDH1, an NADH-dependent allosteric L-lactate dehydrogenase from L. casei, towards phenylpyruvic acid (PPA), its directed modification was conducted based on the semi-rational design. The three variant genes, Lcldh1 Q88R , Lcldh1 I229A and Lcldh1 T235G , were constructed by whole-plasmid PCR as designed theoretically, and expressed in E. coli BL21(DE3), respectively. The purified mutant, L-LcLDH1 Q88R or L-LcLDH1 I229A , displayed the specific activity of 451.5 or 512.4 U/mg towards PPA, by which the asymmetric reduction of PPA afforded L-phenyllactic acid (PLA) with an enantiomeric excess (ee p ) more than 99%. Their catalytic efficiencies (k cat /K m ) without D-fructose-1,6-diphosphate (D-FDP) were 4.8- and 5.2-fold that of L-LcLDH1. Additionally, the k cat /K m values of L-LcLDH1 Q88R and L-LcLDH1 I229A with D-FDP were 168.4- and 8.5-fold higher than those of the same enzymes without D-FDP, respectively. The analysis of catalytic mechanisms by molecular docking (MD) simulation indicated that substituting I229 in L-LcLDH1 with Ala enlarges the space of substrate-binding pocket, and that the replacement of Q88 with Arg makes the inlet of pocket larger than that of L-LcLDH1. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end.

    Science.gov (United States)

    Merkiene, Egle; Gaidamaviciute, Edita; Riauba, Laurynas; Janulaitis, Arvydas; Lagunavicius, Arunas

    2010-08-01

    We improved the target RNA-primed RCA technique for direct detection and analysis of RNA in vitro and in situ. Previously we showed that the 3' --> 5' single-stranded RNA exonucleolytic activity of Phi29 DNA polymerase converts the target RNA into a primer and uses it for RCA initiation. However, in some cases, the single-stranded RNA exoribonucleolytic activity of the polymerase is hindered by strong double-stranded structures at the 3'-end of target RNAs. We demonstrate that in such hampered cases, the double-stranded RNA-specific Escherichia coli RNase III efficiently assists Phi29 DNA polymerase in converting the target RNA into a primer. These observations extend the target RNA-primed RCA possibilities to test RNA sequences distanced far from the 3'-end and customize this technique for the inner RNA sequence analysis.

  14. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

    KAUST Repository

    Butt, Haroon; Eid, Ayman; Ali, Zahir; Atia, Mohamed A. M.; Mokhtar, Morad M.; Hassan, Norhan; Lee, Ciaran M.; Bao, Gang; Mahfouz, Magdy M.

    2017-01-01

    used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate

  15. An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples.

    Directory of Open Access Journals (Sweden)

    Jonathan A Scolnick

    Full Text Available Fusion genes are known to be key drivers of tumor growth in several types of cancer. Traditionally, detecting fusion genes has been a difficult task based on fluorescent in situ hybridization to detect chromosomal abnormalities. More recently, RNA sequencing has enabled an increased pace of fusion gene identification. However, RNA-Seq is inefficient for the identification of fusion genes due to the high number of sequencing reads needed to detect the small number of fusion transcripts present in cells of interest. Here we describe a method, Single Primer Enrichment Technology (SPET, for targeted RNA sequencing that is customizable to any target genes, is simple to use, and efficiently detects gene fusions. Using SPET to target 5701 exons of 401 known cancer fusion genes for sequencing, we were able to identify known and previously unreported gene fusions from both fresh-frozen and formalin-fixed paraffin-embedded (FFPE tissue RNA in both normal tissue and cancer cells.

  16. Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency.

    Directory of Open Access Journals (Sweden)

    Max Schelker

    2016-10-01

    Full Text Available After endocytic uptake, influenza viruses transit early endosomal compartments and eventually reach late endosomes. There, the viral glycoprotein hemagglutinin (HA triggers fusion between endosomal and viral membrane, a critical step that leads to release of the viral segmented genome destined to reach the cell nucleus. Endosomal maturation is a complex process involving acidification of the endosomal lumen as well as endosome motility along microtubules. While the pH drop is clearly critical for the conformational change and membrane fusion activity of HA, the effect of intracellular transport dynamics on the progress of infection remains largely unclear. In this study, we developed a comprehensive mathematical model accounting for the first steps of influenza virus infection. We calibrated our model with experimental data and challenged its predictions using recombinant viruses with altered pH sensitivity of HA. We identified the time point of virus-endosome fusion and thereby the diffusion distance of the released viral genome to the nucleus as a critical bottleneck for efficient virus infection. Further, we concluded and supported experimentally that the viral RNA is subjected to cytosolic degradation strongly limiting the probability of a successful genome import into the nucleus.

  17. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Science.gov (United States)

    Bi, Yanwei; Sun, Le; Gao, Dandan; Ding, Chen; Li, Zhihua; Li, Yadong; Cun, Wei; Li, Qihan

    2014-05-01

    A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas)) RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ) and homology-directed repair (HDR) pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  18. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Directory of Open Access Journals (Sweden)

    Yanwei Bi

    2014-05-01

    Full Text Available A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR-associated (Cas RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ and homology-directed repair (HDR pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  19. Influenza A Virus NS1 Protein Promotes Efficient Nuclear Export of Unspliced Viral M1 mRNA.

    Science.gov (United States)

    Pereira, Carina F; Read, Eliot K C; Wise, Helen M; Amorim, Maria J; Digard, Paul

    2017-08-01

    Influenza A virus mRNAs are transcribed by the viral RNA-dependent RNA polymerase in the cell nucleus before being exported to the cytoplasm for translation. Segment 7 produces two major transcripts: an unspliced mRNA that encodes the M1 matrix protein and a spliced transcript that encodes the M2 ion channel. Export of both mRNAs is dependent on the cellular NXF1/TAP pathway, but it is unclear how they are recruited to the export machinery or how the intron-containing but unspliced M1 mRNA bypasses the normal quality-control checkpoints. Using fluorescent in situ hybridization to monitor segment 7 mRNA localization, we found that cytoplasmic accumulation of unspliced M1 mRNA was inefficient in the absence of NS1, both in the context of segment 7 RNPs reconstituted by plasmid transfection and in mutant virus-infected cells. This effect was independent of any major effect on steady-state levels of segment 7 mRNA or splicing but corresponded to a ∼5-fold reduction in the accumulation of M1. A similar defect in intronless hemagglutinin (HA) mRNA nuclear export was seen with an NS1 mutant virus. Efficient export of M1 mRNA required both an intact NS1 RNA-binding domain and effector domain. Furthermore, while wild-type NS1 interacted with cellular NXF1 and also increased the interaction of segment 7 mRNA with NXF1, mutant NS1 polypeptides unable to promote mRNA export did neither. Thus, we propose that NS1 facilitates late viral gene expression by acting as an adaptor between viral mRNAs and the cellular nuclear export machinery to promote their nuclear export. IMPORTANCE Influenza A virus is a major pathogen of a wide variety of mammalian and avian species that threatens public health and food security. A fuller understanding of the virus life cycle is important to aid control strategies. The virus has a small genome that encodes relatively few proteins that are often multifunctional. Here, we characterize a new function for the NS1 protein, showing that, as well as

  20. Comparative measurement of the efficiency of catalytic after-burning devices on a heavy-duty diesel engine

    Energy Technology Data Exchange (ETDEWEB)

    Pattas, K.N.; Kyriakis, N.A.; Samaras, Z.C.; Aidarinis, J.K.

    1984-01-01

    The effect of three oxidation catalysts (Honeycat DEP 290, Engelhard PTX 623, Herapur 20L) and one catalytic trap oxidizer (Johnson Matthey JM 13/II) on the emissions of a RABA (M.A.N. Licensed) heavy-duty diesel engine has been comparatively studied. Tests were conducted according to EPA 13 mode test to measure CO, total HC, NO/sub x/ and total particulate matter emitted by the engine with and without devices. The test results were also correlated to the total emissions of the Athenian buses through new weighing factors of an ''Athenian 13 mode test''. The engine tests for all four devices resulted in: (1) considerable reduction of the engine's CO and total HC emissions - being already low (2) practically no difference in NO/sub x/ emissions and (3) increase of the total particulate emissions at high load modes.

  1. Modeling and Re-Engineering of Azotobacter vinelandii Alginate Lyase to Enhance Its Catalytic Efficiency for Accelerating Biofilm Degradation.

    Directory of Open Access Journals (Sweden)

    Chul Ho Jang

    Full Text Available Alginate is known to prevent elimination of Pseudomonas aeruginosa biofilms. Alginate lyase (AlgL might therefore facilitate treatment of Pseudomonas aeruginosa-infected cystic fibrosis patients. However, the catalytic activity of wild-type AlgL is not sufficiently high. Therefore, molecular modeling and site-directed mutagenesis of AlgL might assist in enzyme engineering for therapeutic development. AlgL, isolated from Azotobacter vinelandii, catalyzes depolymerization of alginate via a β-elimination reaction. AlgL was modeled based on the crystal structure template of Sphingomonas AlgL species A1-III. Based on this computational analysis, AlgL was subjected to site-directed mutagenesis to improve its catalytic activity. The kcat/Km of the K194E mutant showed a nearly 5-fold increase against the acetylated alginate substrate, as compared to the wild-type. Double and triple mutants (K194E/K245D, K245D/K319A, K194E/K245D/E312D, and K194E/K245D/K319A were also prepared. The most potent mutant was observed to be K194E/K245D/K319A, which has a 10-fold improved kcat value (against acetylated alginate compared to the wild-type enzyme. The antibiofilm effect of both AlgL forms was identified in combination with piperacillin/tazobactam (PT and the disruption effect was significantly higher in mutant AlgL combined with PT than wild-type AlgL. However, for both the wild-type and K194E/K245D/K319A mutant, the use of the AlgL enzyme alone did not show significant antibiofilm effect.

  2. Modeling and Re-Engineering of Azotobacter vinelandii Alginate Lyase to Enhance Its Catalytic Efficiency for Accelerating Biofilm Degradation.

    Science.gov (United States)

    Jang, Chul Ho; Piao, Yu Lan; Huang, Xiaoqin; Yoon, Eun Jeong; Park, So Hee; Lee, Kyoung; Zhan, Chang-Guo; Cho, Hoon

    2016-01-01

    Alginate is known to prevent elimination of Pseudomonas aeruginosa biofilms. Alginate lyase (AlgL) might therefore facilitate treatment of Pseudomonas aeruginosa-infected cystic fibrosis patients. However, the catalytic activity of wild-type AlgL is not sufficiently high. Therefore, molecular modeling and site-directed mutagenesis of AlgL might assist in enzyme engineering for therapeutic development. AlgL, isolated from Azotobacter vinelandii, catalyzes depolymerization of alginate via a β-elimination reaction. AlgL was modeled based on the crystal structure template of Sphingomonas AlgL species A1-III. Based on this computational analysis, AlgL was subjected to site-directed mutagenesis to improve its catalytic activity. The kcat/Km of the K194E mutant showed a nearly 5-fold increase against the acetylated alginate substrate, as compared to the wild-type. Double and triple mutants (K194E/K245D, K245D/K319A, K194E/K245D/E312D, and K194E/K245D/K319A) were also prepared. The most potent mutant was observed to be K194E/K245D/K319A, which has a 10-fold improved kcat value (against acetylated alginate) compared to the wild-type enzyme. The antibiofilm effect of both AlgL forms was identified in combination with piperacillin/tazobactam (PT) and the disruption effect was significantly higher in mutant AlgL combined with PT than wild-type AlgL. However, for both the wild-type and K194E/K245D/K319A mutant, the use of the AlgL enzyme alone did not show significant antibiofilm effect.

  3. Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes.

    Directory of Open Access Journals (Sweden)

    Cornelius Schneider

    Full Text Available Little is known about contacts in the spliceosome between proteins and intron nucleotides surrounding the pre-mRNA branch-site and their dynamics during splicing. We investigated protein-pre-mRNA interactions by UV-induced crosslinking of purified yeast B(act spliceosomes formed on site-specifically labeled pre-mRNA, and analyzed their changes after conversion to catalytically-activated B* and step 1 C complexes, using a purified splicing system. Contacts between nucleotides upstream and downstream of the branch-site and the U2 SF3a/b proteins Prp9, Prp11, Hsh49, Cus1 and Hsh155 were detected, demonstrating that these interactions are evolutionarily conserved. The RES proteins Pml1 and Bud13 were shown to contact the intron downstream of the branch-site. A comparison of the B(act crosslinking pattern versus that of B* and C complexes revealed that U2 and RES protein interactions with the intron are dynamic. Upon step 1 catalysis, Cwc25 contacts with the branch-site region, and enhanced crosslinks of Prp8 and Prp45 with nucleotides surrounding the branch-site were observed. Cwc25's step 1 promoting activity was not dependent on its interaction with pre-mRNA, indicating it acts via protein-protein interactions. These studies provide important insights into the spliceosome's protein-pre-mRNA network and reveal novel RNP remodeling events during the catalytic activation of the spliceosome and step 1 of splicing.

  4. 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.

  5. Mesoporous silica nanorods toward efficient loading and intracellular delivery of siRNA

    Science.gov (United States)

    Chen, Lijue; She, Xiaodong; Wang, Tao; Shigdar, Sarah; Duan, Wei; Kong, Lingxue

    2018-02-01

    The technology of RNA interference (RNAi) that uses small interfering RNA (siRNA) to silence the gene expression with complementary messenger RNA (mRNA) sequence has great potential for the treatment of cancer in which certain genes were usually found overexpressed. However, the carry and delivery of siRNA to the target site in the human body can be challenging for this technology to be used clinically to silence the cancer-related gene expression. In this work, rod shaped mesoporous silica nanoparticles (MSNs) were developed as siRNA delivery system for specific intracellular delivery. The rod MSNs with an aspect ratio of 1.5 had a high surface area of 934.28 m2/g and achieved a siRNA loading of more than 80 mg/g. With the epidermal growth factor (EGF) grafted on the surface of the MSNs, siRNA can be delivered to the epidermal growth factor receptor (EGFR) overexpressed colorectal cancer cells with high intracellular concentration compared to MSNs without EGF and lead to survivin gene knocking down to less than 30%.

  6. Pulsed laser synthesis in liquid of efficient visible-light-active ZnO/rGO nanocomposites for improved photo-catalytic activity

    Science.gov (United States)

    Moqbel, Redhwan A.; Gondal, Mohammed A.; Qahtan, Talal F.; Dastageer, Mohamed A.

    2018-03-01

    In this work the synthesis of visible light active zinc oxide/reduced graphene oxide (ZnO/rGO) nanocomposite by laser induced fragmentation of particulates in liquid, its morphological/optical characterizations, and its application in the process of photo-catalytic degradation of toxic Rhodamine B (RhB) dye under visible radiation were studied. It is observed from the optical and morphological characterization that the anchoring of ZnO on the rGO sheets in ZnO/rGO nanocomposite considerably reduced the aggregation of ZnO (increased surface area), reduced the recombination of photo-induced charge carriers, promoted more adsorption of reactants on the catalytic surface and also enhanced and extended the light absorption in the visible spectral region. With all these improved characteristics of ZnO/rGO nanocomposite, it was found that this material as a photo-catalyst yielded an RhB degradation efficiency of 86%, as compared to the 40% degradation with pure ZnO NPs under the same experimental conditions. In the ZnO/rGO nanocomposite, rGO functions as an electron acceptor to promote charge separation, an aggregation inhibitor to enhance the active surface area, a co-catalyst, a good dye adsorber and also as a supporting matrix for ZnO.

  7. Transition state analogue imprinted polymers as artificial amidases for amino acid p-nitroanilides: morphological effects of polymer network on catalytic efficiency.

    Science.gov (United States)

    Mathew, Divya; Thomas, Benny; Devaky, K S

    2017-11-13

    The morphology of the polymer network - porous/less porous - plays predominant role in the amidase activities of the polymer catalysts in the hydrolytic reactions of amino acid p-nitroanilides. Polymers with the imprints of stable phosphonate analogue of the intermediate of hydrolytic reactions were synthesized as enzyme mimics. Molecular imprinting was carried out in thermodynamically stable porogen dimethyl sulphoxide and unstable porogen chloroform, to investigate the morphological effects of polymers on catalytic amidolysis. It was found that the medium of polymerization has vital influence in the amidase activities of the enzyme mimics. The morphological studies of the polymer catalysts were carried out by scanning electron microscopy and Bruner-Emmett-Teller analysis. The morphology of the polymer catalysts and their amidase activities are found to be dependent on the composition of reaction medium. The polymer catalyst prepared in dimethyl sulphoxide is observed to be efficient in 1:9 acetonitrile (ACN)-Tris HCl buffer and that prepared in chloroform is noticed to be stereo specifically and shape-selectively effective in 9:1 ACN-Tris HCl buffer. The solvent memory effect in catalytic amidolysis was investigated using the polymer prepared in acetonitrile.

  8. Pyrrolic-N-doped graphene oxide/Fe2O3 mesocrystal nanocomposite: Efficient charge transfer and enhanced photo-Fenton catalytic activity

    Science.gov (United States)

    Liu, Bing; Tian, Lihong; Wang, Ran; Yang, Jinfeng; Guan, Rong; Chen, Xiaobo

    2017-11-01

    Though α-Fe2O3 has attracted much attention in photocatalytic or Fenton-catalytic degradation of organic contaminants, its performance is still unsatisfactory due to fast recombination of electrons and holes in photocatalytic process and the difficult conversion of Fe(II) and Fe(III) in Fenton reaction. Herein, a pyrrolic N-doped graphene oxide/Fe2O3 mesocrystal (NG-Fe2O3) nanocomposite with good distribution is synthesized by a simple solvothermal method and adjusting the oxygen-containing groups on graphene oxide. The morphology of NG-Fe2O3 contributes to a relatively large BET surface area and an intimate contact between NG and Fe2O3. These two important factors along with the excellent electro-conductivity of pyrrolic-N doped GO result in the efficient separation of electron-hole pairs and fast conversion of Fe(II)and Fe(III) in photo-Fenton synergistic reaction. Thus, a remarkably improved photo-Fenton catalytic activity of NG-Fe2O3 is obtained. The degrading rate on methyl blue increases by 1.5 times and the conversion rate of glyphosate increases by 2.3 times under visible light irradiation, compared to pristine α-Fe2O3 mesocrystals.

  9. The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during MicroRNA biogenesis

    KAUST Repository

    Liu, Chenggang; Axtell, Michael J.; Fedoroff, Nina V.

    2012-01-01

    Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 mutants accumulate low levels of miRNAs and display

  10. RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.

    Science.gov (United States)

    Orenstein, Yaron; Wang, Yuhao; Berger, Bonnie

    2016-06-15

    Protein-RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein-RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein-RNA structure-based models on an unprecedented scale. Software and models are freely available at http://rck.csail.mit.edu/ bab@mit.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by

  11. The evolution of catalytic function

    Science.gov (United States)

    Maurel, Marie-Christine; Ricard, Jacques

    2006-03-01

    It is very likely that the main driving force of enzyme evolution is the requirement to improve catalytic and regulatory efficiency which results from the intrinsic performance as well as from the spatial and functional organization of enzymes in living cells. Kinetic co-operativity may occur in simple monomeric proteins if they display “slow” conformational transitions, at the cost of catalytic efficiency. Oligomeric enzymes on the other hand can be both efficient and co-operative. We speculate that the main reason for the emergence of co-operative oligomeric enzymes is the need for catalysts that are both cooperative and efficient. As it is not useful for an enzyme to respond to a change of substrate concentration in a complex kinetic way, the emergence of symmetry has its probable origin in a requirement for “functional simplicity”. In a living cell, enzyme are associated with other macromolecules and membranes. The fine tuning of their activity may also be reached through mutations of the microenvironment. Our hypothesis is that these mutations are related to the vectorial transport of molecules, to achieve the hysteresis loops of enzyme reactions generated by the coupling of reaction and diffusion, through the co-operativity brought about by electric interactions between a charged substrate and a membrane, and last but not least, through oscillations. As the physical origins of these effects are very simple and do not require complex molecular devices, it is very likely that the functional advantage generated by the spatial and functional organization of enzyme molecules within the cell have appeared in prebiotic catalysis or very early during the primeval stages of biological evolution. We shall began this paper by presenting the nature of the probable earliest catalysts in the RNA world.

  12. Increased efficiency of exogenous messenger RNA translation in a Krebs ascites cell lysate.

    Science.gov (United States)

    Metafora, S; Terada, M; Dow, L W; Marks, P A; Bank, A

    1972-05-01

    Addition of a 0.5 M KCl wash fraction from rabbit reticulocyte ribosomes causes a 3- to 10-fold increase in the extent of translation of natural mRNAs by Krebs-cell lysates. In the presence of the wash fraction, 1 pmol of rabbit or mouse 10S RNA directs the incorporation of 80 pmol of leucine into rabbit globin. The addition of human 10S RNA results in the synthesis of equal amounts of human alpha and beta chains, identified by column chromatography. The stimulation by the wash fraction is almost completely dependent on added mammalian tRNA. In contrast to the wash fraction from rabbit reticulocytes, the wash fraction isolated from Krebs-cell ribosomes is inhibitory to both endogenous and exogenous mRNA translation. The stimulation by the wash fraction from rabbit ribosomes is not specific for globin mRNAs, but also increases endogenous, phage Qbeta, and viral RNA-directed protein synthesis.

  13. Reversible tetramerization of human TK1 to the high catalytic efficient form is induced by pyrophosphate, in addition to tripolyphosphates, or high enzyme concentration

    DEFF Research Database (Denmark)

    Munch-Petersen, Birgitte

    2009-01-01

    of ATP is necessary for tetramerisation and how the reaction velocity is influenced by the enzyme concentration. The results show that only two or three of the phosphate groups of ATP are necessary for tetramerisation, and that kinetics and tetramerisation are closely related. Furthermore, enzyme...... concentration was found to have a pivotal effect on catalytic efficiency.......Thymidine kinase (TK1) is a key enzyme in the salvage pathway of deoxyribonucleotide metabolism catalyzing the first step in the synthesis of dTTP by the transfer of a gamma-phosphate group from a nucleoside triphosphate to the 5´-hydroxyl group of thymidine forming dTMP. Human TK1 is cytosolic...

  14. mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer.

    Directory of Open Access Journals (Sweden)

    Silvia von der Heyde

    Full Text Available Intrinsic and acquired resistance to the monoclonal antibody drug trastuzumab is a major problem in the treatment of HER2-positive breast cancer. A deeper understanding of the underlying mechanisms could help to develop new agents. Our intention was to detect genes and single nucleotide polymorphisms (SNPs affecting trastuzumab efficiency in cell culture. Three HER2-positive breast cancer cell lines with different resistance phenotypes were analyzed. We chose BT474 as model of trastuzumab sensitivity, HCC1954 as model of intrinsic resistance, and BTR50, derived from BT474, as model of acquired resistance. Based on RNA-Seq data, we performed differential expression analyses on these cell lines with and without trastuzumab treatment. Differentially expressed genes between the resistant cell lines and BT474 are expected to contribute to resistance. Differentially expressed genes between untreated and trastuzumab treated BT474 are expected to contribute to drug efficacy. To exclude false positives from the candidate gene set, we removed genes that were also differentially expressed between untreated and trastuzumab treated BTR50. We further searched for SNPs in the untreated cell lines which could contribute to trastuzumab resistance. The analysis resulted in 54 differentially expressed candidate genes that might be connected to trastuzumab efficiency. 90% of 40 selected candidates were validated by RT-qPCR. ALPP, CALCOCO1, CAV1, CYP1A2 and IGFBP3 were significantly higher expressed in the trastuzumab treated than in the untreated BT474 cell line. GDF15, IL8, LCN2, PTGS2 and 20 other genes were significantly higher expressed in HCC1954 than in BT474, while NCAM2, COLEC12, AFF3, TFF3, NRCAM, GREB1 and TFF1 were significantly lower expressed. Additionally, we inferred SNPs in HCC1954 for CAV1, PTGS2, IL8 and IGFBP3. The latter also had a variation in BTR50. 20% of the validated subset have already been mentioned in literature. For half of them we

  15. The Investigation of Electron Beam Catalytical Oxidation Process Efficiency with Potassium Persulfate in Removal Humic Acid from Aqueous Solutions

    Directory of Open Access Journals (Sweden)

    MT Ghaneian

    2015-05-01

    Results: Based on the results, changes in pH had little effect on the Humic acid removal efficiency. The average, with increasing of pH from 4 to 10, the removal efficiency of humic acid from 72.59% to 73.36% increased, respectively. The results showed that increasing of the dose from 1 to 15 kGy, humic acid removal efficiency increases. Based on results by increasing of persulfate concentration, the removal efficiency increased so that with increasing of concentration of potassium persulfate from 0.1 to 0.5 mmol/100cc, removal efficiency from 69.43% to 83.82% was increased. Kinetic experiments showed that the decomposition of humic acid by electron beam radiation followed the second-order kinetic. Conclusion: The data from this study showed that the aqueous solution containing acid Humic is decomposed effectively by electron beams irradiation. Addition of potassium persulfate can be have significant improvements in removal efficiency of humic acid in the presence of electron beam.

  16. Efficient Inhibition of wear debris-induced inflammation by locally delivered siRNA

    International Nuclear Information System (INIS)

    Peng Xiaochun; Tao Kun; Cheng Tao; Zhu Junfeng; Zhang Xianlong

    2008-01-01

    Aseptic loosening is the most common long-term complication of total joint replacement, which is associated with the generation of wear debris. The purpose of this study was to investigate the inhibitory effect of small interfering RNA (siRNA) targeting tumor necrosis factor-α (TNF-α) on wear debris-induced inflammation. A local delivery of lentivirus-mediated TNF-α siRNA into the modified murine air pouch, which was stimulated by polymethylmethacrylate (PMMA) particles, resulted in significant blockage of TNF-α both in mRNA and protein levels for up to 4 weeks. In addition, significant down-regulation of interleukin-1 (IL-1) and interleukin-6 (IL-6) was observed in TNF-α siRNA-treated pouches. The safety profile of gene therapy was proven by Bioluminescent assay and quantitative fluorescent flux. Histological analysis revealed less inflammatory responses (thinner pouch membrane and decreased cellular infiltration) in TNF-α siRNA-treated pouches. These findings suggest that local delivery of TNF-α siRNA might be an excellent therapeutic candidate to inhibit particle-induced inflammation.

  17. Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues.

    Science.gov (United States)

    Oliveira, R R; Viana, A J C; Reátegui, A C E; Vincentz, M G A

    2015-12-29

    Determination of gene expression is an important tool to study biological processes and relies on the quality of the extracted RNA. Changes in gene expression profiles may be directly related to mutations in regulatory DNA sequences or alterations in DNA cytosine methylation, which is an epigenetic mark. Correlation of gene expression with DNA sequence or epigenetic mark polymorphism is often desirable; for this, a robust protocol to isolate high-quality RNA and DNA simultaneously from the same sample is required. Although commercial kits and protocols are available, they are mainly optimized for animal tissues and, in general, restricted to RNA or DNA extraction, not both. In the present study, we describe an efficient and accessible method to extract both RNA and DNA simultaneously from the same sample of various plant tissues, using small amounts of starting material. The protocol was efficient in the extraction of high-quality nucleic acids from several Arabidopsis thaliana tissues (e.g., leaf, inflorescence stem, flower, fruit, cotyledon, seedlings, root, and embryo) and from other tissues of non-model plants, such as Avicennia schaueriana (Acanthaceae), Theobroma cacao (Malvaceae), Paspalum notatum (Poaceae), and Sorghum bicolor (Poaceae). The obtained nucleic acids were used as templates for downstream analyses, such as mRNA sequencing, quantitative real time-polymerase chain reaction, bisulfite treatment, and others; the results were comparable to those obtained with commercial kits. We believe that this protocol could be applied to a broad range of plant species, help avoid technical and sampling biases, and facilitate several RNA- and DNA-dependent analyses.

  18. Prokaryotic Argonautes - variations on the RNA interference theme

    Science.gov (United States)

    van der Oost, John; Swarts, Daan C.; Jore, Matthijs M.

    2014-01-01

    The discovery of RNA interference (RNAi) has been a major scientific breakthrough. This RNA-guided RNA interference system plays a crucial role in a wide range of regulatory and defense mechanisms in eukaryotes. The key enzyme of the RNAi system is Argonaute (Ago), an endo-ribonuclease that uses a small RNA guide molecule to specifically target a complementary RNA transcript. Two functional classes of eukaryotic Ago have been described: catalytically active Ago that cleaves RNA targets complementary to its guide, and inactive Ago that uses its guide to bind target RNA to down-regulate translation efficiency. A recent comparative genomics study has revealed that Argonaute-like proteins are also encoded by prokaryotic genomes. Interestingly, there is a lot of variation among these prokaryotic Argonaute (pAgo) proteins with respect to domain architecture: some resemble the eukaryotic Ago (long pAgo) containing a complete or disrupted catalytic site, while others are truncated versions (short pAgo) that generally contain an incomplete catalytic site. Prokaryotic Agos with an incomplete catalytic site often co-occur with (predicted) nucleases. Based on this diversity, and on the fact that homologs of other RNAi-related protein components (such as Dicer nucleases) have never been identified in prokaryotes, it has been predicted that variations on the eukaryotic RNAi theme may occur in prokaryotes. PMID:28357239

  19. Development of a software tool and criteria evaluation for efficient design of small interfering RNA

    International Nuclear Information System (INIS)

    Chaudhary, Aparna; Srivastava, Sonam; Garg, Sanjeev

    2011-01-01

    Research highlights: → The developed tool predicted siRNA constructs with better thermodynamic stability and total score based on positional and other criteria. → Off-target silencing below score 30 were observed for the best siRNA constructs for different genes. → Immunostimulation and cytotoxicity motifs considered and penalized in the developed tool. → Both positional and compositional criteria were observed to be important. -- Abstract: RNA interference can be used as a tool for gene silencing mediated by small interfering RNAs (siRNA). The critical step in effective and specific RNAi processing is the selection of suitable constructs. Major design criteria, i.e., Reynolds's design rules, thermodynamic stability, internal repeats, immunostimulatory motifs were emphasized and implemented in the siRNA design tool. The tool provides thermodynamic stability score, GC content and a total score based on other design criteria in the output. The viability of the tool was established with different datasets. In general, the siRNA constructs produced by the tool had better thermodynamic score and positional properties. Comparable thermodynamic scores and better total scores were observed with the existing tools. Moreover, the results generated had comparable off-target silencing effect. Criteria evaluations with additional criteria were achieved in WEKA.

  20. Direct and efficient transfection of mouse neural stem cells and mature neurons by in vivo mRNA electroporation.

    Science.gov (United States)

    Bugeon, Stéphane; de Chevigny, Antoine; Boutin, Camille; Coré, Nathalie; Wild, Stefan; Bosio, Andreas; Cremer, Harold; Beclin, Christophe

    2017-11-01

    In vivo brain electroporation of DNA expression vectors is a widely used method for lineage and gene function studies in the developing and postnatal brain. However, transfection efficiency of DNA is limited and adult brain tissue is refractory to electroporation. Here, we present a systematic study of mRNA as a vector for acute genetic manipulation in the developing and adult brain. We demonstrate that mRNA electroporation is far more efficient than DNA electroporation, and leads to faster and more homogeneous protein expression in vivo Importantly, mRNA electroporation allows the manipulation of neural stem cells and postmitotic neurons in the adult brain using minimally invasive procedures. Finally, we show that this approach can be efficiently used for functional studies, as exemplified by transient overexpression of the neurogenic factor Myt1l and by stably inactivating Dicer nuclease in vivo in adult born olfactory bulb interneurons and in fully integrated cortical projection neurons. © 2017. Published by The Company of Biologists Ltd.

  1. Low-weight polyethylenimine cross-linked 2-hydroxypopyl-ß-cyclodextrin and folic acid as an efficient and nontoxic siRNA carrier for gene silencing and tumor inhibition by VEGF siRNA

    Directory of Open Access Journals (Sweden)

    Li JM

    2013-06-01

    Full Text Available Jin-Ming Li, Yuan-Yuan Wang, Wei Zhang, Hua Su, Liang-Nian Ji, Zong-Wan Mao MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, People's Republic of China Background: Targeted delivery of small interfering RNA (siRNA has been regarded as one of the most important technologies for the development of siRNA therapeutics. However, the need for safe and efficient delivery systems is a barrier to further development of RNA interference therapeutics. In this work, a nontoxic and efficient siRNA carrier delivery system of low molecular weight polyethyleneimine (PEI-600 Da cross-linked with 2-hydroxypopyl-β-cyclodextrin (HP-β-CD and folic acid (FA was synthesized for biomedical application. Methods: The siRNA carrier was prepared using a simple method and characterized by nuclear magnetic resonance and Fourier transform infrared spectroscopy. The siRNA carrier nanoparticles were characterized in terms of morphology, size and zeta potential, stability, efficiency of delivery, and gene silencing efficiency in vitro and in vivo. Results: The siRNA carrier was synthesized successfully. It showed good siRNA binding capacity and ability to protect siRNA. Further, the toxicity of the carrier measured in vitro and in vivo appeared to be negligible, probably because of degradation of the low molecular weight PEI and HP-β-CD in the cytosol. Flow cytometry and confocal microscopy confirmed that the FA receptor-mediated endocytosis of the FA-HP-β-CD-PEI/siRNA complexes was greater than that of the HP-β-CD-PEI/siRNA complexes in FA receptor-enriched HeLa cells. The FA-HP-β-CD-PEI/siRNA complexes also demonstrated excellent gene silencing efficiency in vitro (in the range of 90%, and reduced vascular endothelial growth factor (VEGF protein expression in the presence of 20% serum. FA-HP-β-CD-PEI/siRNA complexes administered via tail vein injection resulted in marked

  2. Natural Variants of the KPC-2 Carbapenemase have Evolved Increased Catalytic Efficiency for Ceftazidime Hydrolysis at the Cost of Enzyme Stability.

    Directory of Open Access Journals (Sweden)

    Shrenik C Mehta

    2015-06-01

    Full Text Available The spread of β-lactamases that hydrolyze penicillins, cephalosporins and carbapenems among Gram-negative bacteria has limited options for treating bacterial infections. Initially, Klebsiella pneumoniae carbapenemase-2 (KPC-2 emerged as a widespread carbapenem hydrolyzing β-lactamase that also hydrolyzes penicillins and cephalosporins but not cephamycins and ceftazidime. In recent years, single and double amino acid substitution variants of KPC-2 have emerged among clinical isolates that show increased resistance to ceftazidime. Because it confers multi-drug resistance, KPC β-lactamase is a threat to public health. In this study, the evolution of KPC-2 function was determined in nine clinically isolated variants by examining the effects of the substitutions on enzyme kinetic parameters, protein stability and antibiotic resistance profile. The results indicate that the amino acid substitutions associated with KPC-2 natural variants lead to increased catalytic efficiency for ceftazidime hydrolysis and a consequent increase in ceftazidime resistance. Single substitutions lead to modest increases in catalytic activity while the double mutants exhibit significantly increased ceftazidime hydrolysis and resistance levels. The P104R, V240G and H274Y substitutions in single and double mutant combinations lead to the largest increases in ceftazidime hydrolysis and resistance. Molecular modeling suggests that the P104R and H274Y mutations could facilitate ceftazidime hydrolysis through increased hydrogen bonding interactions with the substrate while the V240G substitution may enhance backbone flexibility so that larger substrates might be accommodated in the active site. Additionally, we observed a strong correlation between gain of catalytic function for ceftazidime hydrolysis and loss of enzyme stability, which is in agreement with the 'stability-function tradeoff' phenomenon. The high Tm of KPC-2 (66.5°C provides an evolutionary advantage as

  3. A Multifunctional Envelope-Type Nano Device Containing a pH-Sensitive Cationic Lipid for Efficient Delivery of Short Interfering RNA to Hepatocytes In Vivo.

    Science.gov (United States)

    Sato, Yusuke; Harashima, Hideyoshi; Kohara, Michinori

    2016-01-01

    Various types of nanoparticles have been developed with the intent of efficiently delivering short interfering RNA (siRNA) to hepatocytes to date. To achieve efficient SiRNA delivery, various aspects of the delivery processes and physical properties need to be considered. We recently developed an original lipid nanoparticle, a multifunctional envelope-type nano device (MEND) containing YSK05, a pH-sensitive cationic lipid (YSK05-MEND). The YSK05-MEND with SiRNA in its formulation showed hepatocyte-specific uptake and robust gene silencing in hepatocytes after intravenous administration. Here, we describe the procedure used in the preparation and characterization method of the YSK05-MEND.

  4. Catalytic efficiency of natural and synthetic compounds used as laccase-mediators in oxidising veratryl alcohol and a kraft lignin, estimated by electrochemical analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez Arzola, K. [Department of Microbiology and Cell Biology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife (Spain); Arevalo, M.C. [Department of Physical Chemistry, Faculty of Chemistry, University of La Laguna, 38206 La Laguna, Tenerife (Spain)], E-mail: carevalo@ull.es; Falcon, M.A. [Department of Microbiology and Cell Biology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife (Spain)], E-mail: mafalcon@ull.es

    2009-03-30

    The electrochemical properties of eighteen natural and synthetic compounds commonly used to expand the oxidative capacity of laccases were evaluated in an aqueous buffered medium using cyclic voltammetry. This clarifies which compounds fulfil the requisites to be considered as redox mediators or enhancers. Cyclic voltammetry was also applied as a rapid way to assess the catalytic efficiency (CE) of those compounds which oxidise a non-phenolic lignin model (veratryl alcohol, VA) and a kraft lignin (KL). With the exception of gallic acid and catechol, all assayed compounds were capable of oxidising VA with varying CE. However, only some of them were able to oxidise KL. Although the oxidised forms of HBT and acetovanillone were not electrochemically stable, their reduced forms were quickly regenerated in the presence of VA. They thus act as chemical catalysts. Importantly, HBT and HPI did not attack the KL via the same mechanism as in VA oxidation. Electrochemical evidence suggests that violuric acid oxidises both substrates by an electron transfer mechanism, unlike the other N-OH compounds HBT and HPI. Acetovanillone was found to be efficient in oxidising VA and KL, even better than the synthetic mediators TEMPO, violuric acid or ABTS. Most of the compounds produced a generalised increase in the oxidative charge of KL, probably attributed to chain reactions arising between the phenolic and non-phenolic components of this complex molecule.

  5. Catalytic efficiency of natural and synthetic compounds used as laccase-mediators in oxidising veratryl alcohol and a kraft lignin, estimated by electrochemical analysis

    International Nuclear Information System (INIS)

    Gonzalez Arzola, K.; Arevalo, M.C.; Falcon, M.A.

    2009-01-01

    The electrochemical properties of eighteen natural and synthetic compounds commonly used to expand the oxidative capacity of laccases were evaluated in an aqueous buffered medium using cyclic voltammetry. This clarifies which compounds fulfil the requisites to be considered as redox mediators or enhancers. Cyclic voltammetry was also applied as a rapid way to assess the catalytic efficiency (CE) of those compounds which oxidise a non-phenolic lignin model (veratryl alcohol, VA) and a kraft lignin (KL). With the exception of gallic acid and catechol, all assayed compounds were capable of oxidising VA with varying CE. However, only some of them were able to oxidise KL. Although the oxidised forms of HBT and acetovanillone were not electrochemically stable, their reduced forms were quickly regenerated in the presence of VA. They thus act as chemical catalysts. Importantly, HBT and HPI did not attack the KL via the same mechanism as in VA oxidation. Electrochemical evidence suggests that violuric acid oxidises both substrates by an electron transfer mechanism, unlike the other N-OH compounds HBT and HPI. Acetovanillone was found to be efficient in oxidising VA and KL, even better than the synthetic mediators TEMPO, violuric acid or ABTS. Most of the compounds produced a generalised increase in the oxidative charge of KL, probably attributed to chain reactions arising between the phenolic and non-phenolic components of this complex molecule

  6. Identification of high-efficiency 3′GG gRNA motifs in indexed FASTA files with ngg2

    Directory of Open Access Journals (Sweden)

    Elisha D. Roberson

    2015-11-01

    Full Text Available CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3′GG motif, which substantially increases the efficiency of editing at all sites tested in C. elegans. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a Python command-line tool, ngg2, to identify 3′GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes: Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens. I also scanned the genomes of pig (Sus scrofa and African elephant (Loxodonta africana to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3′GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3′GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3′GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3′GG editing sites in any species with an available genome sequence.

  7. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA.

    Science.gov (United States)

    Warren, Luigi; Manos, Philip D; Ahfeldt, Tim; Loh, Yuin-Han; Li, Hu; Lau, Frank; Ebina, Wataru; Mandal, Pankaj K; Smith, Zachary D; Meissner, Alexander; Daley, George Q; Brack, Andrew S; Collins, James J; Cowan, Chad; Schlaeger, Thorsten M; Rossi, Derrick J

    2010-11-05

    Clinical application of induced pluripotent stem cells (iPSCs) is limited by the low efficiency of iPSC derivation and the fact that most protocols modify the genome to effect cellular reprogramming. Moreover, safe and effective means of directing the fate of patient-specific iPSCs toward clinically useful cell types are lacking. Here we describe a simple, nonintegrating strategy for reprogramming cell fate based on administration of synthetic mRNA modified to overcome innate antiviral responses. We show that this approach can reprogram multiple human cell types to pluripotency with efficiencies that greatly surpass established protocols. We further show that the same technology can be used to efficiently direct the differentiation of RNA-induced pluripotent stem cells (RiPSCs) into terminally differentiated myogenic cells. This technology represents a safe, efficient strategy for somatic cell reprogramming and directing cell fate that has broad applicability for basic research, disease modeling, and regenerative medicine. Copyright © 2010 Elsevier Inc. All rights reserved.

  8. A possible contribution of mRNA secondary structure to translation initiation efficiency in Lactococcus lactis

    NARCIS (Netherlands)

    Guchte, Maarten van de; Lende, Ted van der; Kok, Jan; Venema, Gerard

    1991-01-01

    Gene expression signals derived from Lactococcus lactis were linked to lacZ-fused genes with different 5'-nucleotide sequences. Computer predictions of mRNA secondary structure were combined with lacZ expression studies to direct base-substitutions that could possibly influence gene expression.

  9. Modifying the 5'-Cap for Click Reactions of Eukaryotic mRNA and To Tune Translation Efficiency in Living Cells.

    Science.gov (United States)

    Holstein, Josephin M; Anhäuser, Lea; Rentmeister, Andrea

    2016-08-26

    The 5'-cap is a hallmark of eukaryotic mRNAs and plays fundamental roles in RNA metabolism, ranging from quality control to export and translation. Modifying the 5'-cap may thus enable modulation of the underlying processes and investigation or tuning of several biological functions. A straightforward approach is presented for the efficient production of a range of N7-modified caps based on the highly promiscuous methyltransferase Ecm1. We show that these, as well as N(2) -modified 5'-caps, can be used to tune translation of the respective mRNAs both in vitro and in cells. Appropriate modifications allow subsequent bioorthogonal chemistry, as demonstrated by intracellular live-cell labeling of a target mRNA. The efficient and versatile N7 manipulation of the mRNA cap makes mRNAs amenable to both modulation of their biological function and intracellular labeling, and represents a valuable addition to the chemical biology toolbox. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Amphiphilic core shell nanoparticles containing dense polyethyleneimine shells for efficient delivery of microRNA to Kupffer cells

    Directory of Open Access Journals (Sweden)

    Liu Z

    2016-06-01

    Full Text Available Zuojin Liu,1,* Dechao Niu,2,3,* Junyong Zhang,1 Wenfeng Zhang,1 Yuan Yao,2 Pei Li,2 Jianping Gong1 1Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 2Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, 3Lab of Low-Dimensional Materials Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, People’s Republic of China *These authors contributed equally to this work Abstract: Efficient and targeted delivery approach to transfer exogenous genes into macrophages is still a great challenge. Current gene delivery methods often result in low cellular uptake efficiency in vivo in some types of cells, especially for the Kupffer cells (KCs. In this article, we demonstrate that amphiphilic core–shell nanoparticles (NPs consisting of well-defined hydrophobic poly(methyl methacrylate (PMMA cores and branched polyethyleneimine (PEI shells (denoted as PEI@PMMA NPs are efficient nanocarriers to deliver microRNA (miRNA-loaded plasmid to the KCs. Average hydrodynamic diameter of PEI@PMMA NPs was 279 nm with a narrow size distribution. The NPs also possessed positive surface charges up to +30 mV in water, thus enabling effective condensation of negatively charged plasmid DNA. Gel electrophoresis assay showed that the resultant PEI@PMMA NPs were able to completely condense miRNA plasmid at a weight ratio of 25:1 (N/P ratio equal to 45:1. The Cell Counting Kit-8 assay and flow cytometry results showed that the PEI@PMMA/miRNA NPs displayed low cytotoxicity and cell apoptosis activity against the KCs. The maximum cell transfection efficiency reached 34.7% after 48 hours, which is much higher than that obtained by using the commercial Lipofectamine™ 2000 (1.7%. Bio-transmission electron microscope observation revealed that the PEI@PMMA NPs were mainly distributed in

  11. Polycistronic artificial miRNA-mediated resistance to Wheat dwarf virus in barley is highly efficient at low temperature.

    Science.gov (United States)

    Kis, András; Tholt, Gergely; Ivanics, Milán; Várallyay, Éva; Jenes, Barnabás; Havelda, Zoltán

    2016-04-01

    Infection of Wheat dwarf virus (WDV) strains on barley results in dwarf disease, imposing severe economic losses on crop production. As the natural resistance resources against this virus are limited, it is imperative to elaborate a biotechnological approach that will provide effective and safe immunity to a wide range of WDV strains. Because vector insect-mediated WDV infection occurs during cool periods in nature, it is important to identify a technology which is effective at lower temperature. In this study, we designed artificial microRNAs (amiRNAs) using a barley miRNA precursor backbone, which target different conservative sequence elements of the WDV strains. Potential amiRNA sequences were selected to minimize the off-target effects and were tested in a transient sensor system in order to select the most effective constructs at low temperature. On the basis of the data obtained, a polycistronic amiRNA precursor construct (VirusBuster171) was built expressing three amiRNAs simultaneously. The construct was transformed into barley under the control of a constitutive promoter. The transgenic lines were kept at 12-15 °C to mimic autumn and spring conditions in which major WDV infection and accumulation take place. We were able to establish a stable barley transgenic line displaying resistance to insect-mediated WDV infection. Our study demonstrates that amiRNA technology can be an efficient tool for the introduction of highly efficient resistance in barley against a DNA virus belonging to the Geminiviridae family, and this resistance is effective at low temperature where the natural insect vector mediates the infection process. © 2015 BSPP and John Wiley & Sons Ltd.

  12. Highly efficient gene delivery by mRNA electroporation in human hematopoietic cells: superiority to lipofection and passive pulsing of mRNA and to electroporation of plasmid cDNA for tumor antigen loading of dendritic cells.

    Science.gov (United States)

    Van Tendeloo, V F; Ponsaerts, P; Lardon, F; Nijs, G; Lenjou, M; Van Broeckhoven, C; Van Bockstaele, D R; Berneman, Z N

    2001-07-01

    Designing effective strategies to load human dendritic cells (DCs) with tumor antigens is a challenging approach for DC-based tumor vaccines. Here, a cytoplasmic expression system based on mRNA electroporation to efficiently introduce tumor antigens into DCs is described. Preliminary experiments in K562 cells using an enhanced green fluorescent protein (EGFP) reporter gene revealed that mRNA electroporation as compared with plasmid DNA electroporation showed a markedly improved transfection efficiency (89% versus 40% EGFP(+) cells, respectively) and induced a strikingly lower cell toxicity (15% death rate with mRNA versus 51% with plasmid DNA). Next, mRNA electroporation was applied for nonviral transfection of different types of human DCs, including monocyte-derived DCs (Mo-DCs), CD34(+) progenitor-derived DCs (34-DCs) and Langerhans cells (34-LCs). High-level transgene expression by mRNA electroporation was obtained in more than 50% of all DC types. mRNA-electroporated DCs retained their phenotype and maturational potential. Importantly, DCs electroporated with mRNA-encoding Melan-A strongly activated a Melan-A-specific cytotoxic T lymphocyte (CTL) clone in an HLA-restricted manner and were superior to mRNA-lipofected or -pulsed DCs. Optimal stimulation of the CTL occurred when Mo-DCs underwent maturation following mRNA transfection. Strikingly, a nonspecific stimulation of CTL was observed when DCs were transfected with plasmid DNA. The data clearly demonstrate that Mo-DCs electroporated with mRNA efficiently present functional antigenic peptides to cytotoxic T cells. Therefore, electroporation of mRNA-encoding tumor antigens is a powerful technique to charge human dendritic cells with tumor antigens and could serve applications in future DC-based tumor vaccines.

  13. Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding

    Energy Technology Data Exchange (ETDEWEB)

    Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka, E-mail: kinjo@sci.hokudai.ac.jp

    2015-07-31

    Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS{sup SV40}) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesis takes place. GFP-NLS{sup SV40} in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS{sup SV40} formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS{sup SV40} likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS{sup SV40} can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. - Highlights: • Nuclear localization signal-tagged GFP (GFP-NLS) showed clear nuclear localization. • The GFP-NLS dynamically localized not only in the nucleoplasm, but also to the nucleolus. • The nuclear localization of GFP-NLS results from transient oligomerization mediated via RNA binding. • Our NLS-tagging procedure is ideal for use in artificial sequestration of proteins in the nucleus.

  14. Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding

    International Nuclear Information System (INIS)

    Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka

    2015-01-01

    Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS SV40 ) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesis takes place. GFP-NLS SV40 in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS SV40 formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS SV40 likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS SV40 can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. - Highlights: • Nuclear localization signal-tagged GFP (GFP-NLS) showed clear nuclear localization. • The GFP-NLS dynamically localized not only in the nucleoplasm, but also to the nucleolus. • The nuclear localization of GFP-NLS results from transient oligomerization mediated via RNA binding. • Our NLS-tagging procedure is ideal for use in artificial sequestration of proteins in the nucleus

  15. Radiolytic Synthesis of Pt-Ru Catalysts Based on Functional Polymer-Grafted MWNT and Their Catalytic Efficiency for CO and MeOH

    Directory of Open Access Journals (Sweden)

    Dae-Soo Yang

    2011-01-01

    Full Text Available Pt-Ru catalysts based on functional polymer-grafted MWNT (Pt-Ru@FP-MWNT were prepared by radiolytic deposition of Pt-Ru nanoparticles on functional polymer-grafted multiwalled carbon nanotube (FP-MWNT. Three different types of functional polymers, poly(acrylic acid (PAAc, poly(methacrylic acid (PMAc, and poly(vinylphenyl boronic acid (PVPBAc, were grafted on the MWNT surface by radiation-induced graft polymerization (RIGP. Then, Pt-Ru nanoparticles were deposited onto the FP-MWNT supports by the reduction of metal ions using γ-irradiation to obtain Pt-Ru@FP-MWNT catalysts. The Pt-Ru@FP-MWNT catalysts were then characterized by XRD, XPS, TEM ,and elemental analysis. The catalytic efficiency of Pt-Ru@FP-MWNT catalyst was examined for CO stripping and MeOH oxidation for use in a direct methanol fuel cell (DMFC. The Pt-Ru@PVPBAc-MWNT catalyst shows enhanced activity for electro-oxidation of CO and MeOH oxidation over that of the commercial E-TEK catalyst.

  16. Association of mitochondrial lysyl-tRNA synthetase with HIV-1 GagPol involves catalytic domain of the synthetase and transframe and integrase domains of Pol

    Directory of Open Access Journals (Sweden)

    Shalak V. F.

    2011-10-01

    Full Text Available Aim. Analyze the interaction between Lysyl-tRNA synthetase (LysRS and HIV-1 GagPol to know whether a particular N-terminal sequence of mitochondrial LysRS triggers a specific recognition with GagPol. Methods. Yeast two-hybrid analysis, immunoprecipitation. Results. We have shown that LysRS associates with the Pol domain of GagPol. Conclusions. A model of the assembly of the LysRS:tRNA3Lys:GagPol packaging complex is proposed.

  17. Highly efficient reprogramming to pluripotency and directed differentiation of human cells using synthetic modified mRNA

    OpenAIRE

    Warren, Luigi; Manos, Philip D.; Ahfeldt, Tim; Loh, Yuin-Han; Li, Hu; Lau, Frank; Ebina, Wataru; Mandal, Pankaj; Smith, Zachary D.; Meissner, Alexander; Daley, George Q.; Brack, Andrew S.; Collins, James J.; Cowan, Chad; Schlaeger, Thorsten M.

    2010-01-01

    Clinical application of induced pluripotent stem (iPS) cells is limited by the low efficiency of iPS derivation and the fact that most protocols modify the genome to effect cellular reprogramming. Moreover, safe and effective means of directing the fate of patient-specific iPS cells towards clinically useful cell types are lacking. Here we describe a simple, non-integrating strategy for reprogramming cell fate based on administration of synthetic mRNA modified to overcome innate anti-viral re...

  18. Catalytic treatment

    Energy Technology Data Exchange (ETDEWEB)

    Bindley, W T.R.

    1931-04-18

    An apparatus is described for the catalytic treatment of liquids, semi-liquids, and gases comprising a vessel into which the liquid, semi-liquid, or gas to be treated is introduced through a common inlet to a chamber within the vessel whence it passes to contact with a catalyst through radially arranged channels or passages to a common outlet chamber.

  19. Efficient in vitro delivery of Noggin siRNA enhances osteoblastogenesis

    Directory of Open Access Journals (Sweden)

    S. Ghadakzadeh

    2017-11-01

    Full Text Available Several types of serious bone defects would not heal without invasive clinical intervention. One approach to such defects is to enhance the capacity of bone-formation cells. Exogenous bone morphogenetic proteins (BMP have been utilized to positively regulate matrix mineralization and osteoblastogenesis, however, numerous adverse effects are associated with this approach. Noggin, a potent antagonist of BMPs, is an ideal candidate to target and decrease the need for supraphysiological doses of BMPs. In the current research we report a novel siRNA-mediated gene knock-down strategy to down-regulate Noggin. We utilized a lipid nanoparticle (LNP delivery strategy in pre-osteoblastic rat cells. In vitro LNP-siRNA treatment caused inconsequential cell toxicity and transfection was achieved in over 85% of cells. Noggin siRNA treatment successfully down-regulated cellular Noggin protein levels and enhanced BMP signal activity which in turn resulted in significantly increased osteoblast differentiation and extracellular matrix mineralization evidenced by histological assessments. Gene expression analysis showed that targeting Noggin specifically in bone cells would not lead to a compensatory effect from other BMP negative regulators such as Gremlin and Chordin. The results from this study support the notion that novel therapeutics targeting Noggin have the clinically relevant potential to enhance bone formation without the need for toxic doses of exogenous BMPs. Such treatments will undeniably provide safe and economical treatments for individuals whose poor bone repair results in permanent morbidity and disability. Keywords: Biological sciences, Biomedical engineering, Bioengineering, Biotechnology, Cell biology, Genetics

  20. Lipoprotein-biomimetic nanostructure enables efficient targeting delivery of siRNA to Ras-activated glioblastoma cells via macropinocytosis

    Science.gov (United States)

    Huang, Jia-Lin; Jiang, Gan; Song, Qing-Xiang; Gu, Xiao; Hu, Meng; Wang, Xiao-Lin; Song, Hua-Hua; Chen, Le-Pei; Lin, Ying-Ying; Jiang, Di; Chen, Jun; Feng, Jun-Feng; Qiu, Yong-Ming; Jiang, Ji-Yao; Jiang, Xin-Guo; Chen, Hong-Zhuan; Gao, Xiao-Ling

    2017-05-01

    Hyperactivated Ras regulates many oncogenic pathways in several malignant human cancers including glioblastoma and it is an attractive target for cancer therapies. Ras activation in cancer cells drives protein internalization via macropinocytosis as a key nutrient-gaining process. By utilizing this unique endocytosis pathway, here we create a biologically inspired nanostructure that can induce cancer cells to `drink drugs' for targeting activating transcription factor-5 (ATF5), an overexpressed anti-apoptotic transcription factor in glioblastoma. Apolipoprotein E3-reconstituted high-density lipoprotein is used to encapsulate the siRNA-loaded calcium phosphate core and facilitate it to penetrate the blood-brain barrier, thus targeting the glioblastoma cells in a macropinocytosis-dependent manner. The nanostructure carrying ATF5 siRNA exerts remarkable RNA-interfering efficiency, increases glioblastoma cell apoptosis and inhibits tumour cell growth both in vitro and in xenograft tumour models. This strategy of targeting the macropinocytosis caused by Ras activation provides a nanoparticle-based approach for precision therapy in glioblastoma and other Ras-activated cancers.

  1. Efficient mRNA delivery with graphene oxide-polyethylenimine for generation of footprint-free human induced pluripotent stem cells.

    Science.gov (United States)

    Choi, Hye Yeon; Lee, Tae-Jin; Yang, Gwang-Mo; Oh, Jaesur; Won, Jihye; Han, Jihae; Jeong, Gun-Jae; Kim, Jongpil; Kim, Jin-Hoi; Kim, Byung-Soo; Cho, Ssang-Goo

    2016-08-10

    Clinical applications of induced pluripotent stem cells (iPSCs) require development of technologies for the production of "footprint-free" (gene integration-free) iPSCs, which avoid the potential risk of insertional mutagenesis in humans. Previously, several studies have shown that mRNA transfer can generate "footprint-free" iPSCs, but these studies did not use a delivery vehicle and thus repetitive daily transfection was required because of mRNA degradation. Here, we report an mRNA delivery system employing graphene oxide (GO)-polyethylenimine (PEI) complexes for the efficient generation of "footprint-free" iPSCs. GO-PEI complexes were found to be very effective for loading mRNA of reprogramming transcription factors and protection from mRNA degradation by RNase. Dynamic suspension cultures of GO-PEI/RNA complexes-treated cells dramatically increased the reprogramming efficiency and successfully generated rat and human iPSCs from adult adipose tissue-derived fibroblasts without repetitive daily transfection. The iPSCs showed all the hallmarks of pluripotent stem cells including expression of pluripotency genes, epigenetic reprogramming, and differentiation into the three germ layers. These results demonstrate that mRNA delivery using GO-PEI-RNA complexes can efficiently generate "footprint-free" iPSCs, which may advance the translation of iPSC technology into the clinical settings. Copyright © 2016. Published by Elsevier B.V.

  2. Mutant forms of Escherichia coli protein L25 unable to bind to 5S rRNA are incorporated efficiently into the ribosome in vivo.

    Science.gov (United States)

    Anikaev, A Y; Korepanov, A P; Korobeinikova, A V; Kljashtorny, V G; Piendl, W; Nikonov, S V; Garber, M B; Gongadze, G M

    2014-08-01

    5S rRNA-binding ribosomal proteins of the L25 family are an evolutional acquisition of bacteria. Earlier we showed that (i) single replacements in the RNA-binding module of the protein of this family result in destabilization or complete impossibility to form a complex with 5S rRNA in vitro; (ii) ΔL25 ribosomes of Escherichia coli are less efficient in protein synthesis in vivo than the control ribosomes. In the present work, the efficiency of incorporation of the E. coli protein L25 with mutations in the 5S rRNA-binding region into the ribosome in vivo was studied. It was found that the mutations in L25 that abolish its ability to form the complex with free 5S rRNA do not prevent its correct and efficient incorporation into the ribosome. This is supported by the fact that even the presence of a very weakly retained mutant form of the protein in the ribosome has a positive effect on the activity of the translational machinery in vivo. All this suggests the existence of an alternative incorporation pathway for this protein into the ribosome, excluding the preliminary formation of the complex with 5S rRNA. At the same time, the stable L25-5S rRNA contact is important for the retention of the protein within the ribosome, and the conservative amino acid residues of the RNA-binding module play a key role in this.

  3. Enhancing chemosensitivity to gemcitabine via RNA interference targeting the catalytic subunits of protein kinase CK2 in human pancreatic cancer cells

    International Nuclear Information System (INIS)

    Kreutzer, Jan N; Ruzzene, Maria; Guerra, Barbara

    2010-01-01

    Pancreatic cancer is a complex genetic disorder that is characterized by rapid progression, invasiveness, resistance to treatment and high molecular heterogeneity. Various agents have been used in clinical trials showing only modest improvements with respect to gemcitabine-based chemotherapy, which continues to be the standard first-line treatment for this disease. However, owing to the overwhelming molecular alterations that have been reported in pancreatic cancer, there is increasing focus on targeting molecular pathways and networks, rather than individual genes or gene-products with a combination of novel chemotherapeutic agents. Cells were transfected with small interfering RNAs (siRNAs) targeting the individual CK2 subunits. The CK2 protein expression levels were determined and the effect of its down-regulation on chemosensitization of pancreatic cancer cells was investigated. The present study examined the impact on cell death following depletion of the individual protein kinase CK2 catalytic subunits alone or in combination with gemcitabine and the molecular mechanisms by which this effect is achieved. Depletion of the CK2α or -α' subunits in combination with gemcitabine resulted in marked apoptotic and necrotic cell death in PANC-1 cells. We show that the mechanism of cell death is associated with deregulation of distinct survival signaling pathways. Cellular depletion of CK2α leads to phosphorylation and activation of MKK4/JNK while down-regulation of CK2α' exerts major effects on the PI3K/AKT pathway. Results reported here show that the two catalytic subunits of CK2 contribute differently to enhance gemcitabine-induced cell death, the reduced level of CK2α' being the most effective and that simultaneous reduction in the expression of CK2 and other survival factors might be an effective therapeutic strategy for enhancing the sensitivity of human pancreatic cancer towards chemotherapeutic agents

  4. Mutational analysis of the hypervariable region of hepatitis e virus reveals its involvement in the efficiency of viral RNA replication.

    Science.gov (United States)

    Pudupakam, R S; Kenney, Scott P; Córdoba, Laura; Huang, Yao-Wei; Dryman, Barbara A; Leroith, Tanya; Pierson, F William; Meng, Xiang-Jin

    2011-10-01

    The RNA genome of the hepatitis E virus (HEV) contains a hypervariable region (HVR) in ORF1 that tolerates small deletions with respect to infectivity. To further investigate the role of the HVR in HEV replication, we constructed a panel of mutants with overlapping deletions in the N-terminal, central, and C-terminal regions of the HVR by using a genotype 1 human HEV luciferase replicon and analyzed the effects of deletions on viral RNA replication in Huh7 cells. We found that the replication levels of the HVR deletion mutants were markedly reduced in Huh7 cells, suggesting a role of the HVR in viral replication efficiency. To further verify the results, we constructed HVR deletion mutants by using a genetically divergent, nonmammalian avian HEV, and similar effects on viral replication efficiency were observed when the avian HEV mutants were tested in LMH cells. Furthermore, the impact of complete HVR deletion on virus infectivity was tested in chickens, using an avian HEV mutant with a complete HVR deletion. Although the deletion mutant was still replication competent in LMH cells, the complete HVR deletion resulted in a loss of avian HEV infectivity in chickens. Since the HVR exhibits extensive variations in sequence and length among different HEV genotypes, we further examined the interchangeability of HVRs and demonstrated that HVR sequences are functionally exchangeable between HEV genotypes with regard to viral replication and infectivity in vitro, although genotype-specific HVR differences in replication efficiency were observed. The results showed that although the HVR tolerates small deletions with regard to infectivity, it may interact with viral and host factors to modulate the efficiency of HEV replication.

  5. Human norovirus RNA persists in seawater under simulated winter conditions but does not bioaccumulate efficiently in Pacific Oysters (Crassostrea gigas).

    Science.gov (United States)

    Dancer, D; Rangdale, R E; Lowther, J A; Lees, D N

    2010-11-01

    Norovirus (NoV) is the principal agent of bivalve molluscan shellfish-associated gastroenteric illness worldwide. Currently, noncultivable human NoVs can be detected in bivalve molluscan shellfish by using molecular methods such as real-time reverse transcription PCR assays (qRT-PCR). In addition to infectious viruses, this methodology may also detect noninfectious NoV, including fragments of the NoV genome. This study addresses, in part, the implications of qRT-PCR results for the detection of NoV in shellfish in the absence of an infectivity assay. To evaluate environmental persistence, the stability of a short fragment of the NoV genome, spanning the qRT-PCR target in the open reading frame 1/2 junction, was assessed in seawater under artificial environmental conditions simulating winter in the United Kingdom (1 mW/cm² UV irradiation, 8°C) during a 4-week period. Detectable RNA levels decreased exponentially (T₉₀ of approximately 141 h); however, sequences were still detectable for up to 2 weeks. The ability of Pacific oysters (Crassostrea gigas) to bioaccumulate NoV particles (from human feces) and RNA fragments was also compared using qRT-PCR. Oysters exposed to NoV particles subsequently were positive for NoV by qRT-PCR at levels several orders of magnitude in excess of the theoretical limit of detection, whereas oysters exposed to similar quantities of NoV RNA were either negative or positive at significantly lower levels. Therefore, although noninfectious fragments of NoV RNA may persist in the environment under winter conditions, this type of material will not be efficiently bioaccumulated by Pacific oysters and should not significantly contribute to positive qRT-PCR results.

  6. Automated, simple, and efficient influenza RNA extraction from clinical respiratory swabs using TruTip and epMotion.

    Science.gov (United States)

    Griesemer, Sara B; Holmberg, Rebecca; Cooney, Christopher G; Thakore, Nitu; Gindlesperger, Alissa; Knickerbocker, Christopher; Chandler, Darrell P; St George, Kirsten

    2013-09-01

    Rapid, simple and efficient influenza RNA purification from clinical samples is essential for sensitive molecular detection of influenza infection. Automation of the TruTip extraction method can increase sample throughput while maintaining performance. To automate TruTip influenza RNA extraction using an Eppendorf epMotion robotic liquid handler, and to compare its performance to the bioMerieux easyMAG and Qiagen QIAcube instruments. Extraction efficacy and reproducibility of the automated TruTip/epMotion protocol was assessed from influenza-negative respiratory samples spiked with influenza A and B viruses. Clinical extraction performance from 170 influenza A and B-positive respiratory swabs was also evaluated and compared using influenza A and B real-time RT-PCR assays. TruTip/epMotion extraction efficacy was 100% in influenza virus-spiked samples with at least 745 influenza A and 370 influenza B input gene copies per extraction, and exhibited high reproducibility over four log10 concentrations of virus (extraction were also positive following TruTip extraction. Overall Ct value differences obtained between TruTip/epMotion and easyMAG/QIAcube clinical extracts ranged from 1.24 to 1.91. Pairwise comparisons of Ct values showed a high correlation of the TruTip/epMotion protocol to the other methods (R2>0.90). The automated TruTip/epMotion protocol is a simple and rapid extraction method that reproducibly purifies influenza RNA from respiratory swabs, with comparable efficacy and efficiency to both the easyMAG and QIAcube instruments. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Improving the temperature characteristics and catalytic efficiency of a mesophilic xylanase from Aspergillus oryzae, AoXyn11A, by iterative mutagenesis based on in silico design.

    Science.gov (United States)

    Li, Xue-Qing; Wu, Qin; Hu, Die; Wang, Rui; Liu, Yan; Wu, Min-Chen; Li, Jian-Fang

    2017-12-01

    To improve the temperature characteristics and catalytic efficiency of a glycoside hydrolase family (GHF) 11 xylanase from Aspergillus oryzae (AoXyn11A), its variants were predicted based on in silico design. Firstly, Gly 21 with the maximum B-factor value, which was confirmed by molecular dynamics (MD) simulation on the three-dimensional structure of AoXyn11A, was subjected to site-saturation mutagenesis. Thus, one variant with the highest thermostability, AoXyn11A G21I , was selected from the mutagenesis library, E. coli/Aoxyn11A G21X (X: any one of 20 amino acids). Secondly, based on the primary structure multiple alignment of AoXyn11A with seven thermophilic GHF11 xylanases, AoXyn11A Y13F or AoXyn11A G21I-Y13F , was designed by replacing Tyr 13 in AoXyn11A or AoXyn11A G21I with Phe. Finally, three variant-encoding genes, Aoxyn11A G21I , Aoxyn11A Y13F and Aoxyn11A G21I-Y13F , were constructed by two-stage whole-plasmid PCR method, and expressed in Pichia pastoris GS115, respectively. The temperature optimum (T opt ) of recombinant (re) AoXyn11A G21I-Y13F was 60 °C, being 5 °C higher than that of reAoXyn11A G21I or reAoXyn11A Y13F , and 10 °C higher than that of reAoXyn11A. The thermal inactivation half-life (t 1/2 ) of reAoXyn11A G21I-Y13F at 50 °C was 240 min, being 40-, 3.4- and 2.5-fold longer than those of reAoXyn11A, reAoXyn11A G21I and reAoXyn11A Y13F . The melting temperature (T m ) values of reAoXyn11A, reAoXyn11A G21I , reAoXyn11A Y13F and reAoXyn11A G21I-Y13F were 52.3, 56.5, 58.6 and 61.3 °C, respectively. These findings indicated that the iterative mutagenesis of both Gly21Ile and Tyr13Phe improved the temperature characteristics of AoXyn11A in a synergistic mode. Besides those, the catalytic efficiency (k cat /K m ) of reAoXyn11A G21I-Y13F was 473.1 mL mg -1 s -1 , which was 1.65-fold higher than that of reAoXyn11A.

  8. Features of CRISPR-Cas Regulation Key to Highly Efficient and Temporally-Specific crRNA Production

    Directory of Open Access Journals (Sweden)

    Andjela Rodic

    2017-11-01

    Full Text Available Bacterial immune systems, such as CRISPR-Cas or restriction-modification (R-M systems, affect bacterial pathogenicity and antibiotic resistance by modulating horizontal gene flow. A model system for CRISPR-Cas regulation, the Type I-E system from Escherichia coli, is silent under standard laboratory conditions and experimentally observing the dynamics of CRISPR-Cas activation is challenging. Two characteristic features of CRISPR-Cas regulation in E. coli are cooperative transcription repression of cas gene and CRISPR array promoters, and fast non-specific degradation of full length CRISPR transcripts (pre-crRNA. In this work, we use computational modeling to understand how these features affect the system expression dynamics. Signaling which leads to CRISPR-Cas activation is currently unknown, so to bypass this step, we here propose a conceptual setup for cas expression activation, where cas genes are put under transcription control typical for a restriction-modification (R-M system and then introduced into a cell. Known transcription regulation of an R-M system is used as a proxy for currently unknown CRISPR-Cas transcription control, as both systems are characterized by high cooperativity, which is likely related to similar dynamical constraints of their function. We find that the two characteristic CRISPR-Cas control features are responsible for its temporally-specific dynamical response, so that the system makes a steep (switch-like transition from OFF to ON state with a time-delay controlled by pre-crRNA degradation rate. We furthermore find that cooperative transcription regulation qualitatively leads to a cross-over to a regime where, at higher pre-crRNA processing rates, crRNA generation approaches the limit of an infinitely abrupt system induction. We propose that these dynamical properties are associated with rapid expression of CRISPR-Cas components and efficient protection of bacterial cells against foreign DNA. In terms of synthetic

  9. Catalytic process for tritium exchange reaction

    International Nuclear Information System (INIS)

    Hansoo Lee; Kang, H.S.; Paek, S.W.; Hongsuk Chung; Yang Geun Chung; Sook Kyung Lee

    2001-01-01

    The catalytic activities for a hydrogen isotope exchange were measured through the reaction of a vapor and gas mixture. The catalytic activity showed to be comparable with the published data. Since the gas velocity is relatively low, the deactivation was not found clearly during the 5-hour experiment. Hydrogen isotope transfer experiments were also conducted through the liquid phase catalytic exchange reaction column that consisted of a catalytic bed and a hydrophilic bed. The efficiencies of both the catalytic and hydrophilic beds were higher than 0.9, implying that the column performance was excellent. (author)

  10. An unsaturated metal site-promoted approach to construct strongly coupled noble metal/HNb3O8 nanosheets for efficient thermo/photo-catalytic reduction.

    Science.gov (United States)

    Shen, Lijuan; Xia, Yuzhou; Lin, Sen; Liang, Shijing; Wu, Ling

    2017-10-05

    Creating two-dimensional (2D) crystal-metal heterostructures with an ultrathin thickness has spurred increasing research endeavors in catalysis because of its fascinating opportunities in tuning the electronic state at the surface and enhancing the chemical reactivity. Here we report a novel and facile Nb 4+ -assisted strategy for the in situ growth of highly dispersed Pd nanoparticles (NPs) on monolayer HNb 3 O 8 nanosheets (HNb 3 O 8 NS) constituting a 2D Pd/HNb 3 O 8 NS heterostructure composite without using extra reducing agents and stabilizing agents. The Pd NP formation is directed via a redox reaction between an oxidative Pd salt precursor (H 2 PdCl 4 ) and reductive unsaturated surface metal (Nb 4+ ) sites induced by light irradiation on monolayer HNb 3 O 8 NS. The periodic arrangement of metal Nb nodes on HNb 3 O 8 NS leads to a homogeneous distribution of Pd NPs. Density functional theory (DFT) calculations reveal that the direct redox reaction between the Nb 4+ and Pd 2+ ions leads to a strong chemical interaction between the formed Pd metal NPs and the monolayer HNb 3 O 8 support. Consequently, the as-obtained Pd/HNb 3 O 8 composite serves as a highly efficient bifunctional catalyst in both heterogeneous thermocatalytic and photocatalytic selective reduction of aromatic nitro compounds in water under ambient conditions. The achieved high activity originates from the unique 2D nanosheet configuration and in situ Pd incorporation, which leads to a large active surface area, strong metal-support interaction and enhanced charge transport capability. Moreover, this facile Nb 4+ -assisted synthetic route has demonstrated to be general, which can be applied to load other metals such as Au and Pt on monolayer HNb 3 O 8 NS. It is anticipated that this work can extend the facile preparation of noble metal/nanosheet 2D heterostructures, as well as promote the simultaneous capture of duple renewable thermal and photon energy sources to drive an energy efficient

  11. Application of BiFeO3-based on nickel foam composites with a highly efficient catalytic activity and easily recyclable in Fenton-like process under microwave irradiation

    Science.gov (United States)

    Li, Shuo; Zhang, Guangshan; Zheng, Heshan; Zheng, Yongjie; Wang, Peng

    2018-05-01

    In this study, BiFeO3 (BFO) powders decorated on nickel foam (NF) with a high catalytic activity are prepared via a one-step microwave-assisted hydrothermal method. The factors that influence the degradation of bisphenol A (BPA) with BFO/NFs as catalysts are optimized to improve the catalytic activity in a microwave-enhanced Fenton-like process. BFO/NF exhibit a superior catalytic activity with a high BPA removal ratio (98.4%) and TOC removal ratio (69.5%) within 5 min. Results indicate that NF significantly affect the improvement of the catalytic activity of BFO because it served as a source of hydroxyl radicals (•OH) during degradation. The amount of •OH generated by BFO/NF is approximately 1.65-fold higher than that by pure BFO. After six reaction cycles, the stability and reusability of •OH remain high. These findings provide new insights into the synthesis of composites on heterogeneous catalysts with high efficiency and easy recyclability for water treatment applications.

  12. RNA-Seq Analysis of Abdominal Fat Reveals Differences between Modern Commercial Broiler Chickens with High and Low Feed Efficiencies.

    Directory of Open Access Journals (Sweden)

    Zhu Zhuo

    Full Text Available For economic and environmental reasons, chickens with superior feed efficiency (FE are preferred in the broiler chicken industry. High FE (HFE chickens typically have reduced abdominal fat, the major adipose tissue in chickens. In addition to its function of energy storage, adipose tissue is a metabolically active organ that also possesses endocrine and immune regulatory functions. It plays a central role in maintaining energy homeostasis. Comprehensive understanding of the gene expression in the adipose tissue and the biological basis of FE are of significance to optimize selection and breeding strategies. Through gene expression profiling of abdominal fat from high and low FE (LFE commercial broiler chickens, the present study aimed to characterize the differences of gene expression between HFE and LFE chickens. mRNA-seq analysis was carried out on the total RNA of abdominal fat from 10 HFE and 12 LFE commercial broiler chickens, and 1.48 billion of 75-base sequence reads were generated in total. On average, 11,565 genes were expressed (>5 reads/gene/sample in the abdominal fat tissue, of which 286 genes were differentially expressed (DE at q (False Discover Rate 1.3 between HFE and LFE chickens. Expression levels from RNA-seq were confirmed with the NanoString nCounter analysis system. Functional analysis showed that the DE genes were significantly (p < 0.01 enriched in lipid metabolism, coagulation, and immune regulation pathways. Specifically, the LFE chickens had higher expression of lipid synthesis genes and lower expression of triglyceride hydrolysis and cholesterol transport genes. In conclusion, our study reveals the overall differences of gene expression in the abdominal fat from HFE and LFE chickens, and the results suggest that the divergent expression of lipid metabolism genes represents the major differences.

  13. Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation.

    Science.gov (United States)

    Wang, Peng; Yang, Lijiang; Gao, Yi Qin; Zhao, Xin Sheng

    2015-09-03

    H/ACA RNA-guided ribonucleoprotein particle (RNP), the most complicated RNA pseudouridylase so far known, uses H/ACA guide RNA for substrate capture and four proteins (Cbf5, Nop10, L7Ae and Gar1) for pseudouridylation. Although it was shown that Gar1 not only facilitates the product release, but also enhances the catalytic activity, the chemical role that Gar1 plays in this complicated machinery is largely unknown. Kinetics measurement on Pyrococcus furiosus RNPs at different temperatures making use of fluorescence anisotropy showed that Gar1 reduces the catalytic barrier through affecting the activation entropy instead of enthalpy. Site-directed mutagenesis combined with molecular dynamics simulations demonstrated that V149 in the thumb loop of Cbf5 is critical in placing the target uridine to the right position toward catalytic D85 of Cbf5. The enzyme elegantly aligns the position of uridine in the catalytic site with the help of Gar1. In addition, conversion of uridine to pseudouridine results in a rigid syn configuration of the target nucleotide in the active site and causes Gar1 to pull out the thumb. Both factors guarantee the efficient release of the product. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Translation of the flavivirus kunjin NS3 gene in cis but not its RNA sequence or secondary structure is essential for efficient RNA packaging.

    Science.gov (United States)

    Pijlman, Gorben P; Kondratieva, Natasha; Khromykh, Alexander A

    2006-11-01

    Our previous studies using trans-complementation analysis of Kunjin virus (KUN) full-length cDNA clones harboring in-frame deletions in the NS3 gene demonstrated the inability of these defective complemented RNAs to be packaged into virus particles (W. J. Liu, P. L. Sedlak, N. Kondratieva, and A. A. Khromykh, J. Virol. 76:10766-10775). In this study we aimed to establish whether this requirement for NS3 in RNA packaging is determined by the secondary RNA structure of the NS3 gene or by the essential role of the translated NS3 gene product. Multiple silent mutations of three computer-predicted stable RNA structures in the NS3 coding region of KUN replicon RNA aimed at disrupting RNA secondary structure without affecting amino acid sequence did not affect RNA replication and packaging into virus-like particles in the packaging cell line, thus demonstrating that the predicted conserved RNA structures in the NS3 gene do not play a role in RNA replication and/or packaging. In contrast, double frameshift mutations in the NS3 coding region of full-length KUN RNA, producing scrambled NS3 protein but retaining secondary RNA structure, resulted in the loss of ability of these defective RNAs to be packaged into virus particles in complementation experiments in KUN replicon-expressing cells. Furthermore, the more robust complementation-packaging system based on established stable cell lines producing large amounts of complemented replicating NS3-deficient replicon RNAs and infection with KUN virus to provide structural proteins also failed to detect any secreted virus-like particles containing packaged NS3-deficient replicon RNAs. These results have now firmly established the requirement of KUN NS3 protein translated in cis for genome packaging into virus particles.

  15. A small and efficient dimerization/packaging signal of rat VL30 RNA and its use in murine leukemia virus-VL30-derived vectors for gene transfer.

    Science.gov (United States)

    Torrent, C; Gabus, C; Darlix, J L

    1994-02-01

    Retroviral genomes consist of two identical RNA molecules associated at their 5' ends by the dimer linkage structure located in the packaging element (Psi or E) necessary for RNA dimerization in vitro and packaging in vivo. In murine leukemia virus (MLV)-derived vectors designed for gene transfer, the Psi + sequence of 600 nucleotides directs the packaging of recombinant RNAs into MLV virions produced by helper cells. By using in vitro RNA dimerization as a screening system, a sequence of rat VL30 RNA located next to the 5' end of the Harvey mouse sarcoma virus genome and as small as 67 nucleotides was found to form stable dimeric RNA. In addition, a purine-rich sequence located at the 5' end of this VL30 RNA seems to be critical for RNA dimerization. When this VL30 element was extended by 107 nucleotides at its 3' end and inserted into an MLV-derived vector lacking MLV Psi +, it directed the efficient encapsidation of recombinant RNAs into MLV virions. Because this VL30 packaging signal is smaller and more efficient in packaging recombinant RNAs than the MLV Psi + and does not contain gag or glyco-gag coding sequences, its use in MLV-derived vectors should render even more unlikely recombinations which could generate replication-competent viruses. Therefore, utilization of the rat VL30 packaging sequence should improve the biological safety of MLV vectors for human gene transfer.

  16. New self-assembled material based on Ru nanoparticles and 4-sulfocalix[4]arene as an efficient and recyclable catalyst for reduction of brilliant yellow azo dye in water: a new model catalytic reaction

    Energy Technology Data Exchange (ETDEWEB)

    Rambabu, Darsi; Pradeep, Chullikkattil P.; Dhir, Abhimanew, E-mail: abhimanew@iitmandi.ac.in [Indian Institute of Technology (India)

    2016-12-15

    New self-assembled material (Ru@SC) with ruthenium nanoparticles (Ru NPs) and 4-sulfocalix[4]arene (SC) is synthesized in water at room temperature. Ru@SC is characterized by thermal gravimetric analysis, FT-IR, powder x-ray diffraction, TEM and SEM analysis. The size of Ru nanoparticles in the self-assembly is approximately 5 nm. The self-assembled material Ru@SC shows an efficient catalytic reduction of toxic ‘brilliant yellow’ (BY) azo dye. The reduced amine products were successfully separated and confirmed by single-crystal XRD, NMR and UV-Vis spectroscopy. Ru@SC showed a better catalytic activity in comparison with commercial catalysts Ru/C (ruthenium on charcoal 5 %) and Pd/C (palladium on charcoal 5 and 10 %). The catalyst also showed a promising recyclability and heterogeneous nature as a catalyst for reduction of ‘BY’ azo dye.

  17. Nature of the Nucleosomal Barrier to RNA Polymerase II | Center for Cancer Research

    Science.gov (United States)

    In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged into nucleosomes, but in vitro encounters with the nucleosomes induce catalytic inactivation (arrest) of the pol II core enzyme. To determine potential mechanisms making nucleosomes transparent to transcription in vivo, we analyzed the nature of the nucleosome-induced arrest. We found that the arrests

  18. RNA Processing Factor 5 is required for efficient 5' cleavage at a processing site conserved in RNAs of three different mitochondrial genes in Arabidopsis thaliana.

    Science.gov (United States)

    Hauler, Aron; Jonietz, Christian; Stoll, Birgit; Stoll, Katrin; Braun, Hans-Peter; Binder, Stefan

    2013-05-01

    The 5' ends of many mitochondrial transcripts are generated post-transcriptionally. Recently, we identified three RNA PROCESSING FACTORs required for 5' end maturation of different mitochondrial mRNAs in Arabidopsis thaliana. All of these factors are pentatricopeptide repeat proteins (PPRPs), highly similar to RESTORERs OF FERTILTY (RF), that rescue male fertility in cytoplasmic male-sterile lines from different species. Therefore, we suggested a general role of these RF-like PPRPs in mitochondrial 5' processing. We now identified RNA PROCESSING FACTOR 5, a PPRP not classified as an RF-like protein, required for the efficient 5' maturation of the nad6 and atp9 mRNAs as well as 26S rRNA. The precursor molecules of these RNAs share conserved sequence elements, approximately ranging from positions -50 to +9 relative to mature 5' mRNA termini, suggesting these sequences to be at least part of the cis elements required for processing. The knockout of RPF5 has only a moderate influence on 5' processing of atp9 mRNA, whereas the generation of the mature nad6 mRNA and 26S rRNA is almost completely abolished in the mutant. The latter leads to a 50% decrease of total 26S rRNA species, resulting in an imbalance between the large rRNA and 18S rRNA. Despite these severe changes in RNA levels and in the proportion between the 26S and 18S rRNAs, mitochondrial protein levels appear to be unaltered in the mutant, whereas seed germination capacity is markedly reduced. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  19. A non-acid-assisted and non-hydroxyl-radical-related catalytic ozonation with ceria supported copper oxide in efficient oxalate degradation in water

    KAUST Repository

    Zhang, Tao; Li, Weiwei; Croue, Jean-Philippe

    2012-01-01

    with ozone. The optimum CuO loading amount was 12%. The molar ratio of oxalate removed/ozone consumption reached 0.84. The catalytic ozonation was most effective in a neutral pH range (6.7-7.9) and became ineffective when the water solution was acidic

  20. Multifunctional triblock co-polymer mP3/4HB-b-PEG-b-lPEI for efficient intracellular siRNA delivery and gene silencing.

    Science.gov (United States)

    Zhou, Li; Chen, Zhifei; Wang, Feifei; Yang, Xiuqun; Zhang, Biliang

    2013-04-01

    A non-viral siRNA carrier composed of mono-methoxy-poly (3-hydroxybutyrate-co-4-hydroxybutyrate)-block-polyethylene glycol-block-linear polyethyleneimine (mP3/4HB-b-PEG-b-lPEI) was synthesized using 1800 Da linear polyethyleneimine and evaluated for siRNA delivery. Our study demonstrated that siRNA could be efficiently combined with mP3/4HB-b-PEG-b-lPEI (mAG) co-polymer and was protected from nuclease degradation. The combined siRNA were released from the complexes easily under heparin competition. The particle size of the mAG/siRNA complexes was 158 nm, with a ζ-potential of around 28 mV. Atomic force microscopy images displayed spherical and homogeneously distributed complexes. The mAG block co-polymer displayed low cytotoxicity and efficient cellular uptake of Cy3-siRNA in A549 cells by flow cytometry and confocal microscopy. In vitro transfection efficiency of the block co-polymer was assessed using siRNA against luciferase in cultured A549-Luc, HeLa-Luc, HLF-Luc, A375-Luc and MCF-7-Luc cells. A higher transfection efficiency and lower cytotoxicity was obtained by mAG block co-polymer in five cell lines. Furthermore, a remarkable improvement in luciferase gene silencing efficiency of the mAG complex (up to 90-95%) over that of Lipofectamine™ 2000 (70-82%) was observed in HLF-Luc and A375-Luc cells. Additionally, a mAG/p65-siRNA complex also showed a better capability than Lipofectamine™ 2000/p65-siRNA complex to drastically reduce the p65 mRNA level down to 10-16% in HeLa, U251 and HUVEC cells at an N/P ratio of 70. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  1. Efficient replication of the in vitro transcripts from cloned cDNA of tomato black ring virus satellite RNA requires the 48K satellite RNA-encoded protein.

    Science.gov (United States)

    Hemmer, O; Oncino, C; Fritsch, C

    1993-06-01

    Tomato black ring virus isolate L supports the multiplication of a large satellite RNA of 1376 nt which has no common features with the two genomic RNAs except for the terminal motif 5' VPg UUGAAAA and a 3' poly(A) tail. The TBRV sat-RNA contains an ORF for a protein of 48K which is translated both in vitro and in vivo. To determine the function of the 48K protein we have studied the effect of different mutations introduced in the ORF of the cDNA clone on the capacity of transcripts to multiply in Chenopodium quinoa plants or protoplasts when inoculated along with the genomic RNAs. Transcripts in which nucleotides have been substituted within the 5' proximal region of the ORF multiplied poorly even when the modification conserved the 48K protein sequence, suggesting that this portion of the ORF contains cis-acting RNA sequences. Transcripts with alterations in the internal region of the ORF retained their multiplication capacity provided the mutation did not destroy the ORF or modify the length of the protein expressed. The absence of multiplication in plants of transcripts unable to express the 48K protein and their inability to replicate in protoplasts suggest strongly that the sat-RNA translation product itself is implicated in the replication of sat-RNA.

  2. Efficient and nontoxic biological response carrier delivering TNF-α shRNA for gene silencing in a murine model of rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Jialin Song

    2016-08-01

    Full Text Available Small interfering RNA (siRNA is an effective and specific method for silencing genes. However, an efficient and nontoxic carrier is needed to deliver the siRNA into the target cells. Tumor necrosis factor α (TNF-α plays a central role in the occurrence and progression of rheumatoid arthritis. In this study, we pre-synthetized a degradable cationic polymer (PDAPEI from 2,6-pyridinedicarboxaldehyde and low molecular weight polyethyleneimine (PEI, Mw=1.8 kDa as a gene vector for the delivery of TNF-α shRNA. The PDAPEI/pDNA complex showed a suitable particle size and stable zeta potential for transfection. In vitro study of the PDAPEI/pDNA complex revealed a lower cytotoxicity and higher transfection efficiency when transfecting TNF-α shRNA to macrophages by significantly down-regulating the expression of TNF-α. Moreover, the complex was extremely efficient in decreasing the severity of arthritis in mice with collagen-induced arthritis (CIA. PDAPEI delivered TNF-α shRNA has great potential in the treatment of rheumatoid arthritis.

  3. Catalytic exhaust control

    Energy Technology Data Exchange (ETDEWEB)

    Heinemann, H

    1973-09-01

    Recent achievements and problems in the development of exhaust control devices in the USA are reviewed. To meet the 1976 emission standards, catalytic systems for the oxidation of carbon monoxide and hydrocarbons and for the reduction of nitrogen oxides to nitrogen and water are needed. While oxidizing catalysts using platinum, palladium, copper, vanadium, and chromium appplied on alumina or ceramic materials are more or less effective in emission control, there are no catalytic devices for the reduction of nitrogen oxides with the required useful life of 25,000 to 50,000 miles as yet available. In the case of platinum catalysts on monolithic supports, the operating temperature of 650 to 750/sup 0/C as required for the oxidation process may cause inactivation of the catalysts and fusion of the support material. The oxidation of CO and hydrocarbons is inhibited by high concentrations of CO, nitric oxide, and hydrocarbons. The use of catalytic converters requires the use of lead-free or low-lead gasoline. The nitrogen oxides conversion efficiency is considerably influenced by the oxygen-to-CO ratio of the exhaust gas, which makes limitation of this ratio necessary.

  4. Plasma hydrogenated cationic detonation nanodiamonds efficiently deliver to human cells in culture functional siRNA targeting the Ewing sarcoma junction oncogene.

    Science.gov (United States)

    Bertrand, Jean-Rémi; Pioche-Durieu, Catherine; Ayala, Juan; Petit, Tristan; Girard, Hugues A; Malvy, Claude P; Le Cam, Eric; Treussart, François; Arnault, Jean-Charles

    2015-03-01

    The expression of a defective gene can lead to major cell dysfunctions among which cell proliferation and tumor formation. One promising therapeutic strategy consists in silencing the defective gene using small interfering RNA (siRNA). In previous publications we showed that diamond nanocrystals (ND) of primary size 35 nm, rendered cationic by polyethyleneimine-coating, can efficiently deliver siRNA into cell, which further block the expression of EWS/FLI-1 oncogene in a Ewing sarcoma disease model. However, a therapeutic application of such nanodiamonds requires their elimination by the organism, particularly in urine, which is impossible for 35 nm particles. Here, we report that hydrogenated cationic nanodiamonds of primary size 7 nm (ND-H) have also a high affinity for siRNA and are capable of delivering them in cells. With siRNA/ND-H complexes, we measured a high inhibition efficacy of EWS/FLI-1 gene expression in Ewing sarcoma cell line. Electron microscopy investigations showed ND-H in endocytosis compartments, and especially in macropinosomes from which they can escape before siRNA degradation occurred. In addition, the association of EWS/FLI-1 silencing by the siRNA/ND-H complex with a vincristine treatment yielded a potentiation of the toxic effect of this chemotherapeutic drug. Therefore ND-H appears as a promising delivery agent in anti-tumoral gene therapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Efficient Diethylzinc/Gallic Acid and Diethylzinc/Gallic Acid Ester Catalytic Systems for the Ring-Opening Polymerization of rac-Lactide

    Directory of Open Access Journals (Sweden)

    Karolina Żółtowska

    2015-12-01

    Full Text Available Polylactide (PLA represents one of the most promising biomedical polymers due to its biodegradability, bioresorbability and good biocompatibility. This work highlights the synthesis and characterization of PLAs using novel diethylzinc/gallic acid (ZnEt2/GAc and diethylzinc/propyl gallate (ZnEt2/PGAc catalytic systems that are safe for human body. The results of the ring-opening polymerization (ROP of rac-lactide (rac-LA in the presence of zinc-based catalytic systems have shown that, depending on the reaction conditions, “predominantly isotactic”, disyndiotactic or atactic PLA can be obtained. Therefore, the controlled and stereoselective ROP of rac-LA is discussed in detail in this paper.

  6. Antisense targeting of 3' end elements involved in DUX4 mRNA processing is an efficient therapeutic strategy for facioscapulohumeral dystrophy: a new gene-silencing approach.

    Science.gov (United States)

    Marsollier, Anne-Charlotte; Ciszewski, Lukasz; Mariot, Virginie; Popplewell, Linda; Voit, Thomas; Dickson, George; Dumonceaux, Julie

    2016-04-15

    Defects in mRNA 3'end formation have been described to alter transcription termination, transport of the mRNA from the nucleus to the cytoplasm, stability of the mRNA and translation efficiency. Therefore, inhibition of polyadenylation may lead to gene silencing. Here, we choose facioscapulohumeral dystrophy (FSHD) as a model to determine whether or not targeting key 3' end elements involved in mRNA processing using antisense oligonucleotide drugs can be used as a strategy for gene silencing within a potentially therapeutic context. FSHD is a gain-of-function disease characterized by the aberrant expression of the Double homeobox 4 (DUX4) transcription factor leading to altered pathogenic deregulation of multiple genes in muscles. Here, we demonstrate that targeting either the mRNA polyadenylation signal and/or cleavage site is an efficient strategy to down-regulate DUX4 expression and to decrease the abnormally high-pathological expression of genes downstream of DUX4. We conclude that targeting key functional 3' end elements involved in pre-mRNA to mRNA maturation with antisense drugs can lead to efficient gene silencing and is thus a potentially effective therapeutic strategy for at least FSHD. Moreover, polyadenylation is a crucial step in the maturation of almost all eukaryotic mRNAs, and thus all mRNAs are virtually eligible for this antisense-mediated knockdown strategy. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. A non-acid-assisted and non-hydroxyl-radical-related catalytic ozonation with ceria supported copper oxide in efficient oxalate degradation in water

    KAUST Repository

    Zhang, Tao

    2012-06-01

    Oxalate is usually used as a refractory model compound that cannot be effectively removed by ozone and hydroxyl radical oxidation in water. In this study, we found that ceria supported CuO significantly improved oxalate degradation in reaction with ozone. The optimum CuO loading amount was 12%. The molar ratio of oxalate removed/ozone consumption reached 0.84. The catalytic ozonation was most effective in a neutral pH range (6.7-7.9) and became ineffective when the water solution was acidic or alkaline. Moreover, bicarbonate, a ubiquitous hydroxyl radical scavenger in natural waters, significantly improved the catalytic degradation of oxalate. Therefore, the degradation relies on neither hydroxyl radical oxidation nor acid assistance, two pathways usually proposed for catalytic ozonation. These special characters of the catalyst make it suitable to be potentially used for practical degradation of refractory hydrophilic organic matter and compounds in water and wastewater. With in situ characterization, the new surface Cu(II) formed from ozone oxidation of the trace Cu(I) of the catalyst was found to be an active site in coordination with oxalate forming multi-dentate surface complex. It is proposed that the complex can be further oxidized by molecular ozone and then decomposes through intra-molecular electron transfer. The ceria support enhanced the activity of the surface Cu(I)/Cu(II) in this process. © 2012 Elsevier B.V.

  8. The Fabrication of Ga2O3/ZSM-5 Hollow Fibers for Efficient Catalytic Conversion of n-Butane into Light Olefins and Aromatics

    Directory of Open Access Journals (Sweden)

    Jing Han

    2016-01-01

    Full Text Available In this study, the dehydrogenation component of Ga2O3 was introduced into ZSM-5 nanocrystals to prepare Ga2O3/ZSM-5 hollow fiber-based bifunctional catalysts. The physicochemical features of as-prepared catalysts were characterized by means of XRD, BET, SEM, STEM, NH3-TPD, etc., and their performances for the catalytic conversion of n-butane to produce light olefins and aromatics were investigated. The results indicated that a very small amount of gallium can cause a marked enhancement in the catalytic activity of ZSM-5 because of the synergistic effect of the dehydrogenation and aromatization properties of Ga2O3 and the cracking function of ZSM-5. Compared with Ga2O3/ZSM-5 nanoparticles, the unique hierarchical macro-meso-microporosity of the as-prepared hollow fibers can effectively enlarge the bifunctionality by enhancing the accessibility of active sites and the diffusion. Consequently, Ga2O3/ZSM-5 hollow fibers show excellent catalytic conversion of n-butane, with the highest yield of light olefins plus aromatics at 600 °C by 87.6%, which is 56.3%, 24.6%, and 13.3% higher than that of ZSM-5, ZSM-5 zeolite fibers, and Ga2O3/ZSM-5, respectively.

  9. An efficient RuCl3·H2O/I2 catalytic system: A facile access to 3-aroylimidazo[1,2-a]pyridines from 2-aminopyridines and chalcones

    Directory of Open Access Journals (Sweden)

    P.V. Sri Ramya

    2018-01-01

    Full Text Available A simple and efficient protocol has been demonstrated for the preparation of densely functionalized 3-aroylimidazo[1,2-a]pyridines from 2-aminopyridines and chalcones using RuCl3·H2O/I2 catalytic system. The advantages, such as low catalyst loading, broad substrate scope with respect to substitutions on aminopyridines as well as chalcones, stability of heterocycles such as thiophene under the reaction conditions, operationally simple procedure and higher yields makes this approach remarkable for synthetic applications.

  10. Plant 7SL RNA and tRNA(Tyr) genes with inserted antisense sequences are efficiently expressed in an in vitro transcription system from Nicotiana tabacum cells

    Czech Academy of Sciences Publication Activity Database

    Yukawa, Y.; Matoušek, Jaroslav; Grimm, M.; Vrba, Lukáš; Steger, G.; Sugiura, M.; Beier, H.

    2002-01-01

    Roč. 50, - (2002), s. 713-723 ISSN 0167-4412 R&D Projects: GA ČR GA521/99/1591; GA MŠk ME 463 Keywords : antisense RNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.529, year: 2002

  11. A novel tyrosine-modified low molecular weight polyethylenimine (P10Y) for efficient siRNA delivery in vitro and in vivo.

    Science.gov (United States)

    Ewe, Alexander; Przybylski, Susanne; Burkhardt, Jana; Janke, Andreas; Appelhans, Dietmar; Aigner, Achim

    2016-05-28

    The delivery of nucleic acids, particularly of small RNA molecules like siRNAs for the induction of RNA interference (RNAi), still represents a major hurdle with regard to their application in vivo. Possible therapeutic applications thus rely on the development of efficient non-viral gene delivery vectors. While low molecular weight polyethylenimines (PEIs) have been successfully explored, the introduction of chemical modifications offers an avenue towards the development of more efficient vectors. In this paper, we describe the synthesis of a novel tyrosine-modified low-molecular weight polyethylenimine (P10Y) for efficient siRNA complexation and delivery. The comparison with the respective parent PEI reveals that knockdown efficacies are considerably enhanced by the tyrosine modification, as determined in different reporter cell lines, without appreciable cytotoxicity. We furthermore identify optimal conditions for complex preparation as well as for storing or lyophilization of the complexes without loss of biological activity. Beyond reporter cell lines, P10Y/siRNA complexes mediate the efficient knockdown of endogenous target genes and, upon knockdown of the anti-apoptotic oncogene survivin, tumor cell inhibitory effects in different carcinoma cell lines. Pushing the system further towards its therapeutic in vivo application, we demonstrate in mice the delivery of intact siRNAs and distinct biodistribution profiles upon systemic (intravenous or intraperitoneal) injection. No adverse effects (hepatotoxicity, immunostimulation/alterations in immunophenotype, weight loss) are observed. More importantly, profound tumor-inhibitory effects in a melanoma xenograft mouse model are observed upon systemic application of P10Y/siRNA complexes for survivin knockdown, indicating the therapeutic efficacy of P10Y/siRNA complexes. Taken together, we (i) establish tyrosine-modified PEI (P10Y) as efficient platform for siRNA delivery in vitro and in vivo, (ii) identify optimal

  12. Potential roles of placental human beta-defensin-3 and apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3G in prevention of intrauterine transmission of hepatitis B virus.

    Science.gov (United States)

    Bai, Xiaoxia; Tian, Ting; Wang, Peng; Yang, Xiaofu; Wang, Zhengping; Dong, Minyue

    2015-03-01

    Approximately 5% of newborns were infected by hepatitis B virus (HBV) via intrauterine transmission and this is the main reason for high prevalence of HBV in endemic regions. However, the mechanisms by which intrauterine transmission is avoided in most cases remain elusive and placental natural anti-microbial factors may play a role in the prevention of HBV intrauterine transmission. The expression levels of human β-defensin-3 (HBD-3), apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3G (A3G) and mannose binding lectin (MBL) were determined in the placenta of 30 HBV-seronegative pregnant women (controls), 7 HBV-seropositive pregnant women with infants infected via intrauterine transmission (infected group) and 30 HBV-seropositive pregnant women with non-infected infants (non-infected group). The expression of HBD-3, A3G, and MBL of placental trophoblast cell line Swan71 was determined after exposed to HBV. There were significant differences in placental HBD-3 and A3G levels among three groups, but the expression of MBL did not significantly differ. The expressions of HBD-3 and A3G were higher in non-infected group than controls and infected group, but not significantly different between infected group and controls. The exposure to HBV increased significantly the expression of HBD-3, A3G, and MBL by Swan 71. It may be concluded HBV up-regulates HBD-3 and A3G expression in vivo and in vitro in placental trophoblast and lack of this up-regulation is possibly associated with intrauterine transmission of HBV. © 2014 Wiley Periodicals, Inc.

  13. Sequences within both the 5' untranslated region and the Gag gene are important for efficient encapsidation of Mason-Pfizer monkey virus RNA

    International Nuclear Information System (INIS)

    Schmidt, Russell D.; Mustafa, Farah; Lew, Kathy A.; Browning, Mathew T.; Rizvi, Tahir A.

    2003-01-01

    It has previously been shown that the 5' untranslated leader region (UTR), including about 495 bp of the gag gene, is sufficient for the efficient encapsidation and propagation of Mason-Pfizer monkey virus (MPMV) based retroviral vectors. In addition, a deletion upstream of the major splice donor, SD, has been shown to adversely affect MPMV RNA packaging. However, the precise sequence requirement for the encapsidation of MPMV genomic RNA within the 5' UTR and gag remains largely unknown. In this study, we have used a systematic deletion analysis of the 5' UTR and gag gene to define the cis-acting sequences responsible for efficient MPMV RNA packaging. Using an in vivo packaging and transduction assay, our results reveal that the MPMV packaging signal is primarily found within the first 30 bp immediately downstream of the primer binding site. However, its function is dependent upon the presence of the last 23 bp of the 5' UTR and approximately the first 100 bp of the gag gene. Thus, sequences that affect MPMV RNA packaging seem to reside both upstream and downstream of the major splice donor with the downstream region responsible for the efficient functioning of the upstream primary packaging determinant

  14. Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I.

    Science.gov (United States)

    Lama, Lodoe; Ryan, Kevin

    2016-01-01

    Many high-throughput small RNA next-generation sequencing protocols use 5' preadenylylated DNA oligonucleotide adapters during cDNA library preparation. Preadenylylation of the DNA adapter's 5' end frees from ATP-dependence the ligation of the adapter to RNA collections, thereby avoiding ATP-dependent side reactions. However, preadenylylation of the DNA adapters can be costly and difficult. The currently available method for chemical adenylylation of DNA adapters is inefficient and uses techniques not typically practiced in laboratories profiling cellular RNA expression. An alternative enzymatic method using a commercial RNA ligase was recently introduced, but this enzyme works best as a stoichiometric adenylylating reagent rather than a catalyst and can therefore prove costly when several variant adapters are needed or during scale-up or high-throughput adenylylation procedures. Here, we describe a simple, scalable, and highly efficient method for the 5' adenylylation of DNA oligonucleotides using the thermostable RNA ligase 1 from bacteriophage TS2126. Adapters with 3' blocking groups are adenylylated at >95% yield at catalytic enzyme-to-adapter ratios and need not be gel purified before ligation to RNA acceptors. Experimental conditions are also reported that enable DNA adapters with free 3' ends to be 5' adenylylated at >90% efficiency. © 2015 Lama and Ryan; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  15. RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithromycin susceptibility.

    Science.gov (United States)

    Shoji, Tatsuma; Takaya, Akiko; Sato, Yoshiharu; Kimura, Satoshi; Suzuki, Tsutomu; Yamamoto, Tomoko

    2015-10-15

    Adenine at position 752 in a loop of helix 35 from positions 745 to 752 in domain II of 23S rRNA is involved in binding to the ribosome of telithromycin (TEL), a member of ketolides. Methylation of guanine at position 748 by the intrinsic methyltransferase RlmA(II) enhances binding of telithromycin (TEL) to A752 in Streptococcus pneumoniae. We have found that another intrinsic methylation of the adjacent uridine at position 747 enhances G748 methylation by RlmA(II), rendering TEL susceptibility. U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae. Inactivation of RlmCD reduced N1-methylated level of G748 by RlmA(II) in vivo, leading to TEL resistance when the nucleotide A2058, located in domain V of 23S rRNA, was dimethylated by the dimethyltransferase Erm(B). In vitro methylation of rRNA showed that RlmA(II) activity was significantly enhanced by RlmCD-mediated pre-methylation of 23S rRNA. These results suggest that RlmCD-mediated U747 methylation promotes efficient G748 methylation by RlmA(II), thereby facilitating TEL binding to the ribosome. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Tailored synthesis of CuS nanodisks from a new macrocyclic precursor and their efficient catalytic properties on methylene blue dye degradation

    International Nuclear Information System (INIS)

    Islam, D. A.; Chakraborty, A.; Bhattacharya, B.; Sarkar, U.; Acharya, H.

    2016-01-01

    In this study, CuS nanodisks have been synthesized from a tetraaza (N_4) macrocyclic complex precursor by a facile wet chemical method. The crystallinity and morphology of the as-synthesized products were characterized by X-ray diffraction and transmission electron microscopy, which confirm a phase pure crystalline CuS nanostructures with ~15 to 20 nm in dimension with ~5 nm thickness. A possible formation mechanism and growth process of the CuS nanodisks are discussed using thiourea and tetraaza ligand as the sulfur donor and stabilizing agent, respectively. Cyclic N_4 ligand also acts as a binding agent to template-guide the oriented growth of CuS nanodisks. The optimized geometry of ligands and complexes was calculated using B3YLP functional, which indicates that the HOMO in the complex located on metal center and N atoms are weakly bonded to the metal center. The catalytic activity of CuS nanodisks toward MB degradation with light displays the higher MB degradation rate than under dark in the presence of H_2O_2. The C_t/C_0 plot as a function of time displays the higher MB degradation activity of CuS nanoparticles with H_2O_2. The recycle stability of CuS nanoparticles was even found to be >80 % after five cycles studied by repeating the MB degradation with same CuS nanoparticles sample.Graphical AbstractCuS nanostructures synthesized from a tetraaza macrocyclic complex precursor show the disk-like registry with average lateral dimension between 15 and 20 nm and thickness of 5 nm. The catalytic activity of CuS nanodisks toward MB degradation with light displays the higher MB degradation rate than in dark in the presence of H_2O_2.

  17. Tailored synthesis of CuS nanodisks from a new macrocyclic precursor and their efficient catalytic properties on methylene blue dye degradation

    Energy Technology Data Exchange (ETDEWEB)

    Islam, D. A.; Chakraborty, A. [Assam University, Department of Chemistry, Centre for Soft Matters (India); Bhattacharya, B.; Sarkar, U. [Assam University, Department of Physics (India); Acharya, H., E-mail: himadriau@yahoo.co.in [Assam University, Department of Chemistry, Centre for Soft Matters (India)

    2016-05-15

    In this study, CuS nanodisks have been synthesized from a tetraaza (N{sub 4}) macrocyclic complex precursor by a facile wet chemical method. The crystallinity and morphology of the as-synthesized products were characterized by X-ray diffraction and transmission electron microscopy, which confirm a phase pure crystalline CuS nanostructures with ~15 to 20 nm in dimension with ~5 nm thickness. A possible formation mechanism and growth process of the CuS nanodisks are discussed using thiourea and tetraaza ligand as the sulfur donor and stabilizing agent, respectively. Cyclic N{sub 4} ligand also acts as a binding agent to template-guide the oriented growth of CuS nanodisks. The optimized geometry of ligands and complexes was calculated using B3YLP functional, which indicates that the HOMO in the complex located on metal center and N atoms are weakly bonded to the metal center. The catalytic activity of CuS nanodisks toward MB degradation with light displays the higher MB degradation rate than under dark in the presence of H{sub 2}O{sub 2}. The C{sub t}/C{sub 0} plot as a function of time displays the higher MB degradation activity of CuS nanoparticles with H{sub 2}O{sub 2}. The recycle stability of CuS nanoparticles was even found to be >80 % after five cycles studied by repeating the MB degradation with same CuS nanoparticles sample.Graphical AbstractCuS nanostructures synthesized from a tetraaza macrocyclic complex precursor show the disk-like registry with average lateral dimension between 15 and 20 nm and thickness of 5 nm. The catalytic activity of CuS nanodisks toward MB degradation with light displays the higher MB degradation rate than in dark in the presence of H{sub 2}O{sub 2}.

  18. Catalytic modification of cellulose and hemicellulose - Sugarefine

    Energy Technology Data Exchange (ETDEWEB)

    Repo, T. [Helsinki Univ. (Finland),Laboratory of Inorganic Chemistry], email: timo.repo@helsinki.fi

    2012-07-01

    The main goal of the project is to develop catalytic methods for the modification of lignocellulose-based saccharides in the biorefineries. The products of these reactions could be used for example as biofuel components, raw materials for the chemical industry, solvents and precursors for biopolymers. The catalyst development aims at creating efficient, selective and green catalytic methods for profitable use in biorefineries. The project is divided in three work packages: In WP1 (Catalytic dehydration of cellulose) the aim is at developing non-toxic, efficient methods for the catalytic dehydration of cellulose the target molecule being here 5-hydroxymethylfurfural (5-HMF). 5-HMF is an interesting platform chemical for the production of fuel additives, solvents and polymers. In WP2 (Catalytic reduction), the objective of the catalytic reduction studies is to produce commercially interesting monofunctional chemicals, such as 1-butanol or 2-methyltetrahydrofuran (2-MeTHF). In WP3 (Catalytic oxidation), the research focuses on developing a green and efficient oxidation method for producing acids. Whereas acetic and formic acids are bulk chemicals, diacids such as glucaric and xylaric acids are valuable specialty chemicals for detergent, polymer and food production.

  19. An efficient route for catalytic activity promotion via hybrid electro-depositional modification on commercial nickel foam for hydrogen evolution reaction in alkaline water electrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Guanshui; He, Yongwei; Wang, Mei; Zhu, Fuchun; Tang, Bin [Research Institute of Surface Engineering, Taiyuan University of Technology, Yingze West Road 79, Taiyuan 030024 (China); Wang, Xiaoguang, E-mail: wangxiaog1982@163.com [Research Institute of Surface Engineering, Taiyuan University of Technology, Yingze West Road 79, Taiyuan 030024 (China); International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga (Portugal)

    2014-09-15

    Highlights: • Mono-Cu surface modification depress the HER activity of Ni-foam. • Hybrid Ni-foam/Cu0.01/Co0.05 exhibits superior HER performance. • Layer-by-layer structure may contribute to a synergistic promoting effect. - Abstract: In this paper, the single- and hybrid-layered Cu, Ni and Co thin films were electrochemically deposited onto the three-dimensional nickel foam as composite cathode catalyst for hydrogen evolution reaction in alkaline water electrolysis. The morphology, structure and chemical composition of the electrodeposited composite catalysts were investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray analysis (EDX). Electrochemical measurement depicted that, for the case of the monometallic layered samples, the general activity for hydrogen evolution reaction followed the sequence: Ni-foam/Ni > Ni-foam/Co > bare Ni-foam > Ni-foam/Cu. It is noteworthy that, the hybrid-layered Ni-foam/Cu0.01/Co0.05 exhibited the highest catalytic activity towards hydrogen evolution reaction with the current density as high as 2.82 times that of the bare Ni-foam. Moreover, both excellent electrochemical and physical stabilities can also be acquired on the Ni-foam/Cu0.01/Co0.05, making this hybrid-layered composite structure as a promising HER electro-catalyst.

  20. Effect of alginate microencapsulation on the catalytic efficiency and in vitro enzyme-prodrug therapeutic efficacy of cytosine deaminase and of recombinant E. coli expressing cytosine deaminase.

    Science.gov (United States)

    Funaro, Michael G; Nemani, Krishnamurthy V; Chen, Zhihang; Bhujwalla, Zaver M; Griswold, Karl E; Gimi, Barjor

    2016-02-01

    Cytosine deaminase (CD) catalyses the enzymatic conversion of the non-toxic prodrug 5-fluorocytosine (5-FC) to the potent chemotherapeutic form, 5-fluorouracil (5-FU). Intratumoral delivery of CD localises chemotherapy dose while reducing systemic toxicity. Encapsulation in biocompatible microcapsules immunoisolates CD and protects it from degradation. We report on the effect of alginate encapsulation on the catalytic and functional activity of isolated CD and recombinant E. coli engineered to express CD (E. coli(CD)). Alginate microcapsules containing either CD or Escherichia coli(CD) were prepared using ionotropic gelation. Conversion of 5-FC to 5-FU was quantitated in unencapsulated and encapsulated CD/E. coli(CD) using spectrophotometry, with a slower rate of conversion observed following encapsulation. Both encapsulated CD/5-FC and E. coli(CD)/5-FC resulted in cell kill and reduced proliferation of 9 L rat glioma cells, which was comparable to direct 5-FU treatment. Our results show that encapsulation preserves the therapeutic potential of CD and E. coli(CD) is equally effective for enzyme-prodrug therapy.

  1. Efficient procedure for transferring specific human genes into Chinese hamster cell mutants: interspecific transfer of the human genes encoding leucyl- and asparaginyl-tRNA synthetases

    International Nuclear Information System (INIS)

    Cirullo, R.E.; Dana, S.; Wasmuth, J.J.

    1983-01-01

    A simple and efficient procedure for transferring specific human genes into mutant Chinese hamster ovary cell recipients has been developed that does not rely on using calcium phosphate-precipitated high-molecular-weight DNA. Interspecific cell hybrids between human leukocytes and temperature-sensitive Chinese hamster cell mutants with either a thermolabile leucyl-tRNA synthetase or a thermolabile asparaginyl-tRNA synthetase were used as the starting material in these experiments. These hybrids contain only one or a few human chromosomes and require expression of the appropriate human aminoacyl-tRNA synthetase gene to grow at 39 degrees C. Hybrids were exposed to very high doses of gamma-irradiation to extensively fragment the chromosomes and re-fused immediately to the original temperature-sensitive Chinese hamster mutant, and secondary hybrids were isolated at 39 degrees C. Secondary hybrids, which had retained small fragments of the human genome containing the selected gene, were subjected to another round of irradiation, refusion, and selection at 39 degrees C to reduce the amount of human DNA even further. Using this procedure, Chinese hamster cell lines have been constructed that express the human genes encoding either asparaginyl- or leucyl-tRNA synthetase, yet less than 0.1% of their DNA is derived from the human genome, as quantitated by a sensitive dot-blot nucleic acid hybridization procedure

  2. An efficient and high fidelity method for amplification, cloning and sequencing of complete tospovirus genomic RNA segments

    Science.gov (United States)

    Amplification and sequencing of the complete M- and S-RNA segments of Tomato spotted wilt virus and Impatiens necrotic spot virus as a single fragment is useful for whole genome sequencing of tospoviruses co-infecting a single host plant. It avoids issues associated with overlapping amplicon-based ...

  3. Cell-killing efficiency and number of platinum atoms binding to DNA, RNA and protein molecules of HeLa cells treated with combinations of hyperthermia and carboplatin

    International Nuclear Information System (INIS)

    Akaboshi, M.; Kawai, K.; Tanaka, Y.; Takada, J.; Sumino, T.

    1999-01-01

    The effect of hyperthermia on the cell killing efficiency of Pt atoms binding to DNA, RNA and protein molecules of HeLa cells treated with cis-diamine(1,1-cyclobutanedicarboxylato)platinum(II) (CBDCA) was examined. HeLa S-3 cells were treated with 195m Pt-radiolabeled CBDCA for 60 minutes at various temperatures, and the relationship between the lethal effect and the number of Pt atoms binding to DNA, RNA and proteins was examined. The mean lethal concentration (D 0 ) of carboplatin for a 60 min-treatment at 0, 25, 37, 40, 42 and 44 deg C was 671.2, 201.5, 67.3, 33.4, 20.2 and 15.6 μM, respectively. By using identically treated cells, the number of Pt-atoms combined with DNA, RNA and protein molecules were determined in the subcellular fractions. Thus, the D 0 's given as the drug concentrations were replaced with the number of Pt-atoms combined in each fraction. Then, the cell-killing efficiency of the Pt atom was expressed as the reciprocal of the number of Pt-atoms combined and was calculated for each molecule. The efficiency for DNA molecules was 0.699, 1.42, 2.65, 4.84, 7.74 and 8.28x10 4 nucleotides, respectively, for the conditions described above. From 0 to 44 deg C, the cell-killing efficiency of Pt atoms increased by a factor of 11.9. (author)

  4. A novel sodium iodide and ammonium molybdate co-catalytic system for the efficient synthesis of 2-benzimidazoles using hydrogen peroxide under ultrasound irradiation.

    Science.gov (United States)

    Bai, Guo-Yi; Lan, Xing-Wang; Chen, Guo-Feng; Liu, Xiao-Fang; Li, Tian-Yu; Shi, Ling-Juan

    2014-03-01

    The reaction of aldehydes and o-phenylenediamine for the preparation of 2-benzimidazoles has been studied using hydrogen peroxide as an oxidant under ultrasound irradiation at room temperature in this paper. The combination of substoichiometric sodium iodide and ammonium molybdate as co-catalysts, together with using small amounts of hydrogen peroxide, makes this transformation very efficient and attractive under ultrasound. Thus, a mild, green and efficient method is established to carry out this reaction in high yield. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. On the efficient bio-incorporation of 5-hydroxy-tryptophan in recombinant proteins expressed in Escherichia coli with T7 RNA polymerase-based vectors.

    Science.gov (United States)

    Oliveira-Souza, Wellington P; Bronze, Fellipe; Broos, Jaap; Marcondes, Marcelo F M; Oliveira, Vitor

    2017-10-21

    Biosynthetic incorporation of non-canonic amino acids is an attractive strategy to introduce new properties in recombinant proteins. Trp analogs can be incorporated in recombinant proteins replacing regular Trp during protein translation into a Trp-auxotrophic cell host. This straightforward method however, is limited to few analogs recognized and accepted by the cellular protein production machinery. 5-hydroxy-tryptophan (5OH-Trp) can be bio-incorporated using E. coli as expression host however; we have experienced very low incorporation yields - amount of protein containing regular Trp/amount of protein containing the Trp analog - during expressions of 5OH-Trp labeled proteins. Furthermore, this low incorporation yield were verified especially when the widely-used vectors based on the T7 RNA polymerase were used. Testing different 5OH-Trp incorporation protocols we verified that in these T7-based systems, the production of the T7 RNA polymerase is driven by the same elements - lac promoter/IPTG - as the target protein. Consequently, the bio-incorporation of the 5OH-Trp residues also occurs in this crucial enzyme, but, the produced T7 RNA polymerase labeled with 5OH-Trp is inactive or much less active. In the present work, we describe an efficient method to overcome this mentioned problem and bio-incorporate 5OH-Trp in proteins expressed in E. coli., using vectors based on the T7 RNA polymerase-T7 promoter. The two-step induction protocol here described showed incorporation efficiencies of 5OH-Trp higher than 90%. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Update: An efficient synthesis of poly(ethylene glycol)-supported iron(II) porphyrin using a click reaction and its application for the catalytic olefination of aldehydes

    KAUST Repository

    Chinnusamy, Tamilselvi R.; Rodionov, Valentin; Kü hn, Fritz; Reiser, Oliver

    2012-01-01

    The facile synthesis of polyethylene glycol (PEG)-immobilized iron(II) porphyrin using a copper-catalyzed azide-alkyne [3+2] cycloaddition "click" reaction is reported. The prepared complex 5 (PEG-C 51H 39FeN 7O) was found to be an efficient

  7. Aminoacyl-tRNA quality control is required for efficient activation of the TOR pathway regulator Gln3p.

    Science.gov (United States)

    Mohler, Kyle; Mann, Rebecca; Kyle, Amanda; Reynolds, Noah; Ibba, Michael

    2017-09-14

    The aminoacylation status of the cellular tRNA pool regulates both general amino acid control (GAAC) and target of rapamycin (TOR) stress response pathways in yeast. Consequently, fidelity of translation at the level of aminoacyl-tRNA synthesis plays a central role in determining accuracy and sensitivity of stress responses. To investigate effects of translational quality control (QC) on cell physiology under stress conditions, phenotypic microarray analyses were used to identify changes in QC deficient cells. Nitrogen source growth assays showed QC deficient yeast grew differently compared to WT. The QC deficient strain was more tolerant to caffeine treatment than wild type through altered interactions with the TOR and GAAC pathways. Increased caffeine tolerance of the QC deficient strain was consistent with the observation that the activity of Gln3p, a transcription factor controlled by the TOR pathway, is decreased in the QC deficient strain compared to WT. GCN4 translation, which is typically repressed in the absence of nutritional stress, was enhanced in the QC deficient strain through TOR inhibition. QC did not impact cell cycle regulation; however, the chronological lifespan of QC deficient yeast strains decreased compared to wild type, likely due to translational errors and alteration of the TOR-associated regulon. These findings support the idea that changes in translational fidelity provide a mechanism of cellular adaptation by modulating TOR activity. This, in turn, supports a central role for aminoacyl-tRNA synthesis QC in the integrated stress response by maintaining the proper aa-tRNA pools necessary to coordinate the GAAC and TOR.

  8. Mutations in the catalytic core or the C-terminus of murine leukemia virus (MLV) integrase disrupt virion infectivity and exert diverse effects on reverse transcription

    International Nuclear Information System (INIS)

    Steinrigl, Adolf; Nosek, Dagmara; Ertl, Reinhard; Guenzburg, Walter H.; Salmons, Brian; Klein, Dieter

    2007-01-01

    Understanding of the structures and functions of the retroviral integrase (IN), a key enzyme in the viral replication cycle, is essential for developing antiretroviral treatments and facilitating the development of safer gene therapy vehicles. Thus, four MLV IN-mutants were constructed in the context of a retroviral vector system, harbouring either a substitution in the catalytic centre, deletions in the C-terminus, or combinations of both modifications. IN-mutants were tested for their performance in different stages of the viral replication cycle: RNA-packaging; RT-activity; transient and stable infection efficiency; dynamics of reverse transcription and nuclear entry. All mutant vectors packaged viral RNA with wild-type efficiencies and displayed only slight reductions in RT-activity. Deletion of either the IN C-terminus alone, or in addition to part of the catalytic domain exerted contrasting effects on intracellular viral DNA levels, implying that IN influences reverse transcription in more than one direction

  9. A new hypercrosslinked supermicroporous polymer, with scope for sulfonation, and its catalytic potential for the efficient synthesis of biodiesel at room temperature.

    Science.gov (United States)

    Bhunia, Subhajit; Banerjee, Biplab; Bhaumik, Asim

    2015-03-25

    We have designed a new hypercrosslinked supermicroporous polymer (HMP-1) with a BET surface area of 913 m(2) g(-1) by FeCl3 via a catalyzed Friedel-Crafts alkylation reaction between carbazole and α,α'-dibromo-p-xylene. Upon sulfonation HMP-1 yielded a very efficient solid acid catalyst for the production of biodiesels via esterification/transesterification of free fatty acids (FFA)/esters at room temperature.

  10. Update: An efficient synthesis of poly(ethylene glycol)-supported iron(II) porphyrin using a click reaction and its application for the catalytic olefination of aldehydes

    KAUST Repository

    Chinnusamy, Tamilselvi R.

    2012-05-09

    The facile synthesis of polyethylene glycol (PEG)-immobilized iron(II) porphyrin using a copper-catalyzed azide-alkyne [3+2] cycloaddition "click" reaction is reported. The prepared complex 5 (PEG-C 51H 39FeN 7O) was found to be an efficient catalyst for the selective olefination of aldehydes with ethyl diazoacetate in the presence of triphenylphosphine, and afforded excellent olefin yields with high (E) selectivities. The PEG-supported catalyst 5 was readily recovered by precipitation and filtration, and was recycled through ten runs without significant activity loss. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Mutational Analysis of the Hypervariable Region of Hepatitis E Virus Reveals Its Involvement in the Efficiency of Viral RNA Replication ▿

    Science.gov (United States)

    Pudupakam, R. S.; Kenney, Scott P.; Córdoba, Laura; Huang, Yao-Wei; Dryman, Barbara A.; LeRoith, Tanya; Pierson, F. William; Meng, Xiang-Jin

    2011-01-01

    The RNA genome of the hepatitis E virus (HEV) contains a hypervariable region (HVR) in ORF1 that tolerates small deletions with respect to infectivity. To further investigate the role of the HVR in HEV replication, we constructed a panel of mutants with overlapping deletions in the N-terminal, central, and C-terminal regions of the HVR by using a genotype 1 human HEV luciferase replicon and analyzed the effects of deletions on viral RNA replication in Huh7 cells. We found that the replication levels of the HVR deletion mutants were markedly reduced in Huh7 cells, suggesting a role of the HVR in viral replication efficiency. To further verify the results, we constructed HVR deletion mutants by using a genetically divergent, nonmammalian avian HEV, and similar effects on viral replication efficiency were observed when the avian HEV mutants were tested in LMH cells. Furthermore, the impact of complete HVR deletion on virus infectivity was tested in chickens, using an avian HEV mutant with a complete HVR deletion. Although the deletion mutant was still replication competent in LMH cells, the complete HVR deletion resulted in a loss of avian HEV infectivity in chickens. Since the HVR exhibits extensive variations in sequence and length among different HEV genotypes, we further examined the interchangeability of HVRs and demonstrated that HVR sequences are functionally exchangeable between HEV genotypes with regard to viral replication and infectivity in vitro, although genotype-specific HVR differences in replication efficiency were observed. The results showed that although the HVR tolerates small deletions with regard to infectivity, it may interact with viral and host factors to modulate the efficiency of HEV replication. PMID:21775444

  12. Codon optimization of the HIV-1 vpu and vif genes stabilizes their mRNA and allows for highly efficient Rev-independent expression

    International Nuclear Information System (INIS)

    Nguyen, Kim-Lien; Llano, Manuel; Akari, Hirofumi; Miyagi, Eri; Poeschla, Eric M.; Strebel, Klaus; Bour, Stephan

    2004-01-01

    Two HIV-1 accessory proteins, Vpu and Vif, are notoriously difficult to express autonomously in the absence of the viral Tat and Rev proteins. We examined whether the codon bias observed in the vpu and vif genes relative to highly expressed human genes contributes to the Rev dependence and low expression level outside the context of the viral genome. The entire vpu gene as well as the 5' half of the vif gene were codon optimized and the resulting open reading frames (ORFs) (vphu and hvif, respectively) were cloned in autonomous expression vectors under the transcriptional control of the CMV promoter. Codon optimization efficiently removed the expression block observed in the native genes and allowed high levels of Rev- and Tat-independent expression of Vpu and Vif. Most of the higher protein levels detected are accounted for by enhanced steady-state levels of the mRNA encoding the optimized species. Nuclear run-on experiments show for the first time that codon optimization has no effect on the rate of transcriptional initiation or elongation of the vphu mRNA. Instead, optimization of the vpu gene was found to stabilize the vphu mRNA in the nucleus and enhance its export to the cytoplasm. This was achieved by allowing the optimized mRNA to use a new CRM1-independent nuclear export pathway. This work provides a better understanding of the molecular mechanisms underlying the process of codon optimization and introduces novel tools to study the biological functions of the Vpu and Vif proteins independently of other viral proteins

  13. Use of short interfering RNA delivered by cationic liposomes to enable efficient down-regulation of PTPN22 gene in human T lymphocytes.

    Directory of Open Access Journals (Sweden)

    Valentina Perri

    Full Text Available Type 1 diabetes and thyroid disease are T cell-dependent autoimmune endocrinopathies. The standard substitutive administration of the deficient hormones does not halt the autoimmune process; therefore, development of immunotherapies aiming to preserve the residual hormonal cells, is of crucial importance. PTPN22 C1858T mutation encoding for the R620W lymphoid tyrosine phosphatase variant, plays a potential pathophysiological role in autoimmunity. The PTPN22 encoded protein Lyp is a negative regulator of T cell antigen receptor signaling; R620W variant, leading to a gain of function with paradoxical reduced T cell activation, may represent a valid therapeutic target. We aimed to develop novel wild type PTPN22 short interfering RNA duplexes (siRNA and optimize their delivery into Jurkat T cells and PBMC by using liposomal carriers. Conformational stability, size and polydispersion of siRNA in lipoplexes was measured by CD spectroscopy and DLS. Lipoplexes internalization and toxicity evaluation was assessed by confocal microscopy and flow cytometry analysis. Their effect on Lyp expression was evaluated by means of Western Blot and confocal microscopy. Functional assays through engagement of TCR signaling were established to evaluate biological consequences of down-modulation. Both Jurkat T cells and PBMC were efficiently transfected by stable custom lipoplexes. Jurkat T cell morphology and proliferation was not affected. Lipoplexes incorporation was visualized in CD3+ but also in CD3- peripheral blood immunotypes without signs of toxicity, damage or apoptosis. Efficacy in affecting Lyp protein expression was demonstrated in both transfected Jurkat T cells and PBMC. Moreover, impairment of Lyp inhibitory activity was revealed by increase of IL-2 secretion in culture supernatants of PBMC following anti-CD3/CD28 T cell receptor-driven stimulation. The results of our study open the pathway to future trials for the treatment of autoimmune diseases based

  14. Improving clinical laboratory efficiency: a time-motion evaluation of the Abbott m2000 RealTime and Roche COBAS AmpliPrep/COBAS TaqMan PCR systems for the simultaneous quantitation of HIV-1 RNA and HCV RNA.

    Science.gov (United States)

    Amendola, Alessandra; Coen, Sabrina; Belladonna, Stefano; Pulvirenti, F Renato; Clemens, John M; Capobianchi, M Rosaria

    2011-08-01

    Diagnostic laboratories need automation that facilitates efficient processing and workflow management to meet today's challenges for expanding services and reducing cost, yet maintaining the highest levels of quality. Processing efficiency of two commercially available automated systems for quantifying HIV-1 and HCV RNA, Abbott m2000 system and Roche COBAS Ampliprep/COBAS TaqMan 96 (docked) systems (CAP/CTM), was evaluated in a mid/high throughput workflow laboratory using a representative daily workload of 24 HCV and 72 HIV samples. Three test scenarios were evaluated: A) one run with four batches on the CAP/CTM system, B) two runs on the Abbott m2000 and C) one run using the Abbott m2000 maxCycle feature (maxCycle) for co-processing these assays. Cycle times for processing, throughput and hands-on time were evaluated. Overall processing cycle time was 10.3, 9.1 and 7.6 h for Scenarios A), B) and C), respectively. Total hands-on time for each scenario was, in order, 100.0 (A), 90.3 (B) and 61.4 min (C). The interface of an automated analyzer to the laboratory workflow, notably system set up for samples and reagents and clean up functions, are as important as the automation capability of the analyzer for the overall impact to processing efficiency and operator hands-on time.

  15. [Correlation of codon biases and potential secondary structures with mRNA translation efficiency in unicellular organisms].

    Science.gov (United States)

    Vladimirov, N V; Likhoshvaĭ, V A; Matushkin, Iu G

    2007-01-01

    Gene expression is known to correlate with degree of codon bias in many unicellular organisms. However, such correlation is absent in some organisms. Recently we demonstrated that inverted complementary repeats within coding DNA sequence must be considered for proper estimation of translation efficiency, since they may form secondary structures that obstruct ribosome movement. We have developed a program for estimation of potential coding DNA sequence expression in defined unicellular organism using its genome sequence. The program computes elongation efficiency index. Computation is based on estimation of coding DNA sequence elongation efficiency, taking into account three key factors: codon bias, average number of inverted complementary repeats, and free energy of potential stem-loop structures formed by the repeats. The influence of these factors on translation is numerically estimated. An optimal proportion of these factors is computed for each organism individually. Quantitative translational characteristics of 384 unicellular organisms (351 bacteria, 28 archaea, 5 eukaryota) have been computed using their annotated genomes from NCBI GenBank. Five potential evolutionary strategies of translational optimization have been determined among studied organisms. A considerable difference of preferred translational strategies between Bacteria and Archaea has been revealed. Significant correlations between elongation efficiency index and gene expression levels have been shown for two organisms (S. cerevisiae and H. pylori) using available microarray data. The proposed method allows to estimate numerically the coding DNA sequence translation efficiency and to optimize nucleotide composition of heterologous genes in unicellular organisms. http://www.mgs.bionet.nsc.ru/mgs/programs/eei-calculator/.

  16. EFFICIENCY OF REAL-TIME PCR FOR 18S rRNA AMPLIFICATION OF SORBUS DOMESTICA, L.

    Directory of Open Access Journals (Sweden)

    Petronela Poláčeková

    2012-10-01

    Full Text Available Normal 0 21 false false false SK X-NONE X-NONE Nowadays, the awareness is given more and more to underutilized and  unusual fruits. One of them is Sorbus domestica, L. not only as an endangered species, but as well as a promising and economically usable crop. The work was aimed for finding a total genomic DNA isolating methods from fresh plant material and confirmation of the optimized method by the detection of 18S rRNA gene using real-time PCR. Two commercial isolation kits were tested -  Invisorb® Spin Plant Mini Kit and Wizard ® Genomic DNA. Higher purity and yield of DNA isolation kit showed Invisorb kit. The effective and pure PCR amplification was confirmed for Invisorb, too when 20 ng undiluted DNA at annealing temperature of 64.5 °C.doi:10.5219/203

  17. Catalytic Efficiency of Titanium Dioxide (TiO2) and Zeolite ZSM-5 Catalysts in the in-situ Epoxidation of Palm Olein

    Science.gov (United States)

    Yunus, M. Z. Mohd; Jamaludin, S. K.; Abd. Karim, S. F.; Gani, A. Abd; Sauki, A.

    2018-05-01

    Titanium dioxide and zeolite ZSM-5 are the commonly used heterogeneous catalysts in many chemical reactions. They have several advantages such as low cost and environmental friendly. In this study, titanium dioxide and zeolite ZSM-5 act as catalyst in the in-situ epoxidation of palm olein. Epoxidation of palm olein was carried out by using in-situ generated performic acid to produce epoxidized palm olein in a semi-batch reactor at different temperatures (45°C and 60°C) and agitation speed of 400 rpm. The effects of both catalysts are studied to compare their efficiency in catalyzing the in-situ epoxidation. Epoxidized palm olein was analyzed by using percent of relative conversion to oxirane (RCO%) and fourier transform infrared spectroscopy (FTIR). Surface area of the catalysts used were then characterized by using BET. The results indicated that titanium dioxide is a better catalyst in the in-situ epoxidation of palm olein since it provides higher RCO% compared to Zeolite ZSM-5 at 45°C.

  18. An efficient method for the synthesis of photo catalytically active ZnO nanoparticles by a gel-combustion method for the photo-degradation of Caffeine

    Directory of Open Access Journals (Sweden)

    Rajesha Bedre Jagannatha

    2017-01-01

    Full Text Available In this study, Zinc oxide nanoparticles were synthesized by gel-combustion method using a novel bio-fuel tapioca starch pearls, derived from the tubers of Mannihot esculenta, to investigate the photocatalytic degradation of ccaffeine. The ZnO photocatalyst was characterized by X-ray diffraction (XRD, scanning electron microscopy (SEM, and UV-visible spectroscopy. X-ray diffractometry result for the ZnO nanoparticles exhibit normal crystalline phase features. All observed peaks can be indexed to the pure hexagonal wurtzite crystal structures. There are no other impurities in the diffraction peak. In addition, SEM measurement shows that most of the nanoparticles are spongy and spherical in shape and fairly mono dispersed. A significant degradation of the Caffeine was observed when the catalyst was added into the solution even without the UV light exposure. In addition, the photo degradation increaseds with the photocatalyst loading. Besides the photocatalyst loading, the effect of some parameters on the photo degradation efficiency such as initial concentration and pH were also studied.

  19. Including lateral interactions into microkinetic models of catalytic reactions

    DEFF Research Database (Denmark)

    Hellman, Anders; Honkala, Johanna Karoliina

    2007-01-01

    In many catalytic reactions lateral interactions between adsorbates are believed to have a strong influence on the reaction rates. We apply a microkinetic model to explore the effect of lateral interactions and how to efficiently take them into account in a simple catalytic reaction. Three differ...... different approximations are investigated: site, mean-field, and quasichemical approximations. The obtained results are compared to accurate Monte Carlo numbers. In the end, we apply the approximations to a real catalytic reaction, namely, ammonia synthesis....

  20. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis

    Directory of Open Access Journals (Sweden)

    Song Cai

    2011-07-01

    Full Text Available Abstract Background Siraitia grosvenorii (Luohanguo is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chinese medicine. The major bioactive constituents in the fruit extract are the cucurbitane-type triterpene saponins known as mogrosides. Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in S. grosvenorii, especially the late steps of the pathway. Results In this study, a cDNA library generated from of equal amount of RNA taken from S. grosvenorii fruit at 50 days after flowering (DAF and 70 DAF were sequenced using Illumina/Solexa platform. More than 48,755,516 high-quality reads from a cDNA library were generated that was assembled into 43,891 unigenes. De novo assembly and gap-filling generated 43,891 unigenes with an average sequence length of 668 base pairs. A total of 26,308 (59.9% unique sequences were annotated and 11,476 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. cDNA sequences for all of the known enzymes involved in mogrosides backbone synthesis were identified from our library. Additionally, a total of eighty-five cytochrome P450 (CYP450 and ninety UDP-glucosyltransferase (UDPG unigenes were identified, some of which appear to encode enzymes responsible for the conversion of the mogroside backbone into the various mogrosides. Digital gene expression profile (DGE analysis using Solexa sequencing was performed on three important stages of fruit development, and based on their expression pattern, seven CYP450s and five UDPGs were selected as the candidates most likely to be involved in mogrosides biosynthesis. Conclusion A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying

  1. shRNA-Mediated XRCC2 Gene Knockdown Efficiently Sensitizes Colon Tumor Cells to X-ray Irradiation in Vitro and in Vivo

    Directory of Open Access Journals (Sweden)

    Qin Wang

    2014-01-01

    Full Text Available Colon cancer is one of the most common tumors of the digestive tract. Resistance to ionizing radiation (IR decreased therapeutic efficiency in these patients’ radiotherapy. XRCC2 is the key protein of DNA homologous recombination repair, and its high expression is associated with enhanced resistance to DNA damage induced by IR. Here, we investigated the effect of XRCC2 silencing on colon tumor cells’ growth and sensitivity to X-radiation in vitro and in vivo. Colon tumor cells (T84 cell line were cultivated in vitro and tumors originated from the cell line were propagated as xenografts in nude mice. The suppression of XRCC2 expression was achieved by using vector-based short hairpin RNA (shRNA in T84 cells. We found that the knockdown of XRCC2 expression effectively decreased T84 cellular proliferation and colony formation, and led to cell apoptosis and cell cycle arrested in G2/M phase induced by X-radiation in vitro. In addition, tumor xenograft studies suggested that XRCC2 silencing inhibited tumorigenicity after radiation treatment in vivo. Our data suggest that the suppression of XRCC2 expression rendered colon tumor cells more sensitive to radiation therapy in vitro and in vivo, implying XRCC2 as a promising therapeutic target for the treatment of radioresistant human colon cancer.

  2. Structural insights into RNA processing by the human RISC-loading complex.

    Science.gov (United States)

    Wang, Hong-Wei; Noland, Cameron; Siridechadilok, Bunpote; Taylor, David W; Ma, Enbo; Felderer, Karin; Doudna, Jennifer A; Nogales, Eva

    2009-11-01

    Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2.

  3. SHORT COMMUNICATION CATALYTIC KINETIC ...

    African Journals Online (AJOL)

    IV) catalyzes the discoloring reaction of DBS-arsenazo oxidized by potassium bromate, a new catalytic kinetic spectrophotometric method for the determination of trace titanium (IV) was developed. The linear range of the determination of ...

  4. Catalytic distillation process

    Science.gov (United States)

    Smith, L.A. Jr.

    1982-06-22

    A method is described for conducting chemical reactions and fractionation of the reaction mixture comprising feeding reactants to a distillation column reactor into a feed zone and concurrently contacting the reactants with a fixed bed catalytic packing to concurrently carry out the reaction and fractionate the reaction mixture. For example, a method for preparing methyl tertiary butyl ether in high purity from a mixed feed stream of isobutene and normal butene comprising feeding the mixed feed stream to a distillation column reactor into a feed zone at the lower end of a distillation reaction zone, and methanol into the upper end of said distillation reaction zone, which is packed with a properly supported cationic ion exchange resin, contacting the C[sub 4] feed and methanol with the catalytic distillation packing to react methanol and isobutene, and concurrently fractionating the ether from the column below the catalytic zone and removing normal butene overhead above the catalytic zone.

  5. Catalytic distillation structure

    Science.gov (United States)

    Smith, L.A. Jr.

    1984-04-17

    Catalytic distillation structure is described for use in reaction distillation columns, and provides reaction sites and distillation structure consisting of a catalyst component and a resilient component intimately associated therewith. The resilient component has at least about 70 volume % open space and is present with the catalyst component in an amount such that the catalytic distillation structure consists of at least 10 volume % open space. 10 figs.

  6. Catalytic asymmetric synthesis of the alkaloid (+)-myrtine

    NARCIS (Netherlands)

    Pizzuti, Maria Gabriefla; Minnaard, Adriaan J.; Feringa, Ben L.

    2008-01-01

    A new protocol for the asymmetric synthesis of trans-2,6-disubstituted-4-piperidones has been developed using a catalytic enantioselective conjugate addition reaction in combination with a diastereoselective lithiation-substitution sequence; an efficient synthesis of (+)-myrtine has been achieved

  7. I2-SDS-H2O System: A highly Efficient Dual Catalytic Green System for Deprotection of Imines and in Situ Preparation of Bis(indolyl)alkanes from Indoles in Water.

    Science.gov (United States)

    Hazarika, Parasa; Pahari, Pallab; Borah, Manash Jyoti; Konwar, Dilip

    2012-01-01

    A novel catalytic system consisting of I2-SDS-H2O has been developed which cleaves 2,3-diaza-1,3-butadiene, 1-aza-1,3-butadienes, oximes and in presence of indoles in the medium uses the corresponding aldehyde products to produce bis(indolyl)alkanes in situ. This one pot simple and mild dual catalytic system works in water at room temperature under neutral conditions.

  8. Snapshots of Dynamics in Synthesizing N6-isopentenyladenosine at tRNA Anticodon†,‡

    Science.gov (United States)

    Chimnaronk, Sarin; Forouhar, Farhad; Sakai, Junichi; Yao, Min; Tron, Cecile M.; Atta, Mohamed; Fontecave, Marc; Hunt, John F.; Tanaka, Isao

    2009-01-01

    Bacterial and eukaryotic transfer RNAs that decode codons starting with uridine have a hydrophobically-hypermodified adenosine at the position 37 (A37) adjacent to the 3′-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of the crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during modification of RNA. A compact evolutionary inserted domain (herein ‘swinging domain’) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A36 and A38 together to squeeze out A37 into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate-binding of MiaA. PMID:19435325

  9. Pd-catalytic in situ generation of H2O2 from H2 and O2 produced by water electrolysis for the efficient electro-fenton degradation of rhodamine B.

    Science.gov (United States)

    Yuan, Songhu; Fan, Ye; Zhang, Yucheng; Tong, Man; Liao, Peng

    2011-10-01

    A novel electro-Fenton process was developed for wastewater treatment using a modified divided electrolytic system in which H2O2 was generated in situ from electro-generated H2 and O2 in the presence of Pd/C catalyst. Appropriate pH conditions were obtained by the excessive H+ produced at the anode. The performance of the novel process was assessed by Rhodamine B (RhB) degradation in an aqueous solution. Experimental results showed that the accumulation of H2O2 occurred when the pH decreased and time elapsed. The maximum concentration of H2O2 reached 53.1 mg/L within 120 min at pH 2 and a current of 100 mA. Upon the formation of the Fenton reagent by the addition of Fe2+, RhB degraded completely within 30 min at pH 2 with a pseudo first order rate constant of 0.109 ± 0.009 min(-1). An insignificant decline in H2O2 generation and RhB degradation was found after six repetitions. RhB degradation was achieved by the chemisorption of H2O2 on the Pd/C surface, which subsequently decomposed into •OH upon catalysis by Pd0 and Fe2+. The catalytic decomposition of H2O2 to •OH by Fe2+ was more powerful than that by Pd0, which was responsible for the high efficiency of this novel electro-Fenton process.

  10. Correction: β-Amyrin synthase from Euphorbia tirucalli L. functional analyses of the highly conserved aromatic residues Phe413, Tyr259 and Trp257 disclose the importance of the appropriate steric bulk, and cation-π and CH-π interactions for the efficient catalytic action of the polyolefin cyclization cascade.

    Science.gov (United States)

    Ito, Ryousuke; Nakada, Chika; Hoshino, Tsutomu

    2017-01-18

    Correction for 'β-Amyrin synthase from Euphorbia tirucalli L. functional analyses of the highly conserved aromatic residues Phe413, Tyr259 and Trp257 disclose the importance of the appropriate steric bulk, and cation-π and CH-π interactions for the efficient catalytic action of the polyolefin cyclization cascade' by Ryousuke Ito et al., Org. Biomol. Chem., 2017, 15, 177-188.

  11. Catalytic Kinetic Resolution of Biaryl Compounds.

    Science.gov (United States)

    Ma, Gaoyuan; Sibi, Mukund P

    2015-08-10

    Biaryl compounds with axial chirality are very common in synthetic chemistry, especially in catalysis. Axially chiral biaryls are important due to their biological activities and extensive applications in asymmetric catalysis. Thus the development of efficient enantioselective methods for their synthesis has attracted considerable attention. This Minireview discusses the progress made in catalytic kinetic resolution of biaryl compounds and chronicles significant advances made recently in catalytic kinetic resolution of biaryl scaffolds. © 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. MicroRNA-27a decreases the level and efficiency of the LDL receptor and contributes to the dysregulation of cholesterol homeostasis.

    Science.gov (United States)

    Alvarez, M Lucrecia; Khosroheidari, Mahdieh; Eddy, Elena; Done, Stefania C

    2015-10-01

    A strong risk factor for atherosclerosis- the leading cause of heart attacks and strokes- is the elevation of low-density lipoprotein cholesterol (LDL-C) in blood. The LDL receptor (LDLR) is the primary pathway for LDL-C removal from circulation, and their levels are increased by statins -the main treatment for high blood LDL-C. However, statins have low efficiency because they also increase PCSK9 which targets LDLR for degradation. Since microRNAs have recently emerged as key regulators of cholesterol homeostasis, our aim was to identify potential microRNA-based therapeutics to decrease blood LDL-C and prevent atherosclerosis. We over expressed and knocked down miR-27a in HepG2 cells to assess its effect on the expression of key players in the LDLR pathway using PCR Arrays, Elisas, and Western blots. We found that miR-27a decreases LDLR levels by 40% not only through a direct binding to its 3' untranslated region but also indirectly by inducing a 3-fold increase in PCSK9, which enhances LDLR degradation. Interestingly, miR-27a also directly decreases LRP6 and LDLRAP1, two other key players in the LDLR pathway that are required for efficient endocytosis of the LDLR-LDL-C complex in the liver. The inhibition of miR-27a using lock nucleic acids induced a 70% increase in LDLR levels and, therefore, it would be a more efficient treatment for hypercholesterolemia because of its desirable effects not only on LDLR but also on PCSK9. The results presented here provide evidence supporting the potential of miR-27a as a novel therapeutic target for the prevention of atherosclerosis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. Catalytic nanoporous membranes

    Science.gov (United States)

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

    2013-08-27

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

  14. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei

    2015-01-01

    -ray diffraction. A combination of electron microscopy images with X-ray absorption spectra demonstrated that the silver atoms were anchored on five-fold oxygen-terminated cavities on the surface of the support to form highly dense isolated metal active sites, leading to excellent reactivity in catalytic oxidation......Atomically dispersed noble-metal catalysts with highly dense active sites are promising materials with which to maximise metal efficiency and to enhance catalytic performance; however, their fabrication remains challenging because metal atoms are prone to sintering, especially at a high metal...... loading. A dynamic process of formation of isolated metal atom catalytic sites on the surface of the support, which was achieved starting from silver nanoparticles by using a thermal surface-mediated diffusion method, was observed directly by using in situ electron microscopy and in situ synchrotron X...

  15. Steam reformer with catalytic combustor

    Science.gov (United States)

    Voecks, Gerald E. (Inventor)

    1990-01-01

    A steam reformer is disclosed having an annular steam reforming catalyst bed formed by concentric cylinders and having a catalytic combustor located at the center of the innermost cylinder. Fuel is fed into the interior of the catalytic combustor and air is directed at the top of the combustor, creating a catalytic reaction which provides sufficient heat so as to maintain the catalytic reaction in the steam reforming catalyst bed. Alternatively, air is fed into the interior of the catalytic combustor and a fuel mixture is directed at the top. The catalytic combustor provides enhanced radiant and convective heat transfer to the reformer catalyst bed.

  16. 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...

  17. Chondroitin sulfate-polyethylenimine copolymer-coated superparamagnetic iron oxide nanoparticles as an efficient magneto-gene carrier for microRNA-encoding plasmid DNA delivery

    Science.gov (United States)

    Lo, Yu-Lun; Chou, Han-Lin; Liao, Zi-Xian; Huang, Shih-Jer; Ke, Jyun-Han; Liu, Yu-Sheng; Chiu, Chien-Chih; Wang, Li-Fang

    2015-04-01

    MicroRNA-128 (miR-128) is an attractive therapeutic molecule with powerful glioblastoma regulation properties. However, miR-128 lacks biological stability and leads to poor delivery efficacy in clinical applications. In our previous study, we demonstrated two effective transgene carriers, including polyethylenimine (PEI)-decorated superparamagnetic iron oxide nanoparticles (SPIONs) as well as chemically-conjugated chondroitin sulfate-PEI copolymers (CPs). In this contribution, we report optimized conditions for coating CPs onto the surfaces of SPIONs, forming CPIOs, for magneto-gene delivery systems. The optimized weight ratio of the CPs and SPIONs is 2 : 1, which resulted in the formation of a stable particle as a good transgene carrier. The hydrodynamic diameter of the CPIOs is ~136 nm. The gel electrophoresis results demonstrate that the weight ratio of CPIO/DNA required to completely encapsulate pDNA is >=3. The in vitro tests of CPIO/DNA were done in 293 T, CRL5802, and U87-MG cells in the presence and absence of an external magnetic field. The magnetofection efficiency of CPIO/DNA was measured in the three cell lines with or without fetal bovine serum (FBS). CPIO/DNA exhibited remarkably improved gene expression in the presence of the magnetic field and 10% FBS as compared with a gold non-viral standard, PEI/DNA, and a commercial magnetofection reagent, PolyMag/DNA. In addition, CPIO/DNA showed less cytotoxicity than PEI/DNA and PolyMag/DNA against the three cell lines. The transfection efficiency of the magnetoplex improved significantly with an assisted magnetic field. In miR-128 delivery, a microRNA plate array and fluorescence in situ hybridization were used to demonstrate that CPIO/pMIRNA-128 indeed expresses more miR-128 with the assisted magnetic field than without. In a biodistribution test, CPIO/Cy5-DNA showed higher accumulation at the tumor site where an external magnet is placed nearby.MicroRNA-128 (miR-128) is an attractive therapeutic molecule

  18. Catalytic pyrolysis of hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Vail' eva, N A; Buyanov, R A

    1979-01-01

    Catalytic pyrolysis of petroleum fractions (undecane) was performed with the object of clarifying such questions as the mechanism of action of the catalyst, the concepts of activity and selectivity of the catalyst, the role of transport processes, the temperature ranges and limitations of the catalytic process, the effect of the catalyst on secondary processes, and others. Catalysts such as quartz, MgO, Al/sub 2/O/sub 3/, were used. Analysis of the experimental findings and the fact that the distribution of products is independent of the nature of the surface, demonstrate that the pyrolysis of hydrocarbons in the presence of catalysts is based on the heterogeneous-homogeneous radical-chain mechanism of action, and that the role of the catalysts reduces to increasing the concentration of free radicals. The concept of selectivity cannot be applied to catalysts here, since they do not affect the mechanism of the unfolding of the process of pyrolysis and their role consists solely in initiating the process. In catalytic pyrolysis the concepts of kinetic and diffusive domains of unfolding of the catalytic reaction do not apply, and only the outer surface of the catalyst is engaged, whereas the inner surface merely promotes deletorious secondary processes reducing the selectivity of the process and the activity of the catalyst. 6 references, 2 figures.

  19. Catalytic Conversion of Biofuels

    DEFF Research Database (Denmark)

    Jørgensen, Betina

    This thesis describes the catalytic conversion of bioethanol into higher value chemicals. The motivation has been the unavoidable coming depletion of the fossil resources. The thesis is focused on two ways of utilising ethanol; the steam reforming of ethanol to form hydrogen and the partial oxida...

  20. CATALYTIC KINETIC SPECTROPHOTOMETRIC DETERMINATION ...

    African Journals Online (AJOL)

    Preferred Customer

    acetylchlorophosphonazo(CPApA) by hydrogen peroxide in 0.10 M phosphoric acid. A novel catalytic kinetic-spectrophotometric method is proposed for the determination of copper based on this principle. Copper(II) can be determined spectrophotometrically ...

  1. Catalytic methanol dissociation

    International Nuclear Information System (INIS)

    Alcinikov, Y.; Fainberg, V.; Garbar, A.; Gutman, M.; Hetsroni, G.; Shindler, Y.; Tatrtakovsky, L.; Zvirin, Y.

    1998-01-01

    Results of the methanol dissociation study on copper/potassium catalyst with alumina support at various temperatures are presented. The following gaseous and liquid products at. The catalytic methanol dissociation is obtained: hydrogen, carbon monoxide, carbon dioxide, methane, and dimethyl ether. Formation rates of these products are discussed. Activation energies of corresponding reactions are calculated

  2. Heterogeneous catalytic materials solid state chemistry, surface chemistry and catalytic behaviour

    CERN Document Server

    Busca, Guido

    2014-01-01

    Heterogeneous Catalytic Materials discusses experimental methods and the latest developments in three areas of research: heterogeneous catalysis; surface chemistry; and the chemistry of catalysts. Catalytic materials are those solids that allow the chemical reaction to occur efficiently and cost-effectively. This book provides you with all necessary information to synthesize, characterize, and relate the properties of a catalyst to its behavior, enabling you to select the appropriate catalyst for the process and reactor system. Oxides (used both as catalysts and as supports for cata

  3. Concentric catalytic combustor

    Science.gov (United States)

    Bruck, Gerald J [Oviedo, FL; Laster, Walter R [Oviedo, FL

    2009-03-24

    A catalytic combustor (28) includes a tubular pressure boundary element (90) having a longitudinal flow axis (e.g., 56) separating a first portion (94) of a first fluid flow (e.g., 24) from a second portion (95) of the first fluid flow. The pressure boundary element includes a wall (96) having a plurality of separate longitudinally oriented flow paths (98) annularly disposed within the wall and conducting respective portions (100, 101) of a second fluid flow (e.g., 26) therethrough. A catalytic material (32) is disposed on a surface (e.g., 102, 103) of the pressure boundary element exposed to at least one of the first and second portions of the first fluid flow.

  4. Enantioselective catalytic fluorinative aza-semipinacol rearrangement.

    Science.gov (United States)

    Romanov-Michailidis, Fedor; Pupier, Marion; Besnard, Céline; Bürgi, Thomas; Alexakis, Alexandre

    2014-10-03

    An efficient and highly stereoselective fluorinative aza-semipinacol rearrangement is described. The catalytic reaction requires use of Selectfluor in combination with the chiral, enantiopure phosphate anion derived from acid L3. Under optimized conditions, cyclopropylamines A were transformed into β-fluoro cyclobutylimines B in good yields and high levels of diastereo- and enantiocontrol. Furthermore, the optically active cyclobutylimines were reduced diastereoselectively with L-Selectride in the corresponding fluorinated amines C, compounds of significant interest in the pharmacological industry.

  5. Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

    Science.gov (United States)

    Zhu, Yanglong; Stribinskis, Vilius; Ramos, Kenneth S.; Li, Yong

    2006-01-01

    RNase MRP is a eukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase P is a ubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5′ termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata, the internal loop of helix P3 is 100% conserved between MRP and P RNAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of P RNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and P RNA, such as those from Dictyostelium discoideum. These conserved nucleotides between the MRP and P RNAs strongly support the hypothesis that the MRP RNA is derived from the P RNA molecule in early eukaryote evolution. PMID:16540690

  6. Enhanced propylene production in FCC by novel catalytic materials

    Energy Technology Data Exchange (ETDEWEB)

    Kelkar, C.P.; Harris, D.; Xu, M.; Fu, J. [BASF Catalyst LLC, Iselin, NJ (United States)

    2007-07-01

    Fluid catalytic cracking is expected to increasingly supply the additional incremental requirements for propylene. The most efficient route to increase propylene yield from an FCC unit is through the use of medium pore zeolites such as ZSM-5. ZSM-5 zeolite cracks near linear olefins in the gasoline range to LPG olefins such as propylene and butylenes. This paper will describe catalytic approaches to increase gasoline range olefins and the chemistry of ZSM-5 to crack those olefins. The paper will also describe novel catalytic materials designed to increase propylene. (orig.)

  7. Aerobic, catalytic oxidation of alcohols in ionic liquids

    Directory of Open Access Journals (Sweden)

    Souza Roberto F. de

    2006-01-01

    Full Text Available An efficient and simple catalytic system based on RuCl3 dissolved in ionic liquids has been developed for the oxidation of alcohols into aldehydes and ketones under mild conditions. A new fluorinated ionic liquid, 1-n-butyl-3-methylimidazolium pentadecafluorooctanoate, was synthesized and demonstrated better performance that the other ionic liquids employed. Moreover this catalytic system utilizes molecular oxygen as an oxidizing agent, producing water as the only by-product.

  8. Engineering of small interfering RNA-loaded lipidoid-poly(DL-lactic-co-glycolic acid) hybrid nanoparticles for highly efficient and safe gene silencing: A quality by design-based approach.

    Science.gov (United States)

    Thanki, Kaushik; Zeng, Xianghui; Justesen, Sarah; Tejlmann, Sarah; Falkenberg, Emily; Van Driessche, Elize; Mørck Nielsen, Hanne; Franzyk, Henrik; Foged, Camilla

    2017-11-01

    Safety and efficacy of therapeutics based on RNA interference, e.g., small interfering RNA (siRNA), are dependent on the optimal engineering of the delivery technology, which is used for intracellular delivery of siRNA to the cytosol of target cells. We investigated the hypothesis that commonly used and poorly tolerated cationic lipids might be replaced with more efficacious and safe lipidoids as the lipid component of siRNA-loaded lipid-polymer hybrid nanoparticles (LPNs) for achieving more efficient gene silencing at lower and safer doses. However, formulation design of such a complex formulation is highly challenging due to a strong interplay between several contributing factors. Hence, critical formulation variables, i.e. the lipidoid content and siRNA:lipidoid ratio, were initially identified, followed by a systematic quality-by-design approach to define the optimal operating space (OOS), eventually resulting in the identification of a robust, highly efficacious and safe formulation. A 17-run design of experiment with an I-optimal approach was performed to systematically assess the effect of selected variables on critical quality attributes (CQAs), i.e. physicochemical properties (hydrodynamic size, zeta potential, siRNA encapsulation/loading) and the biological performance (in vitro gene silencing and cell viability). Model fitting of the obtained data to construct predictive models revealed non-linear relationships for all CQAs, which can be readily overlooked in one-factor-at-a-time optimization approaches. The response surface methodology further enabled the identification of an OOS that met the desired quality target product profile. The optimized lipidoid-modified LPNs revealed more than 50-fold higher in vitro gene silencing at well-tolerated doses and approx. a twofold increase in siRNA loading as compared to reference LPNs modified with the commonly used cationic lipid dioleyltrimethylammonium propane (DOTAP). Thus, lipidoid-modified LPNs show highly

  9. Catalytic cleavage activities of 10–23 DNAzyme analogs functionalized with an amino group in its catalytic core

    Directory of Open Access Journals (Sweden)

    Qi Wang

    2012-02-01

    Full Text Available Functionalization of the catalytic loop of 10–23 DNAzyme with an amino group was performed by incorporation of 7-(3-aminopropyl-8-aza-7-deaza-2′-deoxyadenosine in different single positions. Among the nine modified positions in the catalytic loop, A9 is the unique position with positive contribution by such modification. These results indicated that more efficient deoxyribozymes remain to be explored by introduction of exogenous functional groups in an appropriate position in the catalytic loop of 10–23 DNAzyme, such as the combination of 7-functional group substituted 8-aza-7-deaza-2′-deoxyadenosine analogs and A9 position.

  10. Rationally evolving tRNAPyl for efficient incorporation of noncanonical amino acids.

    Science.gov (United States)

    Fan, Chenguang; Xiong, Hai; Reynolds, Noah M; Söll, Dieter

    2015-12-15

    Genetic encoding of noncanonical amino acids (ncAAs) into proteins is a powerful approach to study protein functions. Pyrrolysyl-tRNA synthetase (PylRS), a polyspecific aminoacyl-tRNA synthetase in wide use, has facilitated incorporation of a large number of different ncAAs into proteins to date. To make this process more efficient, we rationally evolved tRNA(Pyl) to create tRNA(Pyl-opt) with six nucleotide changes. This improved tRNA was tested as substrate for wild-type PylRS as well as three characterized PylRS variants (N(ϵ)-acetyllysyl-tRNA synthetase [AcKRS], 3-iodo-phenylalanyl-tRNA synthetase [IFRS], a broad specific PylRS variant [PylRS-AA]) to incorporate ncAAs at UAG codons in super-folder green fluorescence protein (sfGFP). tRNA(Pyl-opt) facilitated a 5-fold increase in AcK incorporation into two positions of sfGFP simultaneously. In addition, AcK incorporation into two target proteins (Escherichia coli malate dehydrogenase and human histone H3) caused homogenous acetylation at multiple lysine residues in high yield. Using tRNA(Pyl-opt) with PylRS and various PylRS variants facilitated efficient incorporation of six other ncAAs into sfGFP. Kinetic analyses revealed that the mutations in tRNA(Pyl-opt) had no significant effect on the catalytic efficiency and substrate binding of PylRS enzymes. Thus tRNA(Pyl-opt) should be an excellent replacement of wild-type tRNA(Pyl) for future ncAA incorporation by PylRS enzymes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  12. Catalytic biomass pyrolysis process

    Science.gov (United States)

    Dayton, David C.; Gupta, Raghubir P.; Turk, Brian S.; Kataria, Atish; Shen, Jian-Ping

    2018-04-17

    Described herein are processes for converting a biomass starting material (such as lignocellulosic materials) into a low oxygen containing, stable liquid intermediate that can be refined to make liquid hydrocarbon fuels. More specifically, the process can be a catalytic biomass pyrolysis process wherein an oxygen removing catalyst is employed in the reactor while the biomass is subjected to pyrolysis conditions. The stream exiting the pyrolysis reactor comprises bio-oil having a low oxygen content, and such stream may be subjected to further steps, such as separation and/or condensation to isolate the bio-oil.

  13. Catalytic reforming methods

    Science.gov (United States)

    Tadd, Andrew R; Schwank, Johannes

    2013-05-14

    A catalytic reforming method is disclosed herein. The method includes sequentially supplying a plurality of feedstocks of variable compositions to a reformer. The method further includes adding a respective predetermined co-reactant to each of the plurality of feedstocks to obtain a substantially constant output from the reformer for the plurality of feedstocks. The respective predetermined co-reactant is based on a C/H/O atomic composition for a respective one of the plurality of feedstocks and a predetermined C/H/O atomic composition for the substantially constant output.

  14. RNA Origami

    DEFF Research Database (Denmark)

    Sparvath, Steffen Lynge

    introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...

  15. Efficient Translation of Pelargonium line pattern virus RNAs Relies on a TED-Like 3´-Translational Enhancer that Communicates with the Corresponding 5´-Region through a Long-Distance RNA-RNA Interaction.

    Science.gov (United States)

    Blanco-Pérez, Marta; Pérez-Cañamás, Miryam; Ruiz, Leticia; Hernández, Carmen

    2016-01-01

    Cap-independent translational enhancers (CITEs) have been identified at the 3´-terminal regions of distinct plant positive-strand RNA viruses belonging to families Tombusviridae and Luteoviridae. On the bases of their structural and/or functional requirements, at least six classes of CITEs have been defined whose distribution does not correlate with taxonomy. The so-called TED class has been relatively under-studied and its functionality only confirmed in the case of Satellite tobacco necrosis virus, a parasitic subviral agent. The 3´-untranslated region of the monopartite genome of Pelargonium line pattern virus (PLPV), the recommended type member of a tentative new genus (Pelarspovirus) in the family Tombusviridae, was predicted to contain a TED-like CITE. Similar CITEs can be anticipated in some other related viruses though none has been experimentally verified. Here, in the first place, we have performed a reassessment of the structure of the putative PLPV-TED through in silico predictions and in vitro SHAPE analysis with the full-length PLPV genome, which has indicated that the presumed TED element is larger than previously proposed. The extended conformation of the TED is strongly supported by the pattern of natural sequence variation, thus providing comparative structural evidence in support of the structural data obtained by in silico and in vitro approaches. Next, we have obtained experimental evidence demonstrating the in vivo activity of the PLPV-TED in the genomic (g) RNA, and also in the subgenomic (sg) RNA that the virus produces to express 3´-proximal genes. Besides other structural features, the results have highlighted the key role of long-distance kissing-loop interactions between the 3´-CITE and 5´-proximal hairpins for gRNA and sgRNA translation. Bioassays of CITE mutants have confirmed the importance of the identified 5´-3´ RNA communication for viral infectivity and, moreover, have underlined the strong evolutionary constraints that may

  16. Efficient Translation of Pelargonium line pattern virus RNAs Relies on a TED-Like 3´-Translational Enhancer that Communicates with the Corresponding 5´-Region through a Long-Distance RNA-RNA Interaction.

    Directory of Open Access Journals (Sweden)

    Marta Blanco-Pérez

    Full Text Available Cap-independent translational enhancers (CITEs have been identified at the 3´-terminal regions of distinct plant positive-strand RNA viruses belonging to families Tombusviridae and Luteoviridae. On the bases of their structural and/or functional requirements, at least six classes of CITEs have been defined whose distribution does not correlate with taxonomy. The so-called TED class has been relatively under-studied and its functionality only confirmed in the case of Satellite tobacco necrosis virus, a parasitic subviral agent. The 3´-untranslated region of the monopartite genome of Pelargonium line pattern virus (PLPV, the recommended type member of a tentative new genus (Pelarspovirus in the family Tombusviridae, was predicted to contain a TED-like CITE. Similar CITEs can be anticipated in some other related viruses though none has been experimentally verified. Here, in the first place, we have performed a reassessment of the structure of the putative PLPV-TED through in silico predictions and in vitro SHAPE analysis with the full-length PLPV genome, which has indicated that the presumed TED element is larger than previously proposed. The extended conformation of the TED is strongly supported by the pattern of natural sequence variation, thus providing comparative structural evidence in support of the structural data obtained by in silico and in vitro approaches. Next, we have obtained experimental evidence demonstrating the in vivo activity of the PLPV-TED in the genomic (g RNA, and also in the subgenomic (sg RNA that the virus produces to express 3´-proximal genes. Besides other structural features, the results have highlighted the key role of long-distance kissing-loop interactions between the 3´-CITE and 5´-proximal hairpins for gRNA and sgRNA translation. Bioassays of CITE mutants have confirmed the importance of the identified 5´-3´ RNA communication for viral infectivity and, moreover, have underlined the strong evolutionary

  17. Orion EFT-1 Catalytic Tile Experiment Overview and Flight Measurements

    Science.gov (United States)

    Salazar, Giovanni; Amar, Adam; Hyatt, Andrew; Rezin, Marc D.

    2016-01-01

    This paper describes the design and results of a surface catalysis flight experiment flown on the Orion Multipurpose Crew Vehicle during Exploration Flight Test 1 (EFT1). Similar to previous Space Shuttle catalytic tile experiments, the present test consisted of a highly catalytic coating applied to an instrumented TPS tile. However, the present catalytic tile experiment contained significantly more instrumentation in order to better resolve the heating overshoot caused by the change in surface catalytic efficiency at the interface between two distinct materials. In addition to collecting data with unprecedented spatial resolution of the "overshoot" phenomenon, the experiment was also designed to prove if such a catalytic overshoot would be seen in turbulent flow in high enthalpy regimes. A detailed discussion of the results obtained during EFT1 is presented, as well as the challenges associated with data interpretation of this experiment. Results of material testing carried out in support of this flight experiment are also shown. Finally, an inverse heat conduction technique is employed to reconstruct the flight environments at locations upstream and along the catalytic coating. The data and analysis presented in this work will greatly contribute to our understanding of the catalytic "overshoot" phenomenon, and have a significant impact on the design of future spacecraft.

  18. Modulation of RNA function by aminoglycoside antibiotics.

    Science.gov (United States)

    Schroeder, R; Waldsich, C; Wank, H

    2000-01-04

    One of the most important families of antibiotics are the aminoglycosides, including drugs such as neomycin B, paromomycin, gentamicin and streptomycin. With the discovery of the catalytic potential of RNA, these antibiotics became very popular due to their RNA-binding capacity. They serve for the analysis of RNA function as well as for the study of RNA as a potential therapeutic target. Improvements in RNA structure determination recently provided first insights into the decoding site of the ribosome at high resolution and how aminoglycosides might induce misreading of the genetic code. In addition to inhibiting prokaryotic translation, aminoglycosides inhibit several catalytic RNAs such as self-splicing group I introns, RNase P and small ribozymes in vitro. Furthermore, these antibiotics interfere with human immunodeficiency virus (HIV) replication by disrupting essential RNA-protein contacts. Most exciting is the potential of many RNA-binding antibiotics to stimulate RNA activities, conceiving small-molecule partners for the hypothesis of an ancient RNA world. SELEX (systematic evolution of ligands by exponential enrichment) has been used in this evolutionary game leading to small synthetic RNAs, whose NMR structures gave valuable information on how aminoglycosides interact with RNA, which could possibly be used in applied science.

  19. Role of RNA structure and RNA binding activity of foot-and-mouth disease virus 3C protein in VPg uridylylation and virus replication

    DEFF Research Database (Denmark)

    Nayak, A.; Goodfellow, I. G.; Woolaway, K. E.

    2006-01-01

    The uridylylation of the VPg peptide primer is the first stage in the replication of picornavirus RNA. This process can be achieved in vitro using purified components, including 3B (VPg) with the RNA dependent RNA polymerase (3D(pol)), the precursor 3CD, and an RNA template containing the cre....../bus. We show that certain RNA sequences within the foot-and-mouth disease virus (FMDV) 5' untranslated region but outside of the cre/bus can enhance VPg uridylylation activity. Furthermore, we have shown that the FMDV X protein alone can substitute for 3CD, albeit less efficiently. In addition, the VPg...... precursors, 3B(3)3C and 3B(123)3C, can function as substrates for uridylylation in the absence of added 3C or 3CD. Residues within the FMDV 3C protein involved in interaction with the cre/bus RNA have been identified and are located on the face of the protein opposite from the catalytic site. These residues...

  20. Novel Catalytic Membrane Reactors

    Energy Technology Data Exchange (ETDEWEB)

    Stuart Nemser, PhD

    2010-10-01

    There are many industrial catalytic organic reversible reactions with amines or alcohols that have water as one of the products. Many of these reactions are homogeneously catalyzed. In all cases removal of water facilitates the reaction and produces more of the desired chemical product. By shifting the reaction to right we produce more chemical product with little or no additional capital investment. Many of these reactions can also relate to bioprocesses. Given the large number of water-organic compound separations achievable and the ability of the Compact Membrane Systems, Inc. (CMS) perfluoro membranes to withstand these harsh operating conditions, this is an ideal demonstration system for the water-of-reaction removal using a membrane reactor. Enhanced reaction synthesis is consistent with the DOE objective to lower the energy intensity of U.S. industry 25% by 2017 in accord with the Energy Policy Act of 2005 and to improve the United States manufacturing competitiveness. The objective of this program is to develop the platform technology for enhancing homogeneous catalytic chemical syntheses.

  1. Mutational Analysis of the Hypervariable Region of Hepatitis E Virus Reveals Its Involvement in the Efficiency of Viral RNA Replication ▿

    OpenAIRE

    Pudupakam, R. S.; Kenney, Scott P.; Córdoba, Laura; Huang, Yao-Wei; Dryman, Barbara A.; LeRoith, Tanya; Pierson, F. William; Meng, Xiang-Jin

    2011-01-01

    The RNA genome of the hepatitis E virus (HEV) contains a hypervariable region (HVR) in ORF1 that tolerates small deletions with respect to infectivity. To further investigate the role of the HVR in HEV replication, we constructed a panel of mutants with overlapping deletions in the N-terminal, central, and C-terminal regions of the HVR by using a genotype 1 human HEV luciferase replicon and analyzed the effects of deletions on viral RNA replication in Huh7 cells. We found that the replication...

  2. Processing and structural characterization of porous reforming catalytic films

    International Nuclear Information System (INIS)

    Hou Xianghui; Williams, Jey; Choy, Kwang-Leong

    2006-01-01

    Nickel-based catalysts are often used to reform methanol into hydrogen. The preparation and installation of these catalysts are costly and laborious. As an alternative, directly applying catalytic films onto the separator components can improve the manufacturing efficiency. This paper reports the successful deposition of adherent porous NiO-Al 2 O 3 -based catalytic films with well-controlled stoichiometry, using a single-step Aerosol Assisted Chemical Vapour Deposition (AACVD) method. The microstructure, composition and crystalline phase of the as-deposited catalytic films are characterized using a combination of X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and Fourier Transform Infrared (FTIR) Spectrometer. The results have demonstrated the capability of AACVD to produce porous NiO-Al 2 O 3 -based catalytic films

  3. Catalytic pleat filter bags for combined particulate separation and nitrogen oxides removal from flue gas streams

    International Nuclear Information System (INIS)

    Park, Young Ok; Choi, Ho Kyung

    2010-01-01

    The development of a high temperature catalytically active pleated filter bag with hybrid filter equipment for the combined removal of particles and nitrogen oxides from flue gas streams is presented. A special catalyst load in stainless steel mesh cartridge with a high temperature pleated filter bag followed by optimized catalytic activation was developed to reach the required nitrogen oxides levels and to maintain the higher collection efficiencies. The catalytic properties of the developed high temperature filter bags with hybrid filter equipment were studied and demonstrated in a pilot scale test rig and a demonstration plant using commercial scale of high temperature catalytic pleated filter bags. The performance of the catalytic pleated filter bags were tested under different operating conditions, such as filtration velocity and operating temperature. Moreover, the cleaning efficiency and residual pressure drop of the catalyst loaded cartridges in pleated filter bags were tested. As result of theses studies, the optimum operating conditions for the catalytic pleated filter bags are determined. (author)

  4. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    Extensive studies have been conducted to establish sound basis for design and engineering of reactors for practising such catalytic reactions and for realizing improvements in reactor performance. In this article, application of recent (and not so recent) developments in engineering reactors for catalytic reactions is ...

  5. Flexible Nanosomes (SECosomes) Enable Efficient siRNA Delivery in Cultured Primary Skin Cells and in the Viable Epidermis of Ex Vivo Human Skin

    NARCIS (Netherlands)

    Geusens, Barbara; Van Gele, Mireille; Braat, Sien; De Smedt, Stefaan C.; Stuart, Marc C. A.; Prow, Tarl W.; Sanchez, Washington; Roberts, Michael S.; Sanders, Niek N.; Lambert, Jo

    2010-01-01

    The extent to which nanoscale-engineered systems cross intact human skin and can exert pharmacological effects in viable epidermis is controversial. This research seeks to develop a new lipid-based nanosome that enables the effective delivery of siRNA into human skin. The major finding is that an

  6. Catalytic detritiation of water

    International Nuclear Information System (INIS)

    Rogers, M.L.; Lamberger, P.H.; Ellis, R.E.; Mills, T.K.

    1977-01-01

    A pilot-scale system has been used at Mound Laboratory to investigate the catalytic detritiation of water. A hydrophobic, precious metal catalyst is used to promote the exchange of tritium between liquid water and gaseous hydrogen at 60 0 C. Two columns are used, each 7.5 m long by 2.5 cm ID and packed with catalyst. Water flow is 5-10 cm 3 /min and countercurrent hydrogen flow is 9,000-12,000 cm 3 /min. The equipment, except for the columns, is housed in an inert atmosphere glovebox and is computer controlled. The hydrogen is obtained by electrolysis of a portion of the water stream. Enriched gaseous tritium is withdrawn for further enrichment. A description of the system is included along with an outline of its operation. Recent experimental data are discussed

  7. Enhancement of catalytic efficiency of enzymes through exposure to anhydrous organic solvent at 70 degrees C. Three-dimensional structure of a treated serine proteinase at 2.2 A resolution.

    Science.gov (United States)

    Gupta, M N; Tyagi, R; Sharma, S; Karthikeyan, S; Singh, T P

    2000-05-15

    The enzyme behavior in anhydrous media has important applications in biotechnology. So far chemical modifications and protein engineering have been used to alter the catalytic power of the enzymes. For the first time, it is demonstrated that an exposure of enzyme to anhydrous organic solvents at optimized high temperature enhances its catalytic power through local changes at the binding region. Six enzymes: proteinase K, wheat germ acid phosphatase, alpha-amylase, beta-glucosidase, chymotrypsin and trypsin have been exposed to acetonitrile at 70 degrees C for three hours. The activities of these enzymes were found to be considerably enhanced. In order to understand the basis of this change in the activity of these enzymes, the structure of one of these treated enzymes, proteinase K has been analyzed in detail using X-ray diffraction method. The overall structure of the enzyme is similar to the native structure in aqueous environment. The hydrogen bonding system of the catalytic triad is intact after the treatment. However, the water structure in the substrate binding site undergoes some rearrangement as some of the water molecules are either displaced or completely absent. The most striking observation concerning the water structure pertains to the complete deletion of the water molecule which occupied the position at the so-called oxyanion hole in the active site of the native enzyme. Three acetonitrile molecules were found in the present structure. All the acetonitrile molecules are located in the recognition site. The sites occupied by acetonitrile molecules are independent of water molecules. The acetonitrile molecules are involved in extensive interactions with the protein atoms. All of them are interlinked through water molecules. The methyl group of one of the acetonitrile molecules (CCN1) interacts simultaneously with the hydrophobic side chains of Leu-96, Ile-107, and Leu-133. The development of such a hydrophobic environment at the recognition site

  8. Tunable preparation of ruthenium nanoparticles with superior size-dependent catalytic hydrogenation properties

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Yuan; Luo, Yaodong; Yang, Xuan; Yang, Yaxin; Song, Qijun, E-mail: qsong@jiangnan.edu.cn

    2017-06-15

    Highlights: • A facile and efficient strategy is firstly developed for the synthesis of Ru NPs. • Ru NPs are stable and uniform with the controllable sizes from 2.6 to 51.5 nm. • Ru NPs exhibit size-dependent and superior catalytic hydrogenation activity. - Abstract: Ruthenium (Ru) featured with an unusual catalytic behavior is of great significance in several heterogeneous and electro-catalytic reactions. The preparation of tractable Ru nanocatalysts and the building of highly active catalytic system at ambient temperature remains a grand challenge. Herein, a facile strategy is developed for the controllable preparation of Ru nanoparticles (NPs) with the sizes ranging from 2.6 to 51.5 nm. Ru NPs show superior size-dependent catalytic performance with the best kinetic rate constant as high as −1.52 min{sup −1}, which could far surpass the other traditional noble metals. Ru NPs exert exceedingly efficient low-temperature catalytic activity and good recyclability in the catalytic reduction of nitroaromatic compounds (NACs) and azo dyes. The developed catalytic system provides a distinguishing insight for the artificial preparation of Ru NPs with desired sizes, and allows for the development of rational design rules for exploring catalysts with superior catalytic performances, potentially broadening the applications of metallic NP-enabled catalytic analysis.

  9. Catalytic Combustion of Gasified Waste

    Energy Technology Data Exchange (ETDEWEB)

    Kusar, Henrik

    2003-09-01

    This thesis concerns catalytic combustion for gas turbine application using a low heating-value (LHV) gas, derived from gasified waste. The main research in catalytic combustion focuses on methane as fuel, but an increasing interest is directed towards catalytic combustion of LHV fuels. This thesis shows that it is possible to catalytically combust a LHV gas and to oxidize fuel-bound nitrogen (NH{sub 3}) directly into N{sub 2} without forming NO{sub x} The first part of the thesis gives a background to the system. It defines waste, shortly describes gasification and more thoroughly catalytic combustion. The second part of the present thesis, paper I, concerns the development and testing of potential catalysts for catalytic combustion of LHV gases. The objective of this work was to investigate the possibility to use a stable metal oxide instead of noble metals as ignition catalyst and at the same time reduce the formation of NO{sub x} In paper II pilot-scale tests were carried out to prove the potential of catalytic combustion using real gasified waste and to compare with the results obtained in laboratory scale using a synthetic gas simulating gasified waste. In paper III, selective catalytic oxidation for decreasing the NO{sub x} formation from fuel-bound nitrogen was examined using two different approaches: fuel-lean and fuel-rich conditions. Finally, the last part of the thesis deals with deactivation of catalysts. The various deactivation processes which may affect high-temperature catalytic combustion are reviewed in paper IV. In paper V the poisoning effect of low amounts of sulfur was studied; various metal oxides as well as supported palladium and platinum catalysts were used as catalysts for combustion of a synthetic gas. In conclusion, with the results obtained in this thesis it would be possible to compose a working catalytic system for gas turbine application using a LHV gas.

  10. Engineering of small interfering RNA-loaded lipidoid-poly(DL-lactic-co-glycolic acid) hybrid nanoparticles for highly efficient and safe gene silencing: A quality by design-based approach

    DEFF Research Database (Denmark)

    Thanki, Kaushik; Zeng, Xianghui; Justesen, Sarah

    2017-01-01

    used and poorly tolerated cationic lipids might be replaced with more efficacious and safe lipidoids as the lipid component of siRNA-loaded lipid-polymer hybrid nanoparticles (LPNs) for achieving more efficient gene silencing at lower and safer doses. However, formulation design of such a complex...... formulation is highly challenging due to a strong interplay between several contributing factors. Hence, critical formulation variables, i.e. the lipidoid content and siRNA:lipidoid ratio, were initially identified, followed by a systematic quality-by-design approach to define the optimal operating space (OOS......), eventually resulting in the identification of a robust, highly efficacious and safe formulation. A 17-run design of experiment with an I-optimal approach was performed to systematically assess the effect of selected variables on critical quality attributes (CQAs), i.e. physicochemical properties...

  11. Electrochemical catalytic treatment of phenol wastewater

    International Nuclear Information System (INIS)

    Ma Hongzhu; Zhang Xinhai; Ma Qingliang; Wang Bo

    2009-01-01

    The slurry bed catalytic treatment of contaminated water appears to be a promising alternative for the oxidation of aqueous organic pollutants. In this paper, the electrochemical oxidation of phenol in synthetic wastewater catalyzed by ferric sulfate and potassium permanganate adsorbed onto active bentonite in slurry bed electrolytic reactor with graphite electrode has been investigated. In order to determine the optimum operating condition, the orthogonal experiments were devised and the results revealed that the system of ferric sulfate, potassium permanganate and active bentonite showed a high catalytic efficiency on the process of electrochemical oxidation phenol in initial pH 5. When the initial concentration of phenol was 0.52 g/L (the initial COD 1214 mg/L), up to 99% chemical oxygen demand (COD) removal was obtained in 40 min. According to the experimental results, a possible mechanism of catalytic degradation of phenol was proposed. Environmental estimation was also done and the results showed that the treated wastewater have little impact on plant growth and could totally be applied to irrigation.

  12. Catalytic applications of bio-inspired nanomaterials

    Science.gov (United States)

    Pacardo, Dennis Kien Balaong

    The biomimetic synthesis of Pd nanoparticles was presented using the Pd4 peptide, TSNAVHPTLRHL, isolated from combinatorial phage display library. Using this approach, nearly monodisperse and spherical Pd nanoparticles were generated with an average diameter of 1.9 +/- 0.4 nm. The peptide-based nanocatalyst were employed in the Stille coupling reaction under energy-efficient and environmentally friendly reaction conditions of aqueous solvent, room temperature and very low catalyst loading. To this end, the Pd nanocatalyst generated high turnover frequency (TOF) value and quantitative yields using ≥ 0.005 mol% Pd as well as catalytic activities with different aryl halides containing electron-withdrawing and electron-donating groups. The Pd4-capped Pd nanoparticles followed the atom-leaching mechanism and were found to be selective with respect to substrate identity. On the other hand, the naturally-occurring R5 peptide (SSKKSGSYSGSKGSKRRIL) was employed in the synthesis of biotemplated Pd nanomaterials which showed morphological changes as a function of Pd:peptide ratio. TOF analysis for hydrogenation of olefinic alcohols showed similar catalytic activity regardless of nanomorphology. Determination of catalytic properties of these bio-inspired nanomaterials are important as they serve as model system for alternative green catalyst with applications in industrially important transformations.

  13. Vapor-Driven Propulsion of Catalytic Micromotors

    Science.gov (United States)

    Dong, Renfeng; Li, Jinxing; Rozen, Isaac; Ezhilan, Barath; Xu, Tailin; Christianson, Caleb; Gao, Wei; Saintillan, David; Ren, Biye; Wang, Joseph

    2015-08-01

    Chemically-powered micromotors offer exciting opportunities in diverse fields, including therapeutic delivery, environmental remediation, and nanoscale manufacturing. However, these nanovehicles require direct addition of high concentration of chemical fuel to the motor solution for their propulsion. We report the efficient vapor-powered propulsion of catalytic micromotors without direct addition of fuel to the micromotor solution. Diffusion of hydrazine vapor from the surrounding atmosphere into the sample solution is instead used to trigger rapid movement of iridium-gold Janus microsphere motors. Such operation creates a new type of remotely-triggered and powered catalytic micro/nanomotors that are responsive to their surrounding environment. This new propulsion mechanism is accompanied by unique phenomena, such as the distinct off-on response to the presence of fuel in the surrounding atmosphere, and spatio-temporal dependence of the motor speed borne out of the concentration gradient evolution within the motor solution. The relationship between the motor speed and the variables affecting the fuel concentration distribution is examined using a theoretical model for hydrazine transport, which is in turn used to explain the observed phenomena. The vapor-powered catalytic micro/nanomotors offer new opportunities in gas sensing, threat detection, and environmental monitoring, and open the door for a new class of environmentally-triggered micromotors.

  14. Electrochemical catalytic treatment of phenol wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Ma Hongzhu, E-mail: hzmachem@snnu.edu.cn [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Zhang Xinhai [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Ma Qingliang [Department of Applied Physics, College of Sciences, Taiyuan University of Technology, 030024 Taiyuan (China); Wang Bo [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China)

    2009-06-15

    The slurry bed catalytic treatment of contaminated water appears to be a promising alternative for the oxidation of aqueous organic pollutants. In this paper, the electrochemical oxidation of phenol in synthetic wastewater catalyzed by ferric sulfate and potassium permanganate adsorbed onto active bentonite in slurry bed electrolytic reactor with graphite electrode has been investigated. In order to determine the optimum operating condition, the orthogonal experiments were devised and the results revealed that the system of ferric sulfate, potassium permanganate and active bentonite showed a high catalytic efficiency on the process of electrochemical oxidation phenol in initial pH 5. When the initial concentration of phenol was 0.52 g/L (the initial COD 1214 mg/L), up to 99% chemical oxygen demand (COD) removal was obtained in 40 min. According to the experimental results, a possible mechanism of catalytic degradation of phenol was proposed. Environmental estimation was also done and the results showed that the treated wastewater have little impact on plant growth and could totally be applied to irrigation.

  15. Efficient genome editing in hematopoietic stem cells with helper-dependent Ad5/35 vectors expressing site-specific endonucleases under microRNA regulation

    Directory of Open Access Journals (Sweden)

    Kamola Saydaminova

    Full Text Available Genome editing with site-specific endonucleases has implications for basic biomedical research as well as for gene therapy. We generated helper-dependent, capsid-modified adenovirus (HD-Ad5/35 vectors for zinc-finger nuclease (ZFN– or transcription activator-like effector nuclease (TALEN–mediated genome editing in human CD34+ hematopoietic stem cells (HSCs from mobilized adult donors. The production of these vectors required that ZFN and TALEN expression in HD-Ad5/35 producer 293-Cre cells was suppressed. To do this, we developed a microRNA (miRNA-based system for regulation of gene expression based on miRNA expression profiling of 293-Cre and CD34+ cells. Using miR-183-5p and miR-218-5p based regulation of transgene gene expression, we first produced an HD-Ad5/35 vector expressing a ZFN specific to the HIV coreceptor gene ccr5. We demonstrated that HD-Ad5/35.ZFNmiR vector conferred ccr5 knock out in primitive HSC (i.e., long-term culture initiating cells and NOD/SCID repopulating cells. The ccr5 gene disruption frequency achieved in engrafted HSCs found in the bone marrow of transplanted mice is clinically relevant for HIV therapy considering that these cells can give rise to multiple lineages, including all the lineages that represent targets and reservoirs for HIV. We produced a second HD-Ad5/35 vector expressing a TALEN targeting the DNase hypersensitivity region 2 (HS2 within the globin locus control region. This vector has potential for targeted gene correction in hemoglobinopathies. The miRNA regulated HD-Ad5/35 vector platform for expression of site-specific endonucleases has numerous advantages over currently used vectors as a tool for genome engineering of HSCs for therapeutic purposes.

  16. Catalytic production of biodiesel

    Energy Technology Data Exchange (ETDEWEB)

    Theilgaard Madsen, A.

    2011-07-01

    The focus of this thesis is the catalytic production of diesel from biomass, especially emphasising catalytic conversion of waste vegetable oils and fats. In chapter 1 an introduction to biofuels and a review on different catalytic methods for diesel production from biomass is given. Two of these methods have been used industrially for a number of years already, namely the transesterification (and esterification) of oils and fats with methanol to form fatty acid methyl esters (FAME), and the hydrodeoxygenation (HDO) of fats and oils to form straight-chain alkanes. Other possible routes to diesel include upgrading and deoxygenation of pyrolysis oils or aqueous sludge wastes, condensations and reductions of sugars in aqueous phase (aqueous-phase reforming, APR) for monofunctional hydrocarbons, and gasification of any type of biomass followed by Fischer-Tropsch-synthesis for alkane biofuels. These methods have not yet been industrialised, but may be more promising due to the larger abundance of their potential feedstocks, especially waste feedstocks. Chapter 2 deals with formation of FAME from waste fats and oils. A range of acidic catalysts were tested in a model fat mixture of methanol, lauric acid and trioctanoin. Sulphonic acid-functionalised ionic liquids showed extremely fast convertion of lauric acid to methyl laurate, and trioctanoate was converted to methyl octanoate within 24 h. A catalyst based on a sulphonated carbon-matrix made by pyrolysing (or carbonising) carbohydrates, so-called sulphonated pyrolysed sucrose (SPS), was optimised further. No systematic dependency on pyrolysis and sulphonation conditions could be obtained, however, with respect to esterification activity, but high activity was obtained in the model fat mixture. SPS impregnated on opel-cell Al{sub 2}O{sub 3} and microporous SiO{sub 2} (ISPS) was much less active in the esterification than the original SPS powder due to low loading and thereby low number of strongly acidic sites on the

  17. The ViennaRNA web services.

    Science.gov (United States)

    Gruber, Andreas R; Bernhart, Stephan H; Lorenz, Ronny

    2015-01-01

    The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detection. The ViennaRNA web services can be used free of charge and can be accessed via http://rna.tbi.univie.ac.at.

  18. Chemically-modified cellulose paper as a microstructured catalytic reactor.

    Science.gov (United States)

    Koga, Hirotaka; Kitaoka, Takuya; Isogai, Akira

    2015-01-15

    We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.

  19. Chemically-Modified Cellulose Paper as a Microstructured Catalytic Reactor

    Directory of Open Access Journals (Sweden)

    Hirotaka Koga

    2015-01-01

    Full Text Available We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.

  20. Catalytic stereoselective synthesis of highly substituted indanones via tandem Nazarov cyclization and electrophilic fluorination trapping.

    Science.gov (United States)

    Nie, Jing; Zhu, Hong-Wei; Cui, Han-Feng; Hua, Ming-Qing; Ma, Jun-An

    2007-08-02

    A new catalytic stereoselective tandem transformation via Nazarov cyclization/electrophilic fluorination has been accomplished. This sequence is efficiently catalyzed by a Cu(II) complex to afford fluorine-containing 1-indanone derivatives with two new stereocenters with high diastereoselectivity (trans/cis up to 49/1). Three examples of catalytic enantioselective tandem transformation are presented.

  1. 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.

  2. 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

  3. Catalytic cracking of lignites

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, M.; Nowak, S.; Naegler, T.; Zimmermann, J. [Hochschule Merseburg (Germany); Welscher, J.; Schwieger, W. [Erlangen-Nuernberg Univ. (Germany); Hahn, T. [Halle-Wittenberg Univ., Halle (Germany)

    2013-11-01

    A most important factor for the chemical industry is the availability of cheap raw materials. As the oil price of crude oil is rising alternative feedstocks like coal are coming into focus. This work, the catalytic cracking of lignite is part of the alliance ibi (innovative Braunkohlenintegration) to use lignite as a raw material to produce chemicals. With this new one step process without an input of external hydrogen, mostly propylene, butenes and aromatics and char are formed. The product yield depends on manifold process parameters. The use of acid catalysts (zeolites like MFI) shows the highest amount of the desired products. Hydrogen rich lignites with a molar H/C ratio of > 1 are to be favoured. Due to primary cracking and secondary reactions the ratio between catalyst and lignite, temperature and residence time are the most important parameter to control the product distribution. Experiments at 500 C in a discontinuous rotary kiln reactor show yields up to 32 wt-% of hydrocarbons per lignite (maf - moisture and ash free) and 43 wt-% char, which can be gasified. Particularly, the yields of propylene and butenes as main products can be enhanced four times to about 8 wt-% by the use of catalysts while the tar yield decreases. In order to develop this innovative process catalyst systems fixed on beads were developed for an easy separation and regeneration of the used catalyst from the formed char. (orig.)

  4. Chemistry - Toward efficient hydrogen production at surfaces

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Christensen, Claus H.

    2006-01-01

    Calculations are providing a molecular picture of hydrogen production on catalytic surfaces and within enzymes, knowledge that may guide the design of new, more efficient catalysts for the hydrogen economy.......Calculations are providing a molecular picture of hydrogen production on catalytic surfaces and within enzymes, knowledge that may guide the design of new, more efficient catalysts for the hydrogen economy....

  5. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    126, No. 2, March 2014, pp. 341–351. c Indian Academy of Sciences. ... enhancement was realized by catalyst design, appropriate choice of reactor, better injection and .... Gas–liquid and liquid–solid transport processes in catalytic reactors.5.

  6. Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Risager, Peter Christian; Fahnøe, Ulrik

    2013-01-01

    Background Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described....... This strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. Results A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable...

  7. Progress in catalytic naphtha reforming process: A review

    International Nuclear Information System (INIS)

    Rahimpour, Mohammad Reza; Jafari, Mitra; Iranshahi, Davood

    2013-01-01

    Catalytic naphtha reforming process is a vital process for refineries due to the production of high-octane components, which is intensely demanded in our modern life. The significance of this industrial process induced researchers to investigate different aspects of catalytic naphtha reforming process intensively. Some of the investigators try to improve this process by representing more effective catalysts, while others try to elucidate its kinetic and deactivation mechanisms and design more efficient reactor setups. The amount of these established papers is so much that may confuse some of the researchers who want to find collective information about catalytic naphtha reforming process. In the present paper, the published studies from 1949 until now are categorized into three main groups including finding suitable catalyst, revealing appropriate kinetic and deactivation model, and suggesting efficient reactor configuration and mode of operation. These studies are reviewed separately, and a suitable reference is provided for those who want to have access to generalized information about catalytic naphtha reforming process. Finally, various suggestions for revamping the catalytic naphtha reforming process have been proposed as a guideline for further investigations

  8. Simulation on Toxic Gases in Vehicle Exhaust Equipped with Modified Catalytic Converter : A Review

    Directory of Open Access Journals (Sweden)

    Leman A.M.

    2016-01-01

    Full Text Available Air pollution and global warming is a major issue nowadays. One of the main contributors to be the emission of harmful gases produced by vehicle exhausts lines. The harmful gases like NOx, CO, unburned HC and particulate matter increases the global warming, so catalytic converter plays a vital role in reducing harmful gases. Catalytic converters are used on most vehicles on the road today. This research deals with the gas emission flow in the catalytic converter involving the heat transfer, velocity flow, back pressure and others chemical reaction in the modified catalytic converter by using FeCrAl as a substrate that is treated using the ultrasonic bath and electroplating techniques. The objective of this study is to obtain a quantitative description of the gas emission in the catalytic converter system of automobile exhaust gas using ANSYS Software. The description of the gas emission in the catalytic converter system of automobile exhaust gas using ANSYS Software was simulated in this research in order to provide better efficiency and ease the reusability of the catalytic converter by comparing experimental data with software analysing data. The result will be expected to demonstrate a good approximation of gas emission in the modified catalytic converter simulation data compared to experimental data in order to verify the effectiveness of modified catalytic converter. Therefore studies on simulation of flow through the modified catalytic converter are very important to increase the accuracy of the obtained emission result.

  9. Catalytic Stereoinversion of L-Alanine to Deuterated D-Alanine.

    Science.gov (United States)

    Moozeh, Kimia; So, Soon Mog; Chin, Jik

    2015-08-03

    A combination of an achiral pyridoxal analogue and a chiral base has been developed for catalytic deuteration of L-alanine with inversion of stereochemistry to give deuterated D-alanine under mild conditions (neutral pD and 25 °C) without the use of any protecting groups. This system can also be used for catalytic deuteration of D-alanine with retention of stereochemistry to give deuterated D-alanine. Thus a racemic mixture of alanine can be catalytically deuterated to give an enantiomeric excess of deuterated D-alanine. While catalytic deracemization of alanine is forbidden by the second law of thermodynamics, this system can be used for catalytic deracemization of alanine with deuteration. Such green and biomimetic approach to catalytic stereocontrol provides insights into efficient amino acid transformations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Catalytic Ketone Hydrodeoxygenation Mediated by Highly Electrophilic Phosphonium Cations.

    Science.gov (United States)

    Mehta, Meera; Holthausen, Michael H; Mallov, Ian; Pérez, Manuel; Qu, Zheng-Wang; Grimme, Stefan; Stephan, Douglas W

    2015-07-06

    Ketones are efficiently deoxygenated in the presence of silane using highly electrophilic phosphonium cation (EPC) salts as catalysts, thus affording the corresponding alkane and siloxane. The influence of distinct substitution patterns on the catalytic effectiveness of several EPCs was evaluated. The deoxygenation mechanism was probed by DFT methods. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Enhanced catalytic behavior of Ni alloys in steam methane reforming

    Science.gov (United States)

    Yoon, Yeongpil; Kim, Hanmi; Lee, Jaichan

    2017-08-01

    The dissociation process of methane on Ni and Ni alloys are investigated by density functional theory (DFT) in terms of catalytic efficiency and carbon deposition. Examining the dissociation to CH3, CH2, CH, C, and H is not sufficient to properly predict the catalytic efficiency and carbon deposition, and further investigation of the CO gas-evolving reaction is required to completely understand methane dissociation in steam. The location of alloying element in Ni alloy needed be addressed from the results of ab-inito molecular dynamics (MD). The reaction pathway of methane dissociation associated with CO gas evolution is traced by performing first-principles calculations of the adsorption and activation energies of each dissociation step. During the dissociation process, two alternative reaction steps producing adsorbed C and H or adsorbed CO are critically important in determining coking inhibition as well as H2 gas evolution (i.e., the catalytic efficiency). The theoretical calculations presented here suggest that alloying Ni with Ru is an effective way to reduce carbon deposition and enhance the catalytic efficiency of H2 fueling in solid oxide fuel cells (SOFCs).

  12. OPERATING SPECIFICATIONS OF CATALYTIC CLEANING OF GAS FROM BIOMASS GASIFICATION

    Directory of Open Access Journals (Sweden)

    Martin Lisý

    2015-12-01

    Full Text Available The paper focuses on the theoretical description of the cleaning of syngas from biomass and waste gasification using catalytic methods, and on the verification of the theory through experiments. The main obstruction to using syngas from fluid gasification of organic matter is the presence of various high-boiling point hydrocarbons (i.e., tar in the gas. The elimination of tar from the gas is a key factor in subsequent use of the gas in other technologies for cogeneration of electrical energy and heat. The application of a natural or artificial catalyst for catalytic destruction of tar is one of the methods of secondary elimination of tar from syngas. In our experiments, we used a natural catalyst (dolomite or calcium magnesium carbonate from Horní Lánov with great mechanical and catalytic properties, suitable for our purposes. The advantages of natural catalysts in contrast to artificial catalysts include their availability, low purchase prices and higher resilience to the so-called catalyst poison. Natural calcium catalysts may also capture undesired compounds of sulphure and chlorine. Our paper presents a theoretical description and analysis of catalytic destruction of tar into combustible gas components, and of the impact of dolomite calcination on its efficiency. The efficiency of the technology is verified in laboratories. The facility used for verification was a 150 kW pilot gasification unit with a laboratory catalytic filter. The efficiency of tar elimination reached 99.5%, the tar concentration complied with limits for use of the gas in combustion engines, and the tar content reached approximately 35 mg/mn3. The results of the measurements conducted in laboratories helped us design a pilot technology for catalytic gas cleaning.

  13. Catalytically enhanced combustion process

    International Nuclear Information System (INIS)

    Rodriguez, C.

    1992-01-01

    This patent describes a fuel having improved combustion efficiency. It comprises a petroleum based liquid hydrocarbon; and a combustion catalyst comprising from about 18 to about 21 weight percent naphthalene, from about 75 to about 80 weight percent toluene, and from about 2.8 to about 3.2 weight percent benzyl alcohol

  14. Low and medium heating value coal gas catalytic combustor characterization

    Science.gov (United States)

    Schwab, J. A.

    1982-01-01

    Catalytic combustion with both low and medium heating value coal gases obtained from an operating gasifier was demonstrated. A practical operating range for efficient operation was determined, and also to identify potential problem areas were identified for consideration during stationary gas turbine engine design. The test rig consists of fuel injectors, a fuel-air premixing section, a catalytic reactor with thermocouple instrumentation and a single point, water cooled sample probe. The test rig included inlet and outlet transition pieces and was designed for installation into an existing test loop.

  15. Catalytic Oxidation of Allylic Alcohols to Methyl Esters

    DEFF Research Database (Denmark)

    Gallas-Hulin, Agata; Kotni, Rama Krishna; Nielsen, Martin

    2017-01-01

    Aerobic oxidation of allylic alcohols to methyl esters using gold nanoparticles supported on different metal oxide carriers has been performed successfully under mild conditions (room temperature, 0.1 MPa O2) without significant loss of catalytic activity. The effects of different reaction...... parameters are studied to find the suitable reaction conditions. All catalysts are characterised by XRD, XRF and TEM. Among these catalysts, Au/TiO2 showed the most efficient catalytic activity towards the selective oxidation of allylic alcohols to the corresponding esters. Moreover, the same Au/TiO2...... to synthesize methyl esters from allylic alcohols....

  16. Solvent-free Oxidation of Alcohols and Mild Catalytic Deprotection of ...

    African Journals Online (AJOL)

    tetrabromobenzene- 1,3-disulphonamide (TBBDA) can be used for solvent-free oxidation of primary and secondary alcohols to the corresponding carbonyl compounds without over-oxidation, and efficient catalytic deprotection of various silyl ...

  17. Computer-aided modeling framework – a generic modeling template for catalytic membrane fixed bed reactors

    DEFF Research Database (Denmark)

    Fedorova, Marina; Sin, Gürkan; Gani, Rafiqul

    2013-01-01

    and users to generate and test models systematically, efficiently and reliably. In this way, development of products and processes can be faster, cheaper and very efficient. In this contribution, as part of the framework a generic modeling template for the systematic derivation of problem specific catalytic...... membrane fixed bed models is developed. The application of the modeling template is highlighted with a case study related to the modeling of a catalytic membrane reactor coupling dehydrogenation of ethylbenzene with hydrogenation of nitrobenzene....

  18. Catalytic bioreactors and methods of using same

    Science.gov (United States)

    Worden, Robert Mark; Liu, Yangmu Chloe

    2017-07-25

    Various embodiments provide a bioreactor for producing a bioproduct comprising one or more catalytically active zones located in a housing and adapted to keep two incompatible gaseous reactants separated when in a gas phase, wherein each of the one or more catalytically active zones may comprise a catalytic component retainer and a catalytic component retained within and/or thereon. Each of the catalytically active zones may additionally or alternatively comprise a liquid medium located on either side of the catalytic component retainer. Catalytic component may include a microbial cell culture located within and/or on the catalytic component retainer, a suspended catalytic component suspended in the liquid medium, or a combination thereof. Methods of using various embodiments of the bioreactor to produce a bioproduct, such as isobutanol, are also provided.

  19. A catalytic distillation process for light gas oil hydrodesulfurization

    Energy Technology Data Exchange (ETDEWEB)

    Vargas-Villamil, F.D.; Marroquin, J.O.; Paz, C. de la; Rodriguez, E. [Prog. de Matematicas Aplicadas y Computacion, Prog. de Tratamiento de Crudo Maya, Instituto Mexicano del Petroleo, Mexico City, DF (Mexico)

    2004-07-01

    A light gas oil hydrodesulfurization process via catalytic distillation is developed and compared to a conventional process. By integrating the separation and reaction into a single unit, the catalytic distillation may produce a diesel with low concentration of sulfur compounds at a lower cost than the traditional reaction/separation process. The process proposed in this work is compared to an optimised conventional hydrodesulfurization unit which represents fairly well a plant that belongs to the National System of Refineries. During the optimisation of the conventional process, a compromise is established among the production of diesel and naphtha and the operating costs. The results show that the light gas oil hydrodesulfurization via catalytic distillation is as or more efficient than the conventional process. However, the removal of the sulfur compounds is carried out under less rigorous conditions. This design reduces the fix and operational costs. (author)

  20. Photolytic AND Catalytic Destruction of Organic Waste Water Pollutants

    Science.gov (United States)

    Torosyan, V. F.; Torosyan, E. S.; Kryuchkova, S. O.; Gromov, V. E.

    2017-01-01

    The system: water supply source - potable and industrial water - wastewater - sewage treatment - water supply source is necessary for water supply and efficient utilization of water resources. Up-to-date technologies of waste water biological treatment require for special microorganisms, which are technologically complex and expensive but unable to solve all the problems. Application of photolytic and catalytically-oxidizing destruction is quite promising. However, the most reagents are strong oxidizers in catalytic oxidation of organic substances and can initiate toxic substance generation. Methodic and scientific approaches to assess bread making industry influence on the environment have been developed in this paper in order to support forecasting and taking technological decisions concerning reduction of this influence. Destructive methods have been tested: ultra violet irradiation and catalytic oxidation for extraction of organic compounds from waste water by natural reagents.

  1. Catalytic activity of Au nanoparticles

    DEFF Research Database (Denmark)

    Larsen, Britt Hvolbæk; Janssens, Ton V.W.; Clausen, Bjerne

    2007-01-01

    Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change with par......Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change...... with particle size. We find that the fraction of low-coordinated Au atoms scales approximately with the catalytic activity, suggesting that atoms on the corners and edges of Au nanoparticles are the active sites. This effect is explained using density functional calculations....

  2. RNA-Based Vaccines in Cancer Immunotherapy

    Directory of Open Access Journals (Sweden)

    Megan A. McNamara

    2015-01-01

    Full Text Available RNA vaccines traditionally consist of messenger RNA synthesized by in vitro transcription using a bacteriophage RNA polymerase and template DNA that encodes the antigen(s of interest. Once administered and internalized by host cells, the mRNA transcripts are translated directly in the cytoplasm and then the resulting antigens are presented to antigen presenting cells to stimulate an immune response. Alternatively, dendritic cells can be loaded with either tumor associated antigen mRNA or total tumor RNA and delivered to the host to elicit a specific immune response. In this review, we will explain why RNA vaccines represent an attractive platform for cancer immunotherapy, discuss modifications to RNA structure that have been developed to optimize mRNA vaccine stability and translational efficiency, and describe strategies for nonviral delivery of mRNA vaccines, highlighting key preclinical and clinical data related to cancer immunotherapy.

  3. Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1.

    Directory of Open Access Journals (Sweden)

    Luis Apolonia

    2015-01-01

    Full Text Available The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 proteins are cell-encoded cytidine deaminases, some of which, such as APOBEC3G (A3G and APOBEC3F (A3F, act as potent human immunodeficiency virus type-1 (HIV-1 restriction factors. These proteins require packaging into HIV-1 particles to exert their antiviral activities, but the molecular mechanism by which this occurs is incompletely understood. The nucleocapsid (NC region of HIV-1 Gag is required for efficient incorporation of A3G and A3F, and the interaction between A3G and NC has previously been shown to be RNA-dependent. Here, we address this issue in detail by first determining which RNAs are able to bind to A3G and A3F in HV-1 infected cells, as well as in cell-free virions, using the unbiased individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP method. We show that A3G and A3F bind many different types of RNA, including HIV-1 RNA, cellular mRNAs and small non-coding RNAs such as the Y or 7SL RNAs. Interestingly, A3G/F incorporation is unaffected when the levels of packaged HIV-1 genomic RNA (gRNA and 7SL RNA are reduced, implying that these RNAs are not essential for efficient A3G/F packaging. Confirming earlier work, HIV-1 particles formed with Gag lacking the NC domain (Gag ΔNC fail to encapsidate A3G/F. Here, we exploit this system by demonstrating that the addition of an assortment of heterologous RNA-binding proteins and domains to Gag ΔNC efficiently restored A3G/F packaging, indicating that A3G and A3F have the ability to engage multiple RNAs to ensure viral encapsidation. We propose that the rather indiscriminate RNA binding characteristics of A3G and A3F promote functionality by enabling recruitment into a wide range of retroviral particles whose packaged RNA genomes comprise divergent sequences.

  4. PARAMETRIC EVALUATION OF VOC CONVERSION VIA CATALYTIC INCINERATION

    Directory of Open Access Journals (Sweden)

    Kaskantzis Neto G.

    1997-01-01

    Full Text Available Abstract - A pilot-scale catalytic incineration system was used to investigate the effectiveness of catalytic incineration as a means of reducing volatile organic compound (VOC air pollutants. The objectives of the study were: 1 to investigate the effects of operating and design variables on the reduction efficiency of VOCs; and 2 to evaluate reduction efficiencies for specific compounds in different chemical classes. The study results verified that the following factors affect the catalyst performance: inlet temperature, space velocity, compound type, and compound inlet concentration. Tests showed that reduction efficiencies exceeding 98% were possible, given sufficiently high inlet gas temperatures for the following classes of compounds: alcohols, acetates, ketones, hydrocarbons, and aromatics

  5. A comparative evaluation on the emission characteristics of ceramic and metallic catalytic converter in internal combustion engine

    Science.gov (United States)

    Leman, A. M.; Jajuli, Afiqah; Rahman, Fakhrurrazi; Feriyanto, Dafit; Zakaria, Supaat

    2017-09-01

    Enforcement of a stricter regulation on exhaust emission by many countries has led to utilization of catalytic converter to reduce the harmful pollutant emission. Ceramic and metallic catalytic converters are the most common type of catalytic converter used. The purpose of this study is to evaluate the performance of the ceramic and metallic catalytic converter on its conversion efficiency using experimental measurement. Both catalysts were placed on a modified exhaust system equipped with a Mitshubishi 4G93 single cylinder petrol engine that was tested on an eddy current dynamometer under steady state conditions for several engine speeds. The experimental results show that the metallic catalytic converter reduced a higher percentage of CO up to 98.6% reduction emissions while ceramic catalytic converter had a better reduction efficiency of HC up to 85.4% and 87.2% reduction of NOx.

  6. RNA signal amplifier circuit with integrated fluorescence output.

    Science.gov (United States)

    Akter, Farhima; Yokobayashi, Yohei

    2015-05-15

    We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.

  7. Computational and Physical Analysis of Catalytic Compounds

    Science.gov (United States)

    Wu, Richard; Sohn, Jung Jae; Kyung, Richard

    2015-03-01

    Nanoparticles exhibit unique physical and chemical properties depending on their geometrical properties. For this reason, synthesis of nanoparticles with controlled shape and size is important to use their unique properties. Catalyst supports are usually made of high-surface-area porous oxides or carbon nanomaterials. These support materials stabilize metal catalysts against sintering at high reaction temperatures. Many studies have demonstrated large enhancements of catalytic behavior due to the role of the oxide-metal interface. In this paper, the catalyzing ability of supported nano metal oxides, such as silicon oxide and titanium oxide compounds as catalysts have been analyzed using computational chemistry method. Computational programs such as Gamess and Chemcraft has been used in an effort to compute the efficiencies of catalytic compounds, and bonding energy changes during the optimization convergence. The result illustrates how the metal oxides stabilize and the steps that it takes. The graph of the energy computation step(N) versus energy(kcal/mol) curve shows that the energy of the titania converges faster at the 7th iteration calculation, whereas the silica converges at the 9th iteration calculation.

  8. Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2

    International Nuclear Information System (INIS)

    Eckerle, Lance D.; Albarino, Cesar G.; Ball, L. Andrew.

    2003-01-01

    The nodavirus Flock House virus has a bipartite genome composed of RNAs 1 and 2, which encode the catalytic component of the RNA-dependent RNA polymerase (RdRp) and the capsid protein precursor, respectively. In addition to catalyzing replication of the viral genome, the RdRp also transcribes from RNA1 a subgenomic RNA3, which is both required for and suppressed by RNA2 replication. Here, we show that in the absence of RNA1 replication, FHV RdRp replicated positive-sense RNA3 transcripts fully and copied negative-sense RNA3 transcripts into positive strands. The two nonstructural proteins encoded by RNA3 were dispensable for replication, but sequences in the 3'-terminal 58 nucleotides were required. RNA3 variants that failed to replicate also failed to transactivate RNA2. These results imply that RNA3 is naturally produced both by transcription from RNA1 and by subsequent RNA1-independent replication and that RNA3 replication may be necessary for transactivation of RNA2

  9. Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants.

    Science.gov (United States)

    Liu, Weipeng; Zhu, Minjun; Liu, Hongxing; Wei, Jitao; Zhou, Xiaoming; Xing, Da

    2016-07-15

    Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Catalytic Conversion of Carbohydrates

    DEFF Research Database (Denmark)

    Osmundsen, Christian Mårup

    a renewable route to aromatics. The conversion of biomass by high temperature processes is a desirable prospect due to the high volumetric production rates which can be achieved, and the ability of these types of processes to convert a wide range of substrates. Current processes however typically have rather...... with the production of commodity chemicals from the most abundantly available renewable source of carbon, carbohydrates. The production of alkyl lactates by the Lewis acid catalyzed conversion of hexoses is an interesting alternative to current fermentation based processes. A range of stannosilicates were...... to be an efficient initial conversion step in the utilization of biomass for chemicals production. The shift from an oil based chemical industry to one based on renewable resources is bound to happen sooner or later, however the environmental problems associated with the burning of fossil resources means...

  11. Catalytic properties of niobium compounds

    International Nuclear Information System (INIS)

    Tanabe, K.; Iizuka, T.

    1983-04-01

    The catalytic activity and selectivity of niobium compounds including oxides, salts, organometallic compounds and others are outlined. The application of these compounds as catalysts to diversified reactions is reported. The nature and action of niobium catalysts are characteristic and sometimes anomalous, suggesting the necessity of basic research and the potential use as catalysts for important processes in the chemical industry. (Author) [pt

  12. Catalytic Decoupling of Quantum Information

    DEFF Research Database (Denmark)

    Majenz, Christian; Berta, Mario; Dupuis, Frédéric

    2017-01-01

    The decoupling technique is a fundamental tool in quantum information theory with applications ranging from quantum thermodynamics to quantum many body physics to the study of black hole radiation. In this work we introduce the notion of catalytic decoupling, that is, decoupling in the presence...... and quantum state merging, and leads to a resource theory of decoupling....

  13. Conserved and variable domains of RNase MRP RNA.

    Science.gov (United States)

    Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

    2009-01-01

    Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

  14. Synthesis, spectroscopic characterization and catalytic oxidation ...

    Indian Academy of Sciences (India)

    were characterized by infrared, electronic, electron paramagnetic resonance ... The catalytic oxidation property of ruthenium(III) complexes were also ... cies at room temperature. ..... aldehyde part of Schiff base ligands, catalytic activ- ity of new ...

  15. Cooperation of an RNA Packaging Signal and a Viral Envelope Protein in Coronavirus RNA Packaging

    OpenAIRE

    Narayanan, Krishna; Makino, Shinji

    2001-01-01

    Murine coronavirus mouse hepatitis virus (MHV) produces a genome-length mRNA, mRNA 1, and six or seven species of subgenomic mRNAs in infected cells. Among these mRNAs, only mRNA 1 is efficiently packaged into MHV particles. MHV N protein binds to all MHV mRNAs, whereas envelope M protein interacts only with mRNA 1. This M protein-mRNA 1 interaction most probably determines the selective packaging of mRNA 1 into MHV particles. A short cis-acting MHV RNA packaging signal is necessary and suffi...

  16. Catalytic combustion in gas stoves - Phase II

    Energy Technology Data Exchange (ETDEWEB)

    Hjelm, Anna-Karin [CATATOR AB, Lund (Sweden)

    2003-06-01

    Several independent studies show that gas stoves to some degree contribute to the indoor emissions of NO{sub x} especially in situations were the ventilation flow is poor. The peak-NO{sub x} concentrations can reach several hundred ppb but the integral concentration seldom exceeds about 20 - 50 ppb, which corresponds to an indoor-outdoor ratio of about 1 - 2.5. Epidemiological studies indicate increasing problems with respiratory symptoms in sensitive people at concentrations as low as 15 ppb of NO{sub 2}. Consequently, the NO{sub x}-concentration in homes where gas stoves are used is high enough to cause health effects. However, in situations where the ventilation flow is high (utilisation of ventilation hoods) the NO{sub x}-emissions are not likely to cause any health problems. This study has been aimed at investigating the possibilities to reduce the NO{sub x} emissions from gas stoves by replacing the conventional flame combustion with catalytic combustion. The investigation is requested by Swedish Gas Center, and is a following-up work of an earlier conducted feasibility study presented in April-2002. The present investigation reports on the possibility to use cheap and simple retro-fit catalytic design suggestions for traditional gas stoves. Experiments have been conducted with both natural and town gas, and parameters such as emissions of NO{sub x}, CO and unburned fuel gas and thermal efficiency, etc, have been examined and are discussed. The results show that it is possible to reduce the NO{sub x} emissions up to 80% by a simple retro-fit installation, without decreasing the thermal efficiency of the cooking plate. The measured source strengths correspond to indoor NO{sub x} concentrations that are below or equal to the average outdoor concentration, implying that no additional detrimental health effects are probable. The drawback of the suggested installations is that the concentration of CO and in some cases also CH{sub 4} are increased in the flue gases

  17. Direct catalytic asymmetric aldol-Tishchenko reaction.

    Science.gov (United States)

    Gnanadesikan, Vijay; Horiuchi, Yoshihiro; Ohshima, Takashi; Shibasaki, Masakatsu

    2004-06-30

    A direct catalytic asymmetric aldol reaction of propionate equivalent was achieved via the aldol-Tishchenko reaction. Coupling an irreversible Tishchenko reaction to a reversible aldol reaction overcame the retro-aldol reaction problem and thereby afforded the products in high enantio and diastereoselectivity using 10 mol % of the asymmetric catalyst. A variety of ketones and aldehydes, including propyl and butyl ketones, were coupled efficiently, yielding the corresponding aldol-Tishchenko products in up to 96% yield and 95% ee. Diastereoselectivity was generally below the detection limit of 1H NMR (>98:2). Preliminary studies performed to clarify the mechanism revealed that the aldol products were racemic with no diastereoselectivity. On the other hand, the Tishchenko products were obtained in a highly enantiocontrolled manner.

  18. Smoke emissions from a catalytic wood stove

    International Nuclear Information System (INIS)

    Cowburn, D.A.; Stephens, N.P.J.

    1994-01-01

    The work reported here was concerned with testing a catalytic wood burning stove (roomheater) following the most applicable UK procedures. The identical stove has also been tested in several other nations to their individual procedures. The results will be submitted to the International Energy Agency (IEA) such that appropriate comparisons can be made. The results comprised: burning rate; an indicative appliance efficiency; heat output; carbon dioxide emissions; carbon monoxide emissions; and smoke emissions. These results were determined with the appliance at three nominal burning rates (high, medium and low). Comparing the results with those obtained in other countries indicates good agreement except when the appliance was operated at low burning rates, under which conditions the UK results indicate significantly worse smoke emissions than those measured by other researchers. (author)

  19. Soluble organic nanotubes for catalytic systems

    Science.gov (United States)

    Xiong, Linfeng; Yang, Kunran; Zhang, Hui; Liao, Xiaojuan; Huang, Kun

    2016-03-01

    In this paper, we report a novel method for constructing a soluble organic nanotube supported catalyst system based on single-molecule templating of core-shell bottlebrush copolymers. Various organic or metal catalysts, such as sodium prop-2-yne-1-sulfonate (SPS), 1-(2-(prop-2-yn-1-yloxy)ethyl)-1H-imidazole (PEI) and Pd(OAc)2 were anchored onto the tube walls to functionalize the organic nanotubes via copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Depending on the ‘confined effect’ and the accessible cavity microenvironments of tubular structures, the organic nanotube catalysts showed high catalytic efficiency and site-isolation features. We believe that the soluble organic nanotubes will be very useful for the development of high performance catalyst systems due to their high stability of support, facile functionalization and attractive textural properties.

  20. Soluble organic nanotubes for catalytic systems.

    Science.gov (United States)

    Xiong, Linfeng; Yang, Kunran; Zhang, Hui; Liao, Xiaojuan; Huang, Kun

    2016-03-18

    In this paper, we report a novel method for constructing a soluble organic nanotube supported catalyst system based on single-molecule templating of core–shell bottlebrush copolymers. Various organic or metal catalysts, such as sodium prop-2-yne-1-sulfonate (SPS), 1-(2-(prop-2-yn-1-yloxy)ethyl)-1H-imidazole (PEI) and Pd(OAc)2 were anchored onto the tube walls to functionalize the organic nanotubes via copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Depending on the 'confined effect' and the accessible cavity microenvironments of tubular structures, the organic nanotube catalysts showed high catalytic efficiency and site-isolation features. We believe that the soluble organic nanotubes will be very useful for the development of high performance catalyst systems due to their high stability of support, facile functionalization and attractive textural properties.

  1. A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    2009-03-01

    Full Text Available Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.

  2. Studies on the catalytic rate constant of ribosomal peptidyltransferase.

    Science.gov (United States)

    Synetos, D; Coutsogeorgopoulos, C

    1987-02-20

    A detailed kinetic analysis of a model reaction for the ribosomal peptidyltransferase is described, using fMet-tRNA or Ac-Phe-tRNA as the peptidyl donor and puromycin as the acceptor. The initiation complex (fMet-tRNA X AUG X 70 S ribosome) or (Ac-Phe-tRNA X poly(U) X 70 S ribosome) (complex C) is isolated and then reacted with excess puromycin (S) to give fMet-puromycin or Ac-Phe-puromycin. This reaction (puromycin reaction) is first order at all concentrations of S tested. An important asset of this kinetic analysis is the fact that the relationship between the first order rate constant kobs and [S] shows hyperbolic saturation and that the value of kobs at saturating [S] is a measure of the catalytic rate constant (k cat) of peptidyltransferase in the puromycin reaction. With fMet-tRNA as the donor, this kcat of peptidyltransferase is 8.3 min-1 when the 0.5 M NH4Cl ribosomal wash is present, compared to 3.8 min-1 in its absence. The kcat of peptidyltransferase is 2.0 min-1 when Ac-Phe-tRNA replaces fMet-tRNA in the presence of the ribosomal wash and decreases to 0.8 min-1 in its absence. This kinetic procedure is the best method available for evaluating changes in the activity of peptidyltransferase in vitro. The results suggest that peptidyltransferase is subjected to activation by the binding of fMet-tRNA to the 70 S initiation complex.

  3. Fuel Flexible, Low Emission Catalytic Combustor for Opportunity Fuel Applications

    Energy Technology Data Exchange (ETDEWEB)

    Eteman, Shahrokh

    2013-06-30

    Limited fuel resources, increasing energy demand and stringent emission regulations are drivers to evaluate process off-gases or process waste streams as fuels for power generation. Often these process waste streams have low energy content and/or highly reactive components. Operability of low energy content fuels in gas turbines leads to issues such as unstable and incomplete combustion. On the other hand, fuels containing higher-order hydrocarbons lead to flashback and auto-ignition issues. Due to above reasons, these fuels cannot be used directly without modifications or efficiency penalties in gas turbine engines. To enable the use of these wide variety of fuels in gas turbine engines a rich catalytic lean burn (RCL®) combustion system was developed and tested in a subscale high pressure (10 atm.) rig. The RCL® injector provided stability and extended turndown to low Btu fuels due to catalytic pre-reaction. Previous work has shown promise with fuels such as blast furnace gas (BFG) with LHV of 85 Btu/ft3 successfully combusted. This program extends on this work by further modifying the combustor to achieve greater catalytic stability enhancement. Fuels containing low energy content such as weak natural gas with a Lower Heating Value (LHV) of 6.5 MJ/m3 (180 Btu/ft3 to natural gas fuels containing higher hydrocarbon (e.g ethane) with LHV of 37.6 MJ/m3 (1010 Btu/ft3) were demonstrated with improved combustion stability; an extended turndown (defined as the difference between catalytic and non-catalytic lean blow out) of greater than 250oF was achieved with CO and NOx emissions lower than 5 ppm corrected to 15% O2. In addition, for highly reactive fuels the catalytic region preferentially pre-reacted the higher order hydrocarbons with no events of flashback or auto-ignition allowing a stable and safe operation with low NOx and CO emissions.

  4. RNA oxidation

    DEFF Research Database (Denmark)

    Kjaer, L. K.; Cejvanovic, V.; Henriken, T.

    2015-01-01

    .9 significant hazard ratio for death compared with the quartile with the lowest 8oxoGuo excretion when adjusted for age, sex, BMI, smoker status, s-HbA1c, urine protein excretion and s-cholesterol. We conclude that it is now established that RNA oxidation is an independent risk factor for death in type 2...

  5. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    International Nuclear Information System (INIS)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

    2012-01-01

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a

  6. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    Energy Technology Data Exchange (ETDEWEB)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

    2012-04-15

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

  7. Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme.

    Science.gov (United States)

    Vallecillo-Viejo, Isabel C; Liscovitch-Brauer, Noa; Montiel-Gonzalez, Maria Fernanda; Eisenberg, Eli; Rosenthal, Joshua J C

    2018-01-02

    Site-directed RNA editing (SDRE) is a general strategy for making targeted base changes in RNA molecules. Although the approach is relatively new, several groups, including our own, have been working on its development. The basic strategy has been to couple the catalytic domain of an adenosine (A) to inosine (I) RNA editing enzyme to a guide RNA that is used for targeting. Although highly efficient on-target editing has been reported, off-target events have not been rigorously quantified. In this report we target premature termination codons (PTCs) in messages encoding both a fluorescent reporter protein and the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein transiently transfected into human epithelial cells. We demonstrate that while on-target editing is efficient, off-target editing is extensive, both within the targeted message and across the entire transcriptome of the transfected cells. By redirecting the editing enzymes from the cytoplasm to the nucleus, off-target editing is reduced without compromising the on-target editing efficiency. The addition of the E488Q mutation to the editing enzymes, a common strategy for increasing on-target editing efficiency, causes a tremendous increase in off-target editing. These results underscore the need to reduce promiscuity in current approaches to SDRE.

  8. Heterogeneous Photo catalytic Degradation of Hazardous Waste in Aqueous Suspension

    International Nuclear Information System (INIS)

    Sadek, S.A.; Ebraheem, S.; Friesen, K.J.

    1999-01-01

    The photo catalytic degradation of hazardous waste like chlorinated paraffin compound (1,12-Dichlorodoecane Ded) was investigated in different aquatic media using GC-MSD. The direct photolysis of Ded in HPLC water was considered to be negligible (k = 0.0020+-0.0007h - 1 ) . An acceleration of the photodegradation rate was occurred in presence of different TiO 2 catalyst systems. Molecular oxygen was found to play a vital role in the degradation process. Anatase TiO 2 was proved to be the most efficient one (k=0.7670+-0.0876h -1 ), while the rate constant of the rutile TiO 2 was calculated to be 0.2780+-0.0342h -1 . Improvement of photo catalytic efficiency of rutile TiO 2 was achieved by addition of Fe +2 giving a rate constant =0.6710+-0.0786h -1

  9. NOx Selective Catalytic Reduction (SCR) on Self-Supported V-W-doped TiO2 Nanofibers

    DEFF Research Database (Denmark)

    Marani, Debora; Silva, Rafael Hubert; Dankeaw, Apiwat

    2017-01-01

    Electrospun V–W–TiO2 catalysts, resulting in a solid solution of V and W in the anatase phase, are prepared as nonwoven nanofibers for NOx selective catalytic reduction (SCR). Preliminary catalytic characterization indicates their superior NOx conversion efficiency to the-state-of-the-art materia...

  10. Computational Insights into the High-Fidelity Catalysis of Aminoacyl-tRNA Synthetases

    Science.gov (United States)

    Aboelnga, Mohamed M.

    cysteine and valine, respectively. In chapter 8, an assessment QM/MM study using a variety of DFT functionals to represent the chemically active layer in aminoacylation mechanism of the unnatural amino acid ss-Hydroxynorvaline as catalyzed by Threonyl-tRNA synthetase has been carried out. Overall, it was found that substrate-assisted mechanisms are a common pathway for these enzymes. One important application of such information is to establish the criteria required for any candidate to inhibit the catalytic functions of aaRS, which was applied in chapter 9 to screen potential competitive inhibitors able to efficiently block the bacterial Threonyl-tRNA synthetases. The investigations reported herein should provide atomistic details into the fundamental catalytic mechanisms of the ubiquitous and ancient aaRS enzymes. Consequently, they will also help enable a much-needed deeper understanding of the underlying chemical principles of catalysis in general.

  11. Catalytic Fast Pyrolysis: A Review

    Directory of Open Access Journals (Sweden)

    Theodore Dickerson

    2013-01-01

    Full Text Available Catalytic pyrolysis is a promising thermochemical conversion route for lignocellulosic biomass that produces chemicals and fuels compatible with current, petrochemical infrastructure. Catalytic modifications to pyrolysis bio-oils are geared towards the elimination and substitution of oxygen and oxygen-containing functionalities in addition to increasing the hydrogen to carbon ratio of the final products. Recent progress has focused on both hydrodeoxygenation and hydrogenation of bio-oil using a variety of metal catalysts and the production of aromatics from bio-oil using cracking zeolites. Research is currently focused on developing multi-functional catalysts used in situ that benefit from the advantages of both hydrodeoxygenation and zeolite cracking. Development of robust, highly selective catalysts will help achieve the goal of producing drop-in fuels and petrochemical commodities from wood and other lignocellulosic biomass streams. The current paper will examine these developments by means of a review of existing literature.

  12. Transfecting Human Monocytes with RNA.

    Science.gov (United States)

    Dannull, Jens; Nair, Smita K

    2016-01-01

    Targeting monocytes as a delivery system for drugs or nucleic acids, and thereby harnessing their natural tissue-infiltrating capacity, has become an area of intense investigation in both basic and clinical research. Herein we describe an efficient method to deliver mRNA (messenger RNA) or siRNA (small interfering RNA) into human monocytes by electroporation. This method can be applied in the laboratory to monocytes isolated via magnetic bead-based techniques, or in a clinical setting using monocytes that were collected via counterflow centrifugation elutriation using the Elutra(®) Cell Separation System. We further demonstrate that electroporation of monocytes with RNA represents a robust and highly relevant approach to modify monocytes for cell-based therapies. Last, the procedure described can readily be adapted to monocytes from different species, hence facilitating research in animal models.

  13. Plasma-assisted catalytic ionization using porous nickel plate

    International Nuclear Information System (INIS)

    Oohara, W.; Maeda, T.; Higuchi, T.

    2011-01-01

    Hydrogen atomic pair ions, i.e., H + and H - ions, are produced by plasma-assisted catalytic ionization using a porous nickel plate. Positive ions in a hydrogen plasma generated by dc arc discharge are irradiated to the porous plate, and pair ions are produced from the back of the irradiation plane. It becomes clear that the production quantity of pair ions mainly depends on the irradiation current of positive ions and the irradiation energy affects the production efficiency of H - ions.

  14. Catalytic processes for cleaner fuels

    International Nuclear Information System (INIS)

    Catani, R.; Marchionna, M.; Rossini, S.

    1999-01-01

    More stringent limitations on vehicle emissions require different measurement: fuel reformulation is one of the most important and is calling for a noticeable impact on refinery assets. Composition rangers of the future fuels have been defined on a time scale. In this scenario the evolution of catalytic technologies becomes a fundamental tool for allowing refinery to reach the fixed-by-law targets. In this paper, the refinery process options to meet each specific requirements of reformulated fuels are surveyed [it

  15. Overexpression of miR169o, an Overlapping microRNA in Response to Both Nitrogen Limitation and Bacterial Infection, Promotes Nitrogen Use Efficiency and Susceptibility to Bacterial Blight in Rice.

    Science.gov (United States)

    Chao, Yu; Chen, Yutong; Cao, Yaqian; Chen, Huamin; Wang, Jichun; Bi, Yong-Mei; Tian, Fang; Yang, Fenghuan; Rothstein, Steven J; Zhou, Xueping; He, Chenyang

    2018-03-15

    Limiting nitrogen (N) supply contributes to improved resistance to bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) in susceptible rice (Oryza sativa). To understand the regulatory roles of microRNAs in this phenomenon, sixty-three differentially-expressed overlapping miRNAs in response to Xoo infection and N-limitation stress in rice were identified through deep RNA-sequence and stem loop qRT-PCR. Among these, miR169o was further assessed as a typical overlapping miRNA through the overexpression of the miR169o primary gene. Osa-miR169o-OX plants were taller, and had more biomass accumulation with significantly increased nitrate and total amino acid contents in roots than wild type (WT). Transcript level assays showed that under different N supply conditions miR169o opposite regulated NRT2 which is reduced under normal N supply condition but remarkably induced under N limiting stress. On the other hand, osa-miR169o-OX plants also displayed increased disease lesion lengths and reduced transcriptional levels of defense gene (PR1b, PR10a, PR10b and PAL) compared with WT after inoculation with Xoo. In addition, miR169o impeded Xoo-mediated NRT transcription. Therefore, the overlapping miR169o contributes to increase N use efficiency and negatively regulates the resistance to bacterial blight in rice. Consistently, transient expression of NF-YAs in rice protoplast promoted the transcripts of PR genes and NRT2 genes, while reduced the transcripts of NRT1 genes. Our results provide novel and additional insights into the coordinated regulatory mechanisms of crosstalk between Xoo infection and N-deficiency responses in rice.

  16. Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP.

    Science.gov (United States)

    Perederina, Anna; Khanova, Elena; Quan, Chao; Berezin, Igor; Esakova, Olga; Krasilnikov, Andrey S

    2011-10-01

    Ribonuclease (RNase) MRP is a multicomponent ribonucleoprotein complex closely related to RNase P. RNase MRP and eukaryotic RNase P share most of their protein components, as well as multiple features of their catalytic RNA moieties, but have distinct substrate specificities. While RNase P is practically universally found in all three domains of life, RNase MRP is essential in eukaryotes. The structural organizations of eukaryotic RNase P and RNase MRP are poorly understood. Here, we show that Pop5 and Rpp1, protein components found in both RNase P and RNase MRP, form a heterodimer that binds directly to the conserved area of the putative catalytic domain of RNase MRP RNA. The Pop5/Rpp1 binding site corresponds to the protein binding site in bacterial RNase P RNA. Structural and evolutionary roles of the Pop5/Rpp1 heterodimer in RNases P and MRP are discussed.

  17. Structured materials for catalytic and sensing applications

    Science.gov (United States)

    Hokenek, Selma

    The optical and chemical properties of the materials used in catalytic and sensing applications directly determine the characteristics of the resultant catalyst or sensor. It is well known that a catalyst needs to have high activity, selectivity, and stability to be viable in an industrial setting. The hydrogenation activity of palladium catalysts is known to be excellent, but the industrial applications are limited by the cost of obtaining catalyst in amounts large enough to make their use economical. As a result, alloying palladium with a cheaper, more widely available metal while maintaining the high catalytic activity seen in monometallic catalysts is, therefore, an attractive option. Similarly, the optical properties of nanoscale materials used for sensing must be attuned to their application. By adjusting the shape and composition of nanoparticles used in such applications, very fine changes can be made to the frequency of light that they absorb most efficiently. The design, synthesis, and characterization of (i) size controlled monometallic palladium nanoparticles for catalytic applications, (ii) nickel-palladium bimetallic nanoparticles and (iii) silver-palladium nanoparticles with applications in drug detection and biosensing through surface plasmon resonance, respectively, will be discussed. The composition, size, and shape of the nanoparticles formed were controlled through the use of wet chemistry techniques. After synthesis, the nanoparticles were analyzed using physical and chemical characterization techniques such as X-Ray Diffraction (XRD), Transmission Electron Microscopy (TEM), and Scanning Transmission Electron Microscopy- Energy-Dispersive Spectrometry (STEM-EDX). The Pd and Ni-Pd nanoparticles were then supported on silica for catalytic testing using mass spectrometry. The optical properties of the Ag-Pd nanoparticles in suspension were further investigated using ultraviolet-visible spectrometry (UV-Vis). Monometallic palladium particles have

  18. Catalytic applications of immobilized ionic liquids for synthesis of cyclic carbonates from carbon dioxide and epoxides

    International Nuclear Information System (INIS)

    Kim, Dong-Woo; Roshan, Roshith; Tharun, Jose; Cherian, Amal; Park, Dae-Won

    2013-01-01

    The catalytic applicability of ionic liquids immobilized on various support materials such as silica, polystyrene and biopolymers in the cycloaddition of carbon dioxide with epoxides is reviewed in this work. Comparisons of the catalytic efficiency of these various catalysts have been done from the aspect of turnover number and reusability. The studies revealed that ionic liquids or support materials possessing hydrogen bonding capable groups exhibited enhanced catalytic activity towards cyclic carbonate synthesis. Moreover, the increased quest towards environmentally benign materials has renewed the search for biocompatible materials as support for ionic liquids

  19. New Catalytic DNA Biosensors for Radionuclides and Metal ions

    International Nuclear Information System (INIS)

    Lu, Yi

    2003-01-01

    The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize

  20. Cross-catalytic peptide nucleic acid (PNA) replication based on templated ligation

    DEFF Research Database (Denmark)

    Singhal, Abhishek; Nielsen, Peter E

    2014-01-01

    We report the first PNA self-replicating system based on template directed cross-catalytic ligation, a process analogous to biological replication. Using two template PNAs and four pentameric precursor PNAs, all four possible carbodiimide assisted amide ligation products were detected...... precursors. Cross-catalytic product formation followed product inhibited kinetics, but approximately two replication rounds were observed. Analogous but less efficient replication was found for a similar tetrameric system. These results demonstrate that simpler nucleobase replication systems than natural...

  1. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.

    Science.gov (United States)

    Jiang, F; Kumar, R A; Jones, R A; Patel, D J

    1996-07-11

    The catalytic properties of RNA and its well known role in gene expression and regulation are the consequence of its unique solution structures. Identification of the structural determinants of ligand recognition by RNA molecules is of fundamental importance for understanding the biological functions of RNA, as well as for the rational design of RNA Sequences with specific catalytic activities. Towards this latter end, Szostak et al. used in vitro selection techniques to isolate RNA sequences ('aptamers') containing a high-affinity binding site for ATP, the universal currency of cellular energy, and then used this motif to engineer ribozymes with polynucleotide kinase activity. Here we present the solution structure, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations, of both uniformly and specifically 13C-, 15N-labelled 40-mer RNA containing the ATP-binding motif complexed with AMP. The aptamer adopts an L-shaped structure with two nearly orthogonal stems, each capped proximally by a G x G mismatch pair, binding the AMP ligand at their junction in a GNRA-like motif.

  2. Substrate-Directed Catalytic Selective Chemical Reactions.

    Science.gov (United States)

    Sawano, Takahiro; Yamamoto, Hisashi

    2018-05-04

    The development of highly efficient reactions at only the desired position is one of the most important subjects in organic chemistry. Most of the reactions in current organic chemistry are reagent- or catalyst-controlled reactions, and the regio- and stereoselectivity of the reactions are determined by the inherent nature of the reagent or catalyst. In sharp contrast, substrate-directed reaction determines the selectivity of the reactions by the functional group on the substrate and can strictly distinguish sterically and electronically similar multiple reaction sites in the substrate. In this Perspective, three topics of substrate-directed reaction are mainly reviewed: (1) directing group-assisted epoxidation of alkenes, (2) ring-opening reactions of epoxides by various nucleophiles, and (3) catalytic peptide synthesis. Our newly developed synthetic methods with new ligands including hydroxamic acid derived ligands realized not only highly efficient reactions but also pinpointed reactions at the expected position, demonstrating the substrate-directed reaction as a powerful method to achieve the desired regio- and stereoselective functionalization of molecules from different viewpoints of reagent- or catalyst-controlled reactions.

  3. Progress in controlling the size, composition and nanostructure of supported gold-palladium nanoparticles for catalytic applications

    NARCIS (Netherlands)

    Paalanen, P.P.|info:eu-repo/dai/nl/370602013; Weckhuysen, B.M.|info:eu-repo/dai/nl/285484397; Sankar, M.

    2013-01-01

    This review article gives an overview of the recent developments in the synthesis strategies of supported goldbased bimetallic nanoparticle catalysts. The catalytic efficiency of these supported bimetallic nanoparticles, similar to monometallic nanoparticles, depends on their structural

  4. Investigation of combustion and thermodynamic performance of a lean burn catalytic combustion gas turbine system

    International Nuclear Information System (INIS)

    Yin Juan; Weng Yiwu

    2011-01-01

    The goals of this research were to investigate the combustion and thermodynamic performance of a lean burn catalytic combustion gas turbine. The characteristics of lean burn catalytic combustion were investigated by utilising 1D heterogeneous plug flow model which was validated by experiments. The effects of operating parameters on catalytic combustion were numerically analysed. The system models were built in ASPEN Plus and three independent design variables, i.e. compressor pressure ratio (PR), regenerator effectiveness (RE) and turbine inlet temperature (TIT) were selected to analyse the thermodynamic performance of the thermal cycle. The main results show that: simulations from 1D heterogeneous plug flow model can capture the trend of catalytic combustion and describe the behavior of the catalytic monolith in detail. Inlet temperature is the most significant parameter that impacts operation of the catalytic combustor. When TIT and RE are constant, the increase of PR results in lowering the inlet temperature of the catalytic combustor, which results in decreasing methane conversion. The peak thermal efficiency and the optimal PR at a constant TIT increase with the increase of TIT; and at the constant PR, the thermal efficiency increases with the increase of TIT. However, with lower TIT conditions, the optimal PR and the peak efficiency at a constant TIT of the LBCCGT cycle are relative low to that of the conventional cycle. When TIT and PR are constant, the decrease of RE may result in lower methane conversion. The influences of RE on the methane conversion and the thermal efficiency are more significant at higher PRs. The higher thermal efficiency for the lower RE is achieved at lower PR.

  5. Kinetics of heterogeneous catalytic reactions

    CERN Document Server

    Boudart, Michel

    2014-01-01

    This book is a critical account of the principles of the kinetics of heterogeneous catalytic reactions in the light of recent developments in surface science and catalysis science. Originally published in 1984. The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback editions. The goal of the Princeton Legacy Library is to vastly increase acc

  6. Catalytic Organometallic Reactions of Ammonia

    Science.gov (United States)

    Klinkenberg, Jessica L.

    2012-01-01

    Until recently, ammonia had rarely succumbed to catalytic transformations with homogeneous catalysts, and the development of such reactions that are selective for the formation of single products under mild conditions has encountered numerous challenges. However, recently developed catalysts have allowed several classes of reactions to create products with nitrogen-containing functional groups from ammonia. These reactions include hydroaminomethylation, reductive amination, alkylation, allylic substitution, hydroamination, and cross-coupling. This Minireview describes examples of these processes and the factors that control catalyst activity and selectivity. PMID:20857466

  7. Catalytic cracking of hydrocarbon oils

    Energy Technology Data Exchange (ETDEWEB)

    1940-09-12

    A process is described for the vapor phase catalytic cracking of hydrocarbon oils boiling substantially in the gas oil range. The reaction takes place in the presence of a solid catalyst between 700 to 900/sup 0/F under pressure between atmospheric and 400 psi. A gas containing between 20 and 90 mol % of free hydrogen is used. The reaction is allowed to proceed until consumption of the free begins. The reaction is discontinued at that point and the catalyst is regenerated for further use.

  8. Molecular catalytic coal liquid conversion

    Energy Technology Data Exchange (ETDEWEB)

    Stock, L.M.; Yang, Shiyong [Univ. of Chicago, IL (United States)

    1995-12-31

    This research, which is relevant to the development of new catalytic systems for the improvement of the quality of coal liquids by the addition of dihydrogen, is divided into two tasks. Task 1 centers on the activation of dihydrogen by molecular basic reagents such as hydroxide ion to convert it into a reactive adduct (OH{center_dot}H{sub 2}){sup {minus}} that can reduce organic molecules. Such species should be robust withstanding severe conditions and chemical poisons. Task 2 is focused on an entirely different approach that exploits molecular catalysts, derived from organometallic compounds that are capable of reducing monocyclic aromatic compounds under very mild conditions. Accomplishments and conclusions are discussed.

  9. Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine

    International Nuclear Information System (INIS)

    Kim, Moon-Jung; Lee, Byung Cheon; Hwang, Kwang Yeon; Gladyshev, Vadim N.; Kim, Hwa-Young

    2015-01-01

    Thioredoxin (Trx) is a major thiol-disulfide reductase that plays a role in many biological processes, including DNA replication and redox signaling. Although selenocysteine (Sec)-containing Trxs have been identified in certain bacteria, their enzymatic properties have not been characterized. In this study, we expressed a selenoprotein Trx from Treponema denticola, an oral spirochete, in Escherichia coli and characterized this selenoenzyme and its natural cysteine (Cys) homologue using E. coli Trx1 as a positive control. 75 Se metabolic labeling and mutation analyses showed that the SECIS (Sec insertion sequence) of T. denticola selenoprotein Trx is functional in the E. coli Sec insertion system with specific selenium incorporation into the Sec residue. The selenoprotein Trx exhibited approximately 10-fold higher catalytic activity than the Sec-to-Cys version and natural Cys homologue and E. coli Trx1, suggesting that Sec confers higher catalytic activity on this thiol-disulfide reductase. Kinetic analysis also showed that the selenoprotein Trx had a 30-fold higher K m than Cys-containing homologues, suggesting that this selenoenzyme is adapted to work efficiently with high concentrations of substrate. Collectively, the results of this study support the hypothesis that selenium utilization in oxidoreductase systems is primarily due to the catalytic advantage provided by the rare amino acid, Sec. - Highlights: • The first characterization of a selenoprotein Trx is presented. • The selenoenzyme Trx exhibits 10-fold higher catalytic activity than Cys homologues. • Se utilization in Trx is primarily due to the catalytic advantage provided by Sec residue

  10. Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Moon-Jung [Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717 (Korea, Republic of); Lee, Byung Cheon [Division of Genetics, Department of Medicine, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA 02115 (United States); Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Hwang, Kwang Yeon [Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Gladyshev, Vadim N. [Division of Genetics, Department of Medicine, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA 02115 (United States); Kim, Hwa-Young, E-mail: hykim@ynu.ac.kr [Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717 (Korea, Republic of)

    2015-06-12

    Thioredoxin (Trx) is a major thiol-disulfide reductase that plays a role in many biological processes, including DNA replication and redox signaling. Although selenocysteine (Sec)-containing Trxs have been identified in certain bacteria, their enzymatic properties have not been characterized. In this study, we expressed a selenoprotein Trx from Treponema denticola, an oral spirochete, in Escherichia coli and characterized this selenoenzyme and its natural cysteine (Cys) homologue using E. coli Trx1 as a positive control. {sup 75}Se metabolic labeling and mutation analyses showed that the SECIS (Sec insertion sequence) of T. denticola selenoprotein Trx is functional in the E. coli Sec insertion system with specific selenium incorporation into the Sec residue. The selenoprotein Trx exhibited approximately 10-fold higher catalytic activity than the Sec-to-Cys version and natural Cys homologue and E. coli Trx1, suggesting that Sec confers higher catalytic activity on this thiol-disulfide reductase. Kinetic analysis also showed that the selenoprotein Trx had a 30-fold higher K{sub m} than Cys-containing homologues, suggesting that this selenoenzyme is adapted to work efficiently with high concentrations of substrate. Collectively, the results of this study support the hypothesis that selenium utilization in oxidoreductase systems is primarily due to the catalytic advantage provided by the rare amino acid, Sec. - Highlights: • The first characterization of a selenoprotein Trx is presented. • The selenoenzyme Trx exhibits 10-fold higher catalytic activity than Cys homologues. • Se utilization in Trx is primarily due to the catalytic advantage provided by Sec residue.

  11. Development of a catalytically assisted combustor for a gas turbine

    Energy Technology Data Exchange (ETDEWEB)

    Ozawa, Yasushi; Fujii, Tomoharu; Sato, Mikio [Central Research Institute of Electric Power Industry, 2-6-1 Nagasaka, Yokosuka, Kanagawa 240-01 (Japan); Kanazawa, Takaaki; Inoue, Hitoshi [Kansai Electric Power Company, Inc., 3-11-20 Nakoji, Amagasaki, Hyoho 661 (Japan)

    1999-01-01

    A catalytically assisted low NO{sub x} combustor has been developed which has the advantage of catalyst durability. This combustor is composed of a burner section and a premixed combustion section behind the burner section. The burner system consists of six catalytic combustor segments and six premixing nozzles, which are arranged alternately and in parallel. Fuel flow rate for the catalysts and the premixing nozzles are controlled independently. The catalytic combustion temperature is maintained under 1000C, additional premixed gas is injected from the premixing nozzles into the catalytic combustion gas, and lean premixed combustion at 1300C is carried out in the premixed combustion section. This system was designed to avoid catalytic deactivation at high temperature and thermal or mechanical shock fracture of the honeycomb monolith. In order to maintain the catalyst temperature under 1000C, the combustion characteristics of catalysts at high pressure were investigated using a bench scale reactor and an improved catalyst was selected for the combustor test. A combustor for a 20MW class multi-can type gas turbine was designed and tested under high pressure conditions using LNG fuel. Measurements of NO{sub x}, CO and unburned hydrocarbon were made and other measurements were made to evaluate combustor performance under various combustion temperatures and pressures. As a result of the tests, it was proved that NO{sub x} emission was lower than 10ppm converted at 16% O{sub 2}, combustion efficiency was almost 100% at 1300C of combustor outlet temperature and 13.5ata of combustor inlet pressure

  12. High aspect ratio catalytic reactor and catalyst inserts therefor

    Science.gov (United States)

    Lin, Jiefeng; Kelly, Sean M.

    2018-04-10

    The present invention relates to high efficient tubular catalytic steam reforming reactor configured from about 0.2 inch to about 2 inch inside diameter high temperature metal alloy tube or pipe and loaded with a plurality of rolled catalyst inserts comprising metallic monoliths. The catalyst insert substrate is formed from a single metal foil without a central supporting structure in the form of a spiral monolith. The single metal foil is treated to have 3-dimensional surface features that provide mechanical support and establish open gas channels between each of the rolled layers. This unique geometry accelerates gas mixing and heat transfer and provides a high catalytic active surface area. The small diameter, high aspect ratio tubular catalytic steam reforming reactors loaded with rolled catalyst inserts can be arranged in a multi-pass non-vertical parallel configuration thermally coupled with a heat source to carry out steam reforming of hydrocarbon-containing feeds. The rolled catalyst inserts are self-supported on the reactor wall and enable efficient heat transfer from the reactor wall to the reactor interior, and lower pressure drop than known particulate catalysts. The heat source can be oxygen transport membrane reactors.

  13. Catalytic Ozonation of Phenolic Wastewater: Identification and Toxicity of Intermediates

    Directory of Open Access Journals (Sweden)

    Mahdi Farzadkia

    2014-01-01

    Full Text Available A new strategy in catalytic ozonation removal method for degradation and detoxification of phenol from industrial wastewater was investigated. Magnetic carbon nanocomposite, as a novel catalyst, was synthesized and then used in the catalytic ozonation process (COP and the effects of operational conditions such as initial pH, reaction time, and initial concentration of phenol on the degradation efficiency and the toxicity assay have been investigated. The results showed that the highest catalytic potential was achieved at optimal neutral pH and the removal efficiency of phenol and COD is 98.5% and 69.8%, respectively. First-order modeling demonstrated that the reactions were dependent on the initial concentration of phenol, with kinetic constants varying from 0.038 min−1  ([phenol]o = 1500 mg/L to 1.273 min−1 ([phenol]o = 50 mg/L. Bioassay analysis showed that phenol was highly toxic to Daphnia magna (LC50 96 h=5.6 mg/L. Comparison of toxicity units (TU of row wastewater (36.01 and the treated effluent showed that TU value, after slightly increasing in the first steps of ozonation for construction of more toxic intermediates, severely reduced at the end of reaction (2.23. Thus, COP was able to effectively remove the toxicity of intermediates which were formed during the chemical oxidation of phenolic wastewaters.

  14. Catalytic enantioselective Reformatsky reaction with ketones

    NARCIS (Netherlands)

    Fernandez-Ibanez, M. Angeles; Macia, Beatriz; Minnaard, Adriaan J.; Feringa, Ben L.

    2008-01-01

    Chiral tertiary alcohols were obtained with good yields and enantioselectivities via a catalytic Reformatsky reaction with ketones, including the challenging diaryl ketones, using chiral BINOL derivatives.

  15. Fast prediction of RNA-RNA interaction using heuristic algorithm.

    Science.gov (United States)

    Montaseri, Soheila

    2015-01-01

    Interaction between two RNA molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the RNA-RNA interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two RNAs based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each RNA and binding sites between two RNAs. Furthermore, a parallel version of this method is presented. We describe the algorithm's concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches.

  16. Green technology for conversion of renewable hydrocarbon based on plasma-catalytic approach

    Science.gov (United States)

    Fedirchyk, Igor; Nedybaliuk, Oleg; Chernyak, Valeriy; Demchina, Valentina

    2016-09-01

    The ability to convert renewable biomass into fuels and chemicals is one of the most important steps on our path to green technology and sustainable development. However, the complex composition of biomass poses a major problem for established conversion technologies. The high temperature of thermochemical biomass conversion often leads to the appearance of undesirable byproducts and waste. The catalytic conversion has reduced yield and feedstock range. Plasma-catalytic reforming technology opens a new path for biomass conversion by replacing feedstock-specific catalysts with free radicals generated in the plasma. We studied the plasma-catalytic conversion of several renewable hydrocarbons using the air plasma created by rotating gliding discharge. We found that plasma-catalytic hydrocarbon conversion can be conducted at significantly lower temperatures (500 K) than during the thermochemical ( 1000 K) and catalytic (800 K) conversion. By using gas chromatography, we determined conversion products and found that conversion efficiency of plasma-catalytic conversion reaches over 85%. We used obtained data to determine the energy yield of hydrogen in case of plasma-catalytic reforming of ethanol and compared it with other plasma-based hydrogen-generating systems.

  17. Petrochemical promoters in catalytic cracking

    International Nuclear Information System (INIS)

    Gomez, Maria; Vargas, Clemencia; Lizcano, Javier

    2010-01-01

    This study is based on the current scheme followed by a refinery with available Catalytic Cracking capacity to process new feedstocks such as Straight Run Naphtha and Naphthas from FCC. These feedstocks are of petrochemical interest to produce Ethane, Ethylene, Propylene, i-Butane, Toluene and Xylene. To evaluate the potential of these new streams versus the Cracking-charged Residues, it was performed a detailed chemical analysis on the structural groups in carbons [C1-C12] at the reactor product obtained in pilot plant. A catalyst with and without Propylene Promoter Additive was used. This study analyzes the differences in the chemical composition of the feedstocks, relating them to the yield of each petrochemical product. Straight Run Naphthas with a high content of Naphthenes, and Paraffines n[C5-C12] and i[C7-C12] are selective to the production of i-Butane and Propane, while Naphthas from FCC with a high content of n[C5-C12]Olefins, i-Olefins, and Aromatics are more selective to Propylene, Toluene, and Xylene. Concerning Catalytic Cracking of Naphthas, the Additive has similar selectivity for all the petrochemical products, their yields increase by about one point with 4%wt of Additive, while in cracking of Residues, the Additive increases in three points Propylene yield, corresponding to a selectivity of 50% (?C3= / ?LPG).

  18. Catalytic conversion of light alkanes

    Energy Technology Data Exchange (ETDEWEB)

    Lyons, J.E.

    1992-06-30

    The second Quarterly Report of 1992 on the Catalytic Conversion of Light Alkanes reviews the work done between April 1, 1992 and June 31, 1992 on the Cooperative Agreement. The mission of this work is to devise a new catalyst which can be used in a simple economic process to convert the light alkanes in natural gas to oxygenate products that can either be used as clean-burning, high octane liquid fuels, as fuel components or as precursors to liquid hydrocarbon uwspomdon fuel. During the past quarter we have continued to design, prepare, characterize and test novel catalysts for the mild selective reaction of light hydrocarbons with air or oxygen to produce alcohols directly. These catalysts are designed to form active metal oxo (MO) species and to be uniquely active for the homolytic cleavage of the carbon-hydrogen bonds in light alkanes producing intermediates which can form alcohols. We continue to investigate three molecular environments for the active catalytic species that we are trying to generate: electron-deficient macrocycles (PHASE I), polyoxometallates (PHASE II), and regular oxidic lattices including zeolites and related structures as well as other molecular surface structures having metal oxo groups (PHASE I).

  19. Catalytic converters in the fireplace

    International Nuclear Information System (INIS)

    Kouki, J.

    1995-01-01

    In addition to selecting the appropriate means of heating and using dry fuel, the amount of harmful emissions contained by flue gases produced by fireplaces can be reduced by technical means. One such option is to use an oxidising catalytic converter. Tests at TTS Institute's Heating Studies Experimental Station have focused on two such converters (dense and coarse) mounted in light-weight iron heating stoves. The ability of the dense catalytic converter to oxidise carbon monoxide gases proved to be good. The concentration of carbon monoxide in the flue gases was reduced by as much as 90 %. Measurements conducted by VTT (Technical Research Centre of Finland) showed that the conversion of other gases, e.g. of methane, was good. The exhaust resistance caused by the dense converter was so great as to necessitate the mounting of a fluegas evacuation fan in the chimney for the purpose of creating sufficient draught. When relying on natural draught, the dense converter requires a chimney of at least 7 metres and a by-pass connection while the fire is being lit. In addition, the converter will have to be constructed to be less dense and this will mean that it's capability to oxidise non-combusted gases will be reduced. The coarse converter did not impair the draught but it's oxidising property was insufficient. With the tests over, the converter was not observed to have become blocked up by impurities

  20. Outstanding catalytic activity of ultra-pure platinum nanoparticles.

    Science.gov (United States)

    Januszewska, Aneta; Dercz, Grzegorz; Piwowar, Justyna; Jurczakowski, Rafal; Lewera, Adam

    2013-12-09

    Small (4 nm) nanoparticles with a narrow size distribution, exceptional surface purity, and increased surface order, which exhibits itself as an increased presence of basal crystallographic planes, can be obtained without the use of any surfactant. These nanoparticles can be used in many applications in an as-received state and are threefold more active towards a model catalytic reaction (oxidation of ethylene glycol). Furthermore, the superior properties of this material are interesting not only due to the increase in their intrinsic catalytic activity, but also due to the exceptional surface purity itself. The nanoparticles can be used directly (i.e., as-received, without any cleaning steps) in biomedical applications (i.e., as more efficient drug carriers due to an increased number of adsorption sites) and in energy-harvesting/data-storage devices. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Solid strong base K-Pt/NaY zeolite nano-catalytic system for completed elimination of formaldehyde at room temperature

    Science.gov (United States)

    Song, Shaoqing; Wu, Xi; Lu, Changhai; Wen, Meicheng; Le, Zhanggao; Jiang, Shujuan

    2018-06-01

    Solid strong base nano-catalytic system of K-modification NaY zeolite supported 0.08% Pt (K-Pt/NaY) were constructed for eliminating HCHO at room temperature. In the catalytic process, activation energy over K-Pt/NaY nano-catalytic system was greatly decreased along with the enhanced reaction rate. Characterization and catalytic tests revealed the surface electron structure of K-Pt/NaY was improved, as reflected by the enhanced HCHO adsorption capability, high sbnd OH concentration, and low-temperature reducibility. Therefore, the optimal K-Pt/NaY showed high catalytic efficiency and strong H2O tolerance for HCHO elimination by directly promoting the reaction between active sbnd OH and formate species. These results may suggest a new way for probing the advanced solid strong base nano-catalytic system for the catalytic elimination of indoor HCHO.

  2. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  3. VUV photo-oxidation of gaseous benzene combined with ozone-assisted catalytic oxidation: Effect on transition metal catalyst

    International Nuclear Information System (INIS)

    Huang, Haibao; Lu, Haoxian; Zhan, Yujie; Liu, Gaoyuan; Feng, Qiuyu; Huang, Huiling; Wu, Muyan; Ye, Xinguo

    2017-01-01

    Graphical abstract: Mn nanoparticles are highly dispersed on ZSM-5 and most efficient in benzene degradation in the VUV-OZCO process. - Highlights: • Vacuum UV irradiation is well combined with O_3 catalytic oxidation. • O_3 byproducts was used to enhance catalytic oxidation of VOCs. • Mn/ZSM-5 achieved the best catalytic activity for benzene degradation. - Abstract: Volatile organic compounds (VOCs) cause the major air pollution concern. In this study, a series of ZSM-5 supported transition metals were prepared by impregnation method. They were combined with vacuum UV (VUV) photo-oxidation in a continuous-flow packed-bed reactor and used for the degradation of benzene, a typical toxic VOCs. Compared with VUV photo-oxidation alone, the introduction of catalysts can greatly enhance benzene oxidation under the help of O_3, the by-products from VUV irradiation, via ozone-assisted catalytic oxidation (OZCO). The catalytic activity of transition metals towards benzene oxidation followed the order: Mn > Co > Cu > Ni > Fe. Mn achieved the best catalytic activity due to the strongest capability for O_3 catalytic decomposition and utilization. Benzene and O_3 removal efficiency reached as high as 97% and 100% after 360 min, respectively. O_3 was catalytically decomposed, generating highly reactive oxidants such as ·OH and ·O for benzene oxidation.

  4. VUV photo-oxidation of gaseous benzene combined with ozone-assisted catalytic oxidation: Effect on transition metal catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Haibao, E-mail: seabao8@gmail.com [School of Environmental Science and Engineering, Sun Yat-Sen University (China); Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University) (China); Lu, Haoxian; Zhan, Yujie; Liu, Gaoyuan; Feng, Qiuyu; Huang, Huiling; Wu, Muyan; Ye, Xinguo [School of Environmental Science and Engineering, Sun Yat-Sen University (China)

    2017-01-01

    Graphical abstract: Mn nanoparticles are highly dispersed on ZSM-5 and most efficient in benzene degradation in the VUV-OZCO process. - Highlights: • Vacuum UV irradiation is well combined with O{sub 3} catalytic oxidation. • O{sub 3} byproducts was used to enhance catalytic oxidation of VOCs. • Mn/ZSM-5 achieved the best catalytic activity for benzene degradation. - Abstract: Volatile organic compounds (VOCs) cause the major air pollution concern. In this study, a series of ZSM-5 supported transition metals were prepared by impregnation method. They were combined with vacuum UV (VUV) photo-oxidation in a continuous-flow packed-bed reactor and used for the degradation of benzene, a typical toxic VOCs. Compared with VUV photo-oxidation alone, the introduction of catalysts can greatly enhance benzene oxidation under the help of O{sub 3}, the by-products from VUV irradiation, via ozone-assisted catalytic oxidation (OZCO). The catalytic activity of transition metals towards benzene oxidation followed the order: Mn > Co > Cu > Ni > Fe. Mn achieved the best catalytic activity due to the strongest capability for O{sub 3} catalytic decomposition and utilization. Benzene and O{sub 3} removal efficiency reached as high as 97% and 100% after 360 min, respectively. O{sub 3} was catalytically decomposed, generating highly reactive oxidants such as ·OH and ·O for benzene oxidation.

  5. (Gold core) at (ceria shell) nanostructures for plasmon-enhanced catalytic reactions under visible light

    KAUST Repository

    Wang, Jianfang; Li, Benxia; Gu, Ting; Ming, Tian; Wang, Junxin; Wang, Peng; Yu, Jimmy C.

    2014-01-01

    Driving catalytic reactions with sunlight is an excellent example of sustainable chemistry. A prerequisite of solar-driven catalytic reactions is the development of photocatalysts with high solar-harvesting efficiencies and catalytic activities. Herein, we describe a general approach for uniformly coating ceria on monometallic and bimetallic nanocrystals through heterogeneous nucleation and growth. The method allows for control of the shape, size, and type of the metal core as well as the thickness of the ceria shell. The plasmon shifts of the Au@CeO2 nanostructures resulting from the switching between Ce(IV) and Ce(III) are observed. The selective oxidation of benzyl alcohol to benzaldehyde, one of the fundamental reactions for organic synthesis, performed under both broad-band and monochromatic light, demonstrates the visible-light-driven catalytic activity and reveals the synergistic effect on the enhanced catalysis of the Au@CeO2 nanostructures. © 2014 American Chemical Society.

  6. (Gold core) at (ceria shell) nanostructures for plasmon-enhanced catalytic reactions under visible light

    KAUST Repository

    Wang, Jianfang

    2014-08-26

    Driving catalytic reactions with sunlight is an excellent example of sustainable chemistry. A prerequisite of solar-driven catalytic reactions is the development of photocatalysts with high solar-harvesting efficiencies and catalytic activities. Herein, we describe a general approach for uniformly coating ceria on monometallic and bimetallic nanocrystals through heterogeneous nucleation and growth. The method allows for control of the shape, size, and type of the metal core as well as the thickness of the ceria shell. The plasmon shifts of the Au@CeO2 nanostructures resulting from the switching between Ce(IV) and Ce(III) are observed. The selective oxidation of benzyl alcohol to benzaldehyde, one of the fundamental reactions for organic synthesis, performed under both broad-band and monochromatic light, demonstrates the visible-light-driven catalytic activity and reveals the synergistic effect on the enhanced catalysis of the Au@CeO2 nanostructures. © 2014 American Chemical Society.

  7. Formalization of hydrocarbon conversion scheme of catalytic cracking for mathematical model development

    Science.gov (United States)

    Nazarova, G.; Ivashkina, E.; Ivanchina, E.; Kiseleva, S.; Stebeneva, V.

    2015-11-01

    The issue of improving the energy and resource efficiency of advanced petroleum processing can be solved by the development of adequate mathematical model based on physical and chemical regularities of process reactions with a high predictive potential in the advanced petroleum refining. In this work, the development of formalized hydrocarbon conversion scheme of catalytic cracking was performed using thermodynamic parameters of reaction defined by the Density Functional Theory. The list of reaction was compiled according to the results of feedstock structural-group composition definition, which was done by the n-d-m-method, the Hazelvuda method, qualitative composition of feedstock defined by gas chromatography-mass spectrometry and individual composition of catalytic cracking gasoline fraction. Formalized hydrocarbon conversion scheme of catalytic cracking will become the basis for the development of the catalytic cracking kinetic model.

  8. Heterogeneous catalytic degradation of polyacrylamide solution | Hu ...

    African Journals Online (AJOL)

    Modified with trace metal elements, the catalytic activity of Fe2O3/Al2O3 could be changed greatly. Among various trace metal elements, Fe2O3/Al2O3 catalysts modified with Co and Cu showed great increase on catalytic activity. International Journal of Engineering, Science and Technology, Vol. 2, No. 7, 2010, pp. 110- ...

  9. The use of 125iodine-labeled RNA for detection of the RNA binding to ribosomes

    International Nuclear Information System (INIS)

    Mori, Tomohiko; Fukuda, Mitsuru

    1975-01-01

    The in vitro labeling of RNA with radioactive iodine is the efficient method to obtain the RNA with high specific activity. The present paper reports on the application of this technique to the production of iodine-labeled RNA for use in the experiment of binding RNA to ribosomes. Tobacco mosaic virus (TMV) RNA was used as natural mRNA, and E. coli S-30 preparation was used as a source of ribosomes. The TMV-RNA was prepared by bentonite-phenol extraction from TMV, and the method used for the iodation of RNA was based on the procedure described by Getz et al. The iodine-labeled RNA was incubated in a cell-free protein synthesizing system (S-30) prepared from E. coli K-12. After the incubation, the reaction mixture was layered onto sucrose gradient, centrifuged, and fractionated into 18 fractions. Optical density at 260 nm was measured, and radioactivity was counted, for each fraction. The binding of mRNA to ribosomes occurred even at 0 deg C, and the occurrence of the nonspecific binding was also shown. Consequently, the specific binding, i.e. the formation of the initiation complex being involved in amino acid incorporation, may be estimated by subtracting the radioactivity associated with monosomes in the presence of both rRNA and ATA from that in the presence of rRNA only. It was shown that the iodine-labeled RNA can be used for the studies of binding RNA to ribosomes. (Kako, I.)

  10. Method of fabricating a catalytic structure

    Science.gov (United States)

    Rollins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

    2009-09-22

    A precursor to a catalytic structure comprising zinc oxide and copper oxide. The zinc oxide has a sheet-like morphology or a spherical morphology and the copper oxide comprises particles of copper oxide. The copper oxide is reduced to copper, producing the catalytic structure. The catalytic structure is fabricated by a hydrothermal process. A reaction mixture comprising a zinc salt, a copper salt, a hydroxyl ion source, and a structure-directing agent is formed. The reaction mixture is heated under confined volume conditions to produce the precursor. The copper oxide in the precursor is reduced to copper. A method of hydrogenating a carbon oxide using the catalytic structure is also disclosed, as is a system that includes the catalytic structure.

  11. iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

    Directory of Open Access Journals (Sweden)

    Jittrawan Thaiprasit

    2016-03-01

    Full Text Available RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA

  12. Catalytic hydrogenation of carbon monoxide

    International Nuclear Information System (INIS)

    Wayland, B.B.

    1993-12-01

    Focus of this project is on developing new approaches for hydrogenation of carbon monoxide to produce organic oxygenates at mild conditions. The strategies to accomplish CO reduction are based on favorable thermodynamics manifested by rhodium macrocycles for producing a series of intermediates implicated in the catalytic hydrogenation of CO. Metalloformyl complexes from reactions of H 2 and CO, and CO reductive coupling to form metallo α-diketone species provide alternate routes to organic oxygenates that utilize these species as intermediates. Thermodynamic and kinetic-mechanistic studies are used in guiding the design of new metallospecies to improve the thermodynamic and kinetic factors for individual steps in the overall process. Electronic and steric effects associated with the ligand arrays along with the influences of the reaction medium provide the chemical tools for tuning these factors. Non-macrocyclic ligand complexes that emulate the favorable thermodynamic features associated with rhodium macrocycles, but that also manifest improved reaction kinetics are promising candidates for future development

  13. Selective catalytic oxidation of ammonia

    Energy Technology Data Exchange (ETDEWEB)

    Leppaelahti, J; Koljonen, T [VTT Energy, Espoo (Finland)

    1997-12-31

    In the combustion of fossil fuels, the principal source of nitrogen oxides is nitrogen bound in the fuel structure. In gasification, a large part of fuel nitrogen forms NH{sub 3}, which may form nitrogen oxides during gas combustion. If NH{sub 3} and other nitrogen species could be removed from hot gas, the NO emission could be considerably reduced. However, relatively little attention has been paid to finding new means of removing nitrogen compounds from the hot gasification gas. The possibility of selectively oxidizing NH{sub 3} to N{sub 2} in the hot gasification has been studied at VTT Energy. The largest NH{sub 3} reductions have been achieved by catalytic oxidation on aluminium oxides. (author) (4 refs.)

  14. Non-catalytic recuperative reformer

    Science.gov (United States)

    Khinkis, Mark J.; Kozlov, Aleksandr P.; Kurek, Harry

    2015-12-22

    A non-catalytic recuperative reformer has a flue gas flow path for conducting hot flue gas from a thermal process and a reforming mixture flow path for conducting a reforming mixture. At least a portion of the reforming mixture flow path is embedded in the flue gas flow path to permit heat transfer from the hot flue gas to the reforming mixture. The reforming mixture flow path contains substantially no material commonly used as a catalyst for reforming hydrocarbon fuel (e.g., nickel oxide, platinum group elements or rhenium), but instead the reforming mixture is reformed into a higher calorific fuel via reactions due to the heat transfer and residence time. In a preferred embodiment, extended surfaces of metal material such as stainless steel or metal alloy that are high in nickel content are included within at least a portion of the reforming mixture flow path.

  15. Studies of Catalytic Model Systems

    DEFF Research Database (Denmark)

    Holse, Christian

    The overall topic of this thesis is within the field of catalysis, were model systems of different complexity have been studied utilizing a multipurpose Ultra High Vacuum chamber (UHV). The thesis falls in two different parts. First a simple model system in the form of a ruthenium single crystal...... of the Cu/ZnO nanoparticles is highly relevant to industrial methanol synthesis for which the direct interaction of Cu and ZnO nanocrystals synergistically boost the catalytic activity. The dynamical behavior of the nanoparticles under reducing and oxidizing environments were studied by means of ex situ X......-ray Photoelectron Electron Spectroscopy (XPS) and in situ Transmission Electron Microscopy (TEM). The surface composition of the nanoparticles changes reversibly as the nanoparticles exposed to cycles of high-pressure oxidation and reduction (200 mbar). Furthermore, the presence of metallic Zn is observed by XPS...

  16. Selective catalytic oxidation of ammonia

    Energy Technology Data Exchange (ETDEWEB)

    Leppaelahti, J.; Koljonen, T. [VTT Energy, Espoo (Finland)

    1996-12-31

    In the combustion of fossil fuels, the principal source of nitrogen oxides is nitrogen bound in the fuel structure. In gasification, a large part of fuel nitrogen forms NH{sub 3}, which may form nitrogen oxides during gas combustion. If NH{sub 3} and other nitrogen species could be removed from hot gas, the NO emission could be considerably reduced. However, relatively little attention has been paid to finding new means of removing nitrogen compounds from the hot gasification gas. The possibility of selectively oxidizing NH{sub 3} to N{sub 2} in the hot gasification has been studied at VTT Energy. The largest NH{sub 3} reductions have been achieved by catalytic oxidation on aluminium oxides. (author) (4 refs.)

  17. Additive Manufacturing of Catalytically Active Living Materials.

    Science.gov (United States)

    Saha, Abhijit; Johnston, Trevor G; Shafranek, Ryan T; Goodman, Cassandra J; Zalatan, Jesse G; Storti, Duane W; Ganter, Mark A; Nelson, Alshakim

    2018-04-25

    Living materials, which are composites of living cells residing in a polymeric matrix, are designed to utilize the innate functionalities of the cells to address a broad range of applications such as fermentation and biosensing. Herein, we demonstrate the additive manufacturing of catalytically active living materials (AMCALM) for continuous fermentation. A multi-stimuli-responsive yeast-laden hydrogel ink, based on F127-dimethacrylate, was developed and printed using a direct-write 3D printer. The reversible stimuli-responsive behaviors of the polymer hydrogel inks to temperature and pressure are critical, as they enabled the facile incorporation of yeast cells and subsequent fabrication of 3D lattice constructs. Subsequent photo-cross-linking of the printed polymer hydrogel afforded a robust elastic material. These yeast-laden living materials were metabolically active in the fermentation of glucose into ethanol for 2 weeks in a continuous batch process without significant reduction in efficiency (∼90% yield of ethanol). This cell immobilization platform may potentially be applicable toward other genetically modified yeast strains to produce other high-value chemicals in a continuous biofermentation process.

  18. Plasma-catalytic decomposition of TCE

    Energy Technology Data Exchange (ETDEWEB)

    Vandenbroucke, A.; Morent, R.; De Geyter, N.; Leys, C. [Ghent Univ., Ghent (Belgium). Dept. of Applied Physics; Tuan, N.D.M.; Giraudon, J.M.; Lamonier, J.F. [Univ. des Sciences et Technologies de Lille, Villeneuve (France). Dept. de Catalyse et Chimie du Solide

    2010-07-01

    Volatile organic compounds (VOCs) are gaseous pollutants that pose an environmental hazard due to their high volatility and their possible toxicity. Conventional technologies to reduce the emission of VOCs have their advantages, but they become cost-inefficient when low concentrations have to be treated. In the past 2 decades, non-thermal plasma technology has received growing attention as an alternative and promising remediation method. Non-thermal plasmas are effective because they produce a series of strong oxidizers such as ozone, oxygen radicals and hydroxyl radicals that provide a reactive chemical environment in which VOCs are completely oxidized. This study investigated whether the combination of NTP and catalysis could improve the energy efficiency and the selectivity towards carbon dioxide (CO{sub 2}). Trichloroethylene (TCE) was decomposed by non-thermal plasma generated in a DC-excited atmospheric pressure glow discharge. The production of by-products was qualitatively investigated through FT-IR spectrometry. The results were compared with those from a catalytic reactor. The removal rate of TCE reached a maximum of 78 percent at the highest input energy. The by-products of TCE decomposition were CO{sub 2}, carbon monoxide (CO) hydrochloric acid (HCl) and dichloroacetylchloride. Combining the plasma system with a catalyst located in an oven downstream resulted in a maximum removal of 80 percent, at an energy density of 300 J/L, a catalyst temperature of 373 K and a total air flow rate of 2 slm. 14 refs., 6 figs.

  19. Microchannel Reactor System for Catalytic Hydrogenation

    Energy Technology Data Exchange (ETDEWEB)

    Adeniyi Lawal; Woo Lee; Ron Besser; Donald Kientzler; Luke Achenie

    2010-12-22

    We successfully demonstrated a novel process intensification concept enabled by the development of microchannel reactors, for energy efficient catalytic hydrogenation reactions at moderate temperature, and pressure, and low solvent levels. We designed, fabricated, evaluated, and optimized a laboratory-scale microchannel reactor system for hydrogenation of onitroanisole and a proprietary BMS molecule. In the second phase of the program, as a prelude to full-scale commercialization, we designed and developed a fully-automated skid-mounted multichannel microreactor pilot plant system for multiphase reactions. The system is capable of processing 1 – 10 kg/h of liquid substrate, and an industrially relevant immiscible liquid-liquid was successfully demonstrated on the system. Our microreactor-based pilot plant is one-of-akind. We anticipate that this process intensification concept, if successfully demonstrated, will provide a paradigm-changing basis for replacing existing energy inefficient, cost ineffective, environmentally detrimental slurry semi-batch reactor-based manufacturing practiced in the pharmaceutical and fine chemicals industries.

  20. Catalytic glycerol steam reforming for hydrogen production

    International Nuclear Information System (INIS)

    Dan, Monica; Mihet, Maria; Lazar, Mihaela D.

    2015-01-01

    Hydrogen production from glycerol by steam reforming combine two major advantages: (i) using glycerol as raw material add value to this by product of bio-diesel production which is obtained in large quantities around the world and have a very limited utilization now, and (ii) by implication of water molecules in the reaction the efficiency of hydrogen generation is increased as each mol of glycerol produces 7 mol of H 2 . In this work we present the results obtained in the process of steam reforming of glycerol on Ni/Al 2 O 3 . The catalyst was prepared by wet impregnation method and characterized through different methods: N 2 adsorption-desorption, XRD, TPR. The catalytic study was performed in a stainless steel tubular reactor at atmospheric pressure by varying the reaction conditions: steam/carbon ratio (1-9), gas flow (35 ml/min -133 ml/min), temperature (450-650°C). The gaseous fraction of the reaction products contain: H 2 , CH 4 , CO, CO 2 . The optimum reaction conditions as resulted from this study are: temperature 550°C, Gly:H 2 O ratio 9:1 and Ar flow 133 ml/min. In these conditions the glycerol conversion to gaseous products was 43% and the hydrogen yield was 30%

  1. Catalytic glycerol steam reforming for hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Dan, Monica, E-mail: monica.dan@itim-cj.ro; Mihet, Maria, E-mail: maria.mihet@itim-cj.ro; Lazar, Mihaela D., E-mail: diana.lazar@itim-cj.ro [National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat Street, 400293 Cluj Napoca (Romania)

    2015-12-23

    Hydrogen production from glycerol by steam reforming combine two major advantages: (i) using glycerol as raw material add value to this by product of bio-diesel production which is obtained in large quantities around the world and have a very limited utilization now, and (ii) by implication of water molecules in the reaction the efficiency of hydrogen generation is increased as each mol of glycerol produces 7 mol of H{sub 2}. In this work we present the results obtained in the process of steam reforming of glycerol on Ni/Al{sub 2}O{sub 3}. The catalyst was prepared by wet impregnation method and characterized through different methods: N{sub 2} adsorption-desorption, XRD, TPR. The catalytic study was performed in a stainless steel tubular reactor at atmospheric pressure by varying the reaction conditions: steam/carbon ratio (1-9), gas flow (35 ml/min -133 ml/min), temperature (450-650°C). The gaseous fraction of the reaction products contain: H{sub 2}, CH{sub 4}, CO, CO{sub 2}. The optimum reaction conditions as resulted from this study are: temperature 550°C, Gly:H{sub 2}O ratio 9:1 and Ar flow 133 ml/min. In these conditions the glycerol conversion to gaseous products was 43% and the hydrogen yield was 30%.

  2. Radioisotope applications on fluidized catalytic cracking units

    International Nuclear Information System (INIS)

    Charlton, J.S.

    1997-01-01

    Radioisotopes are used to trace the flow of all the phases of Fluidized Catalytic Cracking process in oil refineries. The gaseous phases, steam, hydrocarbon vapour and air, are generally traced using a noble-gas isotope, 41 Ar, 79 Kr or 85 Kr. An appropriate tracer for the catalyst is produced by irradiating a catalyst sample in a nuclear reactor. The activation products, 140 La and 24 Na provide appropriate radioactive 'labels' for the catalyst, which is reinjected into the FCC. An advantage of this approach is that it facilitates the study of the behaviour of different particle size fractions. Radioisotopes as sealed sources of gamma radiation are used to measure catalyst density variations and density distributions in critical parts of the unit. An important trend in radioisotope applications is the increasing use of the information they produce as inputs to or as validation of, mathematical process models. In line with the increasing sophistication of the models, the technology is undergoing continuous refinement. Developments include the investigation of more efficient, more convenient tracers, the introduction of systems to facilitate more rapid and comprehensive data acquisition and software refinements for enhanced data analysis

  3. Multiple isoforms for the catalytic subunit of PKA in the basal fungal lineage Mucor circinelloides.

    Science.gov (United States)

    Fernández Núñez, Lucas; Ocampo, Josefina; Gottlieb, Alexandra M; Rossi, Silvia; Moreno, Silvia

    2016-12-01

    Protein kinase A (PKA) activity is involved in dimorphism of the basal fungal lineage Mucor. From the recently sequenced genome of Mucor circinelloides we could predict ten catalytic subunits of PKA. From sequence alignment and structural prediction we conclude that the catalytic core of the isoforms is conserved, and the difference between them resides in their amino termini. This high number of isoforms is maintained in the subdivision Mucoromycotina. Each paralogue, when compared to the ones form other fungi is more homologous to one of its orthologs than to its paralogs. All of these fungal isoforms cannot be included in the class I or II in which fungal protein kinases have been classified. mRNA levels for each isoform were measured during aerobic and anaerobic growth. The expression of each isoform is differential and associated to a particular growth stage. We reanalyzed the sequence of PKAC (GI 20218944), the only cloned sequence available until now for a catalytic subunit of M. circinelloides. PKAC cannot be classified as a PKA because of its difference in the conserved C-tail; it shares with PKB a conserved C2 domain in the N-terminus. No catalytic activity could be measured for this protein nor predicted bioinformatically. It can thus be classified as a pseudokinase. Its importance can not be underestimated since it is expressed at the mRNA level in different stages of growth, and its deletion is lethal. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  4. Plasma-catalytic reforming of ethanol: influence of air activation rate and reforming temperature

    International Nuclear Information System (INIS)

    Nedybaliuk, O.A.; Chernyak, V.Ya.; Fedirchuk, I.I.; Demchina, V.P.; Bortyshevsky, V.A.; Korzh, R.V.

    2016-01-01

    This paper presents the study of the influence that air activation rate and reforming temperature have on the gaseous products composition and conversion efficiency during the plasma-catalytic reforming of ethanol. The analysis of product composition showed that the conversion efficiency of ethanol has a maximum in the studied range of reforming temperatures. Researched system provided high reforming efficiency and high hydrogen energy yield at the lower temperatures than traditional conversion technologies

  5. Microwave catalytic NOx and SO{sub 2} removal using FeCu/zeolite as catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Z.S. Wei; G.H. Zeng; Z.R. Xie; C.Y. Ma; X.H. Liu; J.L. Sun; L.H. Liu [Sun Yat-sen University, Guangzhou (China). School of Environmental Science and Engineering

    2011-04-15

    Non-thermal plasma technology is a promising process for flue gas treatment. Microwave catalytic NOx and SO{sub 2} removal simultaneously has been investigated using FeCu/zeolite as catalyst. The experimental results showed that a microwave reactor with FeCu/zeolite only could be used to microwave catalytic oxidative 91.7% NOx to nitrates and 79.6% SO{sub 2} to sulfate; the reaction efficiencies of microwave catalytic reduction of NOx and SO{sub 2} in a microwave reactor with FeCu/zeolite and ammonium bicarbonate (NH{sub 4}HCO{sub 3}) as a reducing agent could be up to 95.8% and 93.4% respectively. Microwave irradiation accentuates catalytic reduction of SO{sub 2} and NOx treatment, and microwave addition can increases SO{sub 2} removal efficiency from 14.5% to 18.7%, and NOx removal efficiency from 13.4% to 18.7%, separately. FeCu/zeolite catalyst was characterized by X-ray diffraction (XRD), X-ray photoelectron spectrum analysis (XPS), scanning electron microscopy (SEM) and the Brunauer Emmett Teller (BET) method. Microwave catalytic NOx and SO{sub 2} removal follows Langmuir-Hinshelwood (L-H) kinetics. 25 refs., 7 figs., 1 tab.

  6. VUV photo-oxidation of gaseous benzene combined with ozone-assisted catalytic oxidation: Effect on transition metal catalyst

    Science.gov (United States)

    Huang, Haibao; Lu, Haoxian; Zhan, Yujie; Liu, Gaoyuan; Feng, Qiuyu; Huang, Huiling; Wu, Muyan; Ye, Xinguo

    2017-01-01

    Volatile organic compounds (VOCs) cause the major air pollution concern. In this study, a series of ZSM-5 supported transition metals were prepared by impregnation method. They were combined with vacuum UV (VUV) photo-oxidation in a continuous-flow packed-bed reactor and used for the degradation of benzene, a typical toxic VOCs. Compared with VUV photo-oxidation alone, the introduction of catalysts can greatly enhance benzene oxidation under the help of O3, the by-products from VUV irradiation, via ozone-assisted catalytic oxidation (OZCO). The catalytic activity of transition metals towards benzene oxidation followed the order: Mn > Co > Cu > Ni > Fe. Mn achieved the best catalytic activity due to the strongest capability for O3 catalytic decomposition and utilization. Benzene and O3 removal efficiency reached as high as 97% and 100% after 360 min, respectively. O3 was catalytically decomposed, generating highly reactive oxidants such as rad OH and rad O for benzene oxidation.

  7. Extracellular RNA Communication (ExRNA)

    Data.gov (United States)

    Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...

  8. Catalytic briquettes from low-rank coal for NO reduction

    Energy Technology Data Exchange (ETDEWEB)

    A. Boyano; M.E. Galvez; R. Moliner; M.J. Lazaro [Instituto de Carboquimica, CSIC, Zaragoza (Spain)

    2007-07-01

    The briquetting is one of the most ancient and widespread techniques of coal agglomeration which is nowadays becoming useless for combustion home applications. However, the social increasing interest in environmental protection opens new applications to this technique, especially in developed countries. In this work, a series of catalytic briquettes were prepared from low-rank Spanish coal and commercial pitch by means of a pressure agglomeration method. After that, they were cured in air and doped by equilibrium impregnation with vanadium compounds. Preparation conditions (especially those of activation and oxidizing process) were changed to study their effects on catalytic behaviour. Catalytic briquettes showed a relative high NO conversion at low temperatures in all cases, however, a strong relation between the preparation process and the reached NO conversion was observed. Preparation procedure has an effect not only on the NO reduction efficiency but also on the mechanical strength of the briquettes as a consequence of the structural and chemical changes carried out during the activation and oxidation procedures. Generally speaking mechanical resistance is enhanced by an optimal porous volume and the creation of new carboxyl groups on surface. Just on the contrary, NO reduction is promoted by high microporous structures and higher amounts of surface oxygen groups. Both facts force to find an optimum point in the preparation produce which will depend on the application. 24 refs., 4 figs., 3 tabs.

  9. RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction

    Science.gov (United States)

    Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

    2014-01-01

    Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA–RNA/RNA–protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA–RNA interactions and 1619 RNA–protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA–RNA/RNA–protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA–RNA/RNA–protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. PMID:24803509

  10. Catalytic strategy used by the myosin motor to hydrolyze ATP.

    Science.gov (United States)

    Kiani, Farooq Ahmad; Fischer, Stefan

    2014-07-22

    Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum-classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO4(2-) state, but in the H2PγO4(-) state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3(-)) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.

  11. Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis.

    Directory of Open Access Journals (Sweden)

    Javad Noorbakhsh

    Full Text Available MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by prokaryotic small non-coding RNAs (sRNAs. Our model uses a combination of analytic techniques as well as computational simulations to calculate the mean-expression and noise profiles of genes regulated by both microRNAs and sRNAs. We find that despite very different molecular machinery and modes of action (catalytic vs stoichiometric, the mean expression levels and noise profiles of microRNA-regulated genes are almost identical to genes regulated by prokaryotic sRNAs. This behavior is extremely robust and persists across a wide range of biologically relevant parameters. We extend our model to study crosstalk between multiple mRNAs that are regulated by a single microRNA and show that noise is a sensitive measure of microRNA-mediated interaction between mRNAs. We conclude by discussing possible experimental strategies for uncovering the microRNA-mRNA interactions and testing the competing endogenous RNA (ceRNA hypothesis.

  12. Evaluation of catalytic combustion of actual coal-derived gas

    Science.gov (United States)

    Blanton, J. C.; Shisler, R. A.

    1982-01-01

    The combustion characteristics of a Pt-Pl catalytic reactor burning coal-derived, low-Btu gas were investigated. A large matrix of test conditions was explored involving variations in fuel/air inlet temperature and velocity, reactor pressure, and combustor exit temperature. Other data recorded included fuel gas composition, reactor temperatures, and exhaust emissions. Operating experience with the reactor was satisfactory. Combustion efficiencies were quite high (over 95 percent) over most of the operating range. Emissions of NOx were quite high (up to 500 ppm V and greater), owing to the high ammonia content of the fuel gas.

  13. Research progress on catalytic denitrification technology in chemical industry

    Science.gov (United States)

    Jin, Yezhi

    2017-12-01

    In recent years, due to the rising emission of NOx annually, attention has been aroused widely by people on more and more severe environmental problems. This paper first discusses applying NOx removal and control technologies and relating chemical principles. Of many technologies, selective reduction reaction (SCR) is the most widely used. Catalysts, the concentration of NOx at the entrance of SCR catalytic reactor, reaction temperature, NH3/NOx mole ratio and NH3 slip rate analyzed later contributes to the removal efficiency of NOx. Finally, the processing and configuration of SCR de-NOx system are briefly introduced.

  14. Low temperature catalytic combustion of natural gas - hydrogen - air mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Newson, E; Roth, F von; Hottinger, P; Truong, T B [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1999-08-01

    The low temperature catalytic combustion of natural gas - air mixtures would allow the development of no-NO{sub x} burners for heating and power applications. Using commercially available catalysts, the room temperature ignition of methane-propane-air mixtures has been shown in laboratory reactors with combustion efficiencies over 95% and maximum temperatures less than 700{sup o}C. After a 500 hour stability test, severe deactivation of both methane and propane oxidation functions was observed. In cooperation with industrial partners, scaleup to 3 kW is being investigated together with startup dynamics and catalyst stability. (author) 3 figs., 3 refs.

  15. Catalytic Wittig and aza-Wittig reactions

    Directory of Open Access Journals (Sweden)

    Zhiqi Lao

    2016-11-01

    Full Text Available This review surveys the literature regarding the development of catalytic versions of the Wittig and aza-Wittig reactions. The first section summarizes how arsenic and tellurium-based catalytic Wittig-type reaction systems were developed first due to the relatively easy reduction of the oxides involved. This is followed by a presentation of the current state of the art regarding phosphine-catalyzed Wittig reactions. The second section covers the field of related catalytic aza-Wittig reactions that are catalyzed by both phosphine oxides and phosphines.

  16. Catalytic models developed through social work

    DEFF Research Database (Denmark)

    Jensen, Mogens

    2015-01-01

    of adolescents placed in out-of-home care and is characterised using three situated cases as empirical data. Afterwards the concept of catalytic processes is briefly presented and then applied in an analysis of pedagogical treatment in the three cases. The result is a different conceptualisation of the social......The article develops the concept of catalytic processes in relation to social work with adolescents in an attempt to both reach a more nuanced understanding of social work and at the same time to develop the concept of catalytic processes in psychology. The social work is pedagogical treatment...

  17. A new approach to inertise the containments during catalytic removal of hydrogen

    International Nuclear Information System (INIS)

    Chakraborty, A.K.; Markandeya, S.G.

    1994-01-01

    Use of catalytic recombiners for the removal of hydrogen during a severe accident has been recommended by the German Reactor Safety Commission (RSK) due to numerous successful demonstrations of their performances. At the early stages of the accident, a huge quantity of hydrogen is expected to be released in some compartments requiring supplementary measures to ensure that the excess hydrogen concentration wouldn't pose a threat of deflagration /1/. In this presentation a new idea based on catalytic removal of hydrogen with simultaneous passive inertisation of the atmosphere is proposed for large dry containments particularly for those compartments where high H 2 -concentrations are expected. During the catalytic oxidation of hydrogen, the large exothermic heat of reaction causes strong heating of the catalytic plates as well as a continuous energy input in the containment. This can be limited if this large heat energy is efficiently used for heating some chemical compounds to release inert gases such as steam and/or CO 2 by dissociation at moderate temperatures. Such compounds can be arranged in the form of thin slabs in good thermal contact with the catalytic plates. Several such compounds have been identified which are capable of releasing steam and CO 2 equivalent to about 40 - 75% of their mass. Preliminary calculations have been carded out to demonstrate the effectiveness of the proposed concept for the case of two such selected chemicals placed adjacent to the catalytic plate type recombiners. The calculations performed show promising results. (author)

  18. Optimization of the catalytic converter internal flow by using 3D-CFD; Sanjigen nagare kaiseki ni yoru shokubai converter nai nagare no saitekika

    Energy Technology Data Exchange (ETDEWEB)

    Toi, M; Sugiura, S [Toyota Motor Corp., Tokyo (Japan)

    1997-10-01

    By using computational fluid dynamics and statistical quality control method, we investigated the contribution of front and rear catalytic converter cone shape for the pressure loss and the partial flow, also led the optimal terms and the predictional formulations efficiently. According to this, we can investigate the optimal position of the catalytic converter from the planning. 8 figs., 6 tabs.

  19. Vacuum-insulated catalytic converter

    Science.gov (United States)

    Benson, David K.

    2001-01-01

    A catalytic converter has an inner canister that contains catalyst-coated substrates and an outer canister that encloses an annular, variable vacuum insulation chamber surrounding the inner canister. An annular tank containing phase-change material for heat storage and release is positioned in the variable vacuum insulation chamber a distance spaced part from the inner canister. A reversible hydrogen getter in the variable vacuum insulation chamber, preferably on a surface of the heat storage tank, releases hydrogen into the variable vacuum insulation chamber to conduct heat when the phase-change material is hot and absorbs the hydrogen to limit heat transfer to radiation when the phase-change material is cool. A porous zeolite trap in the inner canister absorbs and retains hydrocarbons from the exhaust gases when the catalyst-coated substrates and zeolite trap are cold and releases the hydrocarbons for reaction on the catalyst-coated substrate when the zeolite trap and catalyst-coated substrate get hot.

  20. Catalytic hydrotreatment of refinery waste

    Energy Technology Data Exchange (ETDEWEB)

    1989-01-01

    The object of the project is to produce liquid hydrocarbons by the catalytic hydroprocessing of solid refinery wastes (hard pitches) in order to improve the profitability of deep conversion processes and reduce the excess production of heavy fuels. The project was mostly carried out on the ASVAHL demonstration platform site, at Solaize, and hard pitches were produced primarily by deasphalting of atmospheric or vacuum distillation residues. The project includes two experimental phases and an economic evaluation study phase. In phase 1, two granular catalysts were used to transform pitch into standard low sulphur fuel oil: a continuously moving bed, with demetallation and conversion catalyst; a fixed bed, with hydrorefining catalyst. In phase 2 of the project, it was proven that a hydrotreatment process using a finely dispersed catalyst in the feedstock, can, under realistic operating conditions, transform with goods yields hard pitch into distillates that can be refined through standard methods. In phase 3 of the project, it was shown that the economics of such processes are tightly linked to the price differential between white and black oil products, which is expected to increase in the future. Furthermore, the evolution of environmental constraints will impel the use of such methods, thus avoiding the coproduction of polluting solid residues.

  1. Free-standing hierarchical α-MnO2@CuO membrane for catalytic filtration degradation of organic pollutants.

    Science.gov (United States)

    Luo, Xinsheng; Liang, Heng; Qu, Fangshu; Ding, An; Cheng, Xiaoxiang; Tang, Chuyang Y; Li, Guibai

    2018-06-01

    Catalytic membrane, due to its compact reactor assembling, high catalytic performance as well as low energy consumption, has proved to be more attractive for wastewater treatment. In this work, a free-standing α-MnO 2 @CuO membrane with hierarchical nanostructures was prepared and evaluated as the catalytic membrane to generate radicals from peroxymonosulfate (PMS) for the oxidative degradation of organic dyes in aqueous solution. Benefiting from the high mass transport efficiency and the hierarchical nanostructures, a superior catalytic activity of the membrane was observed for organic dyes degradation. As a typical organic dye, more than 99% of methylene blue (MB) was degraded within 0.23 s using dead-end filtration cell. The effects of flow rate, PMS concentration and buffer solution on MB degradation were further investigated. Besides MB, the catalytic membrane also showed excellent performance for the removal of other dyes, such as congo red, methyl orange, rhodamine B, acid chrome blue K and malachite green. Moreover, the mechanism study indicated that OH and SO 4 - generated from the interaction between PMS and Mn/Cu species with different oxidation states mainly accounted for the dyes degradation. The catalytic filtration process using α-MnO 2 @CuO catalytic membrane could provide a novel method for wastewater purification with high efficiency and low energy consumption. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Fuel cell research: Towards efficient energy

    CSIR Research Space (South Africa)

    Rohwer, MB

    2008-11-01

    Full Text Available fuel cells by optimising the loading of catalyst (being expensive noble metals) and ionomer; 2) Improving conventional acidic direct alcohol fuel cells by developing more efficient catalysts and by investigating other fuels than methanol; 3... these components add significantly to the overall cost of a PEMFC. 1 We focused our research activities on: 1) The effect of the loading of catalytic ink on cell performance; 2) The effect of the ionomer content in the catalytic ink; 3) Testing...

  3. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D......, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

  4. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    International Nuclear Information System (INIS)

    Cheng, Xiaofei; Deng, Ping; Cui, Hongguang; Wang, Aiming

    2015-01-01

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  5. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: aiming.wang@agr.gc.ca [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)

    2015-11-15

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  6. Chemistry and engineering of catalytic hydrodesulfurization

    NARCIS (Netherlands)

    Schuit, G.C.A.; Gates, B.C.

    1973-01-01

    A review with 74 refs. on catalytic hydrodesulfurization of pure compds. and petroleum feedstocks, with emphasis on reaction intermediates and structures of Al2O3-supported Ni-W and Co-Mo catalysts. [on SciFinder (R)

  7. RNA Thermodynamic Structural Entropy.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

    Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  8. RNA Thermodynamic Structural Entropy.

    Directory of Open Access Journals (Sweden)

    Juan Antonio Garcia-Martin

    Full Text Available Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs. However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  9. Catalytic Aminohalogenation of Alkenes and Alkynes.

    Science.gov (United States)

    Chemler, Sherry R; Bovino, Michael T

    2013-06-07

    Catalytic aminohalogenation methods enable the regio- and stereoselective vicinal difunctionalization of alkynes, allenes and alkenes with amine and halogen moieties. A range of protocols and reaction mechanisms including organometallic, Lewis base, Lewis acid and Brønsted acid catalysis have been disclosed, enabling the regio- and stereoselective synthesis of halogen-functionalized acyclic amines and nitrogen heterocycles. Recent advances including aminofluorination and catalytic enantioselective aminohalogenation reactions are summarized in this review.

  10. Kinetic catalytic studies of scorpion's hemocyanin

    International Nuclear Information System (INIS)

    Queinnec, E.; Vuillaume, M.; Gardes-Albert, M.; Ferradini, C.; Ducancel, F.

    1991-01-01

    Hemocyanins are copper proteins which function as oxygen carriers in the haemolymph of Molluscs and Arthropods. They possess enzymatic properties: peroxidatic and catalatic activities, although they have neither iron nor porphyrin ring at the active site. The kinetics of the catalytic reaction is described. The reaction of superoxide anion with hemocyanin has been studied using pulse radiolysis at pH 9. The catalytic rate constant is 3.5 X 10 7 mol -1 .l.s -1 [fr

  11. Methylated nucleosides in tRNA and tRNA methyltransferases

    Directory of Open Access Journals (Sweden)

    Hiroyuki eHori

    2014-05-01

    Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

  12. Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    Science.gov (United States)

    Martos, Laura; Fernández-Pardo, Álvaro; Oto, Julia; Medina, Pilar; España, Francisco; Navarro, Silvia

    2017-01-01

    microRNAs are promising biomarkers in biological fluids in several diseases. Different plasma RNA isolation protocols and carriers are available, but their efficiencies have been scarcely compared. Plasma microRNAs were isolated using a phenol and column-based procedure and a column-based procedure, in the presence or absence of two RNA carriers (yeast RNA and MS2 RNA). We evaluated the presence of PCR inhibitors and the relative abundance of certain microRNAs by qRT-PCR. Furthermore, we analyzed the association between different isolation protocols, the relative abundance of the miRNAs in the sample, the GC content and the free energy of microRNAs. In all microRNAs analyzed, the addition of yeast RNA as a carrier in the different isolation protocols used gave lower raw Cq values, indicating higher microRNA recovery. Moreover, this increase in microRNAs recovery was dependent on their own relative abundance in the sample, their GC content and the free-energy of their own most stable secondary structure. Furthermore, the normalization of microRNA levels by an endogenous microRNA is more reliable than the normalization by plasma volume, as it reduced the difference in microRNA fold abundance between the different isolation protocols evaluated. Our thorough study indicates that a standardization of pre- and analytical conditions is necessary to obtain reproducible inter-laboratory results in plasma microRNA studies. PMID:29077772

  13. Biodiesel production through non-catalytic supercritical transesterification: current state and perspectives

    OpenAIRE

    Silva, C. da; Oliveira, J. Vladimir

    2014-01-01

    The inconveniences of the conventional method for biodiesel production by alkaline catalysis suggests research towards alternative methods, with the non-catalytic transesterification using an alcohol at supercritical conditions proposed as a promising technique for biodiesel production. The so-called supercritical method (SCM) has powerful advantages over conventional techniques, such as fast reaction rates, feedstock flexibility, production efficiency and environmentally friendly benefits. H...

  14. SNCR technology for NO sub x reduction in the cement industry. [Selective non-catalytic reduction

    Energy Technology Data Exchange (ETDEWEB)

    Kupper, D; Brentrup, L [Krupp Polysius AG, Beckum (Germany)

    1992-03-01

    This article discusses the selective non-catalytic (SNCR) process for reducing nitrogen oxides in exhaust gases from cement plants. Topics covered include operating experience, injection of additives, selection of the additive, operating costs, reduction efficiency of SNCR, capital expenditure, secondary emissions and cycles of ammonium. (UK).

  15. Nano-Fe 3 O 4 /O 2 : Green, Magnetic and Reusable Catalytic ...

    African Journals Online (AJOL)

    , efficient, heterogeneous and reusable catalytic system for the synthesis of benzimidazoles via the reactions of o-phenylenediamine (1 eq) with aryl aldehydes (1 eq) in excellentyields (85–97 %) and short reaction times (30–100 min) with a ...

  16. Oxidative cracking of n-hexane: a catalytic pathway to olefins

    NARCIS (Netherlands)

    Boyadjian, C.A.

    2010-01-01

    Steam cracking, the major, current existing route for light olefin production, is the most energy consuming process in the chemical industry. The need for an energy efficient processes, urged substantial research work for the development of new catalytic technologies for light olefin production.

  17. Development of advanced mesostructured catalytic coatings on different substrates for fine chemical synthesis

    NARCIS (Netherlands)

    Protasova, L.N.

    2011-01-01

    Catalytic microstructured reactors are becoming widely recognized for their unique properties, such as high surface–to–volume ratios, isothermal conditions due to high heat transfer rates, enhanced safety, and potential applications in chemistry and in chemical industry. The efficient use of

  18. Development of catalytic microreactors by plasma processes: application to wastewater treatment

    NARCIS (Netherlands)

    Da Silva, B.T.

    2015-01-01

    A key aspect in overcoming the energy and environmental challenges is to improve the efficiency of existing and new processes. Nowadays, almost all major chemicals are produced by catalytic processes. However, a better understanding of the reaction pathways and kinetics is needed. In the field of

  19. Catalytic Enantioselective Synthesis of Naturally Occurring Butenolides via Hetero-Allylic Alkylation and Ring Closing Metathesis

    NARCIS (Netherlands)

    Mao, Bin; Geurts, Koen; Fañanás-Mastral, Martín; Zijl, Anthoni W. van; Fletcher, Stephen P.; Minnaard, Adriaan J.; Feringa, Bernard

    2011-01-01

    An efficient catalytic asymmetric synthesis of chiral γ-butenolides was developed based on the hetero-allylic asymmetric alkylation (h-AAA) in combination with ring closing metathesis (RCM). The synthetic potential of the h-AAA-RCM protocol was illustrated with the facile synthesis of (-)-whiskey

  20. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway.

    Science.gov (United States)

    Saito, Yuichiro; Takeda, Jun; Adachi, Kousuke; Nobe, Yuko; Kobayashi, Junya; Hirota, Kouji; Oliveira, Douglas V; Taoka, Masato; Isobe, Toshiaki

    2014-01-01

    Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNA(Ser-Met). To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNA(Ser-Met), suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry-based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute "Domain 1" in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.

  1. Recoding aminoacyl-tRNA synthetases for synthetic biology by rational protein-RNA engineering.

    Science.gov (United States)

    Hadd, Andrew; Perona, John J

    2014-12-19

    We have taken a rational approach to redesigning the amino acid binding and aminoacyl-tRNA pairing specificities of bacterial glutaminyl-tRNA synthetase. The four-stage engineering incorporates generalizable design principles and improves the pairing efficiency of noncognate glutamate with tRNA(Gln) by over 10(5)-fold compared to the wild-type enzyme. Better optimized designs of the protein-RNA complex include substantial reengineering of the globular core region of the tRNA, demonstrating a role for specific tRNA nucleotides in specifying the identity of the genetically encoded amino acid. Principles emerging from this engineering effort open new prospects for combining rational and genetic selection approaches to design novel aminoacyl-tRNA synthetases that ligate noncanonical amino acids onto tRNAs. This will facilitate reconstruction of the cellular translation apparatus for applications in synthetic biology.

  2. Solar photo catalytic treatment of simulated dyestuff effluents

    Energy Technology Data Exchange (ETDEWEB)

    Kositzi, M.; Antoniadis, A.; Poulios, I.; Kiridies, I.; Malato, S.

    2003-07-01

    The photo catalytic organic content reduction of two selected synthetic wastewater from the textile dyeing industry, by the use heterogeneous and homogeneous photo catalytic methods under solar irradiation, has been studied at a pilot plant scale at the Plataforma Solar de Almeria. the effect of two different TiO{sub 2} modifications with oxidants such as H{sub 2}O{sub 2} and Na{sub 2}S{sub 2}O{sub 8}, on the decolorisation and the organic content reduction (DOC) of the wastewater was examined. the TiO{sub 2}/H{sub 2}O{sub 2} system seems to be more efficient in comparison to the synergetic action which appears when using persulfate and TiO{sub 2} in these specific wastewaters. By an accumulation energy of 50 KJ L''-1 the synergetic effect of TiO{sub 2} P-25 with H{sub 2}O{sub 2} and Na{sub 2}S{sub 2}O{sub 8} leads to a 70% and 57% DOC reduction, respectively, in the case of cotton synthetic wastewater, while the decolorisation was almost complete. The photo catalytic decolorisation, as well as the DOC reduction in the case of naylon simulated wastewater is a slower process and by an accumulation energy of 50 KJ L''-1 leads to 54% mineralization in both cases. The Photo-Fenton process in both cases was more efficient for this type of wastewater in comparison to the TiO{sub 2}/oxidant system. An accumulation of energy of 50 KJ L''-1 leads to 90% reduction of the organic content. (Author) 13 refs.

  3. Pathways of cellular internalisation of liposomes delivered siRNA and effects on siRNA engagement with target mRNA and silencing in cancer cells.

    Science.gov (United States)

    Alshehri, Abdullah; Grabowska, Anna; Stolnik, Snow

    2018-02-28

    Design of an efficient delivery system is a generally recognised bottleneck in translation of siRNA technology into clinic. Despite research efforts, cellular processes that determine efficiency of siRNA silencing achieved by different delivery formulations remain unclear. Here, we investigated the mechanism(s) of cellular internalisation of a model siRNA-loaded liposome system in a correlation to the engagement of delivered siRNA with its target and consequent silencing by adopting siRNA molecular beacon technology. Probing of cellular internalisation pathways by a panel of pharmacological inhibitors indicated that clathrin-mediated (dynamin-dependent) endocytosis, macropinocytosis (dynamine independent), and cell membrane cholesterol dependent process(es) (clathrin and caveolea-independent) all play a role in the siRNA-liposomes internalization. The inhibition of either of these entry routes was, in general, mirrored by a reduction in the level of siRNA engagement with its target mRNA, as well as in a reduction of the target gene silencing. A dramatic increase in siRNA engagement with its target RNA was observed on disruption of endosomal membrane (by chloroquine), accompanied with an increased silencing. The work thus illustrates that employing molecular beacon siRNA technology one can start to assess the target RNA engagement - a stage between initial cellular internalization and final gene silencing of siRNA delivery systems.

  4. Catalytic hydrogenation of carbon monoxide

    Energy Technology Data Exchange (ETDEWEB)

    Wayland, B.B.

    1992-12-01

    This project is focused on developing strategies to accomplish the reduction and hydrogenation of carbon monoxide to produce organic oxygenates at mild conditions. Our approaches to this issue are based on the recognition that rhodium macrocycles have unusually favorable thermodynamic values for producing a series of intermediate implicated in the catalytic hydrogenation of CO. Observations of metalloformyl complexes produced by reactions of H{sub 2} and CO, and reductive coupling of CO to form metallo {alpha}-diketone species have suggested a multiplicity of routes to organic oxygenates that utilize these species as intermediates. Thermodynamic and kinetic-mechanistic studies are used in constructing energy profiles for a variety of potential pathways, and these schemes are used in guiding the design of new metallospecies to improve the thermodynamic and kinetic factors for individual steps in the overall process. Variation of the electronic and steric effects associated with the ligand arrays along with the influences of the reaction medium provide the chemical tools for tuning these factors. Emerging knowledge of the factors that contribute to M-H, M-C and M-O bond enthalpies is directing the search for ligand arrays that will expand the range of metal species that have favorable thermodynamic parameters to produce the primary intermediates for CO hydrogenation. Studies of rhodium complexes are being extended to non-macrocyclic ligand complexes that emulate the favorable thermodynamic features associated with rhodium macrocycles, but that also manifest improved reaction kinetics. Multifunctional catalyst systems designed to couple the ability of rhodium complexes to produce formyl and diketone intermediates with a second catalyst that hydrogenates these imtermediates are promising approaches to accomplish CO hydrogenation at mild conditions.

  5. Characterization of the catalytic center of the Ebola virus L polymerase.

    Science.gov (United States)

    Schmidt, Marie Luisa; Hoenen, Thomas

    2017-10-01

    Ebola virus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates. While no licensed therapeutics are available, recently there has been tremendous progress in developing antivirals. Targeting the ribonucleoprotein complex (RNP) proteins, which facilitate genome replication and transcription, and particularly the polymerase L, is a promising antiviral approach since these processes are essential for the virus life cycle. However, until now little is known about L in terms of its structure and function, and in particular the catalytic center of the RNA-dependent RNA polymerase (RdRp) of L, which is one of the most promising molecular targets, has never been experimentally characterized. Using multiple sequence alignments with other negative sense single-stranded RNA viruses we identified the putative catalytic center of the EBOV RdRp. An L protein with mutations in this center was then generated and characterized using various life cycle modelling systems. These systems are based on minigenomes, i.e. miniature versions of the viral genome, in which the viral genes are exchanged against a reporter gene. When such minigenomes are coexpressed with RNP proteins in mammalian cells, the RNP proteins recognize them as authentic templates for replication and transcription, resulting in reporter activity reflecting these processes. Replication-competent minigenome systems indicated that our L catalytic domain mutant was impaired in genome replication and/or transcription, and by using replication-deficient minigenome systems, as well as a novel RT-qPCR-based genome replication assay, we showed that it indeed no longer supported either of these processes. However, it still showed similar expression to wild-type L, and retained its ability to be incorporated into inclusion bodies, which are the sites of EBOV genome replication. We have experimentally defined the catalytic center of the EBOV RdRp, and thus a promising antiviral target regulating an essential

  6. Characterization of the catalytic center of the Ebola virus L polymerase.

    Directory of Open Access Journals (Sweden)

    Marie Luisa Schmidt

    2017-10-01

    Full Text Available Ebola virus (EBOV causes a severe hemorrhagic fever in humans and non-human primates. While no licensed therapeutics are available, recently there has been tremendous progress in developing antivirals. Targeting the ribonucleoprotein complex (RNP proteins, which facilitate genome replication and transcription, and particularly the polymerase L, is a promising antiviral approach since these processes are essential for the virus life cycle. However, until now little is known about L in terms of its structure and function, and in particular the catalytic center of the RNA-dependent RNA polymerase (RdRp of L, which is one of the most promising molecular targets, has never been experimentally characterized.Using multiple sequence alignments with other negative sense single-stranded RNA viruses we identified the putative catalytic center of the EBOV RdRp. An L protein with mutations in this center was then generated and characterized using various life cycle modelling systems. These systems are based on minigenomes, i.e. miniature versions of the viral genome, in which the viral genes are exchanged against a reporter gene. When such minigenomes are coexpressed with RNP proteins in mammalian cells, the RNP proteins recognize them as authentic templates for replication and transcription, resulting in reporter activity reflecting these processes. Replication-competent minigenome systems indicated that our L catalytic domain mutant was impaired in genome replication and/or transcription, and by using replication-deficient minigenome systems, as well as a novel RT-qPCR-based genome replication assay, we showed that it indeed no longer supported either of these processes. However, it still showed similar expression to wild-type L, and retained its ability to be incorporated into inclusion bodies, which are the sites of EBOV genome replication.We have experimentally defined the catalytic center of the EBOV RdRp, and thus a promising antiviral target

  7. Catalytic partial oxidation of pyrolysis oils

    Science.gov (United States)

    Rennard, David Carl

    2009-12-01

    details the catalytic partial oxidation of glycerol without preheat: droplets of glycerol are sprayed directly onto the top of the catalyst bed, where they react autothermally with contact times on the order of tau ≈ 30 ms. The reactive flash volatilization of glycerol results in equilibrium syngas production over Rh-Ce catalysts. In addition, water can be added to the liquid glycerol, resulting in true autothermal reforming. This highly efficient process can increase H2 yields and alter the H2 to CO ratio, allowing for flexibility in syngas quality depending on the purpose. Chapter 5 details the results of a time on stream experiment, in which optimal syngas conditions are chosen. Although conversion is 100% for 450 hours, these experiments demonstrate the deactivation of the catalyst over time. Deactivation is exhibited by decreases in H2 and CO 2 production accompanied by a steady increase in CO and temperature. These results are explained as a loss of water-gas shift equilibration. SEM images suggest catalyst sintering may play a role; EDS indicates the presence of impurities on the catalyst. In addition, the instability of quartz in the reactor is demonstrated by etching, resulting in a hole in the reactor tube at the end of the experiment. These results suggest prevaporization may be desirable in this application, and that quartz is not a suitable material for the reactive flash volatilization of oxygenated fuels. In Chapter 6, pyrolysis oil samples from three sources - poplar, pine, and hardwoods - are explored in the context of catalytic partial oxidation. Lessons derived from the tests with model compounds are applied to reactor design, resulting in the reactive flash vaporization of bio oils. Syngas is successfully produced, though deactivation due to coke and ash deposition keeps H2 below equlibrium. Coke formation is observed on the reactor walls, but is avoided between the fuel injection site and catalyst by increasing the proximity of these in the reactor

  8. Adsorbent catalytic nanoparticles and methods of using the same

    Energy Technology Data Exchange (ETDEWEB)

    Slowing, Igor Ivan; Kandel, Kapil

    2017-01-31

    The present invention provides an adsorbent catalytic nanoparticle including a mesoporous silica nanoparticle having at least one adsorbent functional group bound thereto. The adsorbent catalytic nanoparticle also includes at least one catalytic material. In various embodiments, the present invention provides methods of using and making the adsorbent catalytic nanoparticles. In some examples, the adsorbent catalytic nanoparticles can be used to selectively remove fatty acids from feedstocks for biodiesel, and to hydrotreat the separated fatty acids.

  9. siRNA delivery with lipid-based systems

    DEFF Research Database (Denmark)

    Foged, Camilla

    2012-01-01

    A key hurdle for the further development of RNA interference (RNAi) therapeutics like small interfering RNA (siRNA) is their safe and effective delivery. Lipids are promising and versatile carriers because they are based on Nature's own building blocks and can be provided with properties which......RNA into more hydrophobic lipoplexes, which promote passage of the siRNA across cellular membrane barriers, especially when lipids are added that facilitate membrane fusion. Despite these attractive features, siRNA delivery vehicles are facing a number of challenges such as the limited delivery efficiency...

  10. Functional tuning of the catalytic residue pKa in a de novo designed esterase.

    Science.gov (United States)

    Hiebler, Katharina; Lengyel, Zsófia; Castañeda, Carlos A; Makhlynets, Olga V

    2017-09-01

    AlleyCatE is a de novo designed esterase that can be allosterically regulated by calcium ions. This artificial enzyme has been shown to hydrolyze p-nitrophenyl acetate (pNPA) and 4-nitrophenyl-(2-phenyl)-propanoate (pNPP) with high catalytic efficiency. AlleyCatE was created by introducing a single-histidine residue (His 144 ) into a hydrophobic pocket of calmodulin. In this work, we explore the determinants of catalytic properties of AlleyCatE. We obtained the pK a value of the catalytic histidine using experimental measurements by NMR and pH rate profile and compared these values to those predicted from electrostatics pK a calculations (from both empirical and continuum electrostatics calculations). Surprisingly, the pK a value of the catalytic histidine inside the hydrophobic pocket of calmodulin is elevated as compared to the model compound pK a value of this residue in water. We determined that a short-range favorable interaction with Glu 127 contributes to the elevated pK a of His 144 . We have rationally modulated local electrostatic potential in AlleyCatE to decrease the pK a of its active nucleophile, His 144 , by 0.7 units. As a direct result of the decrease in the His 144 pK a value, catalytic efficiency of the enzyme increased by 45% at pH 6. This work shows that a series of simple NMR experiments that can be performed using low field spectrometers, combined with straightforward computational analysis, provide rapid and accurate guidance to rationally improve catalytic efficiency of histidine-promoted catalysis. Proteins 2017; 85:1656-1665. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  11. Degradation of paracetamol by catalytic wet air oxidation and sequential adsorption - Catalytic wet air oxidation on activated carbons

    Energy Technology Data Exchange (ETDEWEB)

    Quesada-Penate, I. [Universite de Toulouse, INPT, UPS, Laboratoire de Genie Chimique, 4, Allee Emile Monso, F-31432 Toulouse (France); CNRS, Laboratoire de Genie Chimique, F-31432 Toulouse (France); Julcour-Lebigue, C., E-mail: carine.julcour@ensiacet.fr [Universite de Toulouse, INPT, UPS, Laboratoire de Genie Chimique, 4, Allee Emile Monso, F-31432 Toulouse (France); CNRS, Laboratoire de Genie Chimique, F-31432 Toulouse (France); Jauregui-Haza, U. J. [Instituto Superior de Tecnologias y Ciencias Aplicadas, Ave. Salvador Allende y Luaces, Habana (Cuba); Wilhelm, A. M.; Delmas, H. [Universite de Toulouse, INPT, UPS, Laboratoire de Genie Chimique, 4, Allee Emile Monso, F-31432 Toulouse (France); CNRS, Laboratoire de Genie Chimique, F-31432 Toulouse (France)

    2012-06-30

    Highlights: Black-Right-Pointing-Pointer Three activated carbons (AC) compared as adsorbents and oxidation catalysts. Black-Right-Pointing-Pointer Similar evolution for catalytic and adsorptive properties of AC over reuses. Black-Right-Pointing-Pointer Acidic and mesoporous AC to be preferred, despite lower initial efficiency. Black-Right-Pointing-Pointer Oxidative degradation of paracetamol improves biodegradability. Black-Right-Pointing-Pointer Convenient hybrid adsorption-regenerative oxidation process for continuous treatment. - Abstract: The concern about the fate of pharmaceutical products has raised owing to the increasing contamination of rivers, lakes and groundwater. The aim of this paper is to evaluate two different processes for paracetamol removal. The catalytic wet air oxidation (CWAO) of paracetamol on activated carbon was investigated both as a water treatment technique using an autoclave reactor and as a regenerative treatment of the carbon after adsorption in a sequential fixed bed process. Three activated carbons (ACs) from different source materials were used as catalysts: two microporous basic ACs (S23 and C1) and a meso- and micro-porous acidic one (L27). During the first CWAO experiment the adsorption capacity and catalytic performance of fresh S23 and C1 were higher than those of fresh L27 despite its higher surface area. This situation changed after AC reuse, as finally L27 gave the best results after five CWAO cycles. Respirometry tests with activated sludge revealed that in the studied conditions the use of CWAO enhanced the aerobic biodegradability of the effluent. In the ADOX process L27 also showed better oxidation performances and regeneration efficiency. This different ageing was examined through AC physico-chemical properties.

  12. Degradation of paracetamol by catalytic wet air oxidation and sequential adsorption – Catalytic wet air oxidation on activated carbons

    International Nuclear Information System (INIS)

    Quesada-Peñate, I.; Julcour-Lebigue, C.; Jáuregui-Haza, U.J.; Wilhelm, A.M.; Delmas, H.

    2012-01-01

    Highlights: ► Three activated carbons (AC) compared as adsorbents and oxidation catalysts. ► Similar evolution for catalytic and adsorptive properties of AC over reuses. ► Acidic and mesoporous AC to be preferred, despite lower initial efficiency. ► Oxidative degradation of paracetamol improves biodegradability. ► Convenient hybrid adsorption–regenerative oxidation process for continuous treatment. - Abstract: The concern about the fate of pharmaceutical products has raised owing to the increasing contamination of rivers, lakes and groundwater. The aim of this paper is to evaluate two different processes for paracetamol removal. The catalytic wet air oxidation (CWAO) of paracetamol on activated carbon was investigated both as a water treatment technique using an autoclave reactor and as a regenerative treatment of the carbon after adsorption in a sequential fixed bed process. Three activated carbons (ACs) from different source materials were used as catalysts: two microporous basic ACs (S23 and C1) and a meso- and micro-porous acidic one (L27). During the first CWAO experiment the adsorption capacity and catalytic performance of fresh S23 and C1 were higher than those of fresh L27 despite its higher surface area. This situation changed after AC reuse, as finally L27 gave the best results after five CWAO cycles. Respirometry tests with activated sludge revealed that in the studied conditions the use of CWAO enhanced the aerobic biodegradability of the effluent. In the ADOX process L27 also showed better oxidation performances and regeneration efficiency. This different ageing was examined through AC physico-chemical properties.

  13. Combinatorics of RNA-RNA interaction

    DEFF Research Database (Denmark)

    Li, Thomas J X; Reidys, Christian

    2012-01-01

    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

  14. rRNA fragmentation induced by a yeast killer toxin.

    Science.gov (United States)

    Kast, Alene; Klassen, Roland; Meinhardt, Friedhelm

    2014-02-01

    Virus like dsDNA elements (VLE) in yeast were previously shown to encode the killer toxins PaT and zymocin, which target distinct tRNA species via specific anticodon nuclease (ACNase) activities. Here, we characterize a third member of the VLE-encoded toxins, PiT from Pichia inositovora, and identify PiOrf4 as the cytotoxic subunit by conditional expression in Saccharomyces cerevisiae. In contrast to the tRNA targeting toxins, however, neither a change of the wobble uridine modification status by introduction of elp3 or trm9 mutations nor tRNA overexpression rescued from PiOrf4 toxicity. Consistent with a distinct RNA target, expression of PiOrf4 causes specific fragmentation of the 25S and 18S rRNA. A stable cleavage product comprising the first ∼ 130 nucleotides of the 18S rRNA was purified and characterized by linker ligation and subsequent reverse transcription; 3'-termini were mapped to nucleotide 131 and 132 of the 18S rRNA sequence, a region showing some similarity to the anticodon loop of tRNA(Glu)(UUC), the zymocin target. PiOrf4 residues Glu9 and His214, corresponding to catalytic sites Glu9 and His209 in the ACNase subunit of zymocin are essential for in vivo toxicity and rRNA fragmentation, raising the possibility of functionally conserved RNase modules in both proteins. © 2013 John Wiley & Sons Ltd.

  15. Contributions to the theory of catalytic titrations-III Neutralization catalytic titrations.

    Science.gov (United States)

    Gaál, F F; Abramović, B F

    1985-07-01

    Neutralization catalytic titrations of weak monoprotic adds and bases with both volumetric and coulometric addition of the titrant (strong base/acid) have been simulated by taking into account the equilibrium concentration of the catalyst during the titration. The influence of several factors on the shape of the simulated catalytic titration curve has been investigated and is discussed.

  16. Cyclophilin B stimulates RNA synthesis by the HCV RNA dependent RNA polymerase.

    Science.gov (United States)

    Heck, Julie A; Meng, Xiao; Frick, David N

    2009-04-01

    Cyclophilins are cellular peptidyl isomerases that have been implicated in regulating hepatitis C virus (HCV) replication. Cyclophilin B (CypB) is a target of cyclosporin A (CsA), an immunosuppressive drug recently shown to suppress HCV replication in cell culture. Watashi et al. recently demonstrated that CypB is important for efficient HCV replication, and proposed that it mediates the anti-HCV effects of CsA through an interaction with NS5B [Watashi K, Ishii N, Hijikata M, Inoue D, Murata T, Miyanari Y, et al. Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase. Mol Cell 2005;19:111-22]. We examined the effects of purified CypB proteins on the enzymatic activity of NS5B. Recombinant CypB purified from insect cells directly stimulated NS5B-catalyzed RNA synthesis. CypB increased RNA synthesis by NS5B derived from genotype 1a, 1b, and 2a HCV strains. Stimulation appears to arise from an increase in productive RNA binding. NS5B residue Pro540, a previously proposed target of CypB peptidyl-prolyl isomerase activity, is not required for stimulation of RNA synthesis.

  17. Plasma catalytic reforming of methane

    Energy Technology Data Exchange (ETDEWEB)

    Bromberg, L.; Cohn, D.R.; Rabinovich, A. [Massachusetts Inst. of Technology, Cambridge, MA (United States). Plasma Science and Fusion Center; Alexeev, N. [Russian Academy of Sciences, Moscow (Russian Federation). Baikov Inst. of Metallurgy

    1998-08-01

    Thermal plasma technology can be efficiently used in the production of hydrogen and hydrogen-rich gases from methane and a variety of fuels. This paper describes progress in plasma reforming experiments and calculations of high temperature conversion of methane using heterogeneous processes. The thermal plasma is a highly energetic state of matter that is characterized by extremely high temperatures (several thousand degrees Celsius) and high degree of dissociation and substantial degree of ionization. The high temperatures accelerate the reactions involved in the reforming process. Hydrogen-rich gas (50% H{sub 2}, 17% CO and 33% N{sub 2}, for partial oxidation/water shifting) can be efficiently made in compact plasma reformers. Experiments have been carried out in a small device (2--3 kW) and without the use of efficient heat regeneration. For partial oxidation/water shifting, it was determined that the specific energy consumption in the plasma reforming processes is 16 MJ/kg H{sub 2} with high conversion efficiencies. Larger plasmatrons, better reactor thermal insulation, efficient heat regeneration and improved plasma catalysis could also play a major role in specific energy consumption reduction and increasing the methane conversion. A system has been demonstrated for hydrogen production with low CO content ({approximately} 1.5%) with power densities of {approximately} 30 kW (H{sub 2} HHV)/liter of reactor, or {approximately} 10 m{sup 3}/hr H{sub 2} per liter of reactor. Power density should further increase with increased power and improved design.

  18. IN SITU DESTRUCTION OF CHLORINATED HYDROCARBON COMPOUNDS IN GROUNDWATER USING CATALYTIC REDUCTIVE REDUCTIVE DEHALOGENATION IN A REACTIVE WELL: TESTING AND OPERATIONAL EXPERIENCES. (R825421)

    Science.gov (United States)

    A groundwater treatment technology based on catalytic reductive dehalogenation has been developed to efficiently destroy chlorinated hydrocarbons in situ using a reactive well approach. The treatment process utilizes dissolved H2 as an electron donor, in...

  19. Site-specific growth of Au-Pd alloy horns on Au nanorods: A platform for highly sensitive monitoring of catalytic reactions by surface enhancement raman spectroscopy

    KAUST Repository

    Huang, Jianfeng; Zhu, Yihan; Lin, Ming; Wang, Qingxiao; Zhao, Lan; Yang, Yang; Yao, Kexin; Han, Yu

    2013-01-01

    Surface-enhanced Raman scattering (SERS) is a highly sensitive probe for molecular detection. The aim of this study was to develop an efficient platform for investigating the kinetics of catalytic reactions with SERS. To achieve this, we synthesized

  20. Single base mutation in the proα2(I) collagen gene that causes efficient splicing of RNA from exon 27 to exon 29 and synthesis of a shortened but in-frame proα2(I) chain

    International Nuclear Information System (INIS)

    Tromp, G.; Prockop, D.J.

    1988-01-01

    Previous observations demonstrated that a lethal variant of osteogenesis imperfecta had two altered alleles for proα2(I) chains of type I procollagen. One mutation produced a nonfunctioning allele in that there was synthesis of mRNA but no detectable synthesis of proα2(I) chains from the allele. The mutation in the other allele caused synthesis of shortened proα2(I) chains that lacked most or all of the 18 amino acids encoded by exon 28. Subclones of the proα2(I) gene were prepared from the proband's DNA and the DNA sequence was determined for a 582-base-pair (bp) region that extended from the last 30 bp of intervening sequence 26 to the first 26 bp of intervening sequence 29. Data from six independent subclones demonstrated that all had the same sequence as a previously isolated normal clone for the proα2(I) gene except that four subclones had a single base mutation at the 3' end of intervening sequence 27. The mutation was a substitution of guanine for adenine that changed the universal consensus sequence for the 3' splicing site of RNA from -AG- to -GG-. S1 nuclease experiments demonstrated that about half the proα2(I) mRNA in the proband's fibroblasts was abnormally spliced and that the major species of abnormal proα2(I) mRNA was completely spliced from the last codon of exon 27 to the first codon of exon 29. The mutation is apparently unique among RNA splicing mutations of mammalian systems in producing a shortened polypeptide chain that is in-frame in terms of coding sequences, that is used in the subunit assembly of a protein, and that contributes to a lethal phenotype

  1. Analysis of RNA binding by the dengue virus NS5 RNA capping enzyme.

    Directory of Open Access Journals (Sweden)

    Brittney R Henderson

    Full Text Available Flaviviruses are small, capped positive sense RNA viruses that replicate in the cytoplasm of infected cells. Dengue virus and other related flaviviruses have evolved RNA capping enzymes to form the viral RNA cap structure that protects the viral genome and directs efficient viral polyprotein translation. The N-terminal domain of NS5 possesses the methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. The mechanism for flavivirus guanylyltransferase activity is currently unknown, and how the capping enzyme binds its diphosphorylated RNA substrate is important for deciphering how the flavivirus guanylyltransferase functions. In this report we examine how flavivirus NS5 N-terminal capping enzymes bind to the 5' end of the viral RNA using a fluorescence polarization-based RNA binding assay. We observed that the K(D for RNA binding is approximately 200 nM Dengue, Yellow Fever, and West Nile virus capping enzymes. Removal of one or both of the 5' phosphates reduces binding affinity, indicating that the terminal phosphates contribute significantly to binding. RNA binding affinity is negatively affected by the presence of GTP or ATP and positively affected by S-adensyl methoninine (SAM. Structural superpositioning of the dengue virus capping enzyme with the Vaccinia virus VP39 protein bound to RNA suggests how the flavivirus capping enzyme may bind RNA, and mutagenesis analysis of residues in the putative RNA binding site demonstrate that several basic residues are critical for RNA binding. Several mutants show differential binding to 5' di-, mono-, and un-phosphorylated RNAs. The mode of RNA binding appears similar to that found with other methyltransferase enzymes, and a discussion of diphosphorylated RNA binding is presented.

  2. Atomically Precise Metal Nanoclusters for Catalytic Application

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Rongchao [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    2016-11-18

    The central goal of this project is to explore the catalytic application of atomically precise gold nanoclusters. By solving the total structures of ligand-protected nanoclusters, we aim to correlate the catalytic properties of metal nanoclusters with their atomic/electronic structures. Such correlation unravel some fundamental aspects of nanocatalysis, such as the nature of particle size effect, origin of catalytic selectivity, particle-support interactions, the identification of catalytically active centers, etc. The well-defined nanocluster catalysts mediate the knowledge gap between single crystal model catalysts and real-world conventional nanocatalysts. These nanoclusters also hold great promise in catalyzing certain types of reactions with extraordinarily high selectivity. These aims are in line with the overall goals of the catalytic science and technology of DOE and advance the BES mission “to support fundamental research to understand, predict, and ultimately control matter and energy at the level of electrons, atoms, and molecules”. Our group has successfully prepared different sized, robust gold nanoclusters protected by thiolates, such as Au25(SR)18, Au28(SR)20, Au38(SR)24, Au99(SR)42, Au144(SR)60, etc. Some of these nanoclusters have been crystallographically characterized through X-ray crystallography. These ultrasmall nanoclusters (< 2 nm diameter) exhibit discrete electronic structures due to quantum size effect, as opposed to quasicontinuous band structure of conventional metal nanoparticles or bulk metals. The available atomic structures (metal core plus surface ligands) of nanoclusters serve as the basis for structure-property correlations. We have investigated the unique catalytic properties of nanoclusters (i.e. not observed in conventional nanogold catalysts) and revealed the structure-selectivity relationships. Highlights of our

  3. Analysis of intermolecular RNA-RNA recombination by rubella virus

    International Nuclear Information System (INIS)

    Adams, Sandra D.; Tzeng, W.-P.; Chen, M.-H.; Frey, Teryl K.

    2003-01-01

    To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5'-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3'-proximal structural protein (SP) ORF, and maintained the 3' end of the genome, including the putative 3' cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3' half of the genome including the SP-ORF and 3' CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and subgenomic RNAs and thus was generated by RNA-RNA recombination. Using transcripts tagged with a 3'-terminal deletion, it was found that recombinants contained the 3' end derived from the replicative strand, indicating a cis-preference for initiation of negative-strand synthesis. In cotransfections in which the replicative transcript lacked the 3' CSE, recombination occurred, albeit at lower efficiency, indicating that initiation in trans from the NS-ORF can occur. The 3' CSE was sufficient as a nonreplicative transcript, showing that it can serve as a promoter for negative-strand RNA synthesis. While deletion mutagenesis showed that the presence of the junction untranslated region (J-UTR) between the ORFs appeared to be necessary on both transcripts for recombination in this region of the genome, analysis with transcripts tagged with restriction sites showed that the J-UTR was not a hot spot for recombination compared to neighboring regions in both ORFs. Sequence analysis of recombinants revealed that both precise (homologous) and imprecise recombination (aberrant, homologous resulting in duplications) occurred; however, imprecise recombination only involved the J-UTR or the 3' end of the NS-ORF and the J-UTR (maintaining the NS-ORF), indicating

  4. Catalytic immunoglobulin gene delivery in a mouse model of Alzheimer's disease: prophylactic and therapeutic applications.

    Science.gov (United States)

    Kou, Jinghong; Yang, Junling; Lim, Jeong-Eun; Pattanayak, Abhinandan; Song, Min; Planque, Stephanie; Paul, Sudhir; Fukuchi, Ken-Ichiro

    2015-02-01

    Accumulation of amyloid beta-peptide (Aβ) in the brain is hypothesized to be a causal event leading to dementia in Alzheimer's disease (AD). Aβ vaccination removes Aβ deposits from the brain. Aβ immunotherapy, however, may cause T cell- and/or Fc-receptor-mediated brain inflammation and relocate parenchymal Aβ deposits to blood vessels leading to cerebral hemorrhages. Because catalytic antibodies do not form stable immune complexes and Aβ fragments produced by catalytic antibodies are less likely to form aggregates, Aβ-specific catalytic antibodies may have safer therapeutic profiles than reversibly-binding anti-Aβ antibodies. Additionally, catalytic antibodies may remove Aβ more efficiently than binding antibodies because a single catalytic antibody can hydrolyze thousands of Aβ molecules. We previously isolated Aβ-specific catalytic antibody, IgVL5D3, with strong Aβ-hydrolyzing activity. Here, we evaluated the prophylactic and therapeutic efficacy of brain-targeted IgVL5D3 gene delivery via recombinant adeno-associated virus serotype 9 (rAAV9) in an AD mouse model. One single injection of rAAV9-IgVL5D3 into the right ventricle of AD model mice yielded widespread, high expression of IgVL5D3 in the unilateral hemisphere. IgVL5D3 expression was readily detectable in the contralateral hemisphere but to a much lesser extent. IgVL5D3 expression was also confirmed in the cerebrospinal fluid. Prophylactic and therapeutic injection of rAAV9-IgVL5D3 reduced Aβ load in the ipsilateral hippocampus of AD model mice. No evidence of hemorrhages, increased vascular amyloid deposits, increased proinflammatory cytokines, or infiltrating T-cells in the brains was found in the experimental animals. AAV9-mediated anti-Aβ catalytic antibody brain delivery can be prophylactic and therapeutic options for AD.

  5. Preparation of Pd-Diimine@SBA-15 and Its Catalytic Performance for the Suzuki Coupling Reaction

    Directory of Open Access Journals (Sweden)

    Jiahuan Yu

    2016-11-01

    Full Text Available A highly efficient and stable Pd-diimine@SBA-15 catalyst was successfully prepared by immobilizing Pd onto diimine-functionalized mesoporous silica SBA-15. With the help of diimine functional groups grafted onto the SBA-15, Pd could be anchored on a support with high dispersion. Pd-diimine@SBA-15 catalyst exhibited excellent catalytic performance for the Suzuki coupling reaction of electronically diverse aryl halides and phenylboronic acid under mild conditions with an ultralow amount of Pd (0.05 mol % Pd. When the catalyst amount was increased, it could catalyze the coupling reaction of chlorinated aromatics with phenylboronic acid. Compared with the catalytic performances of Pd/SBA-15 and Pd-diimine@SiO2 catalysts, the Pd-diimine@SBA-15 catalyst exhibited higher hydrothermal stability and could be repeatedly used four times without a significant decrease of its catalytic activity.

  6. Effect of High-Pressure Treatment on Catalytic and Physicochemical Properties of Pepsin.

    Science.gov (United States)

    Wang, Jianan; Bai, Tenghui; Ma, Yaping; Ma, Hanjun

    2017-10-11

    For a long time, high-pressure treatment has been used to destroy the compact structures of natural proteins in order to promote subsequent enzymatic hydrolysis. However, there are few reports evaluating the feasibility of directly improving the catalytic capability of proteases by using high-pressure treatments. In this study, the effects of high-pressure treatment on the catalytic capacity and structure of pepsin were investigated, and the relationship between its catalytic properties and changes in its physicochemical properties was explored. It was found that high-pressure treatment could lead to changes of the sulfhydryl group/disulfide bond content, hydrophobicity, hydrodynamic radius, intrinsic viscosity, and subunit composition of pepsin, and the conformational change of pepsin resulted in improvement to its enzymatic activity and hydrolysis efficiency, which had an obvious relationship with the high-pressure treatment conditions.

  7. Multi-Walled Carbon Nanotube-Assisted Electrodeposition of Silver Dendrite Coating as a Catalytic Film

    Directory of Open Access Journals (Sweden)

    Li Fu

    2017-12-01

    Full Text Available A multi-walled carbon nanotube (MWCNT-coated indium tin oxide (ITO slide was used as a platform for the growth of a silver dendrite (Ag-D film using cyclic voltammetry. The particular dendritic nanostructures were formed by the diffusion-limited-aggregation model due to the potential difference between the MWCNTs and the ITO surface. The Ag-D-coated ITO film was then used for the catalytic degradation of methyl orange (MO and methylene blue (MB under static aqueous conditions. The network structure of the Ag-D allows the efficient diffusion of MO and MB, and consequently enhances the catalytic performance. Since the thin film is much easier to use for the post-treatment of powder catalysts, the proposed method shows great potential in many catalytic applications.

  8. Kinetic proofreading at single molecular level: aminoacylation of tRNA(Ile and the role of water as an editor.

    Directory of Open Access Journals (Sweden)

    Mantu Santra

    Full Text Available Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNA(Ile which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case, respectively, in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8×10(2.(4.33×10(2 = 7.8×10(4, (ii the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNA(Ile. The present study shows a non-michaelis type dependence of rate of reaction on tRNA(Ile concentration in case of valine. The overall editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNA(Ile whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low. We find that the presence of additional editing domain in class I editing enzyme makes the kinetic proofreading more efficient through enhanced hydrolysis of wrong product at the editing CP1 domain.

  9. Advanced purification of petroleum refinery wastewater by catalytic vacuum distillation.

    Science.gov (United States)

    Yan, Long; Ma, Hongzhu; Wang, Bo; Mao, Wei; Chen, Yashao

    2010-06-15

    In our work, a new process, catalytic vacuum distillation (CVD) was utilized for purification of petroleum refinery wastewater that was characteristic of high chemical oxygen demand (COD) and salinity. Moreover, various common promoters, like FeCl(3), kaolin, H(2)SO(4) and NaOH were investigated to improve the purification efficiency of CVD. Here, the purification efficiency was estimated by COD testing, electrolytic conductivity, UV-vis spectrum, gas chromatography-mass spectrometry (GC-MS) and pH value. The results showed that NaOH promoted CVD displayed higher efficiency in purification of refinery wastewater than other systems, where the pellucid effluents with low salinity and high COD removal efficiency (99%) were obtained after treatment, and the corresponding pH values of effluents varied from 7 to 9. Furthermore, environment estimation was also tested and the results showed that the effluent had no influence on plant growth. Thus, based on satisfied removal efficiency of COD and salinity achieved simultaneously, NaOH promoted CVD process is an effective approach to purify petroleum refinery wastewater. Copyright 2010 Elsevier B.V. All rights reserved.

  10. Reactivity of organic compounds in catalytic synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Minachev, Kh M; Bragin, O V

    1978-01-01

    A comprehensive review of 1976 Soviet research on catalysis delivered to the 1977 annual session of the USSR Academy of Science Council on Catalysis (Baku 6/16-20/77) covers hydrocarbon reactions, including hydrogenation and hydrogenolysis, dehydrogenation, olefin dimerization and disproportionation, and cyclization and dehydrocyclization (e.g., piperylene cyclization and ethylene cyclotrimerization); catalytic and physicochemical properties of zeolites, including cracking, dehydrogenation, and hydroisomerization catalytic syntheses and conversion of heterocyclic and functional hydrocarbon derivatives, including partial and total oxidation (e.g., of o-xylene to phthalic anhydride); syntheses of thiophenes from alkanes and hydrogen sulfide over certain dehydrogenation catalysts; catalytic syntheses involving carbon oxides ( e.g., the development of a new heterogeneous catalyst for hydroformylation of olefins), and of Co-MgO zeolitic catalysts for synthesis of aliphatic hydrocarbons from carbon dioxide and hydrogen, and fabrication of high-viscosity lubricating oils over bifunctional aluminosilicate catalysts.

  11. Catalytic Organic Transformations Mediated by Actinide Complexes

    Directory of Open Access Journals (Sweden)

    Isabell S. R. Karmel

    2015-10-01

    Full Text Available This review article presents the development of organoactinides and actinide coordination complexes as catalysts for homogeneous organic transformations. This chapter introduces the basic principles of actinide catalysis and deals with the historic development of actinide complexes in catalytic processes. The application of organoactinides in homogeneous catalysis is exemplified in the hydroelementation reactions, such as the hydroamination, hydrosilylation, hydroalkoxylation and hydrothiolation of alkynes. Additionally, the use of actinide coordination complexes for the catalytic polymerization of α-olefins and the ring opening polymerization of cyclic esters is presented. The last part of this review article highlights novel catalytic transformations mediated by actinide compounds and gives an outlook to the further potential of this field.

  12. Modeling and simulation of heterogeneous catalytic processes

    CERN Document Server

    Dixon, Anthony

    2014-01-01

    Heterogeneous catalysis and mathematical modeling are essential components of the continuing search for better utilization of raw materials and energy, with reduced impact on the environment. Numerical modeling of chemical systems has progressed rapidly due to increases in computer power, and is used extensively for analysis, design and development of catalytic reactors and processes. This book presents reviews of the state-of-the-art in modeling of heterogeneous catalytic reactors and processes. Reviews by leading authorities in the respective areas Up-to-date reviews of latest techniques in modeling of catalytic processes Mix of US and European authors, as well as academic/industrial/research institute perspectives Connections between computation and experimental methods in some of the chapters.

  13. Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

    Science.gov (United States)

    Manzoor, Dar; Pal, Sourav

    2015-06-18

    Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand.

  14. Uniformity index measurement technology using thermocouples to improve performance in urea-selective catalytic reduction systems

    Science.gov (United States)

    Park, Sangki; Oh, Jungmo

    2018-05-01

    The current commonly used nitrogen oxides (NOx) emission reduction techniques employ hydrocarbons (HCs), urea solutions, and exhaust gas emissions as the reductants. Two of the primary denitrification NOx (DeNOx) catalyst systems are the HC-lean NOx trap (HC-LNT) catalyst and urea-selective catalytic reduction (urea-SCR) catalyst. The secondary injection method depends on the type of injector, injection pressure, atomization, and spraying technique. In addition, the catalyst reaction efficiency is directly affected by the distribution of injectors; hence, the uniformity index (UI) of the reductant is very important and is the basis for system optimization. The UI of the reductant is an indicator of the NOx conversion efficiency (NCE), and good UI values can reduce the need for a catalyst. Therefore, improving the UI can reduce the cost of producing a catalytic converter, which are expensive due to the high prices of the precious metals contained therein. Accordingly, measurement of the UI is an important process in the development of catalytic systems. Two of the commonly used methods for measuring the reductant UI are (i) measuring the exhaust emissions at many points located upstream/downstream of the catalytic converter and (ii) acquisition of a reductant distribution image on a section of the exhaust pipe upstream of the catalytic converter. The purpose of this study is to develop a system and measurement algorithms to measure the exothermic response distribution in the exhaust gas as the reductant passes through the catalytic converter of the SCR catalyst system using a set of thermocouples downstream of the SCR catalyst. The system is used to measure the reductant UI, which is applied in real-time to the actual SCR system, and the results are compared for various types of mixtures for various engine operating conditions and mixer types in terms of NCE.

  15. Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world.

    Science.gov (United States)

    Soslau, Gerald

    2018-06-14

    The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang. Perhaps the most important support for the concept comes from the fact that some RNA species possess catalytic activity, ribozymes, and that RNA could be reverse transcribe to DNA. The thrust of numerous papers on this topic has been to explore how the available molecules on Earth, at its birth, gave rise to life as we know it today. This paper focuses more on a reverse view of the topic. The "how" molecular building blocks were synthesized is not addressed nor how the "first" RNA molecules were synthesized. We can clearly speculate on the variable environmental conditions and chemistry available on Earth billions of years ago. However, we can never truly replicate the changing conditions or know the chemical composition of Earth at the beginning of time. We can, however, confirm that over millions, perhaps billions of years the basic building blocks for life accumulated sufficiently to initiate evolution to an RNA world followed by our RNA/DNA world. Here we are attempting to take the information from our current knowledge of biology and by inference and extrapolation work backward to hypothesize biological events in the march forward from RNA to DNA. It is proposed that the primordial replicating RNA cell, the ribocyte, evolved from liposomes encompassing required reactants and products for "life" and that ribonucleopeptide complexes formed membrane pores to support bidirectional ion and molecular transport to maintain biological functions and

  16. RNA modifications by oxidation

    DEFF Research Database (Denmark)

    Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper

    2012-01-01

    to encompass various classes of novel regulatory RNAs, including, e.g., microRNAs. It is well known that DNA is constantly oxidized and repaired by complex genome maintenance mechanisms. Analogously, RNA also undergoes significant oxidation, and there are now convincing data suggesting that oxidation......The past decade has provided exciting insights into a novel class of central (small) RNA molecules intimately involved in gene regulation. Only a small percentage of our DNA is translated into proteins by mRNA, yet 80% or more of the DNA is transcribed into RNA, and this RNA has been found......, and the consequent loss of integrity of RNA, is a mechanism for disease development. Oxidized RNA is found in a large variety of diseases, and interest has been especially devoted to degenerative brain diseases such as Alzheimer disease, in which up to 50-70% of specific mRNA molecules are reported oxidized, whereas...

  17. Catalytic Wastewater Treatment Using Pillared Clays

    Science.gov (United States)

    Perathoner, Siglinda; Centi, Gabriele

    After introduction on the use of solid catalysts in wastewater treatment technologies, particularly advanced oxidation processes (AOPs), this review discussed the use of pillared clay (PILC) materials in three applications: (i) wet air catalytic oxidation (WACO), (ii) wet hydrogen peroxide catalytic oxidation (WHPCO) on Cu-PILC and Fe-PILC, and (iii) behavior of Ti-PILC and Fe-PILC in the photocatalytic or photo-Fenton conversion of pollutants. Literature data are critically analyzed to evidence the main direction to further investigate, in particularly with reference to the possible practical application of these technologies to treat industrial, municipal, or agro-food production wastewater.

  18. Thermal and catalytic pyrolysis of plastic waste

    Directory of Open Access Journals (Sweden)

    Débora Almeida

    2016-02-01

    Full Text Available Abstract The amount of plastic waste is growing every year and with that comes an environmental concern regarding this problem. Pyrolysis as a tertiary recycling process is presented as a solution. Pyrolysis can be thermal or catalytical and can be performed under different experimental conditions. These conditions affect the type and amount of product obtained. With the pyrolysis process, products can be obtained with high added value, such as fuel oils and feedstock for new products. Zeolites can be used as catalysts in catalytic pyrolysis and influence the final products obtained.

  19. Janus droplet as a catalytic micromotor

    Science.gov (United States)

    Shklyaev, Sergey

    2015-06-01

    Self-propulsion of a Janus droplet in a solution of surfactant, which reacts on a half of a drop surface, is studied theoretically. The droplet acts as a catalytic motor creating a concentration gradient, which generates its surface-tension-driven motion; the self-propulsion speed is rather high, 60 μ \\text{m/s} and more. This catalytic motor has several advantages over other micromotors: simple manufacturing, easily attained neutral buoyancy. In contrast to a single-fluid droplet, which demonstrates a self-propulsion as a result of symmetry breaking instability, for the Janus one no stability threshold exists; hence, the droplet radius can be scaled down to micrometers.

  20. Catalytic burners in larger boiler appliances

    Energy Technology Data Exchange (ETDEWEB)

    Silversand, Fredrik; Persson, Mikael (Catator AB, Lund (Sweden))

    2009-02-15

    This project focuses on the scale up of a Catator's catalytic burner technology to enable retrofit installation in existing boilers and the design of new innovative combinations of catalytic burners and boilers. Different design approaches are discussed and evaluated in the report and suggestions are made concerning scale-up. Preliminary test data, extracted from a large boiler installation are discussed together with an accurate analysis of technical possibilities following an optimization of the boiler design to benefit from the advantages of catalytic combustion. The experimental work was conducted in close collaboration with ICI Caldaie (ICI), located in Verona, Italy. ICI is a leading European boiler manufacturer in the effect segment ranging from about 20 kWt to several MWt. The study shows that it is possibly to scale up the burner technology and to maintain low emissions. The boilers used in the study were designed around conventional combustion and were consequently not optimized for implementation of catalytic burners. From previous experiences it stands clear that the furnace volume can be dramatically decreased when applying catalytic combustion. In flame combustion, this volume is normally dimensioned to avoid flame impingement on cold surfaces and to facilitate completion of the gas-phase reactions. The emissions of nitrogen oxides can be reduced by decreasing the residence time in the furnace. Even with the over-dimensioned furnace used in this study, we easily reached emission values close to 35 mg/kWh. The emissions of carbon monoxide and unburned hydrocarbons were negligible (less than 5 ppmv). It is possible to decrease the emissions of nitrogen oxides further by designing the furnace/boiler around the catalytic burner, as suggested in the report. Simultaneously, the size of the boiler installation can be reduced greatly, which also will result in material savings, i.e. the production cost can be reduced. It is suggested to optimize the