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Sample records for catalytic rna populations

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

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    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.

  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. 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.

  4. An Efficient Catalytic DNA that Cleaves L-RNA.

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    Kha Tram

    Full Text Available Many DNAzymes have been isolated from synthetic DNA pools to cleave natural RNA (D-RNA substrates and some have been utilized for the design of aptazyme biosensors for bioanalytical applications. Even though these biosensors perform well in simple sample matrices, they do not function effectively in complex biological samples due to ubiquitous RNases that can efficiently cleave D-RNA substrates. To overcome this issue, we set out to develop DNAzymes that cleave L-RNA, the enantiomer of D-RNA, which is known to be completely resistant to RNases. Through in vitro selection we isolated three L-RNA-cleaving DNAzymes from a random-sequence DNA pool. The most active DNAzyme exhibits a catalytic rate constant ~3 min-1 and has a structure that contains a kissing loop, a structural motif that has never been observed with D-RNA-cleaving DNAzymes. Furthermore we have used this DNAzyme and a well-known ATP-binding DNA aptamer to construct an aptazyme sensor and demonstrated that this biosensor can achieve ATP detection in biological samples that contain RNases. The current work lays the foundation for exploring RNA-cleaving DNAzymes for engineering biosensors that are compatible with complex biological samples.

  5. Functional identification of catalytic metal ion binding sites within RNA.

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    James L Hougland

    2005-09-01

    Full Text Available The viability of living systems depends inextricably on enzymes that catalyze phosphoryl transfer reactions. For many enzymes in this class, including several ribozymes, divalent metal ions serve as obligate cofactors. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s. In the Tetrahymena group I intron, previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified three metal ions (MA, MB, and MC that make five interactions with the ribozyme substrates in the reaction's transition state. Here, we combine substrate atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to develop a powerful, general strategy for defining the ligands of catalytic metal ions within RNA. In applying this strategy to the Tetrahymena group I intron, we have identified the pro-SP phosphoryl oxygen at nucleotide C262 as a ribozyme ligand for MC. Our findings establish a direct connection between the ribozyme core and the functionally defined model of the chemical transition state, thereby extending the known set of transition-state interactions and providing information critical for the application of the recent group I intron crystallographic structures to the understanding of catalysis.

  6. A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity

    OpenAIRE

    Cifuentes, Daniel; Xue, Huiling; Taylor, David W.; Patnode, Heather; Mishima, Yuichiro; Cheloufi, Sihem; Ma, Enbo; Mane, Shrikant; Hannon, Gregory J.; Lawson, Nathan D.; Wolfe, Scot A.; Giraldez, Antonio J.

    2010-01-01

    Dicer is a central enzyme in microRNA (miRNA) processing. We identified a Dicer-independent miRNA biogenesis pathway that uses Argonaute2 (Ago2) slicer catalytic activity. In contrast to other miRNAs, miR-451 levels were refractory to dicer loss of function but were reduced in MZago2 (maternal-zygotic) mutants. We found that pre-miR-451 processing requires Ago2 catalytic activity in vivo. MZago2 mutants showed delayed erythropoiesis that could be rescued by wild-type Ago2 or miR-451-duplex bu...

  7. Structural Basis for Telomerase Catalytic Subunit TERT Binding to RNA Template and Telomeric DNA

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    Mitchell, M.; Gillis, A; Futahashi, M; Fujiwara, H; Skordalakes, E

    2010-01-01

    Telomerase is a specialized DNA polymerase that extends the 3{prime} ends of eukaryotic linear chromosomes, a process required for genomic stability and cell viability. Here we present the crystal structure of the active Tribolium castaneum telomerase catalytic subunit, TERT, bound to an RNA-DNA hairpin designed to resemble the putative RNA-templating region and telomeric DNA. The RNA-DNA hybrid adopts a helical structure, docked in the interior cavity of the TERT ring. Contacts between the RNA template and motifs 2 and B{prime} position the solvent-accessible RNA bases close to the enzyme active site for nucleotide binding and selectivity. Nucleic acid binding induces rigid TERT conformational changes to form a tight catalytic complex. Overall, TERT-RNA template and TERT-telomeric DNA associations are remarkably similar to those observed for retroviral reverse transcriptases, suggesting common mechanistic aspects of DNA replication between the two families of enzymes.

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

    OpenAIRE

    Wall Michael E; Ming Dengming; Sanbonmatsu Kevin Y

    2007-01-01

    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 quant...

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

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    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.

  10. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity.

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    Cifuentes, Daniel; Xue, Huiling; Taylor, David W; Patnode, Heather; Mishima, Yuichiro; Cheloufi, Sihem; Ma, Enbo; Mane, Shrikant; Hannon, Gregory J; Lawson, Nathan D; Wolfe, Scot A; Giraldez, Antonio J

    2010-06-25

    Dicer is a central enzyme in microRNA (miRNA) processing. We identified a Dicer-independent miRNA biogenesis pathway that uses Argonaute2 (Ago2) slicer catalytic activity. In contrast to other miRNAs, miR-451 levels were refractory to dicer loss of function but were reduced in MZago2 (maternal-zygotic) mutants. We found that pre-miR-451 processing requires Ago2 catalytic activity in vivo. MZago2 mutants showed delayed erythropoiesis that could be rescued by wild-type Ago2 or miR-451-duplex but not by catalytically dead Ago2. Changing the secondary structure of Dicer-dependent miRNAs to mimic that of pre-miR-451 restored miRNA function and rescued developmental defects in MZdicer mutants, indicating that the pre-miRNA secondary structure determines the processing pathway in vivo. We propose that Ago2-mediated cleavage of pre-miRNAs, followed by uridylation and trimming, generates functional miRNAs independently of Dicer. PMID:20448148

  11. Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA-Programmed Nanoparticle Disassembly.

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    He, Xuewen; Zeng, Tao; Li, Zhi; Wang, Ganglin; Ma, Nan

    2016-02-24

    Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low-abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal-to-background ratio of conventional molecular imaging probes. Herein, we report a class of DNA-templated gold nanoparticle (GNP)-quantum dot (QD) assembly-based probes for catalytic imaging of cancer-related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA-programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non-catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells. PMID:26694689

  12. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase

    OpenAIRE

    Sologub, Marina; Litonin, Dmitry; Anikin, Michael; Mustaev, Arkady; Temiakov, Dmitry

    2009-01-01

    Transcription in human mitochondria is carried out by a single-subunit, T7-like RNA polymerase assisted by several auxiliary factors. We demonstrate that an essential initiation factor, TFB2, forms a network of interactions with DNA near the transcription start site and facilitates promoter melting but may not be essential for promoter recognition. Unexpectedly, catalytic autolabeling reveals that TFB2 interacts with the priming substrate, suggesting that TFB2 acts as a transient component of...

  13. Functional Diversification of Maize RNA Polymerase IV and V subtypes via Alternative Catalytic Subunits

    Energy Technology Data Exchange (ETDEWEB)

    Haag, Jeremy R.; Brower-Toland, Brent; Krieger, Elysia K.; Sidorenko, Lyudmila; Nicora, Carrie D.; Norbeck, Angela D.; Irsigler, Andre; LaRue, Huachun; Brzeski, Jan; Mcginnis, Karen A.; Ivashuta, Sergey; Pasa-Tolic, Ljiljana; Chandler, Vicki L.; Pikaard, Craig S.

    2014-10-01

    Unlike nuclear multisubunit RNA polymerases I, II, and III, whose subunit compositions are conserved throughout eukaryotes, plant RNA polymerases IV and V are nonessential, Pol II-related enzymes whose subunit compositions are still evolving. Whereas Arabidopsis Pols IV and V differ from Pol II in four or five of their 12 subunits, respectively, and differ from one another in three subunits, proteomic ana- lyses show that maize Pols IV and V differ from Pol II in six subunits but differ from each other only in their largest subunits. Use of alternative catalytic second subunits, which are nonredundant for development and paramutation, yields at least two sub- types of Pol IV and three subtypes of Pol V in maize. Pol IV/Pol V associations with MOP1, RMR1, AGO121, Zm_DRD1/CHR127, SHH2a, and SHH2b extend parallels between paramutation in maize and the RNA-directed DNA methylation pathway in Arabidopsis.

  14. Functional Diversification of Maize RNA Polymerase IV and V Subtypes via Alternative Catalytic Subunits

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    Jeremy R. Haag

    2014-10-01

    Full Text Available Unlike nuclear multisubunit RNA polymerases I, II, and III, whose subunit compositions are conserved throughout eukaryotes, plant RNA polymerases IV and V are nonessential, Pol II-related enzymes whose subunit compositions are still evolving. Whereas Arabidopsis Pols IV and V differ from Pol II in four or five of their 12 subunits, respectively, and differ from one another in three subunits, proteomic analyses show that maize Pols IV and V differ from Pol II in six subunits but differ from each other only in their largest subunits. Use of alternative catalytic second subunits, which are nonredundant for development and paramutation, yields at least two subtypes of Pol IV and three subtypes of Pol V in maize. Pol IV/Pol V associations with MOP1, RMR1, AGO121, Zm_DRD1/CHR127, SHH2a, and SHH2b extend parallels between paramutation in maize and the RNA-directed DNA methylation pathway in Arabidopsis.

  15. 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...... vitro, GluRS1 activity is reversibly inactivated upon oxidation by hemin and hydrogen peroxide. The targets for oxidation-based inhibition were found to be cysteines from a SWIM zinc-binding motif located in the tRNA acceptor helix-binding domain. tRNA(Glu) was able to protect GluRS1 against oxidative...

  16. The mRNA expression of apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G in peripheral blood mononuclear cells in patients with chronic hepatitis C and its regulation by interferon-α

    Institute of Scientific and Technical Information of China (English)

    蔡卫平

    2013-01-01

    Objective To study the mRNA expression of apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G(APOBEC3G) in the peripheral blood mononuclear cells(PBMC) in patients with chronic hepatitis C(CHC) and its regulation by exogenous interferon-α

  17. Genetic diagnostic test of hepatocellular carcinoma by telomerase catalytic subunit mRNA.

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    Wada, E; Hisatomi, H; Moritoyo, T; Kanamaru, T; Hikiji, K

    1998-01-01

    This study investigated the relationship between telomerase activity and telomere length and between telomerase reverse transcriptase (hTERT) mRNA and telomere length. Both cancerous and non-cancerous tissues were studied in individuals with hepatic carcinoma. In this study, the telomere length in HCC livers had a wide range, no clear significant correlation was found between hTERT mRNA and telomere length. Telomerase activity was more strongly correlated with hTERT mRNA than with telomere length. The correlation between hTERT mRNA and telomerase activity shown here indicates that hTERT mRNA has potential for cancer diagnosis. PMID:9769378

  18. Enzyme catalytic amplification of miRNA-155 detection with graphene quantum dot-based electrochemical biosensor.

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    Hu, Tianxing; Zhang, Le; Wen, Wei; Zhang, Xiuhua; Wang, Shengfu

    2016-03-15

    A specific and sensitive method was developed for quantitative detection of miRNA by integrating horseradish peroxidase (HRP)-assisted catalytic reaction with a simple electrochemical RNA biosensor. The electrochemical biosensor was constructed by a double-stranded DNA structure. The structure was formed by the hybridization of thiol-tethered oligodeoxynucleotide probes (capture DNA), assembled on the gold electrode surface, with target DNA and aminated indicator probe (NH2-DNA). After the construction of the double-stranded DNA structure, the activated carboxyl groups of graphene quantum dots (GQDs) assembled on NH2-DNA. GQDs were used as a new platform for HRP immobilization through noncovalent assembly. HRP modified biosensor can effectively catalyze the hydrogen peroxide (H2O2)-mediated oxidation of 3,3',5,5'-tetramethylbenzidine (TMB), accompanied by a change from colorless to blue in solution color and an increased electrochemical current signal. Due to GQDs and enzyme catalysis, the proposed biosensor could sensitively detect miRNA-155 from 1 fM to 100 pM with a detection limit of 0.14 fM. High performance of the biosensor is attributed to the large surface-to-volume ratio, excellent compatibility of GQDs. For these advantages, the proposed method holds great potential for analysis of other interesting tumor makers. PMID:26453906

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

    International Nuclear Information System (INIS)

    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

  20. Structural and population genetic determinants of RNA secondary structure evolution

    OpenAIRE

    Piskol, Robert

    2011-01-01

    Since their discovery, RNA molecules have been shown to carry functions that extend far beyond their initially ascribed role as intermediates in protein biosynthesis. These noncoding RNAs (ncRNAs) are involved in fundamental cellular processes including the regulation of gene expression and maintenance of genome stability. In most cases the biogenesis or function of the RNA molecule is only possible if the molecule folds into a characteristic two- and three-dimensional shape via formation of ...

  1. Visualizing transient low-populated structures of RNA.

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    Dethoff, Elizabeth A; Petzold, Katja; Chugh, Jeetender; Casiano-Negroni, Anette; Al-Hashimi, Hashim M

    2012-11-29

    The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized so far involve long-lived species that can be captured by structure characterization techniques. Here we report the nuclear magnetic resonance visualization of RNA transitions towards 'invisible' excited states (ESs), which exist in too little abundance (2-13%) and for too short a duration (45-250 μs) to allow structural characterization by conventional techniques. Transitions towards ESs result in localized rearrangements in base-pairing that alter building block elements of RNA architecture, including helix-junction-helix motifs and apical loops. The ES can inhibit function by sequestering residues involved in recognition and signalling or promote ATP-independent strand exchange. Thus, RNAs do not adopt a single conformation, but rather exist in rapid equilibrium with alternative ESs, which can be stabilized by cellular cues to affect functional outcomes. PMID:23041928

  2. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.

    Science.gov (United States)

    Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

    2011-06-15

    We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ∼15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ∼1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction. PMID:21539371

  3. Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations

    Science.gov (United States)

    Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

    2011-01-01

    We use quantum mechanics/molecular mechanics (QM/MM) simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ~15 kcal mol−1, encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ~1–100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The non-monotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA cleavage reaction. PMID:21539371

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

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    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

  5. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures

    OpenAIRE

    van Dijk, Erwin; Cougot, Nicolas; Meyer, Sylke; Babajko, Sylvie; Wahle, Elmar; Séraphin, Bertrand

    2002-01-01

    We have cloned cDNAs for the human homologues of the yeast Dcp1 and Dcp2 factors involved in the major (5′–3′) and NMD mRNA decay pathways. While yeast Dcp1 has been reported to be the decapping enzyme, we show that recombinant human Dcp2 (hDcp2) is enzymatically active. Dcp2 activity appears evolutionarily conserved. Mutational and biochemical analyses indicate that the hDcp2 MutT/Nudix domain mediates this activity. hDcp2 generates m7GDP and 5′-phosphorylated mRNAs that are 5′–3′ exonucleas...

  6. Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya

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    Aryal Rishi

    2012-12-01

    Full Text Available Abstract Background The small RNAs (sRNA are a regulatory class of RNA mainly represented by the 21 and 24-nucleotide size classes. The cellular sRNAs are processed by RNase III family enzyme dicer (Dicer like in plant from a self-complementary hairpin loop or other type of RNA duplexes. The papaya genome has been sequenced, but its microRNAs and other regulatory RNAs are yet to be analyzed. Results We analyzed the genomic features of the papaya sRNA population from three sRNA deep sequencing libraries made from leaves, flowers, and leaves infected with Papaya Ringspot Virus (PRSV. We also used the deep sequencing data to annotate the micro RNA (miRNA in papaya. We identified 60 miRNAs, 24 of which were conserved in other species, and 36 of which were novel miRNAs specific to papaya. In contrast to the Chargaff’s purine-pyrimidine equilibrium, cellular sRNA was significantly biased towards a purine rich population. Of the two purine bases, higher frequency of adenine was present in 23nt or longer sRNAs, while 22nt or shorter sRNAs were over represented by guanine bases. However, this bias was not observed in the annotated miRNAs in plants. The 21nt species were expressed from fewer loci but expressed at higher levels relative to the 24nt species. The highly expressed 21nt species were clustered in a few isolated locations of the genome. The PRSV infected leaves showed higher accumulation of 21 and 22nt sRNA compared to uninfected leaves. We observed higher accumulation of miRNA* of seven annotated miRNAs in virus-infected tissue, indicating the potential function of miRNA* under stressed conditions. Conclusions We have identified 60 miRNAs in papaya. Our study revealed the asymmetric purine-pyrimidine distribution in cellular sRNA population. The 21nt species of sRNAs have higher expression levels than 24nt sRNA. The miRNA* of some miRNAs shows higher accumulation in PRSV infected tissues, suggesting that these strands are not totally

  7. microRNA Expression Profiling of Side Population Cells in Human Lung Cancer and Preliminary Analysis

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    Xiaotao XU

    2010-07-01

    Full Text Available Background and objective Recent studies indicate that the side population (SP which is an enriched source of cancer stem cells (CSCs is the root cause of tumor growth and development. SP appears to be highly resistant to chemo- and radio-therapy which becomes an important factor in tumor recurrence and metastasis. The aim of this study is to determine the difference of microRNA expression profiles between SP cells and non-SP cells so as to lay necessary basis for research on the function of miRNA in lung cancer stem cells. Methods SP and non-SP cells were isolated using flow cytometry and Hoechst 33342 dye efflux assay from human lung adenocarcinoma A549 cell. The total RNA was extracted. The microarray detection system was employed to analyze whether there was difference in miRNA expression profile between SP and non-SP cells. Results A total of 85 differentially expressed miRNA were found, including 32 over-expression and 53 low-expression miRNA in SP. Conclusion miRNA may play important roles in tumorigenesis of lung cancer stem cell. The study of miRNA contributes to elucidate the molecular mechanism of lung cancer stem cell.

  8. Structure of a low-population binding intermediate in protein-RNA recognition

    Science.gov (United States)

    Bardaro, Michael F.; Aprile, Francesco A.; Varani, Gabriele; Vendruscolo, Michele

    2016-01-01

    The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution. PMID:27286828

  9. Wound-induced changes in mRNA populations in tomato pericarp tissue

    International Nuclear Information System (INIS)

    Immature green tomato pericarp tissue was wounded by cutting into small pieces. At various intervals, ethylene production was monitored and the corresponding tissue harvested for mRNA extraction. Poly (A)+ RNA was fractionated from total RNA using oligo (dT)-cellulose chromatography and was translated in vitro in a rabbit reticulocyte lysate system using 35S-methionine. Labeled products were subjected to one and two dimensional polyacrylamide gel electrophoresis (PAGE) to analyze wound-induced changes in mRNA populations. Analyses of autoradiograms of corresponding single dimension SDS-PAGE showed changes in at least 12 major polypeptides with 6 declining (18, 19, 24, 36, 44, 69 kD) and 6 increasing (21, 41, 46, 54, 75, > 94 kD) after wounding. Among the polypeptides resolved (over 200) on two dimensional PAGE, at least 15 showed dramatic increases in the wounded tissue. Results indicate that wounding of tomato pericarp causes induction of synthesis and accumulation of several mRNA species while inhibiting production of relatively few mRNA species

  10. The effect of secondary compounds on the rumen microbial population structure measured by 16S rRNA and 18S rRNA

    International Nuclear Information System (INIS)

    Full text: Plant secondary compounds in the forages have an important role in determining forage quality. A method for evaluating their effects on microbial population structure was carried out using the in vitro gas syringe system followed by extraction of RNA and gel separation of 16S rRNA and 18S rRNA. Quantification of 16S rRNA and 18S rRNA bands indicated the prokaryote and eukaryote populations, respectively. Five types of plant materials, i.e. Nothopanax scutellarium (Mangkokan) leaves, Morinda citrifolia (Mengkudu) fruit, Sapindus rarak (lerak) fruit and two types of Sesbania sesban leaves (hgh saponin and low saponin) were tested and Pennisetum purpureum (rumput gajah, Indonesian name) was used as a control roughage. Presence of saponin in these plant materials was determined qualitatively by thin layer chromatography. Eukaryote population was found to be significantly affected by the above plant materials. Both types of S. sesban leaves caused total elimination of eukaryotes. S. rarak reduced both eukaryote and prokaryote populations. The observed inhibition of eukaryote population might be due to the presence of saponin in these plant materials. In another experiment, a methanol extract of S. rarak which contained saponin was included and its effect on in vitro fermentation of P. purpureum was evaluated. The results showed that at higher levels of inclusion of S. rarak methanol extract, eukaroytes were totally eliminated. Comparison was made between microbial mass calculated based on difference between apparent undigested residue and true undigested residue and microbial mass calculations based on 16S rRNA and 18S rRNA. Microbial mass calculated by difference method was much higher than the microbial mass calculated on the basis of 16S rRNA and 18S rRNA. The quantification of RNA can be a useful and rapid technique for an accurate assessment of the effect of new forage materials on the microbial population structure. Other parameters from in vitro

  11. Maintaining RNA integrity in a homogeneous population of mammary epithelial cells isolated by Laser Capture Microdissection

    Directory of Open Access Journals (Sweden)

    Helbling Jean-Christophe

    2010-12-01

    Full Text Available Abstract Background Laser-capture microdissection (LCM that enables the isolation of specific cell populations from complex tissues under morphological control is increasingly used for subsequent gene expression studies in cell biology by methods such as real-time quantitative PCR (qPCR, microarrays and most recently by RNA-sequencing. Challenges are i to select precisely and efficiently cells of interest and ii to maintain RNA integrity. The mammary gland which is a complex and heterogeneous tissue, consists of multiple cell types, changing in relative proportion during its development and thus hampering gene expression profiling comparison on whole tissue between physiological stages. During lactation, mammary epithelial cells (MEC are predominant. However several other cell types, including myoepithelial (MMC and immune cells are present, making it difficult to precisely determine the specificity of gene expression to the cell type of origin. In this work, an optimized reliable procedure for producing RNA from alveolar epithelial cells isolated from frozen histological sections of lactating goat, sheep and cow mammary glands using an infrared-laser based Arcturus Veritas LCM (Applied Biosystems® system has been developed. The following steps of the microdissection workflow: cryosectioning, staining, dehydration and harvesting of microdissected cells have been carefully considered and designed to ensure cell capture efficiency without compromising RNA integrity. Results The best results were obtained when staining 8 μm-thick sections with Cresyl violet® (Ambion, Applied Biosystems® and capturing microdissected cells during less than 2 hours before RNA extraction. In addition, particular attention was paid to animal preparation before biopsies or slaughtering (milking and freezing of tissue blocks which were embedded in a cryoprotective compound before being immersed in isopentane. The amount of RNA thus obtained from ca.150 to 250 acini

  12. MG-132 inhibits the TCDD-mediated induction of Cyp1a1 at the catalytic activity but not the mRNA or protein levels in Hepa 1c1c7 cells.

    Science.gov (United States)

    Anwar-Mohamed, Anwar; Elbekai, Reem H; El-Kadi, Ayman O S

    2008-11-10

    Previous studies have shown that 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced degradation of aryl hydrocarbon receptor (AhR) is inhibited by MG-132, a potent inhibitor of the 26S proteasome. Therefore, the current study aims to address the effect of MG-132 on the AhR-regulated gene, cytochrome P450 1a1 (Cyp1a1), using murine hepatoma Hepa 1c1c7 cells. Our results showed that MG-132 at the highest concentration tested, 10 microM significantly increased the Cyp1a1 at mRNA, protein and catalytic activity levels through a transcriptional mechanism. On the other hand, MG-132 further potentiated the TCDD-mediated induction of Cyp1a1 at mRNA but not at protein level. In contrast, MG-132 significantly inhibited the TCDD-mediated induction of Cyp1a1 catalytic activity. In addition, we showed that the decrease in Cyp1a1 catalytic activity is not Cyp specific, as MG-132 significantly inhibited Cyp2b1 and total cytochrome P450 catalytic activities. These results prompted us to examine the effect of MG-132 on total cellular heme content and heme oxygenase-1 (HO-1) mRNA, a rate limiting enzyme of heme degradation. Our results showed that MG-132 significantly induced HO-1 mRNA in a concentration-dependent manner. Furthermore, MG-132 potentiated the induction of HO-1 mRNA by TCDD in a concentration-dependent manner. The induction of HO-1 mRNA level coincided with a decrease in total cellular heme content. In conclusion, the present study demonstrates for the first time that MG-132, despite of increasing Cyp1a1 mRNA expression, it decreases its activity probably through decreasing its heme content. PMID:18835339

  13. Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity.

    Science.gov (United States)

    Murashko, Oleg N; Kaberdin, Vladimir R; Lin-Chao, Sue

    2012-05-01

    RNase E plays an essential role in RNA processing and decay and tethers to the cytoplasmic membrane in Escherichia coli; however, the function of this membrane-protein interaction has remained unclear. Here, we establish a mechanistic role for the RNase E-membrane interaction. The reconstituted highly conserved N-terminal fragment of RNase E (NRne, residues 1-499) binds specifically to anionic phospholipids through electrostatic interactions. The membrane-binding specificity of NRne was confirmed using circular dichroism difference spectroscopy; the dissociation constant (K(d)) for NRne binding to anionic liposomes was 298 nM. E. coli RNase G and RNase E/G homologs from phylogenetically distant Aquifex aeolicus, Haemophilus influenzae Rd, and Synechocystis sp. were found to be membrane-binding proteins. Electrostatic potentials of NRne and its homologs were found to be conserved, highly positive, and spread over a large surface area encompassing four putative membrane-binding regions identified in the "large" domain (amino acids 1-400, consisting of the RNase H, S1, 5'-sensor, and DNase I subdomains) of E. coli NRne. In vitro cleavage assay using liposome-free and liposome-bound NRne and RNA substrates BR13 and GGG-RNAI showed that NRne membrane binding altered its enzymatic activity. Circular dichroism spectroscopy showed no obvious thermotropic structural changes in membrane-bound NRne between 10 and 60 °C, and membrane-bound NRne retained its normal cleavage activity after cooling. Thus, NRne membrane binding induced changes in secondary protein structure and enzymatic activation by stabilizing the protein-folding state and increasing its binding affinity for its substrate. Our results demonstrate that RNase E-membrane interaction enhances the rate of RNA processing and decay. PMID:22509045

  14. RNA-seq transcriptome analysis of a Pseudomonas strain with diversified catalytic properties growth under different culture medium.

    Science.gov (United States)

    Yang, Jia-Wei; Zheng, Dai-Jun; Cui, Bao-Dong; Yang, Min; Chen, Yong-Zheng

    2016-08-01

    Biocatalysis is an emerging strategy for the production of enantio-pure organic molecules. However, lacking of commercially available enzymes restricts the widespread application of biocatalysis. In this study, we report a Pseudomonas strain which exhibited versatile oxidation activity to synthesize chiral sulfoxides when growing under M9-toluene medium and reduction activity to synthesize chiral alcohols when on Luria-Bertani (LB) medium, respectively. Further comparative transcriptome analysis on samples from these two cultural conditions has identified 1038 differentially expressed genes (DEG). Gene Ontology (GO) enrichment and KEGG pathways analysis demonstrate significant changes in protein synthesis, energy metabolism, and biosynthesis of metabolites when cells cultured under different conditions. We have identified eight candidate enzymes from this bacterial which may have the potential to be used for synthesis of chiral alcohol and sulfoxide chemicals. This work provides insights into the mechanism of diversity in catalytic properties of this Pseudomonas strain growth with different cultural conditions, as well as candidate enzymes for further biocatalysis of enantiomerically pure molecules and pharmaceuticals. PMID:27061463

  15. Interaction of human decapping scavenger with 5' mRNA cap analogues: structural requirements for catalytic activity

    International Nuclear Information System (INIS)

    The cap structure is a specific feature of the 5' end of mRNA which plays an important role in the post-transcriptional control in gene expression. A major step of gene regulation occurs at the level of mRNA turnover. Degradation of most eukaryotic mRNAs entails the removal of the cap structure in the various pathways. A human scavenger decapping enzyme (hDcpS) catalyses the cleavage of the residual cap structure m7GpppN and/or short oligonucleotides after the 3' to 5' exosom mediated digestion. In this paper we report a fluorescence study of association process of hDcpS with m7GMP, m7GDP and selected dinucleotide cap analogues resistant to enzymatic hydrolysis. The calculated values of association constants (Kas) and corresponding Gibbs free energies (ΔG0) depend on the type of substituents and their positions in the cap molecule, indicating which structural modifications are crucial for the catalysis

  16. Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil.

    Science.gov (United States)

    Brister, Matthew M; Crespo-Hernández, Carlos E

    2015-11-01

    Investigation of the excited-state dynamics in nucleic acid monomers is an area of active research due to the crucial role these early events play in DNA and RNA photodamage. The dynamics and rate at which the triplet state is populated are key mechanistic pathways yet to be fully elucidated. Direct spectroscopic evidence is presented in this contribution for intersystem crossing dynamics in a uracil derivative, 1-cyclohexyluracil. It is shown that intersystem crossing to the triplet manifold occurs in one picosecond or less in acetonitrile solution-at least an order of magnitude faster than previously estimated experimentally. Broadband transient absorption measurements also reveal the primary electronic relaxation pathways of the uracil chromophore, including the absorption spectra of the (1)ππ*, (1)nπ*, and (3)ππ* states and the rates of vibrational cooling in the ground and (3)ππ* states. The experimental results are supported by density functional calculations. PMID:26538051

  17. Rapid mapping of functional cis-acting RNA elements by recovery of virus from a degenerate RNA population: application to genome segment 10 of bluetongue virus.

    Science.gov (United States)

    Boyce, M; McCrae, M A

    2015-10-01

    The regulatory elements which control the processes of virus replication and gene expression in the Orbivirus genus are uncharacterized in terms of both their locations within genome segments and their specific functions. The reverse genetics system for the type species, Bluetongue virus, has been used in combination with RNA secondary structure prediction to identify and map the positions of cis-acting regions within genome segment 10. Through the simultaneous introduction of variability at multiple nucleotide positions in the rescue RNA population, the functional contribution of these positions was used to map regions containing cis-acting elements essential for virus viability. Nucleotides that were individually lethal when varied mapped within a region of predicted secondary structure involving base pairing between the 5' and 3' ends of the transcript. An extended region of predicted perfect base pairing located within the 3' untranslated region of the genome segment was also found to be required for virus viability. In contrast to the identification of individually lethal mutations, gross alteration of the composition of this predicted stem region was possible, providing the base-pairing potential between the two strands was maintained, identifying a structural feature predicted to be conserved throughout the Orbivirus genus. The approach of identifying cis-acting sequences through sequencing the recovered virus following the rescue of a degenerate RNA population is broadly applicable to viruses where reverse genetics is available. PMID:26248463

  18. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs

    Science.gov (United States)

    In eukaryotes, RNA silencing pathways utilize 20–30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focuse...

  19. 16S rRNA gene sequencing as a tool to study microbial populations in foods and process environments

    DEFF Research Database (Denmark)

    Buschhardt, Tasja; Hansen, Tina Beck; Bahl, Martin Iain; Asser Hansen, Martin; Abu Al-Soud, Waleed; Aabo, Søren

    and their role in food safety. During method optimization, we have identified several factors which distort the characterization of microbial populations, including DNA extraction methods, DNA polymerases, and most importantly the analyzed fragment of the 16S rRNA gene. Methods: This study...... culture methods as cross reference. Results: Taxonomic assignments and abundances of sequences in the total community and in the Enterobacteriaceae subpopulation were affected by the 16S rRNA gene variable region, DNA extraction methods, and polymerases chosen. However, community compositions were very......Introduction: Methodological constraints during culturing and biochemical testing have left the true microbiological diversity of foods and process environments unexplored. Culture-independent molecular methods, such as 16S rRNA gene sequencing, may provide deeper insight into microbial communities...

  20. A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers

    Directory of Open Access Journals (Sweden)

    Matt N Krosch

    2015-12-01

    Full Text Available The rapid uptake of transcriptomic approaches in freshwater ecology has seen a wealth of data produced concerning the ways in which organisms interact with their environment on a molecular level. Typically, such studies focus either at the community level and so don’t require species identifications, or on laboratory strains of known species identity or natural populations of large, easily identifiable taxa. For chironomids, impediments still exist for applying these technologies to natural populations because they are small-bodied and often require time-consuming secondary sorting of stream material and morphological voucher preparation to confirm species diagnosis. These procedures limit the ability to maintain RNA quantity and quality in such organisms because RNA degrades rapidly and gene expression can be altered rapidly in organisms; thereby limiting the inclusion of such taxa in transcriptomic studies. Here, we demonstrate that these limitations can be overcome and outline an optimised protocol for collecting, sorting and preserving chironomid larvae that enables retention of both morphological vouchers and RNA for subsequent transcriptomics purposes. By ensuring that sorting and voucher preparation are completed within <4 hours after collection and that samples are kept cold at all times, we successfully retained both RNA and morphological vouchers from all specimens. Although not prescriptive in specific methodology, we anticipate that this paper will assist in promoting transcriptomic investigations of the sublethal impact on chironomid gene expression of changes to aquatic environments.

  1. Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

    Science.gov (United States)

    Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca

    2015-01-01

    In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples. PMID:26035837

  2. Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

    Directory of Open Access Journals (Sweden)

    Ilario Ferrocino

    Full Text Available In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE. The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.

  3. Characterization of rabbit limbal epithelial side population cells using RNA sequencing and single-cell qRT-PCR.

    Science.gov (United States)

    Kameishi, Sumako; Umemoto, Terumasa; Matsuzaki, Yu; Fujita, Masako; Okano, Teruo; Kato, Takashi; Yamato, Masayuki

    2016-05-01

    Corneal epithelial stem cells reside in the limbus, a transitional zone between the cornea and conjunctiva, and are essential for maintaining homeostasis in the corneal epithelium. Although our previous studies demonstrated that rabbit limbal epithelial side population (SP) cells exhibit stem cell-like phenotypes with Hoechst 33342 staining, the different characteristics and/or populations of these cells remain unclear. Therefore, in this study, we determined the gene expression profiles of limbal epithelial SP cells by RNA sequencing using not only present public databases but also contigs that were created by de novo transcriptome assembly as references for mapping. Our transcriptome data indicated that limbal epithelial SP cells exhibited a stem cell-like phenotype compared with non-SP cells. Importantly, gene ontology analysis following RNA sequencing demonstrated that limbal epithelial SP cells exhibited significantly enhanced expression of mesenchymal/endothelial cell markers rather than epithelial cell markers. Furthermore, single-cell quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) demonstrated that the limbal epithelial SP population consisted of at least two immature cell populations with endothelial- or mesenchymal-like phenotypes. Therefore, our present results may propose the presence of a novel population of corneal epithelial stem cells distinct from conventional epithelial stem cells. PMID:26546824

  4. Developed and evaluated a multiplex mRNA profiling system for body fluid identification in Chinese Han population.

    Science.gov (United States)

    Song, Feng; Luo, Haibo; Hou, Yiping

    2015-10-01

    In forensic casework, identification the cellular origin from a biological sample is crucial to the case investigation and reconstruction in crime scene. DNA/RNA co-extraction for STR typing and human body fluids identification has been proposed as an efficient and comprehensive assay for forensic analysis. Several cell-specific messenger RNA (mRNA) markers for identification of the body fluids have been proposed by previous studies. In this study, a novel multiplex mRNA profiling system included 19 markers was developed and performed by reverse transcription endpoint polymerase chain reaction (RT-PCR). The multiplex combined 3 housekeeping gene markers and 16 cell-specific markers that have been used to identify five types of human body fluids: peripheral blood, semen, saliva, vaginal secretions and menstrual blood. The specificity, sensitivity, stability and detectability of the mixture were explored in our study. Majority of the cell-specific mRNA markers showed high specificity, although cross-reactivity was observed sporadically. Specific profiling for per body fluid was obtained. Moreover, the interpretation guidelines for inference of body fluid types were performed according to the A. Lindenbergh et al. The scoring guidelines can be applied to any RNA multiplex, which was based on six different scoring categories (observed, observed and fits, sporadically observed and fits, not observed, sporadically observed, not reliable, and non-specific due to high input). The simultaneous extraction of DNA showed positive full or partial profiling results of all samples. It demonstrated that the approach of combined STR-profiling and RNA profiling was suitable and reliable to detect the donor and origin of human body fluids in Chinese Han population. PMID:26311108

  5. mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: a population-based simulation study.

    Directory of Open Access Journals (Sweden)

    John Walmsley

    Full Text Available Differences in mRNA expression levels have been observed in failing versus non-failing human hearts for several membrane channel proteins and accessory subunits. These differences may play a causal role in electrophysiological changes observed in human heart failure and atrial fibrillation, such as action potential (AP prolongation, increased AP triangulation, decreased intracellular calcium transient (CaT magnitude and decreased CaT triangulation. Our goal is to investigate whether the information contained in mRNA measurements can be used to predict cardiac electrophysiological remodeling in heart failure using computational modeling. Using mRNA data recently obtained from failing and non-failing human hearts, we construct failing and non-failing cell populations incorporating natural variability and up/down regulation of channel conductivities. Six biomarkers are calculated for each cell in each population, at cycle lengths between 1500 ms and 300 ms. Regression analysis is performed to determine which ion channels drive biomarker variability in failing versus non-failing cardiomyocytes. Our models suggest that reported mRNA expression changes are consistent with AP prolongation, increased AP triangulation, increased CaT duration, decreased CaT triangulation and amplitude, and increased delay between AP and CaT upstrokes in the failing population. Regression analysis reveals that changes in AP biomarkers are driven primarily by reduction in I[Formula: see text], and changes in CaT biomarkers are driven predominantly by reduction in I(Kr and SERCA. In particular, the role of I(CaL is pacing rate dependent. Additionally, alternans developed at fast pacing rates for both failing and non-failing cardiomyocytes, but the underlying mechanisms are different in control and heart failure.

  6. 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.

  7. Evolution of random catalytic networks

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, S.M. [Santa Fe Inst., NM (United States); Reidys, C.M. [Santa Fe Inst., NM (United States)]|[Los Alamos National Lab., NM (United States)

    1997-06-01

    In this paper the authors investigate the evolution of populations of sequences on a random catalytic network. Sequences are mapped into structures, between which are catalytic interactions that determine their instantaneous fitness. The catalytic network is constructed as a random directed graph. They prove that at certain parameter values, the probability of some relevant subgraphs of this graph, for example cycles without outgoing edges, is maximized. Populations evolving under point mutations realize a comparatively small induced subgraph of the complete catalytic network. They present results which show that populations reliably discover and persist on directed cycles in the catalytic graph, though these may be lost because of stochastic effects, and study the effect of population size on this behavior.

  8. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max

    Science.gov (United States)

    Background: Small non-coding RNAs (smRNAs) are known to have major roles in gene regulation in eukaryotes. In plants, knowledge of the biogenesis and mechanisms of action of smRNA classes including microRNAs (miRNAs), short interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs) has been gaine...

  9. A survey of small RNA population during FR-induced apical hook opening

    Directory of Open Access Journals (Sweden)

    Ying eLi

    2014-04-01

    Full Text Available Photomorphogenesis is a mechanism employed by plants to regulate their architecture and developmental program in response to light conditions. As they emerge into light for the first time, dark-grown seedlings employ a rapid and finely-controlled photomorphogenic signaling network. Small RNAs have increasingly been revealed to play an important role in regulating multiple aspects of plant development, by modulating the stability of mRNAs. The rapid alteration of the mRNA transcriptome is a known hallmark of the de-etiolation response, thus we investigated the small RNA transcriptome during this process in specific seedling tissues. Here we describe a survey of the small RNA expression profile in four tissues of etiolated soybean seedlings, the cotyledons, hypocotyl and the convex and concave sides of the apical hook. We also investigate how this profile responds to a one-hour far-red light treatment. Our data suggests that miRNAs show a different global profile between these tissues and treatments, suggesting a possible role for tissue- and treatment-specific expression in the differential morphology of the seedling on de-etiolation. Further evidence for the role of miRNA in light-regulated development is given by the de-etiolation responses of a hypomorphic ago1 mutant, which displays reduced and delayed photomorphogenic responses in apical hook and cotyledon angle to far-red light.

  10. Characterization of viral siRNA populations in honey bee colony collapse disorder.

    Science.gov (United States)

    Chejanovsky, Nor; Ophir, Ron; Schwager, Michal Sharabi; Slabezki, Yossi; Grossman, Smadar; Cox-Foster, Diana

    2014-04-01

    Colony Collapse Disorder (CCD), a special case of collapse of honey bee colonies, has resulted in significant losses for beekeepers. CCD-colonies show abundance of pathogens which suggests that they have a weakened immune system. Since honey bee viruses are major players in colony collapse and given the important role of viral RNA interference (RNAi) in combating viral infections we investigated if CCD-colonies elicit an RNAi response. Deep-sequencing analysis of samples from CCD-colonies from US and Israel revealed abundant small interfering RNAs (siRNA) of 21-22 nucleotides perfectly matching the Israeli acute paralysis virus (IAPV), Kashmir virus and Deformed wing virus genomes. Israeli colonies showed high titers of IAPV and a conserved RNAi-pattern of matching the viral genome. That was also observed in sample analysis from colonies experimentally infected with IAPV. Our results suggest that CCD-colonies set out a siRNA response that is specific against predominant viruses associated with colony losses. PMID:24725944

  11. The simple fool's guide to population genomics via RNA-Seq: An introduction to high-throughput sequencing data analysis

    DEFF Research Database (Denmark)

    De Wit, P.; Pespeni, M.H.; Ladner, J.T.; Barshis, D.J.; Seneca, F.; Jaris, H.; Therkildsen, Nina Overgaard; Morikawa, M.; Palumbi, S.R.

    2012-01-01

    Population Genomics via RNA-seq' (SFG), a document intended to serve as an easy-to-follow protocol, walking a user through one example of high-throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods...... used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http......://sfg.stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom-made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal...

  12. Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations.

    Science.gov (United States)

    Sakaguchi, Aisa; Sarkies, Peter; Simon, Matt; Doebley, Anna-Lisa; Goldstein, Leonard D; Hedges, Ashley; Ikegami, Kohta; Alvares, Stacy M; Yang, Liwei; LaRocque, Jeannine R; Hall, Julie; Miska, Eric A; Ahmed, Shawn

    2014-10-14

    Germ cells are maintained in a pristine non-aging state as they proliferate over generations. Here, we show that a novel function of the Caenorhabditis elegans RNA interference proteins RNAi spreading defective (RSD)-2 and RSD-6 is to promote germ cell immortality at high temperature. rsd mutants cultured at high temperatures became progressively sterile and displayed loss of small interfering RNAs (siRNAs) that target spermatogenesis genes, simple repeats, and transposons. Desilencing of spermatogenesis genes occurred in late-generation rsd mutants, although defective spermatogenesis was insufficient to explain the majority of sterility. Increased expression of repetitive loci occurred in both germ and somatic cells of late-generation rsd mutant adults, suggesting that desilencing of many heterochromatic segments of the genome contributes to sterility. Nuclear RNAi defective (NRDE)-2 promotes nuclear silencing in response to exogenous double-stranded RNA, and our data imply that RSD-2, RSD-6, and NRDE-2 function in a common transgenerational nuclear silencing pathway that responds to endogenous siRNAs. We propose that RSD-2 and RSD-6 promote germ cell immortality at stressful temperatures by maintaining transgenerational epigenetic inheritance of endogenous siRNA populations that promote genome silencing. PMID:25258416

  13. Highly Efficient Self-Replicating RNA Enzymes

    OpenAIRE

    Robertson, Michael P; Joyce, Gerald F.

    2014-01-01

    An RNA enzyme has been developed that catalyzes the joining of oligonucleotide substrates to form additional copies of itself, undergoing self-replication with exponential growth. The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution. The opportunity for inventive evolution within this synthetic genetic system depends on the diversity of the evolving population, which is limited by the catalytic ...

  14. A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing

    Directory of Open Access Journals (Sweden)

    Westenberger Scott J

    2007-05-01

    % recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of T. cruzi guide RNAs. Based on these preferences, a method of predicting T. cruzi guide RNAs using only primary minicircle sequence data was created.

  15. Sulforaphane induces CYP1A1 mRNA, protein, and catalytic activity levels via an AhR-dependent pathway in murine hepatoma Hepa 1c1c7 and human HepG2 cells.

    Science.gov (United States)

    Anwar-Mohamed, Anwar; El-Kadi, Ayman O S

    2009-03-01

    Recent reports have proposed that some naturally occurring phytochemicals can function as anticancer agents mainly through inducing phase II drug detoxification enzymes. Of these phytochemicals, isothiocyanates sulforaphane (SUL), present in broccoli, is by far the most extensively studied. In spite of its positive effect on phase II drug metabolizing enzymes, its effect on the phase I bioactivating enzyme cytochrome P450 1a1 (Cyp1a1) is still a matter of debate. As a first step to investigate this effect, Hepa 1c1c7 and HepG2 cells were treated with various concentration of SUL. Our results showed that SUL-induced CYP1A1 mRNA in a dose- and time-dependent manner. Furthermore, this induction was further reflected on the protein and catalytic activity levels. Investigating the effect of SUL at the transcriptional level revealed that SUL increases the Cyp1a1 mRNA as early as 1h. The RNA polymerase inhibitor actinomycin D (Act-D) completely abolished the SUL-induced Cyp1a1 mRNA. Furthermore, SUL successfully activated AhR transformation and its subsequent binding to the XRE. At the post-transcriptional level, SUL did not affect the levels of existing Cyp1a1 mRNA transcripts. This is the first demonstration that the broccoli-derived SUL can directly induce Cyp1a1 gene expression in an AhR-dependent manner and represents a novel mechanism by which SUL induces this enzyme. PMID:19013013

  16. miRNA as potential biomarkers of breast cancer in the Lebanese population and in young women: a pilot study.

    Directory of Open Access Journals (Sweden)

    Farah J Nassar

    Full Text Available Relative to western populations, the percentage of women diagnosed with breast cancer at a young age in Lebanon is high. While the younger age of the Lebanese population compared to the West certainly contributes to this difference, potential genetic, reproductive and/or biological factors likely play an important role. The objective of this study is to investigate the contribution of miRNAs in this setting through the analysis of the expression of five reported dysregulated miRNAs, miR-148b, miR-10b, miR-21, miR-221, and miR-155 in 20 normal and 57 cancerous breast tissues from Lebanese breast cancer patients. After finding their relative expression by quantitative reverse transcription real time PCR, the results were analyzed with respect to the patients' clinical and histopathology presentations. Compared to normal breast tissues, significant upregulation of miR-155, miR-21 and miR-148b, notable downregulation of miR-10b and non-significant expression of miR-221 were observed in tumor tissues. Moreover, miR-10b was significantly underexpressed in estrogen/progesterone receptor (ER/PR negative tumors relative to ER/PR positive tumor tissues. miR-155 was also significantly overexpressed in postmenopausal patients and in those of age at diagnosis greater than 40 years old as well as in PR negative or in human epidermal growth factor 2 (Her2 positive tissues. This study is the first one to report miRNA expression patterns in Lebanese breast cancer patients. We found that differential miRNA expression in breast cancer could be variable between Lebanese and Western populations. miR-10b was positively correlated with the ER and PR status and miR-155 could be a noteworthy biomarker for the menopausal state, age at diagnosis, PR and Her2 status. Hence, miRNA can be used as biomarkers for early breast cancer detection.

  17. Silencing expression of the catalytic subunit of DNA-dependent protein kinase by small interfering RNA sensitizes human cells for radiation-induced chromosome damage, cell killing, and mutation

    Science.gov (United States)

    Peng, Yuanlin; Zhang, Qinming; Nagasawa, Hatsumi; Okayasu, Ryuichi; Liber, Howard L.; Bedford, Joel S.

    2002-01-01

    Targeted gene silencing in mammalian cells by RNA interference (RNAi) using small interfering RNAs (siRNAs) was recently described by Elbashir et al. (S. M. Elbashir et al., Nature (Lond.), 411: 494-498, 2001). We have used this methodology in several human cell strains to reduce expression of the Prkdc (DNA-PKcs) gene coding for the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) that is involved in the nonhomologous end joining of DNA double-strand breaks. We have also demonstrated a radiosensitization for several phenotypic endpoints of radiation damage. In low-passage normal human fibroblasts, siRNA knock-down of DNA-PKcs resulted in a reduced capacity for restitution of radiation-induced interphase chromosome breaks as measured by premature chromosome condensation, an increased yield of acentric chromosome fragments at the first postirradiation mitosis, and an increased radiosensitivity for cell killing. For three strains of related human lymphoblasts, DNA-PKcs-targeted siRNA transfection resulted in little or no increase in radiosensitivity with respect to cell killing, a 1.5-fold decrease in induced mutant yield in TK6- and p53-null NH32 cells, but about a 2-fold increase in induced mutant yield in p53-mutant WTK1 cells at both the hypoxanthine quanine phosphoribosyl transferase (hprt) and the thymidine kinase loci.

  18. Association of a miRNA-137 Polymorphism with Schizophrenia in a Southern Chinese Han Population

    Directory of Open Access Journals (Sweden)

    Guoda Ma

    2014-01-01

    Full Text Available Both genome wide association study (GWAS and biochemical studies of Caucasian populations indicate a robust association between the miR-137 genetic variant rs1625579 and schizophrenia, but inconsistent results have been reported. To assay the association between this variant and schizophrenia, we genotyped 611 schizophrenic patients from Southern Chinese Han population for the risk single nucleotide polymorphism (SNP rs1625579 using the SNaPshot technique and compared the clinical profiles of different genotypes. Additionally, a meta-analysis was performed using the combined sample groups from five case-control publications and the present study. Both the genotype and allele distributions of the rs1625579 SNP were significantly different between patients and controls (P=0.036 and 0.026, SNP. TT genotype carriers showed slightly lower Brief Assessment of Cognition in Schizophrenia- (BACS- derived working memory performance than G carriers (15.58 ± 9.56 versus 19.71 ± 8.18, P=0.045. In the meta-analysis, we observed a significant association between rs1625579 and schizophrenia under different genetic models (all P<0.05. The results of our study and meta-analysis provide convincing evidence that rs1625579 is significantly associated with schizophrenia. Furthermore, the miR-137 polymorphism influences the working memory performance of schizophrenic patients in a Chinese Han population.

  19. Experimental evolution of an RNA virus in wild birds: evidence for host-dependent impacts on population structure and competitive fitness.

    Directory of Open Access Journals (Sweden)

    Nathan D Grubaugh

    2015-05-01

    Full Text Available Within hosts, RNA viruses form populations that are genetically and phenotypically complex. Heterogeneity in RNA virus genomes arises due to error-prone replication and is reduced by stochastic and selective mechanisms that are incompletely understood. Defining how natural selection shapes RNA virus populations is critical because it can inform treatment paradigms and enhance control efforts. We allowed West Nile virus (WNV to replicate in wild-caught American crows, house sparrows and American robins to assess how natural selection shapes RNA virus populations in ecologically relevant hosts that differ in susceptibility to virus-induced mortality. After five sequential passages in each bird species, we examined the phenotype and population diversity of WNV through fitness competition assays and next generation sequencing. We demonstrate that fitness gains occur in a species-specific manner, with the greatest replicative fitness gains in robin-passaged WNV and the least in WNV passaged in crows. Sequencing data revealed that intrahost WNV populations were strongly influenced by purifying selection and the overall complexity of the viral populations was similar among passaged hosts. However, the selective pressures that control WNV populations seem to be bird species-dependent. Specifically, crow-passaged WNV populations contained the most unique mutations (~1.7× more than sparrows, ~3.4× more than robins and defective genomes (~1.4× greater than sparrows, ~2.7× greater than robins, but the lowest average mutation frequency (about equal to sparrows, ~2.6× lower than robins. Therefore, our data suggest that WNV replication in the most disease-susceptible bird species is positively associated with virus mutational tolerance, likely via complementation, and negatively associated with the strength of selection. These differences in genetic composition most likely have distinct phenotypic consequences for the virus populations. Taken together

  20. RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73.

    Science.gov (United States)

    Liang, Zhikai; Schnable, James C

    2016-01-01

    Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several clearly distinct clades were identified among putatively B73 samples. A number of these clades were defined by the presence of clearly defined genomic blocks containing a haplotype which did not match the published B73 reference genome. The overall proportion of the maize genotype where multiple distinct haplotypes were observed across different research groups was approximately 2.3%. In some cases the relationship among B73 samples generated by different research groups recapitulated mentor/mentee relationships within the maize genetics community. PMID:27348435

  1. RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73

    Science.gov (United States)

    2016-01-01

    Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several clearly distinct clades were identified among putatively B73 samples. A number of these clades were defined by the presence of clearly defined genomic blocks containing a haplotype which did not match the published B73 reference genome. The overall proportion of the maize genotype where multiple distinct haplotypes were observed across different research groups was approximately 2.3%. In some cases the relationship among B73 samples generated by different research groups recapitulated mentor/mentee relationships within the maize genetics community. PMID:27348435

  2. 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.

  3. Catalytic thermal barrier coatings

    Science.gov (United States)

    Kulkarni, Anand A.; Campbell, Christian X.; Subramanian, Ramesh

    2009-06-02

    A catalyst element (30) for high temperature applications such as a gas turbine engine. The catalyst element includes a metal substrate such as a tube (32) having a layer of ceramic thermal barrier coating material (34) disposed on the substrate for thermally insulating the metal substrate from a high temperature fuel/air mixture. The ceramic thermal barrier coating material is formed of a crystal structure populated with base elements but with selected sites of the crystal structure being populated by substitute ions selected to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a higher rate than would the base compound without the ionic substitutions. Precious metal crystallites may be disposed within the crystal structure to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a lower light-off temperature than would the ceramic thermal barrier coating material without the precious metal crystallites.

  4. The mitochondrial tRNA(Gln) T4353C mutation may not be associated with essential hypertension in Han Chinese population.

    Science.gov (United States)

    Meng, Xing; Pei, Hui; Lan, Chao

    2016-09-01

    We reported here the possible role of a mitochondrial tRNA mutation: T4353C in clinical expression of essential hypertension in Chinese population. The human mammalian mitochondrial tRNA database was used to analyze the conservation index of this mutation between different species. Moreover, phylogenetic analysis showed that the T4353C mutation belonged to human mitochondrial haplogroup HV, a West Eurasian haplogroup found throughout Western Asia and Eastern European but was infrequent in China. In addition, structural prediction of the T4353C mutation indicated that this transition did not alter the secondary structure of tRNA(Gln). Together, our data indicated that the T4353C mutation occurred infrequent and may not be associated with essential hypertension in Han Chinese population. PMID:25693701

  5. Tracking the Fragile X Mental Retardation Protein in a Highly Ordered Neuronal RiboNucleoParticles Population: A Link between Stalled Polyribosomes and RNA Granules

    Science.gov (United States)

    Tremblay, Sandra; Jaglin, Xavier; Dury, Alain; Robert, Claude; De Koninck, Paul; Khandjian, Edouard W.

    2016-01-01

    Local translation at the synapse plays key roles in neuron development and activity-dependent synaptic plasticity. mRNAs are translocated from the neuronal soma to the distant synapses as compacted ribonucleoparticles referred to as RNA granules. These contain many RNA-binding proteins, including the Fragile X Mental Retardation Protein (FMRP), the absence of which results in Fragile X Syndrome, the most common inherited form of intellectual disability and the leading genetic cause of autism. Using FMRP as a tracer, we purified a specific population of RNA granules from mouse brain homogenates. Protein composition analyses revealed a strong relationship between polyribosomes and RNA granules. However, the latter have distinct architectural and structural properties, since they are detected as close compact structures as observed by electron microscopy, and converging evidence point to the possibility that these structures emerge from stalled polyribosomes. Time-lapse video microscopy indicated that single granules merge to form cargoes that are transported from the soma to distal locations. Transcriptomic analyses showed that a subset of mRNAs involved in cytoskeleton remodelling and neural development is selectively enriched in RNA granules. One third of the putative mRNA targets described for FMRP appear to be transported in granules and FMRP is more abundant in granules than in polyribosomes. This observation supports a primary role for FMRP in granules biology. Our findings open new avenues for the study of RNA granule dysfunctions in animal models of nervous system disorders, such as Fragile X syndrome. PMID:27462983

  6. Directed evolution of an RNA enzyme

    Science.gov (United States)

    Beaudry, Amber A.; Joyce, Gerald F.

    1992-01-01

    An in vitro evolution procedures was used to obtain RNA enzymes with a particular catalytic function. A population of 10 exp 13 variants of the Tetrahymena ribozyme, a group I ribozyme that catalyzes sequence-specific cleavage of RNA via a phosphoester transfer mechanism, was generated. This enzyme has a limited ability to cleave DNA under conditions of high temperature or high MgCl2 concentration, or both. A selection constraint was imposed on the population of ribozyme variants such that only those individuals that carried out DNA cleavage under physiologic conditions were amplified to produce 'progeny' ribozymes. Mutations were introduced during amplification to maintain heterogeneity in the population. This process was repeated for ten successive generations, resulting in enhanced (100 times) DNA cleavage activity.

  7. Catalytic DNA with phosphatase activity

    OpenAIRE

    Chandrasekar, Jagadeeswaran; Silverman, Scott K.

    2013-01-01

    Catalytic DNA sequences (deoxyribozymes, DNA enzymes, or DNAzymes) have been identified by in vitro selection for various catalytic activities. Expanding the limits of DNA catalysis is an important fundamental objective and may facilitate practical utility of catalysts that can be obtained from entirely unbiased (random) sequence populations. In this study, we show that DNA can catalyze Zn2+-dependent phosphomonoester hydrolysis of tyrosine and serine side chains (i.e., exhibit phosphatase ac...

  8. Nucleolar protein PinX1p regulates telomerase by sequestering its protein catalytic subunit in an inactive complex lacking telomerase RNA

    OpenAIRE

    Lin, Jue; Elizabeth H. Blackburn

    2004-01-01

    Human TRF1-binding protein PinX1 inhibits telomerase activity. Here we report that overexpression of yeast PinX1p (yPinX1p) results in shortened telomeres and decreased in vitro telomerase activity. yPinX1p coimmunoprecipitated withyeast telomerase protein Est2p even in cells lacking the telomerase RNA TLC1, or the telomerase-associated proteins Est1p and Est3p. Est2p regions required for binding to yPinX1p or TLC1 were similar. Furthermore, we found two distinct Est2p complexes exist, contai...

  9. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei

    International Nuclear Information System (INIS)

    Pyrrolysyl-tRNA synthetase (PylRS) from M. mazei has been overexpressed in an N-terminally truncated form PylRS(c270) in Escherichia coli, purified to homogeneity and crystallized by the hanging-drop vapour-diffusion method. Pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei was overexpressed in an N-terminally truncated form PylRS(c270) in Escherichia coli, purified to homogeneity and crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. The native PylRS(c270) crystals in complex with an ATP analogue belonged to space group P64, with unit-cell parameters a = b = 104.88, c = 70.43 Å, α = β = 90, γ = 120°, and diffracted to 1.9 Å resolution. The asymmetric unit contains one molecule of PylRS(c270). Selenomethionine-substituted protein crystals were prepared in order to solve the structure by the MAD phasing method

  10. Populism

    OpenAIRE

    Abts, Koenraad; van Kessel, Stijn

    2015-01-01

    Populism is a concept applied to a wide range of political movements and actors across the globe. There is, at the same time, considerable confusion about the attributes and manifestation of populism, as well as its impact on democracy. This contribution identifies the defining elements of the populist ideology and discusses the varieties in which populism manifests itself, for instance as a component of certain party families. We finally discuss various normative interpretations of populism,...

  11. The use of RNA-dependent RNA polymerase for the taxonomic assignment of Picorna-like viruses (order Picornavirales infecting Apis mellifera L. populations

    Directory of Open Access Journals (Sweden)

    Schroeder Declan C

    2008-01-01

    Full Text Available Abstract Background Single-stranded RNA viruses, infectious to the European honeybee, Apis mellifera L. are known to reside at low levels in colonies, with typically no apparent signs of infection observed in the honeybees. Reverse transcription-PCR (RT-PCR of regions of the RNA-dependent RNA polymerase (RdRp is often used to diagnose their presence in apiaries and also to classify the type of virus detected. Results Analysis of RdRp conserved domains was undertaken on members of the newly defined order, the Picornavirales; focusing in particular on the amino acid residues and motifs known to be conserved. Consensus sequences were compiled using partial and complete honeybee virus sequences published to date. Certain members within the iflaviruses, deformed wing virus (DWV, Kakugo virus (KV and Varroa destructor virus (VDV; and the dicistroviruses, acute bee paralysis virus (ABPV, Israeli paralysis virus (IAPV and Kashmir bee virus (KBV, shared greater than 98% and 92% homology across the RdRp conserved domains, respectively. Conclusion RdRp was validated as a suitable taxonomic marker for the assignment of members of the order Picornavirales, with the potential for use independent of other genetic or phenotypic markers. Despite the current use of the RdRp as a genetic marker for the detection of specific honeybee viruses, we provide overwhelming evidence that care should be taken with the primer set design. We demonstrated that DWV, VDV and KV, or ABPV, IAPV and KBV, respectively are all recent descendents or variants of each other, meaning caution should be applied when assigning presence or absence to any of these viruses when using current RdRp primer sets. Moreover, it is more likely that some primer sets (regardless of what gene is used are too specific and thus are underestimating the diversity of honeybee viruses.

  12. Population Genetic Structure of Legionella pneumophila Inferred from RNA Polymerase Gene (rpoB) and DotA Gene (dotA) Sequences

    OpenAIRE

    Ko, Kwan Soo; Lee, Hae Kyung; Park, Mi-Yeoun; Park, Man-Suk; Lee, Keun-Hwa; Woo, So-Yon; Yun, Yeo-Jun; Kook, Yoon-Hoh

    2002-01-01

    The population structure of Legionella pneumophila was studied by using partial RNA polymerase gene (rpoB) and DotA gene (dotA) sequences. Trees inferred from rpoB sequences showed that two subspecies of L. pneumophila, Legionella pneumophila subsp. pneumophila and Legionella pneumophila subsp. fraseri, were clearly separated genetically. In both rpoB and dotA trees, 79 Korean isolates used in this study constituted six clonal populations, four of which (designated subgroups P-I to P-IV) were...

  13. Population genetic structure of Cheyletus malaccensis (Acari: Cheyletidae) in China based on mitochondrial COI and 12S rRNA genes.

    Science.gov (United States)

    Yang, Xiaoqiang; Ye, Qingtian; Xin, Tianrong; Zou, Zhiwen; Xia, Bin

    2016-06-01

    Cheyletus malaccensis is a predatory mite widely distributed in grain storages. It has been regarded as an important biological control agent for pest mites. In this study, we investigated the population genetic structure of C. malaccensis distributed in China based on the partial regions of mitochondrial COI and 12S rRNA genes. We collected 256 individuals of C. malaccensis from stored grain in 34 sites of China. We detected 50 COI gene haplotypes and nine 12S rRNA gene haplotypes. There were three clades in the haplotype network and Bayesian and maximum parsimony phylogenetic trees based on COI sequences, and two based on 12S rRNA sequences. The clustering of haplotypes was not correlated with their geographical distributions. The analysis of molecular variance, AMOVA, indicated that the genetic differentiation between populations was relatively weak. The major genetic differentiation was found within populations. We suggest that the genetic structure of C. malaccensis observed in this study may be the result of long-term climate fluctuations and recent human disturbances. PMID:26947027

  14. Population-level study of ribosomal RNA genes expression in Tragopogon allotetraplopids of recent and recurrent origin

    Czech Academy of Sciences Publication Activity Database

    Kovařík, Aleš; Matyášek, Roman; Tate, J. A.; Šrubařová, Hana; Yoong, K.Y.; Leitch, A.R.; Soltis, D.E.; Soltis, P.E.

    Prague, 2006. [Groupe Cytogenetique et polyploidie. 05.04.2006-07.04.2006, Bordeaux] Institutional research plan: CEZ:AV0Z50040507 Keywords : RNA * Tragopogon * allotetraploids Subject RIV: BO - Biophysics

  15. Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling

    OpenAIRE

    Ilario Ferrocino; Raffaella Di Cagno; Maria De Angelis; Silvia Turroni; Lucia Vannini; Elena Bancalari; Kalliopi Rantsiou; Gianluigi Cardinali; Erasmo Neviani; Luca Cocolin

    2015-01-01

    In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal micr...

  16. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    Directory of Open Access Journals (Sweden)

    David Kamanda Ngugi

    Full Text Available Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C and salinity (~41 psu from the mixed layer (~200 m to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS region of SAR11 in different depths of the Red Sea's water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen on the population dynamics of this ubiquitous marine bacterium.

  17. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David Kamanda

    2012-11-20

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.

  18. Association of Polymorphic Variants of miRNA Processing Genes with Larynx Cancer Risk in a Polish Population

    OpenAIRE

    Ewa Osuch-Wojcikiewicz; Antoni Bruzgielewicz; Kazimierz Niemczyk; Olga Sieniawska-Buccella; Alicja Nowak; Anna Walczak; Ireneusz Majsterek

    2015-01-01

    Laryngeal cancer (LC) is one of the most prevalent types of head and neck cancer. An increasing interest has been focused on the role of microRNA (miRNAs) in LC development. The study group consisted of 135 larynx cancer patients and 170 cancer-free individuals. Nine polymorphisms of pre-miRNA processing genes, DROSHA (rs6877842), DGCR8 (rs3757, rs417309, and rs1640299), RAN (rs14035), XPO5 (rs11077), DICER1 (rs13078 and rs3742330) and TARBP2 (rs784567), were performed by TaqMan SNP Genotypin...

  19. The Origin of the RNA World a Kinetic Model

    CERN Document Server

    Wattis, J A D; Wattis, Jonathan A. D.; Coveney, Peter V.

    1999-01-01

    The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar but more general chemical assumptions to those of Eigen, namely that catalytic replication can lead to a large population of long chains. In particular, our models incorporate the possibility of (i) direct chain growth, (ii) template-assisted synthesis and (iii) catalysis by RNA replicase ribozymes, all with varying degrees of efficiency. However, in our models the reaction mechanisms are kept `open'; we do not assume the existence of closed hypercycles which sustain a population of long chains. Rather it is the feasibility of the initial emergence of a self-sustaining set of RNA chains from monomeric nucleotides which is our prime concern. We confront directly the central nonlinear features of the problem, which have often been overlooked in previous studies. Our detailed m...

  20. Analysis of hepatic deiodinase 2 mRNA levels in natural fish lake populations exposed to different levels of putative thyroid disrupters

    International Nuclear Information System (INIS)

    Hepatic mRNA levels of the dio2 gene (deiodinase 2), implicated in thyroid hormone homeostasis, were analyzed in trout from six remote lakes in the Pyrenees (Spain) and the Tatra Mountains (Slovakia). Highest levels corresponded to fish from the two coldest lakes in Pyrenees, whereas relatively low levels were found in the Tatra lakes. These values correlated with the presence of highly-brominated polybrominated diphenyl ethers (PBDE) congeners in the muscle of the same animals, reflecting the distribution of these compounds across European mountain ranges. In contrast, cyp1a expression levels, diagnostic for the presence of dioxin-like pollutants, mirrored the distribution of semi-volatile organochlorine compounds, indicating the specificity of the two types of biological responses. Exposure to PDBEs is known to increase transcription of dio2 and other thyroid-related genes in laboratory experiments; we propose that our data reflects the same phenomenon in natural populations, driven by anthropogenic pollutants at the environmental concentrations. - Highlights: • Hepatic deiodinase 2 (dio2) mRNA levels vary among mountain lake trout populations. • High dio2 expression correlated with elevated levels of PBDE 153 and 154 in muscle. • Expression patterns of dio2 and cyp1a diverge among the same fish populations. • Elevated biological responses associated to high loads of specific pollutants. • These data indicate that thyroid disruption may occur in remote ecosystems. - Deionidase dio2 expression as a marker for exposure to putative thyroid disruptors in mountain lake trout

  1. mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: a population-based simulation study.

    OpenAIRE

    Walmsley, J.; Rodriguez, JF; Mirams, GR; Burrage, K; Efimov, IR; Rodriguez, B.

    2013-01-01

    Differences in mRNA expression levels have been observed in failing versus non-failing human hearts for several membrane channel proteins and accessory subunits. These differences may play a causal role in electrophysiological changes observed in human heart failure and atrial fibrillation, such as action potential (AP) prolongation, increased AP triangulation, decreased intracellular calcium transient (CaT) magnitude and decreased CaT triangulation. Our goal is to investigate whether the inf...

  2. Association of Polymorphic Variants of miRNA Processing Genes with Larynx Cancer Risk in a Polish Population

    Directory of Open Access Journals (Sweden)

    Ewa Osuch-Wojcikiewicz

    2015-01-01

    Full Text Available Laryngeal cancer (LC is one of the most prevalent types of head and neck cancer. An increasing interest has been focused on the role of microRNA (miRNAs in LC development. The study group consisted of 135 larynx cancer patients and 170 cancer-free individuals. Nine polymorphisms of pre-miRNA processing genes, DROSHA (rs6877842, DGCR8 (rs3757, rs417309, and rs1640299, RAN (rs14035, XPO5 (rs11077, DICER1 (rs13078 and rs3742330 and TARBP2 (rs784567, were performed by TaqMan SNP Genotyping Assay. It was found that the frequency of the GT and the TT polymorphic variants of XPO5 gene were higher in LC patients than in controls (p<0.0001 and p=0.000183, resp.. In turn, the frequency of the CT genotype of RAN gene was higher in controls than in LC patients (p<0.0001. The TT and the AG of DICER1 gene (p=0.034697 for rs13078 and p=0.0004 for rs3742330 as well as the AG and the GG genotypes of TARBP2 gene (p=0.008335 and p<0.0001, resp. were associated with higher risk of LC occurrence. Our data suggested that polymorphisms of miRNA processing genes might be useful as predictive factors for the LC development.

  3. Identification of Biomphalaria havanensis and Biomphalaria obstructa populations from Cuba using polymerase chain reaction and restriction fragment length polymorphism of the ribosomal RNA intergenic spacer

    Directory of Open Access Journals (Sweden)

    Teofânia HDA Vidigal

    2001-07-01

    Full Text Available In Cuba, several Biomphalaria species have been reported such as B. orbignyi, B. schrammi, B. helophila, B. havanensis and B. peregrina; only the latter three are considered as potential hosts of Schistosoma mansoni. The specific identification of Biomphalaria species is based on anatomical and morphological characters of genital organs and shells. The correct identification of these snails is complicated by the high variation in these characters, similarity among species and in some cases by the small size of the snails. In this paper, we reported the classical morphological identification, the use of PCR and RFLP analysis of the internal transcribed spacer region of the ribosomal RNA genes for molecular identification of seven snail populations from different localities in Cuba. Using morphological and molecular analysis, we showed that among the studied Cuban Biomphalaria populations only B. havanensis and B. obstructa species were found.

  4. RNA-Seq Using Two Populations Reveals Genes and Alleles Controlling Wood Traits and Growth in Eucalyptus nitens

    OpenAIRE

    Thavamanikumar, Saravanan; Southerton, Simon; Thumma, Bala

    2014-01-01

    Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and allele...

  5. ADAR proteins: structure and catalytic mechanism.

    Science.gov (United States)

    Goodman, Rena A; Macbeth, Mark R; Beal, Peter A

    2012-01-01

    Since the discovery of the adenosine deaminase (ADA) acting on RNA (ADAR) family of proteins in 1988 (Bass and Weintraub, Cell 55:1089-1098, 1988) (Wagner et al. Proc Natl Acad Sci U S A 86:2647-2651, 1989), we have learned much about their structure and catalytic mechanism. However, much about these enzymes is still unknown, particularly regarding the selective recognition and processing of specific adenosines within substrate RNAs. While a crystal structure of the catalytic domain of human ADAR2 has been solved, we still lack structural data for an ADAR catalytic domain bound to RNA, and we lack any structural data for other ADARs. However, by analyzing the structural data that is available along with similarities to other deaminases, mutagenesis and other biochemical experiments, we have been able to advance the understanding of how these fascinating enzymes function. PMID:21769729

  6. RNA-Seq reveals 10 novel promising candidate genes affecting milk protein concentration in the Chinese Holstein population.

    Science.gov (United States)

    Li, Cong; Cai, Wentao; Zhou, Chenghao; Yin, Hongwei; Zhang, Ziqi; Loor, Juan J; Sun, Dongxiao; Zhang, Qin; Liu, Jianfeng; Zhang, Shengli

    2016-01-01

    Paired-end RNA sequencing (RNA-Seq) was used to explore the bovine transcriptome from the mammary tissue of 12 Chinese Holstein cows with 6 extremely high and 6 low phenotypic values for milk protein percentage. We defined the differentially expressed transcripts between the two comparison groups, extremely high and low milk protein percentage during the peak lactation (HP vs LP) and during the non-lactating period (HD vs LD), respectively. Within the differentially expressed genes (DEGs), we detected 157 at peak lactation and 497 in the non-lactating period with a highly significant correlation with milk protein concentration. Integrated interpretation of differential gene expression indicated that SERPINA1, CLU, CNTFR, ERBB2, NEDD4L, ANG, GALE, HSPA8, LPAR6 and CD14 are the most promising candidate genes affecting milk protein concentration. Similarly, LTF, FCGR3A, MEGF10, RRM2 and UBE2C are the most promising candidates that in the non-lactating period could help the mammary tissue prevent issues with inflammation and udder disorders. Putative genes will be valuable resources for designing better breeding strategies to optimize the content of milk protein and also to provide new insights into regulation of lactogenesis. PMID:27254118

  7. Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing

    Science.gov (United States)

    Deep sequencing of viruses isolated from infected hosts is an efficient way to measure population-genetic variation and can reveal patterns of dispersal and natural selection. In this study, we mined existing Illumina sequence reads to investigate single-nucleotide polymorphisms (SNPs) within two RN...

  8. Modulation of RNA function by aminoglycoside antibiotics.

    OpenAIRE

    Schroeder, R; Waldsich, C; Wank, H

    2000-01-01

    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...

  9. RNA nanoparticles come of age

    Institute of Scientific and Technical Information of China (English)

    John J.Rossi

    2011-01-01

    @@ RNA has multiple functions in nature, including informa- tional transfer (mRNA) Ill, adaptor function (tRNAs) [2], guide functions (snRNAs, snoRNAs) [3,4]catalytic func- tion (ribozymes and the large ribosomal RNA) [5-7], and environmental sensing (riboswitehes) [8].In contrast, DNA only serves as an information storage molecule, and proteins serve as structural and enzymatic molecules.

  10. Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Dräger, Carolin;

    2015-01-01

    infectious RNA transcripts. Full length sequencing of cDNA clones and deep sequencing of the parental population identified substitutions important for the observed phenotypes. The investigated cDNA clones were furthermore used as the basis for inferring the sequence of functional viruses. Since each unique......-fitness, functional cDNAs and may also pose problems for sequence-based analysis of viral evolution. To address these challenges we have performed a study of the evolution of classical swine fever virus (CSFV) using deep sequencing and analysis of 84 full-length cDNA clones, each representing individual genomes from...... clone must necessarily be the descendant of a functional ancestor, we hypothesized that it should be possible to produce functional clones by reconstructing ancestral sequences. To test this we used phylogenetic methods to infer two ancestral sequences, which were then reconstructed as cDNA clones...

  11. Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population

    Directory of Open Access Journals (Sweden)

    Nezar Noor Al-hebshi

    2016-05-01

    Full Text Available Background: Reports on the composition of oral bacteriome in Arabs are lacking. In addition, the majority of previous studies on other ethnic groups have been limited by low-resolution taxonomic assignment of next-generation sequencing reads. Furthermore, there has been a conflict about the existence of a ‘core’ bacteriome. Objective: The objective of this study was to characterize the healthy core oral bacteriome in a young Arab population at the species level. Methods: Oral rinse DNA samples obtained from 12 stringently selected healthy young subjects of Arab origin were pyrosequenced (454's FLX chemistry for the bacterial 16S V1–V3 hypervariable region at an average depth of 11,500 reads. High-quality, non-chimeric reads ≥380 bp were classified to the species level using the recently described, prioritized, multistage assignment algorithm. A core bacteriome was defined as taxa present in at least 11 samples. The Chao2, abundance-based coverage estimator (ACE, and Shannon indices were computed to assess species richness and diversity. Results: Overall, 557 species-level taxa (211±42 per subject were identified, representing 122 genera and 13 phyla. The core bacteriome comprised 55 species-level taxa belonging to 30 genera and 7 phyla, namely Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Fusobacteria, Saccharibacteria, and SR1. The core species constituted between 67 and 87% of the individual bacteriomes. However, the abundances differed by up to three orders of magnitude among the study subjects. On average, Streptococcus mitis, Rothia mucilaginosa, Haemophilus parainfluenzae, Neisseria flavescence/subflava group, Prevotella melaninogenica, and Veillonella parvula group were the most abundant. Streptococcus sp. C300, a taxon never reported in the oral cavity, was identified as a core species. Species richness was estimated at 586 (Chao2 and 614 (ACE species, whereas diversity (Shannon index averaged at 3.99. Conclusions

  12. Chromosome mapping of 5S rRNA genes differentiates Brazilian populations of Leporellus vittatus (Anostomidae, Characiformes

    Directory of Open Access Journals (Sweden)

    Cecilia Teixeira de Aguilar

    2008-01-01

    Full Text Available Among the anostomid fishes, the genus Leporellus is represented by only three species: L. nattereri, endemic of the Amazon River, L. retropinnis, endemic of the Piracicaba River, and L. vittatus, widely distributed in rivers from Peru, Colombia, Guianas, and different major hydrographic basins of Brazil. A cytogenetic study carried out on specimens of Leporellus vittatus from three major Brazilian hydrographic basins evidenced a karyotype of 54 metacentric and submetacentric chromosomes. C-banding analysis revealed the presence of large pericentromeric heterochromatic segments in all chromosomes and a telomeric block coincident with the NOR sites. Ag, CMA3 or MM staining, and FISH with ribosomal probes located the 45S ribosomal genes on the terminal region of the long arm of the 12th chromosome pair of all populations. Nevertheless, in the specimens from the Paraná and São Francisco Basins the 5S rDNA clusters were interstitially located by FISH on the long arm of the 2nd chromosome pair, while in the specimens from the Tocantins-Araguaia Basin these sites were observed on the long arm of the 9th chromosome pair and on the short arm of the 17th chromosome pair. These data suggest that the species currently named Leporellus vittatus may comprise a complex of cryptic species.

  13. Catalytic cracking process

    Science.gov (United States)

    Lokhandwala, Kaaeid A.; Baker, Richard W.

    2001-01-01

    Processes and apparatus for providing improved catalytic cracking, specifically improved recovery of olefins, LPG or hydrogen from catalytic crackers. The improvement is achieved by passing part of the wet gas stream across membranes selective in favor of light hydrocarbons over hydrogen.

  14. Catalytic distillation structure

    Science.gov (United States)

    Smith, Jr., Lawrence A.

    1984-01-01

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

  15. Carbon transformations in deep granitic groundwater by attached bacterial populations characterized with 16S-rRNA gene sequencing technique and scanning electron microscopy

    International Nuclear Information System (INIS)

    This report presents molecular characterization of attached bacterial populations growing in slowly flowing (1-3 mm s-1) artesian groundwater from deep crystalline bed-rock of the Stripa research mine, south central Sweden. The assimilation rate of CO2 and lactate, and the lactate respiration rates were also determined. The bacteria studied grew in anoxic, high pH, 9-10, and low redox artesian groundwater flowing up through tubings from two levels of a borehole designated V2, 812-820 m and 970-1240 m below ground. The major groups of bacteria were found. Signature bases placed them in the appropriate systematic groups. All belonged to the Proteobacterial groups beta and gamma. One group was found only at the 812-820 m level, where it constituted 63% of the sequenced clones, whereas the second group existed almost exclusively and constituted 85% of the sequenced clones at the 970-1240 m level. The third group was equally distributed between the levels. A few other bacteria were also found. None of the 16S-rRNA genes from the dominating bacteria resembled any of the other by more than 90% similarity, and none of them resembled anything in the database by more than 96%. Temperature did not seem to have any effect on species composition at the deeper level. SEM images showed rods appearing in microcolonies. The difference in population diversity between the two levels studied presumably reflect the different environments. The earlier proposed presence of sulphate reducing bacteria could no be confirmed

  16. Association between mRNA expression of chemotherapy-related genes and clinicopathological features in colorectal cancer: A large-scale population analysis.

    Science.gov (United States)

    Shimamoto, Yuji; Nukatsuka, Mamoru; Takechi, Teiji; Fukushima, Masakazu

    2016-02-01

    To establish the individualized treatment of patients with colorectal cancer, factors associated with chemotherapeutic effects should be identified. However, to the best of our knowledge, few studies are available on this topic, although it is known that the prognosis of patients and sensitivity to chemotherapy depend on the location of the tumor and that the tumor location is important for individualized treatment. In this study, primary tumors obtained from 1,129 patients with colorectal cancer were used to measure the mRNA expression levels of the following genes associated with the effects of standard chemotherapy for colorectal cancer: 5-fluorouracil (5-FU)-related thymidylate synthase (TYMS), dihydropyrimidine dehydrogenase (DPYD) and thymidine phosphorylase (TYMP); folate-related dihydrofolate reductase (DHFR), folylpolyglutamate synthase (FPGS) and gamma-glutamyl hydrolase (GGH); irinotecan-related topoisomerase I (TOP1); oxaliplatin-related excision repair cross-complementing 1 (ERCC1); biologic agent-related vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR). Large-scale population analysis was performed to determine the association of gene expression with the clinicopathological features, in particular, the location of the colorectal cancer. From the results of our analysis of the mRNA expression of these 10 genes, we noted the strongest correlation between DPYD and TYMP, followed by TYMS and DHFR. The location of the colorectal cancer was classified into 4 regions (the right‑ and left-sided colon, rectosigmoid and rectum) and was compared with gene expression. A significant difference in all genes, apart from VEGF, was noted. Of the remaining 9 genes, the highest expression of TYMS and DPYD was observed in the right‑sided colon; the highest expression of GGH and EGFR was noted in the left-sided colon; the highest expression of DHFR, FPGS, TOP1 and ERCC1 was noted in the rectosigmoid, whereas TYMP

  17. Switching off small RNA regulation with trap-mRNA

    DEFF Research Database (Denmark)

    Overgaard, Martin; Johansen, Jesper; Møller-Jensen, Jakob; Valentin-Hansen, Poul

    2009-01-01

    Small non-coding regulatory RNAs in bacteria have been shown predominantly to be tightly regulated at the level of transcription initiation, and sRNAs that function by an antisense mechanism on trans-encoded target mRNAs have been shown or predicted to act stoichiometrically. Here we show that Mic......M, which silences the expression of an outer membrane protein, YbfM under most growth conditions, does not become destabilized by target mRNA overexpression, indicating that the small RNA regulator acts catalytically. Furthermore, our regulatory studies suggested that control of micM expression is unlikely...... to operate at the level of transcription initiation. By employing a highly sensitive genetic screen we uncovered a novel RNA-based regulatory principle in which induction of a trap-mRNA leads to selective degradation of a small regulatory RNA molecule, thereby abolishing the sRNA-based silencing of...

  18. PNA-mediated modulation and redirection of Her-2 pre-mRNA splicing: specific skipping of erbB-2 exon 19 coding for the ATP catalytic domain

    DEFF Research Database (Denmark)

    Pankratova, Stanislava; Nielsen, Birgit N; Shiraishi, Takehiko;

    2010-01-01

    The Her-2 receptor coded for by the proto-oncogenic erbB-2 gene is a clinically validated target for treatment of a significant genetic subclass of breast cancers, and Her-2 is also overexpressed or mutated in a range of other cancers. In an approach to exploit antisense mediated splicing...... oligomers that specifically induce skipping of exon 19 as this exon is coding for the ATP catalytic domain of Her-2, and if expressed such truncated version of the Her-2 protein should be functionally inactive in a dominant negative fashion. Therefore, antisense compounds having efficient erbB-2 exon 19...... skipping activity could be very interesting in terms of drug discovery. In the present study we identified PNA oligomers having such activity in SK-BR-3 and HeLa cancer cells in culture....

  19. Catalytic Synthesis Lactobionic Acid

    Directory of Open Access Journals (Sweden)

    V.G. Borodina

    2014-07-01

    Full Text Available Gold nanoparticles are obtained, characterized and deposited on the carrier. Conducted catalytic synthesis of lactobionic acid from lactose. Received lactobionic acid identify on the IR spectrum.

  20. Catalytic distillation process

    Science.gov (United States)

    Smith, Jr., Lawrence A.

    1982-01-01

    A method 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.

  1. Catalytic Coanda combustion

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, J.D.; Smith, A.G.; Kopmels, M.

    1992-09-16

    A catalytic reaction is enhanced by the use of the Coanda effect to maximise contact between reactant and catalyst. A device utilising this principle comprises a Coanda surface which directs the flow of fuel from a slot to form a primary jet which entrains the surrounding ambient air and forms a combustible mixture for reaction on a catalytic surface. The Coanda surface may have an internal or external nozzle which may be axi-symmetric or two-dimensional. (author)

  2. Catalytic ignition of light hydrocarbons

    Institute of Scientific and Technical Information of China (English)

    K. L. Hohn; C.-C. Huang; C. Cao

    2009-01-01

    Catalytic ignition refers to phenomenon where sufficient energy is released from a catalytic reaction to maintain further reaction without additional extemai heating. This phenomenon is important in the development of catalytic combustion and catalytic partial oxidation processes, both of which have received extensive attention in recent years. In addition, catalytic ignition studies provide experimental data which can be used to test theoretical hydrocarbon oxidation models. For these reasons, catalytic ignition has been frequently studied. This review summarizes the experimental methods used to study catalytic ignition of light hydrocarbons and describes the experimental and theoretical results obtained related to catalytic ignition. The role of catalyst metal, fuel and fuel concentration, and catalyst state in catalytic ignition are examined, and some conclusions are drawn on the mechanism of catalytic ignition.

  3. RNA genetics

    Energy Technology Data Exchange (ETDEWEB)

    Domingo, E. (Instituto de Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Madrid, Canto Blanco, Madrid (ES)); Holland, J.J. (California Univ., San Diego, La Jolla, CA (USA). Dept. of Biology); Ahlquist, P. (Wisconsin Univ., Madison, WI (USA). Dept. of Plant Pathology)

    1988-01-01

    This book contains the proceedings on RNA genetics: Retroviruses, Viroids, and RNA recombination, Volume 2. Topics covered include: Replication of retrovirus genomes, Hepatitis B virus replication, and Evolution of RNA viruses.

  4. RNA Binding Domain of Telomerase Reverse Transcriptase

    OpenAIRE

    Lai, Cary K.; Mitchell, James R.; Collins, Kathleen

    2001-01-01

    Telomerase is a ribonucleoprotein reverse transcriptase that extends the ends of chromosomes. The two telomerase subunits essential for catalysis in vitro are the telomerase reverse transcriptase (TERT) and the telomerase RNA. Using truncations and site-specific mutations, we identified sequence elements of TERT and telomerase RNA required for catalytic activity and protein-RNA interaction for Tetrahymena thermophila telomerase. We found that the TERT amino and carboxyl termini, although evol...

  5. Quantification of Hyphomicrobium Populations in Activated Sludge from an Industrial Wastewater Treatment System as Determined by 16S rRNA Analysis

    OpenAIRE

    Layton, A C; Karanth, P. N.; Lajoie, C. A.; Meyers, A J; Gregory, I. R.; Stapleton, R. D.; Taylor, D E; Sayler, G. S.

    2000-01-01

    The bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rRNA analysis. 16S ribosomal DNA (rDNA) libraries were created from three sludge samples taken on different dates. Partial rRNA gene sequences were obtained for 46 rDNA clones, and nearly complete 16S rRNA sequences were obtained for 18 clones. Seventeen of these clones were members of the beta subdivision, and their sequences showed high homolog...

  6. RNA catalysis and the origins of life

    Science.gov (United States)

    Orgel, Leslie E.

    1986-01-01

    The role of RNA catalysis in the origins of life is considered in connection with the discovery of riboszymes, which are RNA molecules that catalyze sequence-specific hydrolysis and transesterification reactions of RNA substrates. Due to this discovery, theories positing protein-free replication as preceding the appearance of the genetic code are more plausible. The scope of RNA catalysis in biology and chemistry is discussed, and it is noted that the development of methods to select (or predict) RNA sequences with preassigned catalytic functions would be a major contribution to the study of life's origins.

  7. Catalytic coherence transformations

    Science.gov (United States)

    Bu, Kaifeng; Singh, Uttam; Wu, Junde

    2016-04-01

    Catalytic coherence transformations allow the otherwise impossible state transformations using only incoherent operations with the aid of an auxiliary system with finite coherence that is not being consumed in any way. Here we find the necessary and sufficient conditions for the deterministic and stochastic catalytic coherence transformations between a pair of pure quantum states. In particular, we show that the simultaneous decrease of a family of Rényi entropies of the diagonal parts of the states under consideration is a necessary and sufficient condition for the deterministic catalytic coherence transformations. Similarly, for stochastic catalytic coherence transformations we find the necessary and sufficient conditions for achieving a higher optimal probability of conversion. We thus completely characterize the coherence transformations among pure quantum states under incoherent operations. We give numerous examples to elaborate our results. We also explore the possibility of the same system acting as a catalyst for itself and find that indeed self-catalysis is possible. Further, for the cases where no catalytic coherence transformation is possible we provide entanglement-assisted coherence transformations and find the necessary and sufficient conditions for such transformations.

  8. Coordinated DNA dynamics during the human telomerase catalytic cycle

    OpenAIRE

    Joseph W. Parks; Stone, Michael D.

    2014-01-01

    The human telomerase reverse transcriptase (hTERT) utilizes a template within the integral RNA subunit (hTR) to direct extension of telomeres. Telomerase exhibits repeat addition processivity (RAP) and must therefore translocate the nascent DNA product into a new RNA:DNA hybrid register to prime each round of telomere repeat synthesis. Here we use single-molecule FRET and nuclease protection assays to monitor telomere DNA structure and dynamics during the telomerase catalytic cycle. DNA trans...

  9. The construction of a recombinant cDNA library representative of the poly(A)+ mRNA population from normal human lymphocytes.

    OpenAIRE

    Woods, D.; Crampton, J.; Clarke, B.; Williamson, R

    1980-01-01

    A recombinant library has been constructed using the plasmid pAT153 and double stranded cDNA prepared from normal human lymphocyte poly(A)+ RNA. Transformation conditions were optimized to yield approximately 200,000 recombinants per microgram of double stranded cDNA. Statistical analysis as well as sequence complexity analysis of the inserted sequences indicates that the cDNA library is representative of > 99% of the poly(A)+ RNA present in the normal human lymphocyte.

  10. Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP

    OpenAIRE

    IKAWA, YOSHIYA; Tsuda, Kentaro; Matsumura, Shigeyoshi; Atsumi, Shota; Inoue, Tan

    2003-01-01

    A hypothetical evolutionary pathway from a ribozyme to a catalytic RNA–protein complex (RNP) is proposed and examined. In this hypothesis for an early phase of molecular evolution, one RNA–RNA interaction in the starting ribozyme is replaced with an RNA–protein interaction via two intermediary stages. At each stage, the original RNA–RNA interaction and a newly introduced RNA–protein interaction are designed to coexist. The catalytic RNPs corresponding to the intermediary stages were construct...

  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. Forms and Functions of Telomerase RNA

    Science.gov (United States)

    Collins, Kathleen

    Telomerase adds single-stranded telomeric DNA repeats to chromosome ends. Unlike other polymerases involved in genome replication, telomerase synthe¬sizes DNA without use of a DNA template. Instead, the enzyme active site copies a template carried within the integral RNA subunit of the telomerase ribonucleo-protein (RNP) complex. In addition to providing a template, telomerase RNA has non-template motifs with critical functions in the catalytic cycle of repeat synthesis. In its complexity of structure and function, telomerase RNA resembles the non-coding RNAs of RNP machines like the ribosome and spliceosome that evolved from catalytic RNAs of the RNA World. However, unlike these RNPs, telomerase evolved its RNP identity after advent of the Protein World. Insights about telomer-ase have broad significance for understanding non-coding RNA biology as well as chromosome end maintenance and human disease.

  13. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

    Energy Technology Data Exchange (ETDEWEB)

    Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D. [MSKCC

    2014-08-20

    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

  14. Catalytic methanol dissociation

    International Nuclear Information System (INIS)

    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

  15. Catalytic Phosphination and Arsination

    Institute of Scientific and Technical Information of China (English)

    Kwong Fuk Yee; Chan Kin Shing

    2004-01-01

    The catalytic, user-friendly phosphination and arsination of aryl halides and triflates by triphenylphosphine and triphenylarsine using palladium catalysts have provided a facile synthesis of functionalized aryl phosphines and arsines in neutral media. Modification of the cynaoarisne yielded optically active N, As ligands which will be screened in various asymmetric catalysis.

  16. Monolithic catalytic igniters

    Science.gov (United States)

    La Ferla, R.; Tuffias, R. H.; Jang, Q.

    1993-01-01

    Catalytic igniters offer the potential for excellent reliability and simplicity for use with the diergolic bipropellant oxygen/hydrogen as well as with the monopropellant hydrazine. State-of-the-art catalyst beds - noble metal/granular pellet carriers - currently used in hydrazine engines are limited by carrier stability, which limits the hot-fire temperature, and by poor thermal response due to the large thermal mass. Moreover, questions remain with regard to longevity and reliability of these catalysts. In this work, Ultramet investigated the feasibility of fabricating monolithic catalyst beds that overcome the limitations of current catalytic igniters via a combination of chemical vapor deposition (CVD) iridium coatings and chemical vapor infiltration (CVI) refractory ceramic foams. It was found that under all flow conditions and O2:H2 mass ratios tested, a high surface area monolithic bed outperformed a Shell 405 bed. Additionally, it was found that monolithic catalytic igniters, specifically porous ceramic foams fabricated by CVD/CVI processing, can be fabricated whose catalytic performance is better than Shell 405 and with significantly lower flow restriction, from materials that can operate at 2000 C or higher.

  17. Modulation of RNA function by aminoglycoside antibiotics.

    Science.gov (United States)

    Schroeder, R; Waldsich, C; Wank, H

    2000-01-01

    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. PMID:10619838

  18. Kinetic oscillations in the expression of messenger RNA, regulatory protein, and nonprotein coding RNA

    Science.gov (United States)

    Zhdanov, Vladimir P.

    2008-06-01

    The interplay of messenger RNA (mRNA), protein, produced via translation of this RNA, and nonprotein coding RNA (ncRNA) may include regulation of the ncRNA production by protein and (i) ncRNA-mRNA association or (ii) ncRNA-protein association resulting in degradation of the corresponding complex. The kinetic models, describing these two scenarios and taking into account that the association of ncRNA with a target occurs after ncRNA conversion from the initial form to the final form (e.g., from a long RNA to microRNA), are found to predict oscillations provided that the rate of ncRNA formation increases with increasing protein population.

  19. Interaction between Polymorphisms in Pre-MiRNA Genes and Cooking Oil Fume Exposure on the Risk of Lung Cancer in Chinese Non-Smoking Female Population.

    Directory of Open Access Journals (Sweden)

    Zhihua Yin

    Full Text Available Both genetic polymorphisms and environmental risk factors play important roles in the development of human chronic diseases including lung cancer. This is the first case-control study of interaction between polymorphisms in pre-miRNA genes and cooking oil fume exposure on the risk of lung cancer.A hospital-based case-control study of 258 cases and 310 controls was conducted. Six polymorphisms in miRNAs were determined by Taqman allelic discrimination method. The gene-environment interactions were assessed on both additive and multiplicative scale. The statistical analyses were performed mostly with SPSS.The combination of the risk genotypes of five miRNA SNPs (miR-146a rs2910164, miR-196a2 rs11614913, miR-608 rs4919510, miR-27a rs895819 and miR-423 rs6505162 with risk factor (cooking oil fume exposure contributed to a significantly higher risk of lung cancer, and the corresponding ORs (95% confidence intervals were 1.91(1.04-3.52, 1.94 (1.16-3.25, 2.06 (1.22-3.49, 1.76 (1.03-2.98 and 2.13 (1.29-3.51. The individuals with both risk genotypes of miRNA SNPs and exposure to risk factor (cooking oil fumes were in a higher risk of lung cancer than persons with only one of the two risk factors (ORs were 1.91, 1.05 and 1.41 for miR-146a rs2910164, ORs were 1.94, 1.23 and 1.34 for miR-196a2 rs11614913, ORs were 2.06, 1.41 and 1.68 for miR-608 rs4919510, ORs were 1.76, 0.82 and 1.07 for miR-27a rs895819, and ORs were 2.13, 1.15 and 1.02 for miR-423 rs6505162, respectively. All the measures of biological interaction indicate that there were not indeed biological interactions between the six SNPs of miRNAs and exposure to cooking oil fumes on an additive scale. Logistic models suggested that the gene-environment interactions were not statistically significant on a multiplicative scale.The interactions between miRNA SNPs and cooking oil fume exposure suggested by ORs of different combination were not statistically significant.

  20. Detecting deletions, insertions, and single nucleotide substitutions in cloned β-globin genes and new polymorphic nucleotide substitutions in β-globin genes in a Japanese population using ribonuclease cleavage at mismatches in RNA: DNA duplexes

    International Nuclear Information System (INIS)

    The applicability of ribonuclease (RNase) cleavage at mismatches in RNA:DNA duplexes (the RNase cleavage method) for determining nucleotide variant rates was examined in a Japanese population. DNA segments of various lengths obtained from four different regions of one normal and three thalassemic cloned human β-globin genes were inserted into transcription vectors. Sense and antisense RNA probes uniformly labeled with 32P were prepared. When RNA probes of 771 nucleotides (nt) or less were hybridized with cloned DNAs and the resulting duplexes were treated with a mixture of RNases A and T1, the length of products agreed with theoretical values. Twelve possible mismatches were examined. Since both sense and antisense probes were used, uncleavable mismatches such as G:T and G:G which were made from one combination of RNA and DNA strands could be converted to the cleavable C:A and C:C mismatches, respectively, by using the opposite combination. Deletions and insertions of one (G), four(TTCT), five (ATTTT), and 10 (ATTTTATTTT) nt were easily detected. A polymorphic substitution of T to C at position 666 of the second intervening sequence (IVS2-666) of the β-globin gene was detected using genomic DNAs from cell lines established from the peripheral B lymphocytes of 59 unrelated Japanese from Hiroshima or those amplified by polymerase chain reaction (PCR). The frequency of the gene with C at the IVS2-666 (allele C) was 0.48 and that of the gene with T (allene T) was 0.52. Two new polymorphic substitutions of C to A and A to T were detected at nucleotide positions 1789 and 1945 from the capping site, respectively, using genomic DNAs amplified by PCR. We conclude that it would be feasible to use the RNase cleavage method combined with PCR for large-scale screening of variation in chromosomal DNA. (J.P.N.)

  1. Novel 16S rRNA based PCR method targeting Deinococcus spp. and its application to assess the diversity of deinococcal populations in environmental samples.

    Science.gov (United States)

    Chaturvedi, Ruchi; Archana, G

    2012-09-01

    The members of the genus Deinococcus are extensively studied because of their exemplary radiation resistance. Both ionizing and non-ionizing rays are routinely employed to select upon the radiation resistant deinococcal population and isolate them from the majority of radiation sensitive population. There are no studies on the development of molecular tools for the rapid detection and identification of deinococci from a mixed population without causing the bias of radiation enrichment. Here we present a Deinococcus specific two-step hemi-nested PCR for the rapid detection of deinococci from environmental samples. The method is sensitive and specific to detect deinococci without radiation exposure of the sample. The new protocol was successfully employed to detect deinococci from several soil samples from different geographical regions of India. The PCR method could be adapted to a three-step protocol to study the diversity of the environmental deinococcal population by denaturing gradient gel electrophoresis (DGGE). Sequence analysis of the DGGE bands revealed that the samples harbor diverse populations of deinococci, many of which were not recovered by culturing and may represent novel clades. We demonstrate that the genus specific primers are also suitable for the rapid identification of the bacterial isolates that are obtained from a typical radiation enrichment isolation technique. Therefore the primers and the protocols described in this study can be used to study deinococcal diversity from environmental samples and can be employed for the rapid detection of deinococci in samples or identifying pure culture isolates as Deinococcus species. PMID:22609328

  2. Catalytic reforming process

    Energy Technology Data Exchange (ETDEWEB)

    Absil, R.P.; Huss, A. Jr.; McHale, W.D.; Partridge, R.D.

    1989-06-13

    This patent describes a catalytic reforming process which comprises contacting a naphtha range feed with a low acidity extrudate comprising an intermediate and/or a large pore acidic zeolite bound with a low acidity refractory oxide under reforming conditions to provide a reaction product of increased aromatic content, the extrudate having been prepared with at least an extrusion-facilitating amount of a low acidity refractory oxide in colloidal form and containing at least one metal species selected from the platinum group metals.

  3. 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.

  4. Evolution of DNA and RNA as catalysts for chemical reactions.

    Science.gov (United States)

    Jäschke, A; Seelig, B

    2000-06-01

    In vitro selection from combinatorial nucleic acid libraries has provided new RNA and DNA molecules that have catalytic properties. Catalyzed reactions now go far beyond self-modifying reactions of nucleic acid molecules. The future application of in vitro selected RNA and DNA catalysts in bioorganic synthesis appears promising. PMID:10826969

  5. Bifunctional catalytic electrode

    Science.gov (United States)

    Cisar, Alan (Inventor); Murphy, Oliver J. (Inventor); Clarke, Eric (Inventor)

    2005-01-01

    The present invention relates to an oxygen electrode for a unitized regenerative hydrogen-oxygen fuel cell and the unitized regenerative fuel cell having the oxygen electrode. The oxygen electrode contains components electrocatalytically active for the evolution of oxygen from water and the reduction of oxygen to water, and has a structure that supports the flow of both water and gases between the catalytically active surface and a flow field or electrode chamber for bulk flow of the fluids. The electrode has an electrocatalyst layer and a diffusion backing layer interspersed with hydrophilic and hydrophobic regions. The diffusion backing layer consists of a metal core having gas diffusion structures bonded to the metal core.

  6. 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.

  7. Identification of Two RNA-binding Proteins Associated with Human Telomerase RNA

    OpenAIRE

    Le, Siyuan; Sternglanz, Rolf; Greider, Carol W

    2000-01-01

    Telomerase plays a crucial role in telomere maintenance in vivo. To understand telomerase regulation, we have been characterizing components of the enzyme. To date several components of the mammalian telomerase holoenzyme have been identified: the essential RNA component (human telomerase RNA [hTR]), the catalytic subunit human telomerase reverse transcriptase (hTERT), and telomerase-associated protein 1. Here we describe the identification of two new proteins that interact with hTR: hStau an...

  8. Unsteady catalytic processes and sorption-catalytic technologies

    International Nuclear Information System (INIS)

    Catalytic processes that occur under conditions of the targeted unsteady state of the catalyst are considered. The highest efficiency of catalytic processes was found to be ensured by a controlled combination of thermal non-stationarity and unsteady composition of the catalyst surface. The processes based on this principle are analysed, in particular, catalytic selective reduction of nitrogen oxides, deep oxidation of volatile organic impurities, production of sulfur by the Claus process and by hydrogen sulfide decomposition, oxidation of sulfur dioxide, methane steam reforming and anaerobic combustion, selective oxidation of hydrocarbons, etc.

  9. Sequence polymorphism of GroEL gene in natural population of Bacillus and Brevibacillus spp. that showed variation in thermal tolerance capacity and mRNA expression.

    Science.gov (United States)

    Sen, R; Tripathy, S; Padhi, S K; Mohanty, S; Maiti, N K

    2014-10-01

    GroEL, a class I chaperonin, plays an important role in the thermal adaptation of the cell and helps to maintain the viability of the cell under heat shock condition. Function of groEL in vivo depends on the maintenance of proper structure of the protein which in turn depends on the nucleotide and amino acid sequence of the gene. In this study, we investigated the changes in nucleotide and amino acid sequences of the partial groEL gene that may affect the thermotolerance capacity as well as mRNA expression of bacterial isolates. Sequences among the same species having differences in the amino acid level were identified as different alleles. The effect of allelic variation on the groEL gene expression was analyzed by comparison and relative quantification in each allele under thermal shock condition by RT-PCR. Evaluation of K a/K s ratio among the strains of same species showed that the groEL gene of all the species had undergone similar functional constrain during evolution. The strains showing similar thermotolerance capacity was found to carry same allele of groEL gene. The isolates carrying allele having amino acid substitution inside the highly ATP/ADP or Mg(2+)-binding region could not tolerate thermal stress and showed lower expression of the groEL gene. Our results indicate that during evolution of these bacterial species the groEL gene has undergone the process of natural selection, and the isolates have evolved with the groEL allelic sequences that help them to withstand the thermal stress during their interaction with the environment. PMID:24894903

  10. Polymorphisms in pre-miRNA genes and cooking oil fume exposure as well as their interaction on the risk of lung cancer in a Chinese nonsmoking female population

    Science.gov (United States)

    Yin, Zhihua; Li, Hang; Cui, Zhigang; Ren, Yangwu; Li, Xuelian; Wu, Wei; Guan, Peng; Qian, Biyun; Rothman, Nathaniel; Lan, Qing; Zhou, Baosen

    2016-01-01

    Background MicroRNAs (miRNAs) are suggested to be very important in the development of lung cancer. This study assesses the association between polymorphisms in miRNA-related (miR)-26a-1, miR-605, and miR-16-1 genes and risk of lung cancer, as well as the effect of gene–environment interaction between miRNA polymorphisms and cooking fume exposure on lung cancer. Methods A case–control study including 268 diagnosed nonsmoking female lung cancer patients and 266 nonsmoking female controls was carried out. Three miRNA polymorphisms (miR-26a-1 rs7372209, miR-605 rs2043556, and miR-16-1 rs1022960) were analyzed. Both additive and multiplicative interactions were assessed. Results MiR-16-1 rs1022960 may be associated with the risk of lung cancer. Carriers with TT genotype of miR-16-1 rs1022960 were observed to have a decreased risk of lung cancer compared with CC and CT genotype carriers (odds ratio =0.550, 95% confidence interval =0.308–0.983, P=0.044). MiR-26a-1 rs7372209 and miR-605 rs2043556 showed no statistically significant associations with lung cancer risk. There were no significant associations between the three single nucleotide polymorphisms and lung adenocarcinoma. People with exposure to both risk genotypes of miR-26a-1 rs7372209 and cooking oil fumes were more likely to develop lung cancer than those with only genetic risk factor or cooking oil fumes (odds ratios were 2.136, 1.255, and 1.730, respectively). The measures of biological interaction and logistic models indicate that gene–environment interactions were not statistically significant on additive scale or multiplicative scale. Conclusion MiR-16-1 rs1022960 may be associated with the risk of lung cancer in a Chinese nonsmoking female population. The interactions between miRNA polymorphisms (miR-26a-1 rs7372209, miR-605 rs2043556, and miR-16-1 rs1022960) and cooking oil fumes were not statistically significant. PMID:26855588

  11. 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

  12. Structures of two exonucleases involved in controlled RNA turnover in yeast

    DEFF Research Database (Denmark)

    Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich;

    2p is a catalytic subunit of the cytoplasmic deadenylase complex [2], which removes the poly(A) tail in the 3'-end of mRNA, the first and rate-limiting step of controlled mRNA turnover in the general eukaryotic mRNA degradation pathway [3]. The crystal structure of the central part of S. cerevisiae...

  13. Immigration process in catalytic medium

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The longtime behavior of the immigration process associated with a catalytic super-Brownian motion is studied. A large number law is proved in dimension d≤3 and a central limit theorem is proved for dimension d=3.

  14. Mechanism of Action and Antiviral Activity of Benzimidazole-Based Allosteric Inhibitors of the Hepatitis C Virus RNA-Dependent RNA Polymerase

    OpenAIRE

    Tomei, Licia; Altamura, Sergio; Bartholomew, Linda; Biroccio, Antonino; Ceccacci, Alessandra; Pacini, Laura; Narjes, Frank; Gennari, Nadia; Bisbocci, Monica; Incitti, Ilario; Orsatti, Laura; Harper, Steven; Stansfield, Ian; Rowley, Michael; De Francesco, Raffaele

    2003-01-01

    The RNA-dependent RNA polymerase of hepatitis C virus (HCV) is the catalytic subunit of the viral RNA amplification machinery and is an appealing target for the development of new therapeutic agents against HCV infection. Nonnucleoside inhibitors based on a benzimidazole scaffold have been recently reported. Compounds of this class are efficient inhibitors of HCV RNA replication in cell culture, thus providing attractive candidates for further development. Here we report the detailed analysis...

  15. Polymorphisms in pre-miRNA genes and cooking oil fume exposure as well as their interaction on the risk of lung cancer in a Chinese nonsmoking female population

    Directory of Open Access Journals (Sweden)

    Yin Z

    2016-01-01

    were 2.136, 1.255, and 1.730, respectively. The measures of biological interaction and logistic models indicate that gene–environment interactions were not statistically significant on additive scale or multiplicative scale. Conclusion: MiR-16-1 rs1022960 may be associated with the risk of lung cancer in a Chinese nonsmoking female population. The interactions between miRNA polymorphisms (miR-26a-1 rs7372209, miR-605 rs2043556, and miR-16-1 rs1022960 and cooking oil fumes were not statistically significant. Keywords: lung cancer, microRNA, single nucleotide polymorphism, cooking oil fume, interaction

  16. Coordinated DNA dynamics during the human telomerase catalytic cycle

    Science.gov (United States)

    Parks, Joseph W.; Stone, Michael D.

    2014-06-01

    The human telomerase reverse transcriptase (hTERT) utilizes a template within the integral RNA subunit (hTR) to direct extension of telomeres. Telomerase exhibits repeat addition processivity (RAP) and must therefore translocate the nascent DNA product into a new RNA:DNA hybrid register to prime each round of telomere repeat synthesis. Here, we use single-molecule FRET and nuclease protection assays to monitor telomere DNA structure and dynamics during the telomerase catalytic cycle. DNA translocation during RAP proceeds through a previously uncharacterized kinetic substep during which the 3‧-end of the DNA substrate base pairs downstream within the hTR template. The rate constant for DNA primer realignment reveals this step is not rate limiting for RAP, suggesting a second slow conformational change repositions the RNA:DNA hybrid into the telomerase active site and drives the extrusion of the 5‧-end of the DNA primer out of the enzyme complex.

  17. 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...

  18. Mini-ribozymes and freezing environment: a new scenario for the early RNA world

    Directory of Open Access Journals (Sweden)

    A. V. Vlassov

    2005-11-01

    Full Text Available The RNA World hypothesis states that the present-day life, which is based on DNA genomes and protein enzymes, was preceded by a simpler life form based primarily on RNA. During this era, the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA. Though it is a widely accepted scenario, a number of problems remain unsolved. One of the biggest questions is how complex RNAs could evolve, survive and replicate under typically assumed ''warm and wet'' conditions, taking into account that the RNA phosphodiester backbone is chemically unstable under these conditions. We suggest that prebiotic conditions associated with freezing could have been of key importance in the early RNA World, and discuss the role of primitive catalytic RNA in the evolution of RNA size and complexity.

  19. 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

    2015-09-01

    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. PMID:26206671

  20. 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....

  1. Catalytic distillation water recovery subsystem

    Science.gov (United States)

    Budininkas, P.; Rasouli, F.

    1985-01-01

    An integrated engineering breadboard subsystem for the recovery of potable water from untreated urine based on the vapor phase catalytic ammonia removal was designed, fabricated and tested. Unlike other evaporative methods, this process catalytically oxidizes ammonia and volatile hydrocarbons vaporizing with water to innocuous products; therefore, no pretreatment of urine is required. Since the subsystem is fabricated from commercially available components, its volume, weight and power requirements are not optimized; however, it is suitable for zero-g operation. The testing program consists of parametric tests, one month of daily tests and a continuous test of 168 hours duration. The recovered water is clear, odorless, low in ammonia and organic carbon, and requires only an adjustment of its pH to meet potable water standards. The obtained data indicate that the vapor phase catalytic ammonia removal process, if further developed, would also be competitive with other water recovery systems in weight, volume and power requirements.

  2. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    Vivek V Ranade

    2014-03-01

    Catalytic reactions are ubiquitous in chemical and allied industries. A homogeneous or heterogeneous catalyst which provides an alternative route of reaction with lower activation energy and better control on selectivity can make substantial impact on process viability and economics. 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 discussed. Some examples where performance enhancement was realized by catalyst design, appropriate choice of reactor, better injection and dispersion strategies and recent advances in process intensification/ multifunctional reactors are discussed to illustrate the approach.

  3. Biochemistry and Function of the RNA Exosomes

    DEFF Research Database (Denmark)

    Lubas, Michal Szymon; Chlebowski, Aleksander; Dziembowski, Andrzej;

    2012-01-01

    Discovery of the evolutionary conserved RNA exosome was a milestone in RNA biology. First identified as an activity essential for the processing of ribosomal RNA, the exosome has since proved to be central for RNA processing and degradation in both the nucleus and the cytoplasm of eukaryotic cells....... This multisubunit protein complex consists of a catalytically inert 9-subunit core endowed with associated ribonucleolytic activities and further assisted by compartment-specific cofactors required for its activation and substrate targeting. Although many features of exosome biology are known, fundamental aspects...... are still under investigation. In this chapter, we review current biochemical and functional knowledge of eukaryotic exosomes. After introducing some of their nuclear and cytoplasmic functions, we discuss the structural organization and evolutionary aspects of exosome complexes. Finally, we describe...

  4. Exploring tertiary folding in RNA : novel structural motifs in HDV and TYMV RNA studied by NMR spectroscopy

    OpenAIRE

    Kolk, M H

    1999-01-01

    RNA molecules lie at the basis of many cellular processes. They serve as a carrier of information, but can also form intricate complexes with proteins and other RNAs, and can even have catalytic activity, in which case they are called ribozymes. This versatility of RNA function relates to a wide range of structural properties. Apart from the tRNA structure (1973), however, the number of high-resolution structures have long remained very low. Presently, in the midst of a surge of RNA structure...

  5. Catalytic properties of niobium compounds

    International Nuclear Information System (INIS)

    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)

  6. Protein composition of catalytically active human telomerase from immortal cells

    DEFF Research Database (Denmark)

    Cohen, Scott B; Graham, Mark E; Lovrecz, George O;

    2007-01-01

    Telomerase is a ribonucleoprotein enzyme complex that adds 5'-TTAGGG-3' repeats onto the ends of human chromosomes, providing a telomere maintenance mechanism for approximately 90% of human cancers. We have purified human telomerase approximately 10(8)-fold, with the final elution dependent on the...... enzyme's ability to catalyze nucleotide addition onto a DNA oligonucleotide of telomeric sequence, thereby providing specificity for catalytically active telomerase. Mass spectrometric sequencing of the protein components and molecular size determination indicated an enzyme composition of two molecules...... each of telomerase reverse transcriptase, telomerase RNA, and dyskerin....

  7. Population genetics without intraspecific data

    DEFF Research Database (Denmark)

    Thorne, Jeffrey L; Choi, Sang Chul; Yu, Jiaye;

    2007-01-01

    populations, and parameters of interspecific models should have population genetic interpretations. We show, with two examples, how population genetic interpretations can be assigned to evolutionary models. The first example considers the impact of RNA secondary structure on sequence change, and the second...... genetic interpretation. Udgivelsesdato: 2007-Aug...

  8. 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

  9. 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.

  10. Analogies between the tRNA methylating enzymes and tRNA's in embryonic and tumor tissues

    Energy Technology Data Exchange (ETDEWEB)

    Borek, E.

    1975-01-01

    Progress is reported in the following areas of research, role of tRNA in protein synthesis and as a carrier of amino acids; histidine pathway in Salmonella typhimurium; role of tRNA in regulation of translation; ribosomal binding reactions; role of tRNA in hemoglobin synthesis; population of tRNA's in mutant of Drosophila; methylation of tRNA and DNA by dimethylnitrosamine; purification of DNA methylase from HeLa cell nuclei; effects of age on levels of excretion of tRNA breakdown products in cancer patients; and tyrosyl tRNA's in embryonic and adult liver and in hepatomas. (HLW)

  11. Combined catalytic converter and afterburner

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.

    1994-11-30

    This patent describes the combined use of a catalytic converter and afterburner. An afterburner chamber and a catalyst matrix are disposed in series within a casing. A combustible premixed charge is ignited in the afterburner chamber before it enters the catalyst matrix. This invention overcomes the problem encountered in previous designs of some of the premixed charge passing unreacted through the device unless a very long afterburner chamber is used. (UK)

  12. Investigations for designing catalytic recombiners

    International Nuclear Information System (INIS)

    In case of a severe accident in pressurised water reactors (PWR) a high amount of hydrogen up to about 20,000 m3 might be generated and released into the containments. The mixture consisting of hydrogen and oxygen may either burn or detonate, if ignited. In case of detonation the generated shock wave may endanger the components of the plant or the plant itself. Consequently, effective removal of hydrogen is required. The fact that hydrogen and oxygen react exo-thermally on catalytically acting surfaces already at low temperatures generating steam and heat is made use of in catalytic recombiners. They consist of substrates coated with catalyst (mainly platinum or palladium) which are arranged inside a casing. Being passively acting measures, recombiners do not need any additional energy supply. Experimental investigations on catalytic hydrogen recombination are conducted at FZJ (Forschungszentrum Juelich) using three test facilities. The results yield insight in the development potential of contemporary recombiner systems as well as of innovative systems. Detailed investigations on a recombiner section show strong temperature gradients over the surface of a catalytically coated sample. Dependent on the flow velocity, ignition temperature may be reached at the leading edge already at an inlet hydrogen concentration of about 5 vol.-%. The thermal strain of the substrate leads to considerable detachment of catalyst particles probably causing unintended ignition of the flammable mixture. Temperature peaks can be prevented effectively by leaving the first part of the plate uncoated. In order to avoid overheating of the catalyst elements of a recombiner even at high hydrogen concentrations a modular system of porous substrates is proposed. The metallic substrates are coated with platinum at low catalyst densities thus limiting the activity of the single specimen. A modular arrangement of these elements provides high recombination rates over a large hydrogen concentration

  13. New Catalytic DNA Biosensors for Radionuclides and Metal ions

    International Nuclear Information System (INIS)

    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

  14. Measurably evolving populations

    DEFF Research Database (Denmark)

    Drummond, Alexei James; Pybus, Oliver George; Rambaut, Andrew;

    2003-01-01

    processes through time. Populations for which such studies are possible � measurably evolving populations (MEPs) � are characterized by sufficiently long or numerous sampled sequences and a fast mutation rate relative to the available range of sequence sampling times. The impact of sequences sampled through...... time has been most apparent in the disciplines of RNA viral evolution and ancient DNA, where they enable us to estimate divergence times without paleontological calibrations, and to analyze temporal changes in population size, population structure and substitution rates. Thus, MEPs could increase our...

  15. Tertiary structure of bacterial selenocysteine tRNA.

    Science.gov (United States)

    Itoh, Yuzuru; Sekine, Shun-ichi; Suetsugu, Shiro; Yokoyama, Shigeyuki

    2013-07-01

    Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNA(Sec)) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNA(Sec) from the bacterium Aquifex aeolicus, in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri. The bacterial tRNA(Sec) assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNA(Sec)s, A. aeolicus tRNA(Sec) has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNA(Sec) in vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA(Sec). Similar interactions exist in the reported tRNA(Ser) and SerRS complex structure from the bacterium Thermus thermophilus. Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNA(Sec) in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNA(Sec) to enter the SerRS catalytic site. PMID:23649835

  16. Let-7 miRNA-binding site polymorphism in the KRAS 3′UTR; colorectal cancer screening population prevalence and influence on clinical outcome in patients with metastatic colorectal cancer treated with 5-fluorouracil and oxaliplatin +/− cetuximab

    Directory of Open Access Journals (Sweden)

    Kjersem Janne B

    2012-11-01

    Full Text Available Abstract Background Recent studies have reported associations between a variant allele in a let-7 microRNA complementary site (LCS6 within the 3′untranslated region (3′UTR of KRAS (rs61764370 and clinical outcome in metastatic colorectal cancer (mCRC patients receiving cetuximab. The variant allele has also been associated with increased cancer risk. We aimed to reveal the incidence of the variant allele in a colorectal cancer screening population and to investigate the clinical relevance of the variant allele in mCRC patients treated with 1st line Nordic FLOX (bolus 5-fluorouracil/folinic acid and oxaliplatin +/− cetuximab. Methods The feasibility of the variant allele as a risk factor for CRC was investigated by comparing the LCS6 gene frequencies in 197 CRC patients, 1060 individuals with colorectal polyps, and 358 healthy controls. The relationship between clinical outcome and LCS6 genotype was analyzed in 180 mCRC patients receiving Nordic FLOX and 355 patients receiving Nordic FLOX + cetuximab in the NORDIC-VII trial (NCT00145314. Results LCS6 frequencies did not vary between CRC patients (23%, individuals with polyps (20%, and healthy controls (20% (P = 0.50. No statistically significant differences were demonstrated in the NORDIC-VII cohort even if numerically increased progression-free survival (PFS and overall survival (OS were found in patients with the LCS6 variant allele (8.5 (95% CI: 7.3-9.7 months versus 7.8 months (95% CI: 7.4-8.3 months, P = 0.16 and 23.5 (95% CI: 21.6-25.4 months versus 19.5 months (95% CI: 17.8-21.2 months, P = 0.31, respectively. Addition of cetuximab seemed to improve response rate more in variant carriers than in wild-type carriers (from 35% to 57% versus 44% to 47%, however the difference was not statistically significant (interaction P = 0.16. Conclusions The LCS6 variant allele does not seem to be a risk factor for development of colorectal polyps or CRC. No statistically significant effect of the

  17. Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme

    Science.gov (United States)

    Ahmad, Sadeem; Muthukumar, Sowndarya; Kuncha, Santosh Kumar; Routh, Satya Brata; Yerabham, Antony S. K.; Hussain, Tanweer; Kamarthapu, Venu; Kruparani, Shobha P.; Sankaranarayanan, Rajan

    2015-06-01

    Proofreading modules of aminoacyl-tRNA synthetases are responsible for enforcing a high fidelity during translation of the genetic code. They use strategically positioned side chains for specifically targeting incorrect aminoacyl-tRNAs. Here, we show that a unique proofreading module possessing a D-aminoacyl-tRNA deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. We show, using three distinct archaea, that a side-chain-stripped recognition site is fully capable of solving a subtle discrimination problem. While biochemical probing establishes that RNA plays the catalytic role, mechanistic insights from multiple high-resolution snapshots reveal that differential remodelling of the catalytic core at the RNA-peptide interface provides the determinants for correct proofreading activity. The functional crosstalk between RNA and protein elucidated here suggests how primordial enzyme functions could have emerged on RNA-peptide scaffolds before recruitment of specific side chains.

  18. 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...

  19. 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...

  20. Determinants in mammalian telomerase RNA that mediate enzyme processivity and cross-species incompatibility

    OpenAIRE

    Chen, Jiunn-Liang; Greider, Carol W

    2003-01-01

    Telomerase contains two essential components: an RNA molecule that templates telomeric repeat synthesis and a catalytic protein component. Human telomerase is processive, while the mouse enzyme has much lower processivity. We have identified nucleotide determinants in the telomerase RNA that are responsible for this difference in processivity. Mutations adjacent to the template region of human and mouse telomerase RNA significantly altered telomerase processivity both in vitro and in vivo. We...

  1. Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

    OpenAIRE

    Qi, Lei S.; Larson, Matthew H.; Gilbert, Luke A.; Doudna, Jennifer A.; Weissman, Jonathan S.; Arkin, Adam P; Lim, Wendell A.

    2013-01-01

    Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase bindin...

  2. The effect of structure in a long target RNA on ribozyme cleavage efficiency.

    OpenAIRE

    Campbell, T B; McDonald, C K; Hagen, M.

    1997-01-01

    Inhibition of gene expression by catalytic RNA (ribozymes) requires that ribozymes efficiently cleave specific sites within large target RNAs. However, the cleavage of long target RNAs by ribozymes is much less efficient than cleavage of short oligonucleotide substrates because of higher order structure in the long target RNA. To further study the effects of long target RNA structure on ribozyme cleavage efficiency, we determined the accessibility of seven hammerhead ribozyme cleavage sites i...

  3. piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

    OpenAIRE

    Senti, Kirsten-André; Jurczak, Daniel; Sachidanandam, Ravi; Brennecke, Julius

    2015-01-01

    In this study, Senti et al investigate how cytoplasmic post-transcriptional silencing influences transcriptional silencing in the nucleus. They show that Piwi-bound piRNA populations depend almost exclusively on prior piRNA-guided transcript slicing, thus providing further insight into the regulation of piRNA biogenesis in the developing Drosophila ovary.

  4. Structural basis for catalytically restrictive dynamics of a high-energy enzyme state

    Science.gov (United States)

    Kovermann, Michael; Ådén, Jörgen; Grundström, Christin; Elisabeth Sauer-Eriksson, A.; Sauer, Uwe H.; Wolf-Watz, Magnus

    2015-07-01

    An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or `invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power--a key aspect in rational design of enzymes catalysing novel reactions.

  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. 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.

  7. Studies of Catalytic Model Systems

    DEFF Research Database (Denmark)

    Holse, Christian

    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...... observed by XPS as the nanoparticles are reduced. The Cu/ZnO nanoparticles are tested on a  µ-reactor platform and prove to be active towards methanol synthesis, making it an excellent model system for further investigations into activity depended morphology changes....

  8. Catalytic Spectrophotometric Determination of Chromium

    OpenAIRE

    STOYANOVA, Angelina Miltcheva

    2005-01-01

    The catalytic effect of chromium(III) and chromium(VI) on the oxidation of sulfanilic acid by hydrogen peroxide was studied. The reaction was followed spectrophotometrically by measuring the absorbance of the reaction product at 360 nm. Under the optimum conditions 2 calibration graphs (for chromium(III) up to 100 ng mL-1, and for chromium(VI) up to 200 ng mL-1) were obtained, using the ``fixed time'' method with detection limits of 4.9 ng mL-1 and 3.8 ng mL-1, respectively...

  9. Catalytic Combustion of Ethyl Acetate

    OpenAIRE

    ÖZÇELİK, Tuğba GÜRMEN; ATALAY, Süheyda; ALPAY, Erden

    2007-01-01

    The catalytic combustion of ethyl acetate over prepared metal oxide catalysts was investigated. CeO, Co2O3, Mn2O3, Cr2O3, and CeO-Co2O3 catalysts were prepared on monolith supports and they were tested. Before conducting the catalyst experiments, we searched for the homogeneous gas phase combustion reaction of ethyl acetate. According to the homogeneous phase experimental results, 45% of ethyl acetate was converted at the maximum reactor temperature tested (350 °C). All the prepare...

  10. Estimating the temperature of a catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.

    1994-11-02

    A method is described for estimating the temperature in a catalytic converter used in the exhaust system of an internal combustion engine. Pressure sensors monitor the flow resistance across the catalytic converter to provide an indication of the temperature inside. This feedback system allows heating devices to be switched off and thus avoid overheating, while maintaining the catalytic converter's efficiency by assuring that it does not operate below its light off temperature. (UK)

  11. Estimating the temperature of a catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.

    1994-11-02

    A method of estimating the temperature of a catalytic converter used in the exhaust system of an internal combustion engine is described. Heated exhaust gas oxygen (HEGO) sensors are placed upstream and downstream of the catalytic converter. The temperature of the catalytic converter shortly after start-up is measured by monitoring the resistance of the HEGO sensor's heating element. The downstream sensor is used for mixture control and to double check results of the upstream sensor. (UK)

  12. Pin1 Interacts with the Epstein-Barr Virus DNA Polymerase Catalytic Subunit and Regulates Viral DNA Replication

    OpenAIRE

    Narita, Yohei; Murata, Takayuki; Ryo, Akihide; Kawashima, Daisuke; Sugimoto, Atsuko; Kanda, Teru; Kimura, Hiroshi; Tsurumi, Tatsuya

    2013-01-01

    Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) protein is known as a regulator which recognizes phosphorylated Ser/Thr-Pro motifs and increases the rate of cis and trans amide isomer interconversion, thereby altering the conformation of its substrates. We found that Pin1 knockdown using short hairpin RNA (shRNA) technology resulted in strong suppression of productive Epstein-Barr virus (EBV) DNA replication. We further identified the EBV DNA polymerase catalytic subunit, BALF5,...

  13. Nanostructured Catalytic Reactors for Air Purification Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase II project proposes the development of lightweight compact nanostructured catalytic reactors for air purification from toxic gaseous organic...

  14. Nanostructured Catalytic Reactors for Air Purification Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I project proposes the development of lightweight compact nanostructured catalytic reactors for air purification from toxic gaseous organic...

  15. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.

    Science.gov (United States)

    Abudayyeh, Omar O; Gootenberg, Jonathan S; Konermann, Silvana; Joung, Julia; Slaymaker, Ian M; Cox, David B T; Shmakov, Sergey; Makarova, Kira S; Semenova, Ekaterina; Minakhin, Leonid; Severinov, Konstantin; Regev, Aviv; Lander, Eric S; Koonin, Eugene V; Zhang, Feng

    2016-08-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated genes (Cas) adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the class 2 type VI CRISPR-Cas effector C2c2 and demonstrate its RNA-guided ribonuclease function. C2c2 from the bacterium Leptotrichia shahii provides interference against RNA phage. In vitro biochemical analysis shows that C2c2 is guided by a single CRISPR RNA and can be programmed to cleave single-stranded RNA targets carrying complementary protospacers. In bacteria, C2c2 can be programmed to knock down specific mRNAs. Cleavage is mediated by catalytic residues in the two conserved Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domains, mutations of which generate catalytically inactive RNA-binding proteins. These results broaden our understanding of CRISPR-Cas systems and suggest that C2c2 can be used to develop new RNA-targeting tools. PMID:27256883

  16. 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).

  17. Catalytic converters in the fireplace

    International Nuclear Information System (INIS)

    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

  18. Catalytic reforming feed characterisation technique

    Energy Technology Data Exchange (ETDEWEB)

    Larraz Mora, R.; Arvelo Alvarez, R. [Univ. of La Laguna, Chemical Engineering Dept., La Laguna (Spain)

    2002-09-01

    The catalytic reforming of naphtha is one of the major refinery processes, designed to increase the octane number of naphtha or to produce aromatics. The naphtha used as catalytic reformer feedstock usually contains a mixture of paraffins, naphthenes, and aromatics in the carbon number range C{sub 6} to C{sub 10}. The detailed chemical composition of the feed is necessary to predict the aromatics and hydrogen production as well as the operation severity. The analysis of feed naphtha is usually reported in terms of its ASTM distillation curve and API or specific gravity. Since reforming reactions are described in terms of lumped chemical species (paraffins, naphthenes and aromatics), a feed characterisation technique should be useful in order to predict reforming operating conditions and detect feed quality changes. Unfortunately online analyzer applications as cromatography or recently introduced naphtha NMR [1] are scarce in most of refineries. This work proposes an algorithmic characterisation method focusing on its main steps description. The method could help on the subjects previously described, finally a calculation example is shown. (orig.)

  19. Activities of human RRP6 and structure of the human RRP6 catalytic domain

    Energy Technology Data Exchange (ETDEWEB)

    Januszyk, Kurt; Liu, Quansheng; Lima, Christopher D. (SKI)

    2011-08-29

    The eukaryotic RNA exosome is a highly conserved multi-subunit complex that catalyzes degradation and processing of coding and noncoding RNA. A noncatalytic nine-subunit exosome core interacts with Rrp44 and Rrp6, two subunits that possess processive and distributive 3'-to-5' exoribonuclease activity, respectively. While both Rrp6 and Rrp44 are responsible for RNA processing in budding yeast, Rrp6 may play a more prominent role in processing, as it has been demonstrated to be inhibited by stable RNA secondary structure in vitro and because the null allele in budding yeast leads to the buildup of specific structured RNA substrates. Human RRP6, otherwise known as PM/SCL-100 or EXOSC10, shares sequence similarity to budding yeast Rrp6 and is proposed to catalyze 3'-to-5' exoribonuclease activity on a variety of nuclear transcripts including ribosomal RNA subunits, RNA that has been poly-adenylated by TRAMP, as well as other nuclear RNA transcripts destined for processing and/or destruction. To characterize human RRP6, we expressed the full-length enzyme as well as truncation mutants that retain catalytic activity, compared their activities to analogous constructs for Saccharomyces cerevisiae Rrp6, and determined the X-ray structure of a human construct containing the exoribonuclease and HRDC domains that retains catalytic activity. Structural data show that the human active site is more exposed when compared to the yeast structure, and biochemical data suggest that this feature may play a role in the ability of human RRP6 to productively engage and degrade structured RNA substrates more effectively than the analogous budding yeast enzyme.

  20. RNA Viruses and RNAi: Quasispecies Implications for Viral Escape

    OpenAIRE

    Presloid, John B.; Novella, Isabel S.

    2015-01-01

    Due to high mutation rates, populations of RNA viruses exist as a collection of closely related mutants known as a quasispecies. A consequence of error-prone replication is the potential for rapid adaptation of RNA viruses when a selective pressure is applied, including host immune systems and antiviral drugs. RNA interference (RNAi) acts to inhibit protein synthesis by targeting specific mRNAs for degradation and this process has been developed to target RNA viruses, exhibiting their potenti...

  1. Widespread 3′-end uridylation in eukaryotic RNA viruses

    OpenAIRE

    Huo, Yayun; Shen, Jianguo; Wu, Huanian; Zhang, Chao; Guo, Lihua; Yang, Jinguang; Weimin LI

    2016-01-01

    RNA 3′ uridylation occurs pervasively in eukaryotes, but is poorly characterized in viruses. In this study, we demonstrate that a broad array of RNA viruses, including mycoviruses, plant viruses and animal viruses, possess a novel population of RNA species bearing nontemplated oligo(U) or (U)-rich tails, suggesting widespread 3′ uridylation in eukaryotic viruses. Given the biological relevance of 3′ uridylation to eukaryotic RNA degradation, we propose a conserved but as-yet-unknown mechanism...

  2. Functional insights from molecular modeling, docking, and dynamics study of a cypoviral RNA dependent RNA polymerase.

    Science.gov (United States)

    Kundu, Anirban; Dutta, Anirudha; Biswas, Poulomi; Das, Amit Kumar; Ghosh, Ananta Kumar

    2015-09-01

    Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) contains 11 double stranded RNA genome segments and infects tasar silkworm A. mylitta. RNA-dependent RNA polymerase (RdRp) is reported as a key enzyme responsible for propagation of the virus in the host cell but its structure function relationship still remains elusive. Here a computational approach has been taken to compare sequence and secondary structure of AmCPV RdRp with other viral RdRps to identify consensus motifs. Then a reliable pairwise sequence alignment of AmCPV RdRp with its closest sequence structure homologue λ3 RdRp is done to predict three dimensional structure of AmCPV RdRp. After comparing with other structurally known viral RdRps, important sequence and/or structural features involved in substrate entry or binding, polymerase reaction and the product release events have been identified. A conserved RNA pentanucleotide (5'-AGAGC-3') at the 3'-end of virus genome is predicted as cis-acting signal for RNA synthesis and its docking and simulation study along with the model of AmCPV RdRp has allowed to predict mode of template binding by the viral polymerase. It is found that template RNA enters into the catalytic center through nine sequence-independent and two sequence-dependent interactions with the specific amino acid residues. However, number of sequence dependent interactions remains almost same during 10 nano-second simulation time while total number of interactions decreases. Further, docking of N(7)-methyl-GpppG (mRNA cap) on the model as well as prediction of RNA secondary structure has shown the template entry process in the active site. These findings have led to postulate the mechanism of RNA-dependent RNA polymerization process by AmCPV RdRp. To our knowledge, this is the first report to evaluate structure function relationship of a cypoviral RdRp. PMID:26264734

  3. RNA folding and catalysis mediated by iron (II.

    Directory of Open Access Journals (Sweden)

    Shreyas S Athavale

    Full Text Available Mg²⁺ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg²⁺ in RNA folding and function can indeed be served by Fe²⁺. The results of quantum mechanical calculations show that the geometry of coordination of Fe²⁺ by RNA phosphates is similar to that of Mg²⁺. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4-P6 domain RNA is conserved between complexes with Fe²⁺ or Mg²⁺. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg²⁺, and the hammerhead ribozyme are enhanced in the presence of Fe²⁺ compared to Mg²⁺. All chemical footprinting and ribozyme assays in the presence of Fe²⁺ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe²⁺. The combined biochemical and paleogeological data are consistent with a role for Fe²⁺ in an RNA World. RNA and Fe²⁺ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg²⁺ alone.

  4. Baculovirus RNA Polymerase: Activities, Composition, and Evolution

    Institute of Scientific and Technical Information of China (English)

    A.Lorena Passarelli

    2007-01-01

    Baculoviruses are the only nuclear replicating DNA-containing viruses that encode their own DNA-directed RNA polymerase (RNAP). The baculovirus RNAP is specific for the transcription of genes expressed after virus DNA replication. It is composed of four subunits, making it the simplest multisubunit RNAP known. Two subunits contain motifs found at the catalytic center of other RNAPs and a third has capping enzyme functions. The function of the fourth subunit is not known. Structural studies on this unique RNAP will provide new insights into the functions of this enzyme and the regulation of viral genes and may be instrumental to optimize the baculovirus gene expression system.

  5. Acoustics of automotive catalytic converter assemblies

    Science.gov (United States)

    Dickey, Nolan S.; Selamet, Ahmet; Parks, Steve J.; Tallio, Kevin V.; Miazgowicz, Keith D.; Radavich, Paul M.

    2003-10-01

    In an automotive exhaust system, the purpose of the catalytic converter is to reduce pollutant emissions. However, catalytic converters also affect the engine and exhaust system breathing characteristics; they increase backpressure, affect exhaust system acoustic characteristics, and contribute to exhaust manifold tuning. Thus, radiated sound models should include catalytic converters since they can affect both the source characteristics and the exhaust system acoustic behavior. A typical catalytic converter assembly employs a ceramic substrate to carry the catalytically active noble metals. The substrate has numerous parallel tubes and is mounted in a housing with swelling mat or wire mesh around its periphery. Seals at the ends of the substrate can be used to help force flow through the substrate and/or protect the mat material. Typically, catalytic converter studies only consider sound propagation in the small capillary tubes of the substrate. Investigations of the acoustic characteristics of entire catalytic converter assemblies (housing, substrate, seals, and mat) do not appear to be available. This work experimentally investigates the acoustic behavior of catalytic converter assemblies and the contributions of the separate components to sound attenuation. Experimental findings are interpreted with respect to available techniques for modeling sound propagation in ceramic substrates.

  6. Understanding catalytic biomass conversion through data mining

    NARCIS (Netherlands)

    E.J. Ras; B. McKay; G. Rothenberg

    2010-01-01

    Catalytic conversion of biomass is a key challenge that we chemists face in the twenty-first century. Worldwide, research is conducted into obtaining bulk chemicals, polymers and fuels. Our project centres on glucose valorisation via furfural derivatives using catalytic hydrogenation. We present her

  7. Silver nanocluster catalytic microreactors for water purification

    Science.gov (United States)

    Da Silva, B.; Habibi, M.; Ognier, S.; Schelcher, G.; Mostafavi-Amjad, J.; Khalesifard, H. R. M.; Tatoulian, M.; Bonn, D.

    2016-07-01

    A new method for the elaboration of a novel type of catalytic microsystem with a high specific area catalyst is developed. A silver nanocluster catalytic microreactor was elaborated by doping a soda-lime glass with a silver salt. By applying a high power laser beam to the glass, silver nanoclusters are obtained at one of the surfaces which were characterized by BET measurements and AFM. A microfluidic chip was obtained by sealing the silver coated glass with a NOA 81 microchannel. The catalytic activity of the silver nanoclusters was then tested for the efficiency of water purification by using catalytic ozonation to oxidize an organic pollutant. The silver nanoclusters were found to be very stable in the microreactor and efficiently oxidized the pollutant, in spite of the very short residence times in the microchannel. This opens the way to study catalytic reactions in microchannels without the need of introducing the catalyst as a powder or manufacturing complex packed bed microreactors.

  8. Orthogonal gene knock out and activation with a catalytically active Cas9 nuclease

    OpenAIRE

    Dahlman, James E.; Abudayyeh, Omar O.; Joung, Julia; Gootenberg, Jonathan S.; Zhang, Feng; Konermann, Silvana

    2015-01-01

    We have developed a CRISPR-based method that uses catalytically active Cas9 and distinct sgRNA constructs to knock out and activate different genes in the same cell. These sgRNAs, with 14 15 bp target sequences and MS2 binding loops, can activate gene expression using an active Cas9 nuclease, without inducing DSBs. We use these ‘dead RNAs’ to perform orthogonal gene knockout and transcriptional activation in human cells.

  9. Structure and dynamics of a primordial catalytic fold generated by in vitro evolution

    OpenAIRE

    Chao, Fa-An; Morelli, Aleardo; Haugner, John C.; Churchfield, Lewis; Hagmann, Leonardo N.; Shi, Lei; Masterson, Larry R.; Sarangi, Ritimukta; Veglia, Gianluigi; Seelig, Burckhard

    2012-01-01

    Engineering functional protein scaffolds capable of carrying out chemical catalysis is a major challenge in enzyme design. Starting from a non-catalytic protein scaffold, we recently generated a novel RNA ligase by in vitro directed evolution. This artificial enzyme lost its original fold and adopted an entirely novel structure with dramatically enhanced conformational dynamics, demonstrating that a primordial fold with suitable flexibility is sufficient to carry out enzymatic function.

  10. 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.)

  11. Catalytic hydrogenation of carbon monoxide

    International Nuclear Information System (INIS)

    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 H2 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

  12. Catalytic Graphitization of Phenolic Resin

    Institute of Scientific and Technical Information of China (English)

    Mu Zhao; Huaihe Song

    2011-01-01

    The catalytic graphitization of thermal plastic phenolic-formaldehyde resin with the aid of ferric nitrate (FN) was studied in detail. The morphologies and structural features of the products including onion-like carbon nanoparticles and bamboo-shaped carbon nanotubes were investigated by transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), X-ray diffraction and Raman spectroscopy measurements. It was found that with the changes of loading content of FN and residence time at 1000℃, the products exhibited various morphologies. The TEM images showed that bamboo-shaped carbon nanotube consisted of tens of bamboo sticks and onion-like carbon nanoparticle was made up of quasi-spherically concentrically closed carbon nanocages.

  13. Reducing catalytic converter pressure loss

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-06-01

    This article examines why approximately 30--40% of total exhaust-system pressure loss occurs in the catalytic converter and what can be done to reduce pressure loss. High exhaust-system backpressure is of concern in the design of power trains for passenger cars and trucks because it penalizes fuel economy and limits peak power. Pressure losses occur due to fluid shear and turning during turbulent flow in the converter headers and in entry separation and developing laminar-flow boundary layers within the substrate flow passages. Some of the loss mechanisms are coupled. For example, losses in the inlet header are influenced by the presence of the flow resistance of a downstream substrate. Conversely, the flow maldistribution and pressure loss of the substrate(s) depend on the design of the inlet header.

  14. Non-catalytic recuperative reformer

    Energy Technology Data Exchange (ETDEWEB)

    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. Fluctuations in catalytic surface reactions

    CERN Document Server

    Imbihl, R

    2003-01-01

    The internal reaction-induced fluctuations which occur in catalytic CO oxidation on a Pt field emitter tip have been studied using field electron microscopy (FEM) as a spatially resolving method. The structurally heterogeneous Pt tip consists of facets of different orientations with nanoscale dimensions. The FEM resolution of roughly 2 nm corresponds to a few hundred reacting adsorbed particles whose variations in the density are imaged as brightness fluctuations. In the bistable range of the reaction one finds fluctuation-induced transitions between the two stable branches of the reaction kinetics. The fluctuations exhibit a behaviour similar to that of an equilibrium phase transition, i.e. the amplitude diverges upon approaching the bifurcation point terminating the bistable range of the reaction. Simulations with a hybrid Monte Carlo/mean-field model reproduce the experimental observations. Fluctuations on different facets are typically uncorrelated but within a single facet a high degree of spatial cohere...

  16. Catalytic, enantioselective, vinylogous aldol reactions.

    Science.gov (United States)

    Denmark, Scott E; Heemstra, John R; Beutner, Gregory L

    2005-07-25

    In 1935, R. C. Fuson formulated the principle of vinylogy to explain how the influence of a functional group may be felt at a distant point in the molecule when this position is connected by conjugated double-bond linkages to the group. In polar reactions, this concept allows the extension of the electrophilic or nucleophilic character of a functional group through the pi system of a carbon-carbon double bond. This vinylogous extension has been applied to the aldol reaction by employing "extended" dienol ethers derived from gamma-enolizable alpha,beta-unsaturated carbonyl compounds. Since 1994, several methods for the catalytic, enantioselective, vinylogous aldol reaction have appeared, with which varying degrees of regio- (site), enantio-, and diastereoselectivity can be attained. In this Review, the current scope and limitations of this transformation, as well as its application in natural product synthesis, are discussed. PMID:15940727

  17. Electrochemical promotion of catalytic reactions

    Science.gov (United States)

    Imbihl, R.

    2010-05-01

    The electrochemical promotion of heterogeneously catalyzed reactions (EPOC) became feasible through the use of porous metal electrodes interfaced to a solid electrolyte. With the O 2- conducting yttrium stabilized zirconia (YSZ), the Na + conducting β″-Al 2O 3 (β-alumina), and several other types of solid electrolytes the EPOC effect has been demonstrated for about 100 reaction systems in studies conducted mainly in the mbar range. Surface science investigations showed that the physical basis for the EPOC effect lies in the electrochemically induced spillover of oxygen and alkali metal, respectively, onto the surface of the metal electrodes. For the catalytic promotion effect general concepts and mechanistic schemes were proposed but these concepts and schemes are largely speculative. Applying surface analytical tools to EPOC systems the proposed mechanistic schemes can be verified or invalidated. This report summarizes the progress which has been achieved in the mechanistic understanding of the EPOC effect.

  18. Structure–function analysis of vaccinia virus mRNA cap (guanine-N7) methyltransferase

    OpenAIRE

    Zheng, Sushuang; Shuman, Stewart

    2008-01-01

    The guanine-N7 methyltransferase domain of vaccinia virus mRNA capping enzyme is a heterodimer composed of a catalytic subunit and a stimulatory subunit. Structure–function analysis of the catalytic subunit by alanine scanning and conservative substitutions (49 mutations at 25 amino acids) identified 12 functional groups essential for methyltransferase activity in vivo, most of which were essential for cap methylation in vitro. Defects in cap binding were demonstrated for a subset of lethal m...

  19. A Dicer-independent miRNA biogenesis pathway that requires Ago catalysis

    OpenAIRE

    Cheloufi, Sihem; dos Santos, Camila O.; Chong, Mark M.W.; Hannon, Gregory J.

    2010-01-01

    The nucleolytic activity of animal Argonaute proteins is deeply conserved, despite its having no obvious role in microRNA-directed gene regulation. In mice, Ago2 (also known as Eif2c2) is uniquely required for viability, and only this family member retains catalytic competence. To investigate the evolutionary pressure to conserve Argonaute enzymatic activity, we engineered a mouse with catalytically inactive Ago2 alleles. Homozygous mutants died shortly after birth with an obvious anaemia. Ex...

  20. Catalytic converter with thermoelectric generator

    Energy Technology Data Exchange (ETDEWEB)

    Parise, R.J.

    1998-07-01

    The unique design of an electrically heated catalyst (EHC) and the inclusion of an ECO valve in the exhaust of an internal combustion engine will meet the strict new emission requirements, especially at vehicle cold start, adopted by several states in this country as well as in Europe and Japan. The catalytic converter (CC) has been a most useful tool in pollution abatement for the automobile. But the emission requirements are becoming more stringent and, along with other improvements, the CC must be improved to meet these new standards. Coupled with the ECO valve, the EHC can meet these new emission limits. In an internal combustion engine vehicle (ICEV), approximately 80% of the energy consumed leaves the vehicle as waste heat: out the tail pipe, through the radiator, or convected/radiated off the engine. Included with the waste heat out the tail pipe are the products of combustion which must meet strict emission requirements. The design of a new CC is presented here. This is an automobile CC that has the capability of producing electrical power and reducing the quantity of emissions at vehicle cold start, the Thermoelectric Catalytic Power Generator. The CC utilizes the energy of the exothermic reactions that take place in the catalysis substrate to produce electrical energy with a thermoelectric generator. On vehicle cold start, the thermoelectric generator is used as a heat pump to heat the catalyst substrate to reduce the time to catalyst light-off. Thus an electrically heated catalyst (EHC) will be used to augment the abatement of tail pipe emissions. Included with the EHC in the exhaust stream of the automobile is the ECO valve. This valve restricts the flow of pollutants out the tail pipe of the vehicle for a specified amount of time until the EHC comes up to operating temperature. Then the ECO valve opens and allows the full exhaust, now treated by the EHC, to leave the vehicle.

  1. Analyzing MiRNA-LncRNA Interactions.

    Science.gov (United States)

    Paraskevopoulou, Maria D; Hatzigeorgiou, Artemis G

    2016-01-01

    Long noncoding RNAs (lncRNAs) are noncoding transcripts usually longer than 200 nts that have recently emerged as one of the largest and significantly diverse RNA families. The biological role and functions of lncRNAs are still mostly uncharacterized. Their target-mimetic, sponge/decoy function on microRNAs was recently uncovered. miRNAs are a class of noncoding RNA species (~22 nts) that play a central role in posttranscriptional regulation of protein coding genes by mRNA cleavage, direct translational repression and/or mRNA destabilization. LncRNAs can act as miRNA sponges, reducing their regulatory effect on mRNAs. This function introduces an extra layer of complexity in the miRNA-target interaction network. This chapter focuses on the study of miRNA-lncRNA interactions with either in silico or experimentally supported analyses. The proposed methodologies can be appropriately adapted in order to become the backbone of advanced multistep functional miRNA analyses. PMID:26721498

  2. Changes in the level of micro RNA-206 gene expression in patients with type I bipolar disorder before and after treatment and comparison with a control population%双相障碍I型患者治疗前后微小RNA206基因表达水平变化及与对照的比较

    Institute of Scientific and Technical Information of China (English)

    汪作为; 李则挚; 王凌霄; 吴志国; 苑成梅; 洪武; 禹顺英; 方贻儒

    2011-01-01

    Micro RNA-206(miRNA-206) is a potential biomarker of bipolar disorder that has not yet been fully investigated.Objective:Assess the relationship between the level of miRNA-206 in peripheral blood and the clinical state of patients in the manic phase of bipolar disorder.Methods:Thirty-six newly admitted patients in the manic phase of type I bipolar disorder (diagnosed using the Structured Clinical Interview for DSM IV Axis I disorders) and 30 age and gender matched healthy controls were enrolled.miRNA-206 levels in peripheral blood lymphocytes were assessed at the time of enrollment in control subjects and at baseline and at the end of the second,fourth and eighth week of treatment in the patient group.The severity of manic symptoms in the patient group was evaluated at the same time as the miRNA-206 assessments using the Young Mania Rating Scale.Results:There were no statistically significant differences in baseline miRNA-206 levels between patients and controls (Z=-0.02,P =0.988) or,in the patient group,between baseline levels and those at the end of the second ( Z =-0.17,P =0.864),fourth ( Z =-0.86,P =0.392) and eighth ( Z =-1.29,P =0.197) weeks after initiating treatment.There were also no statistically significant correlations between the miRNA-206 level and the severity of manic symptoms at any of the four time points ( rs =0.13,P =0.518; rs =0.12,P =0.532; rs =-0.18,P =0.361 ;and rs =0.02,P=0.912; respectively).Conclusion:The activity of miRNA-206 in peripherally blood lymphocytes does not appear to be a biomarker of type I bipolar disorder or a biomarker for treatment efficacy during the treatment of a manic episode.But the power to detect differences between patients and controls in the study was only 22% so further research with larger samples ( possibly using different techniques to assess miRNA-206 activity) are needed to confirm these findings.%背景 微小RNA206( MicroRNA-206,miRNA-206)可能是双相障碍的生物学标志

  3. Rates of spontaneous mutation among RNA viruses.

    OpenAIRE

    Drake, J W

    1993-01-01

    Simple methods are presented to estimate rates of spontaneous mutation from mutant frequencies and population parameters in RNA viruses. Published mutant frequencies yield a wide range of mutation rates per genome per replication, mainly because mutational targets have usually been small and, thus, poor samples of the mutability of the average base. Nevertheless, there is a clear central tendency for lytic RNA viruses (bacteriophage Q beta, poliomyelitis, vesicular stomatitis, and influenza A...

  4. Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome.

    Science.gov (United States)

    Baranovskiy, Andrey G; Babayeva, Nigar D; Zhang, Yinbo; Gu, Jianyou; Suwa, Yoshiaki; Pavlov, Youri I; Tahirov, Tahir H

    2016-05-01

    The human primosome, a 340-kilodalton complex of primase and DNA polymerase α (Polα), synthesizes chimeric RNA-DNA primers to be extended by replicative DNA polymerases δ and ϵ. The intricate mechanism of concerted primer synthesis by two catalytic centers was an enigma for over three decades. Here we report the crystal structures of two key complexes, the human primosome and the C-terminal domain of the primase large subunit (p58C) with bound DNA/RNA duplex. These structures, along with analysis of primase/polymerase activities, provide a plausible mechanism for all transactions of the primosome including initiation, elongation, accurate counting of RNA primer length, primer transfer to Polα, and concerted autoregulation of alternate activation/inhibition of the catalytic centers. Our findings reveal a central role of p58C in the coordinated actions of two catalytic domains in the primosome and ultimately could impact the design of anticancer drugs. PMID:26975377

  5. Revolutionary systems for catalytic combustion and diesel catalytic particulate traps.

    Energy Technology Data Exchange (ETDEWEB)

    Stuecker, John Nicholas; Witze, Peter O.; Ferrizz, Robert Matthew; Cesarano, Joseph, III; Miller, James Edward

    2004-12-01

    This report is a summary of an LDRD project completed for the development of materials and structures conducive to advancing the state of the art for catalyst supports and diesel particulate traps. An ancillary development for bio-medical bone scaffolding was also realized. Traditionally, a low-pressure drop catalyst support, such as a ceramic honeycomb monolith, is used for catalytic reactions that require high flow rates of gases at high-temperatures. A drawback to the traditional honeycomb monoliths under these operating conditions is poor mass transfer to the catalyst surface in the straight-through channels. ''Robocasting'' is a unique process developed at Sandia National Laboratories that can be used to manufacture ceramic monoliths with alternative 3-dimensional geometries, providing tortuous pathways to increase mass transfer while maintaining low-pressure drops. These alternative 3-dimensional geometries may also provide a foundation for the development of self-regenerating supports capable of trapping and combusting soot particles from a diesel engine exhaust stream. This report describes the structures developed and characterizes the improved catalytic performance that can result. The results show that, relative to honeycomb monolith supports, considerable improvement in mass transfer efficiency is observed for robocast samples synthesized using an FCC-like geometry of alternating rods. Also, there is clearly a trade-off between enhanced mass transfer and increased pressure drop, which can be optimized depending on the particular demands of a given application. Practical applications include the combustion of natural gas for power generation, production of syngas, and hydrogen reforming reactions. The robocast lattice structures also show practicality for diesel particulate trapping. Preliminary results for trapping efficiency are reported as well as the development of electrically resistive lattices that can regenerate the structure

  6. Peptides as catalysts in the RNA world

    DEFF Research Database (Denmark)

    Wieczorek, Rafal; Dörr, Mark; Luisi, Pier Luigi;

    the RNA world concept. Contrary to RNA building blocks, amino acids form quite easily in simulated prebiotic reactions. Also, many prebiotic scenarios for condensation of amino acids into peptides have been proposed and successfully demonstrated experimentally (Rode 1999). We also have growing body of...... experimental evidence showing various catalytic activities associated with short chain peptides, some of them as small as dipeptides. One such peptide, composed of only two amino acid residues; serine and histidine, was reported to exhibit broad hydrolytic activities. The dipeptide SerHis can catalyze the...... hydrolysis of esters, proteins and nucleic acids (Li et al. 2000). The direction of the catalysis either toward hydrolysis or condensation is determined by thermodynamic constraints. In an aqueous medium (a general requirement for prebiotically compatible reactions), hydrolysis is thermodynamically favored...

  7. 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. PMID:24308908

  8. Catalytic activity of nuclease P1: Experiment and theory

    International Nuclear Information System (INIS)

    Nuclease P1 from Penicillium citrinum is a zinc dependent glyco-enzyme that recognizes single stranded DNA and RNA as substrates and hydrolyzes the phosphate ester bond. Nuclease Pl seems to recognize particular conformations of the phosphodiester backbone and shows significant variation in the rate of hydrolytic activity depending upon which nucleosides are coupled by the phosphodiester bond. The efficiency of nuclease Pl in hydrolyzing the phosphodiester bonds of a substrate can be altered by modifications to one of the substrate bases induced by ionizing radiation or oxidative stress. Measurements have been made of the effect of several radiation induced lesions on the catalytic rate of nuclease Pl. A model of the structure of the enzyme has been constructed in order to better understand the binding and activity of this enzyme on various ssDNA substrates

  9. Antisense RNA-based High-Throughput Screen System for Directed Evolution of Quorum Quenching Enzymes.

    Science.gov (United States)

    Han, Sang-Soo; Park, Won-Ji; Kim, Hak-Sung; Kim, Geun-Joong

    2015-11-20

    Quorum quenching (QQ) enzymes, which disrupt the quorum sensing signaling process, have attracted considerable attention as new antimicrobial agents. However, their low catalytic efficiency for quorum sensing molecules remains a challenge. Herein, we present an antisense RNA-based high-throughput screen system for directed evolution of a quorum quenching enzyme. The screening system was constructed by incorporating an antisense RNA (RyhB) into a synthetic module to quantitatively regulate the expression of a reporter gene fused with a sense RNA (sodB). To control the expression of a reporter gene in response to the catalytic activity of a quorum quenching enzyme, the region of interaction and mode between a pair of antisense (RyhB) and sense (sodB) RNAs was designed and optimized through the prediction of the secondary structure of the RNA pair. The screening system constructed was shown to lead to a significant reduction in the false-positive rate (average 42%) in the screening of N-acyl-homoserine lactonase (AiiA) with increased catalytic activity, resulting in a true-positive frequency of up to 76%. The utility and efficiency of the screening system were demonstrated by selecting an AiiA with 31-fold higher catalytic efficiency than the wild-type in three rounds of directed evolution. The present approach can be widely used for the screening of quorum quenching enzymes with the desired catalytic property, as well as for a synthetic network for a stringent regulation of the gene expression. PMID:26366664

  10. RNA structures regulating nidovirus RNA synthesis

    NARCIS (Netherlands)

    Born, Erwin van den

    2006-01-01

    Viruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the

  11. Structure-based identification of catalytic residues.

    Science.gov (United States)

    Yahalom, Ran; Reshef, Dan; Wiener, Ayana; Frankel, Sagiv; Kalisman, Nir; Lerner, Boaz; Keasar, Chen

    2011-06-01

    The identification of catalytic residues is an essential step in functional characterization of enzymes. We present a purely structural approach to this problem, which is motivated by the difficulty of evolution-based methods to annotate structural genomics targets that have few or no homologs in the databases. Our approach combines a state-of-the-art support vector machine (SVM) classifier with novel structural features that augment structural clues by spatial averaging and Z scoring. Special attention is paid to the class imbalance problem that stems from the overwhelming number of non-catalytic residues in enzymes compared to catalytic residues. This problem is tackled by: (1) optimizing the classifier to maximize a performance criterion that considers both Type I and Type II errors in the classification of catalytic and non-catalytic residues; (2) under-sampling non-catalytic residues before SVM training; and (3) during SVM training, penalizing errors in learning catalytic residues more than errors in learning non-catalytic residues. Tested on four enzyme datasets, one specifically designed by us to mimic the structural genomics scenario and three previously evaluated datasets, our structure-based classifier is never inferior to similar structure-based classifiers and comparable to classifiers that use both structural and evolutionary features. In addition to the evaluation of the performance of catalytic residue identification, we also present detailed case studies on three proteins. This analysis suggests that many false positive predictions may correspond to binding sites and other functional residues. A web server that implements the method, our own-designed database, and the source code of the programs are publicly available at http://www.cs.bgu.ac.il/∼meshi/functionPrediction. PMID:21491495

  12. Development of Catalytic Cooking Plates

    Energy Technology Data Exchange (ETDEWEB)

    Hjelm, Anna-Karin; Silversand, Fredrik [CATATOR AB, Lund (Sweden); Tena, Emmanuel; Berger, Marc [Gaz de France (France)

    2004-04-01

    Gas catalytic combustion for gas stoves or cooking plates (closed catalytic burner system with ceramic plates) is a very promising technique in terms of ease of cleaning, power modulation and emissions. Previous investigations show that wire mesh catalysts, prepared and supplied by Catator AB (CAT), seem to be very well suited for such applications. Beside significantly reducing the NOx-emissions, these catalysts offer important advantages such as good design flexibility, low pressure drop and high heat transfer capacity, where the latter leads to a quick thermal response. Prior to this project, Gaz de France (GdF) made a series of measurements with CAT's wire mesh catalysts in their gas cooking plates and compared the measured performance with similar results obtained with theirs cordierite monolith catalysts. Compared to the monolith catalyst, the wire mesh catalyst was found to enable very promising results with respect to both emission levels (<10 mg NO{sub x} /kWh, <5 mg CO/kWh) and life-time (>8000 h vs. 700 h at 200 kW/m{sup 2}). It was however established that the radiation and hence, the thermal efficiency of the cooking plate, was significantly less than is usually measured in combination with the monolith (15 % vs. 32 %). It was believed that the latter could be improved by developing new burner designs based on CAT's wire mesh concept. As a consequence, a collaboration project between GdF, CAT and the Swedish Gas Technology AB was created. This study reports on the design, the construction and the evaluation of new catalytic burners, based on CAT's wire mesh catalysts, used for the combustion of natural gas in gas cooking stoves. The evaluation of the burners was performed with respect to key factors such as thermal efficiency, emission quality and pressure drop, etc, by the use of theoretical simulations and experimental tests. Impacts of parameters such as the the wire mesh number, the wire mesh structure (planar or folded), the

  13. Catalytic reaction in confined flow channel

    Energy Technology Data Exchange (ETDEWEB)

    Van Hassel, Bart A.

    2016-03-29

    A chemical reactor comprises a flow channel, a source, and a destination. The flow channel is configured to house at least one catalytic reaction converting at least a portion of a first nanofluid entering the channel into a second nanofluid exiting the channel. The flow channel includes at least one turbulating flow channel element disposed axially along at least a portion of the flow channel. A plurality of catalytic nanoparticles is dispersed in the first nanofluid and configured to catalytically react the at least one first chemical reactant into the at least one second chemical reaction product in the flow channel.

  14. Evolutionary perspectives of telomerase RNA structure and function.

    Science.gov (United States)

    Podlevsky, Joshua D; Chen, Julian J-L

    2016-08-01

    Telomerase is the eukaryotic solution to the 'end-replication problem' of linear chromosomes by synthesising the highly repetitive DNA constituent of telomeres, the nucleoprotein cap that protects chromosome termini. Functioning as a ribonucleoprotein (RNP) enzyme, telomerase is minimally composed of the highly conserved catalytic telomerase reverse transcriptase (TERT) and essential telomerase RNA (TR) component. Beyond merely providing the template for telomeric DNA synthesis, TR is an innate telomerase component and directly facilitates enzymatic function. TR accomplishes this by having evolved structural elements for stable assembly with the TERT protein and the regulation of the telomerase catalytic cycle. Despite its prominence and prevalence, TR has profoundly diverged in length, sequence, and biogenesis pathway among distinct evolutionary lineages. This diversity has generated numerous structural and mechanistic solutions for ensuring proper RNP formation and high fidelity telomeric DNA synthesis. Telomerase provides unique insights into RNA and protein coevolution within RNP enzymes. PMID:27359343

  15. 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......, 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...... other RNA molecules show virtually no oxidation. The iron-storage disease hemochromatosis exhibits the most prominent general increase in RNA oxidation ever observed. Oxidation of RNA primarily leads to strand breaks and to oxidative base modifications. Oxidized mRNA is recognized by the ribosomes...

  16. Catalytic Chemistry on Oxide Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Asthagiri, Aravind; Dixon, David A.; Dohnalek, Zdenek; Kay, Bruce D.; Rodriquez, Jose A.; Rousseau, Roger J.; Stacchiola, Dario; Weaver, Jason F.

    2016-05-29

    Metal oxides represent one of the most important and widely employed materials in catalysis. Extreme variability of their chemistry provides a unique opportunity to tune their properties and to utilize them for the design of highly active and selective catalysts. For bulk oxides, this can be achieved by varying their stoichiometry, phase, exposed surface facets, defect, dopant densities and numerous other ways. Further, distinct properties from those of bulk oxides can be attained by restricting the oxide dimensionality and preparing them in the form of ultrathin films and nanoclusters as discussed throughout this book. In this chapter we focus on demonstrating such unique catalytic properties brought by the oxide nanoscaling. In the highlighted studies planar models are carefully designed to achieve minimal dispersion of structural motifs and to attain detailed mechanistic understanding of targeted chemical transformations. Detailed level of morphological and structural characterization necessary to achieve this goal is accomplished by employing both high-resolution imaging via scanning probe methods and ensemble-averaged surface sensitive spectroscopic methods. Three prototypical examples illustrating different properties of nanoscaled oxides in different classes of reactions are selected.

  17. Halogen Chemistry on Catalytic Surfaces.

    Science.gov (United States)

    Moser, Maximilian; Pérez-Ramírez, Javier

    2016-01-01

    Halogens are key building blocks for the manufacture of high-value products such as chemicals, plastics, and pharmaceuticals. The catalytic oxidation of HCl and HBr is an attractive route to recover chlorine and bromine in order to ensure the sustainability of the production processes. Very few materials withstand the high corrosiveness and the strong exothermicity of the reactions and among them RuO2 and CeO2-based catalysts have been successfully applied in HCl oxidation. The search for efficient systems for HBr oxidation was initiated by extrapolating the results of HCl oxidation based on the chemical similarity of these reactions. Interestingly, despite its inactivity in HCl oxidation, TiO2 was found to be an outstanding HBr oxidation catalyst, which highlighted that the latter reaction is more complex than previously assumed. Herein, we discuss the results of recent comparative studies of HCl and HBr oxidation on both rutile-type (RuO2, IrO2, and TiO2) and ceria-based catalysts using a combination of advanced experimental and theoretical methods to provide deeper molecular-level understanding of the reactions. This knowledge aids the design of the next-generation catalysts for halogen recycling. PMID:27131113

  18. Vacuum-insulated catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Benson, David K. (Golden, CO)

    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.

  19. Irreducibility in RNA structures

    OpenAIRE

    Jin, Emma Y.; Reidys, Christian M.

    2009-01-01

    In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various distributions: of the numbers of irreducible substructures, their locations and sizes, parameterized in terms of the maximal number of mutually crossing arcs, $k-1$, and the minimal size of stacks $\\sigma$. In particular, we analyze the size of the largest ...

  20. An all RNA hypercycle network

    Science.gov (United States)

    Vaidya, Nilesh; Lehman, Niles

    The RNA world hypothesis suggests RNA-based catalysis and information storage as the first step in the evolution of life on the Earth. The central process of the RNA world was the replica-tion of RNA, which may have involved the joining of oligonucleotides, perhaps by recombination rather than organization along a linear template. To assist this build-up of information, a hy-percycle may have played a significant role by allowing cooperation between autocatalytic units in a cyclic linkage in such a way that there is a mutual survival and regulated growth of all the units involved (1). Compared to non-coupled self-replicating units, which can only sustain a limited amount of genetic information, the hypercycle allows the maintenance of large amounts of information through cooperation among otherwise competitive units. However, hypercycles have never been empirically demonstrated in the absence of cell-like compartmentalization. In the current work, hypercyclic behavior is demonstrated in the autocatalytic assembly of Azoar-cus group I ribozyme (2). Three different constructs of the Azoarcus ribozyme with different internal guide sequences (IGS) -GUG (canonical), GAG, and GCG -are capable of a min-imal amount of self-assembly when broken into two fragments. Here, self-assembly depends on a mismatch with non-complementary sequences, CGU, CAU and CUU, respectively, to be recognized by IGS via autocatalysis. Yet when all three constructs are present in the same reaction vessel, concomitant assembly of all three is enhanced through an interdependent hy-percyclic reaction network. Analysis of these reactions indicates that each system is capable of guiding its own reproduction weakly, along with providing enhanced catalytic support for the reproduction of one other construct system through matched IGS-tag interactions. Also, when co-incubated with non-interacting (i.e., selfish) yet efficient self-assembly systems, the hypercyclic assembly outcompetes the selfish self

  1. Working with RNA

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    Working with RNA is not a special discipline in molecular biology. However, RNA is chemically and structurally different from DNA and a few simple work rules have to be implemented to maintain the integrity of the RNA. Alkaline pH, high temperatures, and heavy metal ions should be avoided when...

  2. Catalytic models developed through social work

    DEFF Research Database (Denmark)

    Jensen, Mogens

    2015-01-01

    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 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...... work with new possibilities of development of the work, but also suggestions for development of the concept of catalytic processes....

  3. Catalytic converters as a source of platinum

    Directory of Open Access Journals (Sweden)

    A. Fornalczyk

    2011-10-01

    Full Text Available The increase of Platinum Group Metals demand in automotive industry is connected with growing amount of cars equipped with the catalytic converters. The paper presents the review of available technologies during recycling process. The possibility of removing platinum from the used catalytic converters applying pyrometallurgical and hyrdometallurgical methods were also investigated. Metals such as Cu, Pb, Ca, Mg, Cd were used in the pyrometallurgical research (catalytic converter was melted with Cu, Pb and Ca or Mg and Cd vapours were blown through the whole carrier. In hydrometallurgical research catalytic converters was dissolved in aqua regia. Analysis of Pt contents in the carrier before and after the process was performed by means of atomic absorption spectroscopy. Obtained result were discussed.

  4. Fast Prediction of RNA-RNA Interaction

    Science.gov (United States)

    Salari, Raheleh; Backofen, Rolf; Sahinalp, S. Cenk

    Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.

  5. Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates

    OpenAIRE

    Shi, Zhongjie; Nicholson, Rhonda H.; Jaggi, Ritu; Nicholson, Allen W.

    2010-01-01

    Ribonuclease III cleaves double-stranded (ds) structures in bacterial RNAs and participates in diverse RNA maturation and decay pathways. Essential insight on the RNase III mechanism of dsRNA cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, Aquifex aeolicus. However, the biochemical properties of A. aeolicus (Aa)-RNase III and the reactivity epitopes of its substrates are not known. The catalytic activity of purified recombinant Aa-RNa...

  6. Kinetic catalytic studies of scorpion's hemocyanin

    International Nuclear Information System (INIS)

    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 107 mol-1.l.s-1

  7. Characterization of Aqueous Peroxomolybdates with Catalytic Applicability

    OpenAIRE

    Taube, Fabian

    2003-01-01

    Abstract This thesis is a summary of five papers, containing equilibrium and structure studies of aqueous molybdate and peroxomolybdate species. Some of the peroxomolybdate species have also been studied in terms of their dynamic and catalytic properties. The primary objective was to characterize species with potential catalytic activity, with emphasis on thebleach process of kraft pulp. For this, potentiometry, EXAFS and 17O, 31P, 1H and 95 Mo NMR have been used. The molybdate speciation in ...

  8. MOBILE COMPLEX FOR CATALYTIC THERMAL WASTE TREATMENT

    OpenAIRE

    Vedi V.E.; Rovenskii A.I.

    2012-01-01

    The design and purpose of the basic units of the mobile waste processing complex “MPK” are described. Experimental data of catalytic purification of exhaust gases are presented. Experimental data on catalytic clearing of final gases of a designed mobile incinerator plant are shown. It is defined, that concentrating of parasitic bridging in waste gases of the complex are considerably smaller, rather than allowed by normative documents.

  9. MOBILE COMPLEX FOR CATALYTIC THERMAL WASTE TREATMENT

    Directory of Open Access Journals (Sweden)

    Vedi V.E.

    2012-12-01

    Full Text Available The design and purpose of the basic units of the mobile waste processing complex “MPK” are described. Experimental data of catalytic purification of exhaust gases are presented. Experimental data on catalytic clearing of final gases of a designed mobile incinerator plant are shown. It is defined, that concentrating of parasitic bridging in waste gases of the complex are considerably smaller, rather than allowed by normative documents.

  10. Temperature Modulation of a Catalytic Gas Sensor

    OpenAIRE

    Eike Brauns; Eva Morsbach; Sebastian Kunz; Marcus Baeumer; Walter Lang

    2014-01-01

    The use of catalytic gas sensors usually offers low selectivity, only based on their different sensitivities for various gases due to their different heats of reaction. Furthermore, the identification of the gas present is not possible, which leads to possible misinterpretation of the sensor signals. The use of micro-machined catalytic gas sensors offers great advantages regarding the response time, which allows advanced analysis of the sensor response. By using temperature modulation, additi...

  11. Catalytic ammonia oxidation to nitrogen (I) oxide

    OpenAIRE

    MASALITINA NATALIYA YUREVNA; SAVENKOV ANATOLIY SERGEEVICH

    2015-01-01

    The process of synthesis of nitrous oxide by low-temperature catalytical oxidation of NH has been investigated for organic synthesis. The investigation has been carried out by the stage separation approach with NH oxidation occurring in several reaction zones, which characterized by different catalytic conditions. The selectivity for N₂O was 92–92,5 % at the ammonia conversion of 98–99.5 % in the optimal temperature range.

  12. Preparation and Catalytic Oxidation Activity on 2-mercaptoethanol of a Novel Catalytic Cellulose Fibres

    Institute of Scientific and Technical Information of China (English)

    YAO Yu-yuan; LI Ying-jie; CHEN Wen-xing; Lü Wang-yang; Lü Su-fang; XU Min-hong; LIU Fan

    2007-01-01

    Cobalt tetra(N-carbonylacylic) aminophthalocyanine was supported on cellulose fibres by graft reaction to obtain a novel polymer catalyst, catalytic cellulose fibres (CCF),and the optimal supporting conditions were pH = 6, 80℃,t = 120 min. The catalytic oxidation activity of CCF towards oxidation of 2-mereaptoethanol (MEA) in aqueous solution was investigated. The experimental results demonstrated that CCF had good catalytic oxidation activity on MEA at room temperature, causing no secondary pollution and remaining efficient for the repetitive tests with no obvious decrease of catalytic activity.

  13. Theoretical studies on sRNA-mediated regulation in bacteria

    Science.gov (United States)

    Chang, Xiao-Xue; Xu, Liu-Fang; Shi, Hua-Lin

    2015-12-01

    Small RNA(sRNA)-mediated post-transcriptional regulation differs from protein-mediated regulation. Through base-pairing, sRNA can regulate the target mRNA in a catalytic or stoichiometric manner. Some theoretical models were built for comparison of the protein-mediated and sRNA-mediated modes in the steady-state behaviors and noise properties. Many experiments demonstrated that a single sRNA can regulate several mRNAs, which causes crosstalk between the targets. Here, we focus on some models in which two target mRNAs are silenced by the same sRNA to discuss their crosstalk features. Additionally, the sequence-function relationship of sRNA and its role in the kinetic process of base-pairing have been highlighted in model building. Project supported by the National Basic Research Program of China (Grant No. 2013CB834100), the National Natural Science Foundation of China (Grant Nos. 11121403 and 11274320), the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y4KF171CJ1), the National Natural Science Foundation for Young Scholar of China (Grant No. 11304115), and the China Postdoctoral Science Foundation (Grant No. 2013M541282).

  14. Synergism and Mutualism in Non-Enzymatic RNA Polymerization

    Directory of Open Access Journals (Sweden)

    Hussein Kaddour

    2014-11-01

    Full Text Available The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the “RNA world” and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life’s building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system.

  15. Low efficiency deasphalting and catalytic cracking

    International Nuclear Information System (INIS)

    This patent describes a process for converting an asphaltene and metals containing heavy hydrocarbon feed to lighter, more valuable products the metals comprising Ni and V. It comprises: demetallizing the feed by deasphalting the feed in a solvent deasphalting means operating at solvent deasphalting conditions including a solvent: feed volume ratio of about 1:1 to 4:1, using a solvent selected from the group of C4 to 400 degrees F. hydrocarbons and mixtures thereof; recovering from the solvent rich fraction a demetallized oil intermediate product, having a boiling range and containing at least 10 wt.% of the asphaltenes, and 5 to 30% of the Ni and V, and at least 10 wt.% of the solvent present in the solvent rich phase produced in the deasphalting means; catalytically cracking the demetallized oil intermediate product in a catalytic cracking means operating at catalytic cracking conditions to produce a catalytically cracked product vapor fraction having a lower boiling range than the boiling range of the demetallized oil intermediate product; and fractionating the catalytically cracked product in a fractionation means to produce catalytically cracked product fractions

  16. Evaluation of mRNA expression of the transcription factors of Th1 and Th2 subsets (T-bet and GATA-3 in periodontal health and disease - A pilot study in south Indian population

    Directory of Open Access Journals (Sweden)

    Nichenametla Rajesh

    2015-01-01

    Full Text Available Background: Based on their respective pro- or anti-inflammatory cytokine profiles, the Th1/Th2 paradigm explains pathogenic mechanisms involved in periodontal disease. Establishment of Th1 and Th2 subsets from a naive T-cell precursor depends on transcriptional regulation. The aim of this study was to compare the expression of master transcription factor regulators T-bet and GATA-3, respectively, to indicate the predominance of Th1 and Th2 subsets in the presence and absence of periodontal disease. Materials and Methods: A gingival tissue biopsy sample was obtained from each of 10 severe periodontitis patients (>5 mm attachment loss and 10 periodontally healthy patients (no attachment loss. Biopsies were immediately processed by real-time reverse transcriptase polymerase chain reaction and the difference in mRNA expression of T-bet and GATA-3 was assessed for each group. Results: The mRNA expression of T-bet was marginally increased about 1.31-fold in disease, while the GATA-3 levels showed a significant decrease of 4.39-fold in disease. Conclusion: The advanced periodontal lesions lack Th2 cells, which produce anti-inflammatory cytokines. The biopsies were therefore dominated by Th1 cells, which activate macrophages and osteoclasts.

  17. Dynamics of 103K/N and 184M/V HIV-1 drug resistant populations: relative comparison in plasma virus RNA versus CD45RO+T cell proviral DNA

    DEFF Research Database (Denmark)

    Jakobsen, Martin Roelsgaard; Tolstrup, M; Bertelsen, L;

    2007-01-01

    BACKGROUND: Viral populations defined by 103K/N and 184M/V as linked or single mutations in the HIV-1 reverse transcriptase gene were investigated in plasma samples and compared with previous findings in the CD45RO(+)T cell compartment. OBJECTIVE: To develop an ARMS assay for plasma virions and to...... investigate the expression of resistance mutations (103N and 184V) and dynamic interactions between proviral DNA and plasma virions. STUDY DESIGN: A clinical cross-sectional study, including 11 patients on lamivudine efavirenz and/or nevirapine therapy. The viral populations were determined by an assay based...

  18. Combinatorics of RNA-RNA interaction.

    Science.gov (United States)

    Li, Thomas J X; Reidys, Christian M

    2012-02-01

    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 their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures. PMID:21541694

  19. Combinatorics of RNA-RNA interaction

    CERN Document Server

    Li, Thomas J X

    2010-01-01

    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 ``zig-zag'' configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.

  20. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    While increasing evidence appoints diverse types of RNA as key players in the regulatory networks underlying cellular differentiation and metabolism, the potential functions of thousands of conserved RNA structures encoded in mammalian genomes remain to be determined. Since the functions of most...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA......-protein pulldown combined with mass spectrometry analysis is applied for in vivo as well as in vitro identification of RNA-binding proteins, the latter succeeding in verifying known RNA-protein interactions. Secondly, acknowledging the significance of flexible promoter usage for the diversification of the...

  1. Fast prediction of RNA-RNA interaction

    Directory of Open Access Journals (Sweden)

    Backofen Rolf

    2010-01-01

    Full Text Available Abstract Background Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s. There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site. Methods In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introduce a fast heuristic method to predict the specific (multiple binding sites of two interacting RNAs. Results We verify the performance of our algorithms for joint structure and binding site prediction on a set of known interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform all competitive approaches.

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

    Directory of Open Access Journals (Sweden)

    Yuki Fujita

    2010-08-01

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

  3. Catalytic and surface oxidation processes on transition metal surfaces

    OpenAIRE

    Jaatinen, Sampsa

    2007-01-01

    Transition metals are technologically important catalytic materials. The transition metal catalysts are used for example in petroleum and fertilizer industry. In the car industry the catalytic materials are used in the catalytic converters. Because of the industrial importance the catalytic metals have been widely studied throughout the past decades. Nonetheless, the oxidation mechanisms of small molecules and the effect of alloying to catalytic properties of metals are not fully understood. ...

  4. On the Structural Context and Identification of Enzyme Catalytic Residues

    OpenAIRE

    Yu-Tung Chien; Shao-Wei Huang

    2013-01-01

    Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The...

  5. Structure of the Tribolium castaneum Telomerase Catalytic Subunit TERT

    Energy Technology Data Exchange (ETDEWEB)

    Gillis,A.; Schuller, A.; Skordalakes, E.

    2008-01-01

    A common hallmark of human cancers is the overexpression of telomerase, a ribonucleoprotein complex that is responsible for maintaining the length and integrity of chromosome ends. Telomere length deregulation and telomerase activation is an early, and perhaps necessary, step in cancer cell evolution. Here we present the high-resolution structure of the Tribolium castaneum catalytic subunit of telomerase, TERT. The protein consists of three highly conserved domains, organized into a ring-like structure that shares common features with retroviral reverse transcriptases, viral RNA polymerases and B-family DNA polymerases. Domain organization places motifs implicated in substrate binding and catalysis in the interior of the ring, which can accommodate seven to eight bases of double-stranded nucleic acid. Modelling of an RNA-DNA heteroduplex in the interior of this ring demonstrates a perfect fit between the protein and the nucleic acid substrate, and positions the 3'-end of the DNA primer at the active site of the enzyme, providing evidence for the formation of an active telomerase elongation complex.

  6. Binding induced RNA conformational changes control substrate recognition and catalysis by the thiostrepton resistance methyltransferase (Tsr).

    Science.gov (United States)

    Kuiper, Emily G; Conn, Graeme L

    2014-09-19

    Ribosomal RNA (rRNA) post-transcriptional modifications are essential for ribosome maturation, translational fidelity, and are one mechanism used by both antibiotic-producing and pathogenic bacteria to resist the effects of antibiotics that target the ribosome. The thiostrepton producer Streptomyces azureus prevents self-intoxication by expressing the thiostrepton-resistance methyltransferase (Tsr), which methylates the 2'-hydroxyl of 23 S rRNA nucleotide adenosine 1067 within the thiostrepton binding site. Tsr is a homodimer with each protomer containing an L30e-like amino-terminal domain (NTD) and a SPOUT methyltransferase family catalytic carboxyl-terminal domain (CTD). We show that both enzyme domains are required for high affinity RNA substrate binding. The Tsr-CTD has intrinsic, weak RNA affinity that is necessary to direct the specific high-affinity Tsr-RNA interaction via NTDs, which have no detectable RNA affinity in isolation. RNA structure probing experiments identify the Tsr footprint on the RNA and structural changes in the substrate, induced specifically upon NTD binding, which are necessary for catalysis by the CTD. Additionally, we identify a key amino acid in each domain responsible for CTD-RNA binding and the observed NTD-dependent RNA structural changes. These studies allow us to develop a model for Tsr-RNA interaction in which the coordinated substrate recognition of each Tsr structural domain is an obligatory pre-catalytic recognition event. Our findings underscore the complexity of substrate recognition by RNA modification enzymes and the potential for direct involvement of the RNA substrate in controlling the process of its modification. PMID:25086036

  7. MeRNA: a Database of Metal Ion Binding Sites in RNAStructures

    Energy Technology Data Exchange (ETDEWEB)

    Stefan, Liliana R.; Zhang, Rui; Levitan, Aaron G.; Hendrix, DonnaF.; Brenner, Steven E.; Holbrook, Stephen R.

    2005-10-05

    Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using original literature references. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature. MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure, and distance from metal to any RNA atom or to water. New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database will further our understanding of the roles of metal ions in RNA folding and catalysis and have applications in structural and functional analysis, RNA design and engineering.

  8. Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers

    OpenAIRE

    Bhadra, Sanchita; Ellington, Andrew D.

    2014-01-01

    Nucleic acid circuits are finding increasing real-life applications in diagnostics and synthetic biology. Although DNA has been the main operator in most nucleic acid circuits, transcriptionally produced RNA circuits could provide powerful alternatives for reagent production and their use in cells. Towards these goals, we have implemented a particular nucleic acid circuit, catalytic hairpin assembly, using RNA for both information storage and processing. Our results demonstrated that the desi...

  9. Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer.

    OpenAIRE

    Vitiello, D; Pecchia, D B; Burke, J M

    2000-01-01

    Small catalytic RNAs like the hairpin ribozyme are proving to be useful intracellular tools; however, most attempts to demonstrate trans-cleavage of RNA by ribozymes in cells have been frustrated by rapid cellular degradation of the cleavage products. Here, we describe a fluorescence resonance energy transfer (FRET) assay that directly monitors cleavage of target RNA in tissue-culture cells. An oligoribonucleotide substrate was modified to inhibit cellular ribonuclease degradation without int...

  10. RNA catalysis, thermodynamics and the origin of life

    OpenAIRE

    Scott, William G.; Abraham Szöke; Josh Blaustein; Sara M O'Rourke; Robertson, Michael P

    2014-01-01

    The RNA World Hypothesis posits that the first self-replicating molecules were RNAs. RNA self-replicases are, in general, assumed to have employed nucleotide 5'-polyphosphates (or their analogues) as substrates for RNA polymerization. The mechanism by which these substrates might be synthesized with sufficient abundance to supply a growing and evolving population of RNAs is problematic for evolutionary hypotheses because non-enzymatic synthesis and assembly of nucleotide 5'-triphosphates (or ...

  11. Ecological and taxonomic variation among human RNA viruses

    OpenAIRE

    Woolhouse, Mark E J; Adair, Kyle

    2013-01-01

    Only a minority of RNA viruses that can infect humans are capable of spreading in human populations independently of a zoonotic reservoir. This is especially true of vector-borne RNA viruses; the majority of these are not transmissible (via the vector) between humans at all. Understanding the biology underlying this observation will help us evaluate the public health risk associated with novel vector-borne RNA viruses.

  12. RNA Viruses Infecting Pest Insects

    Science.gov (United States)

    RNA viruses are viruses whose genetic material is ribonucleic acid (RNA). RNA viruses may be double or single-stranded based on the type of RNA they contain. Single-stranded RNA viruses can be further grouped into negative sense or positive-sense viruses according to the polarity of their RNA. Fur...

  13. A novel liquid system of catalytic hydrogenation

    Institute of Scientific and Technical Information of China (English)

    LI; XiaoNian; XIANG; YiZhi

    2007-01-01

    On the basis that endothermic aqueous-phase reforming of oxygenated hydrocarbons for H2 production and exothermic liquid phase hydrogenation of organic compounds are carried out under extremely close conditions of temperature and pressure over the same type of catalyst, a novel liquid system of catalytic hydrogenation has been proposed, in which hydrogen produced from aqueous-phase reforming of oxygenated hydrocarbons is in situ used for liquid phase hydrogenation of organic compounds. The usage of active hydrogen generated from aqueous-phase reforming of oxygenated hydrocarbons for liquid catalytic hydrogenation of organic compounds could lead to increasing the selectivity to H2 in the aqueous-phase reforming due to the prompt removal of hydrogen on the active centers of the catalyst. Meanwhile, this novel liquid system of catalytic hydrogenation might be a potential method to improve the selectivity to the desired product in liquid phase catalytic hydrogenation of organic compounds. On the other hand, for this novel liquid system of catalytic hydrogenation, some special facilities for H2 generation, storage and transportation in traditional liquid phase hydrogenation industry process are yet not needed. Thus, it would simplify the working process of liquid phase hydrogenation and increase the energy usage and hydrogen productivity.

  14. Electrocatalytic miRNA Detection Using Cobalt Porphyrin-Modified Reduced Graphene Oxide

    Directory of Open Access Journals (Sweden)

    Camille De Souza

    2014-06-01

    Full Text Available Metalated porphyrins have been described to bind nucleic acids. Additionally, cobalt porphyrins present catalytic properties towards oxygen reduction. In this work, a carboxylic acid-functionalized cobalt porphyrin was physisorbed on reduced graphene oxide, then immobilized on glassy carbon electrodes. The carboxylic groups were used to covalently graft amino-terminated oligonucleotide probes which are complementary to a short microRNA target. It was shown that the catalytic oxygen electroreduction on cobalt porphyrin increases upon hybridization of miRNA strand (“signal-on” response. Current changes are amplified compared to non-catalytic amperometric system. Apart from oxygen, no added reagent is necessary. A limit of detection in the sub-nanomolar range was reached. This approach has never been described in the literature.

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

    Directory of Open Access Journals (Sweden)

    Venanzetti Federica

    2010-01-01

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

  16. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei; Hu, Pingping; Chen, Jianmin; Liu, Xi; Tang, Xingfu

    2015-01-01

    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......-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...

  17. Catalytic microreactors for portable power generation

    Energy Technology Data Exchange (ETDEWEB)

    Karagiannidis, Symeon [Paul Scherer Institute, Villigen (Switzerland)

    2011-07-01

    ''Catalytic Microreactors for Portable Power Generation'' addresses a problem of high relevance and increased complexity in energy technology. This thesis outlines an investigation into catalytic and gas-phase combustion characteristics in channel-flow, platinum-coated microreactors. The emphasis of the study is on microreactor/microturbine concepts for portable power generation and the fuels of interest are methane and propane. The author carefully describes numerical and experimental techniques, providing a new insight into the complex interactions between chemical kinetics and molecular transport processes, as well as giving the first detailed report of hetero-/homogeneous chemical reaction mechanisms for catalytic propane combustion. The outcome of this work will be widely applied to the industrial design of micro- and mesoscale combustors. (orig.)

  18. Catalytic nanoarchitectonics for environmentally compatible energy generation

    Directory of Open Access Journals (Sweden)

    Hideki Abe

    2016-01-01

    Full Text Available Environmentally compatible energy management is one of the biggest challenges of the 21st century. Low-temperature conversion of chemical to electrical energy is of particular importance to minimize the impact to the environment while sustaining the consumptive economy. In this review, we shed light on one of the most versatile energy-conversion technologies: heterogeneous catalysts. We establish the integrity of structural tailoring in heterogeneous catalysts at different scales in the context of an emerging paradigm in materials science: catalytic nanoarchitectonics. Fundamental backgrounds of energy-conversion catalysis are first provided together with a perspective through state-of-the-art energy-conversion catalysis including catalytic exhaust remediation, fuel-cell electrocatalysis and photosynthesis of solar fuels. Finally, the future evolution of catalytic nanoarchitectonics is overviewed: possible combinations of heterogeneous catalysts, organic molecules and even enzymes to realize reaction-selective, highly efficient and long-life energy conversion technologies which will meet the challenge we face.

  19. Use catalytic combustion for LHV gases

    Energy Technology Data Exchange (ETDEWEB)

    Tucci, E.R.

    1982-03-01

    This paper shows how low heating value (LHV) waste gases can be combusted to recover energy even when the gases won't burn in a normal manner. Significant energy and economic savings can result by adopting this process. Catalytic combustion is a heterogeneous surface-catalyzed air oxidation of fuel, gaseous or liquid, to generate thermal energy in a flameless mode. The catalytic combustion process is quite complex since it involves numerous catalytic surface and gas-phase chemical reactions. During low temperature surface-catalyzed combustion, as in start-up, the combustion stage is under kinetically controlled conditions. The discussion covers the following topics - combustor substrates; combustor washcoating and catalyzing; combustor operational modes (turbine or tabular modes); applications in coal gasification and in-situ gasification; waste process gases. 16 refs.

  20. Xylan-Degrading Catalytic Flagellar Nanorods.

    Science.gov (United States)

    Klein, Ágnes; Szabó, Veronika; Kovács, Mátyás; Patkó, Dániel; Tóth, Balázs; Vonderviszt, Ferenc

    2015-09-01

    Flagellin, the main component of flagellar filaments, is a protein possessing polymerization ability. In this work, a novel fusion construct of xylanase A from B. subtilis and Salmonella flagellin was created which is applicable to build xylan-degrading catalytic nanorods of high stability. The FliC-XynA chimera when overexpressed in a flagellin deficient Salmonella host strain was secreted into the culture medium by the flagellum-specific export machinery allowing easy purification. Filamentous assemblies displaying high surface density of catalytic sites were produced by ammonium sulfate-induced polymerization. FliC-XynA nanorods were resistant to proteolytic degradation and preserved their enzymatic activity for a long period of time. Furnishing enzymes with self-assembling ability to build catalytic nanorods offers a promising alternative approach to enzyme immobilization onto nanostructured synthetic scaffolds. PMID:25966869

  1. Flow parameters of IC engine catalytic converters

    Energy Technology Data Exchange (ETDEWEB)

    Zmudka, Z.; Postrzednik, S. [Silesian Univ. of Tech., Gliwice (Poland)

    2007-07-01

    Conversion rate of harmful substances is the principal parameter of catalyst work in respect of ecology. However, resistance of exhaust gas flow through the catalytic converter is also essential problem, apart from its chemical efficiency because fitting the catalyst in exhaust system alters flow characteristic of this system significantly. Catalytic converter can be treated as local or linear resistance element of exhaust system. The first model, in which flow resistance generated by a catalyst is treated as local resistance, is more simplified. Resistance number of the converter was calculated using Darcy model. In the second case, exhaust gas flow resistance through catalyst is treated as linear resistance with energy dissipation (linear frictional resistance) distributed linearly along way of exhaust gas flow. Friction number for the tested converter was calculated and analysed. The problem has been illustrated by results of experimental researches of three-way catalytic converter installed in exhaust system of spark ignition engine and its basic analysis. (orig.)

  2. Electro Catalytic Oxidation (ECO) Operation

    Energy Technology Data Exchange (ETDEWEB)

    Morgan Jones

    2011-03-31

    The power industry in the United States is faced with meeting many new regulations to reduce a number of air pollutants including sulfur dioxide, nitrogen oxides, fine particulate matter, and mercury. With over 1,000 power plants in the US, this is a daunting task. In some cases, traditional pollution control technologies such as wet scrubbers and SCRs are not feasible. Powerspan's Electro-Catalytic Oxidation, or ECO{reg_sign} process combines four pollution control devices into a single integrated system that can be installed after a power plant's particulate control device. Besides achieving major reductions in emissions of sulfur dioxide (SO{sub 2}), nitrogen oxides (NOx), fine particulate matter (PM2.5) and mercury (Hg), ECO produces a highly marketable fertilizer, which can help offset the operating costs of the process system. Powerspan has been operating a 50-MW ECO commercial demonstration unit (CDU) at FirstEnergy Corp.'s R.E. Burger Plant near Shadyside, Ohio, since February 2004. In addition to the CDU, a test loop has been constructed beside the CDU to demonstrate higher NOx removal rates and test various scrubber packing types and wet ESP configurations. Furthermore, Powerspan has developed the ECO{reg_sign}{sub 2} technology, a regenerative process that uses a proprietary solvent to capture CO{sub 2} from flue gas. The CO{sub 2} capture takes place after the capture of NOx, SO{sub 2}, mercury, and fine particulate matter. Once the CO{sub 2} is captured, the proprietary solution is regenerated to release CO{sub 2} in a form that is ready for geological storage or beneficial use. Pilot scale testing of ECO{sub 2} began in early 2009 at FirstEnergy's Burger Plant. The ECO{sub 2} pilot unit is designed to process a 1-MW flue gas stream and produce 20 tons of CO{sub 2} per day, achieving a 90% CO{sub 2} capture rate. The ECO{sub 2} pilot program provided the opportunity to confirm process design and cost estimates, and prepare for large

  3. RNA-dependent RNA polymerases of plants

    OpenAIRE

    Fraenkel-Conrat, H

    1983-01-01

    The existence of RNA-dependent RNA polymerases (EC 2.7.7.48) in plants has been definitely proven by their isolation in pure form from cucumber and tobacco in our laboratory and from cowpea at Wageningen. These enzymes are single-chain proteins of 100-130 kilodaltons. They show clear physical and biochemical differences characteristic for a given plant species, even when their amounts in the plants were greatly increased prior to isolation by infection with the same virus. The role of these e...

  4. RNA decay by messenger RNA interferases

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo; Gerdes, Kenn

    2008-01-01

    Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs....

  5. Nonlinear physics approach to RNA cross-replication: Marginal stability, generalized logistic growth, and impacts of degradation

    Energy Technology Data Exchange (ETDEWEB)

    Frank, T.D., E-mail: till.frank@ucd.ie [UCD School of Physics, University College Dublin, Belfield, Dublin 4 (Ireland); Systems Biology Ireland, University College Dublin, Belfield, Dublin 4 (Ireland); Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269 (United States)

    2011-10-24

    Highlights: → RNA cross-replication is a marginally stable but not asymptotically stable process. → RNA enzymes exhibits a generalized logistic growth pattern with exponent equal to 2. → Degradation results in non-symmetric saturation levels of cross-replicating RNAs. -- Abstract: It is nowadays believed that the evolution of life involved as an intermediate step an RNA world. In such an RNA world RNA molecules replicate themselves in catalytic reactions. Recent experiments on cross-replicating RNA support the RNA world hypothesis. We derive a nonlinear mass-action kinetics model to explain logistic growth patterns and non-symmetric saturation levels observed in those experiments. We also demonstrate that fixed points of the RNA growth process are only marginally stable rather than asymptotically stable.

  6. Nonlinear physics approach to RNA cross-replication: Marginal stability, generalized logistic growth, and impacts of degradation

    International Nuclear Information System (INIS)

    Highlights: → RNA cross-replication is a marginally stable but not asymptotically stable process. → RNA enzymes exhibits a generalized logistic growth pattern with exponent equal to 2. → Degradation results in non-symmetric saturation levels of cross-replicating RNAs. -- Abstract: It is nowadays believed that the evolution of life involved as an intermediate step an RNA world. In such an RNA world RNA molecules replicate themselves in catalytic reactions. Recent experiments on cross-replicating RNA support the RNA world hypothesis. We derive a nonlinear mass-action kinetics model to explain logistic growth patterns and non-symmetric saturation levels observed in those experiments. We also demonstrate that fixed points of the RNA growth process are only marginally stable rather than asymptotically stable.

  7. Interaction of tRNA with MEK2 in pancreatic cancer cells

    Science.gov (United States)

    Wang, Xiaoyun; Chow, Christina R.; Ebine, Kazumi; Lee, Jiyoung; Rosner, Marsha R.; Pan, Tao; Munshi, Hidayatullah G.

    2016-01-01

    Although the translational function of tRNA has long been established, extra translational functions of tRNA are still being discovered. We previously developed a computational method to systematically predict new tRNA-protein complexes and experimentally validated six candidate proteins, including the mitogen-activated protein kinase kinase 2 (MEK2), that interact with tRNA in HEK293T cells. However, consequences of the interaction between tRNA and these proteins remain to be elucidated. Here we tested the consequence of the interaction between tRNA and MEK2 in pancreatic cancer cell lines. We also generated disease and drug resistance-derived MEK2 mutants (Q60P, P128Q, S154F, E207K) to evaluate the function of the tRNA-MEK2 interaction. Our results demonstrate that tRNA interacts with the wild-type and mutant MEK2 in pancreatic cancer cells; furthermore, the MEK2 inhibitor U0126 significantly reduces the tRNA-MEK2 interaction. In addition, tRNA affects the catalytic activity of the wild type and mutant MEK2 proteins in different ways. Overall, our findings demonstrate the interaction of tRNA with MEK2 in pancreatic cancer cells and suggest that tRNA may impact MEK2 activity in cancer cells. PMID:27301426

  8. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase

    International Nuclear Information System (INIS)

    The catalytic domain of human Dus2-like enzyme was purified and crystallized, and data were collected to 1.9 Å resolution. Dihydrouridine synthases catalyse the reduction of uridine to dihydrouridine in the D-loop and variable loop of tRNA. The human dihydrouridine synthase HsDus2L has been implicated in the development of pulmonary carcinogenesis. Here, the purification, crystallization and preliminary X-ray characterization of the HsDus2L catalytic domain are reported. The crystals belonged to space group P21 and contained a single molecule of HsDus2L in the asymmetric unit. A complete data set was collected to 1.9 Å resolution using synchrotron radiation

  9. A catalytic surface for amyloid fibril formation

    Energy Technology Data Exchange (ETDEWEB)

    Hammarstroem, P; Ali, M M; Mishra, R; Tengvall, P; Lundstroem, I [Department of Physics, Biology and Chemistry, Linkoeping University, SE-581 83 Linkoeping (Sweden); Svensson, S [Astra Zeneca R and D, SE-151 85 Soedertaelje (Sweden)], E-mail: ingemar@ifm.liu.se

    2008-03-15

    A hydrophobic surface incubated in a solution of protein molecules (insulin monomers) was made into a catalytic surface for amyloid fibril formation by repeatedly incubate, rinse and dry the surface. The present contribution describes how this unexpected transformation occurred and its relation to rapid fibrillation of insulin solutions in contact with the surface. A tentative model of the properties of the catalytic surface is given, corroborated by ellipsometric measurements of the thickness of the organic layer on the surface and by atomic force microscopy. The surfaces used were spontaneously oxidized silicon made hydrophobic through treatment in dichlorodimethylsilane.

  10. 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.

  11. Catalytic Enantioselective Functionalization of Unactivated Terminal Alkenes.

    Science.gov (United States)

    Coombs, John R; Morken, James P

    2016-02-01

    Terminal alkenes are readily available functional groups which appear in α-olefins produced by the chemical industry, and they appear in the products of many contemporary synthetic reactions. While the organic transformations that apply to alkenes are amongst the most studied reactions in all of chemical synthesis, the number of reactions that apply to nonactivated terminal alkenes in a catalytic enantioselective fashion is small in number. This Minireview highlights the cases where stereocontrol in catalytic reactions of 1-alkenes is high enough to be useful for asymmetric synthesis. PMID:26764019

  12. Catalytic gasification of oil-shales

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, A.; Avakyan, T. [I.M. Gubkin Russian State Univ. of Oil and Gas, Moscow (Russian Federation); Strizhakova, Yu. [Samara State Univ. (Russian Federation)

    2012-07-01

    Nowadays, the problem of complex usage of solid fossil fuels as raw materials for obtaining of motor fuels and chemical products is becoming increasingly important. A one of possible solutions of the problem is their gasification with further processing of gaseous and liquid products. In this work we have investigated the process of thermal and catalytic gasification of Baltic and Kashpir oil-shales. We have shown that, as compared with non-catalytic process, using of nickel catalyst in the reaction increases the yield of gas, as well as hydrogen content in it, and decreases the amount of liquid products. (orig.)

  13. Heterogeneous Catalytic Ozonization of Sulfosalicylic Acid

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper describes the potential of heterogeneous catalytic ozonization of sulfo-salicylic acid (SSal). It was found that catalytic ozonization in the presence of Mn-Zr-O (a modified manganese dioxide supported on silica gel) had significantly enhanced the removal rate (72%) of total organic carbon (TOC) compared with that of ozonization alone (19%). The efficient removal rate of TOC was probably due to increasing the adsorption ability of catalyst and accelerating decomposition of ozone to produce more powerful oxidants than ozone.

  14. Mechanism for Coordinated RNA Packaging and Genome Replication by Rotavirus Polymerase VP1

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Xiaohui; McDonald, Sarah M.; Tortorici, M. Alejandra; Tao, Yizhi Jane; Vasquez-Del Carpio, Rodrigo; Nibert, Max L.; Patton, John T.; Harrison, Stephen C. (Harvard-Med); (NIH); (CH-Boston)

    2009-04-08

    Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 {angstrom} resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus {lambda}3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.

  15. RNA with iron(II) as a cofactor catalyses electron transfer

    Science.gov (United States)

    Hsiao, Chiaolong; Chou, I.-Chun; Okafor, C. Denise; Bowman, Jessica C.; O'Neill, Eric B.; Athavale, Shreyas S.; Petrov, Anton S.; Hud, Nicholas V.; Wartell, Roger M.; Harvey, Stephen C.; Williams, Loren Dean

    2013-06-01

    Mg2+ is essential for RNA folding and catalysis. However, for the first 1.5 billion years of life on Earth RNA inhabited an anoxic Earth with abundant and benign Fe2+. We hypothesize that Fe2+ was an RNA cofactor when iron was abundant, and was substantially replaced by Mg2+ during a period known as the ‘great oxidation’, brought on by photosynthesis. Here, we demonstrate that reversing this putative metal substitution in an anoxic environment, by removing Mg2+ and replacing it with Fe2+, expands the catalytic repertoire of RNA. Fe2+ can confer on some RNAs a previously uncharacterized ability to catalyse single-electron transfer. We propose that RNA function, in analogy with protein function, can be understood fully only in the context of association with a range of possible metals. The catalysis of electron transfer, requisite for metabolic activity, may have been attenuated in RNA by photosynthesis and the rise of O2.

  16. An archaeal tRNA-synthetase complex that enhances aminoacylation under extreme conditions

    DEFF Research Database (Denmark)

    Godinic-Mikulcic, Vlatka; Jaric, Jelena; Hausmann, Corinne D;

    2011-01-01

    Aminoacyl-tRNA synthetases (aaRSs) play an integral role in protein synthesis, functioning to attach the correct amino acid with its cognate tRNA molecule. AaRSs are known to associate into higher-order multi-aminoacyl-tRNA synthetase complexes (MSC) involved in archaeal and eukaryotic translation...... the catalytic efficiency of serine attachment to tRNA, but had no effect on the activity of MtArgRS. Further, the most pronounced improvements in the aminoacylation activity of MtSerRS induced by MtArgRS were observed under conditions of elevated temperature and osmolarity. These data indicate that......, although the precise biological role remains largely unknown. To gain further insights into archaeal MSCs, possible protein-protein interactions with the atypical Methanothermobacter thermautotrophicus seryl-tRNA synthetase (MtSerRS) were investigated. Yeast two-hybrid analysis revealed arginyl-tRNA...

  17. Fidelity of a viral RNA polymerase in an intact host: template structure and host factors affect rates of deletion mutations

    Science.gov (United States)

    Plant RNA viruses often have very diverse populations. One of the commonly proposed mechanisms for generating these diverse populations is the error prone RNA-dependent RNA polymerase, based on examples from a number of human and bacterial viruses. This paper describes work to determine the insertio...

  18. Mammalian α-polymerase: cloning of partial complementary DNA and immunobinding of catalytic subunit in crude homogenate protein blots

    International Nuclear Information System (INIS)

    A new polyclonal antibody against the α-polymerase catalytic polypeptide was prepared by using homogeneous HeLa cellα-polymerase. The antibody neutralized α-polymerase activity and was strong and specific for the α-polymerase catalytic polypeptide (M/sub r/ 183,000) in Western blot analysis of crude extracts of HeLa cells. The antibody was used to screen a cDNA library of newborn rat brain poly(A+) RNA in λgt11. A positive phage was identified and plaque purified. This phage, designated λpolα1.2, also was found to be positive with an antibody against Drosophila α-polymerase. The insert in λpolα1.2 (1183 base pairs) contained a poly(A) sequence at the 3' terminus and a short in-phase open reading frame at the 5' terminus. A synthetic oligopeptide (eight amino acids) corresponding to the open reading frame was used to raise antiserum in rabbits. Antibody affinity purified from this serum was found to be immunoreactive against purified α-polymerase by enzyme-linked immunosorbent assay and was capable of immunoprecipitating α-polymerase. This indicated the λpolα1.2 insert encoded an α-polymerase epitope and suggested that the cDNA corresponded to an α-polymerase mRNA. This was confirmed in hybrid selection experiments using pUC9 containing the cDNA insert and poly(A+) RNA from newborn rat brain; the insert hybridized to mRNA capable of encoding α-polymerase catalytic polypeptides. Northern blot analysis of rat brain poly(A+) RNA revealed that this mRNA is ∼5.4 kilobases

  19. Topology of RNA-RNA interaction structures

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Huang, Fenix Wenda; Penner, Robert;

    2012-01-01

    Abstract The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exist...

  20. Preparation of Multiplexed Small RNA Libraries From Plants

    OpenAIRE

    Gilbert, Kerrigan B.; Fahlgren, Noah; Kasschau, Kristin D.; Chapman, Elisabeth J.; Carrington, James C.; Carbonell, Alberto

    2014-01-01

    High-throughput sequencing is a powerful tool for exploring small RNA populations in plants. The ever-increasing output from an Illumina Sequencing System allows for multiplexing multiple samples while still obtaining sufficient data for small RNA discovery and characterization. Here we describe a protocol for generating multiplexed small RNA libraries for sequencing up to 12 samples in one lane of an Illumina HiSeq System single-end, 50 base pair run. RNA ligases are used to add the 3′ and 5...

  1. Widespread 3'-end uridylation in eukaryotic RNA viruses.

    Science.gov (United States)

    Huo, Yayun; Shen, Jianguo; Wu, Huanian; Zhang, Chao; Guo, Lihua; Yang, Jinguang; Li, Weimin

    2016-01-01

    RNA 3' uridylation occurs pervasively in eukaryotes, but is poorly characterized in viruses. In this study, we demonstrate that a broad array of RNA viruses, including mycoviruses, plant viruses and animal viruses, possess a novel population of RNA species bearing nontemplated oligo(U) or (U)-rich tails, suggesting widespread 3' uridylation in eukaryotic viruses. Given the biological relevance of 3' uridylation to eukaryotic RNA degradation, we propose a conserved but as-yet-unknown mechanism in virus-host interaction. PMID:27151171

  2. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification

    OpenAIRE

    Guilinger, John P.; Thompson, David B.; Liu, David R.

    2014-01-01

    Genome editing by Cas9, which cleaves double-stranded DNA at a sequence programmed by a short single-guide RNA (sgRNA), can result in off-target DNA modification that may be detrimental in some applications. To improve DNA cleavage specificity, we generated fusions of catalytically inactive Cas9 and FokI nuclease (fCas9). DNA cleavage by fCas9 requires association of two fCas9 monomers that simultaneously bind target sites ~15 or 25 base pairs apart. In human cells, fCas9 modified target DNA ...

  3. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity.

    Science.gov (United States)

    Itoh, Yuzuru; Bröcker, Markus J; Sekine, Shun-ichi; Söll, Dieter; Yokoyama, Shigeyuki

    2014-04-17

    The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins and is synthesized on its specific tRNA (tRNA(Sec)). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNA(Sec), formed by seryl-tRNA synthetase, to Sec-tRNA(Sec). SelA, a member of the fold-type-I pyridoxal 5'-phosphate-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNA(Sec) revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNA(Sec). The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of "depentamerized" SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I pyridoxal 5'-phosphate-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures. PMID:24456689

  4. RNA Oligomerization in Laboratory Analogues of Alkaline Hydrothermal Vent Systems.

    Science.gov (United States)

    Burcar, Bradley T; Barge, Laura M; Trail, Dustin; Watson, E Bruce; Russell, Michael J; McGown, Linda B

    2015-07-01

    Discovering pathways leading to long-chain RNA formation under feasible prebiotic conditions is an essential step toward demonstrating the viability of the RNA World hypothesis. Intensive research efforts have provided evidence of RNA oligomerization by using circular ribonucleotides, imidazole-activated ribonucleotides with montmorillonite catalyst, and ribonucleotides in the presence of lipids. Additionally, mineral surfaces such as borates, apatite, and calcite have been shown to catalyze the formation of small organic compounds from inorganic precursors (Cleaves, 2008 ), pointing to possible geological sites for the origins of life. Indeed, the catalytic properties of these particular minerals provide compelling evidence for alkaline hydrothermal vents as a potential site for the origins of life since, at these vents, large metal-rich chimney structures can form that have been shown to be energetically favorable to diverse forms of life. Here, we test the ability of iron- and sulfur-rich chimneys to support RNA oligomerization reactions using imidazole-activated and non-activated ribonucleotides. The chimneys were synthesized in the laboratory in aqueous "ocean" solutions under conditions consistent with current understanding of early Earth. Effects of elemental composition, pH, inclusion of catalytic montmorillonite clay, doping of chimneys with small organic compounds, and in situ ribonucleotide activation on RNA polymerization were investigated. These experiments, under certain conditions, showed successful dimerization by using unmodified ribonucleotides, with the generation of RNA oligomers up to 4 units in length when imidazole-activated ribonucleotides were used instead. Elemental analysis of the chimney precipitates and the reaction solutions showed that most of the metal cations that were determined were preferentially partitioned into the chimneys. PMID:26154881

  5. Toward a catalytic site in DNA

    DEFF Research Database (Denmark)

    Jakobsen, Ulla; Rohr, Katja; Vogel, Stefan

    2007-01-01

    A number of functionalized polyaza crown ether building blocks have been incorporated into DNA-conjugates as catalytic Cu(2+) binding sites. The effect of the DNA-conjugate catalyst on the stereochemical outcome of a Cu(2+)-catalyzed Diels-Alder reaction will be presented....

  6. SELECTIVE CATALYTIC REDUCTION MERCURY FIELD SAMPLING PROJECT

    Science.gov (United States)

    A lack of data still exists as to the effect of selective catalytic reduction (SCR), selective noncatalytic reduction (SNCR), and flue gas conditioning on the speciation and removal of mercury (Hg) at power plants. This project investigates the impact that SCR, SNCR, and flue gas...

  7. Toward Facilitative Mentoring and Catalytic Interventions

    Science.gov (United States)

    Smith, Melissa K.; Lewis, Marilyn

    2015-01-01

    In TESOL teacher mentoring, giving advice can be conceptualized as a continuum, ranging from directive to facilitative feedback. The goal, over time, is to lead toward the facilitative end of the continuum and specifically to catalytic interventions that encourage self-reflection and autonomous learning. This study begins by examining research on…

  8. Catalytic reaction dynamics in inhomogeneous networks.

    Science.gov (United States)

    Watanabe, Akitomo; Yakubo, Kousuke

    2014-05-01

    Biochemical reactions in a cell can be modeled by a catalytic reaction network (CRN). It has been reported that catalytic chain reactions occur intermittently in the CRN with a homogeneous random-graph topology and its avalanche-size distribution obeys a power law with the exponent 4/3 [A. Awazu and K. Kaneko, Phys. Rev. E 80, 010902(R) (2009)]. This fact indicates that the catalytic reaction dynamics in homogeneous CRNs exhibits self-organized criticality (SOC). Structures of actual CRNs are, however, known to be highly inhomogeneous. We study the influence of various types of inhomogeneities found in real-world metabolic networks on the universality class of SOC. Our numerical results clarify that SOC keeps its universality class even for networks possessing structural inhomogeneities such as the scale-free property, community structures, and degree correlations. In contrast, if the CRN has inhomogeneous catalytic functionality, the universality class of SOC depends on how widely distributed the number of reaction paths catalyzed by a single chemical species is. PMID:25353843

  9. Novel Metal Nanomaterials and Their Catalytic Applications.

    Science.gov (United States)

    Wang, Jiaqing; Gu, Hongwei

    2015-01-01

    In the rapidly developing areas of nanotechnology, nano-scale materials as heterogeneous catalysts in the synthesis of organic molecules have gotten more and more attention. In this review, we will summarize the synthesis of several new types of noble metal nanostructures (FePt@Cu nanowires, Pt@Fe₂O₃ nanowires and bimetallic Pt@Ir nanocomplexes; Pt-Au heterostructures, Au-Pt bimetallic nanocomplexes and Pt/Pd bimetallic nanodendrites; Au nanowires, CuO@Ag nanowires and a series of Pd nanocatalysts) and their new catalytic applications in our group, to establish heterogeneous catalytic system in "green" environments. Further study shows that these materials have a higher catalytic activity and selectivity than previously reported nanocrystal catalysts in organic reactions, or show a superior electro-catalytic activity for the oxidation of methanol. The whole process might have a great impact to resolve the energy crisis and the environmental crisis that were caused by traditional chemical engineering. Furthermore, we hope that this article will provide a reference point for the noble metal nanomaterials' development that leads to new opportunities in nanocatalysis. PMID:26393550

  10. Catalytic dehydrogenations of ethylbenzene to styrene

    NARCIS (Netherlands)

    Nederlof, C.

    2012-01-01

    This research work on the catalytic dehydrogenation of ethylbenzene (EB) to styrene (ST) had a primary goal of developing improved catalysts for dehydrogenation processes both in CO2 as well as with O2 that can compete with the conventional dehydrogenation process in steam. In order to achieve this

  11. Electrochemical Promotion of Catalytic Reactions Using

    DEFF Research Database (Denmark)

    Petrushina, Irina; Bjerrum, Niels; Cleemann, Lars Nilausen;

    2007-01-01

    This paper presents the results of a study on electrochemical promotion (EP) of catalytic reactions using Pt/C/polybenzimidazole(H3PO4)/Pt/C fuel cell performed by the Energy and Materials Science Group (Technical University of Denmark) during the last 6 years[1-4]. The development of our...

  12. Shungite carbon catalytic effect on coal treatment

    Energy Technology Data Exchange (ETDEWEB)

    Grigorieva, E.N.; Rozhkova, N.N. [Russian Academy of Sciences, Moscow (Russian Federation). Institute for High Temperature

    1999-07-01

    The catalytic ability of shungite carbon in reactions of coal organic matter models appeared to be due to its fullerene structure only. Transition metal sulphides present in shungite carbon are not active in the conditions of coal treatment. Shungite carbon was shown to exhibit an acceleration of thermolysis of coal and organic matter models, mainly dehydrogenation. 5 refs., 1 tabs.

  13. Catalytic oxidation of industrial organic solvent vapors.

    Science.gov (United States)

    Tzortzatou, Katerina; Grigoropoulou, Eleni

    2010-01-01

    In the present study the catalytic oxidation of an industrial organic solvent consisting predominantly of C-9 to C-10 paraffins and napthtenics and derived from low aromatic white spirit on CuO and Pt catalysts was investigated at ambient pressure and temperatures between 330 and 770 K. Catalysts were prepared in the laboratory and compared to commercial ones. Characterization was based on x-ray diffraction (XRD) analysis, x-ray fluorescence (XRF) analysis, scanning electron microscope (SEM) analysis and nitrogen adsorption data. The commercial platinum catalyst was proved highly efficient in the oxidation of the commercial solvent, necessitating lower temperatures for total oxidation. Catalyst loading in active component is clearly not of primordial importance, since its dispersion and crystallinity as well as the presence of other metallic compounds influence also the catalytic activity. In the case of copper catalysts studied, the different support (alumina) characteristics also would contribute to the difference in catalytic activity. Finally, the power law kinetics may successfully be used in order to explain the catalytic oxidation data of the organic solvent, where its constituents are modeled as a single carbon-containing compound. PMID:20390900

  14. Catalytic Converters Maintain Air Quality in Mines

    Science.gov (United States)

    2014-01-01

    At Langley Research Center, engineers developed a tin-oxide based washcoat to prevent oxygen buildup in carbon dioxide lasers used to detect wind shears. Airflow Catalyst Systems Inc. of Rochester, New York, licensed the technology and then adapted the washcoat for use as a catalytic converter to treat the exhaust from diesel mining equipment.

  15. Novel Metal Nanomaterials and Their Catalytic Applications

    Directory of Open Access Journals (Sweden)

    Jiaqing Wang

    2015-09-01

    Full Text Available In the rapidly developing areas of nanotechnology, nano-scale materials as heterogeneous catalysts in the synthesis of organic molecules have gotten more and more attention. In this review, we will summarize the synthesis of several new types of noble metal nanostructures (FePt@Cu nanowires, Pt@Fe2O3 nanowires and bimetallic Pt@Ir nanocomplexes; Pt-Au heterostructures, Au-Pt bimetallic nanocomplexes and Pt/Pd bimetallic nanodendrites; Au nanowires, CuO@Ag nanowires and a series of Pd nanocatalysts and their new catalytic applications in our group, to establish heterogeneous catalytic system in “green” environments. Further study shows that these materials have a higher catalytic activity and selectivity than previously reported nanocrystal catalysts in organic reactions, or show a superior electro-catalytic activity for the oxidation of methanol. The whole process might have a great impact to resolve the energy crisis and the environmental crisis that were caused by traditional chemical engineering. Furthermore, we hope that this article will provide a reference point for the noble metal nanomaterials’ development that leads to new opportunities in nanocatalysis.

  16. Performance characterization of a hydrogen catalytic heater.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Terry Alan; Kanouff, Michael P.

    2010-04-01

    This report describes the performance of a high efficiency, compact heater that uses the catalytic oxidation of hydrogen to provide heat to the GM Hydrogen Storage Demonstration System. The heater was designed to transfer up to 30 kW of heat from the catalytic reaction to a circulating heat transfer fluid. The fluid then transfers the heat to one or more of the four hydrogen storage modules that make up the Demonstration System to drive off the chemically bound hydrogen. The heater consists of three main parts: (1) the reactor, (2) the gas heat recuperator, and (3) oil and gas flow distribution manifolds. The reactor and recuperator are integrated, compact, finned-plate heat exchangers to maximize heat transfer efficiency and minimize mass and volume. Detailed, three-dimensional, multi-physics computational models were used to design and optimize the system. At full power the heater was able to catalytically combust a 10% hydrogen/air mixture flowing at over 80 cubic feet per minute and transfer 30 kW of heat to a 30 gallon per minute flow of oil over a temperature range from 100 C to 220 C. The total efficiency of the catalytic heater, defined as the heat transferred to the oil divided by the inlet hydrogen chemical energy, was characterized and methods for improvement were investigated.

  17. Exact Results for Kinetics of Catalytic Reactions

    OpenAIRE

    Frachebourg, L.; Krapivsky, P. L.

    1995-01-01

    The kinetics of an irreversible catalytic reaction on substrate of arbitrary dimension is examined. In the limit of infinitesimal reaction rate (reaction-controlled limit), we solve the dimer-dimer surface reaction model (or voter model) exactly in arbitrary dimension $D$. The density of reactive interfaces is found to exhibit a power law decay for $D

  18. Catalytic asymmetric synthesis of mycocerosic acid

    NARCIS (Netherlands)

    ter Horst, B.; Feringa, B.L.; J. Minnaard, A.

    2007-01-01

    The first catalytic asymmetric total synthesis of mycocerosic acid was achieved via the application of iterative enantioselective 1,4-addition reactions and allows for the efficient construction of 1,3-polymethyl arrays with full stereocontrol; further exemplified by the synthesis of tetramethyl-dec

  19. Electrochemical promotion of sulfur dioxide catalytic oxidation

    DEFF Research Database (Denmark)

    Petrushina, Irina; Bandur, Viktor; Cappeln, Frederik Vilhelm;

    2000-01-01

    The effect of electrochemical polarization on the catalytic SO2 oxidation in the molten V2O5-K2S2O7 system has been studied using a gold working electrode in the temperature range 400-460 degrees C. A similar experiment has been performed with the industrial catalyst VK-58. The aim of the present...

  20. Catalytic site interactions in yeast OMP synthase

    DEFF Research Database (Denmark)

    Hansen, Michael Riis; Barr, Eric W.; Jensen, Kaj Frank; Willemoës, Martin; Grubmeyer, Charles; Winther, Jakob R.

    2014-01-01

    45 (2006) 5330-5342]. This behavior was investigated in the yeast enzyme by mutations in the conserved catalytic loop and 5-phosphoribosyl-1-diphosphate (PRPP) binding motif. Although the reaction is mechanistically sequential, the wild-type (WT) enzyme shows parallel lines in double reciprocal...

  1. Catalytic treatment of diesel engines, NOx emissions

    International Nuclear Information System (INIS)

    Some aspects of the operation of diesel engines are revised together with the pollutant emissions they produce, as well as the available catalytic technologies for the treatment of diesel emissions. Furthermore the performance of a catalyst developed in the environmental catalysis group for NOx reduction using synthetic gas mixtures simulating the emissions from diesel engines is presented

  2. Catalytic Effect of Tungsten on Anaerobic Digestion Process for Biogas Production from Fruit and Vegetable Wastes

    OpenAIRE

    Das A; Mondal.C

    2013-01-01

    In the recent years global energy crisis increased at a fast pace. Demand for the use of fossil fuels for cooking and other commercial activities increased along with the increasing population of India. Use of renewable sources of energy viz. biogas for cooking etc can somewhat be an alternative for the excessive demand of fossil fuels like LPG. In this study, the catalytic effect of tungsten for maximizing biogas have been presented. Essentially, anaerobic digesti...

  3. Lentivirus-Mediated Short-Hairpin RNA Targeting Protein Phosphatase 4 Regulatory Subunit 1 Inhibits Growth in Breast Cancer

    OpenAIRE

    Qi, Yuying; Hu, Tinghui; Li, Kai; Ye, Renqing; Ye, Zuodong

    2015-01-01

    Purpose Protein phosphatase 4 regulatory subunit 1 (PP4R1), as an interaction partner of the catalytic serine/threonine-protein phosphatase 4 catalytic subunit has been shown to involve in cellular processes and nuclear factor κB signaling. However, the functions of PP4R1 in human breast cancers remain unclear. This study is designed to explore the effect of PP4R1 knockdown on the biological characteristics of breast cancer cells. Methods A lentivirus-mediated short hairpin RNA (shRNA) was de...

  4. Plant RNA binding proteins for control of RNA virus infection

    OpenAIRE

    Huh, Sung Un; Paek, Kyung-Hee

    2013-01-01

    Plant RNA viruses have effective strategies to infect host plants through either direct or indirect interactions with various host proteins, thus suppressing the host immune system. When plant RNA viruses enter host cells exposed RNAs of viruses are recognized by the host immune system through processes such as siRNA-dependent silencing. Interestingly, some host RNA binding proteins have been involved in the inhibition of RNA virus replication, movement, and translation through RNA-specific b...

  5. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis.

    Science.gov (United States)

    Cheloufi, Sihem; Dos Santos, Camila O; Chong, Mark M W; Hannon, Gregory J

    2010-06-01

    The nucleolytic activity of animal Argonaute proteins is deeply conserved, despite its having no obvious role in microRNA-directed gene regulation. In mice, Ago2 (also known as Eif2c2) is uniquely required for viability, and only this family member retains catalytic competence. To investigate the evolutionary pressure to conserve Argonaute enzymatic activity, we engineered a mouse with catalytically inactive Ago2 alleles. Homozygous mutants died shortly after birth with an obvious anaemia. Examination of microRNAs and their potential targets revealed a loss of miR-451, a small RNA important for erythropoiesis. Though this microRNA is processed by Drosha (also known as Rnasen), its maturation does not require Dicer. Instead, the pre-miRNA becomes loaded into Ago and is cleaved by the Ago catalytic centre to generate an intermediate 3' end, which is then further trimmed. Our findings link the conservation of Argonaute catalysis to a conserved mechanism of microRNA biogenesis that is important for vertebrate development. PMID:20424607

  6. Organocatalytic removal of formaldehyde adducts from RNA and DNA bases

    Science.gov (United States)

    Karmakar, Saswata; Harcourt, Emily M.; Hewings, David S.; Lovejoy, Alexander F.; Kurtz, David M.; Ehrenschwender, Thomas; Barandun, Luzi J.; Roost, Caroline; Alizadeh, Ash A.; Kool, Eric T.

    2015-09-01

    Formaldehyde is universally used to fix tissue specimens, where it forms hemiaminal and aminal adducts with biomolecules, hindering the ability to retrieve molecular information. Common methods for removing these adducts involve extended heating, which can cause extensive degradation of nucleic acids, particularly RNA. Here, we show that water-soluble bifunctional catalysts (anthranilates and phosphanilates) speed the reversal of formaldehyde adducts of mononucleotides over standard buffers. Studies with formaldehyde-treated RNA oligonucleotides show that the catalysts enhance adduct removal, restoring unmodified RNA at 37 °C even when extensively modified, while avoiding the high temperatures that promote RNA degradation. Experiments with formalin-fixed, paraffin-embedded cell samples show that the catalysis is compatible with common RNA extraction protocols, with detectable RNA yields increased by 1.5-2.4-fold using a catalyst under optimized conditions and by 7-25-fold compared with a commercial kit. Such catalytic strategies show promise for general use in reversing formaldehyde adducts in clinical specimens.

  7. Ab initio RNA folding

    International Nuclear Information System (INIS)

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding. (topical review)

  8. Ab initio RNA folding

    Science.gov (United States)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  9. Asymmetric Catalytic Reactions Catalyzed by Chiral Titanium Complexes

    Institute of Scientific and Technical Information of China (English)

    FENG; XiaoMing

    2001-01-01

    Chiral titanium complexes is very importance catalyst to asymmetric catalytic reactions. A series of catalytic systems based on titanium-chiral ligands complexes has been reported. This presentation will discuss some of our recent progress on asymmetric catalytic reactions catalyzed by chiral titanium complexes.  ……

  10. Asymmetric Catalytic Reactions Catalyzed by Chiral Titanium Complexes

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Chiral titanium complexes is very importance catalyst to asymmetric catalytic reactions. A series of catalytic systems based on titanium-chiral ligands complexes has been reported. This presentation will discuss some of our recent progress on asymmetric catalytic reactions catalyzed by chiral titanium complexes.

  11. RNA Localization in Astrocytes

    DEFF Research Database (Denmark)

    Thomsen, Rune

    2012-01-01

    Messenger RNA (mRNA) localization is a mechanism by which polarized cells can regulate protein synthesis to specific subcellular compartments in a spatial and temporal manner, and plays a pivotal role in multiple physiological processes from embryonic development to cell differentiation and...... cell protrusions of both cell types. Moreover, the NGS analysis revealed that the mRNA of the intermediate filament proteins nestin and glial fibrilary acidic protein (GFAP) significantlyaccumulatedin astrocyte protrusions, which was examined in closer detail. Fluorescence in situ hybridization (FISH...

  12. Specific miRNA Stabilization by Gld2-Catalyzed Monoadenylation

    Directory of Open Access Journals (Sweden)

    Andrea D’Ambrogio

    2012-12-01

    Full Text Available MicroRNAs (miRNAs are small, noncoding RNAs that inhibit translation and promote mRNA decay. The levels of mature miRNAs are the result of different rates of transcription, processing, and turnover. The noncanonical polymerase Gld2 has been implicated in the stabilization of miR-122, possibly through catalyzing 3′ monoadenylation; however, there is little evidence that this relationship is one of cause and effect. Here, we biochemically characterize Gld2’s involvement in miRNA monoadenylation and its effect on miRNA stability. We find that Gld2 directly monoadenylates and stabilizes specific miRNA populations in human fibroblasts and that sensitivity to monoadenylation-induced stability depends on nucleotides in the miRNA 3′ end. These results establish a mechanism of miRNA stability and resulting posttranscriptional gene regulation.

  13. Mechanisms of human immunodeficiency virus type 2 RNA packaging

    DEFF Research Database (Denmark)

    Ni, Na; Nikolaitchik, Olga A; Dilley, Kari A; Chen, Jianbo; Galli, Andrea; Fu, William; Prasad, V V S P; Ptak, Roger G; Pathak, Vinay K; Hu, Wei-Shau

    2011-01-01

    Human immunodeficiency virus type 2 (HIV-2) has been reported to have a distinct RNA packaging mechanism, referred to as cis packaging, in which Gag proteins package the RNA from which they were translated. We examined the progeny generated from dually infected cell lines that contain two HIV-2...... proviruses, one with a wild-type gag/gag-pol and the other with a mutant gag that cannot express functional Gag/Gag-Pol. Viral titers and RNA analyses revealed that mutant viral RNAs can be packaged at efficiencies comparable to that of viral RNA from which wild-type Gag/Gag-Pol is translated. These results...... particles in the viral population could be altered by changing a 6-nucleotide palindromic sequence at the 5'-untranslated region of the HIV-2 genome. This finding indicates that selection of copackaging RNA partners occurs prior to encapsidation and that HIV-2 Gag proteins primarily package one dimeric RNA...

  14. tRNA-Related Sequences Trigger Systemic mRNA Transport in Plants.

    Science.gov (United States)

    Zhang, Wenna; Thieme, Christoph J; Kollwig, Gregor; Apelt, Federico; Yang, Lei; Winter, Nikola; Andresen, Nadine; Walther, Dirk; Kragler, Friedrich

    2016-06-01

    In plants, protein-coding mRNAs can move via the phloem vasculature to distant tissues, where they may act as non-cell-autonomous signals. Emerging work has identified many phloem-mobile mRNAs, but little is known regarding RNA motifs triggering mobility, the extent of mRNA transport, and the potential of transported mRNAs to be translated into functional proteins after transport. To address these aspects, we produced reporter transcripts harboring tRNA-like structures (TLSs) that were found to be enriched in the phloem stream and in mRNAs moving over chimeric graft junctions. Phenotypic and enzymatic assays on grafted plants indicated that mRNAs harboring a distinctive TLS can move from transgenic roots into wild-type leaves and from transgenic leaves into wild-type flowers or roots; these mRNAs can also be translated into proteins after transport. In addition, we provide evidence that dicistronic mRNA:tRNA transcripts are frequently produced in Arabidopsis thaliana and are enriched in the population of graft-mobile mRNAs. Our results suggest that tRNA-derived sequences with predicted stem-bulge-stem-loop structures are sufficient to mediate mRNA transport and seem to be necessary for the mobility of a large number of endogenous transcripts that can move through graft junctions. PMID:27268430

  15. Folding of the td pre-RNA with the help of the RNA chaperone StpA.

    Science.gov (United States)

    Mayer, O; Waldsich, C; Grossberger, R; Schroeder, R

    2002-11-01

    The td group I intron is inserted in the reading frame of the thymidylate synthase gene, which is mainly devoid of structural elements. In vivo, translation of the pre-mRNA is required for efficient folding of the intron into its splicing-competent structure. The ribosome probably resolves exon-intron interactions that interfere with splicing. Uncoupling splicing from translation, by introducing a non-sense codon into the upstream exon, reduces the splicing efficiency of the mutant pre-mRNA. Alternatively to the ribosome, co-expression of genes that encode proteins with RNA chaperone activity promote folding of the td pre-mRNA in vivo. These proteins also efficiently accelerate folding of the td pre-mRNA in vitro. In order to understand the mechanism of action of RNA chaperones, we probed the impact of the RNA chaperone StpA on the structure of the td intron in vivo and compared it with that of the well characterized Cyt-18 protein, which is a group-I-intron-specific splicing factor. We found that the two proteins have opposite effects on the structure of the td intron. While StpA loosens the three-dimensional structure, Cyt-18 tightens it up. Furthermore, mutations that destabilize the intron structure render the mutants sensitive to StpA, whereas splicing of these mutants is rescued by Cyt-18. Our results provide direct evidence for protein-induced conformational changes within a catalytic RNA in vivo. Whereas StpA resolves tertiary contacts enabling the RNA to refold, Cyt-18 contributes to the stabilization of the native three-dimensional structure. PMID:12440999

  16. Generation of siRNA Nanosheets for Efficient RNA Interference

    Science.gov (United States)

    Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum

    2016-04-01

    After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.

  17. Formation of RNA oligomers on montmorillonite: site of catalysis

    Science.gov (United States)

    Ertem, G.; Ferris, J. P.

    1998-01-01

    Certain montmorillonites catalyze the self condensation of the 5'-phosphorimidazolide of nucleosides in pH 8 aqueous electrolyte solutions at ambient temperatures leading to formation of RNA oligomers. In order to establish the nature of the sites on montmorillonite responsible for this catalytic activity, oligomerization reactions were run with montmorillonites which had been selectively modified (I) at the edges by (a) fluoride treatment, (b) silylation, (c) metaphosphate treatment of the anion exchange sites (II) in the interlayer by (a) saturation with quaternary alkylammonium ions of increasing size, (b) aluminum polyoxo cations. High pressure liquid chromatography, HPLC, analysis of condensation products for their chain lengths and yields indicated that modification at the edges did not affect the catalytic activity to a significant extent, while blocking the interlayer strongly inhibited product formation.

  18. Shapes of interacting RNA complexes

    DEFF Research Database (Denmark)

    Fu, Benjamin Mingming; Reidys, Christian

    2014-01-01

    Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops.This shape-projection preserves the topological core of the RNA complex and for fixed topological...... genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform...... sampling algorithm for shapes of RNA complexes of fixed topological genus....

  19. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

    Directory of Open Access Journals (Sweden)

    Changrui Lu

    Full Text Available BACKGROUND: The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. METHODOLOGY/PRINCIPAL FINDINGS: Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation. CONCLUSION/SIGNIFICANCE: This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

  20. Electronic fingerprinting of RNA.

    OpenAIRE

    Gegenheimer, P

    1988-01-01

    Software has been developed to assist RNA fingerprinting analysis. One program generates, from a DNA sequence data file, the oligonucleotides resulting from digestion of an RNA transcript labeled with any specified nucleotide(s). Oligonucleotides are sorted according to their position on the fingerprint. Expected molar yields and products of secondary redigestion are also indicated. A second program facilitates calculation of experimental molar yields of oligonucleotides.

  1. Reforming of methane in tubes with a catalytic active wall

    International Nuclear Information System (INIS)

    The heterogeneous steam reforming process in tubes with catalytic active inner surface is studied. The purpose of this ivestigation is to find a method of predicting the reaction rate of the catalytic conversion of methane by steam. The dependency of the reaction rate upon the temperature, pressure, gas composition, Reynolds number, geometrical sizes of tubes and catalytic behaviour of the catalytic active inner wall of these tubes has been examined. It was found that the reaction rate mainly depends on the temperature. The reaction rate is limited by the catalytic behaviour and the heat resisting properties of the materials used. (author)

  2. A non-proteolytic role for ubiquitin in deadenylation of MHC-I mRNA by the RNA-binding E3-ligase MEX-3C.

    Science.gov (United States)

    Cano, Florencia; Rapiteanu, Radu; Sebastiaan Winkler, G; Lehner, Paul J

    2015-01-01

    The regulation of protein and mRNA turnover is essential for many cellular processes. We recently showed that ubiquitin--traditionally linked to protein degradation--directly regulates the degradation of mRNAs through the action of a newly identified family of RNA-binding E3 ubiquitin ligases. How ubiquitin regulates mRNA decay remains unclear. Here, we identify a new role for ubiquitin in regulating deadenylation, the initial and often rate-limiting step in mRNA degradation. MEX-3C, a canonical member of this family of RNA-binding ubiquitin ligases, associates with the cytoplasmic deadenylation complexes and ubiquitinates CNOT7(Caf1), the main catalytic subunit of the CCR4-NOT deadenylation machinery. We establish a new role for ubiquitin in regulating MHC-I mRNA deadenylation as ubiquitination of CNOT7 by MEX-3C regulates its deadenylation activity and is required for MHC-I mRNA degradation. Since neither proteasome nor lysosome inhibitors rescued MEX-3C-mediated MHC-I mRNA degradation, our findings suggest a new non-proteolytic function for ubiquitin in the regulation of mRNA decay. PMID:26471122

  3. Promoting Population

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    THE world's population reached 5 billion in 1987,then 6 billion in 1999;now,in 2011,it is 7 billion.For a country with a set birth control policy,the way in which Chinese people and the media view this number has greatly changed.People are increasingly reflecting on the concept of population from a more scientific and rational perspective.This shift is a change from how people perceived population in the past.

  4. Analysis of hapten binding and catalytic determinants in a family of catalytic antibodies.

    Science.gov (United States)

    Ulrich, H D; Schultz, P G

    1998-01-01

    We report here the cloning and kinetic analysis of a family of catalytic antibodies raised against a common transition state (TS) analog hapten, which accelerate a unimolecular oxy-Cope rearrangement. Sequence analysis revealed close homologies among the heavy chains of the catalytically active members of this set of antibodies, which derive mainly from a single germline gene, whereas the light chains can be traced back to several different, but related germline genes. The requirements for hapten binding and catalytic activity were determined by the construction of hybrid antibodies. Characterization of the latter antibodies again indicates a strong conservation of binding site structure among the catalytically active clones. The heavy chain was found to be the determining factor for catalytic efficiency, while the light chain exerted a smaller modulating effect that depended on light chain gene usage and somatic mutations. Within the heavy chain, the catalytic activity of a clone, but not hapten binding affinity, depended on the sequence of the third complementarity determining region (CDR). No correlation between high affinity for the hapten and high rate enhancement was found in the oxy-Cope system, a result that stands in contrast to the expectations from transition state theory. A mechanistic explanation for this observation is provided based on the three-dimensional crystal structure of the most active antibody, AZ-28, in complex with the hapten. This study demonstrates the utility of catalytic antibodies in examining the relationship between binding energy and catalysis in the evolution of biological catalysis, as well as expanding our understanding of the molecular basis of an immune response. PMID:9451442

  5. mRNA turnover rate limits siRNA and microRNA efficacy

    OpenAIRE

    Larsson, Erik; Sander, Chris; Marks, Debora

    2010-01-01

    What determines how strongly an mRNA responds to a microRNA or an siRNA? We know that properties of the sequence match between the small RNA and the mRNA are crucial. However, large-scale validations of siRNA efficacies have shown that certain transcripts remain recalcitrant to perturbation even after repeated redesign of the siRNA (Krueger et al, 2007). Weak response to RNAi may thus be an inherent property of the mRNA, but the underlying factors have proven difficult to uncover. siRNAs indu...

  6. Janus droplet as a catalytic micromotor

    CERN Document Server

    Shklyaev, Sergey

    2015-01-01

    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, $60\\; {\\rm \\mu m/s}$ 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 Janus one no stability threshold exists; hence, the droplet radius can be scaled down to micrometers. The paper was finalized and submitted by Denis S. Goldobin after Sergey Sklyaev had sadly passed away on June 2, 2014.

  7. From Catalytic Reaction Networks to Protocells

    Science.gov (United States)

    Kaneko, Kunihiko

    2013-12-01

    In spite of recent advances, there still remains a large gape between a set of chemical reactions and a biological cell. Here we discuss several theoretical efforts to fill in the gap. The topics cover (i) slow relaxation to equilibrium due to glassy behavior in catalytic reaction networks (ii) consistency between molecule replication and cell growth, as well as energy metabolism (iii) control of a system by minority molecules in mutually catalytic system, which work as a carrier of genetic information, and leading to evolvability (iv) generation of a compartmentalized structure as a cluster of molecules centered around the minority molecule, and division of the cluster accompanied by the replication of minority molecule (v) sequential, logical process over several states from concurrent reaction dynamics, by taking advantage of discreteness in molecule number.

  8. Catalytic extraction processing of contaminated scrap metal

    International Nuclear Information System (INIS)

    Molten Metal Technology was awarded a contract to demonstrate the applicability of the Catalytic Extraction Process, a proprietary process that could be applied to US DOE's inventory of low level mixed waste. This paper is a description of that technology, and included within this document are discussions of: (1) Program objectives, (2) Overall technology review, (3) Organic feed conversion to synthetic gas, (4) Metal, halogen, and transuranic recovery, (5) Demonstrations, (6) Design of the prototype facility, and (7) Results

  9. Thermal and catalytic pyrolysis of plastic waste

    OpenAIRE

    Débora Almeida; Maria de Fátima Marques

    2016-01-01

    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. Zeolit...

  10. Materials for High-Temperature Catalytic Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Ersson, Anders

    2003-04-01

    Catalytic combustion is an environmentally friendly technique to combust fuels in e.g. gas turbines. Introducing a catalyst into the combustion chamber of a gas turbine allows combustion outside the normal flammability limits. Hence, the adiabatic flame temperature may be lowered below the threshold temperature for thermal NO{sub X} formation while maintaining a stable combustion. However, several challenges are connected to the application of catalytic combustion in gas turbines. The first part of this thesis reviews the use of catalytic combustion in gas turbines. The influence of the fuel has been studied and compared over different catalyst materials. The material section is divided into two parts. The first concerns bimetallic palladium catalysts. These catalysts showed a more stable activity compared to their pure palladium counterparts for methane combustion. This was verified both by using an annular reactor at ambient pressure and a pilot-scale reactor at elevated pressures and flows closely resembling the ones found in a gas turbine combustor. The second part concerns high-temperature materials, which may be used either as active or washcoat materials. A novel group of materials for catalysis, i.e. garnets, has been synthesised and tested in combustion of methane, a low-heating value gas and diesel fuel. The garnets showed some interesting abilities especially for combustion of low-heating value, LHV, gas. Two other materials were also studied, i.e. spinels and hexa aluminates, both showed very promising thermal stability and the substituted hexa aluminates also showed a good catalytic activity. Finally, deactivation of the catalyst materials was studied. In this part the sulphur poisoning of palladium, platinum and the above-mentioned complex metal oxides has been studied for combustion of a LHV gas. Platinum and surprisingly the garnet were least deactivated. Palladium was severely affected for methane combustion while the other washcoat materials were

  11. Materials for High-Temperature Catalytic Combustion

    OpenAIRE

    Ersson, Anders

    2003-01-01

    Catalytic combustion is an environmentally friendlytechnique to combust fuels in e.g. gas turbines. Introducing acatalyst into the combustion chamber of a gas turbine allowscombustion outside the normal flammability limits. Hence, theadiabatic flame temperature may be lowered below the thresholdtemperature for thermal NOXformation while maintaining a stable combustion.However, several challenges are connected to the application ofcatalytic combustion in gas turbines. The first part of thisthe...

  12. Catalytic fast pyrolysis of lignocellulosic biomass

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Changjun; Wang, Huamin; Karim, Ayman M.; Sun, Junming; Wang, Yong

    2014-11-21

    Increasing energy demand, especially in the transportation sector, and soaring CO2 emissions necessitate the exploitation of renewable sources of energy. Despite the large variety of new energy Q3 carriers, liquid hydrocarbon still appears to be the most attractive and feasible form of transportation fuel taking into account the energy density, stability and existing infrastructure. Biomass is an abundant, renewable source of energy; however, utilizing it in a cost-effective way is still a substantial challenge. Lignocellulose is composed of three major biopolymers, namely cellulose, hemicellulose and lignin. Fast pyrolysis of biomass is recognized as an efficient and feasible process to selectively convert lignocellulose into a liquid fuel—bio-oil. However bio-oil from fast pyrolysis contains a large amount of oxygen, distributed in hundreds of oxygenates. These oxygenates are the cause of many negative properties, such as low heating values, high corrosiveness, high viscosity, and instability; they also greatly Q4 limit the application of bio-oil particularly as transportation fuel. Hydrocarbons derived from biomass are most attractive because of their high energy density and compatibility with the existing infrastructure. Thus, converting lignocellulose into transportation fuels via catalytic fast pyrolysis has attracted much attention. Many studies related to catalytic fast pyrolysis of biomass have been published. The main challenge of this process is the development of active and stable catalysts that can deal with a large variety of decomposition intermediates from lignocellulose. This review starts with the current understanding of the chemistry in fast pyrolysis of lignocellulose and focuses on the development of catalysts in catalytic fast pyrolysis. Recent progress in the experimental studies on catalytic fast pyrolysis of biomass is also summarized with the emphasis on bio-oil yields and quality.

  13. Computer Aided Enzyme Design and Catalytic Concepts

    OpenAIRE

    Frushicheva, Maria P.; Mills, Matthew J. L.; Schopf, Patrick; Singh, Manoj K.; Warshel, Arieh

    2014-01-01

    Gaining a deeper understanding of enzyme catalysis is of great practical and fundamental importance. Over the years it has become clear that despite advances made in experimental mutational studies, a quantitative understanding of enzyme catalysis will not be possible without the use of computer modeling approaches. While we believe that electrostatic preorganization is by far the most important catalytic factor, convincing the wider scientific community of this may require the demonstration ...

  14. Ubiquitous "glassy" relaxation in catalytic reaction networks

    OpenAIRE

    Awazu, Akinori; Kaneko, Kunihiko

    2009-01-01

    Study of reversible catalytic reaction networks is important not only as an issue for chemical thermodynamics but also for protocells. From extensive numerical simulations and theoretical analysis, slow relaxation dynamics to sustain nonequlibrium states are commonly observed. These dynamics show two types of salient behaviors that are reminiscent of glassy behavior: slow relaxation along with the logarithmic time dependence of the correlation function and the emergence of plateaus in the rel...

  15. RNA Reactions One Molecule at a Time

    OpenAIRE

    Tinoco, Ignacio; Chen, Gang; Qu, Xiaohui

    2010-01-01

    Much of the dynamics information is lost in bulk measurements because of the population averaging. Single-molecule methods measure one molecule at a time; they provide knowledge not obtainable by other means. In this article, we review the application of the two most widely used single-molecule methods—fluorescence resonance energy transfer (FRET) and force versus extension measurements—to several RNA reactions. First, we discuss folding/unfolding studies on a hairpin ribozyme that revealed m...

  16. siRNA for Influenza Therapy

    OpenAIRE

    Sailen Barik

    2010-01-01

    Influenza virus is one of the most prevalent and ancient infections in humans. About a fifth of world's population is infected by influenza virus annually, leading to high morbidity and mortality, particularly in infants, the elderly and the immunocompromised. In the US alone, influenza outbreaks lead to roughly 30,000 deaths each year. Current vaccines and anti-influenza drugs are of limited use due to high mutation rate of the virus and side effects. In recent years, RNA interference, trigg...

  17. Two Arabidopsis ADP-glucose pyrophosphorylase large subunits (APL1 and APL2) are catalytic.

    Science.gov (United States)

    Ventriglia, Tiziana; Kuhn, Misty L; Ruiz, Ma Teresa; Ribeiro-Pedro, Marina; Valverde, Federico; Ballicora, Miguel A; Preiss, Jack; Romero, José M

    2008-09-01

    ADP-glucose (Glc) pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in starch biosynthesis. Higher plant ADP-Glc PPase is a heterotetramer (alpha(2)beta(2)) consisting of two small and two large subunits. There is increasing evidence that suggests that catalytic and regulatory properties of the enzyme from higher plants result from the synergy of both types of subunits. In Arabidopsis (Arabidopsis thaliana), two genes encode small subunits (APS1 and APS2) and four large subunits (APL1-APL4). Here, we show that in Arabidopsis, APL1 and APL2, besides their regulatory role, have catalytic activity. Heterotetramers formed by combinations of a noncatalytic APS1 and the four large subunits showed that APL1 and APL2 exhibited ADP-Glc PPase activity with distinctive sensitivities to the allosteric activator (3-phosphoglycerate). Mutation of the Glc-1-P binding site of Arabidopsis and potato (Solanum tuberosum) isoforms confirmed these observations. To determine the relevance of these activities in planta, a T-DNA mutant of APS1 (aps1) was characterized. aps1 is starchless, lacks ADP-Glc PPase activity, APS1 mRNA, and APS1 protein, and is late flowering in long days. Transgenic lines of the aps1 mutant, expressing an inactivated form of APS1, recovered the wild-type phenotype, indicating that APL1 and APL2 have catalytic activity and may contribute to ADP-Glc synthesis in planta. PMID:18614708

  18. Two Arabidopsis ADP-Glucose Pyrophosphorylase Large Subunits (APL1 and APL2) Are Catalytic1

    Science.gov (United States)

    Ventriglia, Tiziana; Kuhn, Misty L.; Ruiz, Ma Teresa; Ribeiro-Pedro, Marina; Valverde, Federico; Ballicora, Miguel A.; Preiss, Jack; Romero, José M.

    2008-01-01

    ADP-glucose (Glc) pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in starch biosynthesis. Higher plant ADP-Glc PPase is a heterotetramer (α2β2) consisting of two small and two large subunits. There is increasing evidence that suggests that catalytic and regulatory properties of the enzyme from higher plants result from the synergy of both types of subunits. In Arabidopsis (Arabidopsis thaliana), two genes encode small subunits (APS1 and APS2) and four large subunits (APL1–APL4). Here, we show that in Arabidopsis, APL1 and APL2, besides their regulatory role, have catalytic activity. Heterotetramers formed by combinations of a noncatalytic APS1 and the four large subunits showed that APL1 and APL2 exhibited ADP-Glc PPase activity with distinctive sensitivities to the allosteric activator (3-phosphoglycerate). Mutation of the Glc-1-P binding site of Arabidopsis and potato (Solanum tuberosum) isoforms confirmed these observations. To determine the relevance of these activities in planta, a T-DNA mutant of APS1 (aps1) was characterized. aps1 is starchless, lacks ADP-Glc PPase activity, APS1 mRNA, and APS1 protein, and is late flowering in long days. Transgenic lines of the aps1 mutant, expressing an inactivated form of APS1, recovered the wild-type phenotype, indicating that APL1 and APL2 have catalytic activity and may contribute to ADP-Glc synthesis in planta. PMID:18614708

  19. Probing catalytic rate enhancement during intramembrane proteolysis.

    Science.gov (United States)

    Arutyunova, Elena; Smithers, Cameron C; Corradi, Valentina; Espiritu, Adam C; Young, Howard S; Tieleman, D Peter; Lemieux, M Joanne

    2016-09-01

    Rhomboids are ubiquitous intramembrane serine proteases involved in various signaling pathways. While the high-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed an active site comprised of a serine-histidine dyad and an extensive oxyanion hole, the molecular details of rhomboid catalysis were unclear because substrates are unknown for most of the family members. Here we used the only known physiological pair of AarA rhomboid with its psTatA substrate to decipher the contribution of catalytically important residues to the reaction rate enhancement. An MD-refined homology model of AarA was used to identify residues important for catalysis. We demonstrated that the AarA active site geometry is strict and intolerant to alterations. We probed the roles of H83 and N87 oxyanion hole residues and determined that substitution of H83 either abolished AarA activity or reduced the transition state stabilization energy (ΔΔG‡) by 3.1 kcal/mol; substitution of N87 decreased ΔΔG‡ by 1.6-3.9 kcal/mol. Substitution M154, a residue conserved in most rhomboids that stabilizes the catalytic general base, to tyrosine, provided insight into the mechanism of nucleophile generation for the catalytic dyad. This study provides a quantitative evaluation of the role of several residues important for hydrolytic efficiency and oxyanion stabilization during intramembrane proteolysis. PMID:27071148

  20. Catalytic pyrolysis of olive mill wastewater sludge

    Science.gov (United States)

    Abdellaoui, Hamza

    From 2008 to 2013, an average of 2,821.4 kilotons/year of olive oil were produced around the world. The waste product of the olive mill industry consists of solid residue (pomace) and wastewater (OMW). Annually, around 30 million m3 of OMW are produced in the Mediterranean area, 700,000 m3 year?1 in Tunisia alone. OMW is an aqueous effluent characterized by an offensive smell and high organic matter content, including high molecular weight phenolic compounds and long-chain fatty acids. These compounds are highly toxic to micro-organisms and plants, which makes the OMW a serious threat to the environment if not managed properly. The OMW is disposed of in open air evaporation ponds. After evaporation of most of the water, OMWS is left in the bottom of the ponds. In this thesis, the effort has been made to evaluate the catalytic pyrolysis process as a technology to valorize the OMWS. The first section of this research showed that 41.12 wt. % of the OMWS is mostly lipids, which are a good source of energy. The second section proved that catalytic pyrolysis of the OMWS over red mud and HZSM-5 can produce green diesel, and 450 °C is the optimal reaction temperature to maximize the organic yields. The last section revealed that the HSF was behind the good fuel-like properties of the OMWS catalytic oils, whereas the SR hindered the bio-oil yields and quality.

  1. Modeling the Complete Catalytic Cycle of Aspartoacylase.

    Science.gov (United States)

    Kots, Ekaterina D; Khrenova, Maria G; Lushchekina, Sofya V; Varfolomeev, Sergei D; Grigorenko, Bella L; Nemukhin, Alexander V

    2016-05-12

    The complete catalytic cycle of aspartoacylase (ASPA), a zinc-dependent enzyme responsible for cleavage of N-acetyl-l-aspartate, is characterized by the methods of molecular modeling. The reaction energy profile connecting the enzyme-substrate (ES) and the enzyme-product (EP) complexes is constructed by the quantum mechanics/molecular mechanics (QM/MM) method assisted by the molecular dynamics (MD) simulations with the QM/MM potentials. Starting from the crystal structure of ASPA complexed with the intermediate analogue, the minimum-energy geometry configurations and the corresponding transition states are located. The stages of substrate binding to the enzyme active site and release of the products are modeled by MD calculations with the replica-exchange umbrella sampling technique. It is shown that the first reaction steps, nucleophilic attack of a zinc-bound nucleophilic water molecule at the carbonyl carbon and the amide bond cleavage, are consistent with the glutamate-assisted mechanism hypothesized for the zinc-dependent hydrolases. The stages of formation of the products, acetate and l-aspartate, and regeneration of the enzyme are characterized for the first time. The constructed free energy diagram from the reactants to the products suggests that the enzyme regeneration, but not the nucleophilic attack of the catalytic water molecule, corresponds to the rate-determining stage of the full catalytic cycle of ASPA. PMID:27089954

  2. 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.

  3. Catalytic hydrogen recombination for nuclear containments

    International Nuclear Information System (INIS)

    Catalytic recombiners appear to be a credible option for hydrogen mitigation in nuclear containments. The passive operation, versatility and ease of back fitting are appealing for existing stations and new designs. Recently, a generation of wet-proofed catalyst materials have been developed at AECL which are highly specific to H2-O2, are active at ambient temperatures and are being evaluated for containment applications. Two types of catalytic recombiners were evaluated for hydrogen removal in containments based on the AECL catalyst. The first is a catalytic combustor for application in existing air streams such as provided by fans or ventilation systems. The second is an autocatalytic recombiner which uses the enthalpy of reaction to produce natural convective flow over the catalyst elements. Intermediate-scale results obtained in 6 m3 and 10 m3 spherical and cylindrical vessels are given to demonstrate self-starting limits, operating limits, removal capacity, scaling parameters, flow resistance, mixing behaviour in the vicinity of an operating recombiner and sensitivity to poisoning, fouling and radiation. (author). 13 refs., 10 figs

  4. IFP solutions for revamping catalytic reforming units

    Energy Technology Data Exchange (ETDEWEB)

    Gendler, J.L. [HRI, Inc., Princeton, NJ (United States); Domergue, B.; Mank, L. [Inst. Francais du Petrole, Rueil Malmaison (France)

    1996-12-01

    The decision-making process for the refiner considering a revamp of a catalytic reforming unit comprises many factors. These may be grouped in two broad areas: technical and economic. This paper presents the results of a study performed by IFP that illustrates catalytic reforming unit revamp options. Three IFP processes are described and operating conditions, expected yields, and economic data are presented. The following options are discussed: base case Conventional, fixed-bed, semi-regenerative catalytic reformer; Case 1--revamp using IFP Dualforming technology; Case 2--revamp using IFP Dualforming Plus technology; and Case 3--revamp to IFP Octanizing technology. The study illustrates various options for the refiner to balance unit performance improvements with equipment, site, and economic constraints. The study was performed assuming design feedrate of 98.2 tons/hour (20,000 BPSD) in all cases. Because of the increased need for octane in many refineries, the study assumed that operating severity was set at a design value of 100 research octane number clear (RON). In all of the cases in this study, it was assumed that the existing recycle compressor was reused. Operating pressure differences between the cases is discussed separately. Also, in all cases, a booster compressor was included in order to return export hydrogen pressure to that of the conventional unit.

  5. Electrochemical catalytic treatment of phenol wastewater

    International Nuclear Information System (INIS)

    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.

  6. Population Blocks.

    Science.gov (United States)

    Smith, Martin H.

    1992-01-01

    Describes an educational game called "Population Blocks" that is designed to illustrate the concept of exponential growth of the human population and some potential effects of overpopulation. The game material consists of wooden blocks; 18 blocks are painted green (representing land), 7 are painted blue (representing water); and the remaining…

  7. A Complex Small RNA Repertoire Is Generated by a Plant/Fungal-Like Machinery and Effected by a Metazoan-Like Argonaute in the Single-Cell Human Parasite Toxoplasma gondii

    Science.gov (United States)

    Ortet, Philippe; Barakat, Mohamed; Sautel, Céline F.; Kieffer, Sylvie; Garin, Jérôme; Bastien, Olivier; Voinnet, Olivier; Hakimi, Mohamed-Ali

    2010-01-01

    In RNA silencing, small RNAs produced by the RNase-III Dicer guide Argonaute-like proteins as part of RNA-induced silencing complexes (RISC) to regulate gene expression transcriptionally or post-transcriptionally. Here, we have characterized the RNA silencing machinery and exhaustive small RNAome of Toxoplasma gondii, member of the Apicomplexa, a phylum of animal- and human-infecting parasites that cause extensive health and economic damages to human populations worldwide. Remarkably, the small RNA-generating machinery of Toxoplasma is phylogenetically and functionally related to that of plants and fungi, and accounts for an exceptionally diverse array of small RNAs. This array includes conspicuous populations of repeat-associated small interfering RNA (siRNA), which, as in plants, likely generate and maintain heterochromatin at DNA repeats and satellites. Toxoplasma small RNAs also include many microRNAs with clear metazoan-like features whose accumulation is sometimes extremely high and dynamic, an unexpected finding given that Toxoplasma is a unicellular protist. Both plant-like heterochromatic small RNAs and metazoan-like microRNAs bind to a single Argonaute protein, Tg-AGO. Toxoplasma miRNAs co-sediment with polyribosomes, and thus, are likely to act as translational regulators, consistent with the lack of catalytic residues in Tg-AGO. Mass spectrometric analyses of the Tg-AGO protein complex revealed a common set of virtually all known RISC components so far characterized in human and Drosophila, as well as novel proteins involved in RNA metabolism. In agreement with its loading with heterochromatic small RNAs, Tg-AGO also associates substoichiometrically with components of known chromatin-repressing complexes. Thus, a puzzling patchwork of silencing processor and effector proteins from plant, fungal and metazoan origin accounts for the production and action of an unsuspected variety of small RNAs in the single-cell parasite Toxoplasma and possibly in other

  8. Topology of RNA-RNA interaction structures

    CERN Document Server

    Andersen, Jørgen E; Penner, Robert C; Reidys, Christian M

    2011-01-01

    The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting RNAs, called interaction structures, there exist for fixed genus only finitely many irreducible shadows. This implies that for fixed genus there are only finitely many classes of interaction structures. In particular the simplest case of genus zero already provides the formalism for certain types of structures that occur in nature and are not covered by other filtrations. This case of genus zero interaction structures is already of practical interest, is studied here in detail and found to be expressed by a multiple context-free grammar extending the usual one for RNA secondary structures. We show that in $O(n^6)$ time and $O(n^4)$ space complexity, this grammar for genus zero interaction structures provides not only minimum free energy solutions but also the complete partit...

  9. Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense

    Directory of Open Access Journals (Sweden)

    Olson Ken E

    2011-02-01

    Full Text Available Abstract Background Small RNA (sRNA regulatory pathways (SRRPs are important to anti-viral defence in mosquitoes. To identify critical features of the virus infection process in Dengue serotype 2 (DENV2-infected Ae. aegypti, we deep-sequenced small non-coding RNAs. Triplicate biological replicates were used so that rigorous statistical metrics could be applied. Results In addition to virus-derived siRNAs (20-23 nts previously reported for other arbovirus-infected mosquitoes, we show that PIWI pathway sRNAs (piRNAs (24-30 nts and unusually small RNAs (usRNAs (13-19 nts are produced in DENV-infected mosquitoes. We demonstrate that a major catalytic enzyme of the siRNA pathway, Argonaute 2 (Ago2, co-migrates with a ~1 megadalton complex in adults prior to bloodfeeding. sRNAs were cloned and sequenced from Ago2 immunoprecipitations. Viral sRNA patterns change over the course of infection. Host sRNAs were mapped to the published aedine transcriptome and subjected to analysis using edgeR (Bioconductor. We found that sRNA profiles are altered early in DENV2 infection, and mRNA targets from mitochondrial, transcription/translation, and transport functional categories are affected. Moreover, small non-coding RNAs (ncRNAs, such as tRNAs, spliceosomal U RNAs, and snoRNAs are highly enriched in DENV-infected samples at 2 and 4 dpi. Conclusions These data implicate the PIWI pathway in anti-viral defense. Changes to host sRNA profiles indicate that specific cellular processes are affected during DENV infection, such as mitochondrial function and ncRNA levels. Together, these data provide important progress in understanding the DENV2 infection process in Ae. aegypti.

  10. Crystal structures of two eukaryotic nucleases involved in RNA metabolism

    DEFF Research Database (Denmark)

    Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich;

    well as the controlled turnover of these in response to changing surrounding conditions is of vital importance to ensure optimal fitness of a cell. Central to both these processes is the degradation of RNA, either as a means of decreasing the level of particular RNAs or as a way to get rid of aberrant...... of very similar nucleases provide a visualisation of the catalytic cycle of the S. pombe Pop2p protein. In addition, structural comparison of S. pombe Pop2p to other similar proteins identifies Pop2p and deadenylase specific regions near the active site. Contrary to Pop2p Rrp6p is solely a nuclear...

  11. Population crises and population cycles.

    Science.gov (United States)

    Russell, C; Russell, W M

    2000-01-01

    To prevent a population irretrievably depleting its resources, mammals have evolved a behavioural and physiological response to population crisis. When a mammalian population becomes dangerously dense, there is a reversal of behaviour. Co-operation and parental behaviour are replaced by competition, dominance and aggressive violence, leading to high mortality, especially of females and young, and a reduced population. The stress of overpopulation and the resulting violence impairs both the immune and the reproductive systems. Hence epidemics complete the crash of the population, and reproduction is slowed for three or four generations, giving the resources ample time to recover. In some mammal species, crisis and crisis response recur regularly, leading to cycles of population growth and relapse, oscillating about a fixed mean. Population crisis response and population cycles have been equally prominent in the history of human societies. But in man successive advances in food production have made possible growing populations, though with every such advance population soon outgrew resources again. Hence human cycles have been superimposed on a rising curve, producing a saw-tooth graph. Because advances in food production amounted to sudden disturbances in the relations between human populations and their environments, the crisis response in man has failed to avert famine and resource damage. In the large human societies evolved since the coming of settled agriculture and cities, the basic effects of violence, epidemics, famine and resource damage have been mediated by such specifically human disasters as inflation, unemployment, and political tyranny. An account of past crises, periods of relative relief from population pressure, and resulting cycles, is given for a number of regions: China, North Africa and Western Asia, the northern Mediterranean, and north-western Europe. The paper ends with an account of the present world-wide population crisis, and the solution

  12. Imaginary populations

    Directory of Open Access Journals (Sweden)

    A. Martínez–Abraín

    2010-01-01

    Full Text Available A few years ago, Camus & Lima (2002 wrote an essay to stimulate ecologists to think about how we define and use a fundamental concept in ecology: the population. They concluded, concurring with Berryman (2002, that a population is "a group of individuals of the same species that live together in an area of sufficient size to permit normal dispersal and/or migration behaviour and in which population changes are largely the results of birth and death processes". They pointed out that ecologists often forget "to acknowledge that many study units are neither natural nor even units in terms of constituting a population system", and hence claimed that we "require much more accuracy than in past decades in order to be more effective to characterize populations and predict their behaviour". They stated that this is especially necessary "in disciplines such as conservation biology or resource pest management, to avoid reaching wrong conclusions or making inappropriate decisions". As a population ecologist and conservation biologist I totally agree with these authors and, like them, I be¬lieve that greater precision and care is needed in the use and definition of ecological terms. The point I wish to stress here is that we ecologists tend to forget that when we use statistical tools to infer results from our sample to a population we work with what statisticians term "imaginary", "hypothetical" or "potential" popula¬tions. As Zar (1999 states, if our sample data consist of 40 measurements of growth rate in guinea pigs "the population about which conclusions might be drawn is the growth rates of all the guinea pigs that conceivably might have been administered the same food supplement under identical conditions". Such a population does not really exist, and hence it is considered a hypothetical or imaginary population. Compare that definition with the population concept that would be in our minds when performing such measurements. We would probably

  13. Yeast nuclear RNA processing

    Institute of Scientific and Technical Information of China (English)

    Jade; Bernstein; Eric; A; Toth

    2012-01-01

    Nuclear RNA processing requires dynamic and intricately regulated machinery composed of multiple enzymes and their cofactors.In this review,we summarize recent experiments using Saccharomyces cerevisiae as a model system that have yielded important insights regarding the conversion of pre-RNAs to functional RNAs,and the elimination of aberrant RNAs and unneeded intermediates from the nuclear RNA pool.Much progress has been made recently in describing the 3D structure of many elements of the nuclear degradation machinery and its cofactors.Similarly,the regulatory mechanisms that govern RNA processing are gradually coming into focus.Such advances invariably generate many new questions,which we highlight in this review.

  14. Alignments of RNA structures.

    Science.gov (United States)

    Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

    2010-01-01

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia. PMID:20431150

  15. Absence of telomerase activity and telomerase catalytic subunit mRNA in melanocyte cultures

    OpenAIRE

    Dhaene, K.; Vancoillie, G; Lambert, J.; Naeyaert, J M; Van Marck, E

    2000-01-01

    The classic model of activation of telomerase, for which activity has been found in most cancers including cutaneous malignant melanoma (CMM), dictates that enzyme activity is generated by pathological reactivation of telomerase in telomerase-negative somatic cells. However, recent data demonstrated physiological up-regulation in some normal cell types when established as proliferating cultures, indicating that, in some cancer types, telomerase is expressed by the process of up-regulation in ...

  16. Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme

    Czech Academy of Sciences Publication Activity Database

    Krasovská, Maryna V.; Šefčíková, J.; Réblová, Kamila; Schneider, Bohdan; Walter, N.G.; Šponer, Jiří

    2006-01-01

    Roč. 91, č. 2 (2006), s. 626-638. ISSN 0006-3495 R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA AV ČR(CZ) 1QS500040581; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z40550506 Keywords : molecular dynamics * cations * hydration Subject RIV: BO - Biophysics Impact factor: 4.757, year: 2006

  17. Population policy.

    Science.gov (United States)

    1987-03-01

    Participants in the Seminar on Population Policies for Top-level Policy Makers and Program Managers, meeting in Thailand during January 1987, examined the challenges now facing them regarding the implementation of fertility regulation programs in their respective countries -- Bangladesh, China, India, Indonesia, Malaysia, Nepal, Pakistan, the Philippines, the Republic of Korea, and Thailand. This Seminar was organized to coincide with the completion of an Economic and Social Commission for Asia and the Pacific (ESCAP) study investigating the impact and efficiency of family planning programs in the region. Country studies were reviewed at the Seminar along with policy issues about the status of women, incentive and disincentive programs, and socioeconomic factors affecting fertility. In Bangladesh the government recognizes population growth as its top priority problem related to the socioeconomic development of the country and is working to promote a reorientation strategy from the previous clinic-oriented to a multidimensional family welfare program. China's family planning program seeks to postpone marraige, space the births of children between 3-5 years, and promote the 1-child family. Its goal is to reduce the rate of natural increase from 12/1000 in 1978 to 5/1000 by 1985 and 0 by 2000. India's 7th Five-Year-Plan (1986-90) calls for establishing a 2-child family norm by 2000. In Indonesia the government's population policy includes reducing the rate of population growth, achieving a redistribution of the population, adjusting economic factors, and creating prosperous families. The government of Indonesia reversed its policy to reduce the population growth rate in 1984 and announced its goal of achieving a population of 70 million by 2100 in order to support mass consumption industries. It has created an income tax deduction system favoring large families and maternity benefits for women who have up to 5 children as incentives. Nepal's official policy is to

  18. 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

  19. Sensing of RNA viruses

    DEFF Research Database (Denmark)

    Jensen, Søren; Thomsen, Allan Randrup

    2012-01-01

    Our knowledge regarding the contribution of the innate immune system in recognizing and subsequently initiating a host response to an invasion of RNA virus has been rapidly growing over the last decade. Descriptions of the receptors involved and the molecular mechanisms they employ to sense viral...... pathogen-associated molecular patterns have emerged in great detail. This review presents an overview of our current knowledge regarding the receptors used to detect RNA virus invasion, the molecular structures these receptors sense, and the involved downstream signaling pathways....

  20. A Potential Protein-RNA Recognition Event Along the RISC-Loading Pathway from the Structure of A. aeolicus Argonaute with Externally Bound siRNA

    Energy Technology Data Exchange (ETDEWEB)

    Yuan,Y.; Pei, Y.; Chen, H.; Tuschl, T.; Patel, D.

    2006-01-01

    Argonaute proteins are key components of the RNA-induced silencing complex (RISC). They provide both architectural and catalytic functionalities associated with small interfering RNA (siRNA) guide strand recognition and subsequent guide strand-mediated cleavage of complementary mRNAs. We report on the 3.0 {angstrom} crystal structures of 22-mer and 26-mer siRNAs bound to Aquifex aeolicus Argonaute (Aa-Ago), where one 2 nt 3' overhang of the siRNA inserts into a cavity positioned on the outer surface of the PAZ-containing lobe of the bilobal Aa-Ago architecture. The first overhang nucleotide stacks over a tyrosine ring, while the second overhang nucleotide, together with the intervening sugar-phosphate backbone, inserts into a preformed surface cavity. Photochemical crosslinking studies on Aa-Ago with 5-iodoU-labeled single-stranded siRNA and siRNA duplex provide support for this externally bound siRNA-Aa-Ago complex. The structure and biochemical data together provide insights into a protein-RNA recognition event potentially associated with the RISC-loading pathway.

  1. Strategies underlying RNA silencing suppression by negative strand RNA viruses

    OpenAIRE

    Hemmes, J.C.

    2007-01-01

    The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double stranded (ds)RNA ‘trigger’ molecules into small interfering RNAs (siRNAs) by enzymes of the Dicer family. The siRNA molecules are essential components of the RNA induced silencing complex (RISC), which u...

  2. Branched RNA: A New Architecture for RNA Interference

    Directory of Open Access Journals (Sweden)

    Anna Aviñó

    2011-01-01

    Full Text Available Branched RNAs with two and four strands were synthesized. These structures were used to obtain branched siRNA. The branched siRNA duplexes had similar inhibitory capacity as those of unmodified siRNA duplexes, as deduced from gene silencing experiments of the TNF-α protein. Branched RNAs are considered novel structures for siRNA technology, and they provide an innovative tool for specific gene inhibition. As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems.

  3. Studying RNA-protein interactions in vivo by RNA immunoprecipitation

    DEFF Research Database (Denmark)

    Selth, Luke A; Close, Pierre; Svejstrup, Jesper Q

    The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases and...... have significant effects on gene expression. RNA immunoprecipitation (RIP) is a powerful technique used to detect direct and indirect interactions between individual proteins and specific RNA molecules in vivo. Here, we describe RIP methods for both yeast and mammalian cells....

  4. m5C RNA and m5C DNA methyl transferases use different cysteine residues as catalysts.

    Science.gov (United States)

    Liu, Y; Santi, D V

    2000-07-18

    A family of RNA m(5)C methyl transferases (MTases) containing over 55 members in eight subfamilies has been identified recently by an iterative search of the genomic sequence databases by using the known 16S rRNA m(5)C 967 MTase, Fmu, as an initial probe. The RNA m(5)C MTase family contained sequence motifs that were highly homologous to motifs in the DNA m(5)C MTases, including the ProCys sequence that contains the essential Cys catalyst of the functionally similar DNA-modifying enzymes; it was reasonable to assign the Cys nucleophile to be that in the conserved ProCys. The family also contained an additional conserved Cys residue that aligns with the nucleophilic catalyst in m(5)U54 tRNA MTase. Surprisingly, the mutant of the putative Cys catalyst in the ProCys sequence was active and formed a covalent complex with 5-fluorocytosine-containing RNA, whereas the mutant at the other conserved Cys was inactive and unable to form the complex. Thus, notwithstanding the highly homologous sequences and similar functions, the RNA m(5)C MTase uses a different Cys as a catalytic nucleophile than the DNA m(5)C MTases. The catalytic Cys seems to be determined, not by the target base that is modified, but by whether the substrate is DNA or RNA. The function of the conserved ProCys sequence in the RNA m(5)C MTases remains unknown. PMID:10899996

  5. Engineering Metallic Nanoparticles for Enhancing and Probing Catalytic Reactions.

    Science.gov (United States)

    Collins, Gillian; Holmes, Justin D

    2016-07-01

    Recent developments in tailoring the structural and chemical properties of colloidal metal nanoparticles (NPs) have led to significant enhancements in catalyst performance. Controllable colloidal synthesis has also allowed tailor-made NPs to serve as mechanistic probes for catalytic processes. The innovative use of colloidal NPs to gain fundamental insights into catalytic function will be highlighted across a variety of catalytic and electrocatalytic applications. The engineering of future heterogenous catalysts is also moving beyond size, shape and composition considerations. Advancements in understanding structure-property relationships have enabled incorporation of complex features such as tuning surface strain to influence the behavior of catalytic NPs. Exploiting plasmonic properties and altering colloidal surface chemistry through functionalization are also emerging as important areas for rational design of catalytic NPs. This news article will highlight the key developments and challenges to the future design of catalytic NPs. PMID:26823380

  6. Catalytic bioscavengers in nerve agent poisoning: A promising approach?

    Science.gov (United States)

    Worek, Franz; Thiermann, Horst; Wille, Timo

    2016-02-26

    The repeated use of the nerve agent sarin against civilians in Syria in 2013 emphasizes the continuing threat by chemical warfare agents. Multiple studies demonstrated a limited efficacy of standard atropine-oxime treatment in nerve agent poisoning and called for the development of alternative and more effective treatment strategies. A novel approach is the use of stoichiometric or catalytic bioscavengers for detoxification of nerve agents in the systemic circulation prior to distribution into target tissues. Recent progress in the design of enzyme mutants with reversed stereo selectivity resulting in improved catalytic activity and their use in in vivo studies supports the concept of catalytic bioscavengers. Yet, further research is necessary to improve the catalytic activity, substrate spectrum and in vivo biological stability of enzyme mutants. The pros and cons of catalytic bioscavengers will be discussed in detail and future requirements for the development of catalytic bioscavengers will be proposed. PMID:26200600

  7. New Perspectives on DNA and RNA Triplexes As Effectors of Biological Activity.

    Science.gov (United States)

    Bacolla, Albino; Wang, Guliang; Vasquez, Karen M

    2015-12-01

    Since the first description of the canonical B-form DNA double helix, it has been suggested that alternative DNA, DNA-RNA, and RNA structures exist and act as functional genomic elements. Indeed, over the past few years it has become clear that, in addition to serving as a repository for genetic information, genomic DNA elicits biological responses by adopting conformations that differ from the canonical right-handed double helix, and by interacting with RNA molecules to form complex secondary structures. This review focuses on recent advances on three-stranded (triplex) nucleic acids, with an emphasis on DNA-RNA and RNA-RNA interactions. Emerging work reveals that triplex interactions between noncoding RNAs and duplex DNA serve as platforms for delivering site-specific epigenetic marks critical for the regulation of gene expression. Additionally, an increasing body of genetic and structural studies demonstrates that triplex RNA-RNA interactions are essential for performing catalytic and regulatory functions in cellular nucleoprotein complexes, including spliceosomes and telomerases, and for enabling protein recoding during programmed ribosomal frameshifting. Thus, evidence is mounting that DNA and RNA triplex interactions are implemented to perform a range of diverse biological activities in the cell, some of which will be discussed in this review. PMID:26700634

  8. New Perspectives on DNA and RNA Triplexes As Effectors of Biological Activity.

    Directory of Open Access Journals (Sweden)

    Albino Bacolla

    2015-12-01

    Full Text Available Since the first description of the canonical B-form DNA double helix, it has been suggested that alternative DNA, DNA-RNA, and RNA structures exist and act as functional genomic elements. Indeed, over the past few years it has become clear that, in addition to serving as a repository for genetic information, genomic DNA elicits biological responses by adopting conformations that differ from the canonical right-handed double helix, and by interacting with RNA molecules to form complex secondary structures. This review focuses on recent advances on three-stranded (triplex nucleic acids, with an emphasis on DNA-RNA and RNA-RNA interactions. Emerging work reveals that triplex interactions between noncoding RNAs and duplex DNA serve as platforms for delivering site-specific epigenetic marks critical for the regulation of gene expression. Additionally, an increasing body of genetic and structural studies demonstrates that triplex RNA-RNA interactions are essential for performing catalytic and regulatory functions in cellular nucleoprotein complexes, including spliceosomes and telomerases, and for enabling protein recoding during programmed ribosomal frameshifting. Thus, evidence is mounting that DNA and RNA triplex interactions are implemented to perform a range of diverse biological activities in the cell, some of which will be discussed in this review.

  9. The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations

    Science.gov (United States)

    Schaffer, Michelle F.; Peng, Guanya; Spingler, Bernhard; Schnabl, Joachim; Wang, Meitian; Olieric, Vincent; Sigel, Roland K. O.

    2016-01-01

    Due to the polyanionic nature of RNA, the principles of charge neutralization and electrostatic condensation require that cations help to overcome the repulsive forces in order for RNA to adopt a three-dimensional structure. A precise structural knowledge of RNA-metal ion interactions is crucial to understand the mechanism of metal ions in the catalytic or regulatory activity of RNA. We solved the crystal structure of an octameric RNA duplex in the presence of the di- and trivalent metal ions Ca2+, Mn2+, Co2+, Cu2+, Sr2+, and Tb3+. The detailed investigation reveals a unique innersphere interaction to uracil and extends the knowledge of the influence of metal ions for conformational changes in RNA structure. Furthermore, we could demonstrate that an accurate localization of the metal ions in the X-ray structures require the consideration of several crystallographic and geometrical parameters as well as the anomalous difference map. PMID:27355942

  10. Fluid catalytic cracking of biomass pyrolysis vapors

    Energy Technology Data Exchange (ETDEWEB)

    Mante, Ofei Daku [Virginia Polytechnic Institute and State University, Biological Systems Engineering, Blacksburg, VA (United States); Agblevor, Foster A. [Utah State University, Biological Engineering, Logan, UT (United States); McClung, Ron [BASF Inc, Florham, NJ (United States)

    2011-12-15

    Catalytic cracking of pyrolysis oils/vapors offers the opportunity of producing bio-oils which can potentially be coprocessed with petroleum feedstocks in today's oil refinery to produce transportation fuel and chemicals. Catalyst properties and process conditions are critical in producing and maximizing desired product. In our studies, catalyst matrix (kaolin) and two commercial fluid catalytic cracking (FCC) catalysts, FCC-H and FCC-L, with different Y-zeolite contents were investigated. The catalytic cracking of hybrid poplar wood was conducted in a 50-mm bench-scale bubbling fluidized-bed pyrolysis reactor at 465 C with a weight hourly space velocity of 1.5 h{sup -1}. The results showed that the yields and quality of the bio-oils was a function of the Y-zeolite content of the catalyst. The char/coke yield was highest for the higher Y-zeolite catalyst. The organic liquid yields decreased inversely with increase in zeolite content of the catalyst whereas the water and gas yields increased. Analysis of the oils by both Fourier-transform infrared and {sup 13}C-nuclear magnetic resonance indicated that the catalyst with higher zeolite content (FCC-H) was efficient in the removal of compounds like levoglucosan, carboxylic acids and the conversion of methoxylated phenols to substituted phenols and benzenediols. The cracking of pyrolysis products by kaolin suggests that the activity of the FCC catalyst on biomass pyrolysis vapors can be attributed to both Y-zeolite and matrix. The FCC-H catalyst produced much more improved oil. The oil was low in oxygen (22.67 wt.%), high in energy (29.79 MJ/kg) and relatively stable over a 12-month storage period. (orig.)

  11. Catalytic Mechanism of Human Alpha-galactosidase

    Energy Technology Data Exchange (ETDEWEB)

    Guce, A.; Clark, N; Salgado, E; Ivanen, D; Kulinskaya, A; Brumer, H; Garman, S

    2010-01-01

    The enzyme {alpha}-galactosidase ({alpha}-GAL, also known as {alpha}-GAL A; E.C. 3.2.1.22) is responsible for the breakdown of {alpha}-galactosides in the lysosome. Defects in human {alpha}-GAL lead to the development of Fabry disease, a lysosomal storage disorder characterized by the buildup of {alpha}-galactosylated substrates in the tissues. {alpha}-GAL is an active target of clinical research: there are currently two treatment options for Fabry disease, recombinant enzyme replacement therapy (approved in the United States in 2003) and pharmacological chaperone therapy (currently in clinical trials). Previously, we have reported the structure of human {alpha}-GAL, which revealed the overall structure of the enzyme and established the locations of hundreds of mutations that lead to the development of Fabry disease. Here, we describe the catalytic mechanism of the enzyme derived from x-ray crystal structures of each of the four stages of the double displacement reaction mechanism. Use of a difluoro-{alpha}-galactopyranoside allowed trapping of a covalent intermediate. The ensemble of structures reveals distortion of the ligand into a {sup 1}S{sub 3} skew (or twist) boat conformation in the middle of the reaction cycle. The high resolution structures of each step in the catalytic cycle will allow for improved drug design efforts on {alpha}-GAL and other glycoside hydrolase family 27 enzymes by developing ligands that specifically target different states of the catalytic cycle. Additionally, the structures revealed a second ligand-binding site suitable for targeting by novel pharmacological chaperones.

  12. The RNA interference revolution

    Directory of Open Access Journals (Sweden)

    G. Lenz

    2005-12-01

    Full Text Available The discovery of double-stranded RNA-mediated gene silencing has rapidly led to its use as a method of choice for blocking a gene, and has turned it into one of the most discussed topics in cell biology. Although still in its infancy, the field of RNA interference has already produced a vast array of results, mainly in Caenorhabditis elegans, but recently also in mammalian systems. Micro-RNAs are short hairpins of RNA capable of blocking translation, which are transcribed from genomic DNA and are implicated in several aspects from development to cell signaling. The present review discusses the main methods used for gene silencing in cell culture and animal models, including the selection of target sequences, delivery methods and strategies for a successful silencing. Expected developments are briefly discussed, ranging from reverse genetics to therapeutics. Thus, the development of the new paradigm of RNA-mediated gene silencing has produced two important advances: knowledge of a basic cellular mechanism present in the majority of eukaryotic cells and access to a potent and specific new method for gene silencing.

  13. De novo design of catalytic proteins

    OpenAIRE

    Kaplan, J; DeGrado, W. F.

    2004-01-01

    The de novo design of catalytic proteins provides a stringent test of our understanding of enzyme function, while simultaneously laying the groundwork for the design of novel catalysts. Here we describe the design of an O2-dependent phenol oxidase whose structure, sequence, and activity are designed from first principles. The protein catalyzes the two-electron oxidation of 4-aminophenol (kcat/KM = 1,500 M·1·min·1) to the corresponding quinone monoimine by using a diiron cofactor. The catalyti...

  14. Transport in a Microfluidic Catalytic Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Park, H G; Chung, J; Grigoropoulos, C P; Greif, R; Havstad, M; Morse, J D

    2003-04-30

    A study of the heat and mass transfer, flow, and thermodynamics of the reacting flow in a catalytic microreactor is presented. Methanol reforming is utilized in the fuel processing system driving a micro-scale proton exchange membrane fuel cell. Understanding the flow and thermal transport phenomena as well as the reaction mechanisms is essential for improving the efficiency of the reforming process as well as the quality of the processed fuel. Numerical studies have been carried out to characterize the transport in a silicon microfabricated reactor system. On the basis of these results, optimized conditions for fuel processing are determined.

  15. Asymmetric catalytic aziridination of cyclic enones.

    Science.gov (United States)

    De Vincentiis, Francesco; Bencivenni, Giorgio; Pesciaioli, Fabio; Mazzanti, Andrea; Bartoli, Giuseppe; Galzerano, Patrizia; Melchiorre, Paolo

    2010-07-01

    The first catalytic method for the asymmetric aziridination of cyclic enones is described. The presented organocatalytic strategy is based on the use of an easily available organocatalyst that is able to convert a wide range of cyclic enones into the desired aziridines with very high enantiomeric purity and good chemical yield. Such a method may very well open up new opportunities to stereoselectively prepare complex chiral molecules that possess an indane moiety, a framework that is found in a large number of bioactive and pharmaceutically important molecules. PMID:20512797

  16. Catalytic Pyrolysis of Olive Mill Wastewater Sludge

    OpenAIRE

    Abdellaoui, Hamza

    2015-01-01

    Olive mill wastewater sludge (OMWS) is the solid residue that remains in the evaporation ponds after evaporation of the majority of water in the olive mill wastewater (OMW). OMWS is a major environmental pollutant in the olive oil producing regions. Approximately 41.16 wt. % of the OMWS was soluble in hexanes (HSF). The fatty acids in this fraction consist mainly of oleic and palmitic acid. Catalytic pyrolysis of the OMWS over red mud and HZSM-5 has been demonstrated to be an effective techno...

  17. Electrospun Catalytic Support Prepared by Electrospinning Technique

    Czech Academy of Sciences Publication Activity Database

    Soukup, Karel; Topka, Pavel; Petráš, D.; Klusoň, Petr; Šolcová, Olga

    Praha : Orgit, 2012, C4.1. ISBN 978-80-905035-1-9. [International Congress of Chemical and Process Engineering CHISA 2012 and 15th Conference PRES 2012 /20./. Prague (CZ), 25.08.2012-29.08.2012] R&D Projects: GA ČR GPP106/11/P459; GA ČR(CZ) GAP204/11/1206 Institutional support: RVO:67985858 Keywords : catalytic tests * electrospun * gas transport properties Subject RIV: CI - Industrial Chemistry, Chemical Engineering www.chisa.cz/2012

  18. Tritium stripping by a catalytic exchange stripper

    International Nuclear Information System (INIS)

    A catalytic exchange process for stripping elemental tritium from gas streams has been demonstrated. The process uses a catalyzed isotopic exchange reaction between tritium in the gas phase and protium or deuterium in the solid phase on alumina. The reaction is catalyzed by platinum deposited on the alumina. The process has been tested with both tritium and deuterium. Decontamination factors (ration of inlet and outlet tritium concentrations) as high as 1000 have been achieved, depending on inlet concentration. The test results and some demonstrated applications are presented

  19. Catalytic Synthesis Methods for Triazolopyrimidine Derivatives

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A new method for catalyzed synthesis of triazolopyrimidine derivatives is reported. Aikylamine reaction with dialkyl cyanodithioiminocarbonate was catalyzed by quaternary ammonium salts at room temperature to yield 3-alkylamine-5-amino-1,2,4-triazole in good quality and high yields. After imidization and reaction with an α,β-unsaturated acid derivative, the reaction intermediate was hydrolyzed in the presence of a Lewis acid to obtain the target product. This novel catalytic method for triazolopyrimidine derivatives can be carried out under inexpen-sive and mild conditions, and is safe and environmentally friendly. IH NMR results for all intermediates are re-ported.

  20. Thin film porous membranes for catalytic sensors

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, R.C.; Boyle, T.J.; Gardner, T.J. [and others

    1997-06-01

    This paper reports on new and surprising experimental data for catalytic film gas sensing resistors coated with nanoporous sol-gel films to impart selectivity and durability to the sensor structure. This work is the result of attempts to build selectivity and reactivity to the surface of a sensor by modifying it with a series of sol-gel layers. The initial sol-gel SiO{sub 2} layer applied to the sensor surprisingly showed enhanced O{sub 2} interaction with H{sub 2} and reduced susceptibility to poisons such as H{sub 2}S.

  1. Temperature control of a catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.

    1994-06-08

    In an ic engine having a catalytic convertor, the catalyst heater is controlled in dependence upon an estimate of the temperature of the catalyst so that there is no need for a sensor in the hostile environment of the exhaust. A valve indicative of the catalyst temperature is stored and modified in accordance with a model of the catalyst temperature. The model can be a mathematical mood carried out by a signal processor or an electrical model with the catalyst temperature being represented by the charge stored on a capacitor. (Author)

  2. Catalytic asymmetric formal synthesis of beraprost

    Science.gov (United States)

    Kobayashi, Yusuke; Kuramoto, Ryuta

    2015-01-01

    Summary The first catalytic asymmetric synthesis of the key intermediate for beraprost has been achieved through an enantioselective intramolecular oxa-Michael reaction of an α,β-unsaturated amide mediated by a newly developed benzothiadiazine catalyst. The Weinreb amide moiety and bromo substituent of the Michael adduct were utilized for the C–C bond formations to construct the scaffold. All four contiguous stereocenters of the tricyclic core were controlled via Rh-catalyzed stereoselective C–H insertion and the subsequent reduction from the convex face. PMID:26734111

  3. Catalytic deallylation of allyl- and diallylmalonates.

    Science.gov (United States)

    Necas, David; Turský, Matyás; Kotora, Martin

    2004-08-25

    Substituted allylmalonates undergo the selective C-C bond cleavage in the presence of triethylaluminum and a catalytic amount of nickel and ruthenium phosphine complexes, resulting in the loss of the allyl moiety and formation of monosubstituted malonates. Comparison of reactivity of the nickel and ruthenium complexes showed that the use of the former is general with respect to the structure of the substituted allylmalonates, and the activity of the latter depended on the substitution pattern of the double bond of the allylic moiety. The smooth deallylation may encourage the use of the allyl group as a protective group for the acidic hydrogen in malonates. PMID:15315416

  4. Catalytic multi-stage liquefaction (CMSL)

    Energy Technology Data Exchange (ETDEWEB)

    Comolli, A.G.; Ganguli, P.; Karolkiewicz, W.F.; Lee, T.L.K.; Pradhan, V.R.; Popper, G.A.; Smith, T.; Stalzer, R.

    1996-11-01

    Under contract with the U.S. Department of Energy, Hydrocarbon Technologies, Inc. has conducted a series of eleven catalytic, multi-stage, liquefaction (CMSL) bench scale runs between February, 1991, and September, 1995. The purpose of these runs was to investigate novel approaches to liquefaction relating to feedstocks, hydrogen source, improved catalysts as well as processing variables, all of which are designed to lower the cost of producing coal-derived liquid products. This report summarizes the technical assessment of these runs, and in particular the evaluation of the economic impact of the results.

  5. Biomimetic, Catalytic Oxidation in Organic Synthesis

    Institute of Scientific and Technical Information of China (English)

    Shun-lchi Murahashi

    2005-01-01

    @@ 1Introduction Oxidation is one of the most fundamental reactions in organic synthesis. Owing to the current need to develop forward-looking technology that is environmentally acceptable with respect many aspects. The most attractive approaches are biomimetic oxidation reactions that are closely related to the metabolism of living things. The metabolisms are governed by a variety of enzymes such as cytochrome P-450 and flavoenzyme.Simulation of the function of these enzymes with simple transition metal complex catalyst or organic catalysts led to the discovery of biomimetic, catalytic oxidations with peroxides[1]. We extended such biomimetic methods to the oxidation with molecular oxygen under mild conditions.

  6. Heterogeneous Photooxidation of Phenol by Catalytic Membranes

    Institute of Scientific and Technical Information of China (English)

    Enrica Fontananova; Enrico Drioli; Laura Donato; Marcella Bonchio; Mauro Carraro; Gianfranco Scorrano

    2006-01-01

    In this work the heterogenization in polymeric membranes of decatungstate, a photocatalyst for oxidation reactions,was reported. Solid state characterization techniques confirmed that the catalyst structure was preserved within the polymeric membranes. The catalytic membranes were successfully applied in the aerobic photo-oxidation of phenol, one of the main organic pollutants in wastewater, providing stable and recyclable photocatalytic systems. The dependence of the phenol degradation rate by the catalyst loading and transmembrane pressure was shown. By comparison with homogeneous reaction,the catalyst heterogenized in membrane appears to be more efficient concerning the rate of phenol photodegradation and mineralization.

  7. Submicron Polyethylene Particles from Catalytic Emulsion Polymerization

    OpenAIRE

    Bauers, Florian Martin; Thomann, Ralf; Mecking, Stefan

    2003-01-01

    Particles of linear polyethylene (Mn = (2-3)X 10000 g mol-1; Mw/Mn = 2-4) obtained by catalytic emulsion polymerization of ethylene possess a nonspherical, lentil-like shape with an average aspect ratio of ca. 10 and diameters from 30 to > 300 nm, as determined by TEM and AFM. The particle structure results from a stacking of the lamellae along the one shorter axis of the lentils (i.e., their height, by contrast to the diameter). In addition to these multilamellae particles, remarkably, a con...

  8. Catalytic conversion of sulfur dioxide and trioxide

    Energy Technology Data Exchange (ETDEWEB)

    Solov' eva, E.L.; Shenfel' d, B.E.; Kuznetsova, S.M.; Khludenev, A.G.

    1987-11-10

    The reclamation and utilization of sulfur-containing wastes from the flue gas of fossil-fuel power plants and the subsequent reduction in sulfur emission is addressed in this paper. The authors approach this problem from the standpoint of the catalytic oxidation of sulfur dioxide on solid poison-resistant catalysts with subsequent sorption of the sulfur trioxide and its incorporation into the manufacture of sulfuric acid. The catalyst they propose is a polymetallic dust-like waste from the copper-smelting industry comprised mainly of iron and copper oxides. Experiments with this catalyst were carried out using multifactorial experiment planning.

  9. The catalytic residues of Tn3 resolvase

    OpenAIRE

    Olorunniji, F.J.; Stark, W M

    2009-01-01

    To characterize the residues that participate in the catalysis of DNA cleavage and rejoining by the site-specific recombinase Tn3 resolvase, we mutated conserved polar or charged residues in the catalytic domain of an activated resolvase variant. We analysed the effects of mutations at 14 residues on proficiency in binding to the recombination site ('site I'), formation of a synaptic complex between two site Is, DNA cleavage and recombination. Mutations of Y6, R8, S10, D36, R68 and R71 result...

  10. Study and Analysis on Naphtha Catalytic Reforming Reactor Simulation

    Institute of Scientific and Technical Information of China (English)

    Liang Ke min; Song Yongji; Pan Shiwei

    2004-01-01

    A naphtha catalytic reforming unit with four reactors connected in series is analyzed. A physical model is proposed to describe the catalytic reforming radial flow reactor. Kinetics and thermodynamics equations are selected to describe the naphtha catalytic reforming reaction characteristics based on idealizing the complex naphtha mixture to represent the paraffin, naphthene, and aromatic groups with individual compounds. The simulation results based on above models agree very well with actual operating data of process unit.

  11. 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....

  12. Non-thermal plasmas for non-catalytic and catalytic VOC abatement

    International Nuclear Information System (INIS)

    Highlights: → We review the current status of catalytic and non-catalytic VOC abatement based on a vast number of research papers. → The underlying mechanisms of plasma-catalysis for VOC abatement are discussed. → Critical process parameters that determine the influent are discussed and compared. - Abstract: This paper reviews recent achievements and the current status of non-thermal plasma (NTP) technology for the abatement of volatile organic compounds (VOCs). Many reactor configurations have been developed to generate a NTP at atmospheric pressure. Therefore in this review article, the principles of generating NTPs are outlined. Further on, this paper is divided in two equally important parts: plasma-alone and plasma-catalytic systems. Combination of NTP with heterogeneous catalysis has attracted increased attention in order to overcome the weaknesses of plasma-alone systems. An overview is given of the present understanding of the mechanisms involved in plasma-catalytic processes. In both parts (plasma-alone systems and plasma-catalysis), literature on the abatement of VOCs is reviewed in close detail. Special attention is given to the influence of critical process parameters on the removal process.

  13. Catalytically favorable surface patterns in Pt-Au nanoclusters

    KAUST Repository

    Mokkath, Junais Habeeb

    2013-01-01

    Motivated by recent experimental demonstrations of novel PtAu nanoparticles with highly enhanced catalytic properties, we present a systematic theoretical study that explores principal catalytic indicators as a function of the particle size and composition. We find that Pt electronic states in the vicinity of the Fermi level combined with a modified electron distribution in the nanoparticle due to Pt-to-Au charge transfer are the origin of the outstanding catalytic properties. From our model we deduce the catalytically favorable surface patterns that induce ensemble and ligand effects. © The Royal Society of Chemistry 2013.

  14. Messenger RNA (mRNA) nanoparticle tumour vaccination

    Science.gov (United States)

    Phua, Kyle K. L.; Nair, Smita K.; Leong, Kam W.

    2014-06-01

    Use of mRNA-based vaccines for tumour immunotherapy has gained increasing attention in recent years. A growing number of studies applying nanomedicine concepts to mRNA tumour vaccination show that the mRNA delivered in nanoparticle format can generate a more robust immune response. Advances in the past decade have deepened our understanding of gene delivery barriers, mRNA's biological stability and immunological properties, and support the notion for engineering innovations tailored towards a more efficient mRNA nanoparticle vaccine delivery system. In this review we will first examine the suitability of mRNA for engineering manipulations, followed by discussion of a model framework that highlights the barriers to a robust anti-tumour immunity mediated by mRNA encapsulated in nanoparticles. Finally, by consolidating existing literature on mRNA nanoparticle tumour vaccination within the context of this framework, we aim to identify bottlenecks that can be addressed by future nanoengineering research.

  15. Stellar Populations

    Science.gov (United States)

    Peletier, Reynier F.

    2013-10-01

    This is a summary of my lectures during the 2011 Canary Islands Winter School in Puerto de la Cruz. I give an introduction to the field of stellar populations in galaxies, and highlight some new results. Since the title of the Winter School is Secular Evolution in Galaxies I mostly concentrate on nearby galaxies, which are best suited to study this theme. Of course, the understanding of stellar populations is intimately connected to understanding the formation and evolution of galaxies, one of the great outstanding problems of astronomy. We are currently in a situation where very large observational advances have been made in recent years. Galaxies have been detected up to a redshift of ten. A huge effort has to be made so that stellar population theory can catch up with observations. Since most galaxies are far away, information about them has to come from stellar population synthesis of integrated light. Here I will discuss how stellar evolution theory, together with observations in our Milky Way and Local Group, are used as building blocks to analyse these integrated stellar populations.

  16. Knockdown of RNA Interference Pathway Genes in Western Corn Rootworms (Diabrotica virgifera virgifera Le Conte) Demonstrates a Possible Mechanism of Resistance to Lethal dsRNA.

    Science.gov (United States)

    Vélez, Ana María; Khajuria, Chitvan; Wang, Haichuan; Narva, Kenneth E; Siegfried, Blair D

    2016-01-01

    RNA interference (RNAi) is being developed as a potential tool for insect pest management. Increased understanding of the RNAi pathway in target insect pests will provide information to use this technology effectively and to inform decisions related to resistant management strategies for RNAi based traits. Dicer 2 (Dcr2), an endonuclease responsible for formation of small interfering RNA's and Argonaute 2 (Ago2), an essential catalytic component of the RNA-induced silencing complex (RISC) have both been associated with the RNAi pathway in a number of different insect species including the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). We identified both genes from a transcriptome library generated from different tissues and developmental stages of the western corn rootworm, an important target pest for transgenic plants expressing dsRNA targeting essential genes. The expression of these genes was suppressed by more than 90% after injecting gene specific dsRNA into adult rootworms. The injected beetles were then fed vATPase A dsRNA which has previously been demonstrated to cause mortality in western corn rootworm adults. The suppression of both RNAi pathway genes resulted in reduced mortality after subsequent exposure to lethal concentrations of vATPase A dsRNA as well as increased vATPase A expression relative to control treatments. Injections with dsRNA for a non-lethal target sequence (Laccase 2) did not affect mortality or expression caused by vATPase A dsRNA indicating that the results observed with Argo and Dicer dsRNA were not caused by simple competition among different dsRNA's. These results confirm that both genes play an important role in the RNAi pathway for western corn rootworms and indicate that selection pressures that potentially affect the expression of these genes may provide a basis for future studies to understand potential mechanisms of resistance. PMID:27310918

  17. Knockdown of RNA Interference Pathway Genes in Western Corn Rootworms (Diabrotica virgifera virgifera Le Conte Demonstrates a Possible Mechanism of Resistance to Lethal dsRNA.

    Directory of Open Access Journals (Sweden)

    Ana María Vélez

    Full Text Available RNA interference (RNAi is being developed as a potential tool for insect pest management. Increased understanding of the RNAi pathway in target insect pests will provide information to use this technology effectively and to inform decisions related to resistant management strategies for RNAi based traits. Dicer 2 (Dcr2, an endonuclease responsible for formation of small interfering RNA's and Argonaute 2 (Ago2, an essential catalytic component of the RNA-induced silencing complex (RISC have both been associated with the RNAi pathway in a number of different insect species including the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae. We identified both genes from a transcriptome library generated from different tissues and developmental stages of the western corn rootworm, an important target pest for transgenic plants expressing dsRNA targeting essential genes. The expression of these genes was suppressed by more than 90% after injecting gene specific dsRNA into adult rootworms. The injected beetles were then fed vATPase A dsRNA which has previously been demonstrated to cause mortality in western corn rootworm adults. The suppression of both RNAi pathway genes resulted in reduced mortality after subsequent exposure to lethal concentrations of vATPase A dsRNA as well as increased vATPase A expression relative to control treatments. Injections with dsRNA for a non-lethal target sequence (Laccase 2 did not affect mortality or expression caused by vATPase A dsRNA indicating that the results observed with Argo and Dicer dsRNA were not caused by simple competition among different dsRNA's. These results confirm that both genes play an important role in the RNAi pathway for western corn rootworms and indicate that selection pressures that potentially affect the expression of these genes may provide a basis for future studies to understand potential mechanisms of resistance.

  18. Anticodon recognition in evolution: switching tRNA specificity of an aminoacyl-tRNA synthetase by site-directed peptide transplantation.

    Science.gov (United States)

    Brevet, Annie; Chen, Josiane; Commans, Stéphane; Lazennec, Christine; Blanquet, Sylvain; Plateau, Pierre

    2003-08-15

    The highly conserved aspartyl-, asparaginyl-, and lysyl-tRNA synthetases compose one subclass of aminoacyl-tRNA synthetases, called IIb. The three enzymes possess an OB-folded extension at their N terminus. The function of this extension is to specifically recognize the anticodon triplet of the tRNA. Three-dimensional models of bacterial aspartyl- and lysyl-tRNA synthetases complexed to tRNA indicate that a rigid scaffold of amino acid residues along the five beta-strands of the OB-fold accommodates the base U at the center of the anticodon. The binding of the adjacent anticodon bases occurs through interactions with a flexible loop joining strands 4 and 5 (L45). As a result, a switching of the specificity of lysyl-tRNA synthetase from tRNALys (anticodon UUU) toward tRNAAsp (GUC) could be attempted by transplanting the small loop L45 of aspartyl-tRNA synthetase inside lysyl-tRNA synthetase. Upon this transplantation, lysyl-tRNA synthetase loses its capacity to aminoacylate tRNALys. In exchange, the chimeric enzyme acquires the capacity to charge tRNAAsp with lysine. Upon giving the tRNAAsp substrate the discriminator base of tRNALys, the specificity shift is improved. The change of specificity was also established in vivo. Indeed, the transplanted lysyl-tRNA synthetase succeeds in suppressing a missense Lys --> Asp mutation inserted into the beta-lactamase gene. These results functionally establish that sequence variation in a small peptide region of subclass IIb aminoacyl-tRNA synthetases contributes to specification of nucleic acid recognition. Because this peptide element is not part of the core catalytic structure, it may have evolved independently of the active sites of these synthetases. PMID:12766171

  19. Evolution of complexity in RNA-like replicator systems

    Directory of Open Access Journals (Sweden)

    Hogeweg Paulien

    2008-03-01

    Full Text Available Abstract Background The evolution of complexity is among the most important questions in biology. The evolution of complexity is often observed as the increase of genetic information or that of the organizational complexity of a system. It is well recognized that the formation of biological organization – be it of molecules or ecosystems – is ultimately instructed by the genetic information, whereas it is also true that the genetic information is functional only in the context of the organization. Therefore, to obtain a more complete picture of the evolution of complexity, we must study the evolution of both information and organization. Results Here we investigate the evolution of complexity in a simulated RNA-like replicator system. The simplicity of the system allows us to explicitly model the genotype-phenotype-interaction mapping of individual replicators, whereby we avoid preconceiving the functionality of genotypes (information or the ecological organization of replicators in the model. In particular, the model assumes that interactions among replicators – to replicate or to be replicated – depend on their secondary structures and base-pair matching. The results showed that a population of replicators, originally consisting of one genotype, evolves to form a complex ecosystem of up to four species. During this diversification, the species evolve through acquiring unique genotypes with distinct ecological functionality. The analysis of this diversification reveals that parasitic replicators, which have been thought to destabilize the replicator's diversity, actually promote the evolution of diversity through generating a novel "niche" for catalytic replicators. This also makes the current replicator system extremely stable upon the evolution of parasites. The results also show that the stability of the system crucially depends on the spatial pattern formation of replicators. Finally, the evolutionary dynamics is shown to

  20. Catalytic hydrothermal liquefaction of water hyacinth.

    Science.gov (United States)

    Singh, Rawel; Balagurumurthy, Bhavya; Prakash, Aditya; Bhaskar, Thallada

    2015-02-01

    Thermal and catalytic hydrothermal liquefaction of water hyacinth was performed at temperatures from 250 to 300 °C under various water hyacinth:H2O ratio of 1:3, 1:6 and 1:12. Reactions were also carried out under various residence times (15-60 min) as well as catalytic conditions (KOH and K2CO3). The use of alkaline catalysts significantly increased the bio-oil yield. Maximum bio-oil yield (23 wt%) comprising of bio-oil1 and bio-oil2 as well as conversion (89%) were observed with 1N KOH solution. (1)H NMR and (13)C NMR data showed that both bio-oil1 and bio-oil2 have high aliphatic carbon content. FTIR of bio-residue indicated that the usage of alkaline catalyst resulted in bio-residue samples with lesser oxygen functionality indicating that catalyst has a marked effect on nature of the bio-residue and helps to decompose biomass to a greater extent compared to thermal case. PMID:25240515

  1. Aluminosilicate nanoparticles for catalytic hydrocarbon cracking.

    Science.gov (United States)

    Liu, Yu; Pinnavaia, Thomas J

    2003-03-01

    Aluminosilicate nanoparticles containing 9.0-20 nm mesopores were prepared through the use of protozeolitic nanoclusters as the inorganic precursor and starch as a porogen. The calcined, porogen-free composition containing 2 mol % aluminum exhibited the porosity, hydrothermal stability, and acidity needed for the cracking of very large hydrocarbons. In fact, the hydrothermal stability of the nanoparticles to pure steam at 800 degrees C, along with the cumene cracking activity, surpassed the analogous performance properties of ultrastable Y zeolite, the main catalyst component of commercial cracking catalysts. The remarkable hydrothermal stability and catalytic reactivity of the new nanoparticles are attributable to a unique combination of two factors, the presence of protozeolitic nanoclusters in the pore walls and the unprecedented pore wall thickness (7-15 nm). In addition, the excellent catalytic longevity of the nanoparticles is most likely facilitated by the small domain size of the nanoparticles that greatly improves access to the acid sites on the pore walls and minimizes the diffusion length of coke precursors out of the pores. PMID:12603109

  2. Catalytic converter for next generation turbine engines

    Energy Technology Data Exchange (ETDEWEB)

    Saruhan, B.; Schulz, U.; Leyens, C. [German Aerospace Center (DLR), Inst. of Materials Research, Cologne (Germany)

    2004-07-01

    EB-PVD thermal barrier coatings (TBCs) are used on advanced turbine blades to increase the engine efficiency and improve the blade performance. partially yttria stabilized zirconia (PYSZ) is the standard material for current TBC applications. Lower thermal stability of the PYSZ-based TBCs, however, seriously affects the performance at demanding service temperatures. For the new generation turbines where higher operating gas temperatures (> 1200 C) are to expect, the performance of turbine blades can be improved by replacing the state-art-of-material PYSZ with superior thermal barrier coatings which belong to different crystal structures such as magnetoplumbite. Magnetoplumbite structure through its interlocking grain morphology and unique crystal structure provides essentially a sintering resistant, low thermal conductive layer, but also imparts a catalytic layer to reduce the environmentally harmful substances produced during propulsion and increase the catalytic performance. The complex structures of these compounds make it difficult to realize by conventional methods and requires careful adjustment of process parameters. The morphology and crystallographic aspects of these coatings as well as the mechanisms controlling the improvement are highlighted. (orig.)

  3. Study of catalytic phenomena in radiation chemistry

    International Nuclear Information System (INIS)

    Two phenomena have been studied: the action of γ rays from radio-cobalt on the adsorption and catalytic properties of ZnO and NiO in. relationship with the heterogeneous oxidation of CO, and the homogeneous catalysis by OsO4 of the oxidation of various aqueous phase solutes by the same radiation. The prior irradiation of ZnO and of NiO does not modify their catalytic activity but generally increases the adsorption energy of -the gases CO and O2. The influence of the radiations appears to be connected with the presence of traces of water on ZnO and of an excess of oxygen on NiO. Osmium tetroxide which is not degraded by irradiation in acid solution, accelerates the radiolytic oxidation of certain compounds (TeIV, Pt11, As111) in the presence of oxygen, as a result of its sensitizing effect on the oxidation by H2O2. In the case of phosphites on the other hand, OsO4 has a protecting action under certain conditions of acidity and may suppress entirely the chain reaction which characterizes the oxidation of this solute byγ rays. A general mechanism is proposed for these phenomena. The rate constant for the OsO4 + HO2 reaction is calculated to be 5.7 x 105 l.mol-1. sec-1. (author)

  4. Catalytic converter for next generation turbine engines

    International Nuclear Information System (INIS)

    EB-PVD thermal barrier coatings (TBCs) are used on advanced turbine blades to increase the engine efficiency and improve the blade performance. partially yttria stabilized zirconia (PYSZ) is the standard material for current TBC applications. Lower thermal stability of the PYSZ-based TBCs, however, seriously affects the performance at demanding service temperatures. For the new generation turbines where higher operating gas temperatures (> 1200 C) are to expect, the performance of turbine blades can be improved by replacing the state-art-of-material PYSZ with superior thermal barrier coatings which belong to different crystal structures such as magnetoplumbite. Magnetoplumbite structure through its interlocking grain morphology and unique crystal structure provides essentially a sintering resistant, low thermal conductive layer, but also imparts a catalytic layer to reduce the environmentally harmful substances produced during propulsion and increase the catalytic performance. The complex structures of these compounds make it difficult to realize by conventional methods and requires careful adjustment of process parameters. The morphology and crystallographic aspects of these coatings as well as the mechanisms controlling the improvement are highlighted. (orig.)

  5. Numerical and experimental investigations on catalytic recombiners

    International Nuclear Information System (INIS)

    Numerous containments of European light water reactors (LWR) are equipped with passive auto-catalytic recombiners (PAR). These devices are designed for the removal of hydrogen generated during a severe accident in order to avoid serious damage caused by a detonation. PARs make use of the fact that hydrogen and oxygen react exothermally on catalytic surfaces generating steam and heat even below conventional ignition concentrations and temperatures. Activities at ISR aim at overcoming existing limitations of today's systems. These are e.g. limited conversion capacity or unintended ignition of the gaseous mixture due to overheating of the catalyst elements caused by strong reaction heat generation. Experiments at the REKO facilities are conducted in order to achieve a profound understanding of the processes inside a recombiner, such as reaction kinetics or heat and mass transfer. Innovative PAR designs which may overcome existing limitations can be developed based on the knowledge obtained from these experiments. For the analysis of the processes inside a PAR the numerical code REKO-DIREKT is being developed. The code calculates the local catalyst temperatures and the concentration regression along the catalyst plates. For the validation of the model numerous experiments have been performed with different types of coating and different plate arrangements. The first calculations fit well with the experimental results indicating a proper understanding of the fundamental processes. The paper describes the experiments as well as the numerical model and presents model calculations in comparison with experimental results. (authors)

  6. 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......R-138 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....

  7. Strategies underlying RNA silencing suppression by negative strand RNA viruses

    NARCIS (Netherlands)

    Hemmes, J.C.

    2007-01-01

    The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double strand

  8. 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

  9. 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

  10. A closely related group of RNA-dependent RNA polymerases from double-stranded RNA viruses.

    OpenAIRE

    Bruenn, J A

    1993-01-01

    Probably one of the first proteinaceous enzymes was an RNA-dependent RNA polymerase (RDRP). Although there are several conserved motifs present in the RDRPs of most positive and double-stranded RNA (dsRNA) viruses, the RDRPs of the dsRNA viruses show no detectable sequence similarity outside the conserved motifs. There is now, however, a group of dsRNA viruses of lower eucaryotes whose RDRPs are detectably similar. The origin of this sequence similarity appears to be common descent from one o...

  11. Polarographic catalytic wave of hydrogen--Parallel catalytic hydrogen wave of bovine serum albumin in thepresence of oxidants

    Institute of Scientific and Technical Information of China (English)

    过玮; 刘利民; 林洪; 宋俊峰

    2002-01-01

    A polarographic catalytic hydrogen wave of bovine serum albumin (BSA) at about -1.80 V (vs. SCE) in NH4Cl-NH3@H2O buffer is further catalyzed by such oxidants as iodate, persulfate and hydrogen peroxide, producing a kinetic wave. Studies show that the kinetic wave is a parallel catalytic wave of hydrogen, which resulted from that hydrogen ion is electrochemically reduced and chemically regenerated through oxidation of its reduction product, atomic hydrogen, by oxidants mentioned above. It is a new type of poralographic catalytic wave of protein, which is suggested to be named as a parallel catalytic hydrogen wave.

  12. lncRNA-RNA Interactions across the Human Transcriptome

    Science.gov (United States)

    Szcześniak, Michał Wojciech; Makałowska, Izabela

    2016-01-01

    Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of molecular functions and contribute considerably to the observed diversification of eukaryotic transcriptomes and proteomes. Still, however, only ca. 1% of lncRNAs have well established functions and much remains to be done towards decipherment of their biological roles. One of the least studied aspects of lncRNAs biology is their engagement in gene expression regulation through RNA-RNA interactions. By hybridizing with mate RNA molecules, lncRNAs could potentially participate in modulation of pre-mRNA splicing, RNA editing, mRNA stability control, translation activation, or abrogation of miRNA-induced repression. Here, we implemented a similarity-search based method for transcriptome-wide identification of RNA-RNA interactions, which enabled us to find 18,871,097 lncRNA-RNA base-pairings in human. Further analyses showed that the interactions could be involved in processing, stability control and functions of 57,303 transcripts. An extensive use of RNA-Seq data provided support for approximately one third of the interactions, at least in terms of the two RNA components being co-expressed. The results suggest that lncRNA-RNA interactions are broadly used to regulate and diversify the human transcriptome. PMID:26930590

  13. Population dynamics

    Directory of Open Access Journals (Sweden)

    Cooch, E. G.

    2004-06-01

    Full Text Available Increases or decreases in the size of populations over space and time are, arguably, the motivation for much of pure and applied ecological research. The fundamental model for the dynamics of any population is straightforward: the net change over time in the abundance of some population is the simple difference between the number of additions (individuals entering the population minus the number of subtractions (individuals leaving the population. Of course, the precise nature of the pattern and process of these additions and subtractions is often complex, and population biology is often replete with fairly dense mathematical representations of both processes. While there is no doubt that analysis of such abstract descriptions of populations has been of considerable value in advancing our, there has often existed a palpable discomfort when the ‘beautiful math’ is faced with the often ‘ugly realities’ of empirical data. In some cases, this attempted merger is abandoned altogether, because of the paucity of ‘good empirical data’ with which the theoretician can modify and evaluate more conceptually–based models. In some cases, the lack of ‘data’ is more accurately represented as a lack of robust estimates of one or more parameters. It is in this arena that methods developed to analyze multiple encounter data from individually marked organisms has seen perhaps the greatest advances. These methods have rapidly evolved to facilitate not only estimation of one or more vital rates, critical to population modeling and analysis, but also to allow for direct estimation of both the dynamics of populations (e.g., Pradel, 1996, and factors influencing those dynamics (e.g., Nichols et al., 2000. The interconnections between the various vital rates, their estimation, and incorporation into models, was the general subject of our plenary presentation by Hal Caswell (Caswell & Fujiwara, 2004. Caswell notes that although interest has traditionally

  14. In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries

    NARCIS (Netherlands)

    Karrer, E.E.; Lincoln, J.E.; Hogenhout, S.A.; Bennett, A.B.; Bostock, R.M.; Martineau, B.; Lucas, W.J.; Gilchrist, D.G.; Alexander, D.

    1995-01-01

    A method for isolating and cloning mRNA populations from individual cells in living, intact plant tissues is described. The contents of individual cells were aspirated into micropipette tips filled with RNA extraction buffer. The mRNA from these cells was purified by binding to oligo(dT)-linked magn

  15. G-patch domain and KOW motifs-containing protein, GPKOW; a nuclear RNA-binding protein regulated by protein kinase A

    OpenAIRE

    2011-01-01

    Background: Post-transcriptional processing of pre-mRNA takes place in several steps and requires involvement of a number of RNA-binding proteins. How pre-mRNA processing is regulated is in large enigmatic. The catalytic (C) subunit of protein kinase A (PKA) is a serine/threonine kinase, which regulates numerous cellular processes including pre-mRNA splicing. Despite that a significant fraction of the C subunit is found in splicing factor compartments in the nucleus, there are no indications ...

  16. Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila.

    Science.gov (United States)

    Haase, Astrid D; Fenoglio, Silvia; Muerdter, Felix; Guzzardo, Paloma M; Czech, Benjamin; Pappin, Darryl J; Chen, Caifu; Gordon, Assaf; Hannon, Gregory J

    2010-11-15

    Combining RNAi in cultured cells and analysis of mutant animals, we probed the roles of known Piwi-interacting RNA (piRNA) pathway components in the initiation and effector phases of transposon silencing. Squash associated physically with Piwi, and reductions in its expression led to modest transposon derepression without effects on piRNAs, consistent with an effector role. Alterations in Zucchini or Armitage reduced both Piwi protein and piRNAs, indicating functions in the formation of a stable Piwi RISC (RNA-induced silencing complex). Notably, loss of Zucchini or mutations within its catalytic domain led to accumulation of unprocessed precursor transcripts from flamenco, consistent with a role for this putative nuclease in piRNA biogenesis. PMID:20966049

  17. MicroRNA Expression during Bovine Oocyte Maturation and Fertilization

    Science.gov (United States)

    Gilchrist, Graham C.; Tscherner, Allison; Nalpathamkalam, Thomas; Merico, Daniele; LaMarre, Jonathan

    2016-01-01

    Successful fertilization and subsequent embryo development rely on complex molecular processes starting with the development of oocyte competence through maturation. MicroRNAs (miRNAs) are small non-coding RNA molecules that function as gene regulators in many biological systems, including the oocyte and embryo. In order to further explore the roles of miRNAs in oocyte maturation, we employed small RNA sequencing as a screening tool to identify and characterize miRNA populations present in pools of bovine germinal vesicle (GV) oocytes, metaphase II (MII) oocytes, and presumptive zygotes (PZ). Each stage contained a defined miRNA population, some of which showed stable expression while others showed progressive changes between stages that were subsequently confirmed by quantitative reverse transcription polymerase chain reaction (RT-PCR). Bta-miR-155, bta-miR-222, bta-miR-21, bta-let-7d, bta-let-7i, and bta-miR-190a were among the statistically significant differentially expressed miRNAs (p < 0.05). To determine whether changes in specific primary miRNA (pri-miRNA) transcripts were responsible for the observed miRNA changes, we evaluated pri-miR-155, -222 and let-7d expression. Pri-miR-155 and -222 were not detected in GV oocytes but pri-miR-155 was present in MII oocytes, indicating transcription during maturation. In contrast, levels of pri-let-7d decreased during maturation, suggesting that the observed increase in let-7d expression was likely due to processing of the primary transcript. This study demonstrates that both dynamic and stable populations of miRNAs are present in bovine oocytes and zygotes and extend previous studies supporting the importance of the small RNA landscape in the maturing bovine oocyte and early embryo. PMID:26999121

  18. RNA thermodynamic structural entropy

    OpenAIRE

    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 th...

  19. RNA Interference in livestock

    OpenAIRE

    Merkl, Claudia

    2010-01-01

    RNA Interference (RNAi) allows experimental reduction of gene expression, providing a tool for the investigation of gene function, disease therapy and the generation of animal models for human diseases. RNAi offers an opportunity to carry out precise genetic manipulations in a wide variety of species. This thesis describes the use of RNAi to downregulate two porcine genes, the whey protein Beta-Lactoglobulin (BLG) and the tumor suppressor protein p53. BLG is a major component in porcine and r...

  20. The Functions of RNA-Dependent RNA Polymerases in Arabidopsis

    OpenAIRE

    Willmann, Matthew R.; Endres, Matthew W.; Cook, Rebecca T.; Gregory, Brian D.

    2011-01-01

    One recently identified mechanism that regulates mRNA abundance is RNA silencing, and pioneering work in Arabidopsis thaliana and other genetic model organisms helped define this process. RNA silencing pathways are triggered by either self-complementary fold-back structures or the production of double-stranded RNA (dsRNA) that gives rise to small RNAs (smRNAs) known as microRNAs (miRNAs) or small-interfering RNAs (siRNAs). These smRNAs direct sequence-specific regulation of various gene trans...

  1. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  2. Stellar Populations

    NARCIS (Netherlands)

    Peletier, Reynier F.

    2013-01-01

    This is a summary of my lectures during the 2011 Canary Islands Winter School in Puerto de la Cruz. I give an introduction to the field of stellar populations in galaxies, and highlight some new results. Since the title of the Winter School is Secular Evolution in Galaxies I mostly concentrate on ne

  3. Populations games

    Czech Academy of Sciences Publication Activity Database

    Křivan, Vlastimil

    2015-01-01

    Roč. 2, č. 1 (2015), s. 14-19. ISSN 2367-5233. [Featuring International Conferences Biomath 2015. Blagoevgrad, 14.06.2015-19.06.2015] R&D Projects: GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : populations dynamics

  4. Stellar Populations

    CERN Document Server

    Peletier, Reynier

    2012-01-01

    This is a summary of my lectures during the 2011 IAC Winter School in Puerto de la Cruz. I give an introduction to the field of stellar populations in galaxies, and highlight some new results. Since the title of the Winter School was {\\it Secular Evolution of Galaxies} I mostly concentrate on nearby galaxies, which are best suited to study this theme. Of course, the understanding of stellar populations is intimately connected to understanding the formation and evolution of galaxies, one of the great outstanding problems of astronomy. We are currently in a situation where very large observational advances have been made in recent years. Galaxies have been detected up to a redshift of 10. A huge effort has to be made so that stellar population theory can catch up with observations. Since most galaxies are far away, information about them has to come from stellar population synthesis of integrated light. Here I will discuss how stellar evolution theory, together with observations in our Milky Way and Local Group...

  5. Control of mRNA Decapping by Dcp2: an open and shut case?

    OpenAIRE

    Floor, Stephen N.; Jones, Brittnee N.; Gross, John D.

    2008-01-01

    mRNA decapping by Dcp2 is a critical step in several major eukaryotic mRNA decay pathways. Dcp2 forms the catalytic core of a mRNP that is configured for processing diverse substrates by pathway-specific activators. Here we elaborate a model of catalysis by Dcp2 which posits that activity is controlled by a conformational equilibrium between an open, inactive and closed, active form of the enzyme. Structural studies on yeast Dcp2 indicate that the general activator Dcp1 and substrate promote ...

  6. Monitoring of an RNA Multistep Folding Pathway by Isothermal Titration Calorimetry

    OpenAIRE

    Reymond, Cédric; Bisaillon, Martin; Perreault, Jean-Pierre

    2008-01-01

    Isothermal titration calorimetry was used to monitor the energetic landscape of a catalytic RNA, specifically that of the hepatitis delta virus ribozyme. Using mutants that isolated various tertiary interactions, the thermodynamic parameters of several ribozyme-substrate intermediates were determined. The results shed light on the impact of several tertiary interactions on the global structure of the ribozyme. In addition, the data indicate that the formation of the P1.1 pseudoknot is the lim...

  7. CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

    OpenAIRE

    Gilbert, Luke A.; Larson, Matthew H.; Morsut, Leonardo; Liu, Zairan; Brar, Gloria A.; Torres, Sandra E.; Stern-Ginossar, Noam; Brandman, Onn; Whitehead, Evan H.; Doudna, Jennifer A.; Lim, Wendell A.; Weissman, Jonathan S.; Qi, Lei S.

    2013-01-01

    The genetic interrogation and reprogramming of cells requires methods for robust and precise targeting of genes for expression or repression. The CRISPR-associated catalytically inactive dCas9 protein offers a general platform for RNA-guided DNA targeting. Here we show that fusion of dCas9 to effector domains with distinct regulatory functions enables stable and efficient transcriptional repression or activation in human and yeast cells with the site of delivey determined solely by a co-expre...

  8. Invoking Direct Exciton-Plasmon Interactions by Catalytic Ag Deposition on Au Nanoparticles: Photoelectrochemical Bioanalysis with High Efficiency.

    Science.gov (United States)

    Ma, Zheng-Yuan; Xu, Fei; Qin, Yu; Zhao, Wei-Wei; Xu, Jing-Juan; Chen, Hong-Yuan

    2016-04-19

    In this work, direct exciton-plasmon interactions (EPI) between CdS quantum dots (QDs) and Ag nanoparticles (NPs) were invoked ingeniously by catalytic Ag deposition on Au NPs for the stimulation of high efficient damping effect toward the excitonic responses in CdS QDs, on the basis of which a novel photoelectrochemical (PEC) bioanalytical format was achieved for sensitive microRNA detection. Specifically, upon the configurational change from the hairpin probe DNA to the "Y"-shaped ternary conjugate consisting of the original probe DNA, assistant DNA, and the target microRNA, the alkaline phosphatase (ALP) catalytic chemistry would then trigger the transition of the interparticle interplay from the CdS QDs-Au NPs to the CdS QDs-Ag NPs systems for the microRNA detection due to the dependence of the photocurrent quenching on the target concentration. This work not only provided a unique method for EPI generation among the PEC nanosystems but also offered a versatile and general protocol for future PEC bioanalysis development. PMID:27023112

  9. Population success.

    Science.gov (United States)

    1982-01-01

    "The commitment to population programs is now widespread," says Rafael Salas, Executive Director of the UNFPA, in its report "State of World Population." About 80% of the total population of the developing world live in countries which consider their fertility levels too high and would like them reduced. An important impetus came from the World Conference of 1974. The Plan of Action from the conference projected population growth rates in developing countries of 2.0% by 1985. Today it looks as though this projection will be realized. While in 1969, for example, only 26 developing countries had programs aimed at lowering or maintaining fertility levels, by 1980 there were 59. The International Population Conference, recently announced by the UN for 1984, will, it is hoped, help sustain that momentum. Cuba is the country which has shown the greatest decline in birth rate so far. The birth rate fell 47% between 1965-1970 and 1975-1980. Next came China with a 34% decline in the same period. After these came a group of countries--each with populations of over 10 million--with declines of between 15 and 25%: Chile, Colombia, India, Indonesia, the Republic of Korea, Malaysia and Thailand. Though birth rates have been dropping significantly the decline in mortality rates over recent years has been less than was hoped for. The 1974 conference set 74 years as the target for the world's average expectation of life, to be reached by the year 2000. But the UN now predicts that the developing countries will have only reached 63 or 64 years by then. High infant and child mortality rates, particularly in Africa, are among the major causes. The report identifies the status of women as an important determinant of family size. Evidence from the UNFPA-sponsored World Fertility Survey shows that in general the fertility of women decreases as their income increases. It also indicates that women who have been educated and who work outside the home are likely to have smaller families

  10. New pseudodimeric aurones as palm pocket inhibitors of Hepatitis C virus RNA-dependent RNA polymerase.

    Science.gov (United States)

    Meguellati, Amel; Ahmed-Belkacem, Abdelhakim; Nurisso, Alessandra; Yi, Wei; Brillet, Rozenn; Berqouch, Nawel; Chavoutier, Laura; Fortuné, Antoine; Pawlotsky, Jean-Michel; Boumendjel, Ahcène; Peuchmaur, Marine

    2016-06-10

    The NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme for Hepatitis C Virus (HCV) replication. In addition to the catalytic site, this enzyme is characterized by the presence of at least four allosteric pockets making it an interesting target for development of inhibitors as potential anti-HCV drugs. Based on a previous study showing the potential of the naturally occurring aurones as inhibitors of NS5B, we pursued our efforts to focus on pseudodimeric aurones that have never been investigated so far. Hence, 14 original compounds characterized by the presence of a spacer between the benzofuranone moieties were synthesized and investigated as HCV RdRp inhibitors by means of an in vitro assay. The most active inhibitor, pseudodimeric aurone 4, induced high inhibition activity (IC50 = 1.3 μM). Mutagenic and molecular modeling studies reveal that the binding site for the most active derivatives probably is the palm pocket I instead of the thumb pocket I as for the monomeric derivatives. PMID:27017550

  11. tRNA binding, positioning, and modification by the pseudouridine synthase Pus10.

    Science.gov (United States)

    Kamalampeta, Rajashekhar; Keffer-Wilkes, Laura C; Kothe, Ute

    2013-10-23

    Pus10 is the most recently identified pseudouridine synthase found in archaea and higher eukaryotes. It modifies uridine 55 in the TΨC arm of tRNAs. Here, we report the first quantitative biochemical analysis of tRNA binding and pseudouridine formation by Pyrococcus furiosus Pus10. The affinity of Pus10 for both substrate and product tRNA is high (Kd of 30nM), and product formation occurs with a Km of 400nM and a kcat of 0.9s(-1). Site-directed mutagenesis was used to demonstrate that the thumb loop in the catalytic domain is important for efficient catalysis; we propose that the thumb loop positions the tRNA within the active site. Furthermore, a new catalytic arginine residue was identified (arginine 208), which is likely responsible for triggering flipping of the target uridine into the active site of Pus10. Lastly, our data support the proposal that the THUMP-containing domain, found in the N-terminus of Pus10, contributes to binding of tRNA. Together, our findings are consistent with the hypothesis that tRNA binding by Pus10 occurs through an induced-fit mechanism, which is a prerequisite for efficient pseudouridine formation. PMID:23743107

  12. Antibiotic inhibition of the movement of tRNA substrates through a peptidyl transferase cavity

    DEFF Research Database (Denmark)

    Porse, B T; Rodriguez-Fonseca, C; Leviev, I;

    1996-01-01

    The present review attempts to deal with movement of tRNA substrates through the peptidyl transferase centre on the large ribosomal subunit and to explain how this movement is interrupted by antibiotics. It builds on the concept of hybrid tRNA states forming on ribosomes and on the observed...... movement of the 5' end of P-site-bound tRNA relative to the ribosome that occurs on peptide bond formation. The 3' ends of the tRNAs enter, and move through, a catalytic cavity where antibiotics are considered to act by at least three primary mechanisms: (i) they interfere with the entry of the aminoacyl...... moiety into the catalytic cavity before peptide bond formation; (ii) they inhibit movement of the nascent peptide along the peptide channel, a process that may generally involve destabilization of the peptidyl tRNA, and (iii) they prevent movement of the newly deacylated tRNA between the P/P and hybrid P...

  13. Insights into how RNase R degrades structured RNA: analysis of the nuclease domain.

    Science.gov (United States)

    Vincent, Helen A; Deutscher, Murray P

    2009-04-01

    RNase R readily degrades highly structured RNA, whereas its paralogue, RNase II, is unable to do so. Furthermore, the nuclease domain of RNase R, devoid of all canonical RNA-binding domains, is sufficient for this activity. RNase R also binds RNA more tightly within its catalytic channel than does RNase II, which is thought to be important for its unique catalytic properties. To investigate this idea further, certain residues within the nuclease domain channel of RNase R were changed to those found in RNase II. Among the many examined, we identified one amino acid residue, R572, that has a significant role in the properties of RNase R. Conversion of this residue to lysine, as found in RNase II, results in weaker substrate binding within the nuclease domain channel, longer limit products, increased activity against a variety of substrates and a faster substrate on-rate. Most importantly, the mutant encounters difficulty in degrading structured RNA, pausing within a double-stranded region. Additional studies show that degradation of structured substrates is dependent upon temperature, suggesting a role for thermal breathing in the mechanism of action of RNase R. On the basis of these data, we propose a model in which tight binding within the nuclease domain allows RNase R to capitalize on the natural thermal breathing of an RNA duplex to degrade structured RNAs. PMID:19361424

  14. 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)

    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

  15. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    Science.gov (United States)

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

  16. Genetic relatedness of orbiviruses by RNA-RNA blot hybridization

    International Nuclear Information System (INIS)

    RNA-RNA blot hybridization was developed in order to identify type-specific genes among double-stranded (ds) RNA viruses, to assess the genetic relatedness of dsRNA viruses and to classify new strains. Viral dsRNA segments were electrophoresed through 10% polyacrylamide gels, transferred to membranes, and hybridized to [5'32P]-pCp labeled genomic RNA from a related strain. Hybridization was performed at 520C, 50% formamide, 5X SSC. Under these conditions heterologous RNA species must share ≥ 74% sequence homology in order to form stable dsRNA hybrids. Cognate genes of nine members of the Palyam serogroup of orbiviruses were identified and their sequence relatedness to the prototype. Palyam virus, was determined. Reciprocal blot hybridizations were performed using radiolabeled genomic RNA of all members of the Palyam serogroup. Unique and variant genes were identified by lack of cross-homology or by weak homology between segments. Since genes 2 and 6 exhibited the highest degree of sequence variability, response to the vertebrate immune system may be a major cause of sequence divergence among members of a single serogroup. Changuinola serogroup isolates were compared by dot-blot hybridization, while Colorado tick fever (CTF) serogroup isolates were compared by the RNA-RNA blot hybridization procedure described for reovirus and Palyam serogroup isolates. Preliminary blot hybridization data were also obtained on the relatedness of members of different Orbivirus serogroups

  17. Current preclinical small interfering RNA (siRNA)-based conjugate systems for RNA therapeutics.

    Science.gov (United States)

    Lee, Soo Hyeon; Kang, Yoon Young; Jang, Hyo-Eun; Mok, Hyejung

    2016-09-01

    Recent promising clinical results of RNA therapeutics have drawn big attention of academia and industries to RNA therapeutics and their carrier systems. To improve their feasibility in clinics, systemic evaluations of currently available carrier systems under clinical trials and preclinical studies are needed. In this review, we focus on recent noticeable preclinical studies and clinical results regarding siRNA-based conjugates for clinical translations. Advantages and drawbacks of siRNA-based conjugates are discussed, compared to particle-based delivery systems. Then, representative siRNA-based conjugates with aptamers, peptides, carbohydrates, lipids, polymers, and nanostructured materials are introduced. To improve feasibility of siRNA conjugates in preclinical studies, several considerations for the rational design of siRNA conjugates in terms of cleavability, immune responses, multivalent conjugations, and mechanism of action are also presented. Lastly, we discuss lessons from previous preclinical and clinical studies related to siRNA conjugates and perspectives of their clinical applications. PMID:26514375

  18. A reduced-coordinate approach to modeling RNA 3-D structures

    Energy Technology Data Exchange (ETDEWEB)

    Tung, Chang-Shung

    1997-09-01

    With the realization of RNA molecules capable of performing very specific functions (e.g., catalytic RNAs and RNAs that bind ligand with affinity and specificity of an anti-body) and contrary to the traditional view that structure of RNA molecules being functionally passive, it has become clear that studying the 3-dimensional (3-D) folding of RNA molecules is a very important task. In the absence of sufficient number of experimentally determined RNA structures available up-to-date, folding of RNA structures computationally provides an alternative approach in studying the 3-D structure of RNA molecules. We have developed a computational approach for folding RNA 3-D structures. The method is conceptually simple and general. It consists of two major components. The first being the arrangement of all helices in space. Once the helices are positioned and oriented in space, structures of the connecting loops are modeled and inserted between the helices. Any number of structural constraints derived either experimentally or theoretically can be used to guide the folding processes. A conformational sampling approach is developed with structural equilibration using the Metropolis Monte Carlo simulation. The lengths of various loop sizes (ranging from 1 base to 7 bases) are calculated based on a set of RNA structures deposited in PDB as well as a set of loop structures constructed using our method. The validity of using the averaged loop lengths of the connecting loops as distance constraints for arranging the helices in space is studied.

  19. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

    Science.gov (United States)

    Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

    2014-03-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

  20. Packed-bed catalytic cracking of oak derived pyrolytic vapors

    Science.gov (United States)

    Catalytic upgrading of pyrolysis vapors derived from oak was carried out using a fixed-bed catalytic column at 425 deg C. The vapors were drawn by splitting a fraction from the full stream of vapors produced at 500 deg C in a 5 kg/hr bench-scale fast pyrolysis reactor system downstream the cyclone s...

  1. In situ and operando transmission electron microscopy of catalytic materials

    DEFF Research Database (Denmark)

    Crozier, Peter A.; Hansen, Thomas Willum

    2015-01-01

    measurements of gas-phase catalytic products. To overcome this deficiency, operando TEM techniques are being developed that combine atomic characterization with the simultaneous measurement of catalytic products. This article provides a short review of the current status and major developments in the...

  2. Catalytic pyrolysis of oilsand bitumen over nanoporous catalysts.

    Science.gov (United States)

    Lee, See-Hoon; Heo, Hyeon Su; Jeong, Kwang-Eun; Yim, Jin-Heong; Jeon, Jong-Ki; Jung, Kyeong Youl; Ko, Young Soo; Kim, Seung-Soo; Park, Young-Kwon

    2011-01-01

    The catalytic cracking of oilsand bitumen was performed over nanoporous materials at atmospheric conditions. The yield of gas increased with application of nanoporous catalysts, with the catalytic conversion to gas highest for Meso-MFI. The cracking activity seemed to correlate with pore size rather than weak acidity or surface area. PMID:21446540

  3. Protein Structure Is Related to RNA Structural Reactivity In Vivo.

    Science.gov (United States)

    Tang, Yin; Assmann, Sarah M; Bevilacqua, Philip C

    2016-02-27

    We assessed whether in vivo mRNA structural reactivity and the structure of the encoded protein are related. This is the first investigation of such a relationship that utilizes information on RNA structure obtained in living cells. Based on our recent genome-wide Structure-seq analysis in Arabidopsis thaliana, we report that, as a meta property, regions of individual mRNAs that code for protein domains generally have higher reactivity to DMS (dimethyl sulfate), a chemical that covalently modifies accessible As and Cs, than regions that encode protein domain junctions. This relationship is prominent for proteins annotated for catalytic activity and reversed in proteins annotated for binding and transcription regulatory activity. Upon analyzing intrinsically disordered proteins, we found a similar pattern for disordered regions as compared to ordered regions: regions of individual mRNAs that code for ordered regions have significantly higher DMS reactivity than regions that code for intrinsically disordered regions. Based on these effects, we hypothesize that the decreased DMS reactivity of RNA regions that encode protein domain junctions or intrinsically disordered regions may reflect increased RNA structure that may slow translation, allowing time for the nascent protein domain or ordered region of the protein to fold, thereby reducing protein misfolding. In addition, a drop in DMS reactivity was observed on portions of mRNA sequences that correspond to the C-termini of protein domains, suggesting ribosome protection at these mRNA regions. Structural relationships between mRNAs and their encoded proteins may have evolved to allow efficient and accurate protein folding. PMID:26598238

  4. Mapping the active site of vaccinia virus RNA triphosphatase

    International Nuclear Information System (INIS)

    The RNA triphosphatase component of vaccinia virus mRNA capping enzyme (the product of the viral D1 gene) belongs to a family of metal-dependent phosphohydrolases that includes the RNA triphosphatases of fungi, protozoa, Chlorella virus, and baculoviruses. The family is defined by two glutamate-containing motifs (A and C) that form the metal-binding site. Most of the family members resemble the fungal and Chlorella virus enzymes, which have a complex active site located within the hydrophilic interior of a topologically closed eight-stranded β barrel (the so-called ''triphosphate tunnel''). Here we queried whether vaccinia virus capping enzyme is a member of the tunnel subfamily, via mutational mapping of amino acids required for vaccinia triphosphatase activity. We identified four new essential side chains in vaccinia D1 via alanine scanning and illuminated structure-activity relationships by conservative substitutions. Our results, together with previous mutational data, highlight a constellation of six acidic and three basic amino acids that likely compose the vaccinia triphosphatase active site (Glu37, Glu39, Arg77, Lys107, Glu126, Asp159, Lys161, Glu192, and Glu194). These nine essential residues are conserved in all vertebrate and invertebrate poxvirus RNA capping enzymes. We discerned no pattern of clustering of the catalytic residues of the poxvirus triphosphatase that would suggest structural similarity to the tunnel proteins (exclusive of motifs A and C). We infer that the poxvirus triphosphatases are a distinct lineage within the metal-dependent RNA triphosphatase family. Their unique active site, which is completely different from that of the host cell's capping enzyme, recommends the poxvirus RNA triphosphatase as a molecular target for antipoxviral drug discovery

  5. Molecular Detection of Human Telomerase mRNA (hTERT-mRNA in Egyptian Patients with Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Gahan Kamal El-Saeed

    2009-06-01

    Full Text Available Background and Aims: Diagnostic modalities for hepatocellular carcinoma (HCC as markers, sonography, and CT have contributed to the early detection of HCC but are still not sensitive enough. Human telomerase RNA subunit (hTERT-mRNA has been identified in many cancers and claimed to be reactivated in HCC. To investigate hTERT-mRNA in the peripheral blood of HCC and chronic liver disease (CLD patients and correlate its level with alpha feto protein (AFP, the serological marker for HCC.Methods: The study was conducted on 44 patients selected from the National Liver Institute. Patients included Group I (22 patients diagnosed to have HCC, Group II (22 patients with CLD, and 12 apparently healthy volunteers as controls (Group III. All selected individuals were subjected to history taking, a clinical examination, abdominal sonography and laboratory investigations as liver function tests (LFTs, cell blood count (CBC, hepatitis viral markers, AFP, and real-time polymerase chain reaction (PCR Quantitative detection of -mRNA expression, encoding for telomerase catalytic subunit.Results: There was a significant elevation of AFP levels in the HCC group compared to both the CLD and control groups (P < 0.00, P < 0.001. The mean hTERT-mRNA expression in HCC patients was significantly higher than both CLD patients and controls (P < 0.001, P < 0.001. hTERT-mRNA was correlated with AFP and tumor size (P < 0.05, P < 0.001. The AFP cutoff level (185 ng/ml resulted in a 63.6% sensitivity, a 85.3% specificity; a 89.3% positive predictive value (PPV level, a 76.2 % negative predictive value (NPV level and a 83.4% accuracy for HCC prediction. The hTERT-mRNA cutoff level (112.5 copies/ml showed a 77.3% sensitivity, a 97.1% specificity, a 98% PPV level, a 79.2 % NPV level, and an accuracy of 84% for HCC prediction. Combining hTERT-mRNA and AFP increased diagnostic accuracy to 90.5%. Both markers had a 84.1% sensitivity, a 86.4% specificity, a 86.4% PPV level, and a 88

  6. RNA Silencing in Aspergillus nidulans Is Independent of RNA-Dependent RNA Polymerases

    OpenAIRE

    Hammond, T. M.; Keller, N P

    2005-01-01

    The versatility of RNA-dependent RNA polymerases (RDRPs) in eukaryotic gene silencing is perhaps best illustrated in the kingdom Fungi. Biochemical and genetic studies of Schizosaccharomyces pombe and Neurospora crassa show that these types of enzymes are involved in a number of fundamental gene-silencing processes, including heterochromatin regulation and RNA silencing in S. pombe and meiotic silencing and RNA silencing in N. crassa. Here we show that Aspergillus nidulans, another model fung...

  7. Catalytic Decomposition of Methylene Chloride by Sulfated Titania Catalysts

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Catalytic decomposition of methylene chloride in air below 300℃ was studied.Sulfated titania was very effective in converting 959ppm methylene chloride selectively to CO,CO2 and HCl.Complete decomposition of methylene chloride was achieved at low temperature(275℃).It was found that the acidic property of catalyst was a determinant factor for the catalytic activity.The presence of water vapor in the feed stream remarkably reduced the catalytic activity,which could be due to the blockage of acidic sites on the surface of catalyst by water molecules.A bifunctional catalyst comprising copper oxide was developed to improve the selectivity of catalytic oxidation,which indicated that copper oxide can promote the deep oxidation of methylene chloride.The crystal form of TiO2 imposes an important influence upon the catalytic oxidation.

  8. Relationship between structure and catalytic performance of dealuminated Y zeolites

    International Nuclear Information System (INIS)

    Dealuminated Y zeolites which have been prepared by hydrothermal and chemical treatments show differences in catalytic performance when tested fresh; however, these differences disappear after the zeolites have been steamed. The catalytic behavior of fresh and steamed zeolites is directly related to zeolite structural and chemical characteristics. Such characteristics determine the strength and density of acid sites for catalytic cracking. Dealuminated zeolites were characterized using x-ray diffraction, porosimetry, solid-state NMR and elemental analysis. Hexadecane cracking was used as a probe reaction to determine catalytic properties. Cracking activity was found to be proportional to total aluminum content in the zeolite. Product selectivity was dependent on unit cell size, presence of extra framework alumina and spatial distribution of active sites. The results from this study elucidate the role that zeolite structure plays in determining catalytic performance

  9. Catalytically defective ganglioside neuraminidase in mucolipidosis IV

    International Nuclear Information System (INIS)

    Cultured skin fibroblasts from patients with mucolipidosis IV were found to be deficient in neuraminidase activity toward GDsub(la) and GDsub(lb) gangliosides radiolabelled in C3 and C7 analogs of their sialic acid residues. Neuraminidase activities toward 4-methylumbelliferyl-N-acetyl-neuraminic acid, neuraminlactose, and radiolabelled neuraminlactitol, fetuin and α1-acid glycoprotein were within the range of normal controls. Fibroblasts from parents of patients with mucolipidosis IV demonstrated intermediate levels of ganglioside neuraminidase activity and normal levels of glycoprotein neuraminidase activity. The redidual acidic neuraminidase activity toward GDsub(1a) ganglioside in the patients' fibroblasts did not differ from that of controls in its pH optimum and thermostability, but had an abnormal apparent Ksub(m) which was about 18 times higher than that of the normal enzyme. These findings suggest that mucolipidosis IV ia a ganglioside sialidosis due to a catalytically defective ganglioside neuraminidase. (author)

  10. Carbon nanofibers: a versatile catalytic support

    Directory of Open Access Journals (Sweden)

    Nelize Maria de Almeida Coelho

    2008-09-01

    Full Text Available The aim of this article is present an overview of the promising results obtained while using carbon nanofibers based composites as catalyst support for different practical applications: hydrazine decomposition, styrene synthesis, direct oxidation of H2S into elementary sulfur and as fuel-cell electrodes. We have also discussed some prospects of the use of these new materials in total combustion of methane and in ammonia decomposition. The macroscopic carbon nanofibers based composites were prepared by the CVD method (Carbon Vapor Deposition employing a gaseous mixture of hydrogen and ethane. The results showed a high catalytic activity and selectivity in comparison to the traditional catalysts employed in these reactions. The fact was attributed, mainly, to the morphology and the high external surface of the catalyst support.

  11. Scanning electrochemical microscopy of individual catalytic nanoparticles.

    Science.gov (United States)

    Sun, Tong; Yu, Yun; Zacher, Brian J; Mirkin, Michael V

    2014-12-15

    Electrochemistry at individual metal nanoparticles (NPs) can provide new insights into their electrocatalytic behavior. Herein, the electrochemical activity of single AuNPs attached to the catalytically inert carbon surface is mapped by using extremely small (≥3 nm radius) polished nanoelectrodes as tips in the scanning electrochemical microscope (SECM). The use of such small probes resulted in the spatial resolution significantly higher than in previously reported electrochemical images. The currents produced by either rapid electron transfer or the electrocatalytic hydrogen evolution reaction at a single 10 or 20 nm NP were measured and quantitatively analyzed. The developed methodology should be useful for studying the effects of nanoparticle size, geometry, and surface attachment on electrocatalytic activity in real-world application environment. PMID:25332196

  12. Catalytic cracking process with vanadium passivation

    Energy Technology Data Exchange (ETDEWEB)

    Kennedy, J.V.; Jossens, L.W.

    1991-03-26

    This paper discusses a process for the catalytic cracking of metal-containing hydrocarbonaceous feedstock. It comprises contacting the feedstock under cracking conditions with a dual component catalyst composition. The catalyst composition comprises a first component comprising an active cracking catalyst; and a second component, as a separate and distinct entity, the second component comprising the following materials: a calcium and magnesium containing material selected from the group consisting of dolomite, substantially amorphous calcium magnesium silicate, calcium magnesium oxide, calcium magnesium acetate, calcium magnesium carbonate, and calcium magnesium subcarbonate; a magnesium containing material comprising a hydrous magnesium silicate; and a binder selected from the group consisting of kaolin, bentonite, montmorillonite, saponite, hectorite, alumina, silica, titania, zirconia, silica-alumina, and combinations thereof.

  13. Catalytic Conia-ene and related reactions.

    Science.gov (United States)

    Hack, Daniel; Blümel, Marcus; Chauhan, Pankaj; Philipps, Arne R; Enders, Dieter

    2015-10-01

    Since its initial inception, the Conia-ene reaction, known as the intramolecular addition of enols to alkynes or alkenes, has experienced a tremendous development and appealing catalytic protocols have emerged. This review fathoms the underlying mechanistic principles rationalizing how substrate design, substrate activation, and the nature of the catalyst work hand in hand for the efficient synthesis of carbocycles and heterocycles at mild reaction conditions. Nowadays, Conia-ene reactions can be found as part of tandem reactions, and the road for asymmetric versions has already been paved. Based on their broad applicability, Conia-ene reactions have turned into a highly appreciated synthetic tool with impressive examples in natural product synthesis reported in recent years. PMID:26031492

  14. Smoke emissions from a catalytic wood stove

    International Nuclear Information System (INIS)

    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)

  15. Lignin Valorization using Heterogenous Catalytic Oxidation

    DEFF Research Database (Denmark)

    Melián Rodríguez, Mayra; Shunmugavel, Saravanamurugan; Kegnæs, Søren;

    The research interests in biomass conversion to fuels and chemicals has increased significantly in the last decade in view of current problems such as global warming, high oil prices, food crisis and other geopolitical scenarios. Many different reactions and processes to convert biomass into high......-value products and fuels have been proposed in the literature, giving special attention to the conversion of lignocellulosic biomass, which does not compete with food resources and is widely available as a low cost feedstock 1. Lignocellulose biomass is a complex material composed of three main fractions...... complex so different model compounds are often used to study lignin valorization. These model compounds contain the linkages present in lignin, simplifying catalytic analysis and present analytical challenges related to the study of the complicated lignin polymer and the plethora of products that could be...

  16. Ubiquitous ``glassy'' relaxation in catalytic reaction networks

    Science.gov (United States)

    Awazu, Akinori; Kaneko, Kunihiko

    2009-10-01

    Study of reversible catalytic reaction networks is important not only as an issue for chemical thermodynamics but also for protocells. From extensive numerical simulations and theoretical analysis, slow relaxation dynamics to sustain nonequlibrium states are commonly observed. These dynamics show two types of salient behaviors that are reminiscent of glassy behavior: slow relaxation along with the logarithmic time dependence of the correlation function and the emergence of plateaus in the relaxation-time course. The former behavior is explained by the eigenvalue distribution of a Jacobian matrix around the equilibrium state that depends on the distribution of kinetic coefficients of reactions. The latter behavior is associated with kinetic constraints rather than metastable states and is due to the absence of catalysts for chemicals in excess and the negative correlation between two chemical species. Examples are given and generality is discussed with relevance to bottleneck-type dynamics in biochemical reactions as well.

  17. 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.

  18. Catalytic hot gas cleaning of gasification gas

    Energy Technology Data Exchange (ETDEWEB)

    Simell, P. [VTT Energy, Espoo (Finland). Energy Production Technologies

    1997-12-31

    The aim of this work was to study the catalytic cleaning of gasification gas from tars and ammonia. In addition, factors influencing catalytic activity in industrial applications were studied, as well as the effects of different operation conditions and limits. Also the catalytic reactions of tar and ammonia with gasification gas components were studied. The activities of different catalyst materials were measured with laboratory-scale reactors fed by slip streams taken from updraft and fluid bed gasifiers. Carbonate rocks and nickel catalysts proved to be active tar decomposing catalysts. Ammonia decomposition was in turn facilitated by nickel catalysts and iron materials like iron sinter and iron dolomite. Temperatures over 850 deg C were required at 2000{sup -1} space velocity at ambient pressure to achieve almost complete conversions. During catalytic reactions H{sub 2} and CO were formed and H{sub 2}O was consumed in addition to decomposing hydrocarbons and ammonia. Equilibrium gas composition was almost achieved with nickel catalysts at 900 deg C. No deactivation by H{sub 2}S or carbon took place in these conditions. Catalyst blocking by particulates was avoided by using a monolith type of catalyst. The apparent first order kinetic parameters were determined for the most active materials. The activities of dolomite, nickel catalyst and reference materials were measured in different gas atmospheres using laboratory apparatus. This consisted of nitrogen carrier, toluene as tar model compound, ammonia and one of the components H{sub 2}, H{sub 2}O, CO, CO{sub 2}, CO{sub 2}+H{sub 2}O or CO+CO{sub 2}. Also synthetic gasification gas was used. With the dolomite and nickel catalyst the highest toluene decomposition rates were measured with CO{sub 2} and H{sub 2}O. In gasification gas, however, the rate was retarded due to inhibition by reaction products (CO, H{sub 2}, CO{sub 2}). Tar decomposition over dolomite was modelled by benzene reactions with CO{sub 2}, H

  19. Contact structure for use in catalytic distillation

    Science.gov (United States)

    Jones, Jr., Edward M.

    1984-01-01

    A method for conducting catalytic chemical reactions and fractionation of the reaction mixture comprising feeding reactants into a distillation column reactor contracting said reactant in liquid phase with a fixed bed catalyst in the form of a contact catalyst structure consisting of closed porous containers containing the catatlyst for the reaction and a clip means to hold and support said containers, which are disposed above, i.e., on the distillation trays in the tower. The trays have weir means to provide a liquid level on the trays to substantially cover the containers. In other words, the trays function in their ordinary manner with the addition thereto of the catalyst. The reaction mixture is concurrently fractionated in the column.

  20. Biofuel from fast pyrolysis and catalytic hydrodeoxygenation.

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, Douglas C.

    2015-09-04

    This review addresses recent developments in biomass fast pyrolysis bio-oil upgrading by catalytic hydrotreating. The research in the field has expanded dramatically in the past few years with numerous new research groups entering the field while existing efforts from others expand. The issues revolve around the catalyst formulation and operating conditions. Much work in batch reactor tests with precious metal catalysts needs further validation to verify long-term operability in continuous flow systems. The effect of the low level of sulfur in bio-oil needs more study to be better understood. Utilization of the upgraded bio-oil for feedstock to finished fuels is still in an early stage of understanding.

  1. Structural and functional basis for RNA cleavage by Ire1

    Directory of Open Access Journals (Sweden)

    Stroud Robert M

    2011-07-01

    Full Text Available Abstract Background The unfolded protein response (UPR controls the protein folding capacity of the endoplasmic reticulum (ER. Central to this signaling pathway is the ER-resident bifunctional transmembrane kinase/endoribonuclease Ire1. The endoribonuclease (RNase domain of Ire1 initiates a non-conventional mRNA splicing reaction, leading to the production of a transcription factor that controls UPR target genes. The mRNA splicing reaction is an obligatory step of Ire1 signaling, yet its mechanism has remained poorly understood due to the absence of substrate-bound crystal structures of Ire1, the lack of structural similarity between Ire1 and other RNases, and a scarcity of quantitative enzymological data. Here, we experimentally define the active site of Ire1 RNase and quantitatively evaluate the contribution of the key active site residues to catalysis. Results This analysis and two new crystal structures suggest that Ire1 RNase uses histidine H1061 and tyrosine Y1043 as the general acid-general base pair contributing ≥ 7.6 kcal/mol and 1.4 kcal/mol to transition state stabilization, respectively, and asparagine N1057 and arginine R1056 for coordination of the scissile phosphate. Investigation of the stem-loop recognition revealed that additionally to the stem-loops derived from the classic Ire1 substrates HAC1 and Xbp1 mRNA, Ire1 can site-specifically and rapidly cleave anticodon stem-loop (ASL of unmodified tRNAPhe, extending known substrate specificity of Ire1 RNase. Conclusions Our data define the catalytic center of Ire1 RNase and suggest a mechanism of RNA cleavage: each RNase monomer apparently contains a separate catalytic apparatus for RNA cleavage, whereas two RNase subunits contribute to RNA stem-loop docking. Conservation of the key residues among Ire1 homologues suggests that the mechanism elucidated here for yeast Ire1 applies to Ire1 in metazoan cells, and to the only known Ire1 homologue RNase L.

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

    Science.gov (United States)

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

    2016-01-01

    Rice black-streaked dwarf virus (RBSDV) belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA) construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21–24 nt small interfering RNA (siRNA). By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species. PMID:27187354

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

    Directory of Open Access Journals (Sweden)

    Fangquan Wang

    2016-05-01

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

  4. Comprehensive survey of human brain microRNA by deep sequencing

    Directory of Open Access Journals (Sweden)

    Menzel Corinna

    2010-06-01

    Full Text Available Abstract Background MicroRNA (miRNA play an important role in gene expression regulation. At present, the number of annotated miRNA continues to grow rapidly, in part due to advances of high-throughput sequencing techniques. Here, we use deep sequencing to characterize a population of small RNA expressed in human and rhesus macaques brain cortex. Results Based on a total of more than 150 million sequence reads we identify 197 putative novel miRNA, in humans and rhesus macaques, that are highly conserved among mammals. These putative miRNA have significant excess of conserved target sites in genes' 3'UTRs, supporting their functional role in gene regulation. Additionally, in humans and rhesus macaques respectively, we identify 41 and 22 conserved putative miRNA originating from non-coding RNA (ncRNA transcripts. While some of these molecules might function as conventional miRNA, others might be harmful and result in target avoidance. Conclusions Here, we further extend the repertoire of conserved human and rhesus macaque miRNA. Even though our study is based on a single tissue, the coverage depth of our study allows identification of functional miRNA present in brain tissue at background expression levels. Therefore, our study might cover large proportion of the yet unannotated conserved miRNA present in the human genome.

  5. Catalytic combustion in small wood burning appliances

    Energy Technology Data Exchange (ETDEWEB)

    Oravainen, H. [VTT Energy, Jyvaeskylae (Finland)

    1996-12-31

    There is over a million hand fired small heating appliances in Finland where about 5,4 million cubic meters of wood fuel is used. Combustion in such heating appliances is a batch-type process. In early stages of combustion when volatiles are burned, the formation of carbon monoxide (CO) and other combustible gases are difficult to avoid when using fuels that have high volatile matter content. Harmful emissions are formed mostly after each fuel adding but also during char burnout period. When the CO-content in flue gases is, say over 0.5 %, also other harmful emissions will be formed. Methane (CH{sub 4}) and other hydrocarbons are released and the amount of polycyclic aromatic hydrocarbons (PAH)-compounds can be remarkable. Some PAH-compounds are very carcinogenic. It has been estimated that in Finland even more than 90 % of hydrocarbon and PAH emissions are due to small scale wood combustion. Emissions from transportation is excluded from these figures. That is why wood combustion has a net effect on greenhouse gas phenomena. For example carbon monoxide emissions from small scale wood combustion are two fold compared to that of energy production in power plants. Methane emission is of the same order as emission from transportation and seven fold compared with those of energy production. Emissions from small heating appliances can be reduced by developing the combustion techniques, but also by using other means, for example catalytic converters. In certain stages of the batch combustion, temperature is not high enough, gas mixing is not good enough and residence time is too short for complete combustion. When placed to a suitable place inside a heating appliance, a catalytic converter can oxidize unburned gases in the flue gas into compounds that are not harmful to the environment. (3 refs.)

  6. Plasma Catalytic Synthesis of Silver Nanoparticles

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yu-Tao; GUO Ying; MA Teng-Cai

    2011-01-01

    We present the experimental results of plasma catalytic synthesis of colloidal silver nanoparticles, using AgNO3 as the precursor, ethanol as the solvent and reducing agent, and poly vinyl pyrrolidone (PVP) as the macromolecular surfactant. The plasma is generated by an atmospheric argon dielectric barrier discharge jet. Silver nanoparticles are produced instantly once the plasma is ignited. The system is not heated so it is necessary to use traditional chemical methods. The samples are characterized by UV-visible absorbance and transmission electron microscopy. For glow discharge mode no obvious silver nanoparticles are observed. For low voltage filamentary streamer discharge mode a lot of silver nanoparticles with the mean diameter of ~3.5nm are generated and a further increase of the voltage causes the occurrence of agglomeration.%We present the experimental results of plasma catalytic synthesis of colloidal silver nanoparticles,using AgNO3 as the precursor,ethanol as the solvent and reducing agent,and poly vinyl pyrrolidone (PVP) as the macromolecular surfactant.The plasma is generated by an atmospheric argon dielectric barrier discharge jet.Silver nanoparticles are produced instantly once the plasma is ignited.The system is not heated so it is necessary to use traditional chemical methods.The samples are characterized by UV-visible absorbance and transmission electron microscopy.For glow discharge mode no obvious silver nanoparticles are observed.For low voltage filamentary streamer discharge mode a lot of silver nanoparticles with the mean diameter of ~3.5nm are generated and a further increase of the voltage causes the occurrence of agglomeration.The study of silver nanoparticles has been an extremely active area in recent years because of their important physical and chemical properties as a catalyst and antimicrobial reagent,for example.A number of methods for silver nanoparticle preparation have been developed,[1-3] among them chemical reduction is

  7. Experimental catalytic isotopic exchange column control

    International Nuclear Information System (INIS)

    Full text: In this paper we present a method for monitoring and control of the experimental catalytic isotopic exchange column which is part of ETRF (experimental tritium removal facility) of the ICIT Rm. Valcea. The initial data acquisition system based on analogue instruments is now upgraded to a fully digital system. Therefore we chose to use Compact Field Point which is a programmable automation controller (PAC) and LabVIEW software. To operate the catalytic isotopic exchange column there are some control loops that need to be operated simultaneously, namely: the heavy water column feed temperature and flow rate; the hydrogen gas column feed temperature; the flow rate and pressure at the top of the column; the water vapor flow rate; the hydrogen gas temperature at the condenser output. The human machine interface (HMI) realized with LabVIEW software is very friendly. The use of the PAC graphics interface makes isotopic exchange process operation easier for operators and researchers. The HMI has the functions to provide visualization of process parameters, to enable interaction with the process and also to provide alarms and event notification to operators about any abnormal situation in the plant. To interact with the process, detailed displays which contain specific control functions to operate the column, can be used. Usually, the faceplate display shows the controlled process variable and the output of the control loop. Furthermore, the set point and the operating mode of the control loop can be changed. Additionally, detailed information is available related to the parameters of PID controller and the different alarms that can be authorized in this control loop with its corresponding values of activation. (authors)

  8. Population Aging

    OpenAIRE

    Weil, David N.

    2006-01-01

    Population aging is primarily the result of past declines in fertility, which produced a decades long period in which the ratio of dependents to working age adults was reduced. Rising old-age dependency in many countries represents the inevitable passing of this %u201Cdemographic dividend.%u201D Societies use three methods to transfer resources to people in dependent age groups: government, family, and personal saving. In developed countries, families are predominant in supporting children, w...

  9. Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis

    Energy Technology Data Exchange (ETDEWEB)

    Greenwood, Alexander I.; Rogals, Monique J.; De, Soumya [Cornell University, Department of Molecular Biology and Genetics (United States); Lu, Kun Ping [Cancer Biology Program and Biology of Aging Program, Beth Israel Deaconess Medical Center, Harvard Medical School (United States); Kovrigin, Evgenii L. [Marquette University, Chemistry Department (United States); Nicholson, Linda K., E-mail: lkn2@cornell.edu [Cornell University, Department of Molecular Biology and Genetics (United States)

    2011-09-15

    The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation, rigorous enzymatic assays of isomerization are required. However, most measures of isomerase activity require significant constraints on substrate sequence and only yield rate constants for the cis isomer, k{sub cat}{sup cis} and apparent Michaelis constants, K{sub M}{sup App}. By contrast, NMR lineshape analysis is a powerful tool for determining microscopic rates and populations of each state in a complex binding scheme. The isolated catalytic domain of Pin1 was employed as a first step towards elucidating the reaction scheme of the full-length enzyme. A 24-residue phosphopeptide derived from the amyloid precurser protein intracellular domain (AICD) phosphorylated at Thr668 served as a biologically-relevant Pin1 substrate. Specific {sup 13}C labeling at the Pin1-targeted proline residue provided multiple reporters sensitive to individual isomer binding and on-enzyme catalysis. We have performed titration experiments and employed lineshape analysis of phosphopeptide {sup 13}C-{sup 1}H constant time HSQC spectra to determine k{sub cat}{sup cis}, k{sub cat}{sup trans}, K{sub D}{sup cis}, and K{sub D}{sup trans} for the catalytic domain of Pin1 acting on this AICD substrate. The on-enzyme equilibrium value of [E{center_dot}trans]/[E{center_dot}cis] = 3.9 suggests that the catalytic domain of Pin1 is optimized to operate on this substrate near equilibrium in the cellular context. This highlights the power of lineshape analysis for determining the microscopic parameters of enzyme catalysis, and demonstrates the feasibility of future studies of Pin1-PPIase mutants to gain insights on the catalytic mechanism of this important enzyme.

  10. Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis

    International Nuclear Information System (INIS)

    The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation, rigorous enzymatic assays of isomerization are required. However, most measures of isomerase activity require significant constraints on substrate sequence and only yield rate constants for the cis isomer, kcatcis and apparent Michaelis constants, KMApp. By contrast, NMR lineshape analysis is a powerful tool for determining microscopic rates and populations of each state in a complex binding scheme. The isolated catalytic domain of Pin1 was employed as a first step towards elucidating the reaction scheme of the full-length enzyme. A 24-residue phosphopeptide derived from the amyloid precurser protein intracellular domain (AICD) phosphorylated at Thr668 served as a biologically-relevant Pin1 substrate. Specific 13C labeling at the Pin1-targeted proline residue provided multiple reporters sensitive to individual isomer binding and on-enzyme catalysis. We have performed titration experiments and employed lineshape analysis of phosphopeptide 13C–1H constant time HSQC spectra to determine kcatcis, kcattrans, KDcis, and KDtrans for the catalytic domain of Pin1 acting on this AICD substrate. The on-enzyme equilibrium value of [E·trans]/[E·cis] = 3.9 suggests that the catalytic domain of Pin1 is optimized to operate on this substrate near equilibrium in the cellular context. This highlights the power of lineshape analysis for determining the microscopic parameters of enzyme catalysis, and demonstrates the feasibility of future studies of Pin1-PPIase mutants to gain insights on the catalytic mechanism of this important enzyme.

  11. Global Mapping of Human RNA-RNA Interactions.

    Science.gov (United States)

    Sharma, Eesha; Sterne-Weiler, Tim; O'Hanlon, Dave; Blencowe, Benjamin J

    2016-05-19

    The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing, modification, turnover, and translation. To define roles for ncRNAs, we have developed a method enabling the global-scale mapping of RNA-RNA duplexes crosslinked in vivo, "LIGation of interacting RNA followed by high-throughput sequencing" (LIGR-seq). Applying this method in human cells reveals a remarkable landscape of RNA-RNA interactions involving all major classes of ncRNA and mRNA. LIGR-seq data reveal unexpected interactions between small nucleolar (sno)RNAs and mRNAs, including those involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. LIGR-seq thus represents a powerful approach for illuminating the functions of the myriad of uncharacterized RNAs that act via base-pairing interactions. PMID:27184080

  12. Preparation of Pt-Ru hydrophobic catalysts and catalytic activities for liquid phase catalytic exchange reaction

    International Nuclear Information System (INIS)

    Pt/C and Pt-Ru/C catalysts with different ratios of Pt to Ru were synthesized, using ethylene glycol as both the dispersant and reducing agent at 1-2 MPa by microwave-assisted method. The catalysts were characterized by XRD, TEM and XPS. The mean particle sizes of the Pt/C and Pt-Ru/C catalysts were 1.9-2.0 nm. Pt and Ru existed as Pt(0), Pt(II), Pt(IV), Ru(0) and Ru(IV) for Pt-Ru/C catalysts, respectively. The face-centered cubic structure of the active mental particles would be changed upon the addition of Ru gradually. Then polytetrafluoroethylene and carbon-supported Pt and Pt-Ru catalysts were supported on foamed nickel to obtain hydrophobic catalysts. The catalytic activity was increased for liquid phase catalytic exchange (LPCE) when uniform Pt based hydrophobic catalysts was mixed into appropriate Ru. Hydrogen isotope exchange reaction occurs between hydration layer(H2O)nH+(ads)(n≥2) and D atoms due to intact water molecules being on Pt surface for LPCE. Water molecules have a tendency to dissociate to OH(ads) and H(ads) on metal Ru surface, and there is the other reaction path for Pt-Ru binary catalysts, which is probably the main reason of the increase of the catalytic activity of the hydrophobic Pt-Ru catalyst. (authors)

  13. Transfer RNA and human disease.

    Science.gov (United States)

    Abbott, Jamie A; Francklyn, Christopher S; Robey-Bond, Susan M

    2014-01-01

    Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA) genes are "hotspots" for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase), mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers), and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing). Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease. PMID:24917879

  14. The structure and function of catalytic RNAs

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Before the discovery of ribozymes,RNA had been proposed to function as a catalyst,based on the discovery that RNA folded into high-ordered structures as protein did.This hypothesis was confirmed in the 1980s,after the discovery of Tetrahymena group I intron and RNase P ribozyme.There have been about ten ribozymes identified during the past thirty years,as well as the fact that ribosomes function as ribozymes.Advances have been made in understanding the structures and functions of ribozymes,with numerous crystal structures resolved in the past years.Here we review the structure-function relationship of both small and large ribozymes,especially the structural basis of their catalysis.

  15. The structure and function of catalytic RNAs

    Institute of Scientific and Technical Information of China (English)

    WU QiJia; HUANG Lin; ZHANG Yi

    2009-01-01

    Before the discovery of ribozymes, RNA had been proposed to function as a catalyst, based on the discovery that RNA folded into high-ordered structures as protein did. This hypothesis was confirmed in the 1980s, after the discovery of Tetrahymena group I intron and RNase P ribozyme. There have been about ten ribozymes identified during the past thirty years, as well as the fact that ribosomes function as ribozymes. Advances have been made in understanding the structures and functions of ribozymes, with numerous crystal structures resolved in the past years. Here we review the structure-function re-lationship of both small and large ribozymes, especially the structural basis of their catalysis.

  16. 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

  17. Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants.

    Directory of Open Access Journals (Sweden)

    Isabel Weinheimer

    2015-03-01

    Full Text Available Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant and Caenorhabditis elegans (nematode and found that it cleaves double-stranded small interfering RNA (ds-siRNA molecules that are pivotal in the host RNA interference (RNAi pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA--mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3 produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are

  18. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

    Directory of Open Access Journals (Sweden)

    Wasik Szymon

    2010-05-01

    Full Text Available Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA

  19. RNA interference in Lepidoptera

    DEFF Research Database (Denmark)

    Terenius, Ole; Papanicolaou, Alexie; Garbutt, Jennie S.;

    2011-01-01

    Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive...... in RNAi experiments in Lepidoptera are discussed. The review also points to a need to further investigate the mechanism of RNAi in lepidopteran insects and its possible connection to the innate immune response. Our general understanding of RNAi in Lepidoptera will be further aided in the future as...

  20. RNA Catalysis, Thermodynamics and the Origin of Life

    Directory of Open Access Journals (Sweden)

    William G. Scott

    2014-04-01

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

  1. 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

  2. RNA SURVEILLANCE– AN EMERGING ROLE FOR RNA REGULATORY NETWORKS IN AGING

    OpenAIRE

    Montano, Monty; Long, Kimberly

    2010-01-01

    In this review, we describe recent advances in the field of RNA regulatory biology and relate these advances to aging science. We introduce a new term, RNA surveillance, an RNA regulatory process that is conserved in metazoans, and describe how RNA surveillance represents molecular cross-talk between two emerging RNA regulatory systems – RNA interference and RNA editing. We discuss how RNA surveillance mechanisms influence mRNA and microRNA expression and activity during lifespan. Additionall...

  3. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2

    OpenAIRE

    Aglietti, Robin A.; Floor, Stephen N.; McClendon, Chris L.; Matthew P Jacobson; Gross, John D.

    2013-01-01

    Removal of the 5′ cap structure by Dcp2 is a major step in several 5′–3′ mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base ...

  4. Alfalfa mosaic virus coat protein bridges RNA and RNA-dependent RNA polymerase in vitro.

    Science.gov (United States)

    Reichert, Vienna L; Choi, Mehee; Petrillo, Jessica E; Gehrke, Lee

    2007-07-20

    Alfalfa mosaic virus (AMV) RNA replication requires the viral coat protein (CP). AMV CP is an integral component of the viral replicase; moreover, it binds to the viral RNA 3'-termini and induces the formation of multiple new base pairs that organize the RNA conformation. The results described here suggest that AMV coat protein binding defines template selection by organizing the 3'-terminal RNA conformation and by positioning the RNA-dependent RNA polymerase (RdRp) at the initiation site for minus strand synthesis. RNA-protein interactions were analyzed by using a modified Northwestern blotting protocol that included both viral coat protein and labeled RNA in the probe solution ("far-Northwestern blotting"). We observed that labeled RNA alone bound the replicase proteins poorly; however, complex formation was enhanced significantly in the presence of AMV CP. The RNA-replicase bridging function of the AMV CP may represent a mechanism for accurate de novo initiation in the absence of canonical 3' transfer RNA signals. PMID:17400272

  5. RNA Control of HIV-1 Particle Size Polydispersity

    CERN Document Server

    Faivre-Moskalenko, Cendrine; Thomas, Audrey; Tartour, Kevin; Beck, Yvonne; Iazykov, Maksym; Danial, John; Lourdin, Morgane; Muriaux, Delphine; Castelnovo, Martin

    2014-01-01

    HIV-1, an enveloped RNA virus, produces viral particles that are known to be much more heterogeneous in size than is typical of non-enveloped viruses. We present here a novel strategy to study HIV-1 Viral Like Particles (VLP) assembly by measuring the size distribution of these purified VLPs and subsequent viral cores thanks to Atomic Force Microscopy imaging and statistical analysis. This strategy allowed us to identify whether the presence of viral RNA acts as a modulator for VLPs and cores size heterogeneity in a large population of particles. These results are analyzed in the light of a recently proposed statistical physics model for the self-assembly process. In particular, our results reveal that the modulation of size distribution by the presence of viral RNA is qualitatively reproduced, suggesting therefore an entropic origin for the modulation of RNA uptake by the nascent VLP.

  6. RNA Viruses and RNAi: Quasispecies Implications for Viral Escape

    Directory of Open Access Journals (Sweden)

    John B. Presloid

    2015-06-01

    Full Text Available Due to high mutation rates, populations of RNA viruses exist as a collection of closely related mutants known as a quasispecies. A consequence of error-prone replication is the potential for rapid adaptation of RNA viruses when a selective pressure is applied, including host immune systems and antiviral drugs. RNA interference (RNAi acts to inhibit protein synthesis by targeting specific mRNAs for degradation and this process has been developed to target RNA viruses, exhibiting their potential as a therapeutic against infections. However, viruses containing mutations conferring resistance to RNAi were isolated in nearly all cases, underlining the problems of rapid viral evolution. Thus, while promising, the use of RNAi in treating or preventing viral diseases remains fraught with the typical complications that result from high specificity of the target, as seen in other antiviral regimens.

  7. Development of a Universal RNA Beacon for Exogenous Gene Detection

    OpenAIRE

    Guo, Yuanjian; Lu, Zhongju; Cohen, Ira Stephen; Scarlata, Suzanne

    2015-01-01

    RNA beacon technology is a promising method to detect and separate cells expressing a particular gene, but developing a successful, specific beacon can take months and in some cases is impossible. This study reports an off-the-shelf universal beacon that decreases the time and cost of applying beacon technology to select any living cell population transfected with an exogenous gene.

  8. Competing to destroy: a fight between two RNA-degradation systems

    DEFF Research Database (Denmark)

    Thon, Genevieve

    2008-01-01

    The Argonaute-1 (Ago1) protein bound to small interfering RNAs (siRNAs) directs heterochromatin formation in fission yeast. A high-throughput sequencing approach reveals that the composition of the Ago1-bound siRNA population is sensitive to the noncanonical poly(A) polymerase Cid14, indicating...... that the RNA-interference and Cid14-TRAMP RNA-degradation pathways compete for substrates in fission yeast....

  9. RNA regulons and the RNA-protein interaction network

    OpenAIRE

    Imig, J.; Kanitz, A.; Gerber, AP

    2012-01-01

    The development of genome-wide analysis tools has prompted global investigation of the gene expression program, revealing highly coordinated control mechanisms that ensure proper spatiotemporal activity of a cell's macromolecular components. With respect to the regulation of RNA transcripts, the concept of RNA regulons, which – by analogy with DNA regulons in bacteria – refers to the coordinated control of functionally related RNA molecules, has emerged as a unifying theory that describes the...

  10. RNA-RNA interaction prediction based on multiple sequence alignments

    CERN Document Server

    Li, Andrew X; Qin, Jing; Reidys, Christian M

    2010-01-01

    Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes for pairs of RNA sequences. These algorithms and the biological requirement of more reliable interactions motivate to utilize the additional information contained in multiple sequence alignments and to generalize the above framework to the partition function and base pairing probabilities for multiple sequence alignments.

  11. Inhibition of miR-21 in glioma cells using catalytic nucleic acids.

    Science.gov (United States)

    Belter, Agnieszka; Rolle, Katarzyna; Piwecka, Monika; Fedoruk-Wyszomirska, Agnieszka; Naskręt-Barciszewska, Mirosława Z; Barciszewski, Jan

    2016-01-01

    Despite tremendous efforts worldwide, glioblastoma multiforme (GBM) remains a deadly disease for which no cure is available and prognosis is very bad. Recently, miR-21 has emerged as a key omnipotent player in carcinogenesis, including brain tumors. It is recognized as an indicator of glioma prognosis and a prosperous target for anti-tumor therapy. Here we show that rationally designed hammerhead ribozymes and DNAzymes can target miR-21 and/or its precursors. They decrease miR-21 level, and thus silence this oncomiR functions. We demonstrated that anti-miRNA catalytic nucleic acids show a novel terrific arsenal for specific and effective combat against diseases with elevated cellular miR-21 content, such as brain tumors. PMID:27079911

  12. Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario.

    Science.gov (United States)

    Šponer, Judit E; Šponer, Jiří; Nováková, Olga; Brabec, Viktor; Šedo, Ondrej; Zdráhal, Zbyněk; Costanzo, Giovanna; Pino, Samanta; Saladino, Raffaele; Di Mauro, Ernesto

    2016-03-01

    50 years after the historical Miller-Urey experiment, the formamide-based scenario is perhaps the most powerful concurrent hypothesis for the origin of life on our planet besides the traditional HCN-based concept. The information accumulated during the last 15 years in this topic is astonishingly growing and nowadays the formamide-based model represents one of the most complete and coherent pathways leading from simple prebiotic precursors up to the first catalytically active RNA molecules. In this work, we overview the major events of this long pathway that have emerged from recent experimental and theoretical studies, mainly concentrating on the mechanistic, methodological, and structural aspects of this research. PMID:26807661

  13. Indian populations

    CERN Multimedia

    Spahni,J

    1974-01-01

    Le Prof. J.C. Spahni qui a parcouru les Andes, Vénezuela etc. parle de ses expériences et connaissances qu'il a vécu au cours des 14 ans parmi les populations indiennes de la Cordillière des Andes. Il a ramené des objets artisanals indiens lesquels l'auditoire peut acquérir. L'introduction-conférence est suivi d'un film, commenté par lui-même; après l'entracte il y un débat-dialogue avec le public.

  14. Population geography.

    Science.gov (United States)

    Nash, A

    1994-03-01

    Population geographers are involved in contemporary policy issues, the production of quality work, and successful communication of research findings. This article reviewed some contributions population geographers have made to the understanding of the geographic impact of aging and the consequences of migration. Geographers have come late to the study of aging and have focused primarily on four main policy issues: 1) fertility decline, 2) housing demography, 3) aged patterns of housing and migration, and 4) government policy. Fertility decline research has highlighted information diffusion theories for fertility decline by researchers such as Zelinsky, Skeldon, and Noin. Changes in attitudes and the removal on constraints has been examined by Woods. Residential mobility studies have been the focus of researchers such as Gober, Moore, and Clark, and Myers. Regional labor markets and the movement of the "baby boom" through the life course have been examined by Miron, Plane and Rogerson, and Clout, who studied the empty nesters and the movement out of suburbia. Private residential housing has increased for the elderly in England and Wales (Hamnett and Mullings), and seasonal migration of Minnesotans results in lost sales revenues and high health and social costs for those too ill to travel (Craig). Geographers have not accomplished a significant thrust into the literature on demographic aging. Contributions to the transnational and international literature have resulted in internal migration studies by Clout on "counterurbanization" in northwestern industrial Europe, while Fielding, Baltensperger, Marchand and Scott, and Jones have examined the continuing rural-urban migration. The loss of urban population has been associated with inner city problems, the impact of labor supply and market demand, and the revenue and health care consequences in the work of Champion, Gibson, and Champion and Illeris, and Craig. Impacts are felt differently by geographic location, and

  15. Improved catalytic activity of laser generated bimetallic and trimetallic nanoparticles.

    Science.gov (United States)

    Singh, Rina; Soni, R K

    2014-09-01

    We report synthesis of silver nanoparticles, bimetallic (Al2O3@Ag) nanoparticles and trimetallic (Al2O3@AgAu) nanoparticles by nanosecond pulse laser ablation (PLA) in deionized water. Two-step laser ablation methodologies were adopted for the synthesis of bi- and tri-metallic nanoparticles. In this method a silver or gold target was ablated in colloidal solution of γ-alumina nanoparticles prepared by PLA. The TEM image analysis of bimetallic and trimetallic particles reveals deposition of fine silver particles and Ag-Au alloy particles, respectively, on large alumina particles. The laser generated nanoparticles were tested for catalytic reduction of 4-nitrophenol to 4-aminophenol and showed excellent catalytic behaviour. The catalytic rate was greatly improved by incorporation of additional metal in silver nanoparticles. The catalytic efficiency of trimetallic Al2O3@AgAu for reduction of 4-nitrophenol to 4-aminophenol was remarkably enhanced and the catalytic reaction was completed in just 5 sec. Even at very low concentration, both Al2O3@Ag nanoparticles and Al2O3@AgAu nanoparticles showed improved rate of catalytic reduction than monometallic silver nanoparticles. Our results demonstrate that alumina particles in the solution not only provide the active sites for particle dispersion but also improve the catalytic activity. PMID:25924343

  16. Numerical Study of Passive Catalytic Recombiner for Hydrogen Mitigation

    Directory of Open Access Journals (Sweden)

    Pavan K Sharma

    2010-10-01

    Full Text Available A significant amount of hydrogen is expected to be released within the containment of a water cooled power reactor after a severe accident. To reduce the risk of deflagration/detonation various means for hydrogen control have been adopted all over the world. Passive catalytic recombiner with vertical flat catalytic plate is one of such hydrogen mitigating device. Passive catalytic recombiners are designed for the removal of hydrogen generated in order to limit the impact of possible hydrogen combustion. Inside a passive catalytic recombiner, numerous thin steel sheets coated with catalyst material are vertically arranged at the bottom opening of a sheet metal housing forming parallel flow channels for the surrounding gas atmosphere. Already below conventional flammability limits, hydrogen and oxygen react exothermally on the catalytic surfaces forming harmless steam. Detailed numerical simulations and experiments are required for an in-depth knowledge of such plate type catalytic recombiners. Specific finite volume based in-house CFD code has been developed to model and analyse the working of these recombiner. The code has been used to simulate the recombiner device used in the Gx-test series of Battelle-Model Containment (B-MC experiments. The present paper briefly describes the working principle of such passive catalytic recombiner and salient feature of the CFD model developed at Bhabha Atomic Research Centre (BARC. Finally results of the calculations and comparison with existing data are discussed.

  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. Structure of the catalytic domain of the hepatitis C virus NS2-3 protease

    Energy Technology Data Exchange (ETDEWEB)

    Lorenz,I.; Marcotrigiano, J.; Dentzer, T.; Rice, C.

    2006-01-01

    Hepatitis C virus is a major global health problem affecting an estimated 170 million people worldwide. Chronic infection is common and can lead to cirrhosis and liver cancer. There is no vaccine available and current therapies have met with limited success. The viral RNA genome encodes a polyprotein that includes two proteases essential for virus replication. The NS2-3 protease mediates a single cleavage at the NS2/NS3 junction, whereas the NS3-4A protease cleaves at four downstream sites in the polyprotein. NS3-4A is characterized as a serine protease with a chymotrypsin-like fold, but the enzymatic mechanism of the NS2-3 protease remains unresolved. Here we report the crystal structure of the catalytic domain of the NS2-3 protease at 2.3 Angstroms resolution. The structure reveals a dimeric cysteine protease with two composite active sites. For each active site, the catalytic histidine and glutamate residues are contributed by one monomer, and the nucleophilic cysteine by the other. The carboxy-terminal residues remain coordinated in the two active sites, predicting an inactive post-cleavage form. Proteolysis through formation of a composite active site occurs in the context of the viral polyprotein expressed in mammalian cells. These features offer unexpected insights into polyprotein processing by hepatitis C virus and new opportunities for antiviral drug design.

  19. RNA-Dependent RNA Polymerase 6 Is Required for Efficient hpRNA-Induced Gene Silencing in Plants

    OpenAIRE

    Harmoko, Rikno; Fanata, Wahyu Indra Duwi; Yoo, Jae Yong; Ko, Ki Seong; Rim, Yeong Gil; Uddin, Mohammad Nazim; Siswoyo, Tri Agus; Lee, Seung Sik; Kim, Dool Yi; Lee, Sang Yeol; Lee, Kyun Oh

    2013-01-01

    In plants, transgenes with inverted repeats are used to induce efficient RNA silencing, which is also frequently induced by highly transcribed sense transgenes. RNA silencing induced by sense transgenes is dependent on RNA-dependent RNA polymerase 6 (RDR6), which converts single-stranded (ss) RNA into double-stranded (ds) RNA. By contrast, it has been proposed that RNA silencing induced by self-complementary hairpin RNA (hpRNA) does not require RDR6, because the hpRNA can directly fold back o...

  20. Use of chemical modification and mass spectrometry to identify substrate-contacting sites in proteinaceous RNase P, a tRNA processing enzyme.

    Science.gov (United States)

    Chen, Tien-Hao; Tanimoto, Akiko; Shkriabai, Nikoloz; Kvaratskhelia, Mamuka; Wysocki, Vicki; Gopalan, Venkat

    2016-06-20

    Among all enzymes in nature, RNase P is unique in that it can use either an RNA- or a protein-based active site for its function: catalyzing cleavage of the 5'-leader from precursor tRNAs (pre-tRNAs). The well-studied catalytic RNase P RNA uses a specificity module to recognize the pre-tRNA and a catalytic module to perform cleavage. Similarly, the recently discovered proteinaceous RNase P (PRORP) possesses two domains - pentatricopeptide repeat (PPR) and metallonuclease (NYN) - that are present in some other RNA processing factors. Here, we combined chemical modification of lysines and multiple-reaction monitoring mass spectrometry to identify putative substrate-contacting residues in Arabidopsis thaliana PRORP1 (AtPRORP1), and subsequently validated these candidate sites by site-directed mutagenesis. Using biochemical studies to characterize the wild-type (WT) and mutant derivatives, we found that AtPRORP1 exploits specific lysines strategically positioned at the tips of it's V-shaped arms, in the first PPR motif and in the NYN domain proximal to the catalytic center, to bind and cleave pre-tRNA. Our results confirm that the protein- and RNA-based forms of RNase P have distinct modules for substrate recognition and cleavage, an unanticipated parallel in their mode of action. PMID:27166372