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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. 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.

  7. 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...

  8. 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.

  9. Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme

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    Shechner, David M.; Grant, Robert A.; Bagby, Sarah C.; Koldobskaya, Yelena; Piccirilli, Joseph A.; Bartel, David P.; (MIT); (HHMI); (UC)

    2010-09-02

    Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases.

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

    Science.gov (United States)

    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

  11. 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...

  12. 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.

  13. Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme.

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    Krasovska, Maryna V; Sefcikova, Jana; Réblová, Kamila; Schneider, Bohdan; Walter, Nils G; Sponer, Jirí

    2006-07-15

    The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.

  14. Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

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    Kireeva Maria L

    2012-06-01

    Full Text Available Abstract Background During elongation, multi-subunit RNA polymerases (RNAPs cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile “trigger loop” of the catalytic subunit closes on the nucleoside triphosphate (NTP substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the “bridge helix” that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing. Results All atom molecular dynamics simulations of Thermus thermophilus (Tt RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as “switch” residues trade atomic contacts (ion pairs or hydrogen bonds in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a

  15. 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.

  16. Library preparation for highly accurate population sequencing of RNA viruses

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    Acevedo, Ashley; Andino, Raul

    2015-01-01

    Circular resequencing (CirSeq) is a novel technique for efficient and highly accurate next-generation sequencing (NGS) of RNA virus populations. The foundation of this approach is the circularization of fragmented viral RNAs, which are then redundantly encoded into tandem repeats by ‘rolling-circle’ reverse transcription. When sequenced, the redundant copies within each read are aligned to derive a consensus sequence of their initial RNA template. This process yields sequencing data with error rates far below the variant frequencies observed for RNA viruses, facilitating ultra-rare variant detection and accurate measurement of low-frequency variants. Although library preparation takes ~5 d, the high-quality data generated by CirSeq simplifies downstream data analysis, making this approach substantially more tractable for experimentalists. PMID:24967624

  17. The catalytic and the RNA subunits of human telomerase are required to immortalize equid primary fibroblasts.

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    Vidale, Pamela; Magnani, Elisa; Nergadze, Solomon G; Santagostino, Marco; Cristofari, Gael; Smirnova, Alexandra; Mondello, Chiara; Giulotto, Elena

    2012-10-01

    Many human primary somatic cells can be immortalized by inducing telomerase activity through the exogenous expression of the human telomerase catalytic subunit (hTERT). This approach has been extended to the immortalization of cell lines from several mammals. Here, we show that hTERT expression is not sufficient to immortalize primary fibroblasts from three equid species, namely donkey, Burchelli's zebra and Grevy's zebra. In vitro analysis of a reconstituted telomerase composed by hTERT and an equid RNA component of telomerase (TERC) revealed a low activity of this enzyme compared to human telomerase, suggesting a low compatibility of equid and human telomerase subunits. This conclusion was also strengthened by comparison of human and equid TERC sequences, which revealed nucleotide differences in key regions for TERC and TERT interaction. We then succeeded in immortalizing equid fibroblasts by expressing hTERT and hTERC concomitantly. Expression of both human telomerase subunits led to telomerase activity and telomere elongation, indicating that human telomerase is compatible with the other equid telomerase subunits and proteins involved in telomere metabolism. The immortalization procedure described herein could be extended to primary cells from other mammals. The availability of immortal cells from endangered species could be particularly useful for obtaining new information on the organization and function of their genomes, which is relevant for their preservation.

  18. Phosphoinositide-3-kinase, catalytic, alpha polypeptide RNA interference inhibits growth of colon cancer cell SW948

    Institute of Scientific and Technical Information of China (English)

    Wen-Sheng Huang; Tian-Bao Wang; Yao He; Yu-Jun Chen; Shi-Long Zhong; Min Tan

    2012-01-01

    AIM:To investigate the gene knock-down effect by the phosphoinositide-3-kinase,catalytic,alpha polypeptide (PIK3CA)-targeted double-stranded RNA (dsRNA) and its effect on cell proliferation and cycle distribution in SW948.METHODS:Two PIK3CA-targeted dsRNAs were constructed and transfected into SW948 cells.Transfections were performed using lipofectamineTM 2000.The transfection effectiveness was calculated basing on the rate of fluorescence cell of SW948 at 6 h after transfection.Total messenger RNA was extracted from these cells using the RNeasy kit,and semiquantitative reverse transcription polymerase chain reaction was performed to detect the down-regulation of PIK3CA,AKT-1,MYC,and CCND1 gene expression.Cells were harvested,proteins were resolved,and western blot was employed to detect the expression levels of PIK3CA,AKT1,MYC,and CCND1 gene.Cell proliferation was assessed by 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide assay and the inhibition rate was calculated.Soft agar colony formation assay was performed basing on colonies greater than 60 μm in diameter at ×100magnification.The effect on cell cycle distribution and apoptosis was assessed by flow cytometry.All experiments were performed in triplicate.RESULTS:Green fluorescence was observed in SW948cell transfected with plasmid Pgenesil-1,and the transfection effectiveness was about 65%.Forty-eight hours post-transfection,mRNA expression of PIK3CA in SW948 cells was 0.51 ± 0.04 vs 0.49 ± 0.03 vs 0.92± 0.01 vs 0.93 ± 0.03 (P =0.001) in Pgenesil-CA1,Pgenesil-CA2,negative and blank group respectively.mRNA expression of AKT1 was 0.50 ± 0.03 vs 0.48± 0.01 vs 0.93 ± 0.04 vs 0.92 ± 0.02 (P =0.000) in Pgenesil-CA1,Pgenesil-CA2,negative and blank group respectively,mRNA expression of MYC was 0.49 ± 0.01vs 0.50 ± 0.04 vs 0.90 ± 0.02 vs 0.91 ± 0.03 (P =0.001) in the four groups respectively,mRNA expression of CCND1 was 0.45 ± 0.02 vs 0.51 ± 0.01 vs 0.96± 0.03 vs 0.98 ± 0.01 (P =0

  19. 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...

  20. 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

  1. 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

  2. Dynamics of dsRNA mycoviruses in black Aspergillus population.

    NARCIS (Netherlands)

    Diepeningen, van A.D.; Debets, A.J.M.; Hoekstra, R.F.

    2006-01-01

    Approximately 10% of all examined 668 representatives of black Aspergillus species, independent of worldwide location, were infected with double-stranded RNA (dsRNA) mycoviruses. These isometric viruses (25-40 nm diameter) contained a variety of often multiple segments of different dsRNA sizes rangi

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

    Science.gov (United States)

    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

  4. 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 ...

  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. 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

  7. Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA.

    Science.gov (United States)

    Sunita, S; Zhenxing, H; Swaathi, J; Cygler, Miroslaw; Matte, Allan; Sivaraman, J

    2006-06-16

    Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine (Psi) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E.coli RluF at 2.6A resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of Psi-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.

  8. Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA

    Energy Technology Data Exchange (ETDEWEB)

    Sunita,S.; Zhenxing, H.; Swaathi, J.; Cygler, M.; Matte, A.; Sivaraman, J.

    2006-01-01

    Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine ({psi}) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E. coli RluF at 2.6 Angstroms resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of {psi}-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.

  9. Steady-state NTPase activity of Dengue virus NS3: number of catalytic sites, nucleotide specificity and activation by ssRNA.

    Directory of Open Access Journals (Sweden)

    J Jeremías Incicco

    Full Text Available Dengue virus nonstructural protein 3 (NS3 unwinds double stranded RNA driven by the free energy derived from the hydrolysis of nucleoside triphosphates. This paper presents the first systematic and quantitative characterization of the steady-state NTPase activity of DENV NS3 and their interaction with ssRNA. Substrate curves for ATP, GTP, CTP and UTP were obtained, and the specificity order for these nucleotides - evaluated as the ratio (kcat /KM - was GTP[Formula: see text]ATP[Formula: see text]CTP [Formula: see text] UTP, which showed that NS3 have poor ability to discriminate between different NTPs. Competition experiments between the four substrates indicated that all of them are hydrolyzed in one and the same catalytic site of the enzyme. The effect of ssRNA on the ATPase activity of NS3 was studied using poly(A and poly(C. Both RNA molecules produced a 10 fold increase in the turnover rate constant (kcat and a 100 fold decrease in the apparent affinity (KM for ATP. When the ratio [RNA bases]/[NS3] was between 0 and [Formula: see text]20 the ATPase activity was inhibited by increasing both poly(A and poly(C. Using the theory of binding of large ligands (NS3 to a one-dimensional homogeneous lattice of infinite length (RNA we tested the hypothesis that inhibition is the result of crowding of NS3 molecules along the RNA lattices. Finally, we discuss why this hypothesis is consistent with the idea that the ATPase catalytic cycle is tightly coupled to the movement of NS3 helicase along the RNA.

  10. 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

  11. Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli.

    Science.gov (United States)

    Del Campo, Mark; Ofengand, James; Malhotra, Arun

    2004-02-01

    Escherichia coli pseudouridine synthase RluD makes pseudouridines 1911, 1915, and 1917 in the loop of helix 69 in 23S RNA. These are the most highly conserved ribosomal pseudouridines known. Of 11 pseudouridine synthases in E. coli, only cells lacking RluD have severe growth defects and abnormal ribosomes. We have determined the 2.0 A structure of the catalytic domain of RluD (residues 77-326), the first structure of an RluA family member. The catalytic domain folds into a mainly antiparallel beta-sheet flanked by several loops and helices. A positively charged cleft that presumably binds RNA leads to the conserved Asp 139. The RluD N-terminal S4 domain, connected by a flexible linker, is disordered in our structure. RluD is very similar in both catalytic domain structure and active site arrangement to the pseudouridine synthases RsuA, TruB, and TruA. We identify five sequence motifs, two of which are novel, in the RluA, RsuA, TruB, and TruA families, uniting them as one superfamily. These results strongly suggest that four of the five families of pseudouridine synthases arose by divergent evolution. The RluD structure also provides insight into its multisite specificity.

  12. 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.

  13. Ribosomal RNA gene diversity, effective population size, and evolutionary longevity in asexual glomeromycota.

    Science.gov (United States)

    Vankuren, Nicholas W; den Bakker, Henk C; Morton, Joseph B; Pawlowska, Teresa E

    2013-01-01

    Arbuscular mycorrhizal fungi (phylum Glomeromycota) are among the oldest and most successful symbionts of land plants. With no evidence of sexual reproduction, their evolutionary success is inconsistent with the prediction that asexual taxa are vulnerable to extinction due to accumulation of deleterious mutations. To explore why Glomeromycota defy this prediction, we studied ribosomal RNA (rRNA) gene evolution in the Claroideoglomus lineage and estimated effective population size, N(e) , in C. etunicatum. We found that rRNA genes of these fungi exhibit unusual and complex patterns of molecular evolution. In C. etunicatum, these patterns can be collectively explained by an unexpectedly large N(e) combined with imperfect genome-wide and population-level rRNA gene repeat homogenization. The mutations accumulated in rRNA gene sequences indicate that natural selection is effective at purging deleterious mutations in the Claroideoglomus lineage, which is also consistent with the large N(e) of C. etunicatum. We propose that in the near absence of recombination, asexual reproduction involving massively multinucleate spores typical for Glomeromycota is responsible for the improved efficacy of selection relative to drift. We postulate that large effective population sizes contribute to the evolutionary longevity of Glomeromycota.

  14. 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

  15. Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq.

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    Magdy S Alabady

    Full Text Available We describe restriction site associated RNA sequencing (RARseq, an RNAseq-based genotype by sequencing (GBS method. It includes the construction of RNAseq libraries from double stranded cDNA digested with selected restriction enzymes. To test this, we constructed six single- and six-dual-digested RARseq libraries from six F2 pitcher plant individuals and sequenced them on a half of a Miseq run. On average, the de novo approach of population genome analysis detected 544 and 570 RNA SNPs, whereas the reference transcriptome-based approach revealed an average of 1907 and 1876 RNA SNPs per individual, from single- and dual-digested RARseq data, respectively. The average numbers of RNA SNPs and alleles per loci are 1.89 and 2.17, respectively. Our results suggest that the RARseq protocol allows good depth of coverage per loci for detecting RNA SNPs and polymorphic loci for population genomics and mapping analyses. In non-model systems where complete genomes sequences are not always available, RARseq data can be analyzed in reference to the transcriptome. In addition to enriching for functional markers, this method may prove particularly useful in organisms where the genomes are not favorable for DNA GBS.

  16. Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m³U1498) from crystal and solution structures.

    Science.gov (United States)

    Zhang, Heng; Wan, Hua; Gao, Zeng-Qiang; Wei, Yong; Wang, Wen-Jia; Liu, Guang-Feng; Shtykova, Eleonora V; Xu, Jian-Hua; Dong, Yu-Hui

    2012-11-01

    RsmE is the founding member of a new RNA methyltransferase (MTase) family responsible for methylation of U1498 in 16S ribosomal RNA in Escherichia coli. It is well conserved across bacteria and plants and may play an important role in ribosomal intersubunit communication. The crystal structure in monomer showed that it consists of two distinct but structurally related domains: the PUA (pseudouridine synthases and archaeosine-specific transglycosylases)-like RNA recognition and binding domain and the conserved MTase domain with a deep trefoil knot. Analysis of small-angle X-ray scattering data revealed that RsmE forms a flexible dimeric conformation that may be essential for substrate binding. The S-adenosyl-l-methionine (AdoMet)-binding characteristic determined by isothermal titration calorimetry suggested that there is only one AdoMet molecule bound in the subunit of the homodimer. In vitro methylation assay of the mutants based on the RsmE-AdoMet-uridylic acid complex model showed key residues involved in substrate binding and catalysis. Comprehensive comparisons of RsmE with closely related MTases, combined with the biochemical experiments, indicated that the MTase domain of one subunit in dimeric RsmE is responsible for binding of one AdoMet molecule and catalytic process while the PUA-like domain in the other subunit is mainly responsible for recognition of one substrate molecule (the ribosomal RNA fragment and ribosomal protein complex). The methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. In general, our study provides new information on the structure-function relationship of RsmE and thereby suggests a novel catalytic mechanism.

  17. 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

  18. A deep analysis of the small non-coding RNA population in Schistosoma japonicum eggs.

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    Pengfei Cai

    Full Text Available BACKGROUND: Schistosoma japonicum is a parasitic flatworm that causes zoonotic schistosomiasis. The typical outcome of schistosomiasis is hepatic granuloma and fibrosis, which is primarily induced by soluble egg-derived antigens. Although schistosomal eggs represent an important pathogenic stage to the host, the biology of this critical stage is largely unknown. We previously investigated the expression profiles of sncRNAs during different developmental stages of this parasite. However, using small RNA extracted from egg-deposited liver tissues generated limited information about sncRNAs in eggs. Here, we characterized the complete small RNAome in this stage of the parasite after optimization of RNA purification. METHODOLOGY AND PRINCIPAL FINDINGS: A library, SjE, was constructed with the small RNA extracted from S. japonicum eggs and subjected to high-throughput sequencing. The data were depicted by comprehensive bioinformatic analysis to explore the expression features of sncRNAs in the egg stage. MicroRNAs accounted for about one quarter of the total small RNA population in this stage, with a strongly biased expression pattern of certain miRNA family members. Sja-miR-71, sja-miR-71-5p, and sja-miR-36-3p were suggested to play important roles in embryo development. A panel of transfer RNA fragments (tRFs precisely processed from the 5' end of mature tRNAs was identified for the first time, which represented a strong egg stage-biased expression. The tRNA-Ala derived small RNAs were the most highly expressed Sj-tRFs in eggs. Further, the expression of siRNAs from 29 types of well-defined transposable elements (TEs was observed to be relatively stable among different developmental stages. CONCLUSIONS AND SIGNIFICANCE: In this study, we characterized the sncRNA profile in the egg stage of S. japonicum. Featured expression of sncRNAs, especially the tRNA-derived small RNAs, was identified, which was further compared with that of other developmental

  19. Genetic Diversity in Populations of Sepiella maindroni Using 16S rRNA Gene Sequence Analysis

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Part of the 16S rRNA gene is amplified with PCR and sequenced for 5 populations of common Chinese cuttlefish Sepiella maindroni: three from the South China Sea, one from East China Sea and one from Japan. The result shows that a total of 5 nucleotide positions are found to have gaps or insertions of base pairs among these individuals, and 13 positions are examined to be variable in all the sequences, which range from 494 to 509 base pairs. All of the individuals are grouped into 7 haplotypes (h1-h7). No marked genetic difference is observed among those populations. All of the individuals from Nagasaki belong to h1 and the h3 haplotype is found only in the coastal waters of China. AG transition in Nucleotide 255 is suggested to be taken as a kind of genetic marker to identify the populations distributed in East-South China Sea and the Nagasaki waters of Japan.

  20. Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?

    Science.gov (United States)

    Fernández-Calero, Tamara; Cabrera-Cabrera, Florencia; Ehrlich, Ricardo; Marín, Mónica

    2016-01-01

    Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process. PMID:26901226

  1. Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli.

    Science.gov (United States)

    Sivaraman, J; Iannuzzi, Pietro; Cygler, Miroslaw; Matte, Allan

    2004-01-01

    Pseudouridine (5-beta-D-ribofuranosyluracil, Psi) is the most commonly found modified base in RNA. Conversion of uridine to Psi is performed enzymatically in both prokaryotes and eukaryotes by pseudouridine synthases (EC 4.2.1.70). The Escherichia coli Psi-synthase RluD modifies uridine to Psi at positions 1911, 1915 and 1917 within 23S rRNA. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis. Here, we report the crystal structure of the catalytic module of RluD (residues 68-326; DeltaRluD) refined at 1.8A to a final R-factor of 21.8% (R(free)=24.3%). DeltaRluD is a monomeric enzyme having an overall mixed alpha/beta fold. The DeltaRluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic sub-domain. The catalytic sub-domain of DeltaRluD has a similar fold as in TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue superposing in all four structures. Superposition of the crystal structure of TruB bound to a T-stem loop with RluD reveals that similar RNA-protein interactions for the flipped-out uridine base would exist in both structures, implying that base-flipping is necessary for catalysis. This observation also implies that the specificity determinants for site-specific RNA-binding and recognition likely reside in parts of RluD beyond the active site.

  2. Concerning RNA-guided gene drives for the alteration of wild populations

    Science.gov (United States)

    Esvelt, Kevin M; Smidler, Andrea L; Catteruccia, Flaminia; Church, George M

    2014-01-01

    Gene drives may be capable of addressing ecological problems by altering entire populations of wild organisms, but their use has remained largely theoretical due to technical constraints. Here we consider the potential for RNA-guided gene drives based on the CRISPR nuclease Cas9 to serve as a general method for spreading altered traits through wild populations over many generations. We detail likely capabilities, discuss limitations, and provide novel precautionary strategies to control the spread of gene drives and reverse genomic changes. The ability to edit populations of sexual species would offer substantial benefits to humanity and the environment. For example, RNA-guided gene drives could potentially prevent the spread of disease, support agriculture by reversing pesticide and herbicide resistance in insects and weeds, and control damaging invasive species. However, the possibility of unwanted ecological effects and near-certainty of spread across political borders demand careful assessment of each potential application. We call for thoughtful, inclusive, and well-informed public discussions to explore the responsible use of this currently theoretical technology. DOI: http://dx.doi.org/10.7554/eLife.03401.001 PMID:25035423

  3. 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

  4. 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

  5. Mechanism of phenylalanyl-tRNA synthetase of Escherichia coli K. 10. Modulation of catalytic properties by magnesium.

    Science.gov (United States)

    Pimmer, J; Holler, E

    1979-08-21

    The association of phenylalanylptRNA and Mg2+ follows a biphasic concentration dependence as indicated by the active site directed fluorescent indicator 2-p-toluidinyl-naphthalene-6-sulfonate. The macroscopic dissociation constants are 0.16 +/- 0.03 and 4.1 +/- mM. The effect of Mg2+ on the association of enzyme and MgATP, on the synergistic binding of MgATP and L-phenylalaninol, and on the pre-steady-state synthesis and pyrophosphorolysis of the enzyme-phenylalanyladenylate complex in the absence and the presence of tRNA Phe has been measured by established equilibrium and stopped-flow techniques using 2-p-toluidinylnaphthalene-6-sulfonate. At 10 mM Mg2+, the association of enzyme and MgATP is biphasic with dissociation constants of 0.25 +/- 0.03 and 9.1 +/- 1.7 mM. At 2 mM Mg2+, a single dissociation constant of 5.0 +/- 0.5 mM is indicated. The coupling constant of the synergistic reaction is 15 at 1 mM Mg2+ and 290 at 10 mM Mg2+. The Hill constant of the sigmoidal dependence is 3.6. The strengthening of the synergism is believed to reflect a Mg2+-dependent coupling of the synergistic reactions at the two active sites of the enzyme, the coupling being negligible at 1 mM and maximal at 10 mM Mg2+. The pre-steady-state rate of adenylate synthesis is accelerated by the presence of Mg2+. The effect is to decrease the value of the Michaelis-Menten constant of MgATP. Another effect is to increase the rate constant when tRNA Phe is present. At subsaturating [MgATP], the [Mg2+] dependence of the observed rate constant is hyperbolical in the absence and sigmoidal (Hill constant, 3.5) in the presence of tRNA Phe. The rate of the pyrophosphorolysis is enhanced by a decrease of the Michaelis-Menten constant of MgPPi. The effects on the thermodynamics and kinetics parallel the occupancy of the low-affinity Mg2+-binding sites of the enzyme. PMID:224916

  6. 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

  7. Predicting RNA-RNA Interactions Using RNAstructure.

    Science.gov (United States)

    DiChiacchio, Laura; Mathews, David H

    2016-01-01

    RNA-RNA binding is a required step for many regulatory and catalytic processes in the cell. Identifying RNA-RNA hybridization sites is challenging because of the competition between intramolecular and intermolecular structure formation. A complete picture of RNA-RNA binding includes an understanding of single-stranded folding and binding site accessibility, and is strongly concentration-dependent. This chapter provides guidance for using RNAstructure to predict RNA-RNA binding sites and RNA-RNA structures, utilizing free energy minimization and partition function calculations. RNAstructure is freely available at http://rna.urmc.rochester.edu/RNAstructure.html . PMID:27665592

  8. MicroRNA Genetic Variation: From Population Analysis to Functional Implications of Three Allele Variants Associated with Cancer.

    Science.gov (United States)

    Torruella-Loran, Ignasi; Laayouni, Hafid; Dobon, Begoña; Gallego, Alicia; Balcells, Ingrid; Garcia-Ramallo, Eva; Espinosa-Parrilla, Yolanda

    2016-10-01

    Nucleotide variants in microRNA regions have been associated with disease; nevertheless, few studies still have addressed the allele-dependent effect of these changes. We studied microRNA genetic variation in human populations and found that while low-frequency variants accumulate indistinctly in microRNA regions, the mature and seed regions tend to be depleted of high-frequency variants, probably as a result of purifying selection. Comparison of pairwise population fixation indexes among regions showed that the seed had higher population fixation indexes than the other regions, suggesting the existence of local adaptation in the seed region. We further performed functional studies of three microRNA variants associated with cancer (rs2910164:C > G in MIR146A, rs11614913:C > T in MIR196A2, and rs3746444:A > G in both MIR499A and MIR499B). We found differences in the expression between alleles and in the regulation of several genes involved in cancer, such as TP53, KIT, CDH1, CLH, and TERT, which may result in changes in regulatory networks related to tumorigenesis. Furthermore, luciferase-based assays showed that MIR499A could be regulating the cadherin CDH1 and the cell adhesion molecule CLH1 in an allele-dependent fashion. A better understanding of the effect of microRNA variants associated with disease could be key in our way to a more personalized medicine.

  9. 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;

    2015-01-01

    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 reproducible when the same...... methods were used. Conclusions: Altogether, we have shown that conclusions from population studies based on 16S rRNA gene sequencing need to be made with caution. Overcoming the constraints, we believe that population studies can give new research possibilities for e.g. interaction studies, identification......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...

  10. Requirement of catalytically active Tyk2 and accessory signals for the induction of TRAIL mRNA by IFN-beta.

    Science.gov (United States)

    Rani, M R Sandhya; Pandalai, Sudha; Shrock, Jennifer; Almasan, Alex; Ransohoff, Richard M

    2007-09-01

    Tumor necrosis factor (TNF)-related apoptosis-inducing ligand/Apo2 ligand (TRAIL/Apo2L) mRNA was induced preferentially by interferon (IFN)-beta but not IFN-alpha in human fibrosarcoma and primary fibroblast cells. To characterize the signaling components mediating the IFN subtype-specific induction of this gene, we used mutant cell lines lacking individual components involved in signaling by type I IFNs. TRAIL was not induced by IFN-beta in mutant cell lines U2A, U3A, U4A, U5A, and U6A, which lack, respectively, IFN regulatory factor-9 (IRF-9), Stat1, Jak1, IFNAR-2.2, and Stat2, indicating transcription factor IFN-stimulated gene factor 3 (ISGF3) was essential for the induction of this gene. TRAIL was not induced by IFN-beta in U1A (Tyk2 null) or U1A.R930 cells (that express a kinase-deficient point mutant of Tyk2) but was induced in U1A.wt-5 cells (U1A cells expressing wild-type Tyk2), indicating that Tyk2 protein and kinase activity were both required for induction of the gene. Biochemical and genetic analyses revealed the requirement of transcription factor NF-kappa B and phosphoinositide 3-kinase (PI3K) but not extracellular signal-regulated kinase (ERK) for the induction of TRAIL by IFN-beta. Furthermore, the antiproliferative but not antiviral effects of IFN-beta required catalytically active Tyk2, suggesting that expression of genes, such as TRAIL, may play an important role in mediating the biologic effects of IFNs.

  11. 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

  12. 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...

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.

    Science.gov (United States)

    Fernandes, Andrew D; Macklaim, Jean M; Linn, Thomas G; Reid, Gregor; Gloor, Gregory B

    2013-01-01

    Experimental variance is a major challenge when dealing with high-throughput sequencing data. This variance has several sources: sampling replication, technical replication, variability within biological conditions, and variability between biological conditions. The high per-sample cost of RNA-Seq often precludes the large number of experiments needed to partition observed variance into these categories as per standard ANOVA models. We show that the partitioning of within-condition to between-condition variation cannot reasonably be ignored, whether in single-organism RNA-Seq or in Meta-RNA-Seq experiments, and further find that commonly-used RNA-Seq analysis tools, as described in the literature, do not enforce the constraint that the sum of relative expression levels must be one, and thus report expression levels that are systematically distorted. These two factors lead to misleading inferences if not properly accommodated. As it is usually only the biological between-condition and within-condition differences that are of interest, we developed ALDEx, an ANOVA-like differential expression procedure, to identify genes with greater between- to within-condition differences. We show that the presence of differential expression and the magnitude of these comparative differences can be reasonably estimated with even very small sample sizes.

  2. 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...

  3. Duration of Ebola virus RNA persistence in semen of survivors: population-level estimates and projections.

    Science.gov (United States)

    Eggo, Rosalind M; Watson, Conall H; Camacho, Anton; Kucharski, Adam J; Funk, Sebastian; Edmunds, W John

    2015-01-01

    Ebola virus can persist in semen after recovery, potentially for months, which may impact the duration of enhanced surveillance required after interruption of transmission. We combined recent data on viral RNA persistence with weekly disease incidence to estimate the current number of semen-positive men in affected West African countries. We find the number is low, and since few reported sexual transmission events have occurred, the future risk is also likely low, although sexual health promotion remains critical. PMID:26676163

  4. 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

  5. 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

  6. Evaluation the susceptibility of five polymorphisms in microRNA-binding sites to female breast cancer risk in Chinese population.

    Science.gov (United States)

    He, Bang-Shun; Pan, Yu-Qin; Lin, Kang; Ying, Hou-Qun; Wang, Feng; Deng, Qi-Wen; Sun, Hui-Ling; Gao, Tian-Yi; Wang, Shu-Kui

    2015-11-15

    Polymorphisms in microRNA (miRNA) binding site have been widely discussed to be associated with cancer risk; however, the associations were unclear in Chinese population. To investigate the associations of five polymorphisms (rs11097457, rs1434536, rs1970801, rs1044129, rs11169571) in miRNA binding sites with breast cancer risk, a total of 435 female patients with breast cancer and 439 age- and gender-matched tumor-free individuals were enrolled in this case-control study. Sequenom MassARRAY was applied to detect the polymorphisms, and the immunohistochemistry assay was used to measure the expression of estrogen receptor (ER) and progesterone receptor (PR) and CerbB-2. The data showed that these polymorphisms were not associated with breast cancer risk or clinical characters of breast cancer in all participants and sub-group with the exception that, in the sub-group of women with their first menstruation after 14 years old, those who carried rs1970801 T allele (genotype TT/GT) were associated with decreased breast cancer risk. In short, this case-control study provided the evidence that women with their first menstruation after 14 years old and carried rs1970801 T allele (genotype TT/GT) were associated with decreased breast cancer risk.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. Association of genetic variants in lncRNA H19 with risk of colorectal cancer in a Chinese population

    Science.gov (United States)

    Wang, Haixiao; Du, Mulong; Zhu, Lingjun; Chu, Haiyan; Zhang, Zhengdong; Wang, Meilin

    2016-01-01

    Objective The long non-coding RNA (lncRNA) gene, H19, has been involving in multiple biological functions, which also plays a vital role in colorectal cancer carcinogenesis. However, the association between genetic variants in H19 and colorectal cancer susceptibility has not been reported. In this study, we aim to explore whether H19 polymorphisms are related to the susceptibility of colorectal cancer. Methods We conducted a case-control study to evaluate the association between four selected single nucleotide polymorphisms (SNPs) (rs2839698, rs3024270, rs217727, and rs2735971) in H19 and the risk of colorectal cancer in a Chinese population. Results We found that individuals with rs2839698 A allele had a significantly increased risk of colorectal cancer, compared to those carrying G allele [odds ratio (OR) = 1.20, 95% confidence interval (CI) = 1.05–1.36 in additive model]. Further stratified analyses revealed that colon tumor site, well differentiated grade and Duke's stage of C/D were significantly associated with colorectal cancer risk (P cancer, which may be a potential biomarker for predicting colorectal cancer susceptibility. PMID:27027436

  15. 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.

  16. Formation of a catalytically active complex between tRNAAsp and aspartyl-tRNA synthetase from yeast in high concentrations of ammonium sulphate.

    Science.gov (United States)

    Giegé, R; Lorber, B; Ebel, J P; Moras, D; Thierry, J C; Jacrot, B; Zaccai, G

    1982-05-01

    The interactions of yeast tRNAAsp with cognate aspartyl-tRNA synthetase have been studied in high concentrations of either sodium chloride or ammonium sulphate by fluorescence titration and small-angle neutron scattering. In solutions containing more than 1M NaCl no complex is formed and enzymatic activity is abolished. In strong contrast, however, the physical measurements showed the formation of a two-to-one tRNA-enzyme complex, with high affinity, in 1.6 M (NH4)2SO4. Aminoacylation assays under the same salt conditions showed the enzymatic fixation of aspartic acid to tRNAAsp to occur at an appreciable rate. The present study emphasizes that the effects of salts on protein-nucleic acid interactions do not depend only on ionic strength but also on the nature of the salt. This study has allowed a rational approach to the crystallisation of a functional tRNAAsp-aspartyl-tRNA synthetase complex (Giegé, Lorber, Ebel, Thierry and Moras (1980) C.R. Acad. Sci. Paris, série D, 291, 393-396). PMID:7049254

  17. 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...

  18. 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

  19. 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

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

    Directory of Open Access Journals (Sweden)

    Rachid El Fatimy

    2016-07-01

    Full Text Available 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.

  1. 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

  2. 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,...

  3. Polymorphisms in Long Noncoding RNA H19 Contribute to the Protective Effects of Coal Workers’ Pneumoconiosis in a Chinese Population

    Science.gov (United States)

    Wu, Qiuyun; Yan, Weiwen; Han, Ruhui; Yang, Jingjin; Yuan, Jiali; Ji, Xiaoming; Liu, Yi; Ni, Chunhui

    2016-01-01

    The H19 is a kind of long noncoding RNA, which has been implicated in multiple biological functions. However, the associations between genetic variants in H19 and susceptibility of coal workers’ pneumoconiosis (CWP) have been seldom reported. In the present study, three potential polymorphisms (rs2067051, rs217727, and rs2839702) in H19 were genotyped in a case-control study including 703 CWP cases and 705 controls. We found that individuals with the H19 rs2067051 CT/TT genotypes showed a decreased risk of CWP compared with those with the CC genotype (adjusted OR = 0.64, 95%CI = 0.49–0.83, p = 0.001). Further stratified analyses revealed that the associations between variant genotypes of rs2067051 and the risk of CWP were more prominent in subjects of non-smokers (adjusted OR = 0.55, 95%CI = 0.39–0.79, p = 0.001) and CWP patients with Stage I (adjusted OR = 0.63, 95%CI = 0.46–0.86, p = 0.004). Additionally, the protective effects of H19 rs2067051 were also evident in coal miners both with dust exposure years <25 years (adjusted OR = 0.63, 95%CI = 0.42–0.95, p = 0.026) and ≥25 years (adjusted OR = 0.57, 95%CI = 0.40–0.80, p = 0.001). Our results indicated that rs2067051 in the H19 gene is correlated with a deceased risk of CWP in a Chinese population, which may be a potential genetic marker for prevention and intervention of CWP. Further functional studies are warranted to validate our findings. PMID:27626436

  4. 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.

  5. 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...

  6. Axonal localization of neuritin/CPG15 mRNA in neuronal populations through distinct 5' and 3' UTR elements.

    Science.gov (United States)

    Merianda, Tanuja T; Gomes, Cynthia; Yoo, Soonmoon; Vuppalanchi, Deepika; Twiss, Jeffery L

    2013-08-21

    Many neuronal mRNAs are actively transported into distal axons. The 3' untranslated regions (UTRs) of axonal mRNAs often contain cues for their localization. The 3' UTR of neuritin mRNA was shown to be sufficient for localization into axons of hippocampal neurons. Here, we show that neuritin mRNA localizes into axons of rat sensory neurons, but this is predominantly driven by the 5' rather than 3' UTR. Neuritin mRNA shifts from cell body to axon predominantly after nerve crush injury, suggesting that it encodes a growth-associated protein. Consistent with this, overexpression of neuritin increases axon growth but only when its mRNA localizes into the axons. PMID:23966695

  7. 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...

  8. RNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel.

    Science.gov (United States)

    Tannock, Gerald W; Lawley, Blair; Munro, Karen; Sims, Ian M; Lee, Julian; Butts, Christine A; Roy, Nicole

    2014-04-01

    Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope ((13)C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [(13)C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect (13)C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the (13)C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA-stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism.

  9. 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.

  10. 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.

  11. 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...

  12. 植物 RNA 病毒的群体遗传演化研究进展%The Review on the Genetic Evolution of Plant RNA Virus Population

    Institute of Scientific and Technical Information of China (English)

    陈士华; 张慧聪; 李月; 裴扬; 吴兴泉

    2013-01-01

    Plant RNA viruses are characterized by extreme evolutionary capacities that allow them to successfully expand their distribution ranges rapidly and cause serious harm to their host .Studies on the genetic evolutionary histo-ry of plant RNA virus population help to provide the information essential for designing strategies for viruses control -ling.In recent years ,it has been confirmed that plant RNA viruses change their genomes with gene mutation or gene recombination rapidly to form a quasispecies which is a cloud of diverse variants that are genetically linked through mutation .Plant RNA viruses are known to face many narrow genetic bottlenecks and a significant percentage of a pop -ulation is prevented from reproducing during their life cycles ,including the cell-to-cell movements ,infecting the plant systemically ,being transmitted from plant to plant .Genetic bottlenecks can lead to genetic drift or natural selection for the different genome .The genetic structure of plant RNA viruses population alsonare influenced by gene flow .%植物RNA病毒群体的快速演化是其流行成灾的一个重要原因,研究其遗传演化机制对制定病害防治策略具有重要指导意义。目前,已研究证明植物RNA病毒可通过高频突变保持一个动态的遗传变异群体(准种),也可通过基因重组产生新的变异类型。高度变异的病毒群体在进行细胞间运动、组织间系统侵染及植株间水平传播等过程中均会遭遇遗传瓶颈而使群体数量大幅度减少。此时,自然选择或遗传漂变会发挥对群体中不同变异基因型进行筛选的作用。另外,基因漂移也是影响病毒群体遗传结构的一个重要因素。

  13. 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

  14. 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

  15. 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.

  16. 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...

  17. 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

    2016-06-02

    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.

  18. Raman crystallography of RNA.

    Science.gov (United States)

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

    2009-10-01

    Raman crystallography is the application of Raman spectroscopy to single crystals. This technique has been applied to a variety of protein molecules where it has provided unique information about biopolymer folding, substrate binding, and catalysis. Here, we describe the application of Raman crystallography to functional RNA molecules. RNA represents unique opportunities and challenges for Raman crystallography. One issue that confounds studies of RNA is its tendency to adopt multiple non-functional folds. Raman crystallography has the advantage that it isolates a single state of the RNA within the crystal and can evaluate its fold, metal ion binding properties (ligand identity, stoichiometry, and affinity), proton binding properties (identity, stoichiometry, and affinity), and catalytic potential. In particular, base-specific stretches can be identified and then associated with the binding of metal ions and protons. Because measurements are carried out in the hanging drop at ambient, rather than cryo, conditions and because RNA crystals tend to be approximately 70% solvent, RNA dynamics and conformational changes become experimentally accessible. This review focuses on experimental setup and procedures, acquisition and interpretation of Raman data, and determination of physicochemical properties of the RNA. Raman crystallographic and solution biochemical experiments on the HDV RNA enzyme are summarized and found to be in excellent agreement. Remarkably, characterization of the crystalline state has proven to help rather than hinder functional characterization of functional RNA, most likely because the tendency of RNA to fold heterogeneously is limited in a crystalline environment. Future applications of Raman crystallography to RNA are briefly discussed.

  19. 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.

  20. 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.;

    2012-01-01

    High-throughput sequencing technologies are currently revolutionizing the field of biology and medicine, yet bioinformatic challenges in analysing very large data sets have slowed the adoption of these technologies by the community of population biologists. We introduce the 'Simple Fool's Guide t...

  1. Evidence of two lineages of the symbiont 'Candidatus Erwinia dacicola' in Italian populations of Bactrocera oleae (Rossi) based on 16S rRNA gene sequences.

    Science.gov (United States)

    Savio, Claudia; Mazzon, Luca; Martinez-Sañudo, Isabel; Simonato, Mauro; Squartini, Andrea; Girolami, Vincenzo

    2012-01-01

    The close association between the olive fly Bactrocera oleae (Rossi) (Diptera: Tephritidae) and bacteria has been known for more than a century. Recently, the presence of a host-specific, hereditary, unculturable symbiotic bacterium, designated 'Candidatus Erwinia dacicola', has been described inside the cephalic organ of the fly, called the oesophageal bulb. In the present study, the 16S rRNA gene sequence variability of 'Ca. E. dacicola' was examined within and between 26 Italian olive fly populations sampled across areas where olive trees occur in the wild and areas where cultivated olive trees have been introduced through history. The bacterial contents of the oesophageal bulbs of 314 olive flies were analysed and a minimum of 781 bp of the 16S rRNA gene was sequenced. The corresponding host fly genotype was assessed by sequencing a 776 bp portion of the mitochondrial genome. Two 'Ca. E. dacicola' haplotypes were found (htA and htB), one being slightly more prevalent than the other (57%). The two haplotypes did not co-exist in the same individuals, as confirmed by cloning. Interestingly, the olive fly populations of the two main Italian islands, Sicily and Sardinia, appeared to be represented exclusively by the htB and htA haplotypes, respectively, while peninsular populations showed both bacterial haplotypes in different proportions. No significant correlation emerged between the two symbiont haplotypes and the 16 host fly haplotypes observed, suggesting evidence for a mixed model of vertical and horizontal transmission of the symbiont during the fly life cycle.

  2. An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line

    Science.gov (United States)

    Kim, Myung-Chul; Kim, Na-Yon; Seo, Yu-Ri; Kim, Yongbaek

    2016-01-01

    Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology. The RNA-seq data were analyzed with the MeDIP-seq data in an integrated way to identify the epigenetically modified genes that defined the SP. Concomitant changes in mRNA expression and DNA methylation were found in 122 genes, including 118 down-regulated genes with hypermethylation and 4 up-regulated genes with hypomethylation. Gene ontology revealed that a large portion of the genes belonged to the groups of biological processes such as stem cell maintenance, stem cell development, stem cell differentiation, and the negative regulation of the developmental process. Among these genes, BNC1, RPS6KA3, TWSG1 and DUSP15 contained aberrant methylation in the CpG islands of the promoter region, indicating that the genes regulated by DNA methylation characterized a distinct subpopulation of HMM cells. The present study provided valuable information to shed light on the epigenetic contributions to the generation and maintenance of tumor cell heterogeneity.

  3. Polymorphisms in Long Noncoding RNA H19 Contribute to the Protective Effects of Coal Workers' Pneumoconiosis in a Chinese Population.

    Science.gov (United States)

    Wu, Qiuyun; Yan, Weiwen; Han, Ruhui; Yang, Jingjin; Yuan, Jiali; Ji, Xiaoming; Liu, Yi; Ni, Chunhui

    2016-01-01

    The H19 is a kind of long noncoding RNA, which has been implicated in multiple biological functions. However, the associations between genetic variants in H19 and susceptibility of coal workers' pneumoconiosis (CWP) have been seldom reported. In the present study, three potential polymorphisms (rs2067051, rs217727, and rs2839702) in H19 were genotyped in a case-control study including 703 CWP cases and 705 controls. We found that individuals with the H19 rs2067051 CT/TT genotypes showed a decreased risk of CWP compared with those with the CC genotype (adjusted OR = 0.64, 95%CI = 0.49-0.83, p = 0.001). Further stratified analyses revealed that the associations between variant genotypes of rs2067051 and the risk of CWP were more prominent in subjects of non-smokers (adjusted OR = 0.55, 95%CI = 0.39-0.79, p = 0.001) and CWP patients with Stage I (adjusted OR = 0.63, 95%CI = 0.46-0.86, p = 0.004). Additionally, the protective effects of H19 rs2067051 were also evident in coal miners both with dust exposure years genetic marker for prevention and intervention of CWP. Further functional studies are warranted to validate our findings. PMID:27626436

  4. 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

  5. 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.

  6. 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.

  7. Catalytic combustor for hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Mercea, J.; Grecu, E.; Fodor, T.; Kreibik, S.

    1982-01-01

    The performance of catalytic combustors for hydrogen using platinum-supported catalysts is described. Catalytic plates of different sizes were constructed using fibrous and ceramic supports. The temperature distribution as well as the reaction efficiency as a function of the fuel input rate was determined, and a comparison between the performances of different plates is discussed.

  8. High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock Stress.

    Science.gov (United States)

    Zhang, Hanbang; Ehrenkaufer, Gretchen M; Manna, Dipak; Hall, Neil; Singh, Upinder

    2015-01-01

    The human parasite Entamoeba histolytica has an active RNA interference (RNAi) pathway with an extensive repertoire of 27nt small RNAs that silence genes. However the role of this pathway in regulating amebic biology remains unknown. In this study, we address whether silencing via 27nt small RNAs may be a mechanism for controlling gene expression changes during conversion between the trophozoite and cyst stages of the parasite. We sequenced small RNA libraries generated from trophozoites, early cysts, mature cysts, and excysting cells and mapped them to the E. invadens genome. Our results show that, as in E. histolytica, small RNAs in E. invadens are largely ~27nt in length, have an unusual 5'-polyphosphate structure and mediate gene silencing. However, when comparing the libraries from each developmental time-point we found few changes in the composition of the small RNA populations. Furthermore, genes targeted by small RNAs were permanently silenced with no changes in transcript abundance during development. Thus, the E. invadens 27nt small RNA population does not mediate gene expression changes during development. In order to assess the generalizability of our observations, we examined whether small RNAs may be regulating gene expression changes during stress response in E. histolytica. Comparison of the 27nt small RNA populations from E. histolytica trophozoites from basal conditions, or after heat shock or exposure to oxidative stress showed few differences. Similar to data in E. invadens development, genes targeted by small RNAs were consistently silenced and did not change expression under tested stress conditions. Thus, the biological roles of the 27nt small RNA population in Entamoeba remain elusive. However, as the first characterization of the RNAi pathway in E. invadens these data serve as a useful resource for the study of Entamoeba development and open the door to the development of RNAi-based gene silencing tools in E. invadens.

  9. 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

  10. 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.

  11. Catalytic Functions of Standards

    NARCIS (Netherlands)

    K. Blind (Knut)

    2009-01-01

    textabstractThe three different areas and the examples have illustrated several catalytic functions of standards for innovation. First, the standardisation process reduces the time to market of inventions, research results and innovative technologies. Second, standards themselves promote the diffusi

  12. Switching off small RNA regulation with trap-mRNA

    DEFF Research Database (Denmark)

    Overgaard, Martin; Johansen, Jesper; Møller-Jensen, Jakob;

    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 its...

  13. 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....

  14. 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.

  15. Chemical fidelity of an RNA polymerase ribozyme

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  16. 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.

  17. 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...

  18. 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.

  19. 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...

  20. Axonal Localization of Neuritin/CPG15 mRNA in Neuronal Populations through Distinct 5′ and 3′ UTR Elements

    OpenAIRE

    Merianda, Tanuja T.; Gomes, Cynthia; Yoo, Soonmoon; Vuppalanchi, Deepika; Twiss, Jeffery L.

    2013-01-01

    Many neuronal mRNAs are actively transported into distal axons. The 3′ untranslated regions (UTRs) of axonal mRNAs often contain cues for their localization. The 3′ UTR of neuritin mRNA was shown to be sufficient for localization into axons of hippocampal neurons. Here, we show that neuritin mRNA localizes into axons of rat sensory neurons, but this is predominantly driven by the 5′ rather than 3′ UTR. Neuritin mRNA shifts from cell body to axon predominantly after nerve crush injury, suggest...

  1. 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...

  2. Catalytic Conversion of Biofuels

    DEFF Research Database (Denmark)

    Jørgensen, Betina

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

  3. 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.

  4. Catalytic efficiency of designed catalytic proteins.

    Science.gov (United States)

    Korendovych, Ivan V; DeGrado, William F

    2014-08-01

    The de novo design of catalysts that mimic the affinity and specificity of natural enzymes remains one of the Holy Grails of chemistry. Despite decades of concerted effort we are still unable to design catalysts as efficient as enzymes. Here we critically evaluate approaches to (re)design of novel catalytic function in proteins using two test cases: Kemp elimination and ester hydrolysis. We show that the degree of success thus far has been modest when the rate enhancements seen for the designed proteins are compared with the rate enhancements by small molecule catalysts in solvents with properties similar to the active site. Nevertheless, there are reasons for optimism: the design methods are ever improving and the resulting catalyst can be efficiently improved using directed evolution.

  5. 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

    the reconstructed cDNAs were tested in cell culture and pigs. Both reconstructed ancestral genomes proved functional, and displayed distinct phenotypes in vitro and in vivo. We suggest that reconstruction of ancestral viruses is a useful tool for experimental and computational investigations of virulence and viral......RNA viruses have the highest known mutation rates. Consequently it is likely that a high proportion of individual RNA virus genomes, isolated from an infected host, will contain lethal mutations and be non-functional. This is problematic if the aim is to clone and investigate high...... a moderately virulent isolate. In addition to here being used as a model for RNA viruses generally, CSFV has high socioeconomic importance and remains a threat to animal welfare and pig production. We find that the majority of the investigated genomes are non-functional and only 12% produced infectious RNA...

  6. Axonal Localization of Neuritin/CPG15 mRNA in Neuronal Populations through Distinct 5′ and 3′ UTR Elements

    Science.gov (United States)

    Merianda, Tanuja T.; Gomes, Cynthia; Yoo, Soonmoon; Vuppalanchi, Deepika

    2013-01-01

    Many neuronal mRNAs are actively transported into distal axons. The 3′ untranslated regions (UTRs) of axonal mRNAs often contain cues for their localization. The 3′ UTR of neuritin mRNA was shown to be sufficient for localization into axons of hippocampal neurons. Here, we show that neuritin mRNA localizes into axons of rat sensory neurons, but this is predominantly driven by the 5′ rather than 3′ UTR. Neuritin mRNA shifts from cell body to axon predominantly after nerve crush injury, suggesting that it encodes a growth-associated protein. Consistent with this, overexpression of neuritin increases axon growth but only when its mRNA localizes into the axons. PMID:23966695

  7. Characterization of glyphosate resistance in Amaranthus tuberculatus populations.

    Science.gov (United States)

    Lorentz, Lothar; Gaines, Todd A; Nissen, Scott J; Westra, Philip; Strek, Harry J; Dehne, Heinz W; Ruiz-Santaella, Juan Pedro; Beffa, Roland

    2014-08-13

    The evolution of glyphosate-resistant weeds has recently increased dramatically. Six suspected glyphosate-resistant Amaranthus tuberculatus populations were studied to confirm resistance and determine the resistance mechanism. Resistance was confirmed in greenhouse for all six populations with glyphosate resistance factors (R/S) between 5.2 and 7.5. No difference in glyphosate absorption or translocation was observed between resistant and susceptible individuals. No mutation at amino acid positions G101, T102, or P106 was detected in the EPSPS gene coding sequence, the target enzyme of glyphosate. Analysis of EPSPS gene copy number revealed that all glyphosate-resistant populations possessed increased EPSPS gene copy number, and this correlated with increased expression at both RNA and protein levels. EPSPS Vmax and Kcat values were more than doubled in resistant plants, indicating higher levels of catalytically active expressed EPSPS protein. EPSPS gene amplification is the main mechanism contributing to glyphosate resistance in the A. tuberculatus populations analyzed.

  8. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

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

  9. 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.

  10. 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.

  11. Coamplification of eukaryotic DNA with 16S rRNA gene-based PCR primers: possible consequences for population fingerprinting of complex microbial communities.

    Science.gov (United States)

    Huys, Geert; Vanhoutte, Tom; Joossens, Marie; Mahious, Amal S; De Brandt, Evie; Vermeire, Severine; Swings, Jean

    2008-06-01

    The main aim of this study was to evaluate the specificity of three commonly used 16S rRNA gene-based polymerase chain reaction (PCR) primer sets for bacterial community analysis of samples contaminated with eukaryotic DNA. The specificity of primer sets targeting the V3, V3-V5, and V6-V8 hypervariable regions of the 16S rRNA gene was investigated in silico and by community fingerprinting of human and fish intestinal samples. Both in silico and PCR-based analysis revealed cross-reactivity of the V3 and V3-V5 primers with the 18S rRNA gene of human and sturgeon. The consequences of this primer anomaly were illustrated by denaturing gradient gel electrophoresis (DGGE) profiling of microbial communities in human feces and mixed gut of Siberian sturgeon. DGGE profiling indicated that the cross-reactivity of 16S rRNA gene primers with nontarget eukaryotic DNA might lead to an overestimation of bacterial biodiversity. This study has confirmed previous sporadic indications in literature indicating that several commonly applied 16S rRNA gene primer sets lack specificity toward bacteria in the presence of eukaryotic DNA. The phenomenon of cross-reactivity is a potential source of systematic error in all biodiversity studies where no subsequent analysis of individual community amplicons by cloning and sequencing is performed.

  12. A catalytic cracking process

    Energy Technology Data Exchange (ETDEWEB)

    Degnan, T.F.; Helton, T.E.

    1995-07-20

    Heavy oils are subjected to catalytic cracking in the absence of added hydrogen using a catalyst containing a zeolite having the structure of ZSM-12 and a large-pore crystalline zeolite having a Constraint Index less than about 1. The process is able to effect a bulk conversion of the oil at the same time yielding a higher octane gasoline and increased light olefin content. (author)

  13. rs712 polymorphism within let-7 microRNA-binding site might be involved in the initiation and progression of colorectal cancer in Chinese population

    Directory of Open Access Journals (Sweden)

    Jiang QH

    2015-10-01

    Full Text Available Qiang-Hua Jiang,1,* Hong-Xin Peng,2,3,* Yi Zhang,4 Peng Tian,4 Zu-Lian Xi,4 Hao Chen4 1Department of Surgery, Dongyang People’s Hospital, Dongyang, Zhejiang, 2Medical College, Southeast University, 3Central Laboratory, Nanjing First Hospital, Nanjing, Jiangsu, 4Hubei Key Laboratory of Biological Targeted Therapy, Yichang Yiling Hospital, Yichang, Hubei, People’s Republic of China *These authors contributed equally to this work Abstract: rs712 within 3'-untranslated region of KRAS can affect the specific binding between the mRNA and its targeted microRNAs, leading to the activation of KRAS oncogene. However, the possible association between the locus and susceptibility to colorectal cancer (CRC remains unclear. We investigated genotypes of the locus in 586 cases and 476 controls to explore the possible association between them. Results of our case–control study showed that genotypes TT (6.5% vs 2.5%, P=0.002, adjusted odds ratio [OR] =2.810, 95% confidence interval [CI] =1.342–5.488 and GT/TT (36.5% vs 30.5%, P=0.038, adjusted OR =1.342, 95% CI =1.030–1.712 and allele T (21.5% vs 6.5%, P=0.004, adjusted OR =1.328, 95% CI =1.105–1.722 of rs712 were significantly associated with an increased risk of CRC, and the significant association was also observed in the recessive model (TT vs GG/GT, 6.5% vs 2.5%, P=0.003, adjusted OR =0.372, 95% CI =0.191–0.725. However, there was no association between genotype GT and risk of CRC (30.0% vs 28.0%, P=0.235, adjusted OR =1.210, 95% CI =0.903–1.548. Furthermore, genotype GT (P=0.003 and allele T (P=0.003 were significantly associated with poor differentiation, and genotypes GT and TT and allele T were significantly associated with tumor-node-metastases stage III (P=0.001 for GT vs GG, P<0.001 for TT vs GG, and P<0.001 for T vs G and node metastasis (P<0.001 for GT vs GG, P=0.001 for TT vs GG, and P<0.001 for T vs G, respectively. These findings indicated that allele T and genotypes TT and GT

  14. 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.

  15. 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.

  16. 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.)

  17. 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

  18. HYDROGEN TRANSFER IN CATALYTIC CRACKING

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Hydrogen transfer is an important secondary reaction of catalytic cracking reactions, which affects product yield distribution and product quality. It is an exothermic reaction with low activation energy around 43.3 kJ/mol. Catalyst properties and operation parameters in catalytic cracking greatly influence the hydrogen transfer reaction. Satisfactory results are expected through careful selection of proper catalysts and operation conditions.

  19. Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos Shown with 16S rRNA Gene-Based Microbial Community Analysis

    Directory of Open Access Journals (Sweden)

    Isamu Maeda

    2013-01-01

    Full Text Available Jungle Crows (Corvus macrorhynchos prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

  20. 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.

  1. Catalytic quantum error correction

    CERN Document Server

    Brun, T; Hsieh, M H; Brun, Todd; Devetak, Igor; Hsieh, Min-Hsiu

    2006-01-01

    We develop the theory of entanglement-assisted quantum error correcting (EAQEC) codes, a generalization of the stabilizer formalism to the setting in which the sender and receiver have access to pre-shared entanglement. Conventional stabilizer codes are equivalent to dual-containing symplectic codes. In contrast, EAQEC codes do not require the dual-containing condition, which greatly simplifies their construction. We show how any quaternary classical code can be made into a EAQEC code. In particular, efficient modern codes, like LDPC codes, which attain the Shannon capacity, can be made into EAQEC codes attaining the hashing bound. In a quantum computation setting, EAQEC codes give rise to catalytic quantum codes which maintain a region of inherited noiseless qubits. We also give an alternative construction of EAQEC codes by making classical entanglement assisted codes coherent.

  2. 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.

  3. Catalytic and non-catalytic roles for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response.

    Directory of Open Access Journals (Sweden)

    Christina L Stallings

    Full Text Available Recent evidence indicates that the mycobacterial response to DNA double strand breaks (DSBs differs substantially from previously characterized bacteria. These differences include the use of three DSB repair pathways (HR, NHEJ, SSA, and the CarD pathway, which integrates DNA damage with transcription. Here we identify a role for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. Arr is transcriptionally induced following DNA damage and cellular stress. Although Arr is not required for induction of a core set of DNA repair genes, Arr is necessary for suppression of a set of ribosomal protein genes and rRNA during DNA damage, placing Arr in a similar pathway as CarD. Surprisingly, the catalytic activity of Arr is not required for this function, as catalytically inactive Arr was still able to suppress ribosomal protein and rRNA expression during DNA damage. In contrast, Arr substrate binding and catalytic activities were required for regulation of a small subset of other DNA damage responsive genes, indicating that Arr has both catalytic and noncatalytic roles in the DNA damage response. Our findings establish an endogenous cellular function for a mono-ADP-ribosyltransferase apart from its role in mediating Rifampin resistance.

  4. Catalytic and non-catalytic roles for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response.

    Science.gov (United States)

    Stallings, Christina L; Chu, Linda; Li, Lucy X; Glickman, Michael S

    2011-01-01

    Recent evidence indicates that the mycobacterial response to DNA double strand breaks (DSBs) differs substantially from previously characterized bacteria. These differences include the use of three DSB repair pathways (HR, NHEJ, SSA), and the CarD pathway, which integrates DNA damage with transcription. Here we identify a role for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. Arr is transcriptionally induced following DNA damage and cellular stress. Although Arr is not required for induction of a core set of DNA repair genes, Arr is necessary for suppression of a set of ribosomal protein genes and rRNA during DNA damage, placing Arr in a similar pathway as CarD. Surprisingly, the catalytic activity of Arr is not required for this function, as catalytically inactive Arr was still able to suppress ribosomal protein and rRNA expression during DNA damage. In contrast, Arr substrate binding and catalytic activities were required for regulation of a small subset of other DNA damage responsive genes, indicating that Arr has both catalytic and noncatalytic roles in the DNA damage response. Our findings establish an endogenous cellular function for a mono-ADP-ribosyltransferase apart from its role in mediating Rifampin resistance.

  5. 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.

  6. Unsteady catalytic processes and sorption-catalytic technologies

    Energy Technology Data Exchange (ETDEWEB)

    Zagoruiko, A N [G.K. Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)

    2007-07-31

    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.

  7. Integrative approach detected association between genetic variants of microRNA binding sites of TLRs pathway genes and OSCC susceptibility in Chinese Han population.

    Directory of Open Access Journals (Sweden)

    Yun Wang

    Full Text Available Oral squamous cell carcinoma (OSCC is a leading malignancy worldwide; the overall 5-year survival rate is approximately 50%. A variety of proteins in Toll-like receptors (TLRs pathway have been related with the risk of OSCC. However, the influence of genetic variations in TLRs pathway genes on OSCC susceptibility is unclear. Previous studies mainly focused on the coding region of genes, while the UTR region remains unstudied. In the current study, a bioinformatics approach was performed to select candidate single nucleotide polymorphisms (SNPs on microRNA binding sites of TLRs pathway genes related with OSCC. After screening 90 OSCC related TLRs pathway genes, 16 SNPs were selected for genotyping. We found that rs5030486, the polymorphisms on 3' UTR of TRAF6, was significantly associated with OSCC risk. AG genotype of TRAF6 was strongly associated with a decreased risk of OSCC (OR = 0.252; 95% CI = 0.106, 0.598; p = 0.001. In addition, AG genotype was also related with a reduced risk of OSCC progression both in univariable analysis (HR = 0.303, 95% CI = 0.092, 0.995 and multivariable analysis (HR = 0.272, 95% CI = 0.082, 0.903. Furthermore, after detecting the mRNA expression level of TRAF6 in 24 OSCC patients, we found that TRAF6 expression level was significantly different between patients carrying different genotypes at locus rs5030486 (p = 0.013, indicating that rs5030486 of TRAF6 might contribute to OSCC risk by altering TRAF6 expression level. In general, these data indicated that SNP rs5030486 could be a potential bio-marker for OSCC risk and our results might provide new insights into the association of polymorphisms within the non-coding area of genes with cancers.

  8. RNA oxidation

    DEFF Research Database (Denmark)

    Kjaer, L. K.; Cejvanovic, V.; Henriken, T.;

    2015-01-01

    RNA modification has attracted increasing interest as it is realized that epitranscriptomics is important in disease development. In type 2 diabetes we have suggested that high urinary excretion of 8-oxo-2'-Guanosine (8oxoGuo), as a measure of global RNA oxidation, is associated with poor survival.......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...... diabetes. In agreement with our previous finding, DNA oxidation did not show any prognostic value. RNA oxidation represents oxidative stress intracellularly, presumably predominantly in the cytosol. The mechanism of RNA oxidation is not clear, but hypothesized to result from mitochondrial dysfunction...

  9. 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

  10. Study Diadenosine Oligophosphate Triple Catalytic Activity of E.coli Heat-Inducible Lysyl-tRNA Synthetase%大肠杆菌热诱导赖氨酰-tRNA合成酶二腺苷多磷酸三重催化活性研究

    Institute of Scientific and Technical Information of China (English)

    陈晓龙; 徐宇虹

    2013-01-01

    E. coli heat-inducible lysyl-tRNA synthetase (LysU, EC6.1.1.6) is known to be a highly efficient Ap4A/Ap3A synthase with dual catalytic activity: 2ATP→Ap4A+2Pi→Ap3A+3Pi. To get better known on the intermediate reversible model of LysU, LysU was purified and confirmed its structural stability by circular dichroism and intrinsic fluorescence spectrum. An easy-fast ion-exchange chromatography technique was set up and products were sequentially separated for mass spectrometry. Results demonstrated that LysU initially produce 83% Ap4A from ATP, and then turn over Ap4A into 67% Ap3A However, LysU was accidentally discovered can consecutively catalyze AP3A into 85% ADP as the final product. By using AMPPCP and AMPCPP as ATP surrogate, the Ap3A/ADP reaction was blocked. Mechanistic investigations proved that LysU is triple catalytic activity enzyme: 2ATP→Ap4A+2Pi→Ap3A+3Pi→2ADP+2Pi. Therefore, LysU catalyze the formation of Ap4A/Ap3A/ADP via phosphate-based trap mechanism which is either phosphate-base as inorganic phosphate as added ADP, or nucleotide as ADP as added Ap3A%E.coli热诱导赖氨酰-tRNA合成酶(LysU,EC 6.1.1.6)是高效的Ap4A/Ap3A合成酶,已知反应模式为双重动态过程:2ATP→Ap4A+2Pi→Ap3A+3Pi.为进一步研究LysU“中间物可逆”催化模型,表达纯化了LysU蛋白并验证结构稳定性,构建了二腺苷多磷酸产物检测系统并分离了各阶段催化产物,观察了AMPPCP和AMPCPP阻断Ap3A/ADP合成的反应.圆二色光谱和荧光光谱扫描证明纯化后的LysU蛋白结构完整.LysU首先催化ATP合成83%的Ap4A,接着可逆生成67%的ApA.实验中发现,ApA并非LysU二腺苷多磷酸催化反应的终产物,ApA可继续逆生成80%的ADP.以AMPPCP或AMPCPP代替ATP为起始底物,发现无ApA转化ADP反应.上述结果证明LysU具有三重催化活性:2ATP→Ap4A+2Pi→Ap3A+3Pi→2ADP+2Pi,符合“磷酸捕获机制”催化模型:活化的赖氨酰-腺苷中间物捕获核苷酸或磷酸小分

  11. 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...

  12. Catalytic cracking of lignites

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-01

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

  13. Catalytic Membrane Sensors

    Energy Technology Data Exchange (ETDEWEB)

    Boyle, T.J.; Brinker, C.J.; Gardner, T.J.; Hughes, R.C.; Sault, A.G.

    1998-12-01

    The proposed "catalytic membrane sensor" (CMS) was developed to generate a device which would selectively identify a specific reagent in a complex mixture of gases. This was to be accomplished by modifying an existing Hz sensor with a series of thin films. Through selectively sieving the desired component from a complex mixture and identifying it by decomposing it into Hz (and other by-products), a Hz sensor could then be used to detect the presence of the select component. The proposed "sandwich-type" modifications involved the deposition of a catalyst layered between two size selective sol-gel layers on a Pd/Ni resistive Hz sensor. The role of the catalyst was to convert organic materials to Hz and organic by-products. The role of the membraneo was to impart both chemical specificity by molecukir sieving of the analyte and converted product streams, as well as controlling access to the underlying Pd/Ni sensor. Ultimately, an array of these CMS elements encompassing different catalysts and membranes were to be developed which would enable improved selectivity and specificity from a compiex mixture of organic gases via pattern recognition methodologies. We have successfully generated a CMS device by a series of spin-coat deposited methods; however, it was determined that the high temperature required to activate the catalyst, destroys the sensor.

  14. Catalytic gasification of biomass

    Science.gov (United States)

    Robertus, R. J.; Mudge, L. K.; Sealock, L. J., Jr.; Mitchell, D. H.; Weber, S. L.

    1981-12-01

    Methane and methanol synthesis gas can be produced by steam gasification of biomass in the presence of appropriate catalysts. This concept is to use catalysts in a fluidized bed reactor which is heated indirectly. The objective is to determine the technical and economic feasibility of the concept. Technically the concept has been demonstrated on a 50 lb per hr scale. Potential advantages over conventional processes include: no oxygen plant is needed, little tar is produced so gas and water treatment are simplified, and yields and efficiencies are greater than obtained by conventional gasification. Economic studies for a plant processing 2000 T/per day dry wood show that the cost of methanol from wood by catalytic gasification is competitive with the current price of methanol. Similar studies show the cost of methane from wood is competitive with projected future costs of synthetic natural gas. When the plant capacity is decreased to 200 T per day dry wood, neither product is very attractive in today's market.

  15. 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.

  16. Immigration process in catalytic medium

    Institute of Scientific and Technical Information of China (English)

    洪文明; 王梓坤

    2000-01-01

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

  17. 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...

  18. 3'-UTR Polymorphisms in the MiRNA Machinery Genes DROSHA, DICER1, RAN, and XPO5 Are Associated with Colorectal Cancer Risk in a Korean Population.

    Science.gov (United States)

    Cho, Sung Hwan; Ko, Jung Jae; Kim, Jung Oh; Jeon, Young Joo; Yoo, Jung Ki; Oh, Jisu; Oh, Doyeun; Kim, Jong Woo; Kim, Nam Keun

    2015-01-01

    MicroRNAs play an important role in cancer initiation and development. The aim of this study was to investigate whether polymorphisms in miRNA machinery genes are associated with the development of colorectal cancer (CRC). RAN rs14035 CT heterozygotes and T allele carriers (CT + TT) genotypes had lower risk of CRC, while the DICER1 rs3742330, DROSHA rs10719, and XPO5 rs11077 polymorphisms were not associated with CRC in the full study sample. Specifically, male RAN rs14035 CT heterozygotes and XPO5 rs11077 AA genotype (CT/AA) carriers experienced reduced CRC susceptibility (both colon and rectal). Subgroup analysis demonstrated that the combined RAN rs14035 CT + TT genotype was associated with rectal cancer, but not colon cancer. In addition, the DICER1 rs3742330 AG genotype was associated with a significantly increased risk of colon cancer. Stratified analysis revealed the RAN rs14035 combined CT+TT genotype was associated with decreased CRC risk in male patients without diabetes mellitus (DM) and in patients with rectal cancer. In addition, we found the RAN rs14035 CC genotype was related to a decreased risk of CRC with respect to tumor size and metabolism of homocysteine and folate. Furthermore, patients diagnosed with hypertension or DM who carried the DROSHA rs10719 CC genotype showed increased CRC risk, while the XPO5 rs11077 AC+CC genotype led to increased CRC risk in patients with hypertension only. Our results indicate variations in RAN rs14035, DICER1 rs3742330, XPO5 rs11077, and DROSHA rs10719 of Korean patients are significantly associated with their risk of CRC.

  19. Performance of the Aptima High-Risk Human Papillomavirus mRNA Assay in a Referral Population in Comparison with Hybrid Capture 2 and Cytology▿

    Science.gov (United States)

    Clad, Andreas; Reuschenbach, Miriam; Weinschenk, Johanna; Grote, Ruth; Rahmsdorf, Janina; Freudenberg, Nikolaus

    2011-01-01

    This study compared the Aptima human papillomavirus (HPV) (AHPV; Gen-Probe Incorporated) assay, which detects E6/E7 mRNA from 14 high-risk types, the Hybrid Capture 2 HPV DNA (HC2; Qiagen Incorporated) test, and repeat cytology for their ability to detect high-grade cervical lesions (cervical intraepithelial neoplasia grade 2+ [CIN2+]) in women referred to colposcopy due to an abnormal Papanicolaou (Pap) smear. A total of 424 clinical specimens, stored in liquid-based cytology (LBC) vials at room temperature for up to 3 years, were tested by repeat cytology, the AHPV assay, and the HC2 test. Assay results were compared to each other and to histology results. The overall agreement between the AHPV assay and the HC2 test was 88.4%. The sensitivity (specificity) of cytology, the HC2 test, and the AHPV assay for the detection of CIN2+ was 84.9% (66.3%), 91.3% (61.0%), and 91.7% (75.0%) and for the detection of CIN3+ was 93.9% (54.4%), 95.7% (46.0%), and 98.2% (56.3%), respectively. Of the disease-positive specimens containing high-risk HPV (HR HPV) DNA as determined by Linear Array (Roche Diagnostics), the AHPV assay missed 3 CIN2 and 1 microfocal CIN3 specimen, while the HC2 test missed 6 CIN2, 4 CIN3, and 1 cervical carcinoma specimen. The AHPV assay had a sensitivity similar to but a specificity significantly higher (P < 0.0001) than the HC2 test for the detection of CIN2+. The AHPV assay was significantly more sensitive (P = 0.0041) and significantly more specific (P = 0.0163) than cytology for the detection of disease (CIN2+). PMID:21191046

  20. Performance of the Aptima high-risk human papillomavirus mRNA assay in a referral population in comparison with Hybrid Capture 2 and cytology.

    Science.gov (United States)

    Clad, Andreas; Reuschenbach, Miriam; Weinschenk, Johanna; Grote, Ruth; Rahmsdorf, Janina; Freudenberg, Nikolaus

    2011-03-01

    This study compared the Aptima human papillomavirus (HPV) (AHPV; Gen-Probe Incorporated) assay, which detects E6/E7 mRNA from 14 high-risk types, the Hybrid Capture 2 HPV DNA (HC2; Qiagen Incorporated) test, and repeat cytology for their ability to detect high-grade cervical lesions (cervical intraepithelial neoplasia grade 2+ [CIN2+]) in women referred to colposcopy due to an abnormal Papanicolaou (Pap) smear. A total of 424 clinical specimens, stored in liquid-based cytology (LBC) vials at room temperature for up to 3 years, were tested by repeat cytology, the AHPV assay, and the HC2 test. Assay results were compared to each other and to histology results. The overall agreement between the AHPV assay and the HC2 test was 88.4%. The sensitivity (specificity) of cytology, the HC2 test, and the AHPV assay for the detection of CIN2+ was 84.9% (66.3%), 91.3% (61.0%), and 91.7% (75.0%) and for the detection of CIN3+ was 93.9% (54.4%), 95.7% (46.0%), and 98.2% (56.3%), respectively. Of the disease-positive specimens containing high-risk HPV (HR HPV) DNA as determined by Linear Array (Roche Diagnostics), the AHPV assay missed 3 CIN2 and 1 microfocal CIN3 specimen, while the HC2 test missed 6 CIN2, 4 CIN3, and 1 cervical carcinoma specimen. The AHPV assay had a sensitivity similar to but a specificity significantly higher (P < 0.0001) than the HC2 test for the detection of CIN2+. The AHPV assay was significantly more sensitive (P = 0.0041) and significantly more specific (P = 0.0163) than cytology for the detection of disease (CIN2+).

  1. Protein and mRNA levels support the notion that a genetic regulatory circuit controls growth phases in E. coli populations

    Directory of Open Access Journals (Sweden)

    Agustino Martinez-Antonio

    2015-09-01

    Full Text Available Bacterial populations transition between growing and non-growing phases, based on nutrient availability and stresses conditions. The hallmark of a growing state is anabolism, including DNA replication and cell division. In contrast, bacteria in a growth-arrested state acquire a resistant physiology and diminished metabolism. However, there is little knowledge on how this transition occurs at the molecular level. Here, we provide new evidence that a multi-element genetic regulatory circuit might work to maintain genetic control among growth-phase transitions in Escherichia coli. This work contributes to the discovering of design principles behind the performance of biological functions, which could be of relevance on the new disciplines of biological engineering and synthetic biology.

  2. 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

  3. Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts.

    Science.gov (United States)

    Stenger, Drake C; Krugner, Rodrigo; Nouri, Shahideh; Ferriol, Inmaculada; Falk, Bryce W; Sisterson, Mark S

    2016-11-01

    Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of the corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection.

  4. Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes.

    Science.gov (United States)

    Silverman, Scott K

    2016-07-01

    The discovery of natural RNA enzymes (ribozymes) prompted the pursuit of artificial DNA enzymes (deoxyribozymes) by in vitro selection methods. A key motivation is the conceptual and practical advantages of DNA relative to proteins and RNA. Early studies focused on RNA-cleaving deoxyribozymes, and more recent experiments have expanded the breadth of catalytic DNA to many other reactions. Including modified nucleotides has the potential to widen the scope of DNA enzymes even further. Practical applications of deoxyribozymes include their use as sensors for metal ions and small molecules. Structural studies of deoxyribozymes are only now beginning; mechanistic experiments will surely follow. Following the first report 21 years ago, the field of deoxyribozymes has promise for both fundamental and applied advances in chemistry, biology, and other disciplines.

  5. 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.

  6. 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...

  7. RNA signal amplifier circuit with integrated fluorescence output.

    Science.gov (United States)

    Akter, Farhima; Yokobayashi, Yohei

    2015-05-15

    We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.

  8. Hyperexpansion of RNA Bacteriophage Diversity

    Science.gov (United States)

    Krishnamurthy, Siddharth R.; Janowski, Andrew B.; Zhao, Guoyan; Barouch, Dan; Wang, David

    2016-01-01

    Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent. PMID:27010970

  9. Hyperexpansion of RNA Bacteriophage Diversity.

    Directory of Open Access Journals (Sweden)

    Siddharth R Krishnamurthy

    2016-03-01

    Full Text Available Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent.

  10. Hyperexpansion of RNA Bacteriophage Diversity.

    Science.gov (United States)

    Krishnamurthy, Siddharth R; Janowski, Andrew B; Zhao, Guoyan; Barouch, Dan; Wang, David

    2016-03-01

    Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent.

  11. 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.

  12. 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.

  13. 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....

  14. 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

  15. 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.

  16. 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

  17. 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)

  18. Simple, chemoselective, catalytic olefin isomerization.

    Science.gov (United States)

    Crossley, Steven W M; Barabé, Francis; Shenvi, Ryan A

    2014-12-01

    Catalytic amounts of Co(Sal(tBu,tBu))Cl and organosilane irreversibly isomerize terminal alkenes by one position. The same catalysts effect cycloisomerization of dienes and retrocycloisomerization of strained rings. Strong Lewis bases like amines and imidazoles, and labile functionalities like epoxides, are tolerated.

  19. 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...

  20. Synthesis of Glu-tRNA(Gln) by engineered and natural aminoacyl-tRNA synthetases.

    Science.gov (United States)

    Rodríguez-Hernández, Annia; Bhaskaran, Hari; Hadd, Andrew; Perona, John J

    2010-08-10

    A protein engineering approach to delineating which distinct elements of homologous tRNA synthetase architectures are responsible for divergent RNA-amino acid pairing specificities is described. Previously, we constructed a hybrid enzyme in which 23 amino acids from the catalytic domain of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) were replaced with the corresponding residues of human glutamyl-tRNA synthetase (GluRS). The engineered hybrid (GlnRS S1/L1/L2) synthesizes Glu-tRNA(Gln) more than 10(4)-fold more efficiently than GlnRS. Detailed comparison of kinetic parameters between GlnRS S1/L1/L2 and the naturally occurring Methanothermobacter thermautotrophicus GluRS(ND), which is also capable of Glu-tRNA(Gln) synthesis, now shows that both k(cat) and K(m) for glutamate are recapitulated in the engineered enzyme, but that K(m) for tRNA is 200-fold higher. Thus, the simultaneous optimization of paired amino acid and tRNA binding sites found in a naturally occurring enzyme is not recapitulated in a hybrid that is successfully engineered for amino acid complementarity. We infer that the GlnRS architecture has differentiated to match only cognate amino acid-RNA pairs, and that the substrate selection functions do not operate independently of each other. Design and characterization of four additional hybrids identify further residues involved in improving complementarity for glutamate and in communicating between amino acid and tRNA binding sites. The robust catalytic function demonstrated in this engineered system offers a novel platform for exploring the stereochemical origins of coding as a property of the ancient Rossmann fold.

  1. 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....

  2. Purification and Characterization of Recombinant Deinococcus radiodurans RNA Polymerase.

    Science.gov (United States)

    Esyunina, D M; Kulbachinskiy, A V

    2015-10-01

    The radioresistant bacterium Deinococcus radiodurans is one of the most interesting models for studies of cell stress resistance. Analysis of the mechanisms of gene expression in D. radiodurans revealed some specific features of the transcription apparatus that might play a role in cell resistance to DNA-damaging conditions. In particular, RNA polymerase from D. radiodurans forms unstable promoter complexes and during transcription elongation has a much higher rate of RNA cleavage than RNA polymerase from Escherichia coli. Analysis of the structure and functions of D. radiodurans RNA polymerase is complicated due to the absence of convenient genetic systems for making mutations in the RNA polymerase genes and difficulties with enzyme purification. In this work, we developed a system for expression of D. radiodurans RNA polymerase in E. coli cells. We obtained an expression vector encoding all core RNA polymerase subunits and defined optimal conditions for the expression and purification of the RNA polymerase. It was found that D. radiodurans RNA polymerase has much higher rates of RNA cleavage than E. coli RNA polymerase under a wide range of conditions, including variations in the concentration of catalytic magnesium ions and pH values of the reaction buffer. The expression system can be used for further studies of the RNA cleavage reaction and the mechanisms of transcription regulation in D. radiodurans, including analysis of mutant RNA polymerase variants.

  3. How amino acids and peptides shaped the RNA world.

    Science.gov (United States)

    van der Gulik, Peter T S; Speijer, Dave

    2015-01-01

    The "RNA world" hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a "pure RNA ribosome" evolution started out with. Though the oldest center of the ribosome seems "RNA only", we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to basepairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the "RNA world" view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus. We argue that an RNA world completely independent of amino acids never existed. PMID:25607813

  4. 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.

  5. 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)

  6. Thermodynamics of catalytic nanoparticle morphology

    Science.gov (United States)

    Zwolak, Michael; Sharma, Renu; Lin, Pin Ann

    Metallic nanoparticles are an important class of industrial catalysts. The variability of their properties and the environment in which they act, from their chemical nature & surface modification to their dispersion and support, allows their performance to be optimized for many chemical processes useful in, e.g., energy applications and other areas. Their large surface area to volume ratio, as well as varying sizes and faceting, in particular, makes them an efficient source for catalytically active sites. These characteristics of nanoparticles - i.e., their morphology - can often display intriguing behavior as a catalytic process progresses. We develop a thermodynamic model of nanoparticle morphology, one that captures the competition of surface energy with other interactions, to predict structural changes during catalytic processes. Comparing the model to environmental transmission electron microscope images of nickel nanoparticles during carbon nanotube (and other product) growth demonstrates that nickel deformation in response to the nanotube growth is due to a favorable interaction with carbon. Moreover, this deformation is halted due to insufficient volume of the particles. We will discuss the factors that influence morphology and also how the model can be used to extract interaction strengths from experimental observations.

  7. 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

  8. Investigating RNA editing factors from trypanosome mitochondria

    Science.gov (United States)

    Aphasizheva, Inna; Zhang, Liye; Aphasizhev, Ruslan

    2016-01-01

    Mitochondrial U-insertion/deletion mRNA editing is carried out by two principal multiprotein assemblies, enzymatic RNA editing core (RECC) and RNA editing substrate binding (RESC) complexes, and a plethora of auxiliary factors. An integral part of mitochondrial gene expression, editing receives inputs from primary mRNA and gRNA precursor processing pathways, and generates substrates for mRNA polyadenylation and translation. Although nearly all RECC-embedded enzymes have been implicated in specific editing reactions, the majority of proteins that populate the RESC are also essential for generating edited mRNAs. However, lack of recognizable motifs in RESC subunits limits the prowess of bioinformatics in guiding biochemical experiments and elucidating their specific biological functions. In this chapter, we describe a generic workflow for investigating mitochondrial mRNA editing in Trypanosoma brucei and focus on several methods that proved instrumental is assigning definitive functions to editing factors lacking known signature sequences. PMID:27020893

  9. 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

  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. 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...

  12. 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

  13. 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

  14. 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.

  15. Computational Introduction of Catalytic Activity into Proteins.

    Science.gov (United States)

    Bertolani, Steve J; Carlin, Dylan Alexander; Siegel, Justin B

    2016-01-01

    Recently, there have been several successful cases of introducing catalytic activity into proteins. One method that has been used successfully to achieve this is the theozyme placement and enzyme design algorithms implemented in Rosetta Molecular Modeling Suite. Here, we illustrate how to use this software to recapitulate the placement of catalytic residues and ligand into a protein using a theozyme, protein scaffold, and catalytic constraints as input. PMID:27094294

  16. 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)

  17. 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)

  18. Some Aspects of the Catalytic Organic Synthesis

    Institute of Scientific and Technical Information of China (English)

    Anil; K.Saikia

    2007-01-01

    1 Results Catalytic reactions are gaining importance due to its low cost, operational simplicity, high efficiency and selectivity. It is also getting much attention in green synthesis. Many useful organic reactions, including the acylation of alcohols and aldehydes, carbon-carbon, carbon-nitrogen, carbon-sulfur bond forming and oxidation reactions are carried out by catalyst. We are exploring the catalytic acylation of alcohols and aldehydes in a simple and efficient manner. Catalytic activation of unr...

  19. 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...

  20. 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...

  1. 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.)

  2. 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).

  3. 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

  4. 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...

  5. 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,...

  6. 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...

  7. 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...

  8. Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly.

    Science.gov (United States)

    Hardwick, Steven W; Gubbey, Tobias; Hug, Isabelle; Jenal, Urs; Luisi, Ben F

    2012-04-01

    Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3'-5' directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3' end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a 'splayed' conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the α-proteobacteria.

  9. 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...

  10. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold.

    Science.gov (United States)

    Ericsson, Ulrika B; Nordlund, Pär; Hallberg, B Martin

    2004-05-01

    Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine in structural RNA. The pseudouridine synthase TruD, that modifies U13 in tRNA, belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life. We report here the crystal structure of Escherichia coli TruD at 2.0 A resolution. The structure reveals an overall V-shaped molecule with an RNA-binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold.

  11. 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.

  12. CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders.

    Science.gov (United States)

    Weitzer, Stefan; Hanada, Toshikatsu; Penninger, Josef M; Martinez, Javier

    2015-01-01

    Defects in RNA metabolic pathways are well-established causes for neurodegenerative disorders. Several mutations in genes involved in pre-messenger RNA (pre-mRNA) and tRNA metabolism, RNA stability and protein translation have been linked to motor neuron diseases. Our study on a mouse carrying a catalytically inactive version of the RNA kinase CLP1, a component of the tRNA splicing endonuclease complex, revealed a neurological disorder characterized by progressive loss of lower spinal motor neurons. Surprisingly, mutant mice accumulate a novel class of tRNA-derived fragments. In addition, patients with homozygous missense mutations in CLP1 (R140H) were recently identified who suffer from severe motor-sensory defects, cortical dysgenesis and microcephaly, and exhibit alterations in transfer RNA (tRNA) splicing. Here, we review functions of CLP1 in different RNA pathways and provide hypotheses on the role of the tRNA splicing machinery in the generation of tRNA fragments and the molecular links to neurodegenerative disorders. We further immerse the biology of tRNA splicing into topics of (t)RNA metabolism and oxidative stress, putting forward the idea that defects in tRNA processing leading to tRNA fragment accumulation might trigger the development of neurodegenerative diseases.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.)

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  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. 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.

  6. 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

  7. 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...

  8. 基于ITS1-5.8S rRNA-ITS2序列的猪源结肠小袋纤毛虫种群特征分析%Population characterization of Balantidium coli from pigs using ITS1-5.8S rRNA-ITS2 sequence

    Institute of Scientific and Technical Information of China (English)

    王天奇; 窦刚; 闫文朝; 张龙现; 韩利方; 丁轲; 贾川川; 张梦; 于杜鹃

    2011-01-01

    [目的]为了揭示结肠小袋纤毛虫病在环境中的分子传播机制,研究了猪源结肠小袋纤毛虫的种群特征.[方法]用粪便涂片镜检和改进型DMEM培养基从病猪结肠内容物分离结肠小袋纤毛虫滋养体,然后用显微观察、吖啶橙荧光染色法和基于ITS1-5.8s rRNA-ITS2序列的分子标记技术分析了豫西地区猪群中结肠小袋纤毛虫的种群特征.[结果]结果显示,从来自豫西地区8个县市的病猪中共分离了15株小袋纤毛虫,5.8S rRNA序列相似性高达99.4%以上,同属于结肠小袋纤毛虫,根据ITS1/2序列分析结果,MJ-2和SX-1株属于结肠小袋纤毛虫基因型A,其余13株均属于结肠小袋纤毛虫基因型B.MJ-2和SX-1株滋养体形态特征明显区别其他13株,绝大多数呈球形,运动缓慢,粪便中和体外培养的虫体密度较低;而其他13株的滋养体均呈多形性,运动快速活跃,虫体密度较大.吖啶橙荧光染色显示,2种基因型滋养体的核结构没明显差别.[结论]首次报道中国猪源结肠小袋纤毛虫存在2个基因型,其中基因型B为优势种群,为防控人和动物结肠小袋纤毛虫病提供重要参考.%[Objective]To determine the species and genotypes of Balantidium isolated from pigs in Henan province, China.[Methods]Scatoscopy and the modified DMEM media were used to isolate trophozoites of Balantidium from pig feces.The ITS1-5.8S rRNA-ITS2-based molecular marker method, Acridine orange staining ( AO) and microscopic observation were used to determine the population characteristics among different isolates of B.coli from various pigs farms.[Results]We isolated 15 isolates from the pigs at diagnosis in the Animal Hospital of Henan University of Science and Technology from the pig farms of the 8 counties or cities of the west of Henan province in total, and all of them belong to the same species B.coli.MJ-2 and SX-1 isolates were genotype A of B.coli, and the remaining 13 isolates were genotype B

  9. 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

  10. 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.

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

    Science.gov (United States)

    Lama, Lodoe; Ryan, Kevin

    2016-01-01

    Many high-throughput small RNA next-generation sequencing protocols use 5' preadenylylated DNA oligonucleotide adapters during cDNA library preparation. Preadenylylation of the DNA adapter's 5' end frees from ATP-dependence the ligation of the adapter to RNA collections, thereby avoiding ATP-dependent side reactions. However, preadenylylation of the DNA adapters can be costly and difficult. The currently available method for chemical adenylylation of DNA adapters is inefficient and uses techniques not typically practiced in laboratories profiling cellular RNA expression. An alternative enzymatic method using a commercial RNA ligase was recently introduced, but this enzyme works best as a stoichiometric adenylylating reagent rather than a catalyst and can therefore prove costly when several variant adapters are needed or during scale-up or high-throughput adenylylation procedures. Here, we describe a simple, scalable, and highly efficient method for the 5' adenylylation of DNA oligonucleotides using the thermostable RNA ligase 1 from bacteriophage TS2126. Adapters with 3' blocking groups are adenylylated at >95% yield at catalytic enzyme-to-adapter ratios and need not be gel purified before ligation to RNA acceptors. Experimental conditions are also reported that enable DNA adapters with free 3' ends to be 5' adenylylated at >90% efficiency. PMID:26567315

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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....

  18. 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.

  19. 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.

  20. Catalytic Radical Domino Reactions in Organic Synthesis

    Science.gov (United States)

    Sebren, Leanne J.; Devery, James J.; Stephenson, Corey R.J.

    2014-01-01

    Catalytic radical-based domino reactions represent important advances in synthetic organic chemistry. Their development benefits synthesis by providing atom- and step-economical methods to complex molecules. Intricate combinations of radical, cationic, anionic, oxidative/reductive, and transition metal mechanistic steps result in cyclizations, additions, fragmentations, ring-expansions, and rearrangements. This Perspective summarizes recent developments in the field of catalytic domino processes. PMID:24587964

  1. 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.

  2. 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...

  3. 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

  4. RNA modifications by oxidation

    DEFF Research Database (Denmark)

    Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper;

    2012-01-01

    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...... type 2 diabetics; this demonstrates the clinical relevance of RNA oxidation. Taken collectively the available data suggest that RNA oxidation is a contributing factor in several diseases such as diabetes, hemochromatosis, heart failure, and ß-cell destruction. The mechanism involves free iron...

  5. 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.

  6. 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

  7. 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

  8. Catalytic hydrogenation of carbon monoxide

    Energy Technology Data Exchange (ETDEWEB)

    Wayland, B.B.

    1992-12-01

    This project is focused on developing strategies to accomplish the reduction and hydrogenation of carbon monoxide to produce organic oxygenates at mild conditions. Our approaches to this issue are based on the recognition that rhodium macrocycles have unusually favorable thermodynamic values for producing a series of intermediate implicated in the catalytic hydrogenation of CO. Observations of metalloformyl complexes produced by reactions of H{sub 2} and CO, and reductive coupling of CO to form metallo {alpha}-diketone species have suggested a multiplicity of routes to organic oxygenates that utilize these species as intermediates. Thermodynamic and kinetic-mechanistic studies are used in constructing energy profiles for a variety of potential pathways, and these schemes are used in guiding the design of new metallospecies to improve the thermodynamic and kinetic factors for individual steps in the overall process. Variation of the electronic and steric effects associated with the ligand arrays along with the influences of the reaction medium provide the chemical tools for tuning these factors. Emerging knowledge of the factors that contribute to M-H, M-C and M-O bond enthalpies is directing the search for ligand arrays that will expand the range of metal species that have favorable thermodynamic parameters to produce the primary intermediates for CO hydrogenation. Studies of rhodium complexes are being extended to non-macrocyclic ligand complexes that emulate the favorable thermodynamic features associated with rhodium macrocycles, but that also manifest improved reaction kinetics. Multifunctional catalyst systems designed to couple the ability of rhodium complexes to produce formyl and diketone intermediates with a second catalyst that hydrogenates these imtermediates are promising approaches to accomplish CO hydrogenation at mild conditions.

  9. 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...

  10. 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

  11. 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 ...

  12. 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...

  13. Kinetics of catalytically activated duplication in aggregation growth

    Institute of Scientific and Technical Information of China (English)

    Wang Hai-Feng; Lin Zhen-Quan; Gao Yan; Xu Chao

    2009-01-01

    We propose a catalytically activated duplication model to mimic the coagulation and duplication of the DNA polymer system under the catalysis of the primer RNA.In the model,two aggregates of the same species can coagulate themselves and a DNA aggregate of any size can yield a new monomer or double itself with the help of RNA aggregates.By employing the mean-field rate equation approach we analytically investigate the evolution behaviour of the system.For the system with catalysis-driven monomer duplications,the aggregate size distribution of DNA polymers ak(t) always follows a power law in size in the long-time limit,and it decreases with time or approaches a time-independent steady-state form in the case of the duplication rate independent of the size of the mother aggregates,while it increases with time increasing in the case of the duplication rate proportional to the size of the mother aggregates.For the system with complete catalysis-driven duplications,the aggregate size distribution ak(t) approaches a generalized or modified scaling form.

  14. 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.

  15. RNA Localization in Astrocytes

    DEFF Research Database (Denmark)

    Thomsen, Rune

    2012-01-01

    of 18S ribosomal RNA and the Rab13, Pkp4, Ankrd25, and Inpp1 mRNAs in astrocyte protrusions. The Boyden chamber isolated RNA from both primary astrocytes and C8S cells was analyzed by next generation sequencing (NGS), which revealed that >250 polyadenylated (polyA) RNA species accumulated in the cell...

  16. 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 po...

  17. RNA self-assembly and RNA nanotechnology.

    Science.gov (United States)

    Grabow, Wade W; Jaeger, Luc

    2014-06-17

    CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such

  18. 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.

  19. Catalytic coal liquefaction. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Weller, S W

    1981-01-01

    Monolith catalysts of MoO/sub 3/-CoO-Al/sub 2/O/sub 3/ were prepared and tested for coal liquefaction in a stirred autoclave. In general, the monolith catalysts were not as good as particulate catalysts prepared on Corning alumina supports. Measurement of O/sub 2/ chemisorption and BET surface area has been made on a series of Co/Mo/Al/sub 2/O/sub 3/ catalysts obtained from PETC. The catalysts were derived from Cyanamid 1442A and had been tested for coal liquefaction in batch autoclaves and continuous flow units. MoO/sub 3/-Al/sub 2/O/sub 3/ catalysts over the loading range 3.9 to 14.9 wt % MoO/sub 3/ have been studied with respect to BET surface (before and after reduction), O/sub 2/ chemisorption at -78/sup 0/C, redox behavior at 500/sup 0/C, and activity for cyclohexane dehydrogenation at 500/sup 0/C. In connection with the fate of tin catalysts during coal liquefaction, calculations have been made of the relative thermodynamic stability of SnCl/sub 2/, Sn, SnO/sub 2/, and SnS in the presence of H/sub 2/, HCl, H/sub 2/S and H/sub 2/O. Ferrous sulfate dispersed in methylnaphthalene has been shown to be reduced to ferrous sulfide under typical coal hydroliquefaction conditions (1 hour, 450/sup 0/C, 1000 psi initial p/sub H/sub 2//). This suggests that ferrous sulfide may be the common catalytic ingredient when either (a) ferrous sulfate impregnated on powdered coal, or (b) finely divided iron pyrite is used as the catalyst. Old research on impregnated ferrous sulfate, impregnated ferrous halides, and pyrite is consistent with this assumption. Eight Co/Mo/Al/sub 2/O/sub 3/ catalysts from commercial suppliers, along with SnCl/sub 2/, have been studied for the hydrotreating of 1-methylnaphthalene (1-MN) in a stirred autoclave at 450 and 500/sup 0/C.

  20. 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.

  1. 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.

  2. 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.

  3. Cytoplasmic Z-RNA

    Energy Technology Data Exchange (ETDEWEB)

    Zarling, D.A.; Calhoun, C.J.; Hardin, C.C.; Zarling, A.H.

    1987-09-01

    Specific immunochemical probes for Z-RNA were generated and characterized to search for possible Z-RNA-like double helices in cells. Z-RNA was detected in the cytoplasm of fixed protozoan cells by immunofluorescence microscopy using these anti-Z-RNA IgCs. In contrast, autoimmune or experimentally elicited anti-DNA antibodies, specifically reactive with B-DNA or Z-DNA, stained the nuclei. Pre-or nonimmune IgGs did not bind to the cells. RNase A or T1 digestion eliminated anti-Z-RNA IgG binding to cytoplasmic determinants; however, DNase I or mung bean nuclease had no effect. Doxorubicin and ethidium bromide prevented anti-Z-RNA antibody binding; however, actinomycin D, which does not bind double-stranded RNA, did not. Anti-Z-RNA immunofluorescence was specifically blocked in competition assays by synthetic Z-RNA but not Z-DNA, A-RNA, or single-stranded RNAs. Thus, some cytoplasmic sequences in fixed cells exist in the left-handed Z-RNA conformation.

  4. A novel liquid system of catalytic hydrogenation

    Institute of Scientific and Technical Information of China (English)

    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.

  5. 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...

  6. 燃煤型氟中毒病区人群外周血谷胱甘肽硫转移酶mRNA表达%Expression of glutathione S-transferase mRNA in peripheral blood of the population in coal-burning fluorosis area

    Institute of Scientific and Technical Information of China (English)

    吴昌学; 单可人; 官志忠

    2010-01-01

    目的 研究燃煤型氟中毒病区人群外周血谷胱甘肽硫转移酶(GST)基因的mRNA表达,了解氟中毒地区经综合干预后的效果.方法 采集贵州省毕节市燃煤型氟中毒病区患者(氟中毒组)和经综合干预后的患者(氟中毒干预组)外周血样本各50例,以非病区健康人外周血标本50例作为对照,Trizol-酚-氯仿一步法提取总RNA,以SYBR Green I为荧光介质.采用实时荧光定量PCR技术测定外周血细胞GST mRNA表达水平.结果 氟中毒组、氟中毒干预组和对照组外周血细 胞GST mRNA表达分别为38.28±27.22、70.56±37.23和103.46±46.62,组间比较差异有统计学意义(F=3.75,P<0.05).氟中毒组与氟中毒干预组GsT mRNA表达水平较对照组降低(P均<0.05),氟中毒干预组GST mRNA表达水平较氟中毒组升高(P<0.05).结论 燃煤型氟中毒能降低GST在外周血中的表达,经综合干预后可使GST表达有所回升.%Objective To investigate expression of glutathione S-transferase(GST) mRNA in peripheral blood of the population in coal-burning fluorosis area and to evaluate the effect of comprehensive control intervention. Methods Fifty samples of peripheral blood from patients in the coal-buring fluorosis area in Bijie county of Guizhou province were selected as fluorasis group and 50 samples of peripheral blood from patients in area with comprehensive management were selected as intervention group, respectively. Fifty samples from non-endemic fluorosis area were selected as the control group. Total RNA from blood was extracted and purified by the Trizol- Phenol-Chloroform one-step method. Expression of GST mRNA was detected by using SYBR Green I real-time fluorescence quantitative PCR. Results The data of GST mRNA in fluorosis group, intervention group and control group was 38.28±27.22,70.56±37.23 and 103.46 ± 46.62, respectively. There was a significant difference between the groups(F = 3.75, P < 0.05). Decreased expression of GST mRNA in

  7. 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...

  8. 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.

  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. 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.

  11. Catalytic Organic Transformations Mediated by Actinide Complexes

    Directory of Open Access Journals (Sweden)

    Isabell S. R. Karmel

    2015-10-01

    Full Text Available This review article presents the development of organoactinides and actinide coordination complexes as catalysts for homogeneous organic transformations. This chapter introduces the basic principles of actinide catalysis and deals with the historic development of actinide complexes in catalytic processes. The application of organoactinides in homogeneous catalysis is exemplified in the hydroelementation reactions, such as the hydroamination, hydrosilylation, hydroalkoxylation and hydrothiolation of alkynes. Additionally, the use of actinide coordination complexes for the catalytic polymerization of α-olefins and the ring opening polymerization of cyclic esters is presented. The last part of this review article highlights novel catalytic transformations mediated by actinide compounds and gives an outlook to the further potential of this field.

  12. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei;

    2015-01-01

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

  13. Reactivity of organic compounds in catalytic synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Minachev, Kh.M.; Bragin, O.V.

    1978-01-01

    A comprehensive review of 1976 Soviet research on catalysis delivered to the 1977 annual session of the USSR Academy of Science Council on Catalysis (Baku 6/16-20/77) covers hydrocarbon reactions, including hydrogenation and hydrogenolysis, dehydrogenation, olefin dimerization and disproportionation, and cyclization and dehydrocyclization (e.g., piperylene cyclization and ethylene cyclotrimerization); catalytic and physicochemical properties of zeolites, including cracking, dehydrogenation, and hydroisomerization catalytic syntheses and conversion of heterocyclic and functional hydrocarbon derivatives, including partial and total oxidation (e.g., of o-xylene to phthalic anhydride); syntheses of thiophenes from alkanes and hydrogen sulfide over certain dehydrogenation catalysts; catalytic syntheses involving carbon oxides ( e.g., the development of a new heterogeneous catalyst for hydroformylation of olefins), and of Co-MgO zeolitic catalysts for synthesis of aliphatic hydrocarbons from carbon dioxide and hydrogen, and fabrication of high-viscosity lubricating oils over bifunctional aluminosilicate catalysts.

  14. 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.)

  15. 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.

  16. 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

  17. 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

  18. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne;

    2007-01-01

    : the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

  19. Mutational analysis of a ras catalytic domain

    DEFF Research Database (Denmark)

    Willumsen, B M; Papageorge, A G; Kung, H F;

    1986-01-01

    We used linker insertion-deletion mutagenesis to study the catalytic domain of the Harvey murine sarcoma virus v-rasH transforming protein, which is closely related to the cellular rasH protein. The mutants displayed a wide range of in vitro biological activity, from those that induced focal...... transformation of NIH 3T3 cells with approximately the same efficiency as the wild-type v-rasH gene to those that failed to induce any detectable morphologic changes. Correlation of transforming activity with the location of the mutations enabled us to identify three nonoverlapping segments within the catalytic...

  20. 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.

  1. 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.

  2. 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.)

  3. 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.

  4. A conserved loop in polynucleotide phosphorylase (PNPase) essential for both RNA and ADP/phosphate binding.

    Science.gov (United States)

    Carzaniga, Thomas; Mazzantini, Elisa; Nardini, Marco; Regonesi, Maria Elena; Greco, Claudio; Briani, Federica; De Gioia, Luca; Dehò, Gianni; Tortora, Paolo

    2014-02-01

    Polynucleotide phosphorylase (PNPase) reversibly catalyzes RNA phosphorolysis and polymerization of nucleoside diphosphates. Its homotrimeric structure forms a central channel where RNA is accommodated. Each protomer core is formed by two paralogous RNase PH domains: PNPase1, whose function is largely unknown, hosts a conserved FFRR loop interacting with RNA, whereas PNPase2 bears the putative catalytic site, ∼20 Å away from the FFRR loop. To date, little is known regarding PNPase catalytic mechanism. We analyzed the kinetic properties of two Escherichia coli PNPase mutants in the FFRR loop (R79A and R80A), which exhibited a dramatic increase in Km for ADP/Pi binding, but not for poly(A), suggesting that the two residues may be essential for binding ADP and Pi. However, both mutants were severely impaired in shifting RNA electrophoretic mobility, implying that the two arginines contribute also to RNA binding. Additional interactions between RNA and other PNPase domains (such as KH and S1) may preserve the enzymatic activity in R79A and R80A mutants. Inspection of enzyme structure showed that PNPase has evolved a long-range acting hydrogen bonding network that connects the FFRR loop with the catalytic site via the F380 residue. This hypothesis was supported by mutation analysis. Phylogenetic analysis of PNPase domains and RNase PH suggests that such network is a unique feature of PNPase1 domain, which coevolved with the paralogous PNPase2 domain.

  5. 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 ...

  6. 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.

  7. iRNA-seq

    DEFF Research Database (Denmark)

    Madsen, Jesper Grud Skat; Schmidt, Søren Fisker; Larsen, Bjørk Ditlev;

    2015-01-01

    RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we...... have developed an easy, sensitive and accurate novel computational method, IRNA-SEQ: , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using...... current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all...

  8. RNA-modifying enzymes.

    Science.gov (United States)

    Ferré-D'Amaré, Adrian R

    2003-02-01

    A bewildering number of post-transcriptional modifications are introduced into cellular RNAs by enzymes that are often conserved among archaea, bacteria and eukaryotes. The modifications range from those with well-understood functions, such as tRNA aminoacylation, to widespread but more mysterious ones, such as pseudouridylation. Recent structure determinations have included two types of RNA nucleobase modifying enzyme: pseudouridine synthases and tRNA guanine transglycosylases.

  9. 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.

  10. 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.

  11. 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.

  12. Catalytic site interactions in yeast OMP synthase

    DEFF Research Database (Denmark)

    Hansen, Michael Riis; Barr, Eric W.; Jensen, Kaj Frank;

    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...

  13. Lignin Valorization using Heterogenous Catalytic Oxidation

    DEFF Research Database (Denmark)

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

    is 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...

  14. 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.

  15. 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...

  16. 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…

  17. 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

  18. 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.

  19. Rapid Deployment of Rich Catalytic Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Richard S. Tuthill

    2004-06-10

    The overall objective of this research under the Turbines Program is the deployment of fuel flexible rich catalytic combustion technology into high-pressure ratio industrial gas turbines. The resulting combustion systems will provide fuel flexibility for gas turbines to burn coal derived synthesis gas or natural gas and achieve NO{sub x} emissions of 2 ppmvd or less (at 15 percent O{sub 2}), cost effectively. This advance will signify a major step towards environmentally friendly electric power generation and coal-based energy independence for the United States. Under Phase 1 of the Program, Pratt & Whitney (P&W) performed a system integration study of rich catalytic combustion in a small high-pressure ratio industrial gas turbine with a silo combustion system that is easily scalable to a larger multi-chamber gas turbine system. An implementation plan for this technology also was studied. The principal achievement of the Phase 1 effort was the sizing of the catalytic module in a manner which allowed a single reactor (rather than multiple reactors) to be used by the combustion system, a conclusion regarding the amount of air that should be allocated to the reaction zone to achieve low emissions, definition of a combustion staging strategy to achieve low emissions, and mechanical integration of a Ceramic Matrix Composite (CMC) combustor liner with the catalytic module.

  20. 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

  1. 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.

  2. 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....

  3. 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

  4. 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...

  5. 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.

  6. 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 ...

  7. 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...

  8. 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

  9. 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.

  10. 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.  ……

  11. RNA decay by messenger RNA interferases

    DEFF Research Database (Denmark)

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

    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 mR...

  12. 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...

  13. Effect of antisense oligonucleotides targeting telomerase catalytic subunit on tumor cell proliferationin vitro

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    To screen specific antitumor drugs targeting telomerase catalytic subunit (hEST2), 12 different hEST2 antisense oligonucleotides were designed based on hEST2 mRNA second structure and transfected into tumor cell lines by the lipofectin-mediated method. Cell growth activity was evaluated by MTT assay. hEST212 was picked out and its specificity, antitumor tree and continuous effect were analyzed. The results showed that hEST212 had promising antitumor activity in vitro, hEST2 can be used as a pratical target and an antisense drug candidate for cancer.

  14. 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...

  15. Phylogeny and evolution of RNA structure.

    Science.gov (United States)

    Gesell, Tanja; Schuster, Peter

    2014-01-01

    Darwin's conviction that all living beings on Earth are related and the graph of relatedness is tree-shaped has been essentially confirmed by phylogenetic reconstruction first from morphology and later from data obtained by molecular sequencing. Limitations of the phylogenetic tree concept were recognized as more and more sequence information became available. The other path-breaking idea of Darwin, natural selection of fitter variants in populations, is cast into simple mathematical form and extended to mutation-selection dynamics. In this form the theory is directly applicable to RNA evolution in vitro and to virus evolution. Phylogeny and population dynamics of RNA provide complementary insights into evolution and the interplay between the two concepts will be pursued throughout this chapter. The two strategies for understanding evolution are ultimately related through the central paradigm of structural biology: sequence ⇒ structure ⇒ function. We elaborate on the state of the art in modeling both phylogeny and evolution of RNA driven by reproduction and mutation. Thereby the focus will be laid on models for phylogenetic sequence evolution as well as evolution and design of RNA structures with selected examples and notes on simulation methods. In the perspectives an attempt is made to combine molecular structure, population dynamics, and phylogeny in modeling evolution.

  16. 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...

  17. 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)

  18. 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.

  19. Identification of autoantibodies to tyrosil-tRNA synthetase in heart disfunctions

    Directory of Open Access Journals (Sweden)

    Ryabenko D. V.

    2010-09-01

    Full Text Available Aim. To investigate the levels of specific autoantibodies against tyrosyl-tRNA synthetase and its individual modules in the blood serum of people with heart failure caused by dilated cardiomyopathy, myocarditis and ischemic heart disease compared with healthy donors. Methods. Recombinant proteins were obtained using bacterial strains transformed with appropriate plasmid vectors and were purified by chromatography on Ni-NTA-agarose. The levels of specific autoantibodies were investigated by ELISA. Results. The increased levels of autoantibodies specific to tyrosyl-tRNA synthetase, its N-terminal catalytic module and non-catalytic C-module, were found in the blood serum of patients, compared with healthy donors. Conclusions. The results obtained demonstrate the possible role of tyrosyl-tRNA synthetase in adaptive changes of the myocardium in response to stress factors.

  20. Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business.

    Science.gov (United States)

    Wedekind, Joseph E; Dance, Geoffrey S C; Sowden, Mark P; Smith, Harold C

    2003-04-01

    Alteration of mRNA sequence through base modification mRNA editing frequently generates protein diversity. Several proteins have been identified as being similar to C-to-U mRNA editing enzymes based on their structural domains and the occurrence of a catalytic domain characteristic of cytidine deaminases. In light of the hypothesis that these proteins might represent novel mRNA editing systems that could affect proteome diversity, we consider their structure, expression and relevance to biomedically significant processes or pathologies. PMID:12683974

  1. Identification of host factors that regulate the influenza virus RNA polymerase activity.

    Science.gov (United States)

    Momose, F; Handa, H; Nagata, K

    1996-01-01

    Transcription and replication of the influenza virus RNA genome take place in the nuclei of infected cells. Ribonucleoprotein (RNP) complexes consisting of viral RNA, RNA polymerase, and nucleocapsid protein (NP) are proven to be the catalytic unit for RNA synthesis, while it has been indicated that the viral RNA polymerase activity is modulated by host-derived nuclear factors. Here we have identified such host factors present in nuclear extracts prepared from uninfected HeLa cells with biochemical complementation assays using the in vitro RNA synthesis system. The stimulatory activity was not absorbed to phosphocellulose but was tightly bound to Q-Sepharose. The eluate recovered from Q-Sepharose was able to stimulate the RNA synthesis catalyzed by both RNP complexes and purified RNA polymerase and NP. The stimulatory activity was further separated into two distinct fractions, designated RAF-1 (RNA polymerase activating factor-1) and RAF-2 fractions, through phenyl-Sepharose column chromatography. When these fractions were fractionated through a gel filtration column, RAF-1 and RAF-2 activities were recovered in fractions corresponding to the molecular mass of 350 kDa and 60 kDa, respectively. Furthermore, the RAF-2 fraction was shown to contain an inhibitory activity, tentatively designated RIF-1 (RNA polymerase inhibitory factor-1). RIF-1 sedimented as fast as bovine serum albumin in glycerol density gradient centrifugation. Roles of these host factors are discussed in the context of viral RNA transcription and replication.

  2. 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)

  3. Signature motifs of GDP polyribonucleotidyltransferase, a non-segmented negative strand RNA viral mRNA capping enzyme, domain in the L protein are required for covalent enzyme-pRNA intermediate formation.

    Science.gov (United States)

    Neubauer, Julie; Ogino, Minako; Green, Todd J; Ogino, Tomoaki

    2016-01-01

    The unconventional mRNA capping enzyme (GDP polyribonucleotidyltransferase, PRNTase; block V) domain in RNA polymerase L proteins of non-segmented negative strand (NNS) RNA viruses (e.g. rabies, measles, Ebola) contains five collinear sequence elements, Rx(3)Wx(3-8)ΦxGxζx(P/A) (motif A; Φ, hydrophobic; ζ, hydrophilic), (Y/W)ΦGSxT (motif B), W (motif C), HR (motif D) and ζxxΦx(F/Y)QxxΦ (motif E). We performed site-directed mutagenesis of the L protein of vesicular stomatitis virus (VSV, a prototypic NNS RNA virus) to examine participation of these motifs in mRNA capping. Similar to the catalytic residues in motif D, G1100 in motif A, T1157 in motif B, W1188 in motif C, and F1269 and Q1270 in motif E were found to be essential or important for the PRNTase activity in the step of the covalent L-pRNA intermediate formation, but not for the GTPase activity that generates GDP (pRNA acceptor). Cap defective mutations in these residues induced termination of mRNA synthesis at position +40 followed by aberrant stop-start transcription, and abolished virus gene expression in host cells. These results suggest that the conserved motifs constitute the active site of the PRNTase domain and the L-pRNA intermediate formation followed by the cap formation is essential for successful synthesis of full-length mRNAs.

  4. Method and apparatus for a catalytic firebox reactor

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Lance L. (North Haven, CT); Etemad, Shahrokh (Trumbull, CT); Ulkarim, Hasan (Hamden, CT); Castaldi, Marco J. (Bridgeport, CT); Pfefferle, William C. (Madison, CT)

    2001-01-01

    A catalytic firebox reactor employing an exothermic catalytic reaction channel and multiple cooling conduits for creating a partially reacted fuel/oxidant mixture. An oxidation catalyst is deposited on the walls forming the boundary between the multiple cooling conduits and the exothermic catalytic reaction channel, on the side of the walls facing the exothermic catalytic reaction channel. This configuration allows the oxidation catalyst to be backside cooled by any fluid passing through the cooling conduits. The heat of reaction is added to both the fluid in the exothermic catalytic reaction channel and the fluid passing through the cooling conduits. After discharge of the fluids from the exothermic catalytic reaction channel, the fluids mix to create a single combined flow. A further innovation in the reactor incorporates geometric changes in the exothermic catalytic reaction channel to provide streamwise variation of the velocity of the fluids in the reactor.

  5. 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.

  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. Characterization of the in vitro activity of the RNA-dependent RNA polymerase associated with the ribonucleoproteins of rice hoja blanca tenuivirus.

    Science.gov (United States)

    Nguyen, M; Ramirez, B C; Goldbach, R; Haenni, A L

    1997-04-01

    An RNA-dependent RNA polymerase (RdRp) activity associated with the ribonucleoproteins of rice hoja blanca tenuivirus (RHBV) was detected and analyzed. Conditions for in vitro RNA synthesis and for coupled RNA synthesis-translation of RHBV were established. In both cases, synthesis of the viral and viral complementary genomic and subgenomic RNA3 and RNA4 were observed, demonstrating that both transcription and replication occurred. Though coupling of RNA synthesis to translation allowed efficient translation of the newly synthesized subgenomic RNAs, studies of the effect of various inhibitors of protein synthesis revealed that RNA synthesis was independent of translation. Primer extension experiments demonstrated that in the presence of capped exogenous RNAs, a stretch of 10 to 16 nonviral nucleotides was added to the 5' end of a population of newly synthesized viral complementary RNA4. It appears that in addition to RdRp activity, RHBV-associated protein(s) also possessed cap-snatching capacity. PMID:9060614

  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. 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

  10. 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...

  11. 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...

  12. Selective Catalytic Reduction of NO with Methane

    Institute of Scientific and Technical Information of China (English)

    Xiang Gao; Qi Yu; Limin Chen

    2003-01-01

    The removal of nitrogen oxides from exhaust gases has attracted great attention in recent years, and many approaches have been developed depending on the application. Methane, the main component of natural gas, has great potential as a NO reductant. In this paper, a number of catalysts previous reported for this catalytic reduction of NO have been reviewed, including a direct comparison of the relative activities and effective factors of the catalysts. Reaction mechanisms have also been explored preliminarily.

  13. 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.

  14. 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...

  15. Control of a catalytic fluid cracker

    Energy Technology Data Exchange (ETDEWEB)

    Arbel, A.; Huang, Z.; Rinard, I.; Shinnar, R.

    1993-12-13

    Control offers an important tool for savings in refineries, mainly by integration of process models into on-line control. This paper is part of a research effort to better understand problems of partial control; control of a Fluid Catalytic Cracker (FCC) is used as example. Goal is to understand better the control problems of an FCC in context of model based control of a refinery, and to understand the general problem of designing partial control systems.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. Highly sensitive catalytic spectrophotometric determination of ruthenium

    Science.gov (United States)

    Naik, Radhey M.; Srivastava, Abhishek; Prasad, Surendra

    2008-01-01

    A new and highly sensitive catalytic kinetic method (CKM) for the determination of ruthenium(III) has been established based on its catalytic effect on the oxidation of L-phenylalanine ( L-Pheala) by KMnO 4 in highly alkaline medium. The reaction has been followed spectrophotometrically by measuring the decrease in the absorbance at 526 nm. The proposed CKM is based on the fixed time procedure under optimum reaction conditions. It relies on the linear relationship where the change in the absorbance (Δ At) versus added Ru(III) amounts in the range of 0.101-2.526 ng ml -1 is plotted. Under the optimum conditions, the sensitivity of the proposed method, i.e. the limit of detection corresponding to 5 min is 0.08 ng ml -1, and decreases with increased time of analysis. The method is featured with good accuracy and reproducibility for ruthenium(III) determination. The ruthenium(III) has also been determined in presence of several interfering and non-interfering cations, anions and polyaminocarboxylates. No foreign ions interfered in the determination ruthenium(III) up to 20-fold higher concentration of foreign ions. In addition to standard solutions analysis, this method was successfully applied for the quantitative determination of ruthenium(III) in drinking water samples. The method is highly sensitive, selective and very stable. A review of recently published catalytic spectrophotometric methods for the determination of ruthenium(III) has also been presented for comparison.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. A facile lentiviral vector system for expression of doxycycline-inducible shRNAs: knockdown of the pre-miRNA processing enzyme Drosha

    DEFF Research Database (Denmark)

    Aagaard, Lars; Amarzguioui, Mohammed; Sun, Guihua;

    2007-01-01

    RNA interference (RNAi) is a powerful genetic tool for loss-of-function studies in mammalian cells and is also considered a potentially powerful therapeutic modality for the treatment of a variety of human diseases. During the past 3 years a number of systems for conditional RNAi have been develo...... Drosha. Drosha is the core catalytic component of the "microprocessor complex" and cleaves the primary microRNA (miRNA) transcripts into their pre-miRNA hairpin intermediates. We anticipate that our vector will facilitate functional studies of miRNA biogenesis....

  8. 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

  9. A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins1[W

    Science.gov (United States)

    Campos, Bruna Medéia; Sforça, Mauricio Luis; Ambrosio, Andre Luis Berteli; Domingues, Mariane Noronha; Brasil de Souza, Tatiana de Arruda Campos; Barbosa, João Alexandre Ribeiro Gonçalvez; Leme, Adriana Franco Paes; Perez, Carlos Alberto; Whittaker, Sara Britt-Marie; Murakami, Mario Tyago; Zeri, Ana Carolina de Matos; Benedetti, Celso Eduardo

    2013-01-01

    The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism. PMID:23709667

  10. 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 ...... sampling algorithm for shapes of RNA complexes of fixed topological genus.......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...

  11. Turning goals into results: the power of catalytic mechanisms.

    Science.gov (United States)

    Collins, J

    1999-01-01

    Most executives have a big, hairy, audacious goal. They write vision statements, formalize procedures, and develop complicated incentive programs--all in pursuit of that goal. In other words, with the best of intentions, they install layers of stultifying bureaucracy. But it doesn't have to be that way. In this article, Jim Collins introduces the catalytic mechanism, a simple yet powerful managerial tool that helps translate lofty aspirations into concrete reality. Catalytic mechanisms are the crucial link between objectives and performance; they are a galvanizing, nonbureaucratic means to turn one into the other. What's the difference between catalytic mechanisms and most traditional managerial controls? Catalytic mechanisms share five characteristics. First, they produce desired results in unpredictable ways. Second, they distribute power for the benefit of the overall system, often to the discomfort of those who traditionally hold power. Third, catalytic mechanisms have teeth. Fourth, they eject "viruses"--those people who don't share the company's core values. Finally, they produce an ongoing effect. Catalytic mechanisms are just as effective for reaching individual goals as they are for corporate ones. To illustrate how catalytic mechanisms work, the author draws on examples of individuals and organizations that have relied on such mechanisms to achieve their goals. The same catalytic mechanism that works in one organization, however, will not necessarily work in another. Catalytic mechanisms must be tailored to specific goals and situations. To help readers get started, the author offers some general principles that support the process of building catalytic mechanisms effectively. PMID:10539210

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    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 an...

  13. 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...

  14. 广西巴马地区长寿人群沉默信号调节蛋白6基因mRNA的表达%mRNA expression of silent information regulator 6 among population in Bama county of Guangxi

    Institute of Scientific and Technical Information of China (English)

    蒋梅玉; 黄倩倩; 施礼威; 夏天龙; 梁雪; 何敏; 张志勇; 覃健; 韦霄

    2016-01-01

    Objective To analyze mRNA expression of silent information regulator 6 (SIRT6) gene in the blood of population with family history of longevity in Bama county of Guangxi and to explore its association with SIRT6 gene polymorphism and its protein Methods One hundred and thirty-seven people (aged 30 ~ 106, 70 males, 67 females, 6.57% Han nationality, 93.43% Zhuang and Yao nationalities) with family history of longevity (long-lived family history group), and 91 people (aged 22~89, 51 males, 40 females, all Zhuang and Yao nationalities) without family history of longevity were recruited in the study (non-long-lived family history group). Real-time fluorescence quantitative RT-PCR was used to detect mRNA expression of SIRT6 gene in two groups. Results SIRT6 mRNA expression of total and femals in long-lived family history group were higher than those in non-long-lived family history group (P0.05). Conclusion The expression of mRNA in SIRT6 gene may be associated with familial aggregation of longevity in Bama County of Guangxi and high expression of mRNA of SIRT6 in G allele carriers contributes to longevity.%目的:分析广西巴马有长寿家族史人群外周血沉默信号调节蛋白6(SIRT6)基因的mRNA表达水平,探讨其与SIRT6基因多态性及其蛋白的关系。方法:选取广西巴马地区有长寿家族史者(长寿家族史组)137例(年龄30~106岁,男70例,女67例,汉族占6.57%,壮族和瑶族占93.43%),无长寿家族史者(无长寿家族史组)91例(年龄22~89岁,男51例,女40例,均为壮族和瑶族)。采用实时荧光定量RT-PCR方法检测两组人群外周血SIRT6基因mRNA的表达水平。结果:长寿家族史组总体和女性人群外周血SIRT6 mRNA表达水平均高于无长寿家族史组(P<0.05)。长寿家族史组SIRT6基因rs350846位点GG、CG基因型及G等位基因携带者(GG、CG)的SIRT6 mRNA水平均高于无长寿家族史组(P<0.05

  15. 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

  16. Recapitulation of the hairless mouse phenotype using catalytic oligonucleotides: implications for permanent hair removal.

    Science.gov (United States)

    Cserhalmi-Friedman, Peter B; Panteleyev, Andrey A; Christiano, Angela M

    2004-03-01

    Ribozyme technology is widely used to target mRNA in a sequence-specific fashion and thus change the expression pattern of cells or tissues. While the goal of mRNA targeting is usually the cleavage of mutant mRNAs with the prospect of gene therapy for inherited diseases, in certain instances, targeting of wild-type genes can be used therapeutically. Lack of expression of the mouse hairless gene due to inherited mutations leads to the complete and irreversible loss of hair known as atrichia. We designed this study to recapitulate the hairless phenotype in a restricted manner by topical application of deoxyribozyme-targeting molecules to specifically cleave the mouse hairless mRNA. Histological samples taken from treated skin at different times demonstrated a decreased number of hair follicles, an involution of the remaining follicles, a separation of the dermal papillae, and the presence of dermal cysts, all characteristics of the hairless phenotype, but not normally present in the skin of C57Bl/6 J mice. In this study, we successfully recapitulated the hairless phenotype using topically applied target-specific catalytic oligonucleotides designed to cleave the mouse hairless mRNA. Our results demonstrate the feasibility of using ribozyme technology to alter the gene expression in the skin via topical application and provide proof of principle for the development of this strategy for permanent hair removal.

  17. 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.

  18. 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...

  19. 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...

  20. 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 ...

  1. 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)

    Braun, Laurence; Cannella, Dominique; Ortet, Philippe; Barakat, Mohamed; Sautel, Céline F; Kieffer, Sylvie; Garin, Jérôme; Bastien, Olivier; Voinnet, Olivier; Hakimi, Mohamed-Ali

    2010-05-27

    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

  2. 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.

  3. 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

  4. 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.)

  5. 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.

  6. Simultaneous RNA-DNA FISH.

    Science.gov (United States)

    Lai, Lan-Tian; Meng, Zhenyu; Shao, Fangwei; Zhang, Li-Feng

    2016-01-01

    A highly useful tool for studying lncRNAs is simultaneous RNA-DNA FISH, which reveals the localization and quantitative information of RNA and DNA in cellular contexts. However, a simple combination of RNA FISH and DNA FISH often generates disappointing results because the fragile RNA signals are often damaged by the harsh conditions used in DNA FISH for denaturing the DNA. Here, we describe a robust and simple RNA-DNA FISH protocol, in which amino-labeled nucleic acid probes are used for RNA FISH. The method is suitable to detect single-RNA molecules simultaneously with DNA.

  7. A method for controlling catalytic reforming

    Energy Technology Data Exchange (ETDEWEB)

    Karamyshev, M.S.; Denilov, N.A.; Kamyshnikov, A.I.; Kirilin, Yu.A.; Lozinskiy, V.N.; Melman, A.Z.; Ovchinnikova, T.F.; Shpunt, M.I.; Shuvalov, V.V.; Zayashnikov, Ye.N.

    1983-01-01

    In the method for controlling the process of catalytic reforming, which includes mixing the raw material components with the production of a raw material, reforming and isolation of the final products, through changing the relationship of the expenditures of the raw material components relative to the content of the target components in the raw material, in order to support and stabilize an assigned production of the final products, the relationship of the expenditures of the raw material components are changed with correction based on the flow rates of the final products. A block diagram of the installation which realizes the proposed method is cited.

  8. 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.

  9. 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...

  10. 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)

  11. 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.

  12. 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...

  13. 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

  14. 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.

  15. 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.

  16. 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...

  17. 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.

  18. A study on naphtha catalytic reforming reactor simulation and analysis

    Institute of Scientific and Technical Information of China (English)

    LIANG Ke-min; GUO Hai-yan; PAN Shi-wei

    2005-01-01

    A naphtha catalytic reforming unit with four reactors 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 reactions characteristics based on idealizing the complex naphtha mixture by representing the paraffin, naphthene, and aromatic groups by single compounds. The simulation results based above models agree very well with actual operation unit data.

  19. 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…

  20. 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.

  1. 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.

  2. 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.

  3. 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....

  4. 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.

  5. 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

  6. 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.)

  7. Catalytic reactor for low-Btu fuels

    Science.gov (United States)

    Smith, Lance; Etemad, Shahrokh; Karim, Hasan; Pfefferle, William C.

    2009-04-21

    An improved catalytic reactor includes a housing having a plate positioned therein defining a first zone and a second zone, and a plurality of conduits fabricated from a heat conducting material and adapted for conducting a fluid therethrough. The conduits are positioned within the housing such that the conduit exterior surfaces and the housing interior surface within the second zone define a first flow path while the conduit interior surfaces define a second flow path through the second zone and not in fluid communication with the first flow path. The conduit exits define a second flow path exit, the conduit exits and the first flow path exit being proximately located and interspersed. The conduits define at least one expanded section that contacts adjacent conduits thereby spacing the conduits within the second zone and forming first flow path exit flow orifices having an aggregate exit area greater than a defined percent of the housing exit plane area. Lastly, at least a portion of the first flow path defines a catalytically active surface.

  8. 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...... investigation was to study a possible non-Faradaic electrochemical promotion of the liquid-phase catalytic reaction. It has been shown that there are two negative potential promotion areas with maximum effects at approximately -0.1 and -0.2 V, and one positive potential promotion area with the maximum effect...... caused by the negative charge on the electrode. The Faradaic part of the promoting effect under positive polarization has been explained as the electrochemical pushing of the V(V) V(IV) equilibrium in the direction of V(V) formation. It has also been shown that when using the industrial VK-58 catalyst...

  9. Computational and Physical Analysis of Catalytic Compounds

    Science.gov (United States)

    Wu, Richard; Sohn, Jung Jae; Kyung, Richard

    2015-03-01

    Nanoparticles exhibit unique physical and chemical properties depending on their geometrical properties. For this reason, synthesis of nanoparticles with controlled shape and size is important to use their unique properties. Catalyst supports are usually made of high-surface-area porous oxides or carbon nanomaterials. These support materials stabilize metal catalysts against sintering at high reaction temperatures. Many studies have demonstrated large enhancements of catalytic behavior due to the role of the oxide-metal interface. In this paper, the catalyzing ability of supported nano metal oxides, such as silicon oxide and titanium oxide compounds as catalysts have been analyzed using computational chemistry method. Computational programs such as Gamess and Chemcraft has been used in an effort to compute the efficiencies of catalytic compounds, and bonding energy changes during the optimization convergence. The result illustrates how the metal oxides stabilize and the steps that it takes. The graph of the energy computation step(N) versus energy(kcal/mol) curve shows that the energy of the titania converges faster at the 7th iteration calculation, whereas the silica converges at the 9th iteration calculation.

  10. 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

  11. 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.

  12. 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

  13. 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

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

    Directory of Open Access Journals (Sweden)

    Michelle F. Schaffer

    2016-06-01

    Full Text Available 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.

  15. 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

  16. 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.

  17. 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)

    GUO; Wei(过玮); LIU; Limin(刘利民); LIN; Hong(林洪); SONG; Junfeng(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.

  18. 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

  19. 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

  20. Population neuroscience.

    Science.gov (United States)

    Paus, T

    2016-01-01

    Population neuroscience endeavors to identify influences shaping the human brain from conception onwards, thus generating knowledge relevant for building and maintaining brain health throughout the life span. This can be achieved by studying large samples of participants drawn from the general population and evaluated with state-of-the-art tools for assessing (a) genes and their regulation; (b) external and internal environments; and (c) brain properties. This chapter reviews the three elements of population neuroscience (principles, tools, innovations, limitations), and discusses future directions in this field. PMID:27637950

  1. Shaping tRNA

    Science.gov (United States)

    Priano, Christine

    2013-01-01

    This model-building activity provides a quick, visual, hands-on tool that allows students to examine more carefully the cloverleaf structure of a typical tRNA molecule. When used as a supplement to lessons that involve gene expression, this exercise reinforces several concepts in molecular genetics, including nucleotide base-pairing rules, the…

  2. 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.

  3. 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

  4. 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.

  5. A Grammatical Approach to RNA-RNA Interaction Prediction

    Science.gov (United States)

    Kato, Yuki; Akutsu, Tatsuya; Seki, Hiroyuki

    2007-11-01

    Much attention has been paid to two interacting RNA molecules involved in post-transcriptional control of gene expression. Although there have been a few studies on RNA-RNA interaction prediction based on dynamic programming algorithm, no grammar-based approach has been proposed. The purpose of this paper is to provide a new modeling for RNA-RNA interaction based on multiple context-free grammar (MCFG). We present a polynomial time parsing algorithm for finding the most likely derivation tree for the stochastic version of MCFG, which is applicable to RNA joint secondary structure prediction including kissing hairpin loops. Also, elementary tests on RNA-RNA interaction prediction have shown that the proposed method is comparable to Alkan et al.'s method.

  6. 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...

  7. Catalytic activities of platinum nanotubes: a density functional study

    Science.gov (United States)

    Mukherjee, Prajna; Gupta, Bikash C.; Jena, Puru

    2015-10-01

    In this work we investigate the catalytic properties of platinum nanotubes using density functional theory based calculations. In particular, we study the dissociation of hydrogen and oxygen molecules as well as oxidation of CO molecules. The results indicate that platinum nanotubes have good catalytic properties and can be effectively used in converting CO molecule to CO2.

  8. 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...

  9. 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

  10. Functionalized TUD-1: synthesis, characterization and (photo-)catalytic performance

    NARCIS (Netherlands)

    Hamdy M. Saad, M.S.

    2005-01-01

    The new mesoporous material; TUD-1 is chosen of which the synthesis, characterization, and functionalization for (photo)-catalytic performance are extensively investigated in this study. The synthesis of the new catalytic materials M TUD-1 (M = Ti, V, Cr, Mo, Fe, Co and Cu) is carried out through an

  11. 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.

  12. 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

  13. 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

  14. [Apoptotic endonuclease EndoG induces alternative splicing of telomerase catalytic subunit hTERT and death of tumor cells].

    Science.gov (United States)

    Zhdanov, D D; Vasina, D A; Orlova, V S; Gotovtseva, V Y; Bibikova, M V; Pokrovsky, V S; Pokrovskaya, M V; Aleksandrova, S S; Sokolov, N N

    2016-03-01

    Telomerase activity is known to be regulated by alternative splicing of its catalytic subunit hTERT (human Telomerase Reverse Transcriptase) mRNA. Induction of non-active spliced hTERT leads to inhibition of telomerase activity. However, very little is known about the mechanism of hTERT mRNA alternative splicing. The aim of this study was to determine the role of apoptotic endonuclease EndoG in alternative splicing of hTERT and telomerase activity. Strong correlation was found between expression of EndoG and hTERT splice-variants in 12 colon cancer cell lines. Overexpression of EndoG in СаСо-2 cells downregulated the expression of active full-length hTERT variant and upregulated non-active spliced variant. Reduction of full-length hTERT caused downregulation of telomerase activity, dramatically shortening of telomeres length during cell divisions, converting cells to the replicative senescence state, activation of apoptosis and finally cell death. These data indicated the participation of EndoG in alternative splicing of mRNA of telomerase catalytic subunit, regulation of telomerase activity and cell fate. PMID:27420614

  15. 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

  16. 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

  17. 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

  18. Natural RNA circles function as efficient microRNA sponges

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  19. 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.

  20. 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

  1. 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.

  2. Stoichiometric and Catalytic Synthesis of Alkynylphosphines

    Directory of Open Access Journals (Sweden)

    Annie-Claude Gaumont

    2012-12-01

    Full Text Available Alkynylphosphines or their borane complexes are available either through C–P bond forming reactions or through modification of the phosphorus or the alkynyl function of various alkynyl phosphorus derivatives. The latter strategy, and in particular the one involving phosphoryl reduction by alanes or silanes, is the method of choice for preparing primary and secondary alkynylphosphines, while the former strategy is usually employed for the synthesis of tertiary alkynylphosphines or their borane complexes. The classical C–P bond forming methods rely on the reaction between halophosphines or their borane complexes with terminal acetylenes in the presence of a stoichiometric amount of organometallic bases, which precludes the access to alkynylphosphines bearing sensitive functional groups. In less than a decade, efficient catalytic procedures, mostly involving copper complexes and either an electrophilic or a nucleophilic phosphorus reagent, have emerged. By proceeding under mild conditions, these new methods have allowed a significant broadening of the substituent scope and structure complexity.

  3. Studies on Catalytic Conversion of Ethylene

    Institute of Scientific and Technical Information of China (English)

    Fuyu Liu; Chunyi Li; Xue Ding; Xinghua You

    2007-01-01

    FCC dry gas contains a large amount of ethylene.It is used by most of the refineries in China as fuel or simply burned in atmosphere.Few refineries make good use of the dry gas,so the precious ethylene resource in the dry gas is wasted.In this article,the possibility of catalytic conversion of ethylene to C3,C4,and some high molecular weight hydrocarbons in a fixed bed micro-reactor using LTB-1 catalyst,with pure ethylene as feedstock was studied.Effects of reaction temperature,reaction pressure,and feedstock flow rate,on the conversion of ethylene and the distribution of products were investigated to determine the proper reaction parameters to be used in practice.Good results indicate that this study may provide a new way of using the ethylene resource in the FCC dry gas.

  4. 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.

  5. 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

  6. Catalytic Synthesis of Nitriles in Continuous Flow

    DEFF Research Database (Denmark)

    Nordvang, Emily Catherine

    The objective of this thesis is to report the development of a new, alternative process for the flexible production of nitrile compounds in continuous flow. Nitriles are an important class of compounds that find applications as solvents, chemical intermediates and pharmaceutical compounds......, alternative path to acetonitrile from ethanol via the oxidative dehydrogenation of ethylamine. The catalytic activity and product ratios of the batch and continuous flow reactions are compared and the effect of reaction conditions on the reaction is investigated. The effects of ammonia in the reaction...... dehydrogenation of ethylamine and post-reaction purging.Chapter 4 outlines the application of RuO2/Al2O3 catalysts to the oxidative dehydrogenation of benzylamine in air, utilizing a new reaction setup. Again, batch and continuous flow reactions are compared and the effects of reaction conditions, ammonia...

  7. Flame assisted synthesis of catalytic ceramic membranes

    DEFF Research Database (Denmark)

    Johansen, Johnny; Mosleh, Majid; Johannessen, Tue;

    2004-01-01

    will be spherical due to the fast coalescence at the high temperatures in the flame. The primary product from the flame pyrolysis is an aerosol of metal oxide nanoparticles. The aerosol gas from the flame can be utilized for several different purposes, depending on the precursors fed to the flame. With the present...... technology it is possible to make supported catalysts, composite metal oxides, catalytically active surfaces, and porous ceramic membranes. Membrane layers can be formed by using a porous substrate tube (or surface) as a nano-particle filter. The aerosol gas from the flame is led through a porous substrate...... tube, where a part of the gas is sucked through the wall of the substrate, thereby creating a thin filter cake on the inner surface of the substrate tube. The top-layer can be deposited directly on a coarse pore structure. Since the Brownian motion of the aerosol particles is fast compared to the fluid...

  8. 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.

  9. Propulsion Mechanism of Catalytic Microjet Engines

    Science.gov (United States)

    Fomin, Vladimir M.; Hippler, Markus; Magdanz, Veronika; Soler, Lluís; Sanchez, Samuel; Schmidt, Oliver G.

    2014-01-01

    We describe the propulsion mechanism of the catalytic microjet engines that are fabricated using rolled-up nanotech. Microjets have recently shown numerous potential applications in nanorobotics but currently there is a lack of an accurate theoretical model that describes the origin of the motion as well as the mechanism of self-propulsion. The geometric asymmetry of a tubular microjet leads to the development of a capillary force, which tends to propel a bubble toward the larger opening of the tube. Because of this motion in an asymmetric tube, there emerges a momentum transfer to the fluid. In order to compensate this momentum transfer, a jet force acting on the tube occurs. This force, which is counterbalanced by the linear drag force, enables tube velocities of the order of 100 μm/s. This mechanism provides a fundamental explanation for the development of driving forces that are acting on bubbles in tubular microjets. PMID:25177214

  10. Catalytic Hydrolysis of Borohydride for Fuel Cells

    Institute of Scientific and Technical Information of China (English)

    WANG Lianbang; ZHAN Xingyue; YANG Zhenzhen; MA Chun'an

    2011-01-01

    Borohydrides present interesting options for the electrochemical power generation acting either as hydrogen source or anodic fuel for direct borohydride fuel cells(DBFC).In this work,Mg-Ni composite synthesized by mechanically alloying method,used as the catalyst for the hydrolysis of borohydride,has been investigated.Co-doping treatment has been carried out for the purpose of improving the hydrolysis rate further.The as-prepared and Co-doped Mg-Ni composites with low cost showed high catalytic activity to the hydrolysis of borohydride for hydrogen generation.After Co-doping,the hydrogen generation rate was around 280 ml·g-1·min-1.Borohydride would be a promising hydrogen source for fuel cells.

  11. Catalytic Acylation of Ethylidenecyclohexane over Zeolite Catalysts

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Some environmentally friendly catalysts such as HY and H-β zeolites,various cation-exchanged β zeolites,and some other solids have been used in the acylation reaction of ethylidenecyclohexane with acetic anhydride at room temperature to synthesize 3-(1-cyclohexenyl)-2-butanone instead of conventional catalysts.The effect of the amount of HY zeolite used on the acylation reaction was investigated.The yield of the acylated product was 72% in the case of n(ethylidenecyclohexane)∶n(acetic anhydride)∶m(HY zeolite)=1 mmol∶10 mmol∶0.100 g,reaction temperature:25 ℃,and reaction time:2 h.The regenerated HY zeolite showed almost the same catalytic activity as the fresh zeolite.

  12. 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

  13. siRNA for Influenza Therapy

    Directory of Open Access Journals (Sweden)

    Sailen Barik

    2010-07-01

    Full Text Available 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, triggered by synthetic short interfering RNA (siRNA, has rapidly evolved as a potent antiviral regimen. Properly designed siRNAs have been shown to function as potent inhibitors of influenza virus replication. The siRNAs outperform traditional small molecule antivirals in a number of areas, such as ease of design, modest cost, and fast turnaround. Although specificity and tissue delivery remain major bottlenecks in the clinical applications of RNAi in general, intranasal application of siRNA against respiratory viruses including, but not limited to influenza virus, has experienced significant success and optimism, which is reviewed here.

  14. 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.)

  15. 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

  16. 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 ...

  17. 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.

  18. 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

  19. 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 ...

  20. An experimental study of diffusion and convection of multicomponent gases through catalytic and non-catalytic membranes

    NARCIS (Netherlands)

    Veldsink, J.W.; Versteeg, G.F.; Swaaij, W.P.M. van

    1994-01-01

    Diffusion of binary and ternary gases through catalytic and non-catalytic membranes has been studied experimentally at atmospheric pressure. These experiments were conducted in a modified Wicke-Kallenbach diffusion cell consisting of two continuously stirred gas volumes separated by a membrane. The

  1. 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)

  2. 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

  3. 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

  4. 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...... public database at http://insectacentral.org/RNAi will continue to gather information on RNAi experiments. 2010 Elsevier Ltd. All rights reserved....

  5. 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...

  6. 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.

  7. 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.

  8. A miRNA-tRNA mix-up: tRNA origin of proposed miRNA.

    Science.gov (United States)

    Schopman, Nick C T; Heynen, Stephan; Haasnoot, Joost; Berkhout, Ben

    2010-01-01

    The rapid release of new data from DNA genome sequencing projects has led to a variety of misannotations in public databases. Our results suggest that next generation sequencing approaches are particularly prone to such misannotations. Two related miRNA candidates did recently enter the miRBase database, miR-1274b and miR-1274a, but they share identical 18-nucleotide stretches with tRNA (Lys3) and tRNA (Lys5) , respectively. The possibility that the small RNA fragments that led to the description of these two miRNAs originated from the two tRNAs was examined. The ratio of the miR-1274b:miR-1274a fragments does closely resemble the known tRNA lys3:lys5 ratio in the cell. Furthermore, the proposed miRNA hairpins have a very low prediction score and the proposed miRNA genes are in fact endogenous retroviral elements. We searched for other miRNA-mimics in the human genome and found more examples of tRNA-miRNA mimicry. We propose that the corresponding miRNAs should be validated in more detail, as the small RNA fragments that led to their description are likely derived from tRNA processing. PMID:20818168

  9. 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.

  10. 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.

  11. Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition

    Science.gov (United States)

    Borja, Mark S.; Piotukh, Kirill; Freund, Christian; Gross, John D.

    2011-01-01

    Cap hydrolysis is a critical step in several eukaryotic mRNA decay pathways and is carried out by the evolutionarily conserved decapping complex containing Dcp2 at the catalytic core. In yeast, Dcp1 is an essential activator of decapping and coactivators such as Edc1 and Edc2 are thought to enhance activity, though their mechanism remains elusive. Using kinetic analysis we show that a crucial function of Dcp1 is to couple the binding of coactivators of decapping to activation of Dcp2. Edc1 and Edc2 bind Dcp1 via its EVH1 proline recognition site and stimulate decapping by 1000-fold, affecting both the KM for mRNA and rate of the catalytic step. The C-terminus of Edc1 is necessary and sufficient to enhance the catalytic step, while the remainder of the protein likely increases mRNA binding to the decapping complex. Lesions in the Dcp1 EVH1 domain or the Edc1 proline-rich sequence are sufficient to block stimulation. These results identify a new role of Dcp1, which is to link the binding of coactivators to substrate recognition and activation of Dcp2. PMID:21148770

  12. RNA interference of NADPH-cytochrome P450 reductase results in reduced insecticide resistance in the bed bug, Cimex lectularius.

    Directory of Open Access Journals (Sweden)

    Fang Zhu

    Full Text Available BACKGROUND: NADPH-cytochrome P450 reductase (CPR plays a central role in cytochrome P450 action. The genes coding for P450s are not yet fully identified in the bed bug, Cimex lectularius. Hence, we decided to clone cDNA and knockdown the expression of the gene coding for CPR which is suggested to be required for the function of all P450s to determine whether or not P450s are involved in resistance of bed bugs to insecticides. METHODOLOGY/PRINCIPAL FINDINGS: The full length Cimex lectularius CPR (ClCPR cDNA was isolated from a deltamethrin resistant bed bug population (CIN-1 using a combined PCR strategy. Bioinformatics and in silico modeling were employed to identify three conserved binding domains (FMN, FAD, NADP, a FAD binding motif, and the catalytic residues. The critical amino acids involved in FMN, FAD, NADP binding and their putative functions were also analyzed. No signal peptide but a membrane anchor domain with 21 amino acids which facilitates the localization of ClCPR on the endoplasmic reticulum was identified in ClCPR protein. Phylogenetic analysis showed that ClCPR is closer to the CPR from the body louse, Pediculus humanus corporis than to the CPRs from the other insect species studied. The ClCPR gene was ubiquitously expressed in all tissues tested but showed an increase in expression as immature stages develop into adults. We exploited the traumatic insemination mechanism of bed bugs to inject dsRNA and successfully knockdown the expression of the gene coding for ClCPR. Suppression of the ClCPR expression increased susceptibility to deltamethrin in resistant populations but not in the susceptible population of bed bugs. CONCLUSIONS/SIGNIFICANCE: These data suggest that P450-mediated metabolic detoxification may serve as one of the resistance mechanisms in bed bugs.

  13. 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

  14. 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

  15. Mirware: A MiRNA-mRNA Warehouse for Inference on Their Coordination.

    Science.gov (United States)

    Orsini, Massimiliano; Capobianco, Enrico

    2013-01-01

    Cancer is a multifactorial disease the study and analysis of which naturally require the integration of disciplines, and the fusion of omics and clinical evidence. Each informative layer linked to such combined evidence involves a particular type of complexity, in part technology-driven and in part patient-dependent. Therefore, due to data dimensionality and heterogeneity the task for computational scientists is very challenging as it refers to data assimilation, mining and inference. Cancer-associated mechanisms refer to complex entities such as transcription factors and microRNA the influence of which is exerted over many distinct mRNA targets involved in key biological processes, both normal and altered ones. This work aims to propose an open source tool allowing inference on microRNA-target coordination involving cancer-induced dysregulation. By introducing Mirware, a novel warehouse of genes is provided to specifically and uniquely build a cancer repository based on publicly available data from Array Express, and populated by importing from Tarbase and Mirbase all the known associations between microRNAs and target genes. Coordination can be assessed by merging profiling from gene co-expression measurements and clinical evidence integrated to them. Data have been organized by tissue, such that microRNA-mRNA association matrices can be built based on both experimental and predicted data, thus promising to offer a contribution to build a knowledge base clarifying cancer regulation mechanisms.

  16. 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.

  17. 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

  18. Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification.

    Science.gov (United States)

    Tougan, Takahiro; Okuzaki, Daisuke; Nojima, Hiroshi

    2008-09-01

    Linear RNA amplification using T7 RNA polymerase is useful in genome-wide analysis of gene expression using DNA microarrays, but exponential amplification using polymerase chain reaction (PCR) is still required for cDNA library preparation from single-cell quantities of RNA. We have designed a small RNA molecule called chum-RNA that has enabled us to prepare a single-cell cDNA library after four rounds of T7-based linear amplification, without using PCR amplification. Chum-RNA drove cDNA synthesis from only 0.49 femtograms of mRNA (730 mRNA molecules) as a substrate, a quantity that corresponds to a minor population of mRNA molecules in a single mammalian cell. Analysis of the independent cDNA clone of this library (6.6 x 10(5) cfu) suggests that 30-fold RNA amplification occurred in each round of the amplification process. The size distribution and representation of mRNAs in the resulting one-cell cDNA library retained its similarity to that of the million-cell cDNA library. The use of chum-RNA might also facilitate reactions involving other DNA/RNA modifying enzymes whose Michaelis constant (K(m)) values are around 1 mM, allowing them to be activated in the presence of only small quantities of substrate. PMID:18603591

  19. 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

  20. 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

  1. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea.

    Science.gov (United States)

    Lee, Zarraz May-Ping; Bussema, Carl; Schmidt, Thomas M

    2009-01-01

    A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1-15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.

  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. 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.

  4. Glycosidic Bond Conformation Preference Plays a Pivotal Role in Catalysis of RNA Pseudouridylation: A Combined Simulation and Structural Study

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jing; Lv, Chao; Liang, Bo; Chen, Mengen; Yang, Wei; Li, Hong (FSU)

    2010-11-11

    The most abundant chemical modification on RNA is isomerization of uridine (or pseudouridylation) catalyzed by pseudouridine synthases. The catalytic mechanism of this essential process remains largely speculative, partly due to lack of knowledge of the pre-reactive state that is important to the identification of reactive chemical moieties. In the present study, we showed, using orthogonal space random-walk free-energy simulation, that the pre-reactive states of uridine and its reactive derivative 5-fluorouridine, bound to a ribonucleoprotein particle pseudouridine synthase, strongly prefer the syn glycosidic bond conformation, while that of the nonreactive 5-bromouridine-containing substrate is largely populated in the anti conformation state. A high-resolution crystal structure of the 5-bromouridine-containing substrate bound to the ribonucleoprotein particle pseudouridine synthase and enzyme activity assay confirmed the anti nonreactive conformation and provided the molecular basis for its confinement. The observed preference for the syn pre-reactive state by the enzyme-bound uridine may help to distinguish among currently proposed mechanisms.

  5. Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.

    Science.gov (United States)

    Zhou, Jing; Lv, Chao; Liang, Bo; Chen, Mengen; Yang, Wei; Li, Hong

    2010-09-01

    The most abundant chemical modification on RNA is isomerization of uridine (or pseudouridylation) catalyzed by pseudouridine synthases. The catalytic mechanism of this essential process remains largely speculative, partly due to lack of knowledge of the pre-reactive state that is important to the identification of reactive chemical moieties. In the present study, we showed, using orthogonal space random-walk free-energy simulation, that the pre-reactive states of uridine and its reactive derivative 5-fluorouridine, bound to a ribonucleoprotein particle pseudouridine synthase, strongly prefer the syn glycosidic bond conformation, while that of the nonreactive 5-bromouridine-containing substrate is largely populated in the anti conformation state. A high-resolution crystal structure of the 5-bromouridine-containing substrate bound to the ribonucleoprotein particle pseudouridine synthase and enzyme activity assay confirmed the anti nonreactive conformation and provided the molecular basis for its confinement. The observed preference for the syn pre-reactive state by the enzyme-bound uridine may help to distinguish among currently proposed mechanisms.

  6. 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

  7. 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.

  8. 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.

  9. Cell penetrable humanized-VH/V(H)H that inhibit RNA dependent RNA polymerase (NS5B) of HCV.

    Science.gov (United States)

    Thueng-in, Kanyarat; Thanongsaksrikul, Jeeraphong; Srimanote, Potjanee; Bangphoomi, Kunan; Poungpair, Ornnuthchar; Maneewatch, Santi; Choowongkomon, Kiattawee; Chaicumpa, Wanpen

    2012-01-01

    NS5B is pivotal RNA dependent RNA polymerase (RdRp) of HCV and NS5B function interfering halts the virus infective cycle. This work aimed to produce cell penetrable humanized single domain antibodies (SdAb; VH/V(H)H) that interfere with the RdRp activity. Recombinant NS5BΔ55 of genotype 3a HCV with de novo RNA synthetic activity was produced and used in phage biopanning for selecting phage clones that displayed NS5BΔ55 bound VH/V(H)H from a humanized-camel VH/V(H)H display library. VH/V(H)H from E. coli transfected with four selected phage clones inhibited RdRp activity when tested by ELISA inhibition using 3'di-cytidylate 25 nucleotide directed in vitro RNA synthesis. Deduced amino acid sequences of two clones showed V(H)H hallmark and were designated V(H)H6 and V(H)H24; other clones were conventional VH, designated VH9 and VH13. All VH/V(H)H were linked molecularly to a cell penetrating peptide, penetratin. The cell penetrable VH9, VH13, V(H)H6 and V(H)H24 added to culture of Huh7 cells transfected with JHF-1 RNA of genotype 2a HCV reduced the amounts of RNA intracellularly and in culture medium implying that they inhibited the virus replication. VH/V(H)H mimotopes matched with residues scattered on the polymerase fingers, palm and thumb which were likely juxtaposed to form conformational epitopes. Molecular docking revealed that the antibodies covered the RdRp catalytic groove. The transbodies await further studies for in vivo role in inhibiting HCV replication.

  10. 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.

  11. Catalytic partial oxidation of pyrolysis oils

    Science.gov (United States)

    Rennard, David Carl

    2009-12-01

    This thesis explores the catalytic partial oxidation (CPO) of pyrolysis oils to syngas and chemicals. First, an exploration of model compounds and their chemistries under CPO conditions is considered. Then CPO experiments of raw pyrolysis oils are detailed. Finally, plans for future development in this field are discussed. In Chapter 2, organic acids such as propionic acid and lactic acid are oxidized to syngas over Pt catalysts. Equilibrium production of syngas can be achieved over Rh-Ce catalysts; alternatively mechanistic evidence is derived using Pt catalysts in a fuel rich mixture. These experiments show that organic acids, present in pyrolysis oils up to 25%, can undergo CPO to syngas or for the production of chemicals. As the fossil fuels industry also provides organic chemicals such as monomers for plastics, the possibility of deriving such species from pyrolysis oils allows for a greater application of the CPO of biomass. However, chemical production is highly dependent on the originating molecular species. As bio oil comprises up to 400 chemicals, it is essential to understand how difficult it would be to develop a pure product stream. Chapter 3 continues the experimentation from Chapter 2, exploring the CPO of another organic functionality: the ester group. These experiments demonstrate that equilibrium syngas production is possible for esters as well as acids in autothermal operation with contact times as low as tau = 10 ms over Rh-based catalysts. Conversion for these experiments and those with organic acids is >98%, demonstrating the high reactivity of oxygenated compounds on noble metal catalysts. Under CPO conditions, esters decompose in a predictable manner: over Pt and with high fuel to oxygen, non-equilibrium products show a similarity to those from related acids. A mechanism is proposed in which ethyl esters thermally decompose to ethylene and an acid, which decarbonylates homogeneously, driven by heat produced at the catalyst surface. Chapter 4

  12. 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.

  13. Enhanced propylene production in FCC by novel catalytic materials

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-07-01

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

  14. Bring into Full Play the Role of Catalytic Reforming Unit

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    This article after analyzing the current status of catalytic reforming technology in China puts forward a host of problems related with catalytic reforming capacity, feedstock, size and techno-economic indicators. To solve these problems it is proposed to properly increase the catalytic reforming capacity,extend the feedstock source, and eliminate the bottlenecks to boost the capacity of existing units, improve the operating and management level, as well as speed up R&D work, disseminate new technologies, new processes and novel catalysts.

  15. 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 ...

  16. 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

  17. Transfer RNA and human disease

    Directory of Open Access Journals (Sweden)

    Jamie A Abbott

    2014-06-01

    Full Text Available 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.

  18. 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

  19. Identifying microRNA/mRNA dysregulations in ovarian cancer

    Directory of Open Access Journals (Sweden)

    Miles Gregory D

    2012-03-01

    Full Text Available Abstract Background MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC, revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA. Methods TCGA Microarray data was normalized and samples whose class labels (tumour or normal were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. Results We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from

  20. 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...

  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 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

  3. Catalytic glycerol steam reforming for hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Dan, Monica, E-mail: monica.dan@itim-cj.ro; Mihet, Maria, E-mail: maria.mihet@itim-cj.ro; Lazar, Mihaela D., E-mail: diana.lazar@itim-cj.ro [National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat Street, 400293 Cluj Napoca (Romania)

    2015-12-23

    Hydrogen production from glycerol by steam reforming combine two major advantages: (i) using glycerol as raw material add value to this by product of bio-diesel production which is obtained in large quantities around the world and have a very limited utilization now, and (ii) by implication of water molecules in the reaction the efficiency of hydrogen generation is increased as each mol of glycerol produces 7 mol of H{sub 2}. In this work we present the results obtained in the process of steam reforming of glycerol on Ni/Al{sub 2}O{sub 3}. The catalyst was prepared by wet impregnation method and characterized through different methods: N{sub 2} adsorption-desorption, XRD, TPR. The catalytic study was performed in a stainless steel tubular reactor at atmospheric pressure by varying the reaction conditions: steam/carbon ratio (1-9), gas flow (35 ml/min -133 ml/min), temperature (450-650°C). The gaseous fraction of the reaction products contain: H{sub 2}, CH{sub 4}, CO, CO{sub 2}. The optimum reaction conditions as resulted from this study are: temperature 550°C, Gly:H{sub 2}O ratio 9:1 and Ar flow 133 ml/min. In these conditions the glycerol conversion to gaseous products was 43% and the hydrogen yield was 30%.

  4. Catalytic glycerol steam reforming for hydrogen production

    Science.gov (United States)

    Dan, Monica; Mihet, Maria; Lazar, Mihaela D.

    2015-12-01

    Hydrogen production from glycerol by steam reforming combine two major advantages: (i) using glycerol as raw material add value to this by product of bio-diesel production which is obtained in large quantities around the world and have a very limited utilization now, and (ii) by implication of water molecules in the reaction the efficiency of hydrogen generation is increased as each mol of glycerol produces 7 mol of H2. In this work we present the results obtained in the process of steam reforming of glycerol on Ni/Al2O3. The catalyst was prepared by wet impregnation method and characterized through different methods: N2 adsorption-desorption, XRD, TPR. The catalytic study was performed in a stainless steel tubular reactor at atmospheric pressure by varying the reaction conditions: steam/carbon ratio (1-9), gas flow (35 ml/min -133 ml/min), temperature (450-650°C). The gaseous fraction of the reaction products contain: H2, CH4, CO, CO2. The optimum reaction conditions as resulted from this study are: temperature 550°C, Gly:H2O ratio 9:1 and Ar flow 133 ml/min. In these conditions the glycerol conversion to gaseous products was 43% and the hydrogen yield was 30%.

  5. Effective function annotation through catalytic residue conservation.

    Science.gov (United States)

    George, Richard A; Spriggs, Ruth V; Bartlett, Gail J; Gutteridge, Alex; MacArthur, Malcolm W; Porter, Craig T; Al-Lazikani, Bissan; Thornton, Janet M; Swindells, Mark B

    2005-08-30

    Because of the extreme impact of genome sequencing projects, protein sequences without accompanying experimental data now dominate public databases. Homology searches, by providing an opportunity to transfer functional information between related proteins, have become the de facto way to address this. Although a single, well annotated, close relationship will often facilitate sufficient annotation, this situation is not always the case, particularly if mutations are present in important functional residues. When only distant relationships are available, the transfer of function information is more tenuous, and the likelihood of encountering several well annotated proteins with different functions is increased. The consequence for a researcher is a range of candidate functions with little way of knowing which, if any, are correct. Here, we address the problem directly by introducing a computational approach to accurately identify and segregate related proteins into those with a functional similarity and those where function differs. This approach should find a wide range of applications, including the interpretation of genomics/proteomics data and the prioritization of targets for high-throughput structure determination. The method is generic, but here we concentrate on enzymes and apply high-quality catalytic site data. In addition to providing a series of comprehensive benchmarks to show the overall performance of our approach, we illustrate its utility with specific examples that include the correct identification of haptoglobin as a nonenzymatic relative of trypsin, discrimination of acid-d-amino acid ligases from a much larger ligase pool, and the successful annotation of BioH, a structural genomics target.

  6. Catalytic pyrolysis using UZM-39 aluminosilicate zeolite

    Energy Technology Data Exchange (ETDEWEB)

    Nicholas, Christpher P; Boldingh, Edwin P

    2013-12-17

    A new family of coherently grown composites of TUN and IMF zeotypes has been synthesized and show to be effective catalysts for catalytic pyrolysis of biomass. These zeolites are represented by the empirical formula. Na.sub.nM.sub.m.sup.n+R.sub.rQ.sub.qAl.sub1-xE.sub.xSi.sub.yO.s- ub.z where M represents zinc or a metal or metals from Group 1, Group 2, Group 3 or the lanthanide series of the periodic table, R is an A,.OMEGA.-dihalosubstituted paraffin such as 1,4-dibromobutane, Q is a neutral amine containing 5 or fewer carbon atoms such as 1-methylpyrrolidine and E is a framework element such as gallium. The process involves contacting a carbonaceous biomass feedstock with UZM-39 at pyrolysis conditions to produce pyrolysis gases comprising hydrocarbons. The catalyst catalyzes a deoxygenation reaction converting oxygenated hyrdocarbons into hydrocarbons removing the oxygen as carbon oxides and water. A portion of the pyrolysis gases is condensed to produce low oxygen biomass-derived pyrolysis oil.

  7. Catalytic pyrolysis using UZM-39 aluminosilicate zeolite

    Energy Technology Data Exchange (ETDEWEB)

    Nicholas, Christopher P; Boldingh, Edwin P

    2014-10-07

    A new family of coherently grown composites of TUN and IMF zeotypes has been synthesized and shown to be effective catalysts for catalytic pyrolysis of biomass. These zeolites are represented by the empirical formula. Na.sub.nM.sub.m.sup.n+R.sub.rQ.sub.qAl.sub.1-xE.sub.xSi.sub.yO.s- ub.z where M represents zinc or a metal or metals from Group 1, Group 2, Group 3 or the lanthanide series of the periodic table, R is an A,.OMEGA.-dihalosubstituted paraffin such as 1,4-dibromobutane, Q is a neutral amine containing 5 or fewer carbon atoms such as 1-methylpyrrolidine and E is a framework element such as gallium. The process involves contacting a carbonaceous biomass feedstock with UZM-39 at pyrolysis conditions to produce pyrolysis gases comprising hydrocarbons. The catalyst catalyzes a deoxygenation reaction converting oxygenated hydrocarbons into hydrocarbons and removing the oxygen as carbon oxides and water. A portion of the pyrolysis gases is condensed to produce low oxygen biomass-derived pyrolysis oil.

  8. Microchannel Reactor System for Catalytic Hydrogenation

    Energy Technology Data Exchange (ETDEWEB)

    Adeniyi Lawal; Woo Lee; Ron Besser; Donald Kientzler; Luke Achenie

    2010-12-22

    We successfully demonstrated a novel process intensification concept enabled by the development of microchannel reactors, for energy efficient catalytic hydrogenation reactions at moderate temperature, and pressure, and low solvent levels. We designed, fabricated, evaluated, and optimized a laboratory-scale microchannel reactor system for hydrogenation of onitroanisole and a proprietary BMS molecule. In the second phase of the program, as a prelude to full-scale commercialization, we designed and developed a fully-automated skid-mounted multichannel microreactor pilot plant system for multiphase reactions. The system is capable of processing 1 – 10 kg/h of liquid substrate, and an industrially relevant immiscible liquid-liquid was successfully demonstrated on the system. Our microreactor-based pilot plant is one-of-akind. We anticipate that this process intensification concept, if successfully demonstrated, will provide a paradigm-changing basis for replacing existing energy inefficient, cost ineffective, environmentally detrimental slurry semi-batch reactor-based manufacturing practiced in the pharmaceutical and fine chemicals industries.

  9. Catalytic extraction processing of contaminated scrap metal

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, T.P.; Johnston, J.E.; Payea, B.M. [Molten Metal Technology, Inc., Waltham, MA (United States)] [and others

    1995-10-01

    The U.S. Department of Energy issued a Planned Research and Development Announcement (PRDA) in 1993, with the objective of identifying unique technologies which could be applied to the most hazardous waste streams at DOE sites. The combination of radioactive contamination with additional contamination by hazardous constituents such as those identified by the Resource Conservation and Recovery Act (RCRA) pose an especially challenging problem. Traditional remediation technologies are increasingly becoming less acceptable to stakeholders and regulators because of the risks they pose to public health and safety. Desirable recycling technologies were described by the DOE as: (1) easily installed, operated, and maintained; (2) exhibiting superior environmental performance; (3) protective of worker and public health and safety; (4) readily acceptable to a wide spectrum of evaluators; and (5) economically feasible. Molten Metal Technology, Inc. (MMT) was awarded a contract as a result of the PRDA initiative to demonstrate the applicability of Catalytic Extraction Processing (CEP), MMT`s proprietary elemental recycling technology, to DOE`s inventory of low level mixed waste. This includes DOE`s inventory of radioactively- and RCRA-contaminated scrap metal and other waste forms expected to be generated by the decontamination and decommissioning (D&D) of DOE sites.

  10. Process for catalytic flue gas denoxing

    International Nuclear Information System (INIS)

    With the increasing concern for the environment, stringency of legislation and industry's awareness of its own environmental responsibility, the demand for the reduction of emission levels of nitrogen oxides is becoming increasingly urgent. This paper reports that Shell has developed a low temperature catalytic deNOx system for deep removal of nitrogen oxides, which includes a low-pressure-drop reactor. This process is able to achieve over 90% removal of nitrogen oxides and therefore can be expected to meet legislation requirements for the coming years. The development of a low-temperature catalyst makes it possible to operate at temperatures as low as 120 degrees C, compared to 300-400 degrees C for the conventional honeycomb and plate-type catalysts. This allows an add-on construction, which is most often a more economical solution than the retrofits in the hot section required with conventional deNOx catalysts. The Lateral Flow Reactor (LFR), which is used for dust-free flue gas applications, and the Parallel Passage Reactor (PPR) for dust-containing flue gas applications, have been developed to work with pressure drops below 10 mbar

  11. 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

  12. 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

  13. 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

    2007-01-01

    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

  14. Quantification of miRNA-mRNA interactions.

    Science.gov (United States)

    Muniategui, Ander; Nogales-Cadenas, Rubén; Vázquez, Miguél; Aranguren, Xabier L; Agirre, Xabier; Luttun, Aernout; Prosper, Felipe; Pascual-Montano, Alberto; Rubio, Angel

    2012-01-01

    miRNAs are small RNA molecules (' 22nt) that interact with their corresponding target mRNAs inhibiting the translation of the mRNA into proteins and cleaving the target mRNA. This second effect diminishes the overall expression of the target mRNA. Several miRNA-mRNA relationship databases have been deployed, most of them based on sequence complementarities. However, the number of false positives in these databases is large and they do not overlap completely. Recently, it has been proposed to combine expression measurement from both miRNA and mRNA and sequence based predictions to achieve more accurate relationships. In our work, we use LASSO regression with non-positive constraints to integrate both sources of information. LASSO enforces the sparseness of the solution and the non-positive constraints restrict the search of miRNA targets to those with down-regulation effects on the mRNA expression. We named this method TaLasso (miRNA-Target LASSO).We used TaLasso on two public datasets that have paired expression levels of human miRNAs and mRNAs. The top ranked interactions recovered by TaLasso are especially enriched (more than using any other algorithm) in experimentally validated targets. The functions of the genes with mRNA transcripts in the top-ranked interactions are meaningful. This is not the case using other algorithms.TaLasso is available as Matlab or R code. There is also a web-based tool for human miRNAs at http://talasso.cnb.csic.es/.

  15. 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.

  16. Plasma Catalytic Extraction of Oxygen from the Martian Atmosphere Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Plasma catalytic techniques are proposed for the extraction of oxygen from the abundant carbon dioxide contained in the Martian atmosphere (95% CO2).. The Phase I...

  17. Enantiocontrol in Macrocycle Formation from Catalytic MetalCarbene Transformations

    Institute of Scientific and Technical Information of China (English)

    DOYLE, Michael P.; DOYLE, Michael P; HU, Wen-Hao(胡文浩); 胡文浩

    2001-01-01

    The development of catalytic metal carbene transformations for the construction of macrocyclic lactones has dramatically increased their synthetic advantages.This is the first review of this developing methodology.

  18. Mesoporous zeolite single crystals for catalytic hydrocarbon conversion

    DEFF Research Database (Denmark)

    Schmidt, I.; Christensen, C.H.; Hasselriis, Peter;

    2005-01-01

    Recently, mesoporous zeolite single crystals were discovered. They constitute a novel family of materials that features a combined micropore and mesopore architecture within each individual crystal. Here, we briefly summarize recent catalytic results from cracking and isomerization of alkalies, a...

  19. Size-dependent catalytic activity of supported metal clusters

    Science.gov (United States)

    Xu, Z.; Xiao, F.-S.; Purnell, S. K.; Alexeev, O.; Kawi, S.; Deutsch, S. E.; Gates, B. C.

    1994-11-01

    BECAUSE catalysis by metals is a surface phenomenon, many technological catalysts contain small (typically nanometre-sized) supported metal particles with a large fraction of the atoms exposed1. Many reactions, such as hydrocarbon hydrogenations, are structure-insensitive, proceeding at approximately the same rate on metal particles of various sizes provided that they are larger than about 1 nm and show bulk-like metallic behaviour1. But it is not known whether the catalytic properties of metal particles become size-dependent as the particles become so small that they are no longer metallic in character. Here we investigate the catalytic behaviour of precisely defined clusters of just four and six iridium atoms on solid supports. We find that the Ir4 and Ir6 clusters differ in catalytic activity both from each other and from metallic Ir particles. This raises the possibility of tailoring the catalytic behaviour of metal clusters by controlling the cluster size.

  20. Scaling behavior of optimally structured catalytic microfluidic reactors

    DEFF Research Database (Denmark)

    Okkels, Fridolin; Bruus, Henrik

    2007-01-01

    In this study of catalytic microfluidic reactors we show that, when optimally structured, these reactors share underlying scaling properties. The scaling is predicted theoretically and verified numerically. Furthermore, we show how to increase the reaction rate significantly by distributing the...