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Sample records for tar rna structure

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

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    Das Atze T

    2012-07-01

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

  2. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

    Science.gov (United States)

    Al-Hashimi, Hashim M; Gosser, Yuying; Gorin, Andrey; Hu, Weidong; Majumdar, Ananya; Patel, Dinshaw J

    2002-01-11

    Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(+/-4) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture. Copyright 2001 Academic Press.

  3. Deciphering structure-activity relationships in a series of Tat/TAR inhibitors.

    Science.gov (United States)

    Pascale, Lise; González, Alejandro López; Di Giorgio, Audrey; Gaysinski, Marc; Teixido Closa, Jordi; Tejedor, Roger Estrada; Azoulay, Stéphane; Patino, Nadia

    2016-11-01

    A series of pentameric "Polyamide Amino Acids" (PAAs) compounds derived from the same trimeric precursor have been synthesized and investigated as HIV TAR RNA ligands, in the absence and in the presence of a Tat fragment. All PAAs bind TAR with similar sub-micromolar affinities but their ability to compete efficiently with the Tat fragment strongly differs, IC50 ranging from 35 nM to >2 μM. While NMR and CD studies reveal that all PAA interact with TAR at the same site and induce globally the same RNA conformational change upon binding, a comparative thermodynamic study of PAA/TAR equilibria highlights distinct TAR binding modes for Tat competitor and non-competitor PAAs. This led us to suggest two distinct interaction modes that have been further validated by molecular modeling studies. While the binding of Tat competitor PAAs induces a contraction at the TAR bulge region, the binding of non-competitor ones widens it. This could account for the distinct PAA ability to compete with Tat fragment. Our work illustrates how comparative thermodynamic studies of a series of RNA ligands of same chemical family are of value for understanding their binding modes and for rationalizing structure-activity relationships.

  4. DeepMirTar: a deep-learning approach for predicting human miRNA targets.

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    Wen, Ming; Cong, Peisheng; Zhang, Zhimin; Lu, Hongmei; Li, Tonghua

    2018-06-01

    MicroRNAs (miRNAs) are small noncoding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates. In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed, and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance. DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA. lith@tongji.edu.cn, hongmeilu@csu.edu.cn. Supplementary data are available at Bioinformatics online.

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

    OpenAIRE

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

    2009-01-01

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

  6. Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.

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    Pascale, Lise; Azoulay, Stéphane; Di Giorgio, Audrey; Zenacker, Laura; Gaysinski, Marc; Clayette, Pascal; Patino, Nadia

    2013-06-01

    RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous 'polyamide amino acids' (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy-entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets.

  7. A proteomic study of TAR-RNA binding protein (TRBP-associated factors

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    Chi Ya-Hui

    2011-02-01

    Full Text Available Abstract Background The human TAR RNA-binding protein, TRBP, was first identified and cloned based on its high affinity binding to the small hairpin trans-activation responsive (TAR RNA of HIV-1. TRBP has more recently been found to be a constituent of the RNA-induced silencing complex (RISC serving as a Dicer co-factor in the processing of the ~70 nucleotide pre-microRNAs(miRNAs to 21-25 nucleotide mature miRNAs. Findings Using co-immunoprecipitation and protein-identification by mass spectrometry, we characterized intracellular proteins that complex with TRBP. These interacting proteins include those that have been described to act in protein synthesis, RNA modifications and processing, DNA transcription, and cell proliferation. Conclusions Our findings provide a proteome of factors that may cooperate with TRBP in activities such as miRNA processing and in RNA interference by the RISC complex.

  8. HuMiTar: A sequence-based method for prediction of human microRNA targets

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    Chen Ke

    2008-12-01

    Full Text Available Abstract Background MicroRNAs (miRs are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to induce mRNA degradation or mRNA cleavage. The ability to perform accurate, high-throughput identification of physiologically active miR targets would enable functional characterization of individual miRs. Current target prediction methods include traditional approaches that are based on specific base-pairing rules in the miR's seed region and implementation of cross-species conservation of the target site, and machine learning (ML methods that explore patterns that contrast true and false miR-mRNA duplexes. However, in the case of the traditional methods research shows that some seed region matches that are conserved are false positives and that some of the experimentally validated target sites are not conserved. Results We present HuMiTar, a computational method for identifying common targets of miRs, which is based on a scoring function that considers base-pairing for both seed and non-seed positions for human miR-mRNA duplexes. Our design shows that certain non-seed miR nucleotides, such as 14, 18, 13, 11, and 17, are characterized by a strong bias towards formation of Watson-Crick pairing. We contrasted HuMiTar with several representative competing methods on two sets of human miR targets and a set of ten glioblastoma oncogenes. Comparison with the two best performing traditional methods, PicTar and TargetScanS, and a representative ML method that considers the non-seed positions, NBmiRTar, shows that HuMiTar predictions include majority of the predictions of the other three methods. At the same time, the proposed method is also capable of finding more true positive targets as a trade-off for an increased number of predictions. Genome-wide predictions show that the proposed method is characterized by 1.99 signal

  9. Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR RNA.

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    Matthew S Lalonde

    2011-05-01

    Full Text Available The RNA response element TAR plays a critical role in HIV replication by providing a binding site for the recruitment of the viral transactivator protein Tat. Using a structure-guided approach, we have developed a series of conformationally-constrained cyclic peptides that act as structural mimics of the Tat RNA binding region and block Tat-TAR interactions at nanomolar concentrations in vitro. Here we show that these compounds block Tat-dependent transcription in cell-free systems and in cell-based reporter assays. The compounds are also cell permeable, have low toxicity, and inhibit replication of diverse HIV-1 strains, including both CXCR4-tropic and CCR5-tropic primary HIV-1 isolates of the divergent subtypes A, B, C, D and CRF01_AE. In human peripheral blood mononuclear cells, the cyclic peptidomimetic L50 exhibited an IC(50 ∼250 nM. Surprisingly, inhibition of LTR-driven HIV-1 transcription could not account for the full antiviral activity. Timed drug-addition experiments revealed that L-50 has a bi-phasic inhibition curve with the first phase occurring after HIV-1 entry into the host cell and during the initiation of HIV-1 reverse transcription. The second phase coincides with inhibition of HIV-1 transcription. Reconstituted reverse transcription assays confirm that HIV-1 (- strand strong stop DNA synthesis is blocked by L50-TAR RNA interactions in-vitro. These findings are consistent with genetic evidence that TAR plays critical roles both during reverse transcription and during HIV gene expression. Our results suggest that antiviral drugs targeting TAR RNA might be highly effective due to a dual inhibitory mechanism.

  10. A Tat-grafted anti-nucleic acid antibody acquires nuclear-localization property and a preference for TAR RNA

    International Nuclear Information System (INIS)

    Jeong, Jong-Geun; Kim, Dong-Sik; Kim, Yong-Sung; Kwon, Myung-Hee

    2011-01-01

    Highlights: → We generate ' H3 Tat-3D8' by grafting Tat 48-60 peptide to VH CDR of 3D8 scFv antibody. → H3 Tat-3D8 antibody retains nucleic acid binding and hydrolyzing activities. → H3 Tat-3D8 acquires a preference for TAR RNA structure. → Properties of Tat 48-60 is transferred to an antibody via Tat-grafting into a CDR. -- Abstract: The 3D8 single chain variable fragment (3D8 scFv) is an anti-nucleic acid antibody that can hydrolyze nucleic acids and enter the cytosol of cells without reaching the nucleus. The Tat peptide, derived from the basic region of the HIV-1 Tat protein, translocates to cell nuclei and has TAR RNA binding activity. In this study, we generated a Tat-grafted antibody ( H3 Tat-3D8) by replacing complementarity-determining region 3 (CDR3) within the VH domain of the 3D8 scFv with a Tat 48-60 peptide (GRKKRRQRRRPPQ). H3 Tat-3D8 retained the DNA-binding and DNA-hydrolyzing activity of the scFv, and translocated to the nuclei of HeLa cells and preferentially recognized TAR RNA. Thus, the properties associated with the Tat peptide were transferred to the antibody via Tat-grafting without loss of the intrinsic DNA-binding and hydrolyzing activities of the 3D8 scFv antibody.

  11. Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid β-glycosyltransferase Involved in Methicillin Resistance.

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    Solmaz Sobhanifar

    2016-12-01

    Full Text Available In recent years, there has been a growing interest in teichoic acids as targets for antibiotic drug design against major clinical pathogens such as Staphylococcus aureus, reflecting the disquieting increase in antibiotic resistance and the historical success of bacterial cell wall components as drug targets. It is now becoming clear that β-O-GlcNAcylation of S. aureus wall teichoic acids plays a major role in both pathogenicity and antibiotic resistance. Here we present the first structure of S. aureus TarS, the enzyme responsible for polyribitol phosphate β-O-GlcNAcylation. Using a divide and conquer strategy, we obtained crystal structures of various TarS constructs, mapping high resolution overlapping N-terminal and C-terminal structures onto a lower resolution full-length structure that resulted in a high resolution view of the entire enzyme. Using the N-terminal structure that encapsulates the catalytic domain, we furthermore captured several snapshots of TarS, including the native structure, the UDP-GlcNAc donor complex, and the UDP product complex. These structures along with structure-guided mutants allowed us to elucidate various catalytic features and identify key active site residues and catalytic loop rearrangements that provide a valuable platform for anti-MRSA drug design. We furthermore observed for the first time the presence of a trimerization domain composed of stacked carbohydrate binding modules, commonly observed in starch active enzymes, but adapted here for a poly sugar-phosphate glycosyltransferase.

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

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

    2012-01-01

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

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

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    Gregory Upert

    2012-01-01

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

  14. Relevance of carbon structure to formation of tar and liquid alkane during coal pyrolysis

    International Nuclear Information System (INIS)

    Liu, Peng; Le, Jiawei; Wang, Lanlan; Pan, Tieying; Lu, Xilan; Zhang, Dexiang

    2016-01-01

    Highlights: • Curve-fitting method was used to quantify the accurate contents of structural carbon. • Effect of carbon structure in coal with different rank on formation of pyrolysis tar was studied. • Numerical interrelation between carbon types in coal structure and tar yield is elaborated. • Effect of carbon structure on formation of liquid alkane during coal pyrolysis is discussed. - Abstract: The relevance of carbon structure to formation of tar and liquid alkane during coal pyrolysis were discussed extensively. The pyrolysis tests were carried out in a tube reactor at 873 K and keep 15 min. The carbon distribution in coals was investigated by solid state "1"3C nuclear magnetic resonance (N.M.R.). The curve-fitting method was used to quantify the accurate contents of structural carbon. The alkanes in coal tar were analyzed by Gas Chromatograph–Mass Spectrometer (GC–MS). The results show that oxygen-linked aromatic carbon decreases with the increasing of coal rank. The aliphatic carbon contents of Huainan (HN) coal are 44.20%, the highest among the four coals. The carbon types in coal structure have a significant influence on the formation of tar and liquid alkane. The coal tar yields are related to the aliphatic substituted aromatic carbon, CH_2/CH_3 ratio and oxygen-linked carbon in coal so that the increasing order of tar yield is Inner Mongolia lignite (IM, 6.30 wt.%) < Sinkiang coal (SK, 7.55 wt.%) < Shenmu coal (SM, 12.84 wt.%) < HN (16.29 wt.%). The highest contents of oxygen-linked aromatic carbon in IM lead to phenolic compound of 41.06% in IM-tar. The contents of alkane in SM-tar are the highest because the appropriate CH_2/CH_3 ratio and the highest aliphatic side chains on aromatic rings in SM leading to generate aliphatic hydrocarbon with medium molecular weight easily. The mechanism on formation of tar and liquid alkane plays an important role in guiding the industrialization of pyrolysis-based poly-generation producing tar with high

  15. Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.

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    Peddi, Saikiran Reddy; Sivan, Sree Kanth; Manga, Vijjulatha

    2018-02-01

    The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔG bind and experimental pIC 50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC 50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC 50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.

  16. Fast prediction of RNA-RNA interaction using heuristic algorithm.

    Science.gov (United States)

    Montaseri, Soheila

    2015-01-01

    Interaction between two RNA molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the RNA-RNA interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two RNAs based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each RNA and binding sites between two RNAs. Furthermore, a parallel version of this method is presented. We describe the algorithm's concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches.

  17. Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis.

    Science.gov (United States)

    Beltz, Hervé; Clauss, Céline; Piémont, Etienne; Ficheux, Damien; Gorelick, Robert J; Roques, Bernard; Gabus, Caroline; Darlix, Jean-Luc; de Rocquigny, Hugues; Mély, Yves

    2005-05-20

    The nucleocapsid protein (NC) of human immunodeficiency virus type 1 (HIV-1) is formed of two highly conserved CCHC zinc fingers flanked by small basic domains. NC is required for the two obligatory strand transfers in viral DNA synthesis through its nucleic acid chaperoning properties. The first DNA strand transfer relies on NC's ability to bind and destabilize the secondary structure of complementary transactivation response region (cTAR) DNA, to inhibit self-priming, and to promote the annealing of cTAR to TAR RNA. To further investigate NC chaperone properties, our aim was to identify by fluorescence spectroscopy and gel electrophoresis, the NC structural determinants for cTAR binding and destabilization, and for the inhibition of self-primed DNA synthesis on a model system using a series of NC mutants and HIV-1 reverse transcriptase. NC destabilization and self-priming inhibition properties were found to be supported by the two fingers in their proper context and the basic (29)RAPRKKG(35) linker. The strict requirement of the native proximal finger suggests that its hydrophobic platform (Val13, Phe16, Thr24 and Ala25) is crucial for binding, destabilization and inhibition of self-priming. In contrast, only partial folding of the distal finger is required, probably for presenting the Trp37 residue in an appropriate orientation. Also, Trp37 and the hydrophobic residues of the proximal finger appear to be essential for the propagation of the melting from the cTAR ends up to the middle of the stem. Finally, both N-terminal and C-terminal basic domains contribute to cTAR binding but not to its destabilization.

  18. Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, M; Khanna, S [NIIT Univ, Neemrana (India). Dept. of Biotechnology & Bioinformation

    2010-04-15

    In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation-independent communities is available. Coal-tar-contaminated soil was collected, which consisted of 122-122.5 mg g{sup -1} total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal-tar-contaminated soil, targeting the 16S rRNA to characterize (I) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center {alpha}-subunit) common to all PAH dioxygenase enzymes and (iii) {beta}-subunit of dioxygenase. Phylotypes related to Proteobacteria ({Alpha}-, {Epsilon}- and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of alpha-subunit and beta-subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type (2Fe2S) cluster binding site suggested that these gene fragments encode for {alpha}-subunit of dioxygenase gene. Sequencing of the cloned libraries representing {alpha}-subunit gene fragments (Rf1) and beta-subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal-tar-contaminated soil.

  19. Coal Tar and Coal-Tar Pitch

    Science.gov (United States)

    Learn about coal-tar products, which can raise your risk of skin cancer, lung cancer, and other types of cancer. Examples of coal-tar products include creosote, coal-tar pitch, and certain preparations used to treat skin conditions such as eczema, psoriasis, and dandruff.

  20. Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer

    Science.gov (United States)

    Godet, Julien; Kenfack, Cyril; Przybilla, Frédéric; Richert, Ludovic; Duportail, Guy; Mély, Yves

    2013-01-01

    The HIV-1 nucleocapsid protein (NCp7) is a nucleic acid chaperone required during reverse transcription. During the first strand transfer, NCp7 is thought to destabilize cTAR, the (−)DNA copy of the TAR RNA hairpin, and subsequently direct the TAR/cTAR annealing through the zipping of their destabilized stem ends. To further characterize the destabilizing activity of NCp7, we locally probe the structure and dynamics of cTAR by steady-state and time resolved fluorescence spectroscopy. NC(11–55), a truncated NCp7 version corresponding to its zinc-finger domain, was found to bind all over the sequence and to preferentially destabilize the penultimate double-stranded segment in the lower part of the cTAR stem. This destabilization is achieved through zinc-finger–dependent binding of NC to the G10 and G50 residues. Sequence comparison further revealed that C•A mismatches close to the two G residues were critical for fine tuning the stability of the lower part of the cTAR stem and conferring to G10 and G50 the appropriate mobility and accessibility for specific recognition by NC. Our data also highlight the necessary plasticity of NCp7 to adapt to the sequence and structure variability of cTAR to chaperone its annealing with TAR through a specific pathway. PMID:23511968

  1. Coal tar pitch. Interrelations between properties and utilization of coal tar pitch

    Energy Technology Data Exchange (ETDEWEB)

    Collin, G; Koehler, H [Ruetgerswerke A.G., Duisburg (Germany, F.R.)

    1977-06-01

    Coal tar pitch is won as a highly aromatic, thermoplastic residue by destillating coal tar. In this paper the structure as well as the chemical and physical data of this pitch are introduced. In addition to this the actual as well as possible applications are indicated. For example, the pitch can be used for the production of binders, e.g. for electrodes and road construction as well as in combination with plastics for the production of insulating material and corrosion protection material.

  2. Coal tar phototherapy for psoriasis reevaluated: erythemogenic versus suberythemogenic ultraviolet with a tar extract in oil and crude coal tar

    International Nuclear Information System (INIS)

    Lowe, N.J.; Wortzman, M.S.; Breeding, J.; Koudsi, H.; Taylor, L.

    1983-01-01

    Recent studies have questioned the therapeutic value of coal tar versus ultraviolet (UV) radiation and their relative necessity in phototherapy for psoriasis. In this investigation, different aspects of tar phototherapy have been studied in single-blind bilateral paired comparison studies. The effects of 1% crude coal tar were compared with those of petrolatum in conjunction with erythemogenic and suberythemogenic doses of ultraviolet light (UVB) using a FS72 sunlamp tubed cabinet. Crude coal tar was clinically superior to petrolatum with suberythemogenic ultraviolet. With the erythemogenic UVB, petrolatum was equal in efficacy to crude coal tar. Suberythemogenic UVB was also used adjunctively to compare the effects of a 5% concentration of a tar extract in an oil base to 5% crude coal tar in petrolatum or the oil base without tar. The tar extract in oil plus suberythemogenic UVB produced significantly more rapid improvement than the oil base plus UVB. The direct bilateral comparison of equal concentrations of tar extract in oil base versus crude coal tar in petrolatum in a suberythemogenic UV photo regimen revealed no statistical differences between treatments. In a study comparing tar extract in oil and the oil base without ultraviolet radiation, the tar extract in oil side responded more rapidly

  3. Structural evolution of Eucalyptus tar pitch-based carbons during carbonization

    International Nuclear Information System (INIS)

    Prauchner, Marcos J.; Pasa, Vanya M.D.; Molhallem, Nelcy D.S.; Otani, Choyu; Otani, Satika; Pardini, Luiz C.

    2005-01-01

    Wood tar pitches are generated as by-products by the charcoal manufacturing industry. They have a macromolecular structure constituted mainly by phenolic, guaiacylic, and siringylic units common to lignin. Due to their characteristics, biopitches are been investigated as precursors of carbon materials such as carbon fibers, bioelectrodes and activated carbons. In the present work the structural evolution of Eucalyptus tar pitches under carbonization is investigated, which is important for the improvement of planning and control of pitch processing and end-product properties during carbon material production. The studies involve X-ray diffraction and infrared analyses, besides helium density, BET surface area and BJH pore volume measurements. The results showed that the conversion of pitch into carbon basically involves three steps: (1) Up to around 600 deg C the material has an highly disordered structure, being the release of aliphatic side chains and volatiles the main events taking place. (2) Between 600 deg C and 800 deg C, condensation of aromatic rings occurs to form bi-dimensional hexagonal networks so that micro- and mesoporosity are developed. The 800 deg C-coke is constituted by two phases: one highly disordered and another more crystalline. (3) Over 800 deg C, both phases are gradually ordered. As defects are gradually removed, surface area and porosity decrease, approaching zero for the 2100 deg C-coke

  4. A DEVICE AND METHOD FOR MEASURING TAR IN A TAR-ENVIRONMENT

    DEFF Research Database (Denmark)

    2017-01-01

    The present disclosure describes a device and corresponding method for measuring tar in a tar environment, e.g., a tar producing environment such as a stove or a combustion engine, based on UV absorption spectroscopy. A first measurement along an optical path in the tar environment is performed...

  5. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

    Science.gov (United States)

    2018-01-01

    With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

  6. Coal tar in dermatology

    Energy Technology Data Exchange (ETDEWEB)

    Roelofzen, J.H.J.; Aben, K.K.H.; Van Der Valk, P.G.M.; Van Houtum, J.L.M.; Van De Kerkhof, P.C.M.; Kiemeney, L.A.L.M. [Radboud University Nijmegen Medical Center, Nijmegen (Netherlands). Dept. of Dermatology

    2007-07-01

    Coal tar is one of the oldest treatments for psoriasis and eczema. It has anti-inflammatory, antibacterial, antipruritic and antimitotic effects. The short-term side effects are folliculitis, irritation and contact allergy. Coal tar contains carcinogens. The carcinogenicity of coal tar has been shown in animal studies and studies in occupational settings. There is no clear evidence of an increased risk of skin tumors or internal tumors. Until now, most studies have been fairly small and they did not investigate the risk of coal tar alone, but the risk of coal tar combined with other therapies. New, well-designed, epidemiological studies are necessary to assess the risk of skin tumors and other malignancies after dermatological use of coal tar.

  7. Treatment of lignite tars, etc

    Energy Technology Data Exchange (ETDEWEB)

    1936-08-07

    A process is described for treating tars such as lignite tar, shale tar, or peat tar, and similar tars, characterized by the fact that the tar is rectified to about 240/sup 0/C and the residue brought to a temperature above 50/sup 0/C after diluting with a product of the type of gasoline or ligroin at about 30/sup 0/C and treated with selective solvents preferably low-boiling phenols and eventually with water.

  8. Infrared absorption characteristics of hydroxyl groups in coal tars

    Energy Technology Data Exchange (ETDEWEB)

    Cannon, S A; Chu, C J; Hange, R H; Margrave, J L

    1987-01-01

    Tar evolution was observed over a temperature range of 150-600 C for four coals. Pittsburgh bituminous, Illinois No.6, Rawhide subbituminous, and Texas lignite. Isolation of the evolved tars in a nitrogen matrix at 15 degrees K produced better resolved infrared spectra than those in a coal matrix, thus enhancing structural characterization of the tar molecules. Two distinct hydroxyl functional groups in the tar molecules free of hydrogen bonding were identified for the first time without interference from H/sub 2/O absorptions. These absorptions at 3626.5 cm/sup -1/ have been assigned to phenolic hydroxyls. It is suggested that carboxylic and aliphatic hydroxyl groups do not survive the vaporization process. Tars from Illinois No.6 were found to contain the largest amount of phenolic hydroxyl; Pittsburgh No. 8 tar contains approximately half of that for Illinois No.6 while Rawhide and Texas lignite contain much less phenolic than either of the other coals. 10 references, 6 figures, 1 table.

  9. Microstructure and properties of lignite tar and pitch. Part II

    Energy Technology Data Exchange (ETDEWEB)

    Walther, H

    1954-01-01

    Photomicrographs reveal the presence of crystalline wax which affects the working properties in lignite tars and pitch. The crystals are large needles after slow cooling and small after rapid cooling. The crystals are paraffinic in character. All samples were nonhomogeneous. Thus the properties of lignite tar and pitch are varied by the source of the lignite and history of the specimen, neither softening point nor dropping point seems to satisfactorily characterize these tars. The samples exhibit thixotropic behavior characteristic of a structural viscosity and show hysteresis loops on varying the working rate. The variations have hindered use of lignite tars and pitches except where solubility in a solvent such as coal tar oil can be used to advantage.

  10. Indian coal tars. II

    Energy Technology Data Exchange (ETDEWEB)

    Basu, A N; Bhatnagar, J N; Roy, A K

    1954-01-01

    Laboratory experiments were carried out on these efforts: (1) rank and specific-gravity fractions on tar yield; (2) addition of water to the coal charge, or steam during carbonization, on yield of tar and tar acids; (3) the presence of a cracking agent (shale) with and without steam addition on the yield of tar and tar acids (the particular shale used without steam reduced the yield, and the restricted use of steam brought the yield to the former noncatalyzed level); and (4) catalytic effect of three different samples of shale, firebrick, quartz, coke, and silica-alumina on the cracking of tar acids (the most active were two of the shales, a freshly-prepared coke, and the Al/sub 2/O/sub 3/-SiO/sub 2/ catalysts that gave conversion up to 98%). The products were mainly carbon, aromatic hydrocarbons of the naphthalene series and gases (CO and H/sub 2/). The yield of the tar becomes less as coal of lower specific gravity is used or when higher temperatures are used for carbonization. The mineral matter associated with Indian coals acts as a decomposition catalyst for tar acids, as shown by experiments on the decomposition of PhOH at temperatures above 800/sup 0/.

  11. Tar bases in low-temperature coal tar

    Energy Technology Data Exchange (ETDEWEB)

    Sugiura, S; Ueno, H; Yokoyama, H

    1951-01-01

    Tar bases were extracted from three fractions, that boil below 260/sup 0/ at 260/sup 0/ to 280/sup 0/, and 280/sup 0/ to 330/sup 0/, respectively, of the low-temperature tar obtained by the carbonization of Ube coal in a Koppers' vertical retort at approximately 750/sup 0/. These were divided, respectively, into three groups, acetate-forming amine, HCl salt-forming bases (I), and CHCl/sub 3/-soluble bases (II), and further fractionally distilled. From the physical and chemical properties of the fractions thus obtained, it was concluded that low-temperature coal tar contained no low boiling pyridine homologues and that, besides higher homologues of pyridine, nonaromatic, more saturated, and less basic compounds of larger atomic weight and smaller refractive index, such as derivatives of pyrrole and indole, also existed as in crude petroleum.

  12. 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.

  13. Composition of coal tar from pyrolysis and hydropyrolysis of Shenmu coal macerals

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Q.; Li, W.; Chen, H.; Li, B. [Shandong Academy of Sciences, Jinan (China)

    2005-08-15

    To understand the relationship of the tar compositions and the coal macerals, the tars obtained from the pyrolysis and hydropyrolysis of Shenmu coal macerals in a fixed-bed reactor were analysed using GC-MS. And the effects of petrographic component, atmosphere and pressure on the yield of aromatic hydrocarbon, phenols, hydrocarbons, oxygen-containing heterocycle and PAHs were systematically investigated. The results show that there is great difference in the composition and the relative content of long chain hydrocarbons, aromatic hydrocarbons, phenols, oxygen-containing heterocycle and PAHs in tars from vitrinite and inertinite pyrolysis. Vitrinite tar contains high content of hydrocarbon with long chain, and inertinite tar contains high content of aromatic hydrocarbons, phenols, oxygen-containing heterocycle and PAHs. It suggests that vitrinite has lower aromaticity and longer chain in its structure than inertinite, which is in well agreement with the result from {sup 13}C NMR and FT-IR test. The tar yield of hydropyrolysis is higher than that of pyrolysis. With increasing the hydrogen pressure, the yield of tar increases greatly. The content of phenols and naphthalene in vitrinite tar form hydropyrolysis under 0.1 MPa is much lower than that form pyrolysis, while that of inertinite tar changes a little. The difference of tar compositions and relative content during pyrolysis and hydropyrolysis reflects the effect of hydrogenation and hydrocracking reactions and the structure characteristics of the macerals. 12 refs., 3 figs.

  14. The catalytic cracking mechanism of lignite pyrolysis char on tar

    International Nuclear Information System (INIS)

    Lei, Z.; Huibin, H.; Xiangling, S.; Zhenhua, M.; Lei, Z.

    2017-01-01

    The influence of different pyrolysis conditions for tar catalytic cracking will be analyzed according to the lignite pyrolysis char as catalyst on pyrolytic tar in this paper. The pyrolysis char what is the by-product of the cracking of coal has an abundant of pore structure and it has good catalytic activity. On this basis, making the modified catalyst when the pyrolysis char is activation and loads Fe by impregnation method. The cracking mechanism of lignite pyrolytic tar is explored by applying gas chromatograph to analyze splitting products of tar. The experimental results showed that: (1) The effect of tar cracking as the pyrolysis temperature, the heating rate, the volatilization of pyrolysis char and particle size increasing is better and better. The effect of the catalytic and cracking of lignite pyrolysis char in tar is best when the heating rate, the pyrolysis temperature, the volatiles of pyrolysis char, particle size is in specific conditions.(2) The activation of pyrolysis char can improve the catalytic effect of pyrolysis char on the tar cracking. But it reduces the effect of the tar cracking when the pyrolysis char is activation loading Fe. (author)

  15. Process of treating tars

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, C; Hempel, H; Weissenburger, H

    1955-05-05

    A process is described for treating tars or tar oils, especially carbonization tars, characterized in that the tars or tar oils are mixed with benzene or light oils which contain no aromatic material or only slight amounts, or with gas oil in such amounts that the asphalt precipitates, and after separation of the precipitated material the mixture is treated with caustic solution for separation of the phenols, and after separation of the phenolate liquor the mixture is subjected to heating for removal of the dilution medium, then the remaining oil can be used as heating oil or it is submitted to distillation for the purpose of recovering a fuel suitable for diesel motors, while the phenolate liquor is worked up into phenols.

  16. Chemical-composition studies of low-temperature-carbonization coal tar

    Energy Technology Data Exchange (ETDEWEB)

    Edel' shtein, N G; Lanin, V A

    1955-01-01

    Pintsch-oven low-temperature tar was separated into its constituents by conventional methods, and the average of 2 results was neutral asphaltenes 12.56, basic asphaltenes 2.61, acid asphaltenes 18.82, phenols 13.23, bases 2.31, neutral oil 17.66, crystalline paraffins 7.34, silica-gel tars (I) (benzene extract) 15.40, I (acetone extract) 2.47, carbenes 0.45, and carbides and dust 1.44%. The low-temperature-tar asphaltenes and tars differ from shale-oil tars by being lower in C and higher in H, with a considerably higher C:H ratio. Their specific gravity is somewhat higher, and they are cyclic in structure. The asphaltenes and silica-gel tars of coal tar and shale oil were hydrogenated, molecular weights d/sub 4//sup 20/ and n/sub 4//sup 20/ of the separated compounds were determined, and empirical formulas of the hydrogenated compounds calculated. The neutral oil was separated into saturated, intermediate (iodine number 23), unsaturated (iodine number 51), a small quantity of a mixture of unsaturated and aromatic hydrocarbons, and 44.9% aromatic hydrocarbons. While naphthenes seem to be predominantly present in the neutral-oil fraction of shale oil, aromatic hydrocarbons are predominant in coal oil.

  17. MicroRNA-target binding structures mimic microRNA duplex structures in humans.

    Directory of Open Access Journals (Sweden)

    Xi Chen

    Full Text Available Traditionally, researchers match a microRNA guide strand to mRNA sequences using sequence comparisons to predict its potential target genes. However, many of the predictions can be false positives due to limitations in sequence comparison alone. In this work, we consider the association of two related RNA structures that share a common guide strand: the microRNA duplex and the microRNA-target binding structure. We have analyzed thousands of such structure pairs and found many of them share high structural similarity. Therefore, we conclude that when predicting microRNA target genes, considering just the microRNA guide strand matches to gene sequences may not be sufficient--the microRNA duplex structure formed by the guide strand and its companion passenger strand must also be considered. We have developed software to translate RNA binding structure into encoded representations, and we have also created novel automatic comparison methods utilizing such encoded representations to determine RNA structure similarity. Our software and methods can be utilized in the other RNA secondary structure comparisons as well.

  18. Topical tar: Back to the future

    Energy Technology Data Exchange (ETDEWEB)

    Paghdal, K.V.; Schwartz, R.A. [University of Medicine & Dentistry of New Jersey, Newark, NJ (United States)

    2009-08-15

    The use of medicinal tar for dermatologic disorders dates back to the ancient times. Although coal tar is utilized more frequently in modern dermatology, wood tars have also been widely employed. Tar is used mainly in the treatment of chronic stable plaque psoriasis, scalp psoriasis, atopic dermatitis, and seborrheic dermatitis, either alone or in combination therapy with other medications, phototherapy, or both. Many modifications have been made to tar preparations to increase their acceptability, as some dislike its odor, messy application, and staining of clothing. One should consider a tried and true treatment with tar that has led to clearing of lesions and prolonged remission times. Occupational studies have demonstrated the carcinogenicity of tar; however, epidemiologic studies do not confirm similar outcomes when used topically. This article will review the pharmacology, formulations, efficacy, and adverse effects of crude coal tar and other tars in the treatment of selected dermatologic conditions.

  19. Catalytic destruction of tar in biomass derived producer gas

    International Nuclear Information System (INIS)

    Zhang Ruiqin; Brown, Robert C.; Suby, Andrew; Cummer, Keith

    2004-01-01

    The purpose of this study is to investigate catalytic destruction of tar formed during gasification of biomass, with the goal of improving the quality of the producer gas. This work focuses on nickel based catalysts treated with alkali in an effort to promote steam gasification of the coke that deposits on catalyst surfaces. A tar conversion system consisting of a guard bed and catalytic reactor was designed to treat the producer gas from an air blown, fluidized bed biomass gasifier. The guard bed used dolomite to crack the heavy tars. The catalytic reactor was used to evaluate three commercial steam reforming catalysts. These were the ICI46-1 catalyst from Imperial Chemical Industry and Z409 and RZ409 catalysts from Qilu Petrochemical Corp. in China. A 0.5-3 l/min slipstream from a 5 tpd biomass gasifier was used to test the tar conversion system. Gas and tar were sampled before and after the tar conversion system to evaluate the effectiveness of the system. Changes in gas composition as functions of catalytic bed temperature, space velocity and steam/TOC (total organic carbon) ratio are presented. Structural changes in the catalysts during the tests are also described

  20. Removing tar information from cigarette packages may reduce South Korean smokers' misconceptions about low-tar cigarettes

    Directory of Open Access Journals (Sweden)

    Hye-Jin Paek

    2018-03-01

    Full Text Available Background Many smokers still have misconceptions about “light” or “low tar” cigarettes. In South Korea, low-tar (< 3 mg cigarette sales have increased sharply from 1.8% in 2002 to 49.2% in 2015. Although government regulations forbid cigarette packages from displaying messages such as “mild,” “low-tar,” and “light,” numbers indicating tar amounts are still permitted. This study examines whether removing tar information from packaging altogether reduces people's misconceptions about low tar cigarettes. Methods An online experiment was conducted among 531 smokers who were randomly assigned to one of two conditions. In the “tar” condition, 271 participants were shown in random order three cigarette packages for three major brands (Esse, The One, Marlboro with different tar amounts. In the “no-tar” condition, 260 participants were shown the same packages without tar information. Next, participants evaluated which type of cigarette was mildest, least harmful, easier for nonsmokers to start smoking, and easier for smokers to quit. After descriptive statistics were checked, twelve sets of chi-square tests were performed. Results Average age of the participants was 26.22 (14 - 62 years; 53.5% were male. All 12 chi-square tests were statistically significant. Participants in the tar condition judged the lowest-tar cigarette to be mildest, least harmful, easier to start, and easier to quit. In the no-tar condition, for the Korean brands Esse and The One, most respondents evaluated all cigarette types to be the same only for harm, ease of starting, and ease of quitting; for Marlboro, judgments were the same as those in the tar condition except that “easier to quit” was judged to be the same across the three types. Conclusions Banning tar information from cigarette packages may help reduce smokers' misconceptions about low-tar cigarettes. People have inconsistent judgments about differently packaged cigarettes when tar

  1. Distilling tar; distillation, destructive

    Energy Technology Data Exchange (ETDEWEB)

    Brash, P; Young, W

    1866-09-17

    The tarry residue, which separates on treating crude shale oil with sulfuric acid, is redistilled, in the manner described in Specification No. 1278, A.D. 1866, together with shale. Previous to the distillation, the acid is neutralized with lime, or may be separated by blowing steam into the tar and adding salt. The purified tar thus obtained is absorbed by ashes, or is mixed with lime or other alkaline matter, or the shale may be mixed with lime and distilled with the tar, which is allowed to flow over and through the shale during the process. The tar obtained in the purification of natural paraffin may be similarly utilized.

  2. Technology unlocks tar sands energy

    Energy Technology Data Exchange (ETDEWEB)

    Law, C

    1967-09-25

    Tar sand processing technology has been developed primarily in the categories of extraction techniques and in-situ processing. In October, a $235 million venture into tar sand processing will be inspected by visitors from many points on the globe. A synthetic crude of premium quality will be flowing through a 16-in. pipeline from the Tar Island plant site of Great Canadian Oil Sands to Edmonton. This processing plant uses an extractive mining technique. The tar sand pay zone in this area averages approximately 150 ft in thickness with a 50-ft overburden. It has been estimated that the tar sands cannot be exploited when the formation thickness is less than 100 ft and overburden exceeds the same amount. This indicates that extraction techniques can only be used to recover approximately 15% of the tar sand deposits. An in-situ recovery technique developed by Shell of Canada is discussed in detail. In essence it is selective hydraulic fracturing, followed by the injection of emulsifying chemicals and steam.

  3. Upgrading of hydropyrolysis coal tar by hydroprocessing

    Energy Technology Data Exchange (ETDEWEB)

    Haglund, R.; Otterstedt, J.E.; Sterte, J. (Chalmers Univ. of Tech., Goeteborg (Sweden). 1. Dept. of Engineering Chemistry)

    1991-05-01

    Upgrading of a hydropyrolysis coal tar by hydroprocessing was investigated using different process conditions. The response of the hydropyrolysis tar to hydroprocessing was compared to those of a conventional coal tar and two heavy oil fractions. At comparable conditions, the removal of heteroatoms from the hydropyrolysis tar was more effective than from the conventional tar and, in particular, than from the oil fractions. Using conditions typical for hydroprocessing of heavy oil fractions, the contents of N, O as well as S in the hydropyrolysis tar were reduced by more than 90%. Hydroprocessing also resulted in a considerable increase in the gasoline fraction of the tar. (orig.).

  4. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

    Directory of Open Access Journals (Sweden)

    Andronescu Mirela

    2008-08-01

    Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

  5. Preparation of pure phenols from tars

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, J

    1933-02-07

    A process is disclosed for the preparation of pure phenols from brown coal tar, shale tar, or primary tar, characterized in that the raw oil obtained from the tar is carefully fractionated, in a suitable way without or with a slight pressure decrease, or before the fractionation the raw oil is heated to free the prepared phenolate solution from impurities after successful oxidation by passing in steam at a temperature between 100 and 120/sup 0/C.

  6. Analysis of tars produced in biomass gasification

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, J.; Wang, Y.; Kinoshita, C.M. [Univ. of Hawaii, Honolulu, HI (United States)

    1993-12-31

    Parametric tests on tar formation, varying temperature, equivalence ratio, and residence time, are performed on a bench-scale, indirectly-heated fluidized bed gasifier. Prepared tar samples are analyzed in a gas chromatograph (GC) with a flame ionization detector, using a capillary column. Standards containing dominant tar species have been prepared for GC calibration. The identified peaks include single-ring hydrocarbons, such as benzene, to five-ring hydrocarbons, such as perylene; depending on the gasification conditions, the identified species represent about 70 to 90% (mass basis) of the tar constituents. Under all conditions tested, benzene and naphthalene were the most dominant species. Temperature and equivalence ratio have significant effect on tar yield and tar composition. Tar yield decreases with increasing temperature or equivalence ratio. The test results suggest that lower temperature favors the formation of more aromatic tar species with diversified substituent groups, while higher temperature favors the formation of fewer aromatic tar species without substituent groups. Higher temperature or equivalence ratio favors the formation of polyaromatic compounds. Oxygen-containing compounds exist in significant quantities only at temperature below 800{degrees}C and decrease with increasing temperature, equivalence ratio, or residence time.

  7. Determination of phenol in tar

    Energy Technology Data Exchange (ETDEWEB)

    Dierichs, A; Heinichen, G

    1955-01-01

    During low-temperature carbonization of lignite, the phenols and other oxygenated compounds appear both in the aqueous-process liquor and in the tar. Measurements of these oxygenated components resulting from low-temperature carbonization may serve as a parameter for the classification of lignites. However, such measurements are complicated by the instability of the tar and the complex nature of some of the acidic substances. Difficulties with the previous methods of analysis are reviewed. The present method outlines separation of aqueous-process liquor from lignite tar in a Fischer retort, followed by determination of phenols and fatty acids in the tar phase. The jacketed tar receiver is washed with 300 milliliter xylol and treated with aqueous caustic washes. Neutral oils are separated from the aqueous alkali solution. It is then extracted with ether and finally acidified with HCl. Solids are filtered off, and phenols and fatty acids are separated by Na/sub 2/CO/sub 3/ solution.

  8. Hydroconversion of coal tars: effect of the temperature of pyrolysis on the reactivity of tars

    Energy Technology Data Exchange (ETDEWEB)

    Lemberton, J.L.; Touzeyidio, M.; Guisnet, M.

    1988-12-01

    The hydroconversion of a low-temperature and of a high-temperature tar was carried out in the presence of a sulfided Ni and Mo on alumina catalyst - pure or mixed with an acid catalyst (HY zeolite). Significant amounts of light products can be obtained from low temperature tar, formed however through a non-catalytic process. On the contrary, there is a slight catalytic effect during the hydroprocessing of high temperature tar, but the yield in light products is very low. These results can be explained by an extensive poisoning of the NiMo on alumina catalyst by coke which is initiated by the O- and N-containing compounds of the tars. 10 refs., 1 fig., 3 tabs.

  9. Dehydration of hydrated low-temperature tar

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, T

    1949-01-01

    Yoshida examined the mechanism of the dehydration of hydrated low-temperature tar with a microscope. The tar containing free carbon and coal dust is so stable that the removal of the above substances and water by a physical method is very difficult. Addition of light oil produced by fractionation of low-temperature tar facilitates the operations. Yoshida tried using the separate acid, neutral, and basic components of the light oil; the acid oil proved to be most effective. For many reasons it is convenient to use light oil as it is. In this method the quantity of light oil required is 2 to 3 times that of tar. But in supplementing the centrifugal method, the quantity of light oil needed might be only half the amount of tar.

  10. Separating cresote from tars, mineral oils, etc

    Energy Technology Data Exchange (ETDEWEB)

    Erdmann, E

    1921-01-07

    Phenolic bodies are extracted from tars such as lignite, shale, peat, coal, producer and low temperature tars, and from tar distillates and residues and from mineral oils and distillates by washing with a mixture of acetone and water. Acetone extracts of the tars etc., may be mixed with water or aqueous acetone to cause the separation of the oils, while the creosote remains in solution.

  11. Forced evolution of a regulatory RNA helix in the HIV-1 genome

    NARCIS (Netherlands)

    Berkhout, B.; Klaver, B.; Das, A. T.

    1997-01-01

    The 5'and 3'end of the HIV-1 RNA genome forms a repeat (R) element that encodes a double stem-loop structure (the TAR and polyA hairpins). Phylogenetic analysis of the polyA hairpin in different human and simian immunodeficiency viruses suggests that the thermodynamic stability of the helix is

  12. Bioremediation potential of coal-tar-oil-contaminated soil

    International Nuclear Information System (INIS)

    Lajoie, C.A.

    1991-01-01

    The bioremediation of coal tar oil contaminated soil was investigated in 90 day laboratory simulation experiments. The effect of soil moisture, humic acid amendment, and coal tar oil concentration on the rate of disappearance of individual coal tar oil constituents (PAHs and related compounds) was determined by methylene chloride extraction and gas chromatography. Mass balance experiments determined the fate of both the individual 14 C-labeled PAHs phenanthrene, pyrene, and benzo(a)pyrene, and the total coal tar oil carbon. Mineralization, volatilization, incorporation into microbial biomass, disappearance of individual coal tar oil constitutents, and the distribution of residual 14 C-activity in different soil fractions were measured. The rate of disappearance of coal tar oil constituents increased with increasing soil moisture over the experimental range. Humic acid amendment initially enhanced the rate of disappearance, but decreased the extent of disappearance. The amount of contamination removed decreased at higher coal tar oil concentrations. The practical limit for biodegradation in the system tested appeared to be between 1.0 and 2.5% coal tar oil. Mineralization accounted for 40 to 50% of the applied coal tar oil. Volatilization was a minor pathway of disappearance

  13. Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1

    International Nuclear Information System (INIS)

    Das, Chandreyee; Edgcomb, Stephen P.; Peteranderl, Ralph; Chen, Lily; Frankel, Alan D.

    2004-01-01

    Cyclin T1 (CycT1) is a cellular transcription elongation factor that also participates in Tat-mediated activation of several lentiviral promoters. In human immunodeficiency virus (HIV), CycT1 is required for Tat to bind tightly to TAR and interacts in the ternary complex via its Tat-TAR recognition motif (TRM). In the related bovine immunodeficiency virus (BIV), Tat recognizes its cognate TAR element with high affinity and specificity in the absence of CycT1. At both promoters, CycT1 recruits the Cdk9 kinase, which phosphorylates RNA polymerase II to generate processive transcription complexes. To examine the physical properties of CycT1, we purified a functional domain corresponding to residues 1-272 and found that it possesses a stably folded core, as judged by partial proteolysis and circular dichroism experiments. Interestingly, the C-terminal 20 residues corresponding to the TRM appear conformationally flexible or disordered. The TRM of the bovine CycT1 (bCycT1) is similarly sensitive to proteolysis yet differs in sequence from the human protein. In particular, bCycT1 lacks a cysteine at residue 261 known to be critical for HIV but not BIV ternary complex formation, and mutagenesis data are consistent with a proposed role for this cysteine in metal binding. The apparent flexibility of the TRM suggests that conformational rearrangements may accompany formation of CycT1-Tat-TAR ternary complexes and may contribute to different TAR recognition strategies in different lentiviruses

  14. In situ recovery of oil from Utah tar sand: a summary of tar sand research at the Laramie Energy Technology Center

    Energy Technology Data Exchange (ETDEWEB)

    Marchant, L.C.; Westhoff, J.D.

    1985-10-01

    This report describes work done by the United States Department of Energy's Laramie Energy Technology Center from 1971 through 1982 to develop technology for future recovery of oil from US tar sands. Work was concentrated on major US tar sand deposits that are found in Utah. Major objectives of the program were as follows: determine the feasibility of in situ recovery methods applied to tar sand deposits; and establish a system for classifying tar sand deposits relative to those characteristics that would affect the design and operation of various in situ recovery processes. Contents of this report include: (1) characterization of Utah tar sand; (2) laboratory extraction studies relative to Utah tar sand in situ methods; (3) geological site evaluation; (4) environmental assessments and water availability; (5) reverse combustion field experiment, TS-1C; (6) a reverse combustion followed by forward combustion field experiment, TS-2C; (7) tar sand permeability enhancement studies; (8) two-well steam injection experiment; (9) in situ steam-flood experiment, TS-1S; (10) design of a tar sand field experiment for air-stream co-injection, TS-4; (11) wastewater treatment and oil analyses; (12) economic evaluation of an in situ tar sand recovery process; and (13) appendix I (extraction studies involving Utah tar sands, surface methods). 70 figs., 68 tabs.

  15. On topological RNA interaction structures.

    Science.gov (United States)

    Qin, Jing; Reidys, Christian M

    2013-07-01

    Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.

  16. Centrifuge treatment of coal tar

    Energy Technology Data Exchange (ETDEWEB)

    L.A. Kazak; V.Z. Kaidalov; L.F. Syrova; O.S. Miroshnichenko; A.S. Minakov [Giprokoks, the State Institute for the Design of Coke-Industry Enterprises, Kharkov (Ukraine)

    2009-07-15

    New technology is required for the removal of water and heavy fractions from regular coal tar. Centrifuges offer the best option. Purification of coal tar by means of centrifuges at OAO NLMK permits the production of pitch coke or electrode pitch that complies with current standards.

  17. Efficient RNA structure comparison algorithms.

    Science.gov (United States)

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

    2017-12-01

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

  18. Inverse folding of RNA pseudoknot structures

    Directory of Open Access Journals (Sweden)

    Li Linda YM

    2010-06-01

    Full Text Available Abstract Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing, canonical pseudoknot structures. Results In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv, including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http://www.combinatorics.cn/cbpc/inv.html. Conclusions The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.

  19. Coal tar: past, present and future

    Energy Technology Data Exchange (ETDEWEB)

    Thami, G.P.; Sarkar, R. [Government Medical College & Hospital, Chandigarh (India). Dept. of Dermatology & Venerology

    2002-03-01

    Crude coal tar has been used in the treatment of dermatoses for many decades. In the last few years its use has been limited to skin diseases such as psoriasis and chronic dermatitis. Newer topical modalities for psoriasis are being used increasingly for treatment, but have failed to replace crude coal tar as a first-line treatment of psoriasis. The authors review the pharmacology, chemistry and use of crude coal tar in order to reappraise its role as a therapeutic agent in dermatology.

  20. Distillation of tar and tar fractions in the presence of surface-active coke

    Energy Technology Data Exchange (ETDEWEB)

    Jaeppelt, A; Klaus, J

    1943-01-01

    The tar obtained by low-temperature carbonization of Upper Silesian gas coke and fractions from this tar were distilled in the presence of different grades of coke dust with varying surface activity; the coke had been activated by steam in the course of its production by low-temperature carbonization. The surface activity of the coke dusts was measured by determining the heat of wetting with C/sub 6/H/sub 6/. Tar and coke dust, both anhydrous, were mixed in a kneading machine in such proportions that the capillaries of the dust were saturated and enough ''externally'' bound tar was present to permit briquetting. The briquets were distilled without cracking and with steam as heating medium. The yield and quality of the distillate depended on the magnitude of the internal surface of the coke dust used; a mixture of a very active coke from brown coal and tar yielded a distillate with Conradson carbon residue of 1.34 percent, asphalt content 6.1 percent and eta/sub 20/ 5.4/sup 0/ E. as compared with C residue of 10.95 percent, asphalt content 33.5 percent and eta/sub 20/ 123.6/sup 0/ E. of the distillate obtained in the absence of surface-active coke. Even higher-boiling fractions can be improved by this treatment, although it is preferable to use oils with an initial boiling point below 300/sup 0/. The ratio of oil to adsorbent is not critical, but better results were obtained with higher percentages of added coke dust. The process in its present form is not suited for the conversion of crude creosote to useful phenols.

  1. Characteristics and Prediction of RNA Structure

    Directory of Open Access Journals (Sweden)

    Hengwu Li

    2014-01-01

    Full Text Available RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is NP-hard. Most RNAs fold during transcription from DNA into RNA through a hierarchical pathway wherein secondary structures form prior to tertiary structures. Real RNA secondary structures often have local instead of global optimization because of kinetic reasons. The performance of RNA structure prediction may be improved by considering dynamic and hierarchical folding mechanisms. This study is a novel report on RNA folding that accords with the golden mean characteristic based on the statistical analysis of the real RNA secondary structures of all 480 sequences from RNA STRAND, which are validated by NMR or X-ray. The length ratios of domains in these sequences are approximately 0.382L, 0.5L, 0.618L, and L, where L is the sequence length. These points are just the important golden sections of sequence. With this characteristic, an algorithm is designed to predict RNA hierarchical structures and simulate RNA folding by dynamically folding RNA structures according to the above golden section points. The sensitivity and number of predicted pseudoknots of our algorithm are better than those of the Mfold, HotKnots, McQfold, ProbKnot, and Lhw-Zhu algorithms. Experimental results reflect the folding rules of RNA from a new angle that is close to natural folding.

  2. Flash hydropyrolysis of bituminous coal . III. Research on flash hydropyrolysis tar

    Energy Technology Data Exchange (ETDEWEB)

    Dong, M.; Zhu, Z.; He, Y.; Ding, N.; Tang, L. [East China University of Science and Technology, Shanghai (China)

    2000-02-01

    Tar sample obtained by flash hydropyrolysis (FHP) from Dongshen coal at high pressure entrained reactor was investigated. An effect of flash hydropyrolysis temperature on the main components in tar was studied and the quality of the tar was compared with high temperature coke oven tar. The results showed that: the yields of liquid hydrocarbon in FHP tar were more than 15%, which is twofold of that in coke oven tar; the FHP tar has high oil fraction and low pitch; high phenol components and pure condensed polycyclic aromatic hydrocarbon, and low aliphatic hydrocarbon. The components of the FHP tar were simpler than that of high temperature coke oven tar. Therefore, FHP has improved the quantity and quality of tar. 11 refs., 3 figs., 5 tabs.

  3. Physical and performance properties of coal tar urethanes - pipe

    International Nuclear Information System (INIS)

    Hickney, J.; Hendry, M.

    1984-01-01

    The purpose of this paper is to review certain physical properties of coal tar extended urethane coatings designed specifically for use in the pipe coatings market. The blend of coal tar and urethane resins provides a novel finished product with properties cumulatively inherent in its constituents. Typically, coal tar and coal tar pitch offer exceptional water resistance and cathodic alkali resistance when blended with other resins. An example is the standard coal tar epoxies used for many years in the marine markets for shipbottoms

  4. Characterization of acid tar waste from benzol purification | Danha ...

    African Journals Online (AJOL)

    The use of concentrated sulphuric acid to purify benzene, toluene and xylene produces acidic waste known as acid tar. The characterization of the acid tar to determine the composition and physical properties to device a way to use the waste was done. There were three acid tars two from benzene (B acid tar), toluene and ...

  5. The temporal relationship between advertising and sales of low-tar cigarettes.

    Science.gov (United States)

    Reed, Mark B; Anderson, Christy M; Burns, David M

    2006-12-01

    To determine whether a temporal relationship exists between the advertising and sales of low-tar cigarettes. It was hypothesised that increases in the advertising of low-tar cigarettes would precede increases in sales for these cigarettes. The themes of cigarette advertisements were reviewed and coded for 20 low-tar cigarette brands advertised in 13 widely read magazines in the US between 1960 and 1996. These 20 brands represented most of the low-tar cigarette advertisements and cigarette sales from 1967 to 1996. Cigarette sales data were obtained from the 1994 Maxwell report that summarises all cigarette sales from 1925 to 1990. If the advertisement referred to the low-tar attributes of the cigarette advertised, the advertisement was coded as having a low-tar theme and was included in the analysis. Five different graphical presentations of the relationship between the advertising and sales of the 20 low-tar cigarette brands showed a temporal relationship between low-tar advertising and sales for these brands. This relationship was observed for brands that introduced a low-tar alternative into an existing brand family (eg, Marlboro Light) and for new exclusively low-tar brands (eg, Carlton). Despite large increases in the advertising for the exclusively low-tar brands, sales of these brands remained low relative to sales of the low-tar alternative brands. Increases in print advertising of 20 of the most popular low-tar cigarette brands were followed by increases in sales for these cigarettes. Despite increases in the advertising of exclusively low-tar brands in the mid-1970s and early 1980s, the sales of these brands never matched the sales of the low-tar alternative brands. This suggests that it may have been easier to get smokers to switch to low-tar brands within a brand family compared with entirely new low-tar brands. Over the past 30 years, the marketing of low-tar cigarettes as a healthier alternative to higher-tar cigarettes has resulted in these brands

  6. Cancer fear over coal tar products

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-01-01

    Discusses a report by Dutch researchers which suggests that the regular use of coal tar shampoos may significantly increase the risk of cancer due to the high levels of polynuclear aromatic hydrocarbons (PAHs) in the products. The PAH exposure of volunteers using a coal tar anti-dandruff shampoo was studied by measuring the amount of hydroxypyrene, a PAH breakdown product in their urine. Volunteers who had used the shampoo excreted high levels of hydroxypyrene the day after exposure. Excretion by the control group using a non-coal tar anti-dandruff shampoo remained constant. 1 ref., 1 fig.

  7. Hydration dependent dynamics in RNA

    International Nuclear Information System (INIS)

    Olsen, Greg L.; Bardaro, Michael F.; Echodu, Dorothy C.; Drobny, Gary P.; Varani, Gabriele

    2009-01-01

    The essential role played by local and collective motions in RNA function has led to a growing interest in the characterization of RNA dynamics. Recent investigations have revealed that even relatively simple RNAs experience complex motions over multiple time scales covering the entire ms-ps motional range. In this work, we use deuterium solid-state NMR to systematically investigate motions in HIV-1 TAR RNA as a function of hydration. We probe dynamics at three uridine residues in different structural environments ranging from helical to completely unrestrained. We observe distinct and substantial changes in 2 H solid-state relaxation times and lineshapes at each site as hydration levels increase. By comparing solid-state and solution state 13 C relaxation measurements, we establish that ns-μs motions that may be indicative of collective dynamics suddenly arise in the RNA as hydration reaches a critical point coincident with the onset of bulk hydration. Beyond that point, we observe smaller changes in relaxation rates and lineshapes in these highly hydrated solid samples, compared to the dramatic activation of motion occurring at moderate hydration

  8. New windows into retroviral RNA structures.

    Science.gov (United States)

    Jayaraman, Dhivya; Kenyon, Julia Claire

    2018-01-25

    The multiple roles of both viral and cellular RNAs have become increasingly apparent in recent years, and techniques to model them have become significantly more powerful, enabling faster and more accurate visualization of RNA structures. Techniques such as SHAPE (selective 2'OH acylation analysed by primer extension) have revolutionized the field, and have been used to examine RNAs belonging to many and diverse retroviruses. Secondary structure probing reagents such as these have been aided by the development of faster methods of analysis either via capillary or next-generation sequencing, allowing the analysis of entire genomes, and of retroviral RNA structures within virions. Techniques to model the three-dimensional structures of these large RNAs have also recently developed. The flexibility of retroviral RNAs, both structural and functional, is clear from the results of these new experimental techniques. Retroviral RNA structures and structural changes control many stages of the lifecycle, and both the RNA structures themselves and their interactions with ligands are potential new drug targets. In addition, our growing understanding of retroviral RNA structures is aiding our knowledge of cellular RNA form and function.

  9. Predicting RNA Structure Using Mutual Information

    DEFF Research Database (Denmark)

    Freyhult, E.; Moulton, V.; Gardner, P. P.

    2005-01-01

    , to display and predict conserved RNA secondary structure (including pseudoknots) from an alignment. Results: We show that MIfold can be used to predict simple pseudoknots, and that the performance can be adjusted to make it either more sensitive or more selective. We also demonstrate that the overall...... package. Conclusion: MIfold provides a useful supplementary tool to programs such as RNA Structure Logo, RNAalifold and COVE, and should be useful for automatically generating structural predictions for databases such as Rfam. Availability: MIfold is freely available from http......Background: With the ever-increasing number of sequenced RNAs and the establishment of new RNA databases, such as the Comparative RNA Web Site and Rfam, there is a growing need for accurately and automatically predicting RNA structures from multiple alignments. Since RNA secondary structure...

  10. The temporal relationship between advertising and sales of low‐tar cigarettes

    Science.gov (United States)

    Reed, Mark B; Anderson, Christy M; Burns, David M

    2006-01-01

    Objective and hypothesis To determine whether a temporal relationship exists between the advertising and sales of low‐tar cigarettes. It was hypothesised that increases in the advertising of low‐tar cigarettes would precede increases in sales for these cigarettes. Methods The themes of cigarette advertisements were reviewed and coded for 20 low‐tar cigarette brands advertised in 13 widely read magazines in the US between 1960 and 1996. These 20 brands represented most of the low‐tar cigarette advertisements and cigarette sales from 1967 to 1996. Cigarette sales data were obtained from the 1994 Maxwell report that summarises all cigarette sales from 1925 to 1990. If the advertisement referred to the low‐tar attributes of the cigarette advertised, the advertisement was coded as having a low‐tar theme and was included in the analysis. Results Five different graphical presentations of the relationship between the advertising and sales of the 20 low‐tar cigarette brands showed a temporal relationship between low‐tar advertising and sales for these brands. This relationship was observed for brands that introduced a low‐tar alternative into an existing brand family (eg, Marlboro Light) and for new exclusively low‐tar brands (eg, Carlton). Despite large increases in the advertising for the exclusively low‐tar brands, sales of these brands remained low relative to sales of the low‐tar alternative brands. Conclusions Increases in print advertising of 20 of the most popular low‐tar cigarette brands were followed by increases in sales for these cigarettes. Despite increases in the advertising of exclusively low‐tar brands in the mid‐1970s and early 1980s, the sales of these brands never matched the sales of the low‐tar alternative brands. This suggests that it may have been easier to get smokers to switch to low‐tar brands within a brand family compared with entirely new low‐tar brands. Over the past 30 years, the marketing of low‐tar

  11. Characterization of Tar Deposits, Extraction and Sorption Properties

    Directory of Open Access Journals (Sweden)

    Pryszcz Adrian

    2016-06-01

    Full Text Available The main goal of this paper was to characterize and find a useful solution for the decomposition of tar deposits. For the experimental part, tar deposits, formed by polymerization and condensation reactions, were chosen from a storage tank for tars. At first the initial analyses of tar deposits (elemental, thermogravimetric, and calorimetric analyses were performed. After the characterization, the tar deposits were extracted in the Soxhlet extractor by acetone, toluene, and quinolone and activated with potassium hydroxide. As the final step of this work, the sorption characterization on the 3Flex Surface Characterization Analyzer (Micromeritics was performed. The specific surface area of the samples was evaluated using two methods - a single point measurement at p/p0=0.2 and BET method. Micropore and external surface areas were calculated based on a t-plot analysis (carbon black model.

  12. Combinatorial microRNA target predictions

    DEFF Research Database (Denmark)

    Krek, Azra; Grün, Dominic; Poy, Matthew N.

    2005-01-01

    MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript1, 2, 3. Different combinations of microRNAs are expressed...... in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published micro......RNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. We find that vertebrate microRNAs target, on average, roughly 200 transcripts each. Furthermore, our results...

  13. Technological changes illustrated by the coal tar and tar dye industry; Die Wandlung der Technik am Beispiel der Steinkohlenteer- und Teerfarben-Chemie

    Energy Technology Data Exchange (ETDEWEB)

    Collin, G. [Deutsche Gesellschaft fuer Chemisches Apparatewesen, Chemische Technik und Biotechnologie e.V. (DECHEMA), Frankfurt am Main (Germany)

    2001-05-01

    Coal tar was detected in the 17th century in laboratory experiments based on empirical knowledge. In the 18th century industrial revolution, coal tar was an undesired by-product of iron production and coking plants. It was first used in the 19th century for impregnating railway sleepers. Later developments in atomic theory, new chemical symbols and organic element analysis provided the basis for discovering and chemical characterisation of coal tar constituents. Laboratory experiments with these tar constituents resulted in the first synthetic dyes, the postulation of tetravalent carbon and the resulting structural theory in organic chemistry for systematic synthesis of many tar dyes to substitute natural dyes in the textile industry. The technical application of these syntheses was part 2 of the industrial revolution and the foundation of the chemical industry in Germany, which developed rapidly in the 2nd half of the 19th century. Tar dye chemistry has made a significant contribution to Germany's economic growth and the change from an agricultural to an industrialized country. [German] Die Entdeckung des Steinkohlenteers im 17. Jahrhundert basiert auf durch Erfahrungswissen gepraegten Laboratoriumsexperimenten. Im Verlauf der 'Industriellen Revolution' des 18. Jahrhunderts ist der Steinkohlenteer zunaechst ein laestiges Abfallprodukt der Eisengewinnung im Kokshochofen und der Leuchtgasherstellung durch Kohlenverkokung. Erste technische Applikation finden Steinkohlenteeroele im 19. Jahrhundert durch den Eisenbahnbau zur Langzeit-Konservierung der dafuer benoetigten Holzschwellen. Die wissenschaftlichen Erfkenntnisse zur Atomtheorie, eine neue chemische Zeichensprache und die organische Elementaranalyse werden Voraussetzungen zur Entdeckung und chemischen Charakterisierung der Hauptinhaltsstoffe des Steinkohlenteers. Laboratoriumsexperimente mit den entdeckten Teerinhaltsstoffen fuehren zur Erfindung der ersten synthetischen Farbstoffe, die

  14. Preparation of pure phenols from tars

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, J

    1929-06-18

    A process is disclosed for preparing pure phenols from brown coal and shale tar, characterized in that the alkaline extract obtained from the tar is oxidized and concurrently the alkaline solution is separated from the existing impurities by heating with steam at high temperature, which finally reaches at least 150/sup 0/C.

  15. 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...

  16. New method for the exact determination of phenols in low-temperature tar and tar oils

    Energy Technology Data Exchange (ETDEWEB)

    Lambris, G; Haferkorn, H

    1949-01-01

    A 3-gram sample of water-free tar or tar oil containing approximately 50% phenols is dissolved in a mixture of benzene and xylene and a known excess of a 20% KOH solution of known normality saturated with benzene and xylene is added. Weight of the KOH is determined by difference. This mixture is shaken repeatedly in a 300-milliliter separatory funnel. After standing for 0.5 h, the dark or almost black phenolate solution containing the major portion is separated and weighed. Care must be taken to prevent the induction of solids. The phenolate in the residue is extracted with hot water and titrated with 0.2N HCl and 1 ml. Congo red (1:100). If water is present in the tar or tar oil, 100 ml of xylene is added immediately after weighing and the water separated by distillation the weight of which must be determined. Any phenols carried over are dissolved in the small quantity of xylene in the distillate. This quantity is added to the bulk of the xylene. After any remaining phenols are extracted from the tar residue with boiling benzene, the benzene-xylene mixture is treated with KOH as above. The accuracy of the method is estimated to be +-1% as shown by experiments with phenol; o-, m-, and p-cresol; cresol mixture; and pyrocatechol. The weight of the dissolved phenols X is determined by X = c - a + cd/(ab - d) where a = weight of KOH, b = HCl used per gram of KOH, C = weight of major portion of phenolate solution, which is formed by shaking the phenol solution with KOH, d = HCl used for titration of phenolate residue.

  17. On RNA-RNA interaction structures of fixed topological genus.

    Science.gov (United States)

    Fu, Benjamin M M; Han, Hillary S W; Reidys, Christian M

    2015-04-01

    Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and a linear time uniform sampling algorithm for RNA complexes of fixed topological genus. The bijection allows to either reduce the topological genus of a bicellular map directly, or to lose connectivity by decomposing the complex into a pair of single stranded RNA structures. Our main result is proved bijectively. It provides an explicit algorithm of how to rewire the corresponding complexes and an unambiguous decomposition grammar. Using the concept of genus induction, we construct bicellular maps of fixed topological genus g uniformly in linear time. We present various statistics on these topological RNA complexes and compare our findings with biological complexes. Furthermore we show how to construct loop-energy based complexes using our decomposition grammar. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Sunflower oil in the treatment of hot tar burns.

    Science.gov (United States)

    Türegün, M; Oztürk, S; Selmanpakoğlu, N

    1997-08-01

    Hot tar burns compose a unique class of thermal injury, because removal of this highly sticky compound may be very difficult without inflicting additional tissue damage. Early removal of tar facilitates assessment of the burn and improves patient comfort. Although the use of many substances for the painless removal of tar has been described, we used sunflower oil effectively in the treatment of four tar burn patients. This first report describes the practical and successful use of sunflower oil which was easily obtained from the hospital kitchen.

  19. Tar dew point analyser as a tool in biomass gasification

    Energy Technology Data Exchange (ETDEWEB)

    Vreugdenhil, B.J.; Kuipers, J. [ECN Biomass, Coal and Environmental Research, Petten (Netherlands)

    2008-08-15

    Application of the Tar Dew point Analyzer (TDA) in different biomass based gasification systems and subsequent gas cleaning setups has been proven feasible. Such systems include BFB gasifiers, CFB gasifier and fixed bed gasifiers, with tar crackers or different scrubbers for tar removal. Tar dew points obtained with the TDA give direct insight in the performance of the gas cleaning section and help prevent any tar related problems due to condensation. The current TDA is capable of measuring tar dew points between -20 to 200C. This manuscript will present results from 4 different gasification setups. The range of measured tar dew points is -7 to 164C with comparable results from the calculated dew points based on the SPA measurements. Further detail will be presented on the differences between TDA and SPA results and explanations will be given for deviations that occurred. Improvements for the TDA regarding future work will be presented.

  20. Facilitating RNA structure prediction with microarrays.

    Science.gov (United States)

    Kierzek, Elzbieta; Kierzek, Ryszard; Turner, Douglas H; Catrina, Irina E

    2006-01-17

    Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2'-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2'-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.

  1. Low-temperature tar and oil: properties and applications

    Energy Technology Data Exchange (ETDEWEB)

    Heinze, R

    1942-01-01

    In Germany the value of low-temperature tar is largely dependent on its fuel fractions; these vary with the coal and the method of carbonization (external heating or recirculated gases). Brown-coal tars can be processed by distillation, cracking under pressure, hydrogenation under pressure (largest volume of tar is processed by this method) and by solvent extraction, with EtOH, SO/sub 2/, or phenol. Each of these processes is discussed in detail. In the pressure-hydrogenation process, 1.25 kilogram of brown-coal tar yields approximately 1 kilogram of gasoline with an octane number of 60 to 70. Low-temperature tars from bituminous coals can be hydrogenated readily but are not well adapted to solvent extraction. Attempts should be made to produce tar approximating the desired characteristics for fuel directly from the carbonizing apparatus. For laboratory carbonization tests, an approximation to results secured by externally heated retorts is secured by using an insert consisting of a series of perforated trays in the 200-gram Fischer aluminum retort; this reduces the capacity to 100 gram. Fractional condensation is used to separate heavy oil, middle oil, and liquor; low-boiling products are condensed at -20/sup 0/ by solid CO/sub 2/.

  2. Four RNA families with functional transient structures.

    Science.gov (United States)

    Zhu, Jing Yun A; Meyer, Irmtraud M

    2015-01-01

    Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All

  3. Exploring the impact of the side-chain length on peptide/RNA binding events.

    Science.gov (United States)

    Sbicca, Lola; González, Alejandro López; Gresika, Alexandra; Di Giorgio, Audrey; Closa, Jordi Teixido; Tejedor, Roger Estrada; Andréola, Marie-Line; Azoulay, Stéphane; Patino, Nadia

    2017-07-19

    The impact of the amino-acid side-chain length on peptide-RNA binding events has been investigated using HIV-1 Tat derived peptides as ligands and the HIV-1 TAR RNA element as an RNA model. Our studies demonstrate that increasing the length of all peptide side-chains improves unexpectedly the binding affinity (K D ) but reduces the degree of compactness of the peptide-RNA complex. Overall, the side-chain length appears to modulate in an unpredictable way the ability of the peptide to compete with the cognate TAR RNA partner. Beyond the establishment of non-intuitive fundamental relationships, our results open up new perspectives in the design of effective RNA ligand competitors, since a large number of them have already been identified but few studies report on the modulation of the biological activity by modifying in the same way the length of all chains connecting RNA recognition motives to the central scaffold of a ligand.

  4. Process of transforming tars, etc

    Energy Technology Data Exchange (ETDEWEB)

    1929-04-11

    A process is described for treating tars obtained by carbonization, at high or low temperature, of coals, lignites, shales, and other carbonaceous materials or fractions of these tars, for obtaining products of greater value, consisting of polymerizing or saturating the unstable hydrocarbons in the presence of catalyzers by the progressing action particularly of halogenated metals, such as titanium tetrachloride, iron chloride, etc. and applying a known process of recovery, the disclosed process leading to an important reduction of final losses.

  5. Effect of the rate of heating on the quality of the primary tar in low-temperature coal-carbonization process

    Energy Technology Data Exchange (ETDEWEB)

    Turskii, Y I

    1956-01-01

    Two stages are observed. The first stage yields products of the primary and partial decomposition of coal, mainly water, CO/sub 2/, and CO as decomposition products of functional groups (-COOH, > CO, - OH, and so forth). No tar is formed in this stage. The structural decomposition and tar formation occur in the second stage. The rate of heating is important for the quality of the tar obtained. The slow rate of heating with both stages following each other yields a good-quality tar, richer in C and H, with lower O content. In case of high rate of heating both stages overlap. The tar is of poorer quality with higher specific gravity, and contains more O and asphaltenes. The complete experimental data are given in detail.

  6. Mineralization of PAHs in coal-tar impacted aquifer sediments and associated microbial community structure investigated with FISH

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, S W; Ong, S K; Moorman, T B [Iowa State University, Ames, IA (USA)

    2007-11-15

    The microbial community structure and mineralization of polycyclic aromatic hydrocarbons (PAHs) in a coal-tar contaminated aquifer were investigated spatially using fluorescence in situ hybridization (FISH) and in laboratory-scale incubations of the aquifer sediments. DAPI-detected microbial populations in the contaminated sediments were three orders of magnitude greater than nearby uncontaminated sediments, suggesting growth on coal-tar constituents in situ. Actinobacteria, {beta}- and {gamma}-Proteobacteria, and Flavobacteria dominated the in situ aerobic (> 1 mg l{sup -1} dissolved oxygen) microbial community, whereas sulfate-reducing bacteria comprised 37% of the microbial community in the sulfidogenic region of the aquifer. Rapid mineralization of naphthalene and phenanthrene were observed in aerobic laboratory microcosms and resulted in significant enrichment of {beta}- and {gamma}-Proteobacteria potentially explaining their elevated presence in situ. Nitrate- and sulfate-limited mineralization of naphthalene in laboratory microcosms occurred to a small degree in aquifer sediments from locations where groundwater chemistry indicated nitrate- and sulfate-reduction, respectively. The results of this study suggest that FISH may be a useful tool for providing a link between laboratory microcosms and groundwater measurements made in situ necessary to better demonstrate the potential for natural attenuation at complex PAH contaminated sites.

  7. Cold Preparation of Heroin in a Black Tar Market.

    Science.gov (United States)

    Roth, Alexis M; Armenta, Richard F; Wagner, Karla D; Strathdee, Steffanie A; Goldshear, Jesse L; Cuevas-Mota, Jazmine; Garfein, Richard S

    2017-07-29

    Black tar heroin is typically prepared for injection with heat which decreases the risk of HIV transmission by inactivating the virus. We received reports that persons who inject drugs (PWID) in Tijuana, Baja California, Mexico, a black tar heroin market, were using only water to dissolve heroin. Because Tijuana abuts San Diego County, CA, United States, we undertook the present analyses to determine the prevalence of this practice among PWID in San Diego, California. PWID completed quarterly behavioral assessments and serological testing for blood-borne viruses. Bivariate and multivariable logistic regression models were constructed to assess for individual, social, and structural correlates of preparing heroin without heat within the preceding 6 months. Nearly half of black tar heroin users (149/305) reported they had prepared heroin without heat within 6 months. In multivariable analysis, cold preparation was independently associated with younger age (10 year decrease; AOR = 1.25; 95% CI 1.03, 1.53), more drug injecting acquaintances (per 5 acquaintance increase; AOR = 1.05; 95% CI 1.01, 1.09) and prefilled syringe use (injecting drugs from syringes that are already filled with drugs before purchase; AOR = 1.86; 95% CI 1.14, 3.02). Conclusions/Importance: To our knowledge, this is the first paper to report that PWID living in a black tar heroin market are preparing heroin without heat. Additional research is needed to determine whether this is an endemic practice or PWID are engaging in new forms of drug preparation in response to changes in the environment.

  8. Mineral oils, tars. [British patent

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, A M; Handmarch, E

    1933-08-11

    Hydrocarbon materials such as mineral oils and tars from coal, shale, lignite, or peat are freed from phenols and like oxy-bodies by heating under pressure in a closed vessel to a temperature and for a time sufficient to effect reduction of the oxy-bodies, and then removing the water formed by the reaction. 350/sup 0/ to 400/sup 0/C. for 30 to 60 minutes is suitable. Any wax-like constituents are converted to liquids of lower viscosity and settling point. The product may be fractionated to give light oils and a residue of aviation Diesel fuel. In an example, oil from the low-temperature distillation of coal and having a tar acid content of 30 per cent is treated in a tubular converter at 380/sup 0/C. and 400 lb. per sq. in for 40 min., and the benzine toluol, and xylol distilled; the residue has a tar acid content of only 7.6 per cent.

  9. Structural imprints in vivo decode RNA regulatory mechanisms.

    Science.gov (United States)

    Spitale, Robert C; Flynn, Ryan A; Zhang, Qiangfeng Cliff; Crisalli, Pete; Lee, Byron; Jung, Jong-Wha; Kuchelmeister, Hannes Y; Batista, Pedro J; Torre, Eduardo A; Kool, Eric T; Chang, Howard Y

    2015-03-26

    Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N(6)-methyladenosine (m(6)A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.

  10. A Method to Predict the Structure and Stability of RNA/RNA Complexes.

    Science.gov (United States)

    Xu, Xiaojun; Chen, Shi-Jie

    2016-01-01

    RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

  11. Free energy minimization to predict RNA secondary structures and computational RNA design.

    Science.gov (United States)

    Churkin, Alexander; Weinbrand, Lina; Barash, Danny

    2015-01-01

    Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

  12. RNA structure alignment by a unit-vector approach.

    Science.gov (United States)

    Capriotti, Emidio; Marti-Renom, Marc A

    2008-08-15

    The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

  13. Reaction Mechanism of Tar Evolution in Biomass Steam Gasification for Hydrogen Production

    International Nuclear Information System (INIS)

    Shingo Katayama; Masahiro Suzuki; Atsushi Tsutsumi

    2006-01-01

    Reaction mechanism of tar evolution in steam gasification of biomass was investigated with a continuous cross-flow moving bed type differential reactor, in which tar and gases can be fractionated according to reaction time. We estimated that time profile of tar and gas evolution in the gasification of cellulose, xylan, and lignin, and compared it with experimental product time profile of real biomass gasification. The experimental tar evolution rate is different from estimated tar evolution rate. The estimated tar evolution rate has a peak at 20 s. On the other hand, the experimental tar evolution rate at 20 s is little, and tar at initial stage includes more water-soluble and water-insoluble compounds. It can be concluded that in the real biomass steam gasification the evolution of tar from cellulose and lignin component was found to be precipitated by that from hemi-cellulose component. (authors)

  14. Computer-Aided Design of RNA Origami Structures.

    Science.gov (United States)

    Sparvath, Steffen L; Geary, Cody W; Andersen, Ebbe S

    2017-01-01

    RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order.

  15. DECOMPOSITION OF TARS IN MICROWAVE PLASMA – PRELIMINARY RESULTS

    Directory of Open Access Journals (Sweden)

    Mateusz Wnukowski

    2014-07-01

    Full Text Available The paper refers to the main problem connected with biomass gasification - a presence of tar in a product gas. This paper presents preliminary results of tar decomposition in a microwave plasma reactor. It gives a basic insight into the construction and work of the plasma reactor. During the experiment, researches were carried out on toluene as a tar surrogate. As a carrier gas for toluene and as a plasma agent, nitrogen was used. Flow rates of the gases and the microwave generator’s power were constant during the whole experiment. Results of the experiment showed that the decomposition process of toluene was effective because the decomposition efficiency attained above 95%. The main products of tar decomposition were light hydrocarbons and soot. The article also gives plans for further research in a matter of tar removal from the product gas.

  16. Independent alignment of RNA for dynamic studies using residual dipolar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Bardaro, Michael F.; Varani, Gabriele, E-mail: varani@chem.washington.edu [University of Washington, Department of Chemistry (United States)

    2012-09-15

    Molecular motion and dynamics play an essential role in the biological function of many RNAs. An important source of information on biomolecular motion can be found in residual dipolar couplings which contain dynamics information over the entire ms-ps timescale. However, these methods are not fully applicable to RNA because nucleic acid molecules tend to align in a highly collinear manner in different alignment media. As a consequence, information on dynamics that can be obtained with this method is limited. In order to overcome this limitation, we have generated a chimeric RNA containing both the wild type TAR RNA, the target of our investigation of dynamics, as well as the binding site for U1A protein. When U1A protein was bound to the portion of the chimeric RNA containing its binding site, we obtained independent alignment of TAR by exploiting the physical chemical characteristics of this protein. This technique can allow the extraction of new information on RNA dynamics, which is particularly important for time scales not covered by relaxation methods where important RNA motions occur.

  17. Recovery of very viscous lubricating oils from shale-tar, etc

    Energy Technology Data Exchange (ETDEWEB)

    Erdmann, E

    1918-01-22

    A process is disclosed for the recovery of very viscous lubricating oils from brown-coal tar and shale tar, consisting in driving off from the crude tar or the tar freed from volatile constituents after removal of paraffin by precipitation with a volatile solvent such as acetone or one of its homologs, the light oils more or less completely with superheated steam from about 200 to 250/sup 0/C without any outside heating over a free flame.

  18. VAPOR PRESSURES AND HEATS OF VAPORIZATION OF PRIMARY COAL TARS

    Energy Technology Data Exchange (ETDEWEB)

    Eric M. Suuberg; Vahur Oja

    1997-07-01

    This project had as its main focus the determination of vapor pressures of coal pyrolysis tars. It involved performing measurements of these vapor pressures and from them, developing vapor pressure correlations suitable for use in advanced pyrolysis models (those models which explicitly account for mass transport limitations). This report is divided into five main chapters. Each chapter is a relatively stand-alone section. Chapter A reviews the general nature of coal tars and gives a summary of existing vapor pressure correlations for coal tars and model compounds. Chapter B summarizes the main experimental approaches for coal tar preparation and characterization which have been used throughout the project. Chapter C is concerned with the selection of the model compounds for coal pyrolysis tars and reviews the data available to us on the vapor pressures of high boiling point aromatic compounds. This chapter also deals with the question of identifying factors that govern the vapor pressures of coal tar model materials and their mixtures. Chapter D covers the vapor pressures and heats of vaporization of primary cellulose tars. Chapter E discusses the results of the main focus of this study. In summary, this work provides improved understanding of the volatility of coal and cellulose pyrolysis tars. It has resulted in new experimentally verified vapor pressure correlations for use in pyrolysis models. Further research on this topic should aim at developing general vapor pressure correlations for all coal tars, based on their molecular weight together with certain specific chemical characteristics i.e. hydroxyl group content.

  19. Characterization of acid tars

    Energy Technology Data Exchange (ETDEWEB)

    Leonard, Sunday A., E-mail: sunday.leonard@ucl.ac.uk [Department of Civil Environmental and Geomatic Engineering, University College London, Chadwick Building, Gower Street, London, WC1E 6BT (United Kingdom); Stegemann, Julia A. [Department of Civil Environmental and Geomatic Engineering, University College London, Chadwick Building, Gower Street, London, WC1E 6BT (United Kingdom); Roy, Amitava [J. Bennett Johnston, Sr., Centre for Advance Microstructures and Devices (CAMD), 6980 Jefferson Highway, Louisiana State University, Baton Rouge, LA, 70806 (United States)

    2010-03-15

    Acid tars from the processing of petroleum and petrochemicals using sulfuric acid were characterized by gas chromatography/mass spectrometry (GC/MS), inductively coupled plasma/optical emission spectrometry (ICP/OES), differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectrometry, and scanning electron microscopy/energy dispersive X-ray (SEM/EDX) micro-analysis. Leaching of contaminants from the acid tars in 48 h batch tests with distilled water at a liquid-to-solid ratio 10:1 was also studied. GC/MS results show that the samples contained aliphatic hydrocarbons, cyclic hydrocarbons, up to 12 of the 16 USEPA priority polycyclic aromatic hydrocarbons (PAHs), and numerous other organic groups, including organic acids (sulfonic acids, carboxylic acids and aromatic acids), phenyl, nitrile, amide, furans, thiophenes, pyrroles, and phthalates, many of which are toxic. Metals analysis shows that Pb was present in significant concentration. DSC results show different transition peaks in the studied samples, demonstrating their complexity and variability. FTIR analysis further confirmed the presence of the organic groups detected by GC/MS. The SEM/EDX micro-analysis results provided insight on the surface characteristics of the samples and show that contaminants distribution was heterogeneous. The results provide useful data on the composition, complexity, and variability of acid tars; information which hitherto have been scarce in public domain.

  20. Characterization of acid tars

    International Nuclear Information System (INIS)

    Leonard, Sunday A.; Stegemann, Julia A.; Roy, Amitava

    2010-01-01

    Acid tars from the processing of petroleum and petrochemicals using sulfuric acid were characterized by gas chromatography/mass spectrometry (GC/MS), inductively coupled plasma/optical emission spectrometry (ICP/OES), differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectrometry, and scanning electron microscopy/energy dispersive X-ray (SEM/EDX) micro-analysis. Leaching of contaminants from the acid tars in 48 h batch tests with distilled water at a liquid-to-solid ratio 10:1 was also studied. GC/MS results show that the samples contained aliphatic hydrocarbons, cyclic hydrocarbons, up to 12 of the 16 USEPA priority polycyclic aromatic hydrocarbons (PAHs), and numerous other organic groups, including organic acids (sulfonic acids, carboxylic acids and aromatic acids), phenyl, nitrile, amide, furans, thiophenes, pyrroles, and phthalates, many of which are toxic. Metals analysis shows that Pb was present in significant concentration. DSC results show different transition peaks in the studied samples, demonstrating their complexity and variability. FTIR analysis further confirmed the presence of the organic groups detected by GC/MS. The SEM/EDX micro-analysis results provided insight on the surface characteristics of the samples and show that contaminants distribution was heterogeneous. The results provide useful data on the composition, complexity, and variability of acid tars; information which hitherto have been scarce in public domain.

  1. Ultrasound assisted, thermally activated persulfate oxidation of coal tar DNAPLs.

    Science.gov (United States)

    Peng, Libin; Wang, Li; Hu, Xingting; Wu, Peihui; Wang, Xueqing; Huang, Chumei; Wang, Xiangyang; Deng, Dayi

    2016-11-15

    The feasibility of ultrasound assisted, thermally activated persulfate for effective oxidation of twenty 2-6 ringed coal tar PAHs in a biphasic tar/water system and a triphasic tar/soil/water system were investigated and established. The results indicate that ultrasonic assistance, persulfate and elevated reaction temperature are all required to achieve effective oxidation of coal tar PAHs, while the heating needed can be provided by ultrasonic induced heating as well. Further kinetic analysis reveals that the oxidation of individual PAH in the biphasic tar/water system follows the first-order kinetics, and individual PAH oxidation rate is primary determined by the mass transfer coefficients, tar/water interfacial areas, the aqueous solubility of individual PAH and its concentration in coal tar. Based on the kinetic analysis and experimental results, the contributions of ultrasound, persulfate and elevated reaction temperature to PAHs oxidation were characterized, and the effects of ultrasonic intensity and oxidant dosage on PAHs oxidation efficiency were investigated. In addition, the results indicate that individual PAH degradability is closely related to its reactivity as well, and the high reactivity of 4-6 ringed PAHs substantially improves their degradability. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Production of oil from Intermountain West tar sands deposits

    Energy Technology Data Exchange (ETDEWEB)

    Glassett, J.M.; Glassett, J.A.

    1976-03-01

    Six tar sand deposits in the Intermountain West, each containing more than one billion barrels of oil in place, are identified. All of these deposits are in eastern Utah and contain a total of twenty-eight billion barrels of oil. The names of the six deposits arranged in descending order of desirability for large-scale surface-mining oil recovery operations are as follows: Sunnyside, Tar Sand Triangle, Asphalt Ridge, P.R. Spring, Circle Cliffs, and Hill Creek. An overview of each deposit is presented including geology, surface-mining variables, chemical processing variables, environmental aspects, and economics. A comparison of Utah tar sands and Athabasca, Alberta, Canada tar sands is also presented.

  3. Detecting microRNA activity from gene expression data

    LENUS (Irish Health Repository)

    Madden, Stephen F

    2010-05-18

    Abstract Background MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. Results Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. Conclusions We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.

  4. Detecting microRNA activity from gene expression data.

    LENUS (Irish Health Repository)

    Madden, Stephen F

    2010-01-01

    BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. RESULTS: Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. CONCLUSIONS: We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.

  5. Application of organic geochemistry to coastal tar residues from central California

    Energy Technology Data Exchange (ETDEWEB)

    Kvenvolden, K.A.; Rosenbauer, R.J.; Hostettler, F.D.; Lorenson, T.D.

    2000-01-01

    Tar residues are common on the Monterey Bay National Marine Sanctuary. These coastal tar residues have been washed ashore and usually occur on headlands near the high-tide line. In this study, 18 coastal tar residues were collected and analyzed to determine their carbon isotopic compositions and values of selected biomarker ratios. All of the residues have very heavy ({sup 13}C-enriched) carbon isotopic compositions spanning a narrow range ({delta}{sup 13}C = {minus}22.2 to {minus}23.4{per{underscore}thousand}), and 28,30-bisnorhopane is present in all samples. These same geochemical characteristics are found in Monterey Formation oils from which the coastal tar residues were likely derived. These coastal residues could result from natural seeps or from accidental spills. Statistically the coastal tar residues can be organized into three groups, each of which may represent different spill or seep events. Seven samples of potential local representative sources for the tar residues were examined, but none could account for the coastal tars.

  6. A Viral RNA Structural Element Alters Host Recognition of Nonself RNA

    Energy Technology Data Exchange (ETDEWEB)

    Hyde, J. L.; Gardner, C. L.; Kimura, T.; White, J. P.; Liu, G.; Trobaugh, D. W.; Huang, C.; Tonelli, M.; Paessler, S.; Takeda, K.; Klimstra, W. B.; Amarasinghe, G. K.; Diamond, M. S.

    2014-01-30

    Although interferon (IFN) signaling induces genes that limit viral infection, many pathogenic viruses overcome this host response. As an example, 2'-O methylation of the 5' cap of viral RNA subverts mammalian antiviral responses by evading restriction of Ifit1, an IFN-stimulated gene that regulates protein synthesis. However, alphaviruses replicate efficiently in cells expressing Ifit1 even though their genomic RNA has a 5' cap lacking 2'-O methylation. We show that pathogenic alphaviruses use secondary structural motifs within the 5' untranslated region (UTR) of their RNA to alter Ifit1 binding and function. Mutations within the 5'-UTR affecting RNA structural elements enabled restriction by or antagonism of Ifit1 in vitro and in vivo. These results identify an evasion mechanism by which viruses use RNA structural motifs to avoid immune restriction.

  7. Study on tar generated from downdraft gasification of oil palm fronds.

    Science.gov (United States)

    Atnaw, Samson Mekbib; Kueh, Soo Chuan; Sulaiman, Shaharin Anwar

    2014-01-01

    One of the most challenging issues concerning the gasification of oil palm fronds (OPF) is the presence of tar and particulates formed during the process considering its high volatile matter content. In this study, a tar sampling train custom built based on standard tar sampling protocols was used to quantify the gravimetric concentration of tar (g/Nm3) in syngas produced from downdraft gasification of OPF. The amount of char, ash, and solid tar produced from the gasification process was measured in order to account for the mass and carbon conversion efficiency. Elemental analysis of the char and solid tar samples was done using ultimate analysis machine, while the relative concentration of the different compounds in the liquid tar was determined making use of a liquid gas chromatography (GC) unit. Average tar concentration of 4.928 g/Nm3 and 1.923 g/Nm3 was obtained for raw gas and cleaned gas samples, respectively. Tar concentration in the raw gas sample was found to be higher compared to results for other biomass materials, which could be attributed to the higher volatile matter percentage of OPF. Average cleaning efficiency of 61% which is comparable to that of sand bed filter and venturi scrubber cleaning systems reported in the literature was obtained for the cleaning system proposed in the current study.

  8. Study on Tar Generated from Downdraft Gasification of Oil Palm Fronds

    Directory of Open Access Journals (Sweden)

    Samson Mekbib Atnaw

    2014-01-01

    Full Text Available One of the most challenging issues concerning the gasification of oil palm fronds (OPF is the presence of tar and particulates formed during the process considering its high volatile matter content. In this study, a tar sampling train custom built based on standard tar sampling protocols was used to quantify the gravimetric concentration of tar (g/Nm3 in syngas produced from downdraft gasification of OPF. The amount of char, ash, and solid tar produced from the gasification process was measured in order to account for the mass and carbon conversion efficiency. Elemental analysis of the char and solid tar samples was done using ultimate analysis machine, while the relative concentration of the different compounds in the liquid tar was determined making use of a liquid gas chromatography (GC unit. Average tar concentration of 4.928 g/Nm3 and 1.923 g/Nm3 was obtained for raw gas and cleaned gas samples, respectively. Tar concentration in the raw gas sample was found to be higher compared to results for other biomass materials, which could be attributed to the higher volatile matter percentage of OPF. Average cleaning efficiency of 61% which is comparable to that of sand bed filter and venturi scrubber cleaning systems reported in the literature was obtained for the cleaning system proposed in the current study.

  9. Study on Tar Generated from Downdraft Gasification of Oil Palm Fronds

    Science.gov (United States)

    Atnaw, Samson Mekbib; Kueh, Soo Chuan; Sulaiman, Shaharin Anwar

    2014-01-01

    One of the most challenging issues concerning the gasification of oil palm fronds (OPF) is the presence of tar and particulates formed during the process considering its high volatile matter content. In this study, a tar sampling train custom built based on standard tar sampling protocols was used to quantify the gravimetric concentration of tar (g/Nm3) in syngas produced from downdraft gasification of OPF. The amount of char, ash, and solid tar produced from the gasification process was measured in order to account for the mass and carbon conversion efficiency. Elemental analysis of the char and solid tar samples was done using ultimate analysis machine, while the relative concentration of the different compounds in the liquid tar was determined making use of a liquid gas chromatography (GC) unit. Average tar concentration of 4.928 g/Nm3 and 1.923 g/Nm3 was obtained for raw gas and cleaned gas samples, respectively. Tar concentration in the raw gas sample was found to be higher compared to results for other biomass materials, which could be attributed to the higher volatile matter percentage of OPF. Average cleaning efficiency of 61% which is comparable to that of sand bed filter and venturi scrubber cleaning systems reported in the literature was obtained for the cleaning system proposed in the current study. PMID:24526899

  10. DCJ-RNA - double cut and join for RNA secondary structures.

    Science.gov (United States)

    Badr, Ghada H; Al-Aqel, Haifa A

    2017-10-16

    Genome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures. Many studies have been conducted to obtain an algorithm that identifies the minimum number of inversions that are necessary to transform one genome into another; this allows for genome sequence representation in polynomial time. Studies have not been conducted on the topic of rearranging a genome when it is represented as a secondary structure. Unlike sequences, the secondary structure preserves the functionality of the genome. Sequences can be different, but they all share the same structure and, therefore, the same functionality. This paper proposes a double cut and join for RNA secondary structures (DCJ-RNA) algorithm. This algorithm allows for the description of evolutionary scenarios that are based on secondary structures rather than sequences. The main aim of this paper is to suggest an efficient algorithm that can help researchers compare two ribonucleic acid (RNA) secondary structures based on rearrangement operations. The results, which are based on real datasets, show that the algorithm is able to count the minimum number of rearrangement operations, as well as to report an optimum scenario that can increase the similarity between the two structures. The algorithm calculates the distance between structures and reports a scenario based on the minimum rearrangement operations required to make the given structure similar to the other. DCJ-RNA can also be used to measure the distance between the two structures. This can help identify the common functionalities between different species.

  11. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

  12. BTX production by in-situ contact reforming of low-temperature tar from coal with zeolite-derived catalysts; Zeolite kei shokubai wo mochiita sekitan teion tar no sesshoku kaishitsu ni yoru BTX no seisei

    Energy Technology Data Exchange (ETDEWEB)

    Matsunaga, T.; Fuda, K.; Murakami, K.; Kyo, M.; Hosoya, S.; Kobayashi, S. [Akita University, Akita (Japan). Mining College

    1996-10-28

    On BTX production process from low-temperature tar obtained by pyrolysis of coal, the effect of exchanged metallic species and reaction temperature were studied using metallic ion-exchanged Y-zeolite as catalyst. In experiment, three kinds of coals with different produced tar structures such as Taiheiyo and PSOC-830 sub-bituminous coals and Loy Yang brown coal were used. Y-zeolite ion-exchanged with metal chloride aqueous solution was used as catalyst. Zn{sup 2+}, Ni{sup 2+} and In{sup 3+} were used as metal ions to be exchanged. The experiment was conducted by heating a pyrolysis section up to 600{degree}C for one hour after preheating a contact reforming section up to a certain proper temperature. As a result, the Ni system catalyst was effective for BTX production from aromatic-abundant tar, while the Zn system one from lower aromatic tar. In general, relatively high yields of toluene and xylene were obtained at lower temperature, while those of benzene at higher temperature. 4 figs., 1 tab.

  13. RNA2DMut: a web tool for the design and analysis of RNA structure mutations.

    Science.gov (United States)

    Moss, Walter N

    2018-03-01

    With the widespread application of high-throughput sequencing, novel RNA sequences are being discovered at an astonishing rate. The analysis of function, however, lags behind. In both the cis - and trans -regulatory functions of RNA, secondary structure (2D base-pairing) plays essential regulatory roles. In order to test RNA function, it is essential to be able to design and analyze mutations that can affect structure. This was the motivation for the creation of the RNA2DMut web tool. With RNA2DMut, users can enter in RNA sequences to analyze, constrain mutations to specific residues, or limit changes to purines/pyrimidines. The sequence is analyzed at each base to determine the effect of every possible point mutation on 2D structure. The metrics used in RNA2DMut rely on the calculation of the Boltzmann structure ensemble and do not require a robust 2D model of RNA structure for designing mutations. This tool can facilitate a wide array of uses involving RNA: for example, in designing and evaluating mutants for biological assays, interrogating RNA-protein interactions, identifying key regions to alter in SELEX experiments, and improving RNA folding and crystallization properties for structural biology. Additional tools are available to help users introduce other mutations (e.g., indels and substitutions) and evaluate their effects on RNA structure. Example calculations are shown for five RNAs that require 2D structure for their function: the MALAT1 mascRNA, an influenza virus splicing regulatory motif, the EBER2 viral noncoding RNA, the Xist lncRNA repA region, and human Y RNA 5. RNA2DMut can be accessed at https://rna2dmut.bb.iastate.edu/. © 2018 Moss; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  14. Ensemble-based prediction of RNA secondary structures.

    Science.gov (United States)

    Aghaeepour, Nima; Hoos, Holger H

    2013-04-24

    Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between

  15. Final Safety Assessment of Coal Tar as Used in Cosmetics

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-07-01

    Coal Tar is a semisolid by-product obtained in the destructive distillation of bituminous coal, which functions in cosmetic products as a cosmetic biocide and denaturant-antidandruff agent is also listed as a function, but this is considered an over-the-counter (OTC) drug use. In 2002, Coal Tar was reported to the Food and Drug Administration (FDA) to be used in four formulations, all of which appear to be OTC drug products. Coal Tar is monographed by the FDA as Category I (safe and effective) OTC drug ingredient for use in the treatment of dandruff, seborrhoea, and psoriasis. Coal Tar is absorbed through the skin of animals and humans and is systemically distributed. Although the Cosmetic Ingredient Review (CIR) Expert Panel believes that Coal Tar use as an antidandruff ingredient in OTC drug preparations is adequately addressed by the FDA regulations, the Panel also believes that the appropriate concentration of use of Coal Tar in cosmetic formulations should be that level that does not have a biological effect in the user. Additional data needed to make a safety assessment include product types in which Coal Tar is used (other than as an OTC drug ingredient), use concentrations, and the maximum concentration that does not induce a biological effect in users.

  16. RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.

    Science.gov (United States)

    Schnattinger, Thomas; Schöning, Uwe; Marchfelder, Anita; Kestler, Hans A

    2013-12-01

    Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.

  17. UTILIZATION OF AQUEOUS-TAR CONDENSATES FORMED DURING GASIFICATION

    Directory of Open Access Journals (Sweden)

    Anna Kwiecińska

    2016-11-01

    Full Text Available Gasification of solid fuels is an alternative process for energy production using conventional and renewable fuels. Apart from desired compounds, i.e. carbon oxide, hydrogen and methane, the produced gas contains complex organic (tars and inorganic (carbonizate, ammonia contaminants. Those substances, together with water vapor, condensate during cooling of the process gas, what results in the formation of aqueous-tar condensate, which requires proper methods of utilization. The management of this stream is crucial for commercialization and application of the gasification technology. In the paper the treatment of aqueous-tar condensates formed during biomass gasification process is discussed. The removal of tars from the stream was based on their spontaneous separation. The aqueous stream was subjected to ultrafiltration operated at different pressures. Such a treatment configuration enabled to obtain highly concentrated retentate, which could be recycled to the gasifier, and filtrate, which could be subjected to further treatment.

  18. APOBEC3G inhibits HIV-1 RNA elongation by inactivating the viral trans-activation response element.

    Science.gov (United States)

    Nowarski, Roni; Prabhu, Ponnandy; Kenig, Edan; Smith, Yoav; Britan-Rosich, Elena; Kotler, Moshe

    2014-07-29

    Deamination of cytidine residues in viral DNA is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient human immunodeficiency virus type 1 (HIV-1) replication. dC-to-dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here, we demonstrate that A3G provides an additional layer of defense against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. We further show that free single-stranded DNA (ssDNA) termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3'+5' ends is sufficient for A3G deamination. These results identify A3G as an efficient mutator and that deamination of (-)SSDNA results in an early block of HIV-1 transcription. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Evaluation of lignite tar

    Energy Technology Data Exchange (ETDEWEB)

    Gossedin, A

    1946-01-01

    Tar from the low-temperature (450/sup 0/) carbonization of lignite from Bouches-du-Rhone was hydrogenated in the presence of a catalyst based on MoS/sub 2/ with a 3:1 H:N mixture. Processing (at 470/sup 0/ and 400 atmospheres) for maximum production of gasoline yielded 86 wt % of a product of boiling 55 to 186/sup 0/ and motor octane number 75. An alternative is to hydrogenate with a view to producing solvents and lubricants. For this purpose the tar was separated by distillation (at 20 millimeters, cutting at 220/sup 0/) into two fractions of equal volume. On hydrogenation (at 300/sup 0/ and 400 atmospheres) the light part yields a gasoline H/sub 2/O-soluble cut, a highly aromatic solvent fraction, a heavier cut (280/sup 0/ to 320/sup 0/) suitable as a plasticizer, and a phenol fraction. The heavier part of the tar is hydrogenated (at 380/sup 0/ and 400 atmospheres) to give spindle oil and lubricating oil of medium eta (11.2 centistokes at 98.2/sup 0/), moderate eta index (64), good pour point (-7/sup 0/), and good oxidizing characteristics. The overall yield of products from the two portions is 86.9% (gasoline and solvent 32, light phenols 9.7, spindle oil 14.2, medium lubricating oil 25.7, wax, 5.3%).

  20. Modeling Tar Recirculation in Biomass Fluidized Bed Gasification

    NARCIS (Netherlands)

    Heineken, Wolfram; De la Cuesta de Cal, Daniel; Zobel, Nico

    2016-01-01

    A biomass gasification model is proposed and applied to investigate the benefits of tar recirculation within a gasification plant. In the model, tar is represented by the four species phenol, toluene, naphthalene, and benzene. The model is spatially one-dimensional, assuming plug flow for the

  1. RNA 3D modules in genome-wide predictions of RNA 2D structure

    DEFF Research Database (Denmark)

    Theis, Corinna; Zirbel, Craig L; Zu Siederdissen, Christian Höner

    2015-01-01

    . These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D......Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational...... approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution...

  2. RNA secondary structure prediction using soft computing.

    Science.gov (United States)

    Ray, Shubhra Sankar; Pal, Sankar K

    2013-01-01

    Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

  3. A folding algorithm for extended RNA secondary structures.

    Science.gov (United States)

    Höner zu Siederdissen, Christian; Bernhart, Stephan H; Stadler, Peter F; Hofacker, Ivo L

    2011-07-01

    RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

  4. 48 CFR Appendix to Part 1252 - Tar Matrix

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Tar Matrix Appendix to Part 1252 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Pt. 1252, App. Appendix to Part 1252—Tar Matrix ER27DE05.000...

  5. Low-temperature tar from bituminous coal and its further treatment

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, C J

    1950-01-01

    High-temperature carbonization of bituminous coal yields only 3 to 4 percent tar, as compared with 8 to 10 percent or even more for low-temperature carbonization. The yield of phenols is 20 to 30 times as great from the low-temperature tar. Five conditions that must be met by a satisfactory low-temperature carbonization process are listed. The only method that satisfies all of these conditions is the Brennstoff-Technik (BT) process, in which iron retorts with movable walls are used. One disadvantage of most of the other processes is the high-pitch content of the tar. These tars are processed further to a neutral oil and a phenol-containing oil which are good diesel fuels with high-cetane numbers; the neutral oil can be fractionated to give oils of high-, medium-, and low-cetane number. Attempts to fractionate the tar oil by solvents have not proved commercially useful. However, the tar can be diluted with low-temperature light oil and phenols extracted with NaOH solution without distillation. Some difficulty is found, owing to the simultaneous extraction of viscous resins and other products that are readily removed from the phenols by distillation.

  6. Evaluation of Gravimetric Tar Determination in Particle Samples

    DEFF Research Database (Denmark)

    Hindsgaul, Claus; Henriksen, Ulrik B.; Bentzen, Jens Dall

    2000-01-01

    A comparison of tar determination of particles from a down-draft gasifier using soxhlet extractions (with anisole, dichloromethane and acetone) and pyrolysis of the particles.......A comparison of tar determination of particles from a down-draft gasifier using soxhlet extractions (with anisole, dichloromethane and acetone) and pyrolysis of the particles....

  7. GC/MS analysis of coal tar composition produced from coal pyrolysis

    African Journals Online (AJOL)

    Coal tar is a significant product generated from coal pyrolysis. A detailed analytical study on its composition and chemical structure will be of great advantage to its further processing and utilization. Using a combined method of planigraphy-gas chromatograph/mass spectroscopy (GC/MS), this work presents a composition ...

  8. Experimental comparison of biomass chars with other catalysts for tar reduction

    NARCIS (Netherlands)

    Abu El-Rub, Ziad; Bramer, Eduard A.; Brem, Gerrit

    2008-01-01

    In this paper the potential of using biomass char as a catalyst for tar reduction is discussed. Biomass char is compared with other known catalysts used for tar conversion. Model tar compounds, phenol and naphthalene, were used to test char and other catalysts. Tests were carried out in a fixed bed

  9. Coal-tar based pavement sealant toxicity to freshwater macroinvertebrates

    International Nuclear Information System (INIS)

    Bryer, Pamela J.; Scoggins, Mateo; McClintock, Nancy L.

    2010-01-01

    Non-point-source pollution is a major source of ecological impairment in urban stream systems. Recent work suggests that coal-tar pavement sealants, used extensively to protect parking areas, may be contributing a large portion of the polycyclic aromatic hydrocarbon (PAH) loading seen in urban stream sediments. The hypothesis that dried coal-tar pavement sealant flake could alter the macroinvertebrate communities native to streams in Austin, TX was tested using a controlled outdoor laboratory type approach. The treatment groups were: control, low, medium, and high with total PAH concentrations (TPAH = sum of 16 EPA priority pollutant PAHs) of 0.1, 7.5, 18.4, and 300 mg/kg respectively. The low, medium, and high treatments were created via the addition of dried coal-tar pavement sealant to a sterile soil. At the start of the 24-day exposure, sediment from a minimally impacted local reference site containing a community of live sediment-dwelling benthic macroinvertebrates was added to each replicate. An exposure-dependent response was found for several stream health measures and for several individual taxa. There were community differences in abundance (P = 0.0004) and richness (P < 0.0001) between treatments in addition to specific taxa responses, displaying a clear negative relationship with the amount of coal-tar sealant flake. These results support the hypothesis that coal-tar pavement sealants contain bioavailable PAHs that may harm aquatic environments. - Coal-tar pavement sealants degrade stream invertebrate communities.

  10. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

    Science.gov (United States)

    Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

    2016-04-20

    RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Fatgraph models of RNA structure

    Directory of Open Access Journals (Sweden)

    Huang Fenix

    2017-01-01

    Full Text Available In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We discuss various notions of coarse-grained RNA structures and relate them to fatgraphs.We motivate and discuss the main intuition behind the fatgraph model and showcase its applicability to canonical as well as noncanonical base pairs. Recent discoveries regarding novel recursions of pseudoknotted (pk configurations as well as their translation into context-free grammars for pk-structures are discussed. This is shown to allow for extending the concept of partition functions of sequences w.r.t. a fixed structure having non-crossing arcs to pk-structures. We discuss minimum free energy folding of pk-structures and combine these above results outlining how to obtain an inverse folding algorithm for PK structures.

  12. 29 CFR 1910.1002 - Coal tar pitch volatiles; interpretation of term.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 6 2010-07-01 2010-07-01 false Coal tar pitch volatiles; interpretation of term. 1910.1002... Hazardous Substances § 1910.1002 Coal tar pitch volatiles; interpretation of term. As used in § 1910.1000 (Table Z-1), coal tar pitch volatiles include the fused polycyclic hydrocarbons which volatilize from the...

  13. Global Analysis of RNA Secondary Structure in Two Metazoans

    Directory of Open Access Journals (Sweden)

    Fan Li

    2012-01-01

    Full Text Available The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA] and unpaired (single-stranded RNA [ssRNA] components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.

  14. Regulatory effects of cotranscriptional RNA structure formation and transitions.

    Science.gov (United States)

    Liu, Sheng-Rui; Hu, Chun-Gen; Zhang, Jin-Zhi

    2016-09-01

    RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

  15. Athabasca tar sand reservoir properties derived from cores and logs

    International Nuclear Information System (INIS)

    Woodhouse, R.

    1976-01-01

    Log interpretation parameters for the Athabasca Tar Sand Lease No. 24 have been determined by careful correlation with Dean and Stark core analysis data. Significant expansion of Athabasca cores occurs as overburden pressure is removed. In the more shaly sands the core analysis procedures remove adsorbed water from the clays leading to further overestimation of porosity and free water volume. Log interpretation parameters (R/sub w/ = 0.5 ohm . m and m = n = 1.5) were defined by correlation with the weight of tar as a fraction of the weight of rock solids (grain or dry weight fraction of tar). This quantity is independent of the water content of the cores, whereas porosity and the weight of tar as a fraction of the bulk weight of fluids plus solids (bulk weight fraction) are both dependent on water content. Charts are provided for the conversion of bulk weight fraction of fluids to porosity; grain weight fraction of fluids to porosity; log derived porosity and core grain weight tar to water saturation. Example results show that the core analysis grain weight fraction of tar is adequately matched by the log analyses. The log results provide a better representation of the reservoir fluid volumes than the core analysis data

  16. ncRNA consensus secondary structure derivation using grammar strings.

    Science.gov (United States)

    Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

    2011-04-01

    Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.

  17. Corrosion test by low-temperature coal tar

    Energy Technology Data Exchange (ETDEWEB)

    Ando, S; Yamamoto, S

    1952-01-01

    Corrosive actions of various fractions of low-temperature coal tar against mild steel or Cr 13-steel were compared at their boiling states. Corrosions became severe when the boiling points exceeded 240/sup 0/. The acidic fractions were more corrosive. In all instances, corrosion was excessive at the beginning of immersion testing and then gradually became mild; boiling accelerated the corrosion. Cr 13-steel was corrosion-resistant to low-temperature coal-tar fractions.

  18. On the importance of cotranscriptional RNA structure formation

    Science.gov (United States)

    Lai, Daniel; Proctor, Jeff R.; Meyer, Irmtraud M.

    2013-01-01

    The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation. PMID:24131802

  19. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.

    Science.gov (United States)

    Jiang, F; Kumar, R A; Jones, R A; Patel, D J

    1996-07-11

    The catalytic properties of RNA and its well known role in gene expression and regulation are the consequence of its unique solution structures. Identification of the structural determinants of ligand recognition by RNA molecules is of fundamental importance for understanding the biological functions of RNA, as well as for the rational design of RNA Sequences with specific catalytic activities. Towards this latter end, Szostak et al. used in vitro selection techniques to isolate RNA sequences ('aptamers') containing a high-affinity binding site for ATP, the universal currency of cellular energy, and then used this motif to engineer ribozymes with polynucleotide kinase activity. Here we present the solution structure, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations, of both uniformly and specifically 13C-, 15N-labelled 40-mer RNA containing the ATP-binding motif complexed with AMP. The aptamer adopts an L-shaped structure with two nearly orthogonal stems, each capped proximally by a G x G mismatch pair, binding the AMP ligand at their junction in a GNRA-like motif.

  20. Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

    Science.gov (United States)

    Watters, Kyle E; Choudhary, Krishna; Aviran, Sharon; Perry, Keith L

    2018-01-01

    Abstract In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3′ untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites. PMID:29294088

  1. Protein Structure and the Sequential Structure of mRNA

    DEFF Research Database (Denmark)

    Brunak, Søren; Engelbrecht, Jacob

    1996-01-01

    entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment, By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets, These signals do not originate from......A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed, We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting...... protein, The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain, A complete search for GenBank nucleotide sequences coding for structural...

  2. Effect of water addition in a microwave assisted thermal cracking of biomass tar models

    International Nuclear Information System (INIS)

    Warsita, Aris; Al-attab, K.A.; Zainal, Z.A.

    2017-01-01

    Highlights: • Effective tar thermal treatment with water addition using microwave is proposed. • The reactor temperature of 1200 °C can be reached quickly at bed height 120 mm. • The optimum water to tar ratio W/T was 0.3 for tar models. • Temperature greatly effect tar removal at various W/T rates. - Abstract: Producer gas from biomass gasification is plagued by the presence of tar which causes pipe blockages. Thermal and catalytic treatments in a microwave reactor have been shown to be effective methods in removing tar from producer gas. A question arises as to the possibility of enhancing the removal mechanism by adding water into the reactor. Toluene and naphthalene were used as tar models in the present study with N_2 as the carrier gas followed by the use of simulated producer gas. Thermal treatment with various amount of water was added at temperatures in the range of 800–1200 °C. The tar removal efficiency obtained 95.83% at the optimum temperature of 1200 °C for naphthalene in for toluene 96.32% at 1050 °C at water to tar ratio (W/T) of 0.3. This study shows that the removal of tar by microwave irradiation with water addition is a significant and effective method in tar cracking.

  3. Sampling of tar from sewage sludge gasification using solid phase adsorption.

    Science.gov (United States)

    Ortiz González, Isabel; Pérez Pastor, Rosa Ma; Sánchez Hervás, José Ma

    2012-06-01

    Sewage sludge is a residue from wastewater treatment plants which is considered to be harmful to the environment and all living organisms. Gasification technology is a potential source of renewable energy that converts the sewage sludge into gases that can be used to generate energy or as raw material in chemical synthesis processes. But tar produced during gasification is one of the problems for the implementation of the gasification technology. Tar can condense on pipes and filters and may cause blockage and corrosion in the engines and turbines. Consequently, to minimize tar content in syngas, the ability to quantify tar levels in process streams is essential. The aim of this work was to develop an accurate tar sampling and analysis methodology using solid phase adsorption (SPA) in order to apply it to tar sampling from sewage sludge gasification gases. Four types of commercial SPA cartridges have been tested to determine the most suitable one for the sampling of individual tar compounds in such streams. Afterwards, the capacity, breakthrough volume and sample stability of the Supelclean™ ENVI-Carb/NH(2), which is identified as the most suitable, have been determined. Basically, no significant influences from water, H(2)S or NH(3) were detected. The cartridge was used in sampling real samples, and comparable results were obtained with the present and traditional methods.

  4. High-throughput determination of RNA structure by proximity ligation.

    Science.gov (United States)

    Ramani, Vijay; Qiu, Ruolan; Shendure, Jay

    2015-09-01

    We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures.

  5. A semi-supervised learning approach for RNA secondary structure prediction.

    Science.gov (United States)

    Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

    2015-08-01

    RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Occupational coal tar dermatitis

    Energy Technology Data Exchange (ETDEWEB)

    Conde-Salazar, L; Guimaraens, D; Romero, L V; Gonzalez, M A

    1987-04-01

    The paper describes the allergic reaction to coal tar of a man handling it in a factory. The reaction appeared in the form of eczema on his trunk, arms and legs, but his hands were not affected as he had been wearing gloves. 1 ref.

  7. 179 Extraction of Coal-tar Pitch by Supercritical Carbon Dioxide ...

    African Journals Online (AJOL)

    Meyer

    Several extractions of coal-tar pitch were performed using supercritical fluid ..... pressure and temperature, unlike exhaustive extraction, which involves a change in ... mechanism that is operative on extracting coal-tar pitch components with.

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

    Science.gov (United States)

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

    2008-07-01

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

  9. RNAstructure: software for RNA secondary structure prediction and analysis.

    Science.gov (United States)

    Reuter, Jessica S; Mathews, David H

    2010-03-15

    To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

  10. 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

  11. RNA Thermodynamic Structural Entropy.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

    Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  12. Contact sensitivity to newsprint: a rare manifestation of coal tar allergy

    Energy Technology Data Exchange (ETDEWEB)

    Illchyshyn, A; Cartwright, P H; Smith, A G

    1987-07-01

    Contact dermatitis due to coal tar is infrequently reported in spite of the fact that it consists of a mixture of 10,000 constituents, and is still often used to treat both eczema and psoriasis. Discusses patient with coal tar sensitivity in whom the source of exacerbation of her dermatitis is shown to be newsprint, a common product containing coal tar-derived material. 6 refs.

  13. Coal tar phototoxicity: characteristics of the smarting reaction

    International Nuclear Information System (INIS)

    Diette, K.M.; Gange, R.W.; Stern, R.S.; Arndt, K.A.; Parrish, J.A.

    1985-01-01

    The properties and ultraviolet exposure parameters of tar smarts were examined in an effort to elucidate the mechanisms involved. It was show that irradiation with 1 minimal smarting dose (MSD) of UVA immediately following tar removal lowered the MSD for 6 h, demonstrated by subsequent challenge with UVA. Following 3 MSDs this memory effect was demonstrable for 24 h. The smarting reaction was area dependent--smaller areas of exposure require higher doses of UVA to induce smarting. Smarting followed reciprocity over a 6-fold range of irradiances (2-12.5 mW/cm2) but higher irradiances required higher doses of UVA, perhaps due to a delay in the recognition and reporting of smarting. The smarting reaction and delayed erythema due to UVA and tar were equally blocked by sunscreen

  14. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  15. Solving RNA's structural secrets: interaction with antibodies and crystal structure of a nuclease resistant RNA

    International Nuclear Information System (INIS)

    Wallace, S.T.

    1998-10-01

    This Ph.D. thesis concerns the structural characterization of RNA. The work is split into two sections: 1) in vitro selection and characterization of RNAs which bind antibiotics and 2) crystal structure of a nuclease resistant RNA molecule used in antisense applications. Understanding antibiotic-RNA interactions is crucial in aiding rational drug design. We were interested in studying antibiotic interactions with RNAs small enough to characterize at the molecular and possibly at the atomic level. In order to do so, we previously performed in vitro selection to find small RNAs which bind to the peptide antibiotic viomycin and the aminoglycoside antibiotic streptomycin. The characterization of the viomycin-binding RNAs revealed the necessity of a pseudoknot-structure in order to interact with the antibiotic. The RNAs which were selected to interact with streptomycin require the presence of magnesium to bind the antibiotic. One of the RNAs, upon interacting with streptomycin undergoes a significant conformational change spanning the entire RNA sequence needed to bind the antibiotic. In a quest to design oligodeoxynucleotides (ODNs) which are able to specifically bid and inactivate the mRNA of a gene, it is necessary to fulfill two criteria: 1) increase binding affinity between the ODN and the target RNA and 2) increase the ODN's resistance to nuclease degradation. An ODN with an aminopropyl modification at the 2' position of its ribose has emerged as the most successful candidate at fulfilling both criteria. It is the most nuclease resistant modification known to date. We were interested in explaining how this modification is able to circumvent degradation by nucleases. A dodecamer containing a single 2'-O-aminopropyl modified nucleotide was crystallized and the structure was solved to a resolution of 1.6 A. In an attempt to explain the nuclease resistance, the crystal coordinates were modeled into the active exonuclease site of DNA polymerase I. We propose the

  16. Coal-tar based pavement sealant toxicity to freshwater macroinvertebrates

    Energy Technology Data Exchange (ETDEWEB)

    Bryer, P.J.; Scoggins, M.; McClintock, N.L. [Lamar University, Beaumont, TX (United States). Dept. of Biology

    2010-05-15

    Non-point-source pollution is a major source of ecological impairment in urban stream systems. Recent work suggests that coal-tar pavement sealants, used extensively to protect parking areas, may be contributing a large portion of the polycyclic aromatic hydrocarbon (PAH) loading seen in urban stream sediments. The hypothesis that dried coal-tar pavement sealant flake could alter the macroinvertebrate communities native to streams in Austin, TX was tested using a controlled outdoor laboratory type approach. The treatment groups were: control, low, medium, and high with total PAH concentrations (TPAH = sum of 16 EPA priority pollutant PAHs) of 0.1, 7.5, 18.4, & 300 mg/kg respectively. The low, medium, and high treatments were created via the addition of dried coal-tar pavement sealant to a sterile soil. At the start of the 24-day exposure, sediment from a minimally impacted local reference site containing a community of live sediment-dwelling benthic macroinvertebrates was added to each replicate. An exposure-dependent response was found for several stream health measures and for several individual taxa. There were community differences in abundance (P = 0.0004) and richness (P < 0.0001) between treatments in addition to specific taxa responses, displaying a clear negative relationship with the amount of coal-tar sealant flake. These results support the hypothesis that coal-tar pavement sealants contain bioavailable PAHs that may harm aquatic environments.

  17. Chemical and physical characteristics of tar samples from selected Manufactured Gas Plant (MGP) sites

    International Nuclear Information System (INIS)

    Ripp, J.; Taylor, B.; Mauro, D.; Young, M.

    1993-05-01

    A multiyear, multidisciplinary project concerning the toxicity of former Manufactured Gas Plant (MGP) tarry residues was initiated by EPRI under the Environmental Behavior of Organic Substances (EBOS) Program. This report concerns one portion of that work -- the collection and chemical characterization of tar samples from several former MGP sites. META Environmental, Inc. and Atlantic Environmental Services, Inc. were contracted by EPRI to collect several samples of tarry residues from former MGP sites with varied historical gas production processes and from several parts of the country. The eight tars collected during this program were physically very different. Some tars were fluid and easily pumped from existing wells, while other tars were thicker, semi-solid, or solid. Although care was taken to collect only tar, the nature of the residues at several sites made it impossible not to collect other material, such as soil, gravel, and plant matter. After the samples were collected, they were analyzed for 37 organic compounds, 8 metals, and cyanide. In addition, elemental analysis was performed on the tar samples for carbon, hydrogen, oxygen, sulfur and nitrogen content and several physical/chemical properties were determined for each tar. The tars were mixed together in different batches and distributed to researchers for use in animal toxicity studies. The results of this work show that, although the tars were produced from different processes and stored in different manners, they had some chemical similarities. All of the tars, with the exception of one unusual solid tar, contained similar relative abundances of polycyclic aromatic hydrocarbons (PAHs)

  18. Thermodynamic analysis of tar reforming through auto-thermal reforming process

    Energy Technology Data Exchange (ETDEWEB)

    Nurhadi, N., E-mail: nurhadi@tekmira.esdm.go.id; Diniyati, Dahlia; Efendi, M. Ade Andriansyah [R& D Centre for Mineral and Coal Technology, Jln. Jend.Sudirman no. 623, Bandung. Telp. 022-6030483 (Malaysia); Istadi, I. [Department of Chemical Engineering, Diponegoro University, Jln. Jl. Prof. Soedarto, SH, Semarang (Malaysia)

    2015-12-29

    Fixed bed gasification is a simple and suitable technology for small scale power generation. One of the disadvantages of this technology is producing tar. So far, tar is not utilized yet and being waste that should be treated into a more useful product. This paper presents a thermodynamic analysis of tar conversion into gas producer through non-catalytic auto-thermal reforming technology. Tar was converted into components, C, H, O, N and S, and then reacted with oxidant such as mixture of air or pure oxygen. Thus, this reaction occurred auto-thermally and reached chemical equilibrium. The sensitivity analysis resulted that the most promising process performance occurred at flow rate of air was reached 43% of stoichiometry while temperature of process is 1100°C, the addition of pure oxygen is 40% and preheating of oxidant flow is 250°C. The yield of the most promising process performance between 11.15-11.17 kmol/h and cold gas efficiency was between 73.8-73.9%.The results of this study indicated that thermodynamically the conversion of tar into producer gas through non-catalytic auto-thermal reformingis more promising.

  19. A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure.

    Science.gov (United States)

    Zhang, Jinwei; Landick, Robert

    2016-04-01

    The vectorial (5'-to-3' at varying velocity) synthesis of RNA by cellular RNA polymerases (RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived, pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here, we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNAP and nascent RNA structure. We categorize and rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Pelagic tar and plastic in the Gulf of Alaska and Bering Sea: 1975

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, D G

    1977-07-01

    Seventy-one tows of 740 m/sup 2/ each were made in search of pelagic tar and plastics in the Gulf of Alaska and Bering Sea during the period October 1974 to October 1975. Tar was observed on nine occasions while plastics were found six times. The arithmetic mean value of tar abundance, 3.3 x 10/sup -3/ mg/m/sup 2/, is considerably lower than most other oceanic areas for which values have been reported. Gas chromatographic analysis of this tar indicates that it is more extensively weathered than tar from the north Atlantic. An estimate of the abundance of tar lumps too small to be sampled by net tows is made based on the assumption that there are equal weights of particles in logarithmetically equal size intervals. The abundance of pelagic plastics is also low.

  1. Extraction of low-temperature tar by various alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Hara, N; Osawa, M; Azuma, H

    1948-01-01

    MeOH was the most effective of the alcohols tested (MeOH to pentanol) in extracting acid components from low-temperature tar. The optimum concentrations of MeOH were 70 to 80% for 1 extraction and 70 to 75% for repeated or continuous extractions when the solvent-tar ratio was 1:1. By 2 to 3 extractions neutral oil could be separated in about 90% yield including > 3% acidic oil.

  2. Accelerated probabilistic inference of RNA structure evolution

    Directory of Open Access Journals (Sweden)

    Holmes Ian

    2005-03-01

    Full Text Available Abstract Background Pairwise stochastic context-free grammars (Pair SCFGs are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License.

  3. Visualization of RNA structure models within the Integrative Genomics Viewer.

    Science.gov (United States)

    Busan, Steven; Weeks, Kevin M

    2017-07-01

    Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  4. Automated and fast building of three-dimensional RNA structures.

    Science.gov (United States)

    Zhao, Yunjie; Huang, Yangyu; Gong, Zhou; Wang, Yanjie; Man, Jianfen; Xiao, Yi

    2012-01-01

    Building tertiary structures of non-coding RNA is required to understand their functions and design new molecules. Current algorithms of RNA tertiary structure prediction give satisfactory accuracy only for small size and simple topology and many of them need manual manipulation. Here, we present an automated and fast program, 3dRNA, for RNA tertiary structure prediction with reasonable accuracy for RNAs of larger size and complex topology.

  5. Dermal uptake of polycyclic aromatic hydrocarbons after hairwash with coal-tar shampoo

    Energy Technology Data Exchange (ETDEWEB)

    Schooten, F.-J. van; Moonen, E.J.C.; Rhijnsburger, E.; Agen, B. van; Thijssen, H.H.W.; Kleinjans, J.C.S. [University of Limburg, Maastricht (Netherlands). Dept. of Health Risk Analysis and Toxicology

    1994-11-26

    Describes an experiment to assess the dermal uptake of polycyclic aromatic hydrocarbons (PAHs) after hairwashing with coal tar antidandruff shampoo. The urinary excretion of 1-hydroxypyrene (1-OH-P), a PAH metabolile was used to assess internal dose of PAH. A single use of coal tar shampoo resulted in increased 1-OH-P excretion in all members of the experimental group compared with the control group using a non-coal tar antidandruff shampoo. It is suggested that repeated use of coal tar shampoo would result in a high internal dose of carcinogenic PAH. 5 refs., 1 fig.

  6. Iron-based materials as tar cracking catalyst in waste gasification

    Energy Technology Data Exchange (ETDEWEB)

    Nordgreen, Thomas

    2011-07-01

    The treatment of municipal solid waste (MSW) in Sweden has changed during the past decades due to national legislation and European Union directives. The former landfills have more or less been abandoned in favour of material recycling and waste incineration. On a yearly basis approximately 2.2 million tonnes waste are incinerated in Sweden with heat recovery and to some extent also with electricity generation, though at a low efficiency. It is desirable to alter this utilisation and instead employ MSW as fuel in a fluid bed gasification process. Then electrical energy may be produced at a much higher efficiency. However, MSW contain about 1 % chlorine in the form of ordinary table salt (NaCl) from food scraps. This implies that the tar cracking catalyst, dolomite, which is normally employed in gasification, will suffer from poisoning if applied under such conditions. Then the tar cracking capacity will be reduced or vanish completely with time. Consequently, an alternative catalyst, more resistant to chlorine, is needed. Preliminary research at KTH has indicated that iron in its metallic state may possess tar cracking ability. With this information at hand and participating in the project 'Energy from Waste' an experimental campaign was launched. Numerous experiments were conducted using iron as tar cracking catalyst. First iron sinter pellets from LKAB were employed. They were reduced in situ with a stream of hydrogen before they were applied. Later iron-based granules from Hoeganaes AB were tested. These materials were delivered in the metallic state. In all tests the KTH atmospheric fluidised bed gasifier with a secondary catalytic reactor housing the catalytic material was deployed. Mostly, the applied fuel was birch. The results show that metallic iron possesses an intrinsic ability, almost in the range of dolomite, to crack tars. Calculations indicate that iron may be more resistant to chlorine than dolomite. The exploration of metallic iron

  7. Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.

    Science.gov (United States)

    Boerneke, Mark A; Dibrov, Sergey M; Hermann, Thomas

    2016-03-14

    RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Secondary reactions of tar during thermochemical biomass conversion[Dissertation 14341

    Energy Technology Data Exchange (ETDEWEB)

    Morf, P.O.

    2001-07-01

    This dissertation submitted to the Swiss Federal Institute of Technology in Zurich presents and discusses the results obtained during the examination of the processes involved in the formation and conversion of tar in biomass gasification plant. Details are given on the laboratory reactor system used to provide separated tar production and conversion for the purposes of the experiments carried out. The results of analyses made of the tar and the gaseous products obtained after its conversion at various temperatures are presented. The development of kinetic models using the results of the experiments that were carried out is described. The results of the experiments and modelling are compared with the corresponding results obtained using a full-scale down-draft, fixed-bed gasifier. The author is of the opinion that the reaction conditions found in full-scale gasifiers can be well simulated using heterogeneous tar conversion experiments using the lab reactor system.

  9. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter....

  10. Tar loads on Omani beaches

    International Nuclear Information System (INIS)

    Badawy, M.I.; Al-Harthy, F.T.

    1991-01-01

    Owing to Oman's geographic position and long coastal line, the coastal areas of Oman are particularly vulnerable to oil pollution from normal tanker operations, illegal discharges, and accidental spills as well as local sources of oil input. UNEP carried out a survey on the coasts of Oman to determine the major sources of oil pollution and concluded that the major shoreline pollution problems in Oman arose from operational discharges of oil from passing vessels traffic. The oil, because of the high sea and air temperatures in the area, was subjected to relatively high rates of evaporation and photo-oxidation and tended to arrive at the coast as heavy petroleum particulate residues (tar balls). The aim of the present study was to measure the loads of tar balls in Omani coastal areas and to identify the source of oil pollutants on beaches

  11. Decomposition of tar in gas from updraft gasifier by thermal cracking

    DEFF Research Database (Denmark)

    Brandt, Peder; Henriksen, Ulrik Birk

    2000-01-01

    Continuing earlier work with tar reduction by partial oxidation of pyrolysis gas [1] thermal cracking has been evaluated as a gas cleaning process. The work has been focusing on cleaning gas from updraft gasifiers, and the long term purpose is to develop a tar cleaning unit based on thermal...... cracking. An experimental set-up has been built, in which a flow of contaminated gas can be heated up to 1290°C in a reactor made of pure Al2O3. Four measurements were made. Three with gas from a pyrolysis unit simulating updraft gasifier, and one with gas from an updraft gasifier. Cracking temperatures...... was 1200, 1250 and 1290°C, and the residence time at this temperature was 0.5 second. The measurements show that at the selected residence time of 0.5 second, the gas flow in a thermal tar cracking unit has to be heated to at least 1250°C to achieve sufficient tar cleaning. At 1290°C, a tar content as low...

  12. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

    Science.gov (United States)

    Puton, Tomasz; Kozlowski, Lukasz P.; Rother, Kristian M.; Bujnicki, Janusz M.

    2013-01-01

    We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks. PMID:23435231

  13. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.

    Science.gov (United States)

    Puton, Tomasz; Kozlowski, Lukasz P; Rother, Kristian M; Bujnicki, Janusz M

    2013-04-01

    We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks.

  14. Monitoring of tar contents in gases. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, Finn [ChimneyLab Europe ApS, Hadsten (Denmark); Houmann Jakobsen, H. [BioSynergi Proces ApS, Hoersholm (Denmark)

    2012-08-15

    The purpose of this project is to develop and test a relative cheap and simple online tar measuring method, which can monitor the tar content in product gas from thermal gasification. The measuring principle is absorption of tar from sample gas in Isopropanol (IPA), and measuring on this solution by UV-spectrophotometer. Continuous sampling of tar containing producer gas turned out to be a larger problem than earlier foreseen. The best solution was decided to be sampling with higher flows, and afterwards cleaning the IPA in activated carbon. The ambitions for continuous sampling had to be decreased to 1 week, where the IPA and the activated carbon is contaminated by tar and has to be replaced. However this requires larger amounts of IPA and activated carbon. For IPA the weekly consumption was 12-15 Litres and for activated carbon 10 Litres. The whole analyzer unit turned out to be more complex than first projected, mainly because of the increased amounts of IPA. The best mist filter, with respect to pressure drop, efficiency and retention time is a combination of glass wool and quarts wool. The unit has been tested on gas; 20 kW pellets burner for 116 hours. Harbooere updraft gasifier for 519 hours. Skive fluid bed gasifier for 879 hours. There have during the project period been several simple practical problems such as bubbles in the IPA, increasing pressure drop over the activated carbon bed, dropout of UV data acquisition program and increasing baseline. The principle showed from the beginning some good results, with the limitation of 1 week continuous operation, but at the 5. period in Skive the baseline was increasing all the time, and it was not possible to solve this problem. (LN)

  15. Small catalytic RNA: Structure, function and application

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-04-01

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

  16. Modelling the low-tar BIG gasification concept[Biomass Integrated gasification

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, Lars; Elmegaard, B.; Qvale, B.; Henriksen, Ulrrik [Technical univ. of Denmark (Denmark); Bentzen, J.D.; Hummelshoej, R. [COWI A/S (Denmark)

    2007-07-01

    A low-tar, high-efficient biomass gasification concept for medium- to large-scale power plants has been designed. The concept is named 'Low-Tar BIG' (BIG = Biomass Integrated Gasification). The concept is based on separate pyrolysis and gasification units. The volatile gases from the pyrolysis (containing tar) are partially oxidised in a separate chamber, and hereby the tar content is dramatically reduced. Thus, the investment, and running cost of a gas cleaning system can be reduced, and the reliability can be increased. Both pyrolysis and gasification chamber are bubbling fluid beds, fluidised with steam. For moist fuels, the gasifier can be integrated with a steam drying process, where the produced steam is used in the pyrolysis/gasification chamber. In this paper, mathematical models and results from initial tests of a laboratory Low-Tar BIG gasifier are presented. Two types of models are presented: 1. The gasifier-dryer applied in different power plant systems: Gas engine, Simple cycle gas turbine, Recuperated gas turbine and Integrated Gasification and Combined Cycle (IGCC). The paper determines the differences in efficiency of these systems and shows that the gasifier will be applicable for very different fuels with different moisture contents, depending on the system. 2. A thermodynamic Low-Tar BIG model. This model is based on mass and heat balance between four reactors: Pyrolysis, partial oxidation, gasification, gas-solid mixer. The paper describes the results from this study and compares the results to actual laboratory tests. The study shows, that the Low-Tar BIG process can use very wet fuels (up to 65-70% moist) and still produce heat and power with a remarkable high electric efficiency. Hereby the process offers the unique combination of large scale gasification and low-cost gas cleaning and use of low-cost fuels which very likely is the necessary combination that will lead to a breakthrough of gasification technology. (au)

  17. Creating fluid injectivity in tar sands formations

    Science.gov (United States)

    Stegemeier, George Leo; Beer, Gary Lee; Zhang, Etuan

    2010-06-08

    Methods for treating a tar sands formation are described herein. Methods for treating a tar sands may include heating a portion of a hydrocarbon layer in the formation from one or more heaters located in the portion. The heat may be controlled to increase the permeability of at least part of the portion to create an injection zone in the portion with an average permeability sufficient to allow injection of a fluid through the injection zone. A drive fluid and/or an oxidizing fluid may be provided into the injection zone. At least some hydrocarbons are produced from the portion.

  18. The identification and functional annotation of RNA structures conserved in vertebrates

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus

    2017-01-01

    Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure-b......-structured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.......Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure......-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins...

  19. Computational RNA secondary structure design: empirical complexity and improved methods

    Directory of Open Access Journals (Sweden)

    Condon Anne

    2007-01-01

    Full Text Available Abstract Background We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. Results To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures and the performance of the RNA-SSD algorithm. The scaling analysis on random and biologically motivated structures supports the hypothesis that the running time of both algorithms scales polynomially with the size of the structure. We also found that the algorithms are in general faster when constraints are placed only on paired bases in the structure. Furthermore, we prove that, according to the standard thermodynamic model, for some structures that the RNA-SSD algorithm was unable to design, there exists no sequence whose minimum free energy structure is the target structure. Conclusion Our analysis helps to better understand the strengths and limitations of both the RNA-SSD and RNAinverse algorithms, and suggests ways in which the performance of these algorithms can be further improved.

  20. Landscape and variation of RNA secondary structure across the human transcriptome.

    Science.gov (United States)

    Wan, Yue; Qu, Kun; Zhang, Qiangfeng Cliff; Flynn, Ryan A; Manor, Ohad; Ouyang, Zhengqing; Zhang, Jiajing; Spitale, Robert C; Snyder, Michael P; Segal, Eran; Chang, Howard Y

    2014-01-30

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comprehensive RSS map of human coding and non-coding RNAs. We identify unique RSS signatures that demarcate open reading frames and splicing junctions, and define authentic microRNA-binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1,900 transcribed single nucleotide variants (approximately 15% of all transcribed single nucleotide variants) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSSs. Selective depletion of 'riboSNitches' versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3' untranslated regions, binding sites of microRNAs and RNA-binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.

  1. Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

    Science.gov (United States)

    Vacchi-Suzzi, Caterina; Hahne, Florian; Scheubel, Philippe; Marcellin, Magali; Dubost, Valerie; Westphal, Magdalena; Boeglen, Catherine; Büchmann-Møller, Stine; Cheung, Ming Sin; Cordier, André; De Benedetto, Christopher; Deurinck, Mark; Frei, Moritz; Moulin, Pierre; Oakeley, Edward; Grenet, Olivier; Grevot, Armelle; Stull, Robert; Theil, Diethilde; Moggs, Jonathan G; Marrer, Estelle; Couttet, Philippe

    2013-01-01

    MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves) in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744) and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*). The relative abundance of myocardium-enriched (miR-1) and valve-enriched (miR-125b-5p and miR-204) microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

  2. Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

    Directory of Open Access Journals (Sweden)

    Caterina Vacchi-Suzzi

    Full Text Available MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744 and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*. The relative abundance of myocardium-enriched (miR-1 and valve-enriched (miR-125b-5p and miR-204 microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

  3. The separate effects of tar and nicotine on the cigarette smoking manoeuvre

    International Nuclear Information System (INIS)

    Woodman, G.; Newman, S.P.; Paiva, D.; Clarke, S.W.

    1987-01-01

    The separate effects of tar and nicotine on the cigarette smoking manoeuvre were investigated. Each of ten asymptomatic habitual smokers smoked three different commercially available cigarettes in a randomised order. The brands were chosen such that two had the same tar yield (10 mg) and two had the same nicotine yield (1.4 mg). The volume of smoke inhaled into the lungs was measured by tracing the smoke with the inert gas 81 Kr m . Puffing indices were recorded using an electronic smoking analyser and flowhead/cigarette holder. There was no difference in the total volume of smoke puffed from each of the cigarette brands. With cigarettes of the samme tar level, the total inhaled smoke volume was lower with the higher nicotine cigarette (P<0.05): by contrast, with cigarettes of the same nicotine level, the toal inhaled smoke volume was lower with the lower tar cigarette (P<0.02). Tar and nicotine appear to exercise independent control over the volume of smoke inhaled. (author)

  4. Dissolution and transport of coal tar compounds in fractured clay-rich residuum

    DEFF Research Database (Denmark)

    Vulava, Vijay M.; McKay, Larry D.; Broholm, Mette Martina

    2012-01-01

    the importance of rapid dissolution and transport through the fracture networks. The concentrations continued to rise but did not reach the corresponding effective solubility limit in most cases. Compounds that were less soluble and those that were more susceptible to sorption or matrix diffusion eluted...... at a much slower rate. Analysis of contaminant concentrations in microcore residuum samples indicated that all 10 compounds had spread throughout the entire monolith and had diffused into the fine-grained matrix between fractures. These data suggest that the predominantly fine pore structure did not appear......We investigated the dissolution and transport of organic contaminants from a crude coal tar mixture in a monolith of fractured clay-rich residuum. An electrolyte solution was eluted through the residuum monolith containing a small emplaced source of coal tar under biologically inhibited and mildly...

  5. Structural basis of genomic RNA (gRNA) dimerization and packaging determinants of mouse mammary tumor virus (MMTV).

    Science.gov (United States)

    Aktar, Suriya J; Vivet-Boudou, Valérie; Ali, Lizna M; Jabeen, Ayesha; Kalloush, Rawan M; Richer, Delphine; Mustafa, Farah; Marquet, Roland; Rizvi, Tahir A

    2014-11-14

    One of the hallmarks of retroviral life cycle is the efficient and specific packaging of two copies of retroviral gRNA in the form of a non-covalent RNA dimer by the assembling virions. It is becoming increasingly clear that the process of dimerization is closely linked with gRNA packaging, and in some retroviruses, the latter depends on the former. Earlier mutational analysis of the 5' end of the MMTV genome indicated that MMTV gRNA packaging determinants comprise sequences both within the 5' untranslated region (5' UTR) and the beginning of gag. The RNA secondary structure of MMTV gRNA packaging sequences was elucidated employing selective 2'hydroxyl acylation analyzed by primer extension (SHAPE). SHAPE analyses revealed the presence of a U5/Gag long-range interaction (U5/Gag LRI), not predicted by minimum free-energy structure predictions that potentially stabilizes the global structure of this region. Structure conservation along with base-pair covariations between different strains of MMTV further supported the SHAPE-validated model. The 5' region of the MMTV gRNA contains multiple palindromic (pal) sequences that could initiate intermolecular interaction during RNA dimerization. In vitro RNA dimerization, SHAPE analysis, and structure prediction approaches on a series of pal mutants revealed that MMTV RNA utilizes a palindromic point of contact to initiate intermolecular interactions between two gRNAs, leading to dimerization. This contact point resides within pal II (5' CGGCCG 3') at the 5' UTR and contains a canonical "GC" dyad and therefore likely constitutes the MMTV RNA dimerization initiation site (DIS). Further analyses of these pal mutants employing in vivo genetic approaches indicate that pal II, as well as pal sequences located in the primer binding site (PBS) are both required for efficient MMTV gRNA packaging. Employing structural prediction, biochemical, and genetic approaches, we show that pal II functions as a primary point of contact between

  6. 21 CFR 740.18 - Coal tar hair dyes posing a risk of cancer.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Coal tar hair dyes posing a risk of cancer. 740.18... (CONTINUED) COSMETICS COSMETIC PRODUCT WARNING STATEMENTS Warning Statements § 740.18 Coal tar hair dyes... coal tar hair dye containing any ingredient listed in paragraph (b) of this section shall bear, in...

  7. Gasification of municipal solid waste in a downdraft gasifier: Analysis of tar formation

    Directory of Open Access Journals (Sweden)

    Tabitha Geoffrey Etutu

    2016-04-01

    Full Text Available In this study, municipal solid waste (MSW from a dumpsite was converted into refuse derived fuel (RDF and used as feedstock for an air-blown gasification process. The gasification process was conducted in a 10 kg.hr -1 downdraft gasifier at different air flow rates of 300, 350, 400, 450 and 550 NL.min1 at atmospheric pressure in order to investigate the quantity and quality of tar formed. It was shown that the increase in the air flow rate from 300 NL.min1 to 550 NL.min1 led to an increase in the oxidation temperature from 719°C to 870°C and an increase in the reduction temperature from 585°C to 750°C, respectively. Tar was reduced from 15 g.Nm3 to 4.7 g.Nm3 respectively. Heavy tar compounds (>C17 e.g. pyrene and phenathrene, decreased with the increase in the light tar compounds (tar reduction through a tar cracking process.

  8. Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

    Science.gov (United States)

    Spanò, M.; Lillo, F.; Miccichè, S.; Mantegna, R. N.

    2008-10-01

    By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups, hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact, we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.

  9. Recognition of DNA/RNA bulges by antimicrobial and antitumor metallohelices

    Czech Academy of Sciences Publication Activity Database

    Malina, Jaroslav; Scott, P.; Brabec, Viktor

    2015-01-01

    Roč. 44, č. 33 (2015), s. 14656-14665 ISSN 1477-9226 R&D Projects: GA ČR(CZ) GAP205/11/0856 Institutional support: RVO:68081707 Keywords : CONTAINING DEOXYTRIDECANUCLEOTIDE DUPLEXES * HIV -1 TAR RNA * METALLOSUPRAMOLECULAR CYLINDERS Subject RIV: BO - Biophysics Impact factor: 4.177, year: 2015

  10. 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.

  11. Main component analysis of nuclear magnetic resonance /sup 1/H and /sup 13/C quantitative spectra of hydrogenation products of tars from Kansk-Achinsk Achinsk and Cheremkhovsk coals

    Energy Technology Data Exchange (ETDEWEB)

    Kushnarev, D.F.; Polonov, V.M.; Donskikh, V.I.; Rokhina, E.F.; Kalabin, G.A.

    1986-03-01

    Possibility is discussed of examining nuclear magnetic resonance /sup 1/H and /sup 13/C quantitative spectra of coal tar hydrogenation products using main component factorial analysis and applying special mathematical methods of processing experimental data. Nuclear magnetic resonance spectra of hydrogenation products of low temperature Cheremkhovsk coal carbonization tar and rapid pyrolysis Kansk-Achinsk coal tar were obtained on a WP-200SY (Bruker) spectrometer at 50.3 and 200.1 MHz, respectively. Data processing was carried out on an ODRA-1304 computer. Comparative correlation of parameters are given of tars and hydrogenation products which consist of hydrogenation of aromatic cycles and destruction of alkyl substituents, and factorial loads on structural parameters of tar hydrogenation products. 11 references.

  12. Reconstruction of ancestral RNA sequences under multiple structural constraints

    OpenAIRE

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

    2016-01-01

    Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

  13. Functional RNA structures throughout the Hepatitis C Virus genome.

    Science.gov (United States)

    Adams, Rebecca L; Pirakitikulr, Nathan; Pyle, Anna Marie

    2017-06-01

    The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated analysis of RNA folding on a genome-wide scale, revealing novel structures and networks of interactions. These studies have underscored the active role played by RNA in every function of HCV and they open the door to new types of RNA-targeted therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9).

    Science.gov (United States)

    Fu, Qinqin; Yuan, Y Adam

    2013-03-01

    Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.

  15. Landscape and variation of RNA secondary structure across the human transcriptome.

    OpenAIRE

    Wan, Y; Qu, K; Zhang, QC; Flynn, RA; Manor, O; Ouyang, Z; Zhang, J; Spitale, RC; Snyder, MP; Segal, E; Chang, HY

    2014-01-01

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comp...

  16. An automated procedure for covariation-based detection of RNA structure

    International Nuclear Information System (INIS)

    Winker, S.; Overbeek, R.; Woese, C.R.; Olsen, G.J.; Pfluger, N.

    1989-12-01

    This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential bondings of secondary and tertiary structure, but also provides the covariation evidence that supports the proposed bondings, and any counter-evidence that can be detected in the known sequences. A small number of previously unknown bondings have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. Currently, we are systematically studying mitochondrial rRNA. Our goal is to detect tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosome structure. Our colleagues in biology have begun experiments to test certain hypotheses suggested by an examination of our program's output. These experiments involve sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. The hope is that the 23S ribosomal RNA of these species will exhibit corresponding complementary variation or generalized covariation. 24 refs

  17. An automated procedure for covariation-based detection of RNA structure

    Energy Technology Data Exchange (ETDEWEB)

    Winker, S.; Overbeek, R.; Woese, C.R.; Olsen, G.J.; Pfluger, N.

    1989-12-01

    This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential bondings of secondary and tertiary structure, but also provides the covariation evidence that supports the proposed bondings, and any counter-evidence that can be detected in the known sequences. A small number of previously unknown bondings have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. Currently, we are systematically studying mitochondrial rRNA. Our goal is to detect tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosome structure. Our colleagues in biology have begun experiments to test certain hypotheses suggested by an examination of our program's output. These experiments involve sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. The hope is that the 23S ribosomal RNA of these species will exhibit corresponding complementary variation or generalized covariation. 24 refs.

  18. A comprehensive comparison of comparative RNA structure prediction approaches

    DEFF Research Database (Denmark)

    Gardner, P. P.; Giegerich, R.

    2004-01-01

    -finding and multiple-sequence-alignment algorithms. Results Here we evaluate a number of RNA folding algorithms using reliable RNA data-sets and compare their relative performance. Conclusions We conclude that comparative data can enhance structure prediction but structure-prediction-algorithms vary widely in terms......Background An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene...

  19. Recovery of very viscous lubricating oils from shale-tar, etc

    Energy Technology Data Exchange (ETDEWEB)

    Erdmann, E

    1919-09-10

    Modification of the process covered by German Patent 335,190 for recovering very viscous lubricating oils, consisting, in place of brown-coal tar, deparafinned peat tar being subjected to the treatment with superheated steam from about 200 to 250/sup 0/C or to heating in vacuum at a temperature below 250/sup 0/C.

  20. MultiSETTER: web server for multiple RNA structure comparison.

    Science.gov (United States)

    Čech, Petr; Hoksza, David; Svozil, Daniel

    2015-08-12

    Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

  1. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B.; Andersen, E.S.; Damgaard, C.

    2004-01-01

    Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions...

  2. Inhaled smoke volume and puff indices with cigarettes of different tar and nicotine levels

    International Nuclear Information System (INIS)

    Woodman, G.; Newman, S.P.; Pavia, D.; Clarke, S.W.

    1987-01-01

    Ten asymptomatic smokers each smoked a low, low-to-middle and a middle tar cigarette with approximately the same tar-to-nicotine ratio, in a randomised order. The inhaled smoke volume was measured by tracing the smoke with the inert gas 81 Kr m . Puffing indices were recorded using an electronic smoking analyser and flowhead/cigarette holder. Throughout the study neither the mean inhaled smoke volume per puff nor the total inhaled smoke volume per cigarette changed significantly; however, the mean and total puff volumes were largest with the low tar cigarette and decreased with the higher tar brands. Puff volume was related to puff work (r s =0.83,P s =0.10,P>0.1). It is concluded that when switched between brands with the same tar-to-nicotine ratio, smokers increase their puff volumes with a lower tar cigarette but do not change the volume of smoke inhaled. Puff work and puff resistance were significantly correlated (r s =0.45,P<0.02). (author)

  3. Analysis of low-temperature tar fractions

    Energy Technology Data Exchange (ETDEWEB)

    Kikkawa, S; Yamada, F

    1952-01-01

    A preliminary comparative study was made on the applicability of the methods commonly used for the type analysis of petroleum products to the low-temperature tar fractions. The usability of chromatography was also studied.

  4. Catalytic Pyrolysis of Tar Model Compound with Various Bio-Char Catalysts to Recycle Char from Biomass Pyrolysis

    Directory of Open Access Journals (Sweden)

    Jinmiao Liu

    2016-03-01

    Full Text Available Tar and char can be regarded as unwanted byproducts during the gasification process. In this study, three types of catalyst, i.e., biomass char (bio-char, nickel supported on biomass (Ni+bio-char, and nickel supported on bio-char (bio-char+Ni, were studied to compare the catalytic effects of different preparation methods on tar model compound removal. The structural characteristics of the three catalysts were also investigated by X-ray diffraction (XRD, scanning electron microscopy (SEM, and Brunauer-Emmett-Teller (BET methods. The results revealed that Ni+bio-char catalyst showed much higher activity for the reformation of toluene (C7H8 as a tar model compound than the other two catalysts. Toluene could be completely converted to small gas molecules at a conversion rate of 99.92% at 800 °C, and the maximum yield of gas was 432 mL/(mL C7H8. In particular, the H2 and CH4 yields were 339 and 85 mL/(mL C7H8 at 850 °C, respectively. An N2 absorption-desorption experiment demonstrated that the specific surface area of Ni+bio-char was 32.87 times that of bio-char and 8.39 times that of bio-char+Ni. Moreover, metallic nickel (Ni0 particles could be generated in the carbon matrix of Ni+bio-char catalyst. SEM analysis confirmed that the Ni+bio-char catalyst had a more porous structure. Nickel supported on biomass might be a promising catalyst for tar reformation because of its excellent catalytic activities.

  5. RNA secondary structure image - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us fRNAdb RNA secondary structure image Data detail Data name RNA secondary structure image DOI... 10.18908/lsdba.nbdc00452-005 Description of data contents RNA secondary structure images - png.zip: RNA secondary structure image...s (PNG) - pdf.zip: RNA secondary structure images (PDF) - thumbnail.zip: Thumbnails of... RNA secondary structure images Data file File name: RNA_secondary_structure_image... File URL: ftp://ftp.biosciencedbc.jp/archive/frnadb/LATEST/RNA_secondary_structure_image File size: 9.6 GB

  6. Acid Tar Lagoons: Management and Recovery

    Science.gov (United States)

    Bohers, Anna; Hroncová, Emília; Ladomerský, Juraj

    2017-04-01

    This contribution presents the issue with possibility of definitive removal of dangerous environmental burden in Slovakia - serious historical problem of two acid tar lagoons. In relation to their removal, no technology has been found so far - technologically and economically suitable, what caused problems with its management. Locality Predajná is well known in Slovakia by its character of contrasts: it is situated in the picturesque landscape of National Park buffer zone of Nízke Tatry, on the other site it is contaminated by 229 211m3 of acid tar with its characteristics of toxicity, carcinogenicity, teratogenicity, mutagenicity and toxicity especially for animals and plants. Acid tar in two landfills with depth of 1m in case of the first lagoon and 9,5m in case of the second lagoon is a waste product derived from operation of Petrochema Dubová - refinery and petrochemical plant whose activity was to process the crude oil through processes of sulfonation and adsorption technology for producing lubricating and special oils, synthetic detergents and special white oils for cosmetic and medical purposes. A part of acid tar was incinerated in two incineration plats. Concentration of SO2 in combustion gases was too high and it was not possible to decrease it under the value of 2000 mg.mn-3 [LADOMERSKÝ, J. - SAMEŠOVÁ, D.: Reduction in sulfur dioxide emissions waste gases of incineration plant. Acta facultatis ecologiae. 1999, p. 217-223]. That is why it was necessary to put them out of operation. Later, because of public opposition it was not possible to build a new incineration plat corresponding to the state of the art. Even though actual Slovak and European legislative for protection of environment against such impacts, neither of tried methods - bio or non-biologic treatment methods - was proved as suitable for processing or for recovery in the reason of different factors admission: i.e. strong aggressivity, difficulty with handling because of its sludgy and

  7. Assessment of ground-water contamination by coal-tar derivatives, St. Louis Park area, Minnesota

    Science.gov (United States)

    Hult, M.F.

    1984-01-01

    Operation of a coal-tar distillation and wood-preserving facility in St. Louis Park, Minnesota, during 1918-72 contaminated ground water with coal-tar derivatives and inorganic chemicals. Coal-tar derivatives entered the groundwater system through three major paths: (1) Spills and drippings that percolated to the water table, (2) surface runoff and plant process water that was discharged to wetlands south of the former plant site, and (3) movement of coal tar directly into bedrock aquifers through a multiaquifer well on the site.

  8. The Regulatory and Kinase Domains but Not the Interdomain Linker Determine Human Double-stranded RNA-activated Kinase (PKR) Sensitivity to Inhibition by Viral Non-coding RNAs.

    Science.gov (United States)

    Sunita, S; Schwartz, Samantha L; Conn, Graeme L

    2015-11-20

    Double-stranded RNA (dsRNA)-activated protein kinase (PKR) is an important component of the innate immune system that presents a crucial first line of defense against viral infection. PKR has a modular architecture comprising a regulatory N-terminal dsRNA binding domain and a C-terminal kinase domain interposed by an unstructured ∼80-residue interdomain linker (IDL). Guided by sequence alignment, we created IDL deletions in human PKR (hPKR) and regulatory/kinase domain swap human-rat chimeric PKRs to assess the contributions of each domain and the IDL to regulation of the kinase activity by RNA. Using circular dichroism spectroscopy, limited proteolysis, kinase assays, and isothermal titration calorimetry, we show that each PKR protein is properly folded with similar domain boundaries and that each exhibits comparable polyinosinic-cytidylic (poly(rI:rC)) dsRNA activation profiles and binding affinities for adenoviral virus-associated RNA I (VA RNAI) and HIV-1 trans-activation response (TAR) RNA. From these results we conclude that the IDL of PKR is not required for RNA binding or mediating changes in protein conformation or domain interactions necessary for PKR regulation by RNA. In contrast, inhibition of rat PKR by VA RNAI and TAR RNA was found to be weaker than for hPKR by 7- and >300-fold, respectively, and each human-rat chimeric domain-swapped protein showed intermediate levels of inhibition. These findings indicate that PKR sequence or structural elements in the kinase domain, present in hPKR but absent in rat PKR, are exploited by viral non-coding RNAs to accomplish efficient inhibition of PKR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Simulation of Trajectories of Tar Ball Transport to the Goa Coast

    Digital Repository Service at National Institute of Oceanography (India)

    Suneel, V.; Vethamony, P.; VinodKumar, K.; Babu, M.T.; Prasad, V.S.R.

    Arrival of tar balls to the Goa coast during pre- and southwest monsoon seasons has been a regular phenomenon in the past few years. In one such event, we observed tar ball deposits along the Goa coast during August 2010, April 2011 and May 2011...

  10. Vfold: a web server for RNA structure and folding thermodynamics prediction.

    Science.gov (United States)

    Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

    2014-01-01

    The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

  11. The Legend of Hot Tar or Pitch as a Defensive Weapon

    DEFF Research Database (Denmark)

    Atzbach, Rainer

    2015-01-01

    research. In reality, this way of fighting can only be seen as a legend, i.e. a story with only a relative truth at its core. This paper will examine the origin of this historical tradition and its archaeological and architectural sources. The chemical and physical properties of tar pitch and its...... production and use during the Middle Ages will be discussed with special focus on the application of tar pitch as an ingredient in medieval and post-medieval thermal weapons (especially Greek Fire, the firebomb and the fire arrow). The punishment of tarring and feathering will also be considered...

  12. Ensamblajes urbanos: la TAR y el examen de la ciudad

    Directory of Open Access Journals (Sweden)

    Ignacio Farías

    2011-03-01

    Full Text Available Este artículo presenta nuevas perspectivas de investigación y desafíos analíticos que la teoría del actor-red (TAR abre para los estudios urbanos. En primer lugar, se revisan cómo los principios de relacionalidad híbrida y asociatividad plana de la TAR están siendo adoptados en los estudios urbanos para ampliar simétricamente la ecología urbana a no-humanos e impugnar concepciones escalares del espacio y economías urbanas. A continuación, se propone que la TAR trae consigo un desafío más fundamental relativo a la concepción de la ciudad como objeto de estudio. Mientras su comprensión habitual como objeto espacial, entidad político-económica y/o forma sociocultural subraya su carácter singular, estable y delimitado, la TAR permite pensar la ciudad como un objeto múltiple y decentrado. La noción de ensamblajes urbanos se introduce entonces para dar cuenta de la circulación y devenir de la ciudad en múltiples redes híbridas y translocales. El artículo concluye sopesando algunas de las consecuencias de este exámen de la ciudad, especialmente el reposicionamiento del problema de la complejidad, urbana en este caso, como punto, si no de partida, entonces al menos de llegada para la TAR.

  13. Copyrolysis of coal with coke-oven gas. III. Analysis of tar

    Energy Technology Data Exchange (ETDEWEB)

    Liao, H.; Sun, C.; Li, B.; Liu, Z. [Chinese Academy of Sciences, Taiyuan (China). State Key Laboratory of Coal Conversion, Institute of Coal Chemistry

    1998-02-01

    Tars from copyrolysis of Xianfeng lignite with coke-oven gas (COG) at different pressures (0.1-5 MPa) and heating rates (5-25{degree}C/min) to a final temperature of 650{degree}C were analyzed and compared with hydropyrolysis under the same H{sub 2} partial pressure. The results indicated that high contents of BTX, PCX and naphthalene were found in the tar from copyrolysis of Xianfeng lignite with COG. Pressure and heating rate have important effects on tar yields and the contents of BTX, PCX and naphthalene in oil. Increasing pressure and decreasing heating rate enhance the tar yields and result in high yields of BTX and PCX. When compared with hydropyrolysis under the same H{sub 2} partial pressure, the tar yield increases by 1.2 times and the yields of BTX, PCX and naphthalene by about 1.6, 1.3 and 1.6 times, respectively. At the same total pressure (3MPa), the yields of BTX and naphthalene from copyrolysis are equal to those from hydropyrolysis. The results reveal that other components in COG, such as methane, carbon monoxide etc., are of importance for pyrolysis behaviour of coal under COG and improvement of oil qualities. 5 refs., 5 figs., 2 tabs.

  14. Rclick: a web server for comparison of RNA 3D structures.

    Science.gov (United States)

    Nguyen, Minh N; Verma, Chandra

    2015-03-15

    RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  15. HD-RNAS: An automated hierarchical database of RNA structures

    Directory of Open Access Journals (Sweden)

    Shubhra Sankar eRay

    2012-04-01

    Full Text Available One of the important goals of most biological investigations is to classify and organize the experimental findings so that they are readily useful for deriving generalized rules. Although there is a huge amount of information on RNA structures in PDB, there are redundant files, ambiguous synthetic sequences etc. Moreover, a systematic hierarchical organization, reflecting RNA classification, is missing in PDB. In this investigation, we have classified all the available RNA crystal structures from PDB through a programmatic approach. Hence, it would be now a simple assignment to regularly update the classification as and when new structures are released. The classification can further determine (i a non-redundant set of RNA structures and (ii if available, a set of structures of identical sequence and function, which can highlight structural polymorphism, ligand-induced conformational alterations etc. Presently, we have classified the available structures (2095 PDB entries having RNA chain longer than 9 nucleotides solved by X-ray crystallography or NMR spectroscopy into nine functional classes. The structures of same function and same source are mostly seen to be similar with subtle differences depending on their functional complexation. The web-server is available online at http://www.saha.ac.in/biop/www/HD-RNAS.html and is updated regularly.

  16. Identification of sources of tar balls deposited along the Goa coast, India, using fingerprinting techniques

    International Nuclear Information System (INIS)

    Suneel, V.; Vethamony, P.; Zakaria, M.P.; Naik, B.G.; Prasad, K.V.S.R.

    2013-01-01

    Highlights: ► This is first fingerprinting study in India on identification of source of tar balls. ► Tar balls were formed from tanker-wash spills and they resemble floating tar ball. ► δ 13 C values of Bombay High crude oil and the present tar balls do not match. ► Compound specific stable carbon isotope analysis confirmed the source of tar balls. ► Source is confirmed as the South East Asian Crude Oil and not the Bombay High crude. -- Abstract: Deposition of tar balls along the coast of Goa, India is a common phenomenon during the southwest monsoon. Representative tar ball samples collected from various beaches of Goa and one Bombay High (BH) crude oil sample were subjected to fingerprint analysis based on diagnostic ratios of n-alkane, biomarkers of pentacyclic tri-terpanes and compound specific stable carbon isotope (δ 13 C) analysis to confirm the source. The results were compared with the published data of Middle East Crude Oil (MECO) and South East Asian Crude Oil (SEACO). The results revealed that the tar balls were from tanker-wash derived spills. The study also confirmed that the source is not the BH, but SEACO. The present study suggests that the biomarkers of alkanes and hopanes coupled with stable carbon isotope analysis act as a powerful tool for tracing the source of tar balls, particularly when the source specific biomarkers fail to distinguish the source

  17. 29 CFR 1926.1102 - Coal tar pitch volatiles; interpretation of term.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Coal tar pitch volatiles; interpretation of term. 1926.1102 Section 1926.1102 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH... Hazardous Substances § 1926.1102 Coal tar pitch volatiles; interpretation of term. Note: The requirements...

  18. A review of the primary measures for tar elimination in biomass gasification processes

    International Nuclear Information System (INIS)

    Devi, Lopamudra; Ptasinski, K.J.; Janssen, F.J.J.G.

    2003-01-01

    Tar formation is one of the major problems to deal with during biomass gasification. Tar condenses at reduced temperature, thus blocking and fouling process equipments such as engines and turbines. Considerable efforts have been directed on tar removal from fuel gas. Tar removal technologies can broadly be divided into two approaches; hot gas cleaning after the gasifier (secondary methods), and treatments inside the gasifier (primary methods). Although secondary methods are proven to be effective, treatments inside the gasifier are gaining much attention as these may eliminate the need for downstream cleanup. In primary treatment, the gasifier is optimized to produce a fuel gas with minimum tar concentration. The different approaches of primary treatment are (a) proper selection of operating parameters, (b) use of bed additive/catalyst, and (c) gasifier modifications. The operating parameters such as temperature, gasifying agent, equivalence ratio, residence time, etc. play an important role in formation and decomposition of tar. There is a potential of using some active bed additives such as dolomite, olivine, char, etc. inside the gasifier. Ni-based catalyst are reported to be very effective not only for tar reduction, but also for decreasing the amount of nitrogenous compounds such as ammonia. Also, reactor modification can improve the quality of the product gas. The concepts of two-stage gasification and secondary air injection in the gasifier are of prime importance. Some aspects of primary methods and the research and development in this area are reviewed and cited in the present paper

  19. A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction

    Science.gov (United States)

    Al-Khatib, Ra’ed M.; Abdullah, Rosni; Rashid, Nur’Aini Abdul

    2010-01-01

    RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods. PMID:20458364

  20. A method for rapid similarity analysis of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Liu Na

    2006-11-01

    Full Text Available Abstract Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

  1. Reconstruction of ancestral RNA sequences under multiple structural constraints.

    Science.gov (United States)

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

    2016-11-11

    Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  2. Solid state 13 C NMR quantitative study of wood tar pitches

    International Nuclear Information System (INIS)

    Prauchner, Marcos Juliano; Pasa, Vanya Marcia Duarte; Menezes, Sonia Maria Cabral de

    1999-01-01

    In this work, solid-state 13 C NMR is used with other techniques to characterize Eucalyptus tar pitches and to follow their polymerization reactions. The pitches are the residues of distillation (about 50% m;m) of the tar generated in Eucalyptus slow pyrolysis for charcoal production in metal industry

  3. 29 CFR 1915.1002 - Coal tar pitch volatiles; interpretation of term.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 7 2010-07-01 2010-07-01 false Coal tar pitch volatiles; interpretation of term. 1915.1002 Section 1915.1002 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH... Toxic and Hazardous Substances § 1915.1002 Coal tar pitch volatiles; interpretation of term. Note: The...

  4. Solving the RNA polymerase I structural puzzle

    Energy Technology Data Exchange (ETDEWEB)

    Moreno-Morcillo, María [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Taylor, Nicholas M. I. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Gruene, Tim [Georg-August-University, Tammannstrasse 4, 37077 Göttingen (Germany); Legrand, Pierre [SOLEIL Synchrotron, L’Orme de Merisiers, Saint Aubin, Gif-sur-Yvette (France); Rashid, Umar J. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Ruiz, Federico M. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Steuerwald, Ulrich; Müller, Christoph W. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Fernández-Tornero, Carlos, E-mail: cftornero@cib.csic.es [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany)

    2014-10-01

    Details of the RNA polymerase I crystal structure determination provide a framework for solution of the structures of other multi-subunit complexes. Simple crystallographic experiments are described to extract relevant biological information such as the location of the enzyme active site. Knowing the structure of multi-subunit complexes is critical to understand basic cellular functions. However, when crystals of these complexes can be obtained they rarely diffract beyond 3 Å resolution, which complicates X-ray structure determination and refinement. The crystal structure of RNA polymerase I, an essential cellular machine that synthesizes the precursor of ribosomal RNA in the nucleolus of eukaryotic cells, has recently been solved. Here, the crucial steps that were undertaken to build the atomic model of this multi-subunit enzyme are reported, emphasizing how simple crystallographic experiments can be used to extract relevant biological information. In particular, this report discusses the combination of poor molecular replacement and experimental phases, the application of multi-crystal averaging and the use of anomalous scatterers as sequence markers to guide tracing and to locate the active site. The methods outlined here will likely serve as a reference for future structural determination of large complexes at low resolution.

  5. Avoiding tar formation in biocoke production from waste biomass

    International Nuclear Information System (INIS)

    Adrados, A.; De Marco, I.; Lopez-Urionabarrenechea, A.; Solar, J.; Caballero, B.

    2015-01-01

    This paper focuses in avoiding tar formation and in optimizing pyrolysis gas (maximizing H 2 and CO) in the production of biocoke from waste lignocellulosic biomass. In order to obtain metallurgical grade biochar (biocoke) slow heating rate and high temperature are required. Under such conditions useless pyrolysis liquids, mainly composed of water together with some heavy-sticky tars, are obtained. In order to make biocoke a cost-effective process it is necessary to optimize pyrolysis vapors avoiding tar formation and maximizing the amount and quality of both coke and gases. With this objective, in this work different heating rates (3–20 °C min −1 ) and catalysts (zeolite, Ni/CeO 2 –Al 2 O 3 ) have been tested in a two step pyrolysis process. Olive tree cuttings have been pyrolyzed in a 3.5 L batch reactor at 750 °C and the vapors generated have been thermally and catalytically treated at 900 °C in a second tubular reactor. About 25 wt.% biocoke useful as reducing agent in certain metallurgical processes, ≈57 wt.% gases with near 50 vol.% H 2 , and no tar production has been achieved when a heating rate of 3 °C min −1 and the homemade Ni/CeO 2 –Al 2 O 3 catalyst were used. - Highlights: • Metallurgical grade biochar was obtained by olive waste pyrolysis. • Low heating rates avoid tar formation and increase gas and biochar yields. • Ni/CeO 2 –Al 2 O 3 was better than HZSM5 zeolite for vapor upgrading in a second step. • Ni/CeO 2 –Al 2 O 3 and 3 °C min −1 gave the maximum H 2 , gas and biochar yields

  6. Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

    DEFF Research Database (Denmark)

    Link, Todd M; Valentin-Hansen, Poul; Brennan, Richard G

    2009-01-01

    (A) RNA, A(15). The structure reveals a unique RNA binding mechanism. Unlike uridine-containing sequences, which bind to the "proximal" face, the poly(A) tract binds to the "distal" face of Hfq using 6 tripartite binding motifs. Each motif consists of an adenosine specificity site (A site), which......Hfq is a small, highly abundant hexameric protein that is found in many bacteria and plays a critical role in mRNA expression and RNA stability. As an "RNA chaperone," Hfq binds AU-rich sequences and facilitates the trans annealing of small RNAs (sRNAs) to their target mRNAs, typically resulting...... in the down-regulation of gene expression. Hfq also plays a key role in bacterial RNA decay by binding tightly to polyadenylate [poly(A)] tracts. The structural mechanism by which Hfq recognizes and binds poly(A) is unknown. Here, we report the crystal structure of Escherichia coli Hfq bound to the poly...

  7. 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

  8. Cancer risk estimation for mixtures of coal tars and benzo(a)pyrene

    International Nuclear Information System (INIS)

    Gaylor, D.W.; Culp, S.J.; Goldstein, L.S.; Beland, F.A.

    2000-01-01

    Two-year chronic bioassays were conducted by using B6C3F1 female mice fed several concentrations of two different mixtures of coal tars from manufactured gas waste sites or benzo(a)pyrene (BaP). The purpose of the study was to obtain estimates of cancer potency of coal tar mixtures, by using conventional regulatory methods, for use in manufactured gas waste site remediation. A secondary purpose was to investigate the validity of using the concentration of a single potent carcinogen, in this case benzo(a)pyrene, to estimate the relative risk for a coal tar mixture. The study has shown that BaP dominates the cancer risk when its concentration is greater than 6,300 ppm in the coal tar mixture. In this case the most sensitive tissue site is the forestomach. Using low-dose linear extrapolation, the lifetime cancer risk for humans is estimated to be: Risk -4 (ppm coal tar in total diet) + 240 x 10 -4 (ppm BaP in total diet), based on forestomach tumors. If the BaP concentration in the coal tar mixture is less than 6,300 ppm, the more likely case, then lung tumors provide the largest estimated upper limit of risk, Risk -4 (ppm coal tar in total diet), with no contribution of BaP to lung tumors. The upper limit of the cancer potency (slope factor) for lifetime oral exposure to benzo(a)pyrene is 1.2 x 10 -3 per microg per kg body weight per day from this Good Laboratory Practice (GLP) study compared with the current value of 7.3 x 10 -3 per microg per kg body weight per day listed in the US EPA Integrated Risk Information System

  9. Experimental and theoretical evaluation of the performance of a tar solar water heater

    International Nuclear Information System (INIS)

    Ammari, H.D.; Nimir, Y.L.

    2003-01-01

    The paper presents an experimental and theoretical evaluation of the performance of a tar solar water heater and comparison with that of a conventional type collector. The performance of both collectors is assessed under the same conditions. Both of the collectors have the same surface area and are glazed. The conventional type has the water tubes welded to the absorber plate, whereas in the tar type, the tar acts as an absorber plate that covers the water tubes. The theoretical model for each collector type, with the transient effects taken into account, is based on a control volume and a time base in the related energy equations. By considering a small element of the collector in each case, three partial differential equations were developed for each collector and were solved numerically by the Runge-Kutta method of the fifth order. A good agreement was achieved between the numerical and experimental results for both the conventional and tar collectors, indicating the feasibility of employing the theoretical model in the design of flat plate solar collectors. The results also showed that the conventional collector is more efficient than the tar type during most of the daylight, but the tar collector had the added advantage of better conservation of energy in late afternoon and evening

  10. Estimating release of polycyclic aromatic hydrocarbons from coal tar at manufactured-gas plant sites

    International Nuclear Information System (INIS)

    Loehr, R.C.; Rao, P.S.C.; Lee, L.S.; Okuda, I.

    1992-08-01

    One component of the EPRI's research on Envirorunental Behavior of Organic Substances (EBOS) consists of developing information and models to predict releases of monocyclic and polycyclic aromatic hydrocarbons (MAHs and PAHs) to groundwater from coal tars and contaminated soils at MGP sites. The results of this report focus primarily on release of PAHs from coal tars. There are at least two approaches to predicting the release of organic chemicals from coal tar to water. The simplest method to estimate aqueous concentrations is to assume that water solubility of a PAH compound released from the tar can be defined by equilibrium precipitation-dissolution reactions. Application of Raoult's law is another method to predict aqueous concentrations, which requires the assumption of ''ideal'' behavior for partitioning of PAHs between the tar and water phases. To evaluate the applicability of these two methods for predicting PAH releases, laboratory experiments were conducted with eight coal tar samples from former MGP sites across the country. Migration of chemicals in the environment and resulting contaminant plumes in groundwater are determined by leachate concentrations of the chemicals. The use of equilibrium precipitation-dissolution reactions will usually result in an overestimation of PAH concentrations in the leachate from a coal tar source, and thus the resulting PAH concentrations in groundwater. Raoult's law appears to be a more accurate approach to predicting the release of several PAHs from coal tars. Furthermore, if nonequilibrium conditions prevail, aqueous-phase PAH concentrations will be even lower than those predicted using Raoult's law

  11. Release of polyaromatic hydrocarbons from coal tar contaminated soils

    International Nuclear Information System (INIS)

    Priddy, N.D.; Lee, L.S.

    1996-01-01

    A variety of process wastes generated from manufactured gas production (MGP) have contaminated soils and groundwater at production and disposal sites. Coal tar, consisting of a complex mixture of hydrocarbons present as a nonaqueous phase liquid, makes up a large portion of MGP wastes. Of the compounds in coal tar, polyaromatic hydrocarbons (PAHs) are the major constituents of environmental concern due to their potential mutagenic and carcinogenic hazards. Characterization of the release of PAHs from the waste-soil matrix is essential to quantifying long-term environmental impacts in soils and groundwater. Currently, conservative estimates for the release of PAHs to the groundwater are made assuming equilibrium conditions and using relationships derived from artificially contaminated soils. Preliminary work suggests that aged coal tar contaminated soils have much lower rates of desorption and a greater affinity for retaining organic contaminants. To obtain better estimates of desorption rates, the release of PAHs from a coal tar soil was investigated using a flow-interruption, miscible displacement technique. Methanol/water solutions were employed to enhance PAH concentrations above limits of detection. For each methanol/water solution employed, a series of flow interrupts of varying times was invoked. Release rates from each methanol/water solution were estimated from the increase in concentration with duration of flow interruption. Aqueous-phase release rates were then estimated by extrapolation using a log-linear cosolvency model

  12. URS DataBase: universe of RNA structures and their motifs.

    Science.gov (United States)

    Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

    2016-01-01

    The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.

  13. Extraction of tar acids with methanol from low-temperature tar

    Energy Technology Data Exchange (ETDEWEB)

    Funasaka, W; Yokogawa, C; Suga, S

    1948-01-01

    From 20 grams crude middle oil, boiling at 200/sup 0/ to 250/sup 0/, acid content 40%, tar acids were extracted at 20/sup 0/ to 30/sup 0/ with MeOH for comparison with EtOH, NMe/sub 3/, and ethylene glycol. When 80% MeOH is used, the oil extracted amounts to 61%, including 9% acids, if the ratio of crude oil and solvent is kept at 1:2. EtOH is inferior to MeOH. The properties of the crude oil and the purified oil extracted with 80% MeOH are described.

  14. Evolution of bacterial community during bioremediation of PAHs in a coal tar contaminated soil

    Energy Technology Data Exchange (ETDEWEB)

    Lors, C.; Ryngaert, A.; Perie, F.; Diels, L.; Damidot, D. [University of Lille, Lille (France)

    2010-11-15

    The monitoring of a windrow treatment applied to soil contaminated by mostly 2, 3- and 4-ring PAHs produced by coal tar distillation was performed by following the evolution of both PAH concentration and the bacterial community. Total and PAH-degrading bacterial community structures were followed by 165 rRNA PCR-DGGE in parallel with quantification by bacterial counts and 16 PAH measurements. Six months of biological treatment led to a strong decrease in 2-, 3- and 4-ring PAH concentrations (98, 97 and 82%, respectively). This result was associated with the activity of bacterial PAH-degraders belonging mainly to the Gamma proteobacteria, in particular the Enterobacteria and Pseudomonas genera which were detected over the course of the treatment. This group was considered to be a good bioindicator to determine the potential PAH biodegradation of contaminated soil. Conversely other species like the Beta proteobacteria were detected after 3 months when 2-, 3- and 4-ring PAHs were almost completely degraded. Thus presence of the Beta proteobacteria group could be considered a good candidate indicator to estimate the endpoint of biotreatment of this type of PAH contaminated soil.

  15. Approaches to link RNA secondary structures with splicing regulation

    DEFF Research Database (Denmark)

    Plass, Mireya; Eyras, Eduardo

    2014-01-01

    In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitat...... describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3' splice site (3'ss).......In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either...

  16. High-Throughput Sequencing Based Methods of RNA Structure Investigation

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan

    In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental...... and computational protocol for detecting the reverse transcription termination sites (RTTS-Seq). This protocol was subsequently applied to hydroxyl radical footprinting of three dimensional RNA structures to give a probing signal that correlates well with the RNA backbone solvent accessibility. Moreover, we applied...

  17. The identification and functional annotation of RNA structures conserved in vertebrates

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus

    2017-01-01

    Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure...... (RBPs) or (ii) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared...... expression and shared structure despite low abundance and low sequence identity. About 30k CRS regions are located near coding or long non-coding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their non-structured...

  18. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  19. Tar Removal from Biomass Producer Gas by Using Biochar

    DEFF Research Database (Denmark)

    Ravenni, Giulia; Henriksen, Ulrik Birk; Ahrenfeldt, Jesper

    2017-01-01

    The biomass-derived char (biochar) produced in the gasifier as a residue, is a potential solution for removing tars from producer gas. This work investigates the interaction between tar compounds and biochar. Residual biochar from a TwoStage gasifier was tested as bed material in a laboratory setup....... Phenol and naphthalene were chosen as model tars, and entrained in a nitrogen flow. The gaseous stream was sampled before and after the biochar bed to evaluate the extent of conversion. The biochar bed (30g) was tested at 250°C, 500°C and 600°C, with for 3 consecutive hours. The compounds concentration...... in the gas phase was quantified by stable isotope dilution analysis, using Gas Chromatography-Mass Spectrometry (GC-MS). Results showed a significant effect of biochar on the removal of phenol, at all temperatures. Naphthalene was removed less efficiently at higher temperature, and this trend was even more...

  20. Solvent refining of low-temperature tar with liquid ammonia

    Energy Technology Data Exchange (ETDEWEB)

    Ishida, K

    1953-01-01

    The middle fractions of low-temperature tar were treated with mixed solutions of H/sub 2/O and liquid NH/sub 3/ at 0/sup 0/ and 20/sup 0/, and with liquid NH/sub 3/ at -10, 0, + 10, and 20/sup 0/, and phase equilibrium between tar acids, neutral oil, and solvents were studied. The distribution ratio ranged from less than 1 to greater than 1 when the solvent contained about 20 percent (by weight) H/sub 2/O. When the solvent contained less than 85 percent (by weight) NH/sub 3/, the yield of extract was small but the purity of phenols in the extracted oil was above 90 percent. Solvent containing about 85 percent NH/sub 3/ (by weight) is considered optimum for separating tar acids from oils. A novel definition is proposed for solvent selectivity as the difference between the concentration of the solute in the extract layer, on a solvent-free basis, and the concentration in the raffinate layer.

  1. Reconstruction of ancestral RNA sequences under multiple structural constraints

    Directory of Open Access Journals (Sweden)

    Olivier Tremblay-Savard

    2016-11-01

    Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  2. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

    DEFF Research Database (Denmark)

    Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2013-01-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general...... comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22495 3D modules in all PDB files results in 977 internal loop...

  3. Trace metals in heavy crude oils and tar sand bitumens

    Energy Technology Data Exchange (ETDEWEB)

    Reynolds, J.G.

    1990-11-28

    Fe, Ni, and V are considered trace impurities in heavy crude oils and tar sand bitumens. In order to understand the importance of these metals, we have examined several properties: (1) bulk metals levels, (2) distribution in separated fractions, (3) size behavior in feeds and during processing, (4) speciation as a function of size, and (5) correlations with rheological properties. Some of the results of these studies show: (1) V and Ni have roughly bimodal size distributions, (2) groupings were seen based on location, size distribution, and Ni/V ratio of the sample, (3) Fe profiles are distinctively different, having a unimodal distribution with a maximum at relatively large molecular size, (4) Fe concentrations in the tar sand bitumens suggest possible fines solubilization in some cases, (5) SARA separated fractions show possible correlations of metals with asphaltene properties suggesting secondary and tertiary structure interactions, and (6) ICP-MS examination for soluble ultra-trace metal impurities show the possibility of unexpected elements such as U, Th, Mo, and others at concentrations in the ppB to ppM range. 39 refs., 13 figs., 5 tabs.

  4. Retroviral RNA Dimerization: From Structure to Functions

    Directory of Open Access Journals (Sweden)

    Noé Dubois

    2018-03-01

    Full Text Available The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…, the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.

  5. Ukrainian brown-coal tars recovered at low-temperature carbonization with solid heating medium

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, V I; Govorova, R P; Fadeicheva, A G; Kigel, T B; Chernykh, M K

    1955-01-01

    Three samples of tar were recovered in the laboratory from brown coals carbonized at 375/sup 0/ to 456/sup 0/ +- 25/sup 0/ in a retort with inner heating by solid circulating medium, namely, semicoke (ratio: 4 or 3:1) first heated to 700/sup 0/. One comparative (parallel) experiment was carried out in a retort with inner heating by inert gases entering the retort at 580/sup 0/ to 600/sup 0/ and leaving it at 115/sup 0/ to 120/sup 0/. The tars that were recovered from the retort with the solid heating medium contained a high percentage of coal dust and moisture, which were separated from the tars in supercentrifuges (15,000 rpm). Four samples of cleaned tars were fractionated in a Cu flask with a 2-ball fractional column. The tars from the retort with the solid-heating medium are characterized by increased yield of the petroleum-ether fraction (16.3 or 19.3%) and decreased yield of the paraffin fraction (15.1 to 21.2%) in comparison with those of tar from the retort with gas heating (5.9% of the petroleum ether fraction and 36.5% of paraffin fraction). The yield of paraffin from the paraffin fraction also decreased from 90.6% to 62.6-74.3%. This result shows that in the first case the carbonized products were cracked to a higher degree than those from the retort with gas heating. In raw phenols recovered from fractions of investigated tars, the yield of the phenol-cresol fraction (182/sup 0/ to 204/sup 0/) decreased from 25.9% to 13.0-18.9%.

  6. Analysis of the environmental control technology for tar sand development

    Energy Technology Data Exchange (ETDEWEB)

    de Nevers, N.; Glenne, B.; Bryner, C.

    1979-06-01

    The environmental technology for control of air pollution, water pollution, and for the disposal, stabilization, and vegetation of the waste tar sand were thoroughly investigated. Although some difficulties may be encountered in any of these undertakings, it seems clear that the air and water pollution problems can be solved to meet any applicable standard. Currently there are two large-scale plants producing liquid fuels from tar sands in Alberta, Canada which use similar technology involving surface mining, hot water extraction, and surface disposal of waste sand. These projects all meet the Canadian environmental control regulations in force at the time they began. The largest US deposits of tar sands are much smaller than the Canadian; 95 percent are located in the state of Utah. Their economics do not appear as attractive as the Canadian deposits. The environmental control costs are not large enough to make an otherwise economic project uneconomic. The most serious environmental conflict likely to occur over the recovery of liquid fuels from the US deposits of tar sands is that caused by the proximity of the deposits to national parks, national monuments, and a national recreation area in Utah. These areas have very stringent air pollution requirements; and even if the air pollution control requirements can be met, there may still be adequate opposition to large-scale mining ventures in these areas to prevent their commercial exploitation. Another environmental constraint may be water rights availability.Essentially all of the water running in the Colorado river basin is now legally allocated. Barring new interpretations of the legality of water rights purchase, Utah tar sands developments should be able to obtain water by purchasing existing irrigation water rights.

  7. Catalytic decomposition of tar derived from wood waste pyrolysis using Indonesian low grade iron ore as catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Wicakso, Doni Rahmat [Chemical Engineering Department, Faculty of Engineering, Lambung Mangkurat University, Jalan A. Yani KM. 36 Banjarbaru, 70714, South Kalimantan (Indonesia); Chemical Engineering Department, Faculty of Engineering, Gadjah Mada University, Jalan Grafika No. 2 Bulaksumur, Yogyakarta, 55281 (Indonesia); Sutijan; Rochmadi [Chemical Engineering Department, Faculty of Engineering, Gadjah Mada University, Jalan Grafika No. 2 Bulaksumur, Yogyakarta, 55281 (Indonesia); Budiman, Arief, E-mail: abudiman@ugm.ac.id [Chemical Engineering Department, Faculty of Engineering, Gadjah Mada University, Jalan Grafika No. 2 Bulaksumur, Yogyakarta, 55281 (Indonesia); Center for Energy Studies, Gadjah Mada University, Sekip K1A, Yogyakarta, 55281 (Indonesia)

    2016-06-03

    Low grade iron ore can be used as an alternative catalyst for bio-tar decomposition. Compared to other catalysts, such as Ni, Rd, Ru, Pd and Pt, iron ore is cheaper. The objective of this research was to investigate the effect of using low grade iron ore as catalyst for tar catalytic decomposition in fixed bed reactor. Tar used in this experiment was pyrolysis product of wood waste while the catalyst was Indonesian low grade iron ore. The variables studied were temperatures between 500 – 600 °C and catalyst weight between 0 – 40 gram. The first step, tar was evaporated at 450 °C to produce tar vapor. Then, tar vapor was flowed to fixed bed reactor filled low grade iron ore. Gas and tar vapor from reactor was cooled, then the liquid and uncondensable gas were analyzed by GC/MS. The catalyst, after experiment, was weighed to calculate total carbon deposited into catalyst pores. The results showed that the tar components that were heavy and light hydrocarbon were decomposed and cracked within the iron ore pores to from gases, light hydrocarbon (bio-oil) and carbon, thus decreasing content tar in bio-oil and increasing the total gas product. In conclusion, the more low grade iron ore used as catalyst, the tar content in the liquid decrease, the H{sup 2} productivity increased and calorimetric value of bio-oil increased.

  8. Tar in road system wastes - bibliographic study - quick characterization methods; Le goudron dans les dechets du reseau routier - etude bibliographique - methodes de caracterisation rapides

    Energy Technology Data Exchange (ETDEWEB)

    Brazillet, C.; Domas, J.; Pepin, G.

    2001-12-15

    In the framework of the european regulations on the wastes management, the road structure wastes present a particularly problem because of the tar content and of the toxic associated polycyclic aromatic hydrocarbons. In order to chose the elimination or the valorization of these roads wastes, it is necessary to measure the tar content. After a presentation of the study objectives, a bibliographic study of the context, the challenges, the hydrocarbons, the tar characterization and the today situation of the french road network, the author presents the methods of PAH detection with a special attention on the well known methods: the PAK marker, the TSE and the toluene spot. (A.L.B.)

  9. Evolving stochastic context-free grammars for RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Anderson, James WJ; Tataru, Paula Cristina; Stains, Joe

    2012-01-01

    Background Stochastic Context-Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs potentially useful for RNA secondary structure prediction is very large, but a few...... to structure prediction as has been previously suggested. Results These search techniques were applied to predict RNA secondary structure on a maximal data set and revealed new and interesting grammars, though none are dramatically better than classic grammars. In general, results showed that many grammars...... with quite different structure could have very similar predictive ability. Many ambiguous grammars were found which were at least as effective as the best current unambiguous grammars. Conclusions Overall the method of evolving SCFGs for RNA secondary structure prediction proved effective in finding many...

  10. Phytotoxicity and Plant Productivity Analysis of Tar-Enriched Biochars

    Science.gov (United States)

    Keller, M. L.; Masiello, C. A.; Dugan, B.; Rudgers, J. A.; Capareda, S. C.

    2008-12-01

    Biochar is one of the three by-products obtained by the pyrolysis of organic material, the other two being syngas and bio-oil. The pyrolysis of biomass has generated a great amount of interest in recent years as all three by-products can be put toward beneficial uses. As part of a larger project designed to evaluate the hydrologic impact of biochar soil amendment, we generated a biochar through fast pyrolysis (less than 2 minutes) of sorghum stock at 600°C. In the initial biochar production run, the char bin was not purged with nitrogen. This inadvertent change in pyrolysis conditions produced a fast-pyrolysis biochar enriched with tars. We chose not to discard this batch, however, and instead used it to test the impact of tar-enriched biochars on plants. A suite of phytotoxicity tests were run to assess the effects of tar-rich biochar on plant germination and plant productivity. We designed the experiment to test for negative effects, using an organic carbon and nutrient-rich, greenhouse- optimized potting medium instead of soil. We used Black Seeded Simpson lettuce (Lactuca sativa) as the test organism. We found that even when tars are present within biochar, biochar amendment up to 10% by weight caused increased lettuce germination rates and increased biomass productivity. In this presentation, we will report the statistical significance of our germination and biomass data, as well as present preliminary data on how biochar amendment affects soil hydrologic properties.

  11. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

    Directory of Open Access Journals (Sweden)

    Chen Chun

    2008-03-01

    Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool

  12. Carbon materials for syngas conditioning and tar removal

    International Nuclear Information System (INIS)

    Romero Millán, Lina María; Sierra Vargas, Fabio Emiro

    2017-01-01

    Within the framework of worldwide energy context, the development of technologies and processes for energy production form renewable and non-conventional sources is a priority. According to this, gasification is an interesting process that converts different kinds of organic materials in fuel gases. The main issue related with this process is the fact that the producer gas contains also contaminants and tars that are undesirable for the gas usage in internal combustion motors or turbines. The present work aims to analyze the actual state of the existing methods to remove tars form gasification fuel gases, emphasizing the use of different kinds of carbon materials. (author)

  13. Process from removing benzine, toluene, etc. , from petroleum residues, coal tar, and shale tar, etc

    Energy Technology Data Exchange (ETDEWEB)

    Hlawaty, F

    1888-08-11

    A process is described for the preparation of ligroin and its homologs as well as naphthalene and anthracene consisting in leading superheated water vapor into a mixture of petroleum residues (or mineral coal tar, etc.) heated to about 400/sup 0/C with cellulosic substances as sage shreds, sea grass, or straw, with addition of caustic alkali.

  14. RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

    Science.gov (United States)

    Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

    2018-01-01

    RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

  15. Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

    KAUST Repository

    Chawla, Mohit

    2018-04-01

    The main objective of the thesis is to carry out structural bioinformatics study along with usage of advanced quantum chemical methods to look at the structural stability and energetics of RNA building blocks. The main focus of the work described here lies on understanding the reasons behind the intrinsic stability of key interactions in nucleic acids. Crystal structures of RNA molecules exhibit fascinating variety of non-covalent interactions, which play an important role in maintaining the three dimensional structures. An accurate atomic level description of these interactions in the structural building blocks of RNA is a key to understand the structure-function relationship in these molecules. An effort has been made to link the conclusions drawn from quantum chemical computations on RNA base pairs in wide biochemical context of their occurrence in RNA structures. The initial attention was on the impact of natural and non-natural modifications of the nucleic acid bases on the structure and stability of base pairs that they are involved in. In the remaining sections we cover other molecular interactions shaping nucleic acids, as the interaction between ribose and the bases, and the fluoride sensing riboswitch system in order to investigate structure and dynamics of nucleic acids at the atomic level and to gain insight into the physical chemistry behind.

  16. Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

    KAUST Repository

    Chawla, Mohit

    2018-01-01

    The main objective of the thesis is to carry out structural bioinformatics study along with usage of advanced quantum chemical methods to look at the structural stability and energetics of RNA building blocks. The main focus of the work described here lies on understanding the reasons behind the intrinsic stability of key interactions in nucleic acids. Crystal structures of RNA molecules exhibit fascinating variety of non-covalent interactions, which play an important role in maintaining the three dimensional structures. An accurate atomic level description of these interactions in the structural building blocks of RNA is a key to understand the structure-function relationship in these molecules. An effort has been made to link the conclusions drawn from quantum chemical computations on RNA base pairs in wide biochemical context of their occurrence in RNA structures. The initial attention was on the impact of natural and non-natural modifications of the nucleic acid bases on the structure and stability of base pairs that they are involved in. In the remaining sections we cover other molecular interactions shaping nucleic acids, as the interaction between ribose and the bases, and the fluoride sensing riboswitch system in order to investigate structure and dynamics of nucleic acids at the atomic level and to gain insight into the physical chemistry behind.

  17. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

    Science.gov (United States)

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

  18. Secondary structural entropy in RNA switch (Riboswitch) identification.

    Science.gov (United States)

    Manzourolajdad, Amirhossein; Arnold, Jonathan

    2015-04-28

    RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. Various tests show that there

  19. Carbazole is a naturally occurring inhibitor of angiogenesis and inflammation isolated from antipsoriatic coal tar

    Energy Technology Data Exchange (ETDEWEB)

    Jack L. Arbiser; Baskaran Govindarajan; Traci E. Battle; Rebecca Lynch; David A. Frank; Masuko Ushio-Fukai; Betsy N. Perry; David F. Stern; G. Tim Bowden; Anquan Liu; Eva Klein; Pawel J. Kolodziejski; N. Tony Eissa; Chowdhury F. Hossain; Dale G. Nagle [Emory University School of Medicine, Atlanta, GA (United States). Department of Dermatology

    2006-06-15

    Coal tar is one of the oldest and an effective treatment for psoriasis. Coal tar has been directly applied to the skin, or used in combination with UV light as part of the Goeckerman treatment. The use of coal tar has caused long-term remissions in psoriasis, but has fallen out of favor because the treatment requires hospitalization and coal tar is poorly acceptable aesthetically to patients. Thus, determining the active antipsoriatic component of coal tar is of considerable therapeutic interest. We fractionated coal tar into its components, and tested them using the SVR angiogenesis inhibitor assay. Treatment of SVR endothelial cells with coal tar fractions resulted in the isolation of a single fraction with antiangiogenic activity. The active antiangiogenic compound in coal tar is carbazole. In addition to antiangiogenic activity, carbazole inhibited the production of inflammatory IL-15 by human mononuclear cells. IL-15 is elevated in psoriasis and is thought to contribute to psoriatic inflammation. Carbazole treatment also reduced activity of inducible nitric oxide synthase (iNOS), which is proinflammatory and elevated in psoriasis. The effect of carbazole on upstream pathways in human psoriasis was determined, and carbazole was shown to inhibit signal transducer and activator of transcription (stat)3-mediated transcription, which has been shown to be relevant in human psoriasis. IL-15, iNOS, and stat3 activation require the activation of the small GTPase rac for optimal activity. Carbazole was found to inhibit rac activation as a mechanism for its inhibition of downstream inflammatory and angiogenic pathways. Given its antiangiogenic and anti-inflammatory activities, carbazole is likely a major component of the antipsoriatic activity of coal tar. Carbazole and derivatives may be useful in the therapy of human psoriasis.

  20. Comprehensive database of Manufactured Gas Plant tars. Part C. Heterocyclic and hydroxylated polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Gallacher, Christopher; Thomas, Russell; Lord, Richard; Kalin, Robert M; Taylor, Chris

    2017-08-15

    Coal tars are a mixture of organic and inorganic compounds that were by-products from the manufactured gas and coke making industries. The tar compositions varied depending on many factors such as the temperature of production and the type of retort used. For this reason a comprehensive database of the compounds found in different tar types is of value to understand both how their compositions differ and what potential chemical hazards are present. This study focuses on the heterocyclic and hydroxylated compounds present in a database produced from 16 different tars from five different production processes. Samples of coal tar were extracted using accelerated solvent extraction (ASE) and derivatized post-extraction using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS). The derivatized samples were analysed using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS). A total of 865 heterocyclic compounds and 359 hydroxylated polycyclic aromatic hydrocarbons (PAHs) were detected in 16 tar samples produced by five different processes. The contents of both heterocyclic and hydroxylated PAHs varied greatly with the production process used, with the heterocyclic compounds giving information about the feedstock used. Of the 359 hydroxylated PAHs detected the majority would not have been be detected without the use of derivatization. Coal tars produced using different production processes and feedstocks yielded tars with significantly different heterocyclic and hydroxylated contents. The concentrations of the individual heterocyclic compounds varied greatly even within the different production processes and provided information about the feedstock used to produce the tars. The hydroxylated PAH content of the samples provided important analytical information that would otherwise not have been obtained without the use of derivatization and GCxGC/TOFMS. Copyright © 2017 John Wiley & Sons, Ltd.

  1. Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction.

    Science.gov (United States)

    Yang, Yuedong; Li, Xiaomei; Zhao, Huiying; Zhan, Jian; Wang, Jihua; Zhou, Yaoqi

    2017-01-01

    As most RNA structures are elusive to structure determination, obtaining solvent accessible surface areas (ASAs) of nucleotides in an RNA structure is an important first step to characterize potential functional sites and core structural regions. Here, we developed RNAsnap, the first machine-learning method trained on protein-bound RNA structures for solvent accessibility prediction. Built on sequence profiles from multiple sequence alignment (RNAsnap-prof), the method provided robust prediction in fivefold cross-validation and an independent test (Pearson correlation coefficients, r, between predicted and actual ASA values are 0.66 and 0.63, respectively). Application of the method to 6178 mRNAs revealed its positive correlation to mRNA accessibility by dimethyl sulphate (DMS) experimentally measured in vivo (r = 0.37) but not in vitro (r = 0.07), despite the lack of training on mRNAs and the fact that DMS accessibility is only an approximation to solvent accessibility. We further found strong association across coding and noncoding regions between predicted solvent accessibility of the mutation site of a single nucleotide variant (SNV) and the frequency of that variant in the population for 2.2 million SNVs obtained in the 1000 Genomes Project. Moreover, mapping solvent accessibility of RNAs to the human genome indicated that introns, 5' cap of 5' and 3' cap of 3' untranslated regions, are more solvent accessible, consistent with their respective functional roles. These results support conformational selections as the mechanism for the formation of RNA-protein complexes and highlight the utility of genome-scale characterization of RNA tertiary structures by RNAsnap. The server and its stand-alone downloadable version are available at http://sparks-lab.org. © 2016 Yang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  2. Tar removal from biosyngas in the biomass gasification process. (Liquid + liquid) equilibrium {water + solvent (paraxylene and methyl hexadecanoate) + model molecules of tar (benzene, toluene, phenol)}

    International Nuclear Information System (INIS)

    Bassil, Georgio; Mokbel, Ilham; Abou Naccoul, Ramy; Stephan, Juliette; Jose, Jacques; Goutaudier, Christelle

    2012-01-01

    Highlights: ► (Liquid + liquid) equilibria at atmospheric pressure. ► Solubility of benzene (or toluene or phenol) in paraxylene at (303 to 343) K. ► Solubility of benzene (or toluene or phenol) in methyl palmitate or methyl hexadecanoate at (303 to 343) K. ► Correlation of LLE using NRTL model. - Abstract: Tar is generated in the process by the condensation of the gas resulting from biomass gasification. The objective of this work is a contribution to the database on thermodynamic quantity which will be useful at the operation of tar removal from aqueous medium. With this aim, (liquid + liquid) equilibrium of {water + solvent (paraxylene and methyl hexadecanoate) + model molecules of tar (benzene, toluene, phenol)} was studied at temperatures (303.2, 323.2, and 343.2) K. The data obtained were correlated with the non-random two-liquid (NRTL) model.

  3. Influence of cigarette filter ventilation on smokers' mouth level exposure to tar and nicotine.

    Science.gov (United States)

    Caraway, John W; Ashley, Madeleine; Bowman, Sheri A; Chen, Peter; Errington, Graham; Prasad, Krishna; Nelson, Paul R; Shepperd, Christopher J; Fearon, Ian M

    2017-12-01

    Cigarette filter ventilation allows air to be drawn into the filter, diluting the cigarette smoke. Although machine smoking reveals that toxicant yields are reduced, it does not predict human yields. The objective of this study was to investigate the relationship between cigarette filter ventilation and mouth level exposure (MLE) to tar and nicotine in cigarette smokers. We collated and reviewed data from 11 studies across 9 countries, in studies performed between 2005 and 2013 which contained data on MLE from 156 products with filter ventilation between 0% and 87%. MLE among 7534 participants to tar and nicotine was estimated using the part-filter analysis method from spent filter tips. For each of the countries, MLE to tar and nicotine tended to decrease as filter ventilation increased. Across countries, per-cigarette MLE to tar and nicotine decreased as filter ventilation increased from 0% to 87%. Daily MLE to tar and nicotine also decreased across the range of increasing filter ventilation. These data suggest that on average smokers of highly ventilated cigarettes are exposed to lower amounts of nicotine and tar per cigarette and per day than smokers of cigarettes with lower levels of ventilation. Copyright © 2017 British American Tobacco. Published by Elsevier Inc. All rights reserved.

  4. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

    Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is re......Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious...

  5. Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

    Energy Technology Data Exchange (ETDEWEB)

    Mosley, Ralph T.; Edwards, Thomas E.; Murakami, Eisuke; Lam, Angela M.; Grice, Rena L.; Du, Jinfa; Sofia, Michael J.; Furman, Philip A.; Otto, Michael J. (Pharmasset); (Emerald)

    2012-08-01

    The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory {beta}-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory {beta}-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.

  6. Creating and maintaining a gas cap in tar sands formations

    Science.gov (United States)

    Vinegar, Harold J.; Karanikas, John Michael; Dinkoruk, Deniz Sumnu; Wellington, Scott Lee

    2010-03-16

    Methods for treating a tar sands formation are disclosed herein. Methods for treating a tar sands formation may include providing heat to at least part of a hydrocarbon layer in the formation from one or more heaters located in the formation. Pressure may be allowed to increase in an upper portion of the formation to provide a gas cap in the upper portion. At least some hydrocarbons are produced from a lower portion of the formation.

  7. Investigation of RNA Structure by High-Throughput SHAPE-Based Probing Methods

    DEFF Research Database (Denmark)

    Poulsen, Line Dahl

    of highthroughput SHAPE-based approaches to investigate RNA structure based on novel SHAPE reagents that permit selection of full-length cDNAs. The SHAPE Selection (SHAPES) method is applied to the foot-and-mouth disease virus (FMDV) plus strand RNA genome, and the data is used to construct a genome-wide structural...... that they are functional. The SHAPES method is further applied to the hepatitis C virus (HCV), where the data is used to refine known and predicted structures. Over the past years, the interest of studying RNA structure in their native environment has been increased, and to allow studying RNA structure inside living cells...... using the SHAPE Selection approach, I introduce a biotinylated probing reagent. This chemical can cross cell membranes and reacts with RNA inside the cells, allowing the structural conformations to be studied in the context of physiological relevant conditions in living cells. The methods and results...

  8. The documentation of tar balls on oiled shorelines : lessons from the New Carissa, Oregon

    International Nuclear Information System (INIS)

    Owens, E.H.; Zimlicki-Owens, L.M.; Lamarche, A.; Reimer, P.D.; Martin, C.A.

    2000-01-01

    The New Carissa, carrying approximately 400,000 gallons of fuel oils ran aground on the outer shore of North Spit, in the vicinity of Coos Bay, Oregon, on February 4, 1999. The oil was released directly into the nearshore surf zone. Following the spill, a stretch of approximately 300 km of the coast of Oregon was surveyed and monitored. The need for the documentation of stranded tar balls in the neighbourhood of the spill site prompted the implementation of a long-term observation program. Initially, Shoreline Clean-up and Assessment Technique (SCAT) reporting procedures were required. Heavy oiling was followed by stranded oil taking the form of tar balls. The amount of oil on the shoreline decreased and the SCAT procedures alone were no longer adequate. They provided estimations of oil quantities that were too high and failed to provide any discrimination between amounts of oil observed on the beaches. A new reporting technique called Beach Assessment Reporting was designed to overcome the difficulties and record adequately the character and frequency of stranded tar balls. Maps, tables and histograms of stranded tar ball volumes and concentrations were discussed. Since the data spanned nine orders of magnitude at times, the semi-logarithmic scale time series plots of the concentration of the tar balls was used in order to identify trends. Conventional histograms only identified large values and camouflaged smaller trends in the time series. A direct method for describing tar ball concentrations geographically proved to be the use of weekly maximum tar ball concentration maps by segment. 10 refs., 2 tabs., 9 figs

  9. Comparative assessment of coal tars obtained from 10 former manufactured gas plant sites in the eastern United States

    Energy Technology Data Exchange (ETDEWEB)

    Brown, D.G.; Gupta, L.; Kim, T.H.; Moo-Young, H.K.; Coleman, A.J. [Lehigh University, Bethlehem, PA (United States). Dept. of Civil & Environmental Engineering

    2006-11-15

    A comparative analysis was performed on eleven coal tars obtained from former manufactured gas plant sites in the eastern United States. Bulk properties analyzed included percent ash, Karl Fisher water content, viscosity and average molecular weight. Chemical properties included monocyclic- and polycyclic-aromatic hydrocarbon (PAH) concentrations, alkylated aromatic concentrations, and concentrations of aliphatic and aromatic fractions. It was found that there was at least an order-of-magnitude variation in all properties measured between the eleven coal tars. Additionally, two coal tars obtained from the same manufactured gas plant site had very different properties, highlighting that there can be wide variations in coal tar properties from different samples obtained from the same site. Similarities were also observed between the coal tars. The relative chemical distributions were similar for all coal tars, and the coal tars predominantly consisted of PAHs, with naphthalene being the single-most prevalent compound. The C{sub 9-22} aromatic fraction, an indicator of all PAHs up to a molecular weight of approximately 276 g mole{sup -1}, showed a strong power-law relationship with the coal tar average molecular weight (MWct). And the concentrations of individual PAHs decreased linearly as MWct increased up to ca. 1000 g mole{sup -1}, above which they remained low and variable. Implications of these properties and their variation with MWct on groundwater quality are discussed. Ultimately, while these similarities do allow generalities to be made about coal tars, the wide range of coal tar bulk and chemical properties reported here highlights the complex nature of coal tars.

  10. RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

    Science.gov (United States)

    Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

    2017-01-21

    RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA

  11. Study of RNA structures with a connection to random matrix theory

    International Nuclear Information System (INIS)

    Bhadola, Pradeep; Deo, Nivedita

    2015-01-01

    This manuscript investigates the level of complexity and thermodynamic properties of the real RNA structures and compares the properties with the random RNA sequences. A discussion on the similarities of thermodynamical properties of the real structures with the non linear random matrix model of RNA folding is presented. The structural information contained in the PDB file is exploited to get the base pairing information. The complexity of an RNA structure is defined by a topological quantity called genus which is calculated from the base pairing information. Thermodynamic analysis of the real structures is done numerically. The real structures have a minimum free energy which is very small compared to the randomly generated sequences of the same length. This analysis suggests that there are specific patterns in the structures which are preserved during the evolution of the sequences and certain sequences are discarded by the evolutionary process. Further analyzing the sequences of a fixed length reveal that the RNA structures exist in ensembles i.e. although all the sequences in the ensemble have different series of nucleotides (sequence) they fold into structures that have the same pairs of hydrogen bonding as well as the same minimum free energy. The specific heat of the RNA molecule is numerically estimated at different lengths. The specific heat curve with temperature shows a bump and for some RNA, a double peak behavior is observed. The same behavior is seen in the study of the random matrix model with non linear interaction of RNA folding. The bump in the non linear matrix model can be controlled by the change in the interaction strength.

  12. Physicochemical Approaches for the Remediation of Former Manufactured Gas Plant Tars

    Science.gov (United States)

    Hauswirth, S.; Miller, C. T.

    2014-12-01

    Former manufactured gas plant (FMGP) tars are one of the most challenging non-aqueous phase liquid (NAPL) contaminants to remediate due to their complex chemical composition, high viscosities, and ability to alter wettability. In this work, we investigate several in situ remediation techniques for the removal of tar from porous media. Batch and column experiments were conducted to test the effectiveness of mobilization, solubilization, and chemical oxidation remediation approaches. Alkaline (NaOH), surfactant (Triton X-100), and polymer (xanthan gum) agents were used in various combinations to reduce tar-water interfacial tension, increase flushing solution viscosity, and increase the solubilities of tar components. Base-activated sodium persulfate was used alone and in combination with surfactant to chemically oxidized tar components. The effectiveness of each method was assessed in terms of both removal of PAHs from the system and reduction of dissolved-phase effluent polycyclic aromatic hydrocarbon (PAH) concentrations. In column studies, alkaline-polymer (AP) and alkaline-surfactant-polymer (ASP) solutions efficiently mobilized 81-93% and 95-96% of residual PAHs, respectively, within two pore volumes. The impact of AP flushing on dissolved-phase PAH concentrations was relatively low; however, the concentrations of several low molar mass PAHs were significantly reduced after ASP flushing. Surfactant-polymer (SP) solutions removed over 99% of residual PAHs through a combination of mobilization and solubilization, and reduced the post-remediation, dissolved-phase total PAH concentration by 98.4-99.1%. Degradation of residual PAHs by base-activated sodium persulfate was relatively low (30-50%), and had little impact on dissolved-phase PAH concentrations.

  13. The identification and functional annotation of RNA structures conserved in vertebrates.

    Science.gov (United States)

    Seemann, Stefan E; Mirza, Aashiq H; Hansen, Claus; Bang-Berthelsen, Claus H; Garde, Christian; Christensen-Dalsgaard, Mikkel; Torarinsson, Elfar; Yao, Zizhen; Workman, Christopher T; Pociot, Flemming; Nielsen, Henrik; Tommerup, Niels; Ruzzo, Walter L; Gorodkin, Jan

    2017-08-01

    Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality. © 2017 Seemann et al.; Published by Cold Spring Harbor Laboratory Press.

  14. A novel knowledge-based potential for RNA 3D structure evaluation

    Science.gov (United States)

    Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang

    2018-03-01

    Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).

  15. An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation.

    Science.gov (United States)

    Ingemarsdotter, Carin K; Zeng, Jingwei; Long, Ziqi; Lever, Andrew M L; Kenyon, Julia C

    2018-03-14

    NSC260594, a quinolinium derivative from the NCI diversity set II compound library, was previously identified in a target-based assay as an inhibitor of the interaction between the HIV-1 (ψ) stem-loop 3 (SL3) RNA and Gag. This compound was shown to exhibit potent antiviral activity. Here, the effects of this compound on individual stages of the viral lifecycle were examined by qRT-PCR, ELISA and Western blot, to see if its actions were specific to the viral packaging stage. The structural effects of NSC260594 binding to the HIV-1 gRNA were also examined by SHAPE and dimerization assays. Treatment of cells with NSC260594 did not reduce the number of integration events of incoming virus, and treatment of virus producing cells did not affect the level of intracellular Gag protein or viral particle release as determined by immunoblot. However, NSC260594 reduced the incorporation of gRNA into virions by up to 82%, without affecting levels of gRNA inside the cell. This reduction in packaging correlated closely with the reduction in infectivity of the released viral particles. To establish the structural effects of NSC260594 on the HIV-1 gRNA, we performed SHAPE analyses to pinpoint RNA structural changes. NSC260594 had a stabilizing effect on the wild type RNA that was not confined to SL3, but that was propagated across the structure. A packaging mutant lacking SL3 did not show this effect. NSC260594 acts as a specific inhibitor of HIV-1 RNA packaging. No other viral functions are affected. Its action involves preventing the interaction of Gag with SL3 by stabilizing this small RNA stem-loop which then leads to stabilization of the global packaging signal region (psi or ψ). This confirms data, previously only shown in analyses of isolated SL3 oligonucleotides, that SL3 is structurally labile in the presence of Gag and that this is critical for the complete psi region to be able to adopt different conformations. Since replication is otherwise unaffected by NSC260594

  16. MCTBI: a web server for predicting metal ion effects in RNA structures.

    Science.gov (United States)

    Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

    2017-08-01

    Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  17. The purification of coal tar by the addition of quinoline and Zn(oh)/sub 2/

    International Nuclear Information System (INIS)

    Zhou, P.; Chen, Q.L.; Ao, X.Q.; Kang, C

    2017-01-01

    The coal tar was purified by the addition of quinoline and Zn(OH)2, in order to decrease the content of carbon and inorganic oxide particles. The effect on the viscosity and ash content of the coal tar were investigated by altering temperature, time, and the amount of quinolone and Zn(OH)2 . When the volume ratio between quinolone and coal tar was 20:1 and the static time was 24 h. The viscosity of three layers decreased with rising temperature. When the static temperature and time was 45 °C and 24 h, respectively. The viscosity of three layers decreased with the arising amount of quinoline. And when the volume ratio between quinolone and coal tar was 20:1 and the temperature was 45 °C. The viscosity of three layers decreased first and then increased with the prolonging of static time. And when the static time of coal tar was 24 h, the viscosity of coal tar is the lowest. Because of the lower viscosity of coal tar, decreasing the content of carbon and ash particles in upper and middle layer, the ash content decreased from 0.168% to 0.092%. The addition of Zn(OH)2 can lead ash content in middle layer decrease to 0.058%. Zn2SiO4 and ZnAl2O4 may be produced due to the reaction between Zn (OH) 2 and SiO2 or Al2O3, which can settle down easily. The results show that the content of carbon and inorganic oxide particles in upper-middle-class (the middle 4/5 of the whole volume) decreased with the addition of quinolone and Zn(OH)2 . When the volume ratio between quinolone and coal tar was 50:2, quality ratio between coal tar and Zn(OH)2 was 20000:1, the mixture were heated up to 45 °C at atmospheric pressure and keeping this constant temperature for 24 h, the ash content in upper-middle-class can decreased to 0.058%. (author)

  18. tRNA-like structure regulates translation of Brome mosaic virus RNA.

    Science.gov (United States)

    Barends, Sharief; Rudinger-Thirion, Joëlle; Florentz, Catherine; Giegé, Richard; Pleij, Cornelis W A; Kraal, Barend

    2004-04-01

    For various groups of plant viruses, the genomic RNAs end with a tRNA-like structure (TLS) instead of the 3' poly(A) tail of common mRNAs. The actual function of these TLSs has long been enigmatic. Recently, however, it became clear that for turnip yellow mosaic virus, a tymovirus, the valylated TLS(TYMV) of the single genomic RNA functions as a bait for host ribosomes and directs them to the internal initiation site of translation (with N-terminal valine) of the second open reading frame for the polyprotein. This discovery prompted us to investigate whether the much larger TLSs of a different genus of viruses have a comparable function in translation. Brome mosaic virus (BMV), a bromovirus, has a tripartite RNA genome with a subgenomic RNA4 for coat protein expression. All four RNAs carry a highly conserved and bulky 3' TLS(BMV) (about 200 nucleotides) with determinants for tyrosylation. We discovered TLS(BMV)-catalyzed self-tyrosylation of the tyrosyl-tRNA synthetase but could not clearly detect tyrosine incorporation into any virus-encoded protein. We established that BMV proteins do not need TLS(BMV) tyrosylation for their initiation. However, disruption of the TLSs strongly reduced the translation of genomic RNA1, RNA2, and less strongly, RNA3, whereas coat protein expression from RNA4 remained unaffected. This aberrant translation could be partially restored by providing the TLS(BMV) in trans. Intriguingly, a subdomain of the TLS(BMV) could even almost fully restore translation to the original pattern. We discuss here a model with a central and dominant role for the TLS(BMV) during the BMV infection cycle.

  19. Rapid NMR screening of RNA secondary structure and binding

    International Nuclear Information System (INIS)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald

    2015-01-01

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA

  20. Rapid NMR screening of RNA secondary structure and binding

    Energy Technology Data Exchange (ETDEWEB)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de [Johann Wolfgang Goethe-Universität, Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ) (Germany)

    2015-09-15

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.

  1. Material Properties and Characteristics for Development of an Expert System for Coal-Tar Sealers

    National Research Council Canada - National Science Library

    Shoenberger, James

    2001-01-01

    .... Several coal-tar mixtures that varied with source of the coal-tar emulsion, amount of aggregate, and amount of polymer used in the mixtures were evaluated for their field performance and material properties...

  2. Disease-associated mutations that alter the RNA structural ensemble.

    Directory of Open Access Journals (Sweden)

    Matthew Halvorsen

    2010-08-01

    Full Text Available Genome-wide association studies (GWAS often identify disease-associated mutations in intergenic and non-coding regions of the genome. Given the high percentage of the human genome that is transcribed, we postulate that for some observed associations the disease phenotype is caused by a structural rearrangement in a regulatory region of the RNA transcript. To identify such mutations, we have performed a genome-wide analysis of all known disease-associated Single Nucleotide Polymorphisms (SNPs from the Human Gene Mutation Database (HGMD that map to the untranslated regions (UTRs of a gene. Rather than using minimum free energy approaches (e.g. mFold, we use a partition function calculation that takes into consideration the ensemble of possible RNA conformations for a given sequence. We identified in the human genome disease-associated SNPs that significantly alter the global conformation of the UTR to which they map. For six disease-states (Hyperferritinemia Cataract Syndrome, beta-Thalassemia, Cartilage-Hair Hypoplasia, Retinoblastoma, Chronic Obstructive Pulmonary Disease (COPD, and Hypertension, we identified multiple SNPs in UTRs that alter the mRNA structural ensemble of the associated genes. Using a Boltzmann sampling procedure for sub-optimal RNA structures, we are able to characterize and visualize the nature of the conformational changes induced by the disease-associated mutations in the structural ensemble. We observe in several cases (specifically the 5' UTRs of FTL and RB1 SNP-induced conformational changes analogous to those observed in bacterial regulatory Riboswitches when specific ligands bind. We propose that the UTR and SNP combinations we identify constitute a "RiboSNitch," that is a regulatory RNA in which a specific SNP has a structural consequence that results in a disease phenotype. Our SNPfold algorithm can help identify RiboSNitches by leveraging GWAS data and an analysis of the mRNA structural ensemble.

  3. Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.

    Science.gov (United States)

    Hagio, Taichi; Sakuraba, Shun; Iwakiri, Junichi; Mori, Ryota; Asai, Kiyoshi

    2018-02-19

    It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single 'best' structures, and do not produce alternative structures. There are bioinformatics tools to predict suboptimal structures, but it is difficult to detect which alternative secondary structures are essential. We proposed a new computational method to detect essential alternative secondary structures from RNA sequences by decomposing the base-pairing probability matrix. The decomposition is calculated by a newly implemented software tool, RintW, which efficiently computes the base-pairing probability distributions over the Hamming distance from arbitrary reference secondary structures. The proposed approach has been demonstrated on ROSE element RNA thermometer sequence and Lysine RNA ribo-switch, showing that the proposed approach captures conformational changes in secondary structures. We have shown that alternative secondary structures are captured by decomposing base-paring probabilities over Hamming distance. Source code is available from http://www.ncRNA.org/RintW .

  4. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

    Science.gov (United States)

    Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B

    2016-01-29

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Structural Chemistry of Human RNA Methyltransferases.

    Science.gov (United States)

    Schapira, Matthieu

    2016-03-18

    RNA methyltransferases (RNMTs) play important roles in RNA stability, splicing, and epigenetic mechanisms. They constitute a promising target class that is underexplored by the medicinal chemistry community. Information of relevance to drug design can be extracted from the rich structural coverage of human RNMTs. In this work, the structural chemistry of this protein family is analyzed in depth. Unlike most methyltransferases, RNMTs generally feature a substrate-binding site that is largely open on the cofactor-binding pocket, favoring the design of bisubstrate inhibitors. Substrate purine or pyrimidines are often sandwiched between hydrophobic walls that can accommodate planar ring systems. When the substrate base is laying on a shallow surface, a 5' flanking base is sometimes anchored in a druggable cavity. The cofactor-binding site is structurally more diverse than in protein methyltransferases and more druggable in SPOUT than in Rossman-fold enzymes. Finally, conformational plasticity observed both at the substrate and cofactor binding sites may be a challenge for structure-based drug design. The landscape drawn here may inform ongoing efforts toward the discovery of the first human RNMT inhibitors.

  6. Paleontological overview of oil shale and tar sands areas in Colorado, Utah, and Wyoming.

    Energy Technology Data Exchange (ETDEWEB)

    Murphey, P. C.; Daitch, D.; Environmental Science Division

    2009-02-11

    In August 2005, the U.S. Congress enacted the Energy Policy Act of 2005, Public Law 109-58. In Section 369 of this Act, also known as the ''Oil Shale, Tar Sands, and Other Strategic Unconventional Fuels Act of 2005,'' Congress declared that oil shale and tar sands (and other unconventional fuels) are strategically important domestic energy resources that should be developed to reduce the nation's growing dependence on oil from politically and economically unstable foreign sources. In addition, Congress declared that both research- and commercial-scale development of oil shale and tar sands should (1) be conducted in an environmentally sound manner using management practices that will minimize potential impacts, (2) occur with an emphasis on sustainability, and (3) benefit the United States while taking into account concerns of the affected states and communities. To support this declaration of policy, Congress directed the Secretary of the Interior to undertake a series of steps, several of which are directly related to the development of a commercial leasing program for oil shale and tar sands. One of these steps was the completion of a programmatic environmental impact statement (PEIS) to analyze the impacts of a commercial leasing program for oil shale and tar sands resources on public lands, with an emphasis on the most geologically prospective lands in Colorado, Utah, and Wyoming. For oil shale, the scope of the PEIS analysis includes public lands within the Green River, Washakie, Uinta, and Piceance Creek Basins. For tar sands, the scope includes Special Tar Sand Areas (STSAs) located in Utah. This paleontological resources overview report was prepared in support of the Oil Shale and Tar Sands Resource Management Plan Amendments to Address Land Use Allocations in Colorado, Utah, and Wyoming and PEIS, and it is intended to be used by Bureau of Land Management (BLM) regional paleontologists and field office staff to support future

  7. RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.

    Science.gov (United States)

    Ghosh, Pritha; Mathew, Oommen K; Sowdhamini, Ramanathan

    2016-10-07

    RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information. The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search. RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential

  8. Strategies for measuring evolutionary conservation of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Hofacker Ivo L

    2008-02-01

    Full Text Available Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. Results We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. Conclusion Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.

  9. Biomass Gasifier ''Tars'': Their Nature, Formation, and Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Milne, T. A.; Evans, R. J. (National Renewable Energy Laboratory); Abatzaglou, N. (Kemestrie, Inc.)

    1998-11-01

    The main purpose of this review is to update the information on gasification tar, the most cumbersome and problematic parameter in any gasification commercialization effort. The work aims to present to the community the scientific and practical aspects of tar formation and conversion (removal) during gasification as a function of the various technological and technical parameters and variables.

  10. Structural Analysis of Monomeric RNA-Dependent Polymerases: Evolutionary and Therapeutic Implications.

    Directory of Open Access Journals (Sweden)

    Rodrigo Jácome

    Full Text Available The crystal structures of monomeric RNA-dependent RNA polymerases and reverse transcriptases of more than 20 different viruses are available in the Protein Data Bank. They all share the characteristic right-hand shape of DNA- and RNA polymerases formed by the fingers, palm and thumb subdomains, and, in many cases, "fingertips" that extend from the fingers towards the thumb subdomain, giving the viral enzyme a closed right-hand appearance. Six conserved structural motifs that contain key residues for the proper functioning of the enzyme have been identified in all these RNA-dependent polymerases. These enzymes share a two divalent metal-ion mechanism of polymerization in which two conserved aspartate residues coordinate the interactions with the metal ions to catalyze the nucleotidyl transfer reaction. The recent availability of crystal structures of polymerases of the Orthomyxoviridae and Bunyaviridae families allowed us to make pairwise comparisons of the tertiary structures of polymerases belonging to the four main RNA viral groups, which has led to a phylogenetic tree in which single-stranded negative RNA viral polymerases have been included for the first time. This has also allowed us to use a homology-based structural prediction approach to develop a general three-dimensional model of the Ebola virus RNA-dependent RNA polymerase. Our model includes several of the conserved structural motifs and residues described in other viral RNA-dependent RNA polymerases that define the catalytic and highly conserved palm subdomain, as well as portions of the fingers and thumb subdomains. The results presented here help to understand the current use and apparent success of antivirals, i.e. Brincidofovir, Lamivudine and Favipiravir, originally aimed at other types of polymerases, to counteract the Ebola virus infection.

  11. Dual vapor extraction on acidic sludge tar at a former refinery

    International Nuclear Information System (INIS)

    Lear, P.R.; Beall, P.; Townsend, S.

    1996-01-01

    OHM Remediation Services Corp conducted a pilot-scale demonstration for a novel application of dual vapor extraction technology for the pretreatment of the acid tar sludge material. The acid tar sludge comprised of approximately 60% asphaltene hydrocarbon material, 20% clay, and up to 20% sulfuric acid (H 2 SO 4 ). The liquid layer in the bottom of the pits has a low pH ( 2 ) gas which is released with the sludge material is excavated or handled. The objective of the dual vapor extraction was to remove the SO 2 vapors and liquid layer containing sulfuric acid prior to any further treatment. The dual vapor extraction would reduce the amount of alkaline reagent required for neutralization while eliminating the health and safety concerns. Overall, the DVE pilot demonstration successfully showed that both liquids and vapors could be removed from the acid tar sludge material. The liquid present in the lower portions of the pits will have pH values of 1.0 or less and acidities on the order of 5% H 2 SO 4 . The liquid removed from the acid tar sludge material by a DVE system will have slightly higher pH (∼1.5) and lower alkalinities (∼3% H 2 SO 4 ). The SO 2 concentration in the vapors removed by the DVE system will be variable with initial levels approaching 1,200 ppmv SO 2 . The SO 2 concentration in the vapor phase should decrease with time. A caustic scrubber solution will remove any SO 2 from the vapor phase. After DVE treatment, the acid tar sludge material would have a slightly increased pH and a decreased SO 2 concentration

  12. Toxicity of coal-tar and asphalt sealants to eastern newts, Notophthalmus viridescens

    Energy Technology Data Exchange (ETDEWEB)

    Bommarito, T.; Sparling, D.W.; Halbrook, R.S. [South Illinois University, Carbondale, IL (United States). Cooperative Wildlife Research Laboratory

    2010-09-15

    Between 1970 and 2000 the concentration of total polycyclic aromatic hydrocarbons (TPAH) in several lakes across the country increased whereas those of other persistent organic pollutants (POPs) tended to remain stable or declined. Urbanized watersheds experienced greater rises in TPAH concentration compared to non-urban lakes. Sources for urban PAHs include industrial wastes, vehicular exhausts and oil leaks and sealants from pavement surfaces. Both coal-tar and asphalt sealants are used to protect surfaces but runoff from surfaces coated with coal-tar can have mean concentrations of 3500 mg TPAHs kg{sup -1}, much higher than runoff from asphalt-sealed or cement surfaces. Unaltered parent compounds of PAHs can have many lethal and sublethal toxic effects, but oxidation and UV radiation can alter the toxicity of these compounds, sometimes creating degradates that are many times more toxic than parent compounds. The purposes of this study were to determine if coal-tar sealants can be toxic to adult eastern newts (Notophthalmus viridescens) and to compare the toxicity of coal-tar sealant to that of asphalt sealant. Newts were exposed to sediments containing dried sealants ranging from 0 mg kg{sup -1} to 1500 mg kg{sup -1} under simultaneous exposure to UV radiation and visible light to determine concentration/response relationships. No significant mortality occurred with any treatment. Significant effects due to sealants included decreased righting ability and diminished liver enzyme activities. Coal-tar sealant was more effective in inducing these changes than was asphalt sealant.

  13. Tar analysis from biomass gasification by means of online fluorescence spectroscopy

    Science.gov (United States)

    Baumhakl, Christoph; Karellas, Sotirios

    2011-07-01

    Optical methods in gas analysis are very valuable mainly due to their non-intrusive character. That gives the possibility to use them for in-situ or online measurements with only optical intervention in the measurement volume. In processes like the gasification of biomass, it is of high importance to monitor the gas quality in order to use the product gas in proper machines for energy production following the restrictions in the gas composition but also improving its quality, which leads to high efficient systems. One of the main problems in the biomass gasification process is the formation of tars. These higher hydrocarbons can lead to problems in the operation of the energy system. Up to date, the state of the art method used widely for the determination of tars is a standardized offline measurement system, the so-called "Tar Protocol". The aim of this work is to describe an innovative, online, optical method for determining the tar content of the product gas by means of fluorescence spectroscopy. This method uses optical sources and detectors that can be found in the market at low cost and therefore it is very attractive, especially for industrial applications where cost efficiency followed by medium to high precision are of high importance.

  14. Tar ball concentrations in the ocean around the Cape of Good Hope before and after a major oil spill

    Energy Technology Data Exchange (ETDEWEB)

    Eagle, G A; Green, A; Williams, J

    1979-11-01

    From August 1977 to August 1978, tar ball concentrations around the southwestern coast of South Africa were sampled. Prior to a tanker collision on December 16, 1977, the area was relatively free of floating tar. Following the collision, tar ball concentrations increased; tar was transported by wind and currents, at average speeds of about 1 km/hr. In areas of slack currents, tar was observed for as long as 8 months after the spill. Results provided information about surface current trends.

  15. Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase.

    Science.gov (United States)

    Poranen, Minna M; Salgado, Paula S; Koivunen, Minni R L; Wright, Sam; Bamford, Dennis H; Stuart, David I; Grimes, Jonathan M

    2008-11-01

    The biological role of manganese (Mn(2+)) has been a long-standing puzzle, since at low concentrations it activates several polymerases whilst at higher concentrations it inhibits. Viral RNA polymerases possess a common architecture, reminiscent of a closed right hand. The RNA-dependent RNA polymerase (RdRp) of bacteriophage 6 is one of the best understood examples of this important class of polymerases. We have probed the role of Mn(2+) by biochemical, biophysical and structural analyses of the wild-type enzyme and of a mutant form with an altered Mn(2+)-binding site (E491 to Q). The E491Q mutant has much reduced affinity for Mn(2+), reduced RNA binding and a compromised elongation rate. Loss of Mn(2+) binding structurally stabilizes the enzyme. These data and a re-examination of the structures of other viral RNA polymerases clarify the role of manganese in the activation of polymerization: Mn(2+) coordination of a catalytic aspartate is necessary to allow the active site to properly engage with the triphosphates of the incoming NTPs. The structural flexibility caused by Mn(2+) is also important for the enzyme dynamics, explaining the requirement for manganese throughout RNA polymerization.

  16. Advances in RNA Structure Determination | Center for Cancer Research

    Science.gov (United States)

    The recent years have witnessed a revolution in the field of RNA structure and function. Until recently the main contribution of RNA in cellular and disease functions was considered to be a role defined by the central dogma, namely DNA codes for mRNAs, which in turn encode for proteins, a notion facilitated by non-coding ribosomal RNA and tRNA. It was also assumed at the time

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

    Science.gov (United States)

    Chen, Jiawen; Zhang, Wenbing

    2012-12-01

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

  18. Structural Studies of RNA Helicases Involved in Eukaryotic Pre-mRNA Splicing, Ribosome Biogenesis, and Translation Initiation

    DEFF Research Database (Denmark)

    He, Yangzi

    and ligates the neighbouring exons to generate mature mRNAs. Prp43 is an RNA helicase of the DEAH/RHA family. In yeast, once mRNAs are released, Prp43 catalyzes the disassembly of spliceosomes. The 18S, 5.8S and 25S rRNAs are transcribed as a single polycistronic transcript—the 35S pre......-rRNA. It is nucleolytically cleaved and chemically modified to generate mature rRNAs, which assemble with ribosomal proteins to form the ribosome. Prp43 is required for the processing of the 18S rRNA. Using X-ray crystallography, I determined a high resolution structure of Prp43 bound to ADP, the first structure of a DEAH....../RHA helicase. It defined the conserved structural features of all DEAH/RHA helicases, and unveiled a novel nucleotide binding site. Additionally a preliminary low resolution structure of a ternary complex comprising Prp43, a non-hydrolyzable ATP analogue, and a single-stranded RNA, was obtained. The ribosome...

  19. Skin cancer in patients with psoriasis treated with coal tar. A 25-year follow-up study

    International Nuclear Information System (INIS)

    Pittelkow, M.R.; Perry, H.O.; Muller, S.A.; Maughan, W.Z.; O'Brien, P.C.

    1981-01-01

    For many years, crude coal tar has been used for the treatment of psoriasis. The possible carcinogenic effect of crude coal tar and ultraviolet (UV) radiation (Goeckerman regimen), considered individually or in combination, has been of some concern to physicians. A 25-year follow-up study was completed on 280 patients with psoriasis who were hospitalized and treated with crude coal tar and UV radiation at the Mayo Clinic, Rochester, Minn, during the years 1950 through 1954. The results of this study suggest that the incidence of skin cancer is not appreciably increased above the expected incidence for the general population when patients are treated with coal tar ointments. It seems that the Goeckerman regimen (topical crude coal tar combined with UV radiation) can be used with minimal risk for skin cancer in the treatment of psoriasis

  20. Volatilization of polycyclic aromatic hydrocarbons from coal-tar-sealed pavement

    Science.gov (United States)

    Van Metre, Peter C.; Majewski, Michael S.; Mahler, Barbara J.; Foreman, William T.; Braun, Christopher L.; Wilson, Jennifer T.; Burbank, Teresa L.

    2012-01-01

    Coal-tar-based pavement sealants, a major source of PAHs to urban water bodies, are a potential source of volatile PAHs to the atmosphere. An initial assessment of volatilization of PAHs from coal-tar-sealed pavement is presented here in which we measured summertime gas-phase PAH concentrations 0.03 m and 1.28 m above the pavement surface of seven sealed (six with coal-tar-based sealant and one with asphalt-based sealant) and three unsealed (two asphalt and one concrete) parking lots in central Texas. PAHs also were measured in parking lot dust. The geometric mean concentration of the sum of eight frequently detected PAHs (ΣPAH8) in the 0.03-m samples above sealed lots (1320 ng m-3) during the hottest part of the day was 20 times greater than that above unsealed lots (66.5 ng m-3). The geometric mean concentration in the 1.28-m samples above sealed lots (138 ng m-3) was five times greater than above unsealed lots (26.0 ng m-3). Estimated PAH flux from the sealed lots was 60 times greater than that from unsealed lots (geometric means of 88 and 1.4 μg m-2 h-1, respectively). Although the data set presented here is small, the much higher estimated fluxes from sealed pavement than from unsealed pavement indicate that coal-tar-based sealants are emitting PAHs to urban air at high rates compared to other paved surfaces.

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

    Science.gov (United States)

    Byun, Yanga; Han, Kyungsook

    2016-06-01

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

  2. Detailed grouping and functional composition of neutral substances in low-temperature tar

    Energy Technology Data Exchange (ETDEWEB)

    Kalechits, I V; Salimgareeva, F G; Popova, N I; Kurbangaleeva, D K; Klykova, G G

    1955-01-01

    The grouping and the functional composition of the neutral substances in coal tar were characterized by means of adsorption on silica gel with subsequent chemical analysis of each fraction. The neutral materials were obtained by consecutive treatment of a C/sub 6/H/sub 6/ solution of coal tar with 10 percent alkali and 5 percent H/sub 2/SO/sub 4/ to remove the phenols and the bases. The data show that of the neutral substances (only 75% were identified) 40.5% were aromatic hydrocarbons. Based on a study of all of the data, it was proposed that 90% of the composition of coal tars is aromatic. The physical constants of the separated fractions were determined and are presented in tabular form.

  3. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.

    Directory of Open Access Journals (Sweden)

    Pablo Cordero

    2015-11-01

    Full Text Available Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral infection [corrected]. We report herein that high-throughput chemical experiments can isolate an RNA's multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2 and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states' structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10% and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization.

  4. Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

    Science.gov (United States)

    Lorenz, William A.; Clote, Peter

    2011-01-01

    An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server

  5. Computing the partition function for kinetically trapped RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    William A Lorenz

    Full Text Available An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in O(n3 time and O(n2 space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1 the number of locally optimal structures is far fewer than the total number of structures--indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2 the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3 the (modified maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected

  6. Response of microbial activities and diversity to PAHs contamination at coal tar contaminated land

    Science.gov (United States)

    Zhao, Xiaohui; Sun, Yujiao; Ding, Aizhong; Zhang, Dan; Zhang, Dayi

    2015-04-01

    Coal tar is one of the most hazardous and concerned organic pollutants and the main hazards are polycyclic aromatic hydrocarbons (PAHs). The indigenous microorganisms in soils are capable to degrade PAHs, with essential roles in biochemical process for PAHs natural attenuation. This study investigated 48 soil samples (from 8 depths of 6 boreholes) in Beijing coking and chemistry plant (China) and revealed the correlation between PAHs contamination, soil enzyme activities and microbial community structure, by 16S rRNA denaturing gradient gel electrophoresis (DGGE). At the site, the key contaminants were identified as naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene, and the total PAHs concentration ranged from 0.1 to 923.9 mg/kg dry soil. The total PAHs contamination level was positively correlated (pcatalase activities (0.554-6.230 mL 0.02 M KMnO4/g•h) and dehydrogenase activities (1.9-30.4 TF μg/g•h soil), showing the significant response of microbial population and degrading functions to the organic contamination in soils. The PAHs contamination stimulated the PAHs degrading microbes and promoted their biochemical roles in situ. The positive relationship between bacteria count and dehydrogenase activities (p<0.05) suggested the dominancy of PAHs degrading bacteria in the microbial community. More interestingly, the microbial community deterioration was uncovered via the decline of microbial biodiversity (richness from 16S rRNA DGGE) against total PAHs concentration (p<0.05). Our research described the spatial profiles of PAHs contamination and soil microbial functions at the PAHs heavily contaminated sites, offering deeper understanding on the roles of indigenous microbial community in natural attenuation process.

  7. A combinatorial enumeration problem of RNA secondary structures

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... interesting combinatorial questions (Chen et al., 2005;. Liu, 2006; Schmitt and Waterman 1994; Stein and. Waterman 1978). The research on the enumeration of. RNA secondary structures becomes one of the hot topics in Computational Molecular Biology. An RNA molecule is described by its sequences of.

  8. The crystal structure and RNA-binding of an orthomyxovirus nucleoprotein.

    Directory of Open Access Journals (Sweden)

    Wenjie Zheng

    2013-09-01

    Full Text Available Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV (genus Isavirus. As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ~12 nts of RNA, shorter than the 24-28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions.

  9. The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases

    Directory of Open Access Journals (Sweden)

    Dutartre Hélène

    2005-10-01

    Full Text Available Abstract Background The Flaviviridae virus family includes major human and animal pathogens. The RNA dependent RNA polymerase (RdRp plays a central role in the replication process, and thus is a validated target for antiviral drugs. Despite the increasing structural and enzymatic characterization of viral RdRps, detailed molecular replication mechanisms remain unclear. The hepatitis C virus (HCV is a major human pathogen difficult to study in cultured cells. The bovine viral diarrhea virus (BVDV is often used as a surrogate model to screen antiviral drugs against HCV. The structure of BVDV RdRp has been recently published. It presents several differences relative to HCV RdRp. These differences raise questions about the relevance of BVDV as a surrogate model, and cast novel interest on the "GB" virus C (GBV-C. Indeed, GBV-C is genetically closer to HCV than BVDV, and can lead to productive infection of cultured cells. There is no structural data for the GBV-C RdRp yet. Results We show in this study that the GBV-C RdRp is closest to the HCV RdRp. We report a 3D model of the GBV-C RdRp, developed using sequence-to-structure threading and comparative modeling based on the atomic coordinates of the HCV RdRp structure. Analysis of the predicted structural features in the phylogenetic context of the RNA polymerase family allows rationalizing most of the experimental data available. Both available structures and our model are explored to examine the catalytic cleft, allosteric and substrate binding sites. Conclusion Computational methods were used to infer evolutionary relationships and to predict the structure of a viral RNA polymerase. Docking a GTP molecule into the structure allows defining a GTP binding pocket in the GBV-C RdRp, such as that of BVDV. The resulting model suggests a new proposition for the mechanism of RNA synthesis, and may prove useful to design new experiments to implement our knowledge on the initiation mechanism of RNA

  10. Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

    Energy Technology Data Exchange (ETDEWEB)

    Teplova, Marianna; Farazi, Thalia A.; Tuschl, Thomas; Patel, Dinshaw J.

    2015-09-08

    Abstract

    RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutationsin vivo.

  11. Investigation of RNA structure in satellite panicum mosaic virus

    International Nuclear Information System (INIS)

    Makino, D.L.; Day, J.; Larson, S.B.; McPherson, A.

    2006-01-01

    Three new crystal forms of satellite panicum mosaic virus (SPMV) were grown and their structures solved from X-ray diffraction data using molecular replacement techniques. The crystals were grown under conditions of pH and ionic strength that were appreciably different then those used for the original structure determination. In rhombohedral crystals grown at pH 8.5 and low ionic strength PEG 3350 solutions, Fourier syntheses revealed segments, ten amino acid residues long, of amino-terminal polypeptides not previously seen, as well as masses of electron density within concavities on the interior of the capsid, which appeared in the neighborhoods of icosahedral five- and threefold axes. The densities were compatible with secondary structural domains of RNA, and they included a segment of double helical RNA of about four to five base pairs oriented, at least approximately, along the fivefold axes. The distribution of RNA observed for SPMV appears to be distinctly different than the encapsidated nucleic acid conformation previously suggested for another satellite virus, satellite tobacco mosaic virus. This study further shows that analysis of viruses in crystals grown under different chemical conditions may reveal additional information regarding the structure of encapsidated RNA

  12. RNA secondary structures of the bacteriophage phi6 packaging regions.

    Science.gov (United States)

    Pirttimaa, M J; Bamford, D H

    2000-06-01

    Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.

  13. Research and information needs for management of tar sands development. Interim report Apr-May 83

    Energy Technology Data Exchange (ETDEWEB)

    1983-05-01

    The report discusses important research and information needs for federal lease management of lands with tar sands resources. Short-term needs include more complete definition and characterization of deposits, hydrology, and regions downwind from tar sands areas. Longer-term needs include demonstration-scale operations to resolve production, waste management, and reclamation problems and to provide opportunities for measurement, analysis, and assessment of mining and processing wastes and emissions. Most of the known federal tar sands resource is in eastern Utah and contains about 25 billion barrels of bitumen. Recent legislation provides that existing mining claims and oil and gas leases may be converted to combined hydrocarbon leases including tar sands. Federal approval, which must be applied for by November 1983, is a condition for conversion.

  14. Self containment, a property of modular RNA structures, distinguishes microRNAs.

    Directory of Open Access Journals (Sweden)

    Miler T Lee

    2008-08-01

    Full Text Available RNA molecules will tend to adopt a folded conformation through the pairing of bases on a single strand; the resulting so-called secondary structure is critical to the function of many types of RNA. The secondary structure of a particular substring of functional RNA may depend on its surrounding sequence. Yet, some RNAs such as microRNAs retain their specific structures during biogenesis, which involves extraction of the substructure from a larger structural context, while other functional RNAs may be composed of a fusion of independent substructures. Such observations raise the question of whether particular functional RNA substructures may be selected for invariance of secondary structure to their surrounding nucleotide context. We define the property of self containment to be the tendency for an RNA sequence to robustly adopt the same optimal secondary structure regardless of whether it exists in isolation or is a substring of a longer sequence of arbitrary nucleotide content. We measured degree of self containment using a scoring method we call the self-containment index and found that miRNA stem loops exhibit high self containment, consistent with the requirement for structural invariance imposed by the miRNA biogenesis pathway, while most other structured RNAs do not. Further analysis revealed a trend toward higher self containment among clustered and conserved miRNAs, suggesting that high self containment may be a characteristic of novel miRNAs acquiring new genomic contexts. We found that miRNAs display significantly enhanced self containment compared to other functional RNAs, but we also found a trend toward natural selection for self containment in most functional RNA classes. We suggest that self containment arises out of selection for robustness against perturbations, invariance during biogenesis, and modular composition of structural function. Analysis of self containment will be important for both annotation and design of functional

  15. Investigation of sulfur-polycyclic aromatic hydrocarbon in coal derived tars of pyrolysis and hydropyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Chen, H.; Li, B.; Zhang, B. [Chinese Academy of Sciences, Taiyuan (China). State Key Laboratory of Coal Conversion

    1999-07-01

    A study was undertaken to characterize sulphur forms in coal derived tars from pyrolysis and hydropyrolysis of bituminous coal and lignite. The pyrolysis tars were analyzed for content of polycyclic aromatic sulfur hydrocarbons (PASH). 5 refs., 3 figs., 3 tabs.

  16. Crystallization and preliminary X-ray diffraction analysis of the periplasmic domain of the Escherichia coli aspartate receptor Tar and its complex with aspartate

    Energy Technology Data Exchange (ETDEWEB)

    Mise, Takeshi; Matsunami, Hideyuki; Samatey, Fadel A.; Maruyama, Ichiro N., E-mail: ichi@oist.jp [Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495 (Japan)

    2014-08-27

    The periplasmic domain of the E. coli aspartate receptor Tar was cloned, expressed, purified and crystallized with and without bound ligand. The crystals obtained diffracted to resolutions of 1.58 and 1.95 Å, respectively. The cell-surface receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni{sup 2+}. To understand the molecular mechanisms underlying the induction of Tar activity by its ligands, the Escherichia coli Tar periplasmic domain with and without bound aspartate (Asp-Tar and apo-Tar, respectively) were each crystallized in two different forms. Using ammonium sulfate as a precipitant, crystals of apo-Tar1 and Asp-Tar1 were grown and diffracted to resolutions of 2.10 and 2.40 Å, respectively. Alternatively, using sodium chloride as a precipitant, crystals of apo-Tar2 and Asp-Tar2 were grown and diffracted to resolutions of 1.95 and 1.58 Å, respectively. Crystals of apo-Tar1 and Asp-Tar1 adopted space group P4{sub 1}2{sub 1}2, while those of apo-Tar2 and Asp-Tar2 adopted space groups P2{sub 1}2{sub 1}2{sub 1} and C2, respectively.

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

    Science.gov (United States)

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

    2009-11-01

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

  18. The role of char and tar in determining the gas-phase partitioning of nitrogen during biomass gasification

    International Nuclear Information System (INIS)

    Broer, Karl M.; Brown, Robert C.

    2015-01-01

    Highlights: • Switchgrass was gasified at an equivalence ratio of zero and 650–850 °C. • Short residence times were employed to minimize secondary reactions. • Char- and tar-bound nitrogen, NH_3, HCN, and N_2 were all significant products. • Increasing temperature leads to increased release of gaseous nitrogen compounds. • Kinetic models of gasification should include nitrogen release from char and tar. - Abstract: Gasification is an attractive option for converting biomass into fuels and chemicals. Most biomass contains significant amounts of fuel-bound nitrogen (FBN), which partially converts into ammonia (NH_3) and hydrogen cyanide (HCN) during gasification. These nitrogen compounds are problematic as they can lead to NO_X emissions or catalyst poisoning in downstream applications of syngas. FBN can convert to other products as well, including diatomic nitrogen (N_2), char-bound nitrogen (char-N), and tar-bound nitrogen (tar-N). Efforts to predict concentrations of NH_3 and HCN have been hindered by a lack of accurate, comprehensive measurements of nitrogen partitioning among gasification products. The present study gasified switchgrass under allothermal, short residence time conditions and measured NH_3, HCN, char-N, and tar-N as a function of temperature in the range of 650–850 °C with diatomic nitrogen determined by difference. It was found that a major portion of FBN was retained in the char and tar products. As temperature was increased, char and tar were consumed, releasing nitrogen as gaseous NH_3 and HCN. This increase in undesirable nitrogen compounds is contrary to the predictions of most gasification models, which overlook the presence of significant nitrogen in char and tar even if they include tar cracking and char gasification reactions. The results of this study demonstrate that gas-phase reactions alone are not sufficient to predict the fate of nitrogen during gasification. In order for modeling efforts to obtain more accurate

  19. Trans-acting RNAs as molecular probes for monitoring time-dependent structural change of an RNA complex adapting two structures.

    Science.gov (United States)

    Maeda, Yuri; Furuta, Hiroyuki; Ikawa, Yoshiya

    2011-03-01

    As dynamic structural changes are pivotal for the functions of some classes of RNA molecule, it is important to develop methods to monitor structural changes in RNA in a time-dependent manner without chemical modification. Based on previous reports that trans-acting RNAs can be used as probes for analysis and control of 3D structures of target RNAs, we applied this method to monitor time-dependent structural changes in RNA. We designed and performed a proof-of-principle study using a simple model RNA complex that adopts two different structures as a target. The time-dependent structural changes in the target RNA were successfully monitored using two trans-acting RNAs, which stably form a ternary complex with the bimolecular target RNA and act as a catalyst to join two RNA fragments of the target complex, respectively. Copyright © 2010 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  20. An image processing approach to computing distances between RNA secondary structures dot plots

    Directory of Open Access Journals (Sweden)

    Sapiro Guillermo

    2009-02-01

    Full Text Available Abstract Background Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA structure of interest in a database of structures. Several methods are available for computing distances between RNAs represented as strings or graphs, but none utilize the RNA representation with dot plots. Since dot plots are essentially digital images, there is a clear motivation to devise an algorithm for computing the distance between dot plots based on image processing methods. Results We have developed a new metric dubbed 'DoPloCompare', which compares two RNA structures. The method is based on comparing dot plot diagrams that represent the secondary structures. When analyzing two diagrams and motivated by image processing, the distance is based on a combination of histogram correlations and a geometrical distance measure. We introduce, describe, and illustrate the procedure by two applications that utilize this metric on RNA sequences. The first application is the RNA design problem, where the goal is to find the nucleotide sequence for a given secondary structure. Examples where our proposed distance measure outperforms others are given. The second application locates peculiar point mutations that induce significant structural alternations relative to the wild type predicted secondary structure. The approach reported in the past to solve this problem was tested on several RNA sequences with known secondary structures to affirm their prediction, as well as on a data set of ribosomal pieces. These pieces were computationally cut from a ribosome for which an experimentally derived secondary structure is available, and on each piece the prediction conveys similarity to the experimental result. Our newly proposed distance measure shows benefit in this problem as well when compared to standard methods used for assessing

  1. TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

    Science.gov (United States)

    Wiebe, Nicholas J P; Meyer, Irmtraud M

    2010-06-24

    The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular

  2. Prediction of RNA secondary structures: from theory to models and real molecules

    International Nuclear Information System (INIS)

    Schuster, Peter

    2006-01-01

    RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA

  3. Structure of Drosophila Oskar reveals a novel RNA binding protein

    Science.gov (United States)

    Yang, Na; Yu, Zhenyu; Hu, Menglong; Wang, Mingzhu; Lehmann, Ruth; Xu, Rui-Ming

    2015-01-01

    Oskar (Osk) protein plays critical roles during Drosophila germ cell development, yet its functions in germ-line formation and body patterning remain poorly understood. This situation contrasts sharply with the vast knowledge about the function and mechanism of osk mRNA localization. Osk is predicted to have an N-terminal LOTUS domain (Osk-N), which has been suggested to bind RNA, and a C-terminal hydrolase-like domain (Osk-C) of unknown function. Here, we report the crystal structures of Osk-N and Osk-C. Osk-N shows a homodimer of winged-helix–fold modules, but without detectable RNA-binding activity. Osk-C has a lipase-fold structure but lacks critical catalytic residues at the putative active site. Surprisingly, we found that Osk-C binds the 3′UTRs of osk and nanos mRNA in vitro. Mutational studies identified a region of Osk-C important for mRNA binding. These results suggest possible functions of Osk in the regulation of stability, regulation of translation, and localization of relevant mRNAs through direct interaction with their 3′UTRs, and provide structural insights into a novel protein–RNA interaction motif involving a hydrolase-related domain. PMID:26324911

  4. Potential contributions of asphalt and coal tar to black carbon quantification in urban dust, soils, and sediments

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Y.; Mahler, B.J.; Van Metre, P.C.; Ligouis, B.; Werth, C.J. [University of Illinois Urbana Champaign, Urbana, IL (USA). Dept. of Civil & Environmental Engineering

    2010-12-01

    Measurements of black carbon (BC) using either chemical or thermal oxidation methods are generally thought to indicate the amount of char and/or soot present in a sample. In urban environments, however, asphalt and coal-tar particles worn from pavement are ubiquitous and, because of their pyrogenic origin, could contribute to measurements of BC. Here we explored the effect of the presence of asphalt and coal-tar particles on the quantification of BC in a range of urban environmental sample types, and evaluated biases in the different methods used for quantifying BC. Samples evaluated were pavement dust, residential and commercial area soils, lake sediments from a small urban watershed, and reference materials of asphalt and coal tar. Total BC was quantified using chemical treatment through acid dichromate (Cr{sub 2}O{sub 7}) oxidation and chemo-thermal oxidation at 375{sup o}C (CTO-375). BC species, including soot and char/charcoal, asphalt, and coal tar, were quantified with organic petrographic analysis. Comparison of results by the two oxidation methods and organic petrography indicates that both coal tar and asphalt contribute to BC quantified by Cr{sub 2}O{sub 7} oxidation, and that coal tar contributes to BC quantified by CTO-375. These results are supported by treatment of asphalt and coal-tar reference samples with Cr2O7 oxidation and CTO-375. The reference asphalt is resistant to Cr{sub 2}O{sub 7} oxidation but not to CTO-375, and the reference coal tar is resistant to both Cr2O7 oxidation and CTO-375. These results indicate that coal tar and/or asphalt can contribute to BC measurements in samples from urban areas using Cr{sub 2}O{sub 7} oxidation or CTO-375, and caution is advised when interpreting BC measurements made with these methods.

  5. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

    Science.gov (United States)

    Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

    2013-04-02

    A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

  6. PFB air gasification of biomass. Investigation of product formation and problematic issues related to ammonia, tar and alkali

    Energy Technology Data Exchange (ETDEWEB)

    Padban, Nader

    2000-09-01

    Fluidised bed thermal gasification of biomass is an effective route that results in 100 % conversion of the fuel. In contrast to chemical, enzymatic or anaerobic methods of biomass treatment, the thermal conversion leaves no contaminated residue after the process. The product gas evolved within thermal conversion can be used in several applications such as: fuel for gas turbines, combustion engines and fuel cells, and raw material for production of chemicals and synthetic liquid fuels. This thesis treats a part of the experimental data from two different gasifiers: a 90 kW{sub th} pressurised fluidised bubbling bed gasifier at Lund University and a 18 MW{sub th} circulating fluidised bed gasifier integrated with gas turbine (IGCC) in Vaernamo. A series of parallel and consecutive chemical reactions is involved in thermal gasification, giving origin to formation of a variety of products. These products can be classified within three major groups: gases, tars and oils, and char. The proportion of these categories of species in the final product is a matter of the gasifier design and the process parameters. The thesis addresses the technical and theoretical aspects of the biomass thermochemical conversion and presents a new approach in describing the gasification reactions. There is an evidence of fuel effect on the characteristics of the final products: a mixture of plastic waste (polyethylene) and biomass results in higher concentration of linear hydrocarbons in the gas than gasification of pure biomass. Mixing the biomass with textile waste (containing aromatic structure) results in a high degree of formation of aromatic compounds and light tars. Three topic questions within biomass gasification, namely: tar, NO{sub x} and alkali are discussed in the thesis. The experimental results show that gasification at high ER or high temperature decreases the total amount of the tars and simultaneously reduces the contents of the oxygenated and alkyl-substituted poly

  7. Initiation of translation in bacteria by a structured eukaryotic IRES RNA.

    Science.gov (United States)

    Colussi, Timothy M; Costantino, David A; Zhu, Jianyu; Donohue, John Paul; Korostelev, Andrei A; Jaafar, Zane A; Plank, Terra-Dawn M; Noller, Harry F; Kieft, Jeffrey S

    2015-03-05

    The central dogma of gene expression (DNA to RNA to protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. However, the core structures and conformational dynamics of ribosomes that are responsible for the translation steps that take place after initiation are ancient and conserved across the domains of life. We wanted to explore whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by transfer RNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA, but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence and provides an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.

  8. Volatilization of polycyclic aromatic hydrocarbons from coal-tar-sealed pavement.

    Science.gov (United States)

    Van Metre, Peter C; Majewski, Michael S; Mahler, Barbara J; Foreman, William T; Braun, Christopher L; Wilson, Jennifer T; Burbank, Teresa L

    2012-06-01

    Coal-tar-based pavement sealants, a major source of PAHs to urban water bodies, are a potential source of volatile PAHs to the atmosphere. An initial assessment of volatilization of PAHs from coal-tar-sealed pavement is presented here in which we measured summertime gas-phase PAH concentrations 0.03 m and 1.28 m above the pavement surface of seven sealed (six with coal-tar-based sealant and one with asphalt-based sealant) and three unsealed (two asphalt and one concrete) parking lots in central Texas. PAHs also were measured in parking lot dust. The geometric mean concentration of the sum of eight frequently detected PAHs (ΣPAH(8)) in the 0.03-m samples above sealed lots (1320 ng m(-3)) during the hottest part of the day was 20 times greater than that above unsealed lots (66.5 ng m(-3)). The geometric mean concentration in the 1.28-m samples above sealed lots (138 ng m(-3)) was five times greater than above unsealed lots (26.0 ng m(-3)). Estimated PAH flux from the sealed lots was 60 times greater than that from unsealed lots (geometric means of 88 and 1.4 μg m(-2) h(-1), respectively). Although the data set presented here is small, the much higher estimated fluxes from sealed pavement than from unsealed pavement indicate that coal-tar-based sealants are emitting PAHs to urban air at high rates compared to other paved surfaces. Published by Elsevier Ltd.

  9. UTILIZATION OF ACTIVATED ZEOLITE AS MOLECULAR SIEVE IN CHROMATOGRAPHIC COLUMN FOR SEPARATION OF COAL TAR COMPOUNDS

    Directory of Open Access Journals (Sweden)

    Dwi Retno Nurotul Wahidiyah

    2010-06-01

    Full Text Available Application of activated zeolite (ZAA as molecular sieve to separate compounds of coal tar from vaccum fractional distillation, have been done. The size of zeolite was 10-20 mesh and used as solid phase in column chromatography with length of 30 cm. The first step of the research was coal pyrolisis and the product (tar was distillated by fractional column and vaccum system at reduced pressure 44 cmHg and maximum temperature at 200 oC. The distillate from this procedure was flowed to the column chromatography of zeolite (ZAA. The compound absorbed by zeolite was eluted with varying solvents, i.e: CCl4, acetone and ethanol. Each fraction was then analyzed by gas chromatography. The results showed, zeolite have a capability to separate the compounds of tar and it tends to absorb medium hydrocarbon. The nonpolar eluent [CCl4] gives the better result in eluting tar compound than polar (ethanol or medium polar eluents (acetone.   Keywords: zeolite, coal tar, column chromatography

  10. Development of secondary chamber for tar cracking-improvement of wood pyrolysis performance in pre-vacuum chamber

    Science.gov (United States)

    Siahaan, S.; Homma, H.; Homma, H.

    2018-02-01

    Energy crisis and global warming, in other words, climate change are critical topics discussed in various parts of the world. Global warming primarily result from too much emission of carbon dioxide (CO2) in the atmosphere. To mitigate global warming, or climate change and improve electrification in rural areas, wood pyrolysis technology is developed in a laboratory scale, of which gases are directly applicable to the gas engine generator. Our laboratory has developed a prototype of wood pyrolysis plant with a pre-vacuum chamber. However, tar yield was around 40 wt% of feedstock. This research aims to reduce tar yield by secondary tar cracking. For the secondary tar cracking, a secondary pre-vacuum chamber is installed after primary pre-vacuum chamber. Gases generated in the primary pre-vacuum chamber are lead into the secondary chamber that is heated up to 1000 K. This paper reports performance of the secondary chamber for secondary tar cracking in homogeneous mode and heterogeneous mode with char.

  11. Web-Beagle: a web server for the alignment of RNA secondary structures.

    Science.gov (United States)

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-07-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Structure of noncoding RNA is a determinant of function of RNA binding proteins in transcriptional regulation

    Directory of Open Access Journals (Sweden)

    Oyoshi Takanori

    2012-01-01

    Full Text Available Abstract The majority of the noncoding regions of mammalian genomes have been found to be transcribed to generate noncoding RNAs (ncRNAs, resulting in intense interest in their biological roles. During the past decade, numerous ncRNAs and aptamers have been identified as regulators of transcription. 6S RNA, first described as a ncRNA in E. coli, mimics an open promoter structure, which has a large bulge with two hairpin/stalk structures that regulate transcription through interactions with RNA polymerase. B2 RNA, which has stem-loops and unstructured single-stranded regions, represses transcription of mRNA in response to various stresses, including heat shock in mouse cells. The interaction of TLS (translocated in liposarcoma with CBP/p300 was induced by ncRNAs that bind to TLS, and this in turn results in inhibition of CBP/p300 histone acetyltransferase (HAT activity in human cells. Transcription regulator EWS (Ewing's sarcoma, which is highly related to TLS, and TLS specifically bind to G-quadruplex structures in vitro. The carboxy terminus containing the Arg-Gly-Gly (RGG repeat domains in these proteins are necessary for cis-repression of transcription activation and HAT activity by the N-terminal glutamine-rich domain. Especially, the RGG domain in the carboxy terminus of EWS is important for the G-quadruplex specific binding. Together, these data suggest that functions of EWS and TLS are modulated by specific structures of ncRNAs.

  13. On infrared spectroscopic analysis of transfer RNA secondary structure

    Energy Technology Data Exchange (ETDEWEB)

    Semenov, M A; Starikov, E B

    1987-07-14

    Various techniques of IR spectroscopy in the 1550-1750 cm/sup -1/ region employed to analyse the tRNA secondary structure are discussed and a novel improved method is proposed. The main novel features of this method are the approximation of tRNA helical region spectra by catalogue carbonyl absorption bands and approximation of tRNA nonhelical region spectra by those of homopolyribonucleotides. The IR spectra of tRNA/sub yeast//sup phe/ and tRNA/sub E.coli//sup fmet/ in the carbonyl vibration region are explained on the basis of calculated transition moment coupling.

  14. RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

    Science.gov (United States)

    Kanamori, Hiroshi; Yuhashi, Kazuhito; Ohnishi, Shin; Koike, Kazuhiko; Kodama, Tatsuhiko

    2010-05-01

    The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important cis-acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem-loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. In vitro RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem-loop structure of the negative strand in the replication process.

  15. IDENTIFICATION OF SOME CARCINOGENIC POLYCYCLIC AROMATIC HYDROCARBONS IN BANGLADESHI VEHICLES EXHAUST TAR BY GAS CHROMATOGRAPHY-MASS SPECTROPHOTOMETER

    Directory of Open Access Journals (Sweden)

    M. Amzad Hossain

    2010-06-01

    Full Text Available A more sensitive GC-MS method has been established for the determination of some carcinogenic polycyclic aromatic hydrocarbons (PAHs in vehicles exhaust tar samples. The tar samples were extracted using dichloromethane (DMC: n-hexane solvent mixture. A multi-layer clean-up (silica gel/sodium sulphate column was used, followed by glass fiber filter (GFF paper. The method was successfully applied to determine a number of PAHs present in exhaust tar sample of different vehicles of the Atomic Energy Centre, Dhaka, Bangladesh.   Keywords: Carcinogenic polycyclic aromatic hydrocarbons, vehicles tar samples, identification, GC-MS/MS

  16. Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

    Science.gov (United States)

    Schlundt, Andreas; Tants, Jan-Niklas; Sattler, Michael

    2017-04-15

    Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain

  17. Coal-tar based pavement sealant toxicity to freshwater macroinvertebrates.

    Science.gov (United States)

    Bryer, Pamela J; Scoggins, Mateo; McClintock, Nancy L

    2010-05-01

    Non-point-source pollution is a major source of ecological impairment in urban stream systems. Recent work suggests that coal-tar pavement sealants, used extensively to protect parking areas, may be contributing a large portion of the polycyclic aromatic hydrocarbon (PAH) loading seen in urban stream sediments. The hypothesis that dried coal-tar pavement sealant flake could alter the macroinvertebrate communities native to streams in Austin, TX was tested using a controlled outdoor laboratory type approach. The treatment groups were: control, low, medium, and high with total PAH concentrations (TPAH = sum of 16 EPA priority pollutant PAHs) of 0.1, 7.5, 18.4, & 300 mg/kg respectively. The low, medium, and high treatments were created via the addition of dried coal-tar pavement sealant to a sterile soil. At the start of the 24-day exposure, sediment from a minimally impacted local reference site containing a community of live sediment-dwelling benthic macroinvertebrates was added to each replicate. An exposure-dependent response was found for several stream health measures and for several individual taxa. There were community differences in abundance (P = 0.0004) and richness (P pavement sealants contain bioavailable PAHs that may harm aquatic environments. Copyright 2009 Elsevier Ltd. All rights reserved.

  18. Solvent extraction of Southern US tar sands

    Energy Technology Data Exchange (ETDEWEB)

    Penney, W.R.

    1990-01-01

    The Department of Chemical Engineering at the University of Arkansas, in association with Diversified Petroleum Recovery, Inc. (DPR) of Little Rock, Arkansas, has been developing a solvent extraction process for the recovery of bitumen from tar sands for the past five years. The unique feature of the process is that the bitumen is recovered from the solvent by contacting with a co-solvent, which causes the bitumen to precipitate. The overall purpose of this project is to study both the technical and economic feasibility of applying this technology for recovery of bitumen from tar sands by (1) investigating the socioeconmic factors which affect (a) plant siting and (b) the market value of recovered bitumen; (2) operating a process demonstration unit at the rate of 1 lb/hr recovered bitumen while producing clean sand and recyclable solvents; and (3) determine the economic conditions which will make a bitumen recovery project economical. DPR has analyzed the historical trends of domestic production, consumption, discoveries and reserves of crude oil. They have started an investigation of the volatility in the price of crude oil and of gasoline prices and of the differential between gasoline and crude oil. DPR continues to analyze the geographical movement and demand for asphalt products. Utah does not appear economically attractive as a site for a bitumen from tar sands asphalt plant. Oklahoma sites are now being studied. This report also contains the quarterly progress report from a University of Nevada study to determine bitumen composition, oxygen uptake rates, and viscosities of Alabama and Utah bitumens. Both reports have been indexed separately for inclusion on the data base.

  19. Pelagic tar, dissolved/dispersed petroleum hydrocarbons and plastic distribution in the Cretan Sea, Greece

    Energy Technology Data Exchange (ETDEWEB)

    Kornilios, S.; Drakopoulos, P.G.; Dounas, C. [Institute of Marine Biology of Crete, Iraklio (Greece). Environmental Dept.

    1998-12-01

    During the first cruise of R/V `Philia` in July 1997 within the framework of the TALOS programme supported by the Greek Ministry of Physical Planning and Public Works, the sampling of floating tar, litter and sea water for dissolved/dispersed petroleum hydrocarbons (DDPH) was carried out in the Cretan Sea. Analysis of these data has allowed a first assessment of the status of floating marine pollution in the region. DDPH measurements showed a mean concentration of 0.145 {mu}g/l of chrysene equivalents (n = 24). Tar and plastics concentrations were in the range of 1-4280 and 0-1160 {mu}g/m{sup 2}, respectively. Mean pelagic tar concentration was 318 {mu}g/m{sup 2}, more than two times higher than what was reported for the area in previous studies. Based on in situ hydrographic observations there is strong evidence that most of the floating tar enters the Cretan Sea through the Ionian Sea. (author)

  20. Pelagic tar, dissolved/dispersed petroleum hydrocarbons and plastic distribution in the Cretan Sea, Greece

    Energy Technology Data Exchange (ETDEWEB)

    Kornilios, S.; Drakopoulos, P.G.; Dounas, C. [Institute of Marine Biology of Crete, Iraklio (Greece). Environmental Dept.

    1998-12-01

    During the first cruise of R/V 'Philia' in July 1997 within the framework of the TALOS programme supported by the Greek Ministry of Physical Planning and Public Works, the sampling of floating tar, litter and sea water for dissolved/dispersed petroleum hydrocarbons (DDPH) was carried out in the Cretan Sea. Analysis of these data has allowed a first assessment of the status of floating marine pollution in the region. DDPH measurements showed a mean concentration of 0.145 {mu}g/l of chrysene equivalents (n = 24). Tar and plastics concentrations were in the range of 1-4280 and 0-1160 {mu}g/m{sup 2}, respectively. Mean pelagic tar concentration was 318 {mu}g/m{sup 2}, more than two times higher than what was reported for the area in previous studies. Based on in situ hydrographic observations there is strong evidence that most of the floating tar enters the Cretan Sea through the Ionian Sea. (author)

  1. Pelagic tar, dissolved/dispersed petroleum hydrocarbons and plastic distribution in the Cretan Sea, Greece

    International Nuclear Information System (INIS)

    Kornilios, S.; Drakopoulos, P.G.; Dounas, C.

    1998-01-01

    During the first cruise of R/V 'Philia' in July 1997 within the framework of the TALOS programme supported by the Greek Ministry of Physical Planning and Public Works, the sampling of floating tar, litter and sea water for dissolved/dispersed petroleum hydrocarbons (DDPH) was carried out in the Cretan Sea. Analysis of these data has allowed a first assessment of the status of floating marine pollution in the region. DDPH measurements showed a mean concentration of 0.145 μg/l of chrysene equivalents (n = 24). Tar and plastics concentrations were in the range of 1-4280 and 0-1160 μg/m 2 , respectively. Mean pelagic tar concentration was 318 μg/m 2 , more than two times higher than what was reported for the area in previous studies. Based on in situ hydrographic observations there is strong evidence that most of the floating tar enters the Cretan Sea through the Ionian Sea. (author)

  2. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

    Science.gov (United States)

    Shi, Jieming; Li, Xi; Dong, Min; Graham, Mitchell; Yadav, Nehul; Liang, Chun

    2017-01-01

    Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.

  3. JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

    Science.gov (United States)

    Dong, Min; Graham, Mitchell; Yadav, Nehul

    2017-01-01

    Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

  4. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    Jieming Shi

    Full Text Available Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.

  5. 77 FR 48431 - Safety Zone for Fireworks Display, Pamlico and Tar Rivers; Washington, NC

    Science.gov (United States)

    2012-08-14

    ... near the Pamlico and Tar Rivers to commemorate Beaufort County's 300th anniversary. The temporary... 1625-AA00 Safety Zone for Fireworks Display, Pamlico and Tar Rivers; Washington, NC AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone on...

  6. The extraction of bitumen from western tar sands. Annual report, July 1990--July 1991

    Energy Technology Data Exchange (ETDEWEB)

    Oblad, A.G.; Bunger, J.W.; Deo, M.D.; Hanson, F.V.; Miller, J.D.; Seader, J.D.

    1992-04-01

    Contents of this report include the following: executive summary; characterization of the native bitumen from the Whiterocks oil sand deposit; influence of carboxylic acid content on bitumen viscosity; water based oil sand separation technology; extraction of bitumen from western oil sands by an energy-efficient thermal method; large- diameter fluidized bed reactor studies; rotary kiln pyrolysis of oil sand; catalytic upgrading of bitumen and bitumen derived liquids; ebullieted bed hydrotreating and hydrocracking; super critical fluid extraction; bitumen upgrading; 232 references; Appendix A--Whiterocks tar sand deposit bibliography; Appendix B--Asphalt Ridge tar sand deposit bibliography; and Appendix C--University of Utah tar sands bibliography.

  7. Selected constituents in the smokes of U. S. commercial cigaretts: tar, nicotine, carbon monoxide and carbon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Jenkins, R.A.; Quincy, R.B.; Guerin, M.R.

    1979-05-01

    One hundred twenty-one brands of United States commercial cigarettes were analyzed for their deliveries of tar, nicotine, carbon monoxide, and carbon dioxide under standard analytical smoking conditions. The sample included both filter and nonfilter cigarettes. Comparisons of carbon monoxide deliveries over the range of observed tar deliveries indicated a very high correlation between CO and tar for filter cigarettes, but nonfilter cigarettes tended to produce much less CO than would have been predicted from their tar deliveries. Comparison of ORNL nicotine values for specific brands with those determined by the Federal Trade Commission yield no statistically significant differences between laboratories. 4 figures, 6 tables.

  8. Some studies on tar pillets at Veraval coast (Gujarat)

    Digital Repository Service at National Institute of Oceanography (India)

    Kadam, A.N.

    Infrared spectroscopic (IR) analysis indicated that the tar pillets contain saturated hydrocarbons particularly higher homologues of n-paraffins, unsaturated and carbonyl type of polar compounds. Gas chromatographic (GLC) fingerprint pattern...

  9. Hydrogen production from biomass tar by catalytic steam reforming

    International Nuclear Information System (INIS)

    Yoon, Sang Jun; Choi, Young-Chan; Lee, Jae-Goo

    2010-01-01

    The catalytic steam reforming of model biomass tar, toluene being a major component, was performed at various conditions of temperature, steam injection rate, catalyst size, and space time. Two kinds of nickel-based commercial catalyst, the Katalco 46-3Q and the Katalco 46-6Q, were evaluated and compared with dolomite catalyst. Production of hydrogen generally increased with reaction temperature, steam injection rate and space time and decreased with catalyst size. In particular, zirconia-promoted nickel-based catalyst, Katalco 46-6Q, showed a higher tar conversion efficiency and shows 100% conversion even relatively lower temperature conditions of 600 deg. C. Apparent activation energy was estimated to 94 and 57 kJ/mol for dolomite and nickel-based catalyst respectively.

  10. Integrating chemical footprinting data into RNA secondary structure prediction.

    Directory of Open Access Journals (Sweden)

    Kourosh Zarringhalam

    Full Text Available Chemical and enzymatic footprinting experiments, such as shape (selective 2'-hydroxyl acylation analyzed by primer extension, yield important information about RNA secondary structure. Indeed, since the [Formula: see text]-hydroxyl is reactive at flexible (loop regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA nucleotides are base-paired. Recently, low error rates in secondary structure prediction have been reported for three RNAs of moderate size, by including base stacking pseudo-energy terms derived from shape data into the computation of minimum free energy secondary structure. Here, we describe a novel method, RNAsc (RNA soft constraints, which includes pseudo-energy terms for each nucleotide position, rather than only for base stacking positions. We prove that RNAsc is self-consistent, in the sense that the nucleotide-specific probabilities of being unpaired in the low energy Boltzmann ensemble always become more closely correlated with the input shape data after application of RNAsc. From this mathematical perspective, the secondary structure predicted by RNAsc should be 'correct', in as much as the shape data is 'correct'. We benchmark RNAsc against the previously mentioned method for eight RNAs, for which both shape data and native structures are known, to find the same accuracy in 7 out of 8 cases, and an improvement of 25% in one case. Furthermore, we present what appears to be the first direct comparison of shape data and in-line probing data, by comparing yeast asp-tRNA shape data from the literature with data from in-line probing experiments we have recently performed. With respect to several criteria, we find that shape data appear to be more robust than in-line probing data, at least in the case of asp-tRNA.

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

    Science.gov (United States)

    Will, Sebastian; Jabbari, Hosna

    2016-01-01

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

  12. Luminescence monitoring of oil or tar contamination for industrial hygiene

    International Nuclear Information System (INIS)

    Gammage, R.B.; Vo-Dinh, T.

    1980-01-01

    Synfuel plants produce potentially carcinogenic oils and tars. Exposure of workers to these tars and oils is difficult to avoid completely and occurs via direct contact with dirty surfaces or condensation of escaped fumes onto or within the body. Surface skin, measurements are made directly with a near-ultraviolet luminoscope employing a fiber optics lightguide and a stethoscopic cap pressed against the skin. This instrument is especially suitable for measuring ng to μg/cm 2 amounts of residual contamination remaining on the surface of the skin after washing. To minimize the potential for carcinogenicity, the excitating ultraviolet light intensity is only 1/100th that of sunlight. (orig.)

  13. Heavy crude and tar sands - the long-term oil reserve

    Energy Technology Data Exchange (ETDEWEB)

    Barnea, J

    1984-10-01

    It appears that heavy crude and tar sands occur in many sedimentary areas, and estimates of known world-wide quantities exceed those known for conventional light crude resources. Although there are not precise figures available, production could be as high as three million barrels per day, with Venezuela, the US, and Canada the largest producers. There are different scales to measure the costs of production because of differences in the quality of various types of heavy crude and tar sands. Economic development of these resources should banish fears of oil scarcity in the foreseeable future. A center for information exchange through international meetings and publications is under development.

  14. Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

    Science.gov (United States)

    Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

    2005-01-01

    Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

  15. Effects of electric current upon catalytic steam reforming of biomass gasification tar model compounds to syngas

    International Nuclear Information System (INIS)

    Tao, Jun; Lu, Qiang; Dong, Changqing; Du, Xiaoze; Dahlquist, Erik

    2015-01-01

    Highlights: • ECR technique was proposed to convert biomass gasification tar model compounds. • Electric current enhanced the reforming efficiency remarkably. • The highest toluene conversion reached 99.9%. • Ni–CeO 2 /γ-Al 2 O 3 exhibited good stability during the ECR performance. - Abstract: Electrochemical catalytic reforming (ECR) technique, known as electric current enhanced catalytic reforming technique, was proposed to convert the biomass gasification tar into syngas. In this study, Ni–CeO 2 /γ-Al 2 O 3 catalyst was prepared, and toluene was employed as the major feedstock for ECR experiments using a fixed-bed lab-scale setup where thermal electrons could be generated and provided to the catalyst. Several factors, including the electric current intensity, reaction temperature and steam/carbon (S/C) ratio, were investigated to reveal their effects on the conversion of toluene as well as the composition of the gas products. Moreover, toluene, two other tar model compounds (benzene and 1-methylnaphthalene) and real tar (tar-containing wastewater) were subjected to the long period catalytic stability tests. All the used catalysts were analyzed to determine their carbon contents. The results indicated that the presence of electric current enhanced the catalytic performance remarkably. The toluene conversion reached 99.9% under the electric current of 4 A, catalytic temperature of 800 °C and S/C ratio of 3. Stable conversion performances of benzene, 1-methylnaphthalene and tar-containing wastewater were also observed in the ECR process. H 2 and CO were the major gas products, while CO 2 and CH 4 were the minor ones. Due to the promising capability, the ECR technique deserves further investigation and application for efficient tar conversion

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

    DEFF Research Database (Denmark)

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

    RNA serves a number of functions in the cell: mRNAs are the carriers of information between gene and protein, tRNAs and rRNAs are involved in the synthesis of proteins, whereas a number of additional RNA species are responsible for other functions in the cell. The quality of the different RNAs...... RNAs. We have solved the structures of two nucleases involved in 3'-5' degradation of RNA; the S. pombe Pop2p and the S. cerevisiae Rrp6p. Pop2p is part of the main cytoplasmatic deadenylation complex in yeast, which also contains the nuclease Ccr4p. Deadenylation, where the poly(A)-tail is removed...... specific transcripts. Here, we present the crystal structure of the S. pombe Pop2p protein to 1.4 Å resolution. The high resolution structure provides a clear picture of the active site architecture. Structural alignment of single nucleotides and poly(A)-oligonucleotides from earlier co-crystal structures...

  17. Network Properties of the Ensemble of RNA Structures

    Science.gov (United States)

    Clote, Peter; Bayegan, Amir

    2015-01-01

    We describe the first dynamic programming algorithm that computes the expected degree for the network, or graph G = (V, E) of all secondary structures of a given RNA sequence a = a 1, …, a n. Here, the nodes V correspond to all secondary structures of a, while an edge exists between nodes s, t if the secondary structure t can be obtained from s by adding, removing or shifting a base pair. Since secondary structure kinetics programs implement the Gillespie algorithm, which simulates a random walk on the network of secondary structures, the expected network degree may provide a better understanding of kinetics of RNA folding when allowing defect diffusion, helix zippering, and related conformation transformations. We determine the correlation between expected network degree, contact order, conformational entropy, and expected number of native contacts for a benchmarking dataset of RNAs. Source code is available at http://bioinformatics.bc.edu/clotelab/RNAexpNumNbors. PMID:26488894

  18. Pyrolysis kinetics of phenols from lignite semicoking tar

    Energy Technology Data Exchange (ETDEWEB)

    Platonov, V.V.; Polovetskaya, O.S.; Proskuryakov, V.A.; Shavyrina, O.A. [Leo Tolstoy Tula State Pedag University, Tula (Russian Federation)

    2002-11-01

    The features of pyrolysis of phenols from lignite semicoking tar were studied. The activation energy and order of the reactions of accumulation of methane, hydrogen, carbon monoxide and dioxide, naphthalene and its methyl homologs, phenols, and isomeric cresols and dimethylphenols were determined.

  19. Pyrolysis of aseptic packages (tetrapak) in a laboratory screw type reactor and secondary thermal/catalytic tar decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Haydary, J., E-mail: juma.haydary@stuba.sk [Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava (Slovakia); Susa, D.; Dudáš, J. [Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava (Slovakia)

    2013-05-15

    Highlights: ► Pyrolysis of aseptic packages was carried out in a laboratory flow reactor. ► Distribution of tetrapak into the product yields was obtained. ► Composition of the pyrolysis products was estimated. ► Secondary thermal and catalytic decomposition of tars was studied. ► Two types of catalysts (dolomite and red clay marked AFRC) were used. - Abstract: Pyrolysis of aseptic packages (tetrapak cartons) in a laboratory apparatus using a flow screw type reactor and a secondary catalytic reactor for tar cracking was studied. The pyrolysis experiments were realized at temperatures ranging from 650 °C to 850 °C aimed at maximizing of the amount of the gas product and reducing its tar content. Distribution of tetrapak into the product yields at different conditions was obtained. The presence of H{sub 2}, CO, CH{sub 4}, CO{sub 2} and light hydrocarbons, HCx, in the gas product was observed. The Aluminum foil was easily separated from the solid product. The rest part of char was characterized by proximate and elemental analysis and calorimetric measurements. The total organic carbon in the tar product was estimated by elemental analysis of tars. Two types of catalysts (dolomite and red clay marked AFRC) were used for catalytic thermal tar decomposition. Three series of experiments (without catalyst in a secondary cracking reactor, with dolomite and with AFRC) at temperatures of 650, 700, 750, 800 and 850 °C were carried out. Both types of catalysts have significantly affected the content of tars and other components in pyrolytic gases. The effect of catalyst on the tetrapack distribution into the product yield on the composition of gas and on the total organic carbon in the tar product is presented in this work.

  20. Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

    Science.gov (United States)

    Sloma, Michael F.; Mathews, David H.

    2016-01-01

    RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

  1. Machine-smoking studies of cigarette filter color to estimate tar yield by visual assessment and through the use of a colorimeter.

    Science.gov (United States)

    Morton, Michael J; Williams, David L; Hjorth, Heather B; Smith, Jennifer H

    2010-04-01

    This paper explores using the intensity of the stain on the end of the filter ("filter color") as a vehicle for estimating cigarette tar yield, both by instrument reading of the filter color and by visual comparison to a template. The correlation of machine-measured tar yield to filter color measured with a colorimeter was reasonably strong and was relatively unaffected by different puff volumes or different tobacco moistures. However, the correlation of filter color to machine-measured nicotine yield was affected by the moisture content of the cigarette. Filter color, as measured by a colorimeter, was generally comparable to filter extraction of either nicotine or solanesol in its correlation to machine-smoked tar yields. It was found that the color of the tar stain changes over time. Panelists could generally correctly order the filters from machine-smoked cigarettes by tar yield using the intensity of the tar stain. However, there was considerable variation in the panelist-to-panelist tar yield estimates. The wide person-to-person variation in tar yield estimates, and other factors discussed in the text could severely limit the usefulness and practicality of this approach for visually estimating the tar yield of machine-smoked cigarettes. Copyright 2009 Elsevier Inc. All rights reserved.

  2. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

    Science.gov (United States)

    Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

    2014-01-30

    RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

  3. Fungal cultures of tar bush and creosote bush for production of two phenolic antioxidants (pyrocatechol and gallic acid).

    Science.gov (United States)

    Ventura, J; Gutiérrez-Sanchez, G; Rodríguez-Herrera, R; Aguilar, C N

    2009-01-01

    'Tar bush' and 'creosote bush' were substrates of fungal cultivation for tannase production and gallic acid and pyrocatechol accumulation. Aspergillus niger GH1 grew similarly on both plant materials under solid state culture conditions, reaching maximal levels after 4 d. Fungal strain degraded all tannin content of creosote bush after 4 d of fermentation and >75 % of tar bush after 5 d. Higher level of tannase activity was detected in tar bush fermentation. Biotransformation of tannins to gallic acid was high (93 % in creosote bush and 89 % in tar bush). Pyrocatechol was released poorly. Kinetic parameters of tannin conversion were calculated.

  4. Family physicians and youth tobacco-free education: outcomes of the Colorado Tar Wars program.

    Science.gov (United States)

    Cain, Jeffrey J; Dickinson, W Perry; Fernald, Douglas; Bublitz, Caroline; Dickinson, L Miriam; West, David

    2006-01-01

    Tar Wars is a national school-based tobacco-free education program operated by the American Academy of Family Physicians. The Tar Wars lesson uses an interactive 45-min session taught by volunteer family physicians in 4th- and 5th-grade classrooms and focuses on the short-term image-based consequences of tobacco use. In this study, we evaluated the effectiveness of the Tar Wars program in Colorado with both quantitative and qualitative measures. Students participating in the quantitative evaluation were tested before and after a Tar Wars teaching session using a 14-question test covering the short-term and image-based consequences of tobacco use, cost of smoking, tobacco advertising, and social norms of tobacco use. Qualitative evaluation of the program included guided telephone interviews and focus groups with participating students, teachers, and presenters. Quantitative evaluation showed statistically significant improvement in correct responses for the 14 questions measured with an average increase in correct responses from 8.95 to 10.23. Three areas recommended by the Centers for Disease Control (CDC) for youth tobacco prevention showed greater change in correct responses, including cost of smoking, truth of tobacco advertising, and peer norms of tobacco use. Qualitative evaluation found that the overall message of the session was well received, that previously known tobacco information was reinforced by its presentation in a novel format, and that new information learned included cost of smoking, truth of tobacco advertising, and peer norms of tobacco use. The Tar Wars lesson plan is effective in increasing students' understanding about the short-term consequences of tobacco use, cost of tobacco use, truth of tobacco advertising, and peer norms. Tar Wars meets the CDC guidelines as one component of effective comprehensive youth tobacco prevention.

  5. Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

    Science.gov (United States)

    Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

    2009-08-28

    The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

  6. No Increased Risk of Cancer after Coal Tar Treatment in Patients with Psoriasis or Eczema

    NARCIS (Netherlands)

    Roelofzen, Judith H. J.; Aben, Katja K. H.; Oldenhof, Ursula T. H.; Coenraads, Pieter-Jan; Alkemade, Hans A.; van de Kerkhof, Peter C. M.; van der Valk, Pieter G. M.; Kiemeney, Lambertus A. L. M.

    Coal tar is an effective treatment for psoriasis and eczema, but it contains several carcinogenic compounds. Occupational and animal studies have shown an increased risk of cancer after exposure to coal tar. Many dermatologists have abandoned this treatment for safety reasons, although the risk of

  7. Tar removal from biomass derived fuel gas by pulsed corona discharges: chemical kinetic study II

    NARCIS (Netherlands)

    Nair, S.A.; Yan, K.; Pemen, A.J.M.; Heesch, van E.J.M.; Ptasinski, K.J.; Drinkenburg, A.A.H.

    2005-01-01

    Tar (heavy hydrocarbon or poly aromatic hydrocarbon (PAH)) removal from biomass derived fuel gas is one of the biggest obstacles in its utilization for power generation. We have investigated pulsed corona as a method for tar removal. Our previous experimental results indicate the energy consumption

  8. De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences

    DEFF Research Database (Denmark)

    Ruzzo, Walter L; Gorodkin, Jan

    2014-01-01

    De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphas...... on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.......De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis...

  9. Abating coal tar seepage into surface water bodies using sheet piles with sealed interlocks

    International Nuclear Information System (INIS)

    Collingwood, B.I.; Boscardin, M.D.; Murdock, R.F.

    1995-01-01

    A former coal tar processing facility processed crude coal tar supplied from manufactured gas plants in the area. Coal-tar-contaminated ground water from the site was observed seeping through an existing timber bulkhead along a tidal river and producing a multicolored sheen on the surface of the river. As part of a short-term measure to abate the seepage into the river, 64-m long anchored sheet pile wall with sheet pile wing walls at each end was constructed inland of the of the timber bulkhead. The sheet piles extended to low-permeability soils at depth and the interlocks of the sheet piles were provided with polyurethane rubber seals. Based on postconstruction observations for leakage and sheens related to leakage, the steel sheet piles with polyurethane rubber interlock seals appeared to provide a successful seal and abate coal-tar-contaminated ground water seepage into the river. The tie rod penetration sealing proved to be a more problematic detail, but through several postconstruction grouting episodes, an effective seal was produced

  10. Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.

    Science.gov (United States)

    Roubelakis, Maria G; Zotos, Pantelis; Papachristoudis, Georgios; Michalopoulos, Ioannis; Pappa, Kalliopi I; Anagnou, Nicholas P; Kossida, Sophia

    2009-06-16

    microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation. Predicting or verifying mRNA targets of specific miRNAs is a difficult process of great importance. GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology (GO), in order to extract the main attributes of sets of proteins. GOmir represents a new tool incorporating two separate Java applications integrated into one stand-alone Java application. GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering. Additionally, a reverse search initiated by a potential target can also be conducted. GOmir can freely be downloaded BRFAA.

  11. {sup 13}C relaxation in an RNA hairpin

    Energy Technology Data Exchange (ETDEWEB)

    King, G.C. [Univ. of South Wales, Kensington (Australia)]|[Rice Univ., Houston, TX (United States); Akratos, C. [Univ. of South Wales, Kensington (Australia); Xi, Z.; Michnica, M.J. [Rice Univ., Houston, TX (United States)

    1994-12-01

    This initial survey of {sup 13}C relaxation in the {triangle}TAR RNA element has generated a number of interesting results that should prove generally useful for future studies. The most readily comparable study in the literature monitored {sup 13}C relaxation of the methyl groups from unusual bases in tRNA{sup Phe}. The study, which used T{sub 1} and NOE data only, reported order parameters for the methyl group axis that ranged between 0.51 and 0.97-a range similar to that observed here. However, they reported a breakdown of the standard order parameter analysis at higher (118-MHz {sup 13}C) frequencies, which should serve to emphasize the need for a thorough exploration of suitable motional models.

  12. Coliquefaction of coal, tar sand bitumen and plastic (interaction among coal, bitumen and plastic); Sekitan/tar sand bitumen/plastic no kyoekika ni okeru kyozon busshitsu no eikyo

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, H.; Okuyama, Y.; Matsubara, K. [NKK Corp., Tokyo (Japan); Kamo, T.; Sato, Y. [National Institute for Resources and Environment, Tsukuba (Japan)

    1996-10-28

    For the improvement of economy, coliquefaction of coal, tar sand bitumen and plastic was performed under low hydrogen pressure, to investigate the influence of interaction among these on the liquefaction characteristics. For comparison, coliquefaction was also performed under the hydrogen pressure same as the NEDOL process. In addition, for clarifying its reaction mechanism, coliquefaction of dibenzyl and plastic was performed as a model experiment, to illustrate the distribution of products and composition of oil, and to discuss the interaction between dibenzyl and various plastics, and between various plastics. Under direct coal liquefaction conditions, coprocessing of Tanito Harum coal, Athabasca tar sand and plastic was carried out under low hydrogen pressure with an autoclave. The observed value of oil yield was higher than the calculated value based on the values from separate liquefaction of coal and plastic, which suggested the interaction between coal and the mixed plastic. The results of coliquefaction of coal, tar sand bitumen and plastic could be explained from the obtained oil yield and its composition by the coliquefaction of dibenzyl and plastic. 2 refs., 3 tabs.

  13. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

    Science.gov (United States)

    Al-Khatib, Ra'ed M; Rashid, Nur'Aini Abdul; Abdullah, Rosni

    2011-08-01

    The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

  14. Unzippers, Resolvers and Sensors: A Structural and Functional Biochemistry Tale of RNA Helicases

    Directory of Open Access Journals (Sweden)

    Ana Lúcia Leitão

    2015-01-01

    Full Text Available The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.

  15. Numerical simulation of vortex pyrolysis reactors for condensable tar production from biomass

    Energy Technology Data Exchange (ETDEWEB)

    Miller, R.S.; Bellan, J. [California Inst. of Tech., Pasadena, CA (United States). Jet Propulsion Lab.

    1998-08-01

    A numerical study is performed in order to evaluate the performance and optimal operating conditions of vortex pyrolysis reactors used for condensable tar production from biomass. A detailed mathematical model of porous biomass particle pyrolysis is coupled with a compressible Reynolds stress transport model for the turbulent reactor swirling flow. An initial evaluation of particle dimensionality effects is made through comparisons of single- (1D) and multi-dimensional particle simulations and reveals that the 1D particle model results in conservative estimates for total pyrolysis conversion times and tar collection. The observed deviations are due predominantly to geometry effects while directional effects from thermal conductivity and permeability variations are relatively small. Rapid ablative particle heating rates are attributed to a mechanical fragmentation of the biomass particles that is modeled using a critical porosity for matrix breakup. Optimal thermal conditions for tar production are observed for 900 K. Effects of biomass identity, particle size distribution, and reactor geometry and scale are discussed.

  16. Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).

    Science.gov (United States)

    Watters, Kyle E; Lucks, Julius B

    2016-01-01

    Mapping RNA structure with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry has proven to be a versatile method for characterizing RNA structure in a variety of contexts. SHAPE reagents covalently modify RNAs in a structure-dependent manner to create adducts at the 2'-OH group of the ribose backbone at nucleotides that are structurally flexible. The positions of these adducts are detected using reverse transcriptase (RT) primer extension, which stops one nucleotide before the modification, to create a pool of cDNAs whose lengths reflect the location of SHAPE modification. Quantification of the cDNA pools is used to estimate the "reactivity" of each nucleotide in an RNA molecule to the SHAPE reagent. High reactivities indicate nucleotides that are structurally flexible, while low reactivities indicate nucleotides that are inflexible. These SHAPE reactivities can then be used to infer RNA structures by restraining RNA structure prediction algorithms. Here, we provide a state-of-the-art protocol describing how to perform in vitro RNA structure probing with SHAPE chemistry using next-generation sequencing to quantify cDNA pools and estimate reactivities (SHAPE-Seq). The use of next-generation sequencing allows for higher throughput, more consistent data analysis, and multiplexing capabilities. The technique described herein, SHAPE-Seq v2.0, uses a universal reverse transcription priming site that is ligated to the RNA after SHAPE modification. The introduced priming site allows for the structural analysis of an RNA independent of its sequence.

  17. Analysis of the use of coal tar as a binder in bituminous mixtures, using Marshall and Ramcodes methodologies

    International Nuclear Information System (INIS)

    Ochoa-Díaz, R

    2013-01-01

    This paper presents an alternative use of coal tar, a by-product of the steel industry, given the problems of accumulation and negative environmental impact. Therefore, it is necessary to analyze the incorporation of coal tar as a binder in paving mixtures. First, this paper presents the origin, description of the main characteristics, and properties of tar. Then, this paper evaluates the mix of coal tar by means of the RAMCODES and Marshall methodologies to determine its resistance. The results of the tests explain the physical and mechanical properties of the mix. Taking into account the results of both methods, this paper makes a comparison to determine the suitability of the RAMCODES methodology in the mix design. Finally, it analyzes the alternatives to coal tar that can be used as binders in bituminous mixes for pavement and the advantages of their uses under some specific conditions

  18. Quantitative analysis of phenol and alkylphenols in Brazilian coal tar

    Directory of Open Access Journals (Sweden)

    Elina Bastos Caramão

    2004-04-01

    Full Text Available The main purpose of this work is the identification and quantification of phenolic compounds in coal tar samples from a ceramics factory in Cocal (SC, Brazil. The samples were subjected to preparative scale liquid chromatography, using Amberlyst A-27TM ion-exchange resin as stationary phase. The fractions obtained were classified as "acids" and "BN" (bases and neutrals. The identification and quantification of phenols, in the acid fraction, was made by gas chromatography coupled to mass spectrometry (GC/MS. Nearly twenty-five phenols were identified in the samples and nine of them were also quantified. The results showed that coal tar has large quantities of phenolic compounds of industrial interest.

  19. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Weinberg Zasha

    2011-01-01

    Full Text Available Abstract Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

  20. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

    Science.gov (United States)

    2011-01-01

    Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

  1. R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

    Science.gov (United States)

    Weinberg, Zasha; Breaker, Ronald R

    2011-01-04

    With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

  2. Understanding the fate and transport of petroleum hydrocarbons from coal tar within gasholders.

    Science.gov (United States)

    Coulon, Frédéric; Orsi, Roberto; Turner, Claire; Walton, Chris; Daly, Paddy; Pollard, Simon J T

    2009-02-01

    Coal tars have been identified as posing a threat to human health due to their toxic, mutagenic and carcinogenic characteristics. Workers involved in former gasholders decommissioning are potentially exposed to relevant concentrations of volatile and semi-volatile hydrocarbons upon opening up derelict tanks and during tar excavation/removal. While information on contaminated sites air-quality and its implications on medium-long term exposure is available, acute exposure issues associated with the execution of critical tasks are less understood. Calculations indicated that the concentration of a given contaminant in the gasholder vapour phase only depends on the coal tar composition, being only barely affected by the presence of water in the gasholder and the tar volume/void space ratio. Fugacity modelling suggested that risk-critical compounds such as benzene, naphthalene and other monocyclic and polycyclic aromatic hydrocarbons may gather in the gasholder air phase at significant concentrations. Gasholder emissions were measured on-site and compared with the workplace exposure limits (WELs) currently in use in UK. While levels for most of the toxic compounds were far lower than WELs, benzene air-concentrations where found to be above the accepted threshold. In addition due to the long exposure periods involved in gasholder decommissioning and the significant contribution given by naphthalene to the total coal tar vapour concentration, the adoption of a WEL for naphthalene may need to be considered to support operators in preventing human health risk at the workplace. The Level I fugacity approach used in this study demonstrated its suitability for applications to sealed environments such as gasholders and its further refining could provide a useful tool for land remediation risk assessors.

  3. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

    Science.gov (United States)

    Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O'Connor, Mary; Shapiro, Bruce A

    2008-10-01

    One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes.

  4. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler☆

    Science.gov (United States)

    Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O’Connor, Mary; Shapiro, Bruce A.

    2013-01-01

    One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes. PMID:18838281

  5. Preparation, Characterization, and Activation of Co-Mo/Y Zeolite Catalyst for Coal Tar Conversion to Liquid Fuel

    Directory of Open Access Journals (Sweden)

    Didi Dwi Anggoro

    2017-05-01

    Full Text Available One of many efforts to convert coal tar into alternative liquid fuel is by hydrocracking. This research aims to determine the impregnation of Co-Mo/Y zeolite, its characteristics, the effect of impregnation temperature and time, and also the best Co-Mo/Y zeolite impregnation condition for the conversion of coal tar. This research was conducted in several steps, impregnating Co from Co(NO32.6H2O and Mo from (NH46Mo7O24.4H2O into Zeolite Y in liquid media, drying at 100 °C for 24 hours, and calcination at 550 °C for 3 hours. Coal tar was then reacted with hydrogen gas (as a reactant, and Co-Mo/Zeolite Y (as a catalyst was conducted at 350 °C. Characteristic analysis showed that Co and Mo had impregnated into the Y zeolite, as well as it made no change of catalyst’s structure and increased the total acidity. The higher of impregnation temperature was increased the catalyst crystallinity, total acidity, and yield of gasoline. The longer impregnation time was reduced crystallinity value, but total acidity and yield were increased. GC analysis showed that products included into the gasoline product (C8, C9, and C10. Copyright © 2017 BCREC Group. All rights reserved Received: 13rd November 2016; Revised: 12nd February 2017; Accepted: 16th February 2017 How to Cite: Anggoro, D.D., Buchori, L., Silaen, G.C., Utami, R.N. (2017. Preparation, Characterization, and Activation of Co-Mo/Y Zeolite Catalyst for Coal Tar Conversion to Liquid Fuel. Bulletin of Chemical Reaction Engineering & Catalysis, 12 (2: 219-226 (doi:10.9767/bcrec.12.2.768.219-226 Permalink/DOI: http://dx.doi.org/10.9767/bcrec.12.2.768.219-226

  6. Source identification of a tar residue from Mumbai Beach

    Digital Repository Service at National Institute of Oceanography (India)

    Kadam, A; Rokade, M.A

    A tar residue from Mumbai Beach, Maharashtra, India was matched with the suspected source sample from a tanker using UV, IR and GLC techniques. Negligible differences in several ratios of UV absorbances and ratios of infrared transmittances...

  7. Bi-objective integer programming for RNA secondary structure prediction with pseudoknots.

    Science.gov (United States)

    Legendre, Audrey; Angel, Eric; Tahi, Fariza

    2018-01-15

    RNA structure prediction is an important field in bioinformatics, and numerous methods and tools have been proposed. Pseudoknots are specific motifs of RNA secondary structures that are difficult to predict. Almost all existing methods are based on a single model and return one solution, often missing the real structure. An alternative approach would be to combine different models and return a (small) set of solutions, maximizing its quality and diversity in order to increase the probability that it contains the real structure. We propose here an original method for predicting RNA secondary structures with pseudoknots, based on integer programming. We developed a generic bi-objective integer programming algorithm allowing to return optimal and sub-optimal solutions optimizing simultaneously two models. This algorithm was then applied to the combination of two known models of RNA secondary structure prediction, namely MEA and MFE. The resulting tool, called BiokoP, is compared with the other methods in the literature. The results show that the best solution (structure with the highest F 1 -score) is, in most cases, given by BiokoP. Moreover, the results of BiokoP are homogeneous, regardless of the pseudoknot type or the presence or not of pseudoknots. Indeed, the F 1 -scores are always higher than 70% for any number of solutions returned. The results obtained by BiokoP show that combining the MEA and the MFE models, as well as returning several optimal and several sub-optimal solutions, allow to improve the prediction of secondary structures. One perspective of our work is to combine better mono-criterion models, in particular to combine a model based on the comparative approach with the MEA and the MFE models. This leads to develop in the future a new multi-objective algorithm to combine more than two models. BiokoP is available on the EvryRNA platform: https://EvryRNA.ibisc.univ-evry.fr .

  8. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them.

    Science.gov (United States)

    Leppek, Kathrin; Das, Rhiju; Barna, Maria

    2018-03-01

    RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.

  9. Anomalous capillary flow of coal tar pitches

    Energy Technology Data Exchange (ETDEWEB)

    Saint Romain, J.L.; Lahaye, J.; Ehrburger, P.; Couderc, P.

    1986-06-01

    Capillary flow of liquid coal tar pitch into a coke bed was studied. Anomalies in the flow could not be attributed to a plugging effect for mesophase content lower than 20 wt%. The flow behaviour of small pitch droplets can be correlated with the change in physicochemical properties, as measured by the glass transition temperature, on penetration into the coke bed. 4 references.

  10. Comparative structural analysis of human DEAD-box RNA helicases.

    Science.gov (United States)

    Schütz, Patrick; Karlberg, Tobias; van den Berg, Susanne; Collins, Ruairi; Lehtiö, Lari; Högbom, Martin; Holmberg-Schiavone, Lovisa; Tempel, Wolfram; Park, Hee-Won; Hammarström, Martin; Moche, Martin; Thorsell, Ann-Gerd; Schüler, Herwig

    2010-09-30

    DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

  11. Comparative structural analysis of human DEAD-box RNA helicases.

    Directory of Open Access Journals (Sweden)

    Patrick Schütz

    2010-09-01

    Full Text Available DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

  12. An evolutionary model for protein-coding regions with conserved RNA structure

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Forsberg, Roald; Meyer, Irmtraud Margret

    2004-01-01

    in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagious" context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume...... components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses......Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair...

  13. Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

    Directory of Open Access Journals (Sweden)

    Oleg M Ganichkin

    Full Text Available Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec.We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

  14. Biogeochemical gradients above a coal tar DNAPL

    Energy Technology Data Exchange (ETDEWEB)

    Scherr, Kerstin E., E-mail: kerstin.brandstaetter-scherr@boku.ac.at [University of Natural Resources and Life Sciences Vienna (BOKU), Department IFA-Tulln, Institute for Environmental Biotechnology, Konrad Lorenz Strasse 20, 3430 Tulln (Austria); Backes, Diana [University of Natural Resources and Life Sciences Vienna (BOKU), Department IFA-Tulln, Institute for Environmental Biotechnology, Konrad Lorenz Strasse 20, 3430 Tulln (Austria); Scarlett, Alan G. [University of Plymouth, Petroleum and Environmental Geochemistry Group, Biogeochemistry Research Centre, Drake Circus, Plymouth, Devon PL4 8AA (United Kingdom); Lantschbauer, Wolfgang [Government of Upper Austria, Directorate for Environment and Water Management, Division for Environmental Protection, Kärntner Strasse 10-12, 4021 Linz (Austria); Nahold, Manfred [GUT Gruppe Umwelt und Technik GmbH, Ingenieurbüro für Technischen Umweltschutz, Plesching 15, 4040 Linz (Austria)

    2016-09-01

    Naturally occurring distribution and attenuation processes can keep hydrocarbon emissions from dense non aqueous phase liquids (DNAPL) into the adjacent groundwater at a minimum. In a historically coal tar DNAPL-impacted site, the de facto absence of a plume sparked investigations regarding the character of natural attenuation and DNAPL resolubilization processes at the site. Steep vertical gradients of polycyclic aromatic hydrocarbons, microbial community composition, secondary water quality and redox-parameters were found to occur between the DNAPL-proximal and shallow waters. While methanogenic and mixed-electron acceptor conditions prevailed close to the DNAPL, aerobic conditions and very low dissolved contaminant concentrations were identified in three meters vertical distance from the phase. Comprehensive two-dimensional gas chromatography–mass spectrometry (GC × GC–MS) proved to be an efficient tool to characterize the behavior of the present complex contaminant mixture. Medium to low bioavailability of ferric iron and manganese oxides of aquifer samples was detected via incubation with Shewanella alga and evidence for iron and manganese reduction was collected. In contrast, 16S rDNA phylogenetic analysis revealed the absence of common iron reducing bacteria. Aerobic hydrocarbon degraders were abundant in shallow horizons, while nitrate reducers were dominating in deeper aquifer regions, in addition to a low relative abundance of methanogenic archaea. Partial Least Squares – Canonical Correspondence Analysis (PLS-CCA) suggested that nitrate and oxygen concentrations had the greatest impact on aquifer community structure in on- and offsite wells, which had a similarly high biodiversity (H’ and Chao1). Overall, slow hydrocarbon dissolution from the DNAPL appears to dominate natural attenuation processes. This site may serve as a model for developing legal and technical strategies for the treatment of DNAPL-impacted sites where contaminant plumes are

  15. Differential accumulation of nif structural gene mRNA in Azotobacter vinelandii.

    Science.gov (United States)

    Hamilton, Trinity L; Jacobson, Marty; Ludwig, Marcus; Boyd, Eric S; Bryant, Donald A; Dean, Dennis R; Peters, John W

    2011-09-01

    Northern analysis was employed to investigate mRNA produced by mutant strains of Azotobacter vinelandii with defined deletions in the nif structural genes and in the intergenic noncoding regions. The results indicate that intergenic RNA secondary structures effect the differential accumulation of transcripts, supporting the high Fe protein-to-MoFe protein ratio required for optimal diazotrophic growth.

  16. A role for nuclear energy in the recovery of oil from the tar sands of Alberta

    International Nuclear Information System (INIS)

    Puttagunta, V.R.; Sochaski, R.O.; Robertson, R.F.S.

    1976-12-01

    Techniques of oil recovery from the tar sands and the energy requirements of this operation are described. Fossil fuels, and CANDU reactors are examined as competitive sources of energy for the tar sands plants. The CANDU-OCR reactor appears to have the necessary flexibility to fit into many of the possible methods of recovering oil from the tar sands. Cost comparisons of fossil and nuclear sources show that, for the supply of process steam, the nuclear source is competitive under the criteria of debt financing or low discount rates on capital, continued escalation, and long plant capital write-off period. (author)

  17. Stochastic sampling of the RNA structural alignment space.

    Science.gov (United States)

    Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

    2009-07-01

    A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

  18. Topological classification and enumeration of RNA structures by genus

    DEFF Research Database (Denmark)

    Andersen, Joergen Ellegard; Penner, Robert C.; Reidys, Christian

    2013-01-01

    To an RNA pseudoknot structure is naturally associated a topological surface, which has its associated genus, and structures can thus be classified by the genus. Based on earlier work of Harer-Zagier, we compute the generating function for the number of those structures of fixed genus and minimum...

  19. Evolution of the RNase P RNA structural domain in Leptospira spp

    NARCIS (Netherlands)

    Ravishankar, Vigneshwaran; Ahmed, Ahmed; Sivagnanam, Ulaganathan; Muthuraman, Krishnaraja; Karthikaichamy, Anbarasu; Wilson, Herald A.; Devendran, Ajay; Hartskeerl, Rudy A.; Raj, Stephen M. L.

    2014-01-01

    We have employed the RNase P RNA (RPR) gene, which is present as single copy in chromosome I of Leptospira spp. to investigate the phylogeny of structural domains present in the RNA subunit of the tRNA processing enzyme, RNase P. RPR gene sequences of 150 strains derived from NCBI database along

  20. Stuck in the tar sands : how the federal government's proposed climate change strategy lets oil companies off the hook

    International Nuclear Information System (INIS)

    2008-10-01

    The credibility of any federal climate change strategy must be measured against its ability to reduce emissions from the tar sands. However, the federal government has proposed a climate change strategy that would allow tar sands producers to double their total emissions over the next decade. This report discussed how the federal government's proposed climate change strategy lets oil companies off the hook. The report discussed the problems and harmful effects associated with tar sands development, including greenhouse gas emissions; water depletion and pollution; toxic air emissions; destruction of the boreal forest; violation of native rights; threat to energy security; and negative socio-economic spin-off from an overheated economy. The federal government's proposed strategy was also assessed in terms of its weak greenhouse gas targets; ignoring the recent growth in tar sands emissions; adopting intensity-based targets instead of hard caps on greenhouse gas pollution, allowing total emissions from the tar sands to keep climbing; putting off critical measures until 2018; awarding oil companies hundreds of millions of dollars in credits for meeting targets they have already adopted voluntarily; lowballing the price of oil and downplaying future growth in tar sands emissions; ignoring huge portions of the oil industry's greenhouse gas pollution; letting oil companies buy their way out at rockbottom prices instead of forcing them to reduce their own emissions; and subsidizing increased tar sands production. It was concluded that the federal government's proposed plan to reduce greenhouse gas emissions was inadequate, because it failed to crack down on rising greenhouse gas emissions from the tar sands, one of Canada's most carbon intensive and fastest growing industries. 29 refs., 1 appendix

  1. Recovery of naphthalene, anthracene, etc. , from tar

    Energy Technology Data Exchange (ETDEWEB)

    1920-12-25

    A process is described for the recovery of naphthalene, anthracene, and the like from tar oils and similar liquors, characterized in that the oil is treated in a rapidly rotating hammer mill, such as a colloid mill, with water sufficient, in the presence or absence of suitable solvents, for the only portion preferably in the presence of emulsifiers; and is filtered through a filter with fine pores.

  2. Lab-scale pyrolysis of the Automotive Shredder Residue light fraction and characterization of tar and solid products.

    Science.gov (United States)

    Anzano, Manuela; Collina, Elena; Piccinelli, Elsa; Lasagni, Marina

    2017-06-01

    The general aim of this study is the recovery of Automotive Shredder Residue (ASR). The ASR light fraction, or car fluff, that was collected at an Italian shredding plant was pyrolysed at various temperatures (500-800°C) in a lab-scale reactor. The condensable gases (tar) and solid residue yields increased with decreasing temperature, and these products were characterized to suggest a potential use to reclaim them. The higher heating value (HHV) of tar was 34-37MJ/kg, which is comparable with those of fossil fuels. Furthermore, the ash content was low (0.06-4.98%). Thus, tar can be used as an alternative fuel. With this prospect, the concentrations of polychlorinated dibenzodioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) in tar were determined. The toxicity of tar changes with temperature (1-5ng I-TEQ/g), and the PCDFs significantly contribute to tar toxicity, which was 75-100% with a maximum of 99.6% at 700°C. Regarding the characterization of the solid residue, the low HHV (2.4-3.3MJ/kg) does not make it suitable for energy recovery. Regarding material recovery, we considered its use as a filler in construction materials or a secondary source for metals. It shows a high metal concentration (280,000-395,000mg/kg), which is similar at different pyrolysis temperatures. At 500°C, polycyclic aromatic hydrocarbons (PAHs) were not detected in the solid residue, whereas the maximum total PAH concentration (19.41ng/g, 700°C) was lower than that in fly ash from MSWI. In conclusion, 500°C is a suitable pyrolysis temperature to obtain valuable tar and solid residue. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Concentrations of polycyclic aromatic hydrocarbons (PAHs) and azaarenes in runoff from coal-tar- and asphalt-sealcoated pavement

    International Nuclear Information System (INIS)

    Mahler, Barbara J.; Van Metre, Peter C.; Foreman, William T.

    2014-01-01

    Coal-tar-based sealcoat, used extensively on parking lots and driveways in North America, is a potent source of PAHs. We investigated how concentrations and assemblages of PAHs and azaarenes in runoff from pavement newly sealed with coal-tar-based (CT) or asphalt-based (AS) sealcoat changed over time. Samples of simulated runoff were collected from pavement 5 h to 111 d following application of AS or CT sealcoat. Concentrations of the sum of 16 PAHs (median concentrations of 328 and 35 μg/L for CT and AS runoff, respectively) in runoff varied relatively little, but rapid decreases in concentrations of azaarenes and low molecular weight PAHs were offset by increases in high molecular weight PAHs. The results demonstrate that runoff from CT-sealcoated pavement, in particular, continues to contain elevated concentrations of PAHs long after a 24-h curing time, with implications for the fate, transport, and ecotoxicological effects of contaminants in runoff from CT-sealcoated pavement. - Highlights: • We compare PAH and azaarene concentrations in runoff from coal-tar- and asphalt-sealed pavement. • Concentrations in coal-tar-sealcoat runoff greatly exceeded those in asphalt-sealcoat runoff. • Decreases in azaarenes and LMW PAHs were offset by increases in HMW PAHs. • PAH concentrations in coal-tar-sealcoat runoff remained high for months after application. - Concentrations of PAHs in runoff from pavement with coal-tar-based sealcoat continue to be elevated for at least 3 months following sealcoat application

  4. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

    Science.gov (United States)

    Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M; Weissman, Jonathan S; Rouskin, Silvi

    2017-01-01

    Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.

  5. Modeling the structure of RNA molecules with small-angle X-ray scattering data.

    Directory of Open Access Journals (Sweden)

    Michal Jan Gajda

    Full Text Available We propose a novel fragment assembly method for low-resolution modeling of RNA and show how it may be used along with small-angle X-ray solution scattering (SAXS data to model low-resolution structures of particles having as many as 12 independent secondary structure elements. We assessed this model-building procedure by using both artificial data on a previously proposed benchmark and publicly available data. With the artificial data, SAXS-guided models show better similarity to native structures than ROSETTA decoys. The publicly available data showed that SAXS-guided models can be used to reinterpret RNA structures previously deposited in the Protein Data Bank. Our approach allows for fast and efficient building of de novo models of RNA using approximate secondary structures that can be readily obtained from existing bioinformatic approaches. We also offer a rigorous assessment of the resolving power of SAXS in the case of small RNA structures, along with a small multimetric benchmark of the proposed method.

  6. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  7. Random generation of RNA secondary structures according to native distributions

    Directory of Open Access Journals (Sweden)

    Nebel Markus E

    2011-10-01

    Full Text Available Abstract Background Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest. Results In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure. Compared to well-known sampling approaches used in several structure prediction tools (such as SFold ours has two major advantages: Firstly, after a preprocessing step in time O(n2 for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity Om⋅n⋅ log(n while other algorithms typically have a runtime in O(m⋅n2. Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with

  8. PAH volatilization following application of coal-tar-based pavement sealant

    Science.gov (United States)

    Van Metre, Peter C.; Majewski, Michael S.; Mahler, Barbara J.; Foreman, William T.; Braun, Christopher L.; Wilson, Jennifer T.; Burbank, Teresa L.

    2012-01-01

    Coal-tar-based pavement sealants, a major source of PAHs to urban water bodies, have recently been identified as a source of volatile PAHs to the atmosphere. We tracked the volatilization of PAHs for 1 year after application of a coal-tar-based pavement sealant by measuring gas-phase PAH concentrations above the pavement surface and solid-phase PAH concentrations in sealant scraped from the surface. Gas-phase concentrations at two heights (0.03 and 1.28 m) and wind speed were used to estimate volatilization flux. The sum of the concentrations of eight frequently detected PAHs (ΣPAH8) in the 0.03-m sample 1.6 h after application (297,000 ng m-3) was about 5000 times greater than that previously reported for the same height above unsealed parking lots (66 ng m-3). Flux at 1.6 h after application was estimated at 45,000 μg m-2 h-1 and decreased rapidly during the 45 days after application to 160 μg m-2 h-1. Loss of PAHs from the adhered sealant also was rapid, with about a 50% decrease in solid-phase ΣPAH8 concentration over the 45 days after application. There was general agreement, given the uncertainties, in the estimated mass of ΣPAH8 lost to the atmosphere on the basis of air sampling (2–3 g m-2) and adhered sealant sampling (6 g m-2) during the first 16 days after application, translating to a loss to the atmosphere of one-quarter to one-half of the PAHs in the sealcoat product. Combining the estimated mass of ΣPAH8 released to the atmosphere with a national-use estimate of coal-tar-based sealant suggests that PAH emissions from new coal-tar-based sealcoat applications each year (~1000 Mg) are larger than annual vehicle emissions of PAHs for the United States.

  9. UPF201 Archaeal Specific Family Members Reveals Structural Similarity to RNA-Binding Proteins but Low Likelihood for RNA-Binding Function

    Energy Technology Data Exchange (ETDEWEB)

    Rao, K.N.; Swaminathan, S.; Burley, S. K.

    2008-12-11

    We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10-40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel {beta}-sheet and five {alpha}-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.

  10. Secondary structure of 5S RNA: NMR experiments on RNA molecules partially labeled with Nitrogen-15

    International Nuclear Information System (INIS)

    Gewirth, D.T.; Abo, S.R.; Leontis, N.B.; Moore, P.B.

    1987-01-01

    A method has been found for reassembling fragment 1 of Escherichia coli 5S RNA from mixtures containing strand III (bases 69-87) and the complex consisting of strand II (bases 89-120) and strand IV (bases 1-11). The reassembled molecule is identical with unreconstituted fragment 1. With this technique, fragment 1 molecules have been constructed 15 N-labeled either in strand III or in the strand II-strand IV complex. Spectroscopic data obtained with these partially labeled molecules show that the terminal helix of 5S RNA includes the GU and GC base pairs at positions 9 and 10 which the standard model for 5S secondary structure predicts but that these base pairs are unstable both in the fragment and in native 5S RNA. The data also assign three resonances to the helix V region of the molecule (bases 70-77 and 99-106). None of these resonances has a normal chemical shift even though two of them correspond to AU or GU base pairs in the standard model. The implications of these findings for the authors understanding of the structure of 5S RNA and its complex with ribosomal protein L25 are discussed

  11. The search for a source rock for the giant Tar Sand triangle accumulation, southeastern Utah

    Science.gov (United States)

    Huntoon, J.E.; Hansley, P.L.; Naeser, N.D.

    1999-01-01

    A large proportion (about 36%) of the world's oil resource is contained in accumulations of heavy oil or tar. In these large deposits of degraded oil, the oil in place represents only a fraction of what was present at the time of accumulation. In many of these deposits, the source of the oil is unknown, and the oil is thought to have migrated over long distances to the reservoirs. The Tar Sand triangle in southeastern Utah contains the largest tar sand accumulation in the United States, with 6.3 billion bbl of heavy oil estimated to be in place. The deposit is thought to have originally contained 13-16 billion bbl prior to the biodegradation, water washing, and erosion that have taken place since the middle - late Tertiary. The source of the oil is unknown. The tar is primarily contained within the Lower Permian White Rim Sandstone, but extends into permeable parts of overlying and underlying beds. Oil is interpreted to have migrated into the White Rim sometime during the Tertiary when the formation was at a depth of approximately 3500 m. This conclusion is based on integration of fluid inclusion analysis, time-temperature reconstruction, and apatite fission-track modeling for the White Rim Sandstone. Homogenization temperatures cluster around 85-90??C for primary fluid inclusions in authigenic, nonferroan dolomite in the White Rim. The fluid inclusions are associated with fluorescent oil-bearing inclusions, indicating that dolomite precipitation was coeval with oil migration. Burial reconstruction suggests that the White Rim Sandstone reached its maximum burial depth from 60 to 24 Ma, and that maximum burial was followed by unroofing from 24 to 0 Ma. Time-temperature modeling indicates that the formation experienced temperatures of 85-90??C from about 35 to 40 Ma during maximum burial. Maximum formation temperatures of about 105-110??C were reached at about 24 Ma, just prior to unroofing. Thermal modeling is used to examine the history of potential source rocks

  12. nRC: non-coding RNA Classifier based on structural features.

    Science.gov (United States)

    Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

    2017-01-01

    Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

  13. Selective small-molecule inhibition of an RNA structural element

    Energy Technology Data Exchange (ETDEWEB)

    Howe, John A.; Wang, Hao; Fischmann, Thierry O.; Balibar, Carl J.; Xiao, Li; Galgoci, Andrew M.; Malinverni, Juliana C.; Mayhood, Todd; Villafania, Artjohn; Nahvi, Ali; Murgolo, Nicholas; Barbieri, Christopher M.; Mann, Paul A.; Carr, Donna; Xia, Ellen; Zuck, Paul; Riley, Dan; Painter, Ronald E.; Walker, Scott S.; Sherborne, Brad; de Jesus, Reynalda; Pan, Weidong; Plotkin, Michael A.; Wu, Jin; Rindgen, Diane; Cummings, John; Garlisi, Charles G.; Zhang, Rumin; Sheth, Payal R.; Gill, Charles J.; Tang, Haifeng; Roemer , Terry (Merck)

    2015-09-30

    Riboswitches are non-coding RNA structures located in messenger RNAs that bind endogenous ligands, such as a specific metabolite or ion, to regulate gene expression. As such, riboswitches serve as a novel, yet largely unexploited, class of emerging drug targets. Demonstrating this potential, however, has proven difficult and is restricted to structurally similar antimetabolites and semi-synthetic analogues of their cognate ligand, thus greatly restricting the chemical space and selectivity sought for such inhibitors. Here we report the discovery and characterization of ribocil, a highly selective chemical modulator of bacterial riboflavin riboswitches, which was identified in a phenotypic screen and acts as a structurally distinct synthetic mimic of the natural ligand, flavin mononucleotide, to repress riboswitch-mediated ribB gene expression and inhibit bacterial cell growth. Our findings indicate that non-coding RNA structural elements may be more broadly targeted by synthetic small molecules than previously expected.

  14. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    Science.gov (United States)

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

  15. Marketing 'less harmful, low-tar' cigarettes is a key strategy of the industry to counter tobacco control in China.

    Science.gov (United States)

    Yang, Gonghuan

    2014-03-01

    While the 'low-tar' scheme has been widely recognised as a misleading tactic used by the tobacco industry to deceive the public about the true risks of cigarette smoking, a similar campaign using the slogan of 'less harmful, low tar' was launched by the Chinese tobacco industry, that is, State Tobacco Monopoly Administration/China National Tobacco Corporation and began to gain traction during the last decade. Despite the fact that no sufficient research evidence supports the claims made by the industry that these cigarettes are safer, the Chinese tobacco industry has continued to promote them using various health claims. As a result, the production and sales of 'less harmful, low-tar' cigarettes have increased dramatically since 2000. Recently, a tobacco industry senior researcher, whose main research area is 'less harmful, low-tar' cigarettes, was elected as an Academician to the prestigious Chinese Academy of Engineering for his contribution to developing 'less harmful, low-tar' cigarettes. The tobacco researcher's election caused an outcry from the tobacco control community and the general public in China. This paper discusses the Chinese tobacco industry's 'less harmful, low-tar' initiatives and calls for the Chinese government to stop the execution of this deceptive strategy for tobacco marketing.

  16. Quantitative determination of acid oils in low-temperature coal tar by means of fractional distillation

    Energy Technology Data Exchange (ETDEWEB)

    Jaeger, A

    1950-01-01

    The aromatic hydroxy compounds in low-temperature tar were separated, and 75 compounds in the boiling range 180/sup 0/ to 320/sup 0/ isolated by means of fractional distillation in packed columns of at least 45 theoretical plates. Mixtures not separable by fractionation were separated by means of other physicochemical or chemical methods. Hydroxy compounds with boiling point up to 230/sup 0/C were detemined quantitatively, as were the phenols present in low-temperature carbonization liquors. With the Krupp-Lurgi process of low-temperature carbonization, 1.8% phenol, 1.8% o-cresol, and 3.6% m-p-cresols were formed. The tar contained up to 1.3% 1:3:5-xylenol and up to 0.9% 1:2:4-xylenol. Of the 12.1% v/v of phenol, cresols, and xylenols present in tar, 11.2% were determined quantitatively, and 9 hydroxy compounds were identified in the remaining 0.9%. On the basis of these investigations, a technical plant that permitted the recovery of pure low-temperature tar phenols and the preparation of a number of different phenol resins from the mixtures was erected.

  17. Studies estimating the dermal bioavailability of polynuclear aromatic hydrocarbons from manufactured plant tar-contaminated soils

    International Nuclear Information System (INIS)

    Roy, T.A.; Krueger, A.J.; Taylor, B.B.; Mauro, D.M.; Goldstein, L.S.

    1998-01-01

    In vitro percutaneous absorption studies were performed with contaminated soils or organic extracts of contaminated soils collected at manufactured gas plant (MGP) sites. The MGP tar contaminated soils were found to contain a group of targeted polynuclear aromatic hydrocarbons (PAH) at levels ranging from 10 to 2400 mg/kg. The soil extracts contained target PAH at levels ranging from 12 000 - 34 000 mg/kg. Dermal penetration rates of target PAH from the MGP tar-contaminated soils/soil extracts were determined experimentally through human skin using 3 H-benzo(a)pyrene (BaP) as a surrogate. Results from three MGP sites showed reductions of 2-3 orders of magnitude in PAH absorption through human skin from the most contaminated soils in comparison to the soil extracts. Reduction in PAH penetration can be attributed to PAH concentration and (soil) matrix properties. PAH dermal flux values are used to determine site-specific dermally absorbed dose (DAD) and chronic daily intake (CDI) which are essential terms required to estimate risk associated with human exposure to MGP tar and MGP tar-contaminated soils. 21 refs., 4 figs., 3 tabs

  18. Tar removal from biomass gasification streams: processes and catalysts; Remocao do alcatrao de correntes de gaseificacao de biomassa: processos e catalisadores

    Energy Technology Data Exchange (ETDEWEB)

    Quitete, Cristina P.B. [Centro de Pesquisa e Desenvolvimento Leopoldo Americo Miguez de Mello (CENPES/PETROBRAS), Rio de Janeiro, RJ (Brazil). Processos de Conversao de Biomassa; Souza, Mariana M.V.M., E-mail: mmattos@eq.ufrj.br [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Centro de Tecnologia. Escola de Quimica

    2014-07-01

    Biomass gasification is a technology that has attracted great interest in synthesis of biofuels and oxo alcohols. However, this gas contains several contaminants, including tar, which need to be removed. Removal of tar is particularly critical because it can lead to operational problems. This review discusses the major pathways to remove tar, with a particular focus on the catalytic steam reforming of tar. Few catalysts have shown promising results; however, long-term studies in the context of real biomass gasification streams are required to realize their potential. (author)

  19. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

    Science.gov (United States)

    Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

    2009-01-01

    The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

  20. A quantitative analysis of secondary RNA structure using domination based parameters on trees

    Directory of Open Access Journals (Sweden)

    Zou Yue

    2006-03-01

    Full Text Available Abstract Background It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. Results The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. Conclusion Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These

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

    Science.gov (United States)

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

    2006-11-01

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

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

    Science.gov (United States)

    White, Neil A; Hoogstraten, Charles G

    2017-09-01

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

  3. Human papillomavirus and tar hypothesis for squamous cell cervical ...

    Indian Academy of Sciences (India)

    2010-08-09

    Aug 9, 2010 ... Keywords. Cervical cancer; co-factors; human papillomavirus; tar-based vaginal douche; tobacco smoke; wood smoke. Author Affiliations. Christina Bennett1 Allen E Kuhn2 Harry W Haverkos3. Indiana University School of Medicine, Indianapolis, Indiana 46202-5149, USA; Suite 300, Hamilton Mason Road ...

  4. Coal-tar-based sealcoated pavement: A major PAH source to urban stream sediments

    International Nuclear Information System (INIS)

    Witter, Amy E.; Nguyen, Minh H.; Baidar, Sunil; Sak, Peter B.

    2014-01-01

    We used land-use analysis, PAH concentrations and assemblages, and multivariate statistics to identify sediment PAH sources in a small (∼1303 km 2 ) urbanizing watershed located in South-Central, Pennsylvania, USA. A geographic information system (GIS) was employed to quantify land-use features that may serve as PAH sources. Urban PAH concentrations were three times higher than rural levels, and were significantly and highly correlated with combined residential/commercial/industrial land use. Principal components analysis (PCA) was used to group sediments with similar PAH assemblages, and correlation analysis compared PAH sediment assemblages to common PAH sources. The strongest correlations were observed between rural sediments (n = 7) and coke-oven emissions sources (r = 0.69–0.78, n = 5), and between urban sediments (n = 22) and coal-tar-based sealcoat dust (r = 0.94, n = 47) suggesting that coal-tar-based sealcoat is an important urban PAH source in this watershed linked to residential and commercial/industrial land use. -- Highlights: • Total PAH concentrations were measured at 35 sites along an urbanizing land-use gradient. • PAH concentrations increased with increasing urban land-use. • Urban land-use metrics were measured at three spatial scales using GIS. • PAH assemblages indicate coal-tar-based sealcoat is a major urban PAH source. • PAH assemblages indicate coke-oven emissions are an important rural PAH source. -- Coal-tar-based sealcoated pavement is a major PAH source to urban freshwater stream sediments in south-central Pennsylvania, USA

  5. Social-cognitive remediation in schizophrenia: generalization of effects of the Training of Affect Recognition (TAR).

    Science.gov (United States)

    Wölwer, Wolfgang; Frommann, Nicole

    2011-09-01

    In the last decade, several social cognitive remediation programs have been developed for use in schizophrenia. Though existing evidence indicates that such programs can improve social cognition, which is essential for successful social functioning, it remains unclear whether the improvements generalize to social cognitive domains not primarily addressed by the intervention and whether the improved test performance transfers into everyday social functioning. The present study investigated whether, beyond its known effects on facial affect recognition, the Training of Affect Recognition (TAR) has effects on prosodic affect recognition, theory of mind (ToM) performance, social competence in a role-play task, and more general social and occupational functioning. Thirty-eight inpatients with a diagnosis of schizophrenia or schizoaffective disorder were randomly assigned to 6 weeks of treatment with the TAR--primarily targeted at facial affect recognition-or Cognitive Remediation Training (CRT)--primarily targeted at neurocognition. Intention-to-treat analyses found significantly larger pre-post improvements with TAR than with CRT in prosodic affect recognition, ToM, and social competence and a trend effect in global social functioning. However, the effects on ToM and social competence were no longer significant in the smaller group of patients who completed treatment according to protocol. Results suggest that TAR effects generalize to other social cognitive domains not primarily addressed. TAR may also enhance social skills and social functioning, although this has to be confirmed. Results are discussed with regard to the need to improve functional outcome in schizophrenia against the background of current evidence from other social cognitive remediation approaches.

  6. Combinatorics of RNA-RNA interaction

    DEFF Research Database (Denmark)

    Li, Thomas J X; Reidys, Christian

    2012-01-01

    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

  7. RNA secondary structures of the bacteriophage phi6 packaging regions.

    OpenAIRE

    Pirttimaa, M J; Bamford, D H

    2000-01-01

    Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models ...

  8. CentroidFold: a web server for RNA secondary structure prediction

    OpenAIRE

    Sato, Kengo; Hamada, Michiaki; Asai, Kiyoshi; Mituyama, Toutai

    2009-01-01

    The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the ser...

  9. Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

    Science.gov (United States)

    Leppek, Kathrin; Das, Rhiju; Barna, Maria

    2017-01-01

    RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5′ untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5′ UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms. PMID:29165424

  10. The ins and outs of lncRNA structure: How, why and what comes next?

    Science.gov (United States)

    Blythe, Amanda J; Fox, Archa H; Bond, Charles S

    2016-01-01

    The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. GC content around splice sites affects splicing through pre-mRNA secondary structures

    Directory of Open Access Journals (Sweden)

    Chen Liang

    2011-01-01

    Full Text Available Abstract Background Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens, mice (Mus musculus, fruit flies (Drosophila melanogaster, and nematodes (Caenorhabditis elegans to further investigate this phenomenon. Results We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures. Conclusion All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.

  12. Tar sands showdown : Canada and the new politics of oil in an age of climate change

    International Nuclear Information System (INIS)

    Clarke, T.

    2009-01-01

    This book outlined the social and environmental issues facing the oil sands industry in Canada, including economic sovereignty, energy security, water rights and free trade. The tar sands have become vital to the Canadian economy, as they have the potential to increase Canada's foreign oil output by 4 to 5 times in the next 15 years. The author discussed the ecological and social impact of the Alberta tar sands and the real cost of development to Albertans and Canadians. Tar sands oil production generates more than 3 times the amount of greenhouse gas emissions than conventional oil production. The industry is also becoming a prime example of the abuse of water sources. The author emphasized the need to build an alternative energy future in an age of global warming. The main objective of this book was to help stimulate a nation-wide public debate about the tar sands and the critical issues at stake regarding Canada's energy future and an environmental strategy for more sustainable development. refs., tabs., figs.

  13. A Structural Overview of RNA-Dependent RNA Polymerases from the Flaviviridae Family

    Directory of Open Access Journals (Sweden)

    Jiqin Wu

    2015-06-01

    Full Text Available RNA-dependent RNA polymerases (RdRPs from the Flaviviridae family are representatives of viral polymerases that carry out RNA synthesis through a de novo initiation mechanism. They share a ≈ 600-residue polymerase core that displays a canonical viral RdRP architecture resembling an encircled right hand with palm, fingers, and thumb domains surrounding the active site. Polymerase catalytic motifs A–E in the palm and motifs F/G in the fingers are shared by all viral RdRPs with sequence and/or structural conservations regardless of the mechanism of initiation. Different from RdRPs carrying out primer-dependent initiation, Flaviviridae and other de novo RdRPs utilize a priming element often integrated in the thumb domain to facilitate primer-independent initiation. Upon the transition to the elongation phase, this priming element needs to undergo currently unresolved conformational rearrangements to accommodate the growth of the template-product RNA duplex. In the genera of Flavivirus and Pestivirus, the polymerase module in the C-terminal part of the RdRP protein may be regulated in cis by the N-terminal region of the same polypeptide. Either being a methyltransferase in Flavivirus or a functionally unclarified module in Pestivirus, this region could play auxiliary roles for the canonical folding and/or the catalysis of the polymerase, through defined intra-molecular interactions.

  14. Gc/ms analysis of coal tar composition produced from coal

    African Journals Online (AJOL)

    Coal pyrolysis is one of the significant approaches for the comprehensive utilization ... planigraphy-GC/MS; therefore a satisfactory analytical result obtained, which .... Among the aliphatic group of the coal tar, the proportion of alkene is larger ...

  15. A comparative method for finding and folding RNA secondary structures within protein-coding regions

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Meyer, Irmtraud Margret; Forsberg, Roald

    2004-01-01

    that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known...... secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD....

  16. In situ heat treatment of a tar sands formation after drive process treatment

    Science.gov (United States)

    Vinegar, Harold J.; Stanecki, John

    2010-09-21

    A method for treating a tar sands formation includes providing a drive fluid to a hydrocarbon containing layer of the tar sands formation to mobilize at least some hydrocarbons in the layer. At least some first hydrocarbons from the layer are produced. Heat is provided to the layer from one or more heaters located in the formation. At least some second hydrocarbons are produced from the layer of the formation. The second hydrocarbons include at least some hydrocarbons that are upgraded compared to the first hydrocarbons produced by using the drive fluid.

  17. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

    Science.gov (United States)

    Boudard, Mélanie; Bernauer, Julie; Barth, Dominique; Cohen, Johanne; Denise, Alain

    2015-01-01

    Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

  18. Cigarettes, lung cancer, and coronary heart disease: the effects of inhalation and tar yield.

    Science.gov (United States)

    Higenbottam, T; Shipley, M J; Rose, G

    1982-06-01

    Ten-year mortality rates for lung cancer and coronary heart disease have been related to cigarette smoking habits in 17 475 male civil servants aged 40-64 and in sample of 8089 male British residents aged 35-69. Both diseases were more frequent in smokers. Lung cancer rates were higher overall for "non-inhalers", particularly in heavy smokers. Tar yield correlated with the risk of lung cancer in non-inhalers but less so in inhalers. Conversely, coronary deaths were more common among inhalers, and the effect of tar/nicotine yield (such as it was) was confined to inhalers. It appears that there are subtle interactions between the amount smoked, the tar/nicotine yield of the cigarette, and the style of smoking. Thus the effects of a change in cigarette characteristics are hard to predict, and they may be different for respiratory and cardiovascular disease.

  19. Properties of gasification-derived char and its utilization for catalytic tar reforming

    Science.gov (United States)

    Qian, Kezhen

    Char is a low-value byproduct of biomass gasification and pyrolysis with many potential applications, such as soil amendment and the synthesis of activated carbon. The overall goal of the proposed research was to develop novel methods to use char derived from gasification for high-value applications in syngas conditioning. The first objective was to investigate effects of gasification condition and feedstock on properties of char derived from fluidized bed gasification. Results show that the surface areas of most of the char were 1--10 m 2/g and increased as the equivalence ratio increased. Char moisture and fixed carbon contents decreased while ash content increased as equivalence ratio increased. The next objective was to study the properties of sorghum and red cedar char derived from downdraft gasifier. Red cedar char contained more aliphatic carbon and o-alkyl carbon than sorghum char. Char derived from downdraft gasification had higher heating values and lower ash contents than char derived from fluidized bed gasification. The gasification reactivity of red cedar char was higher than that of sorghum char. Then, red cedar char based catalysts were developed with different preparation method to reform toluene and naphthalene as model tars. The catalyst prepared with nickel nitrate was found to be better than that with nickel acetate. The nickel particle size of catalyst impregnated with nickel nitrate was smaller than that of catalyst impregnated with nickel acetate. The particle size of catalyst impregnated with nickel acetate decreased by hydrazine reduction. The catalyst impregnated with nickel nitrate had the highest toluene removal efficiency, which was 70%--100% at 600--800 °C. The presence of naphthalene in tar reduced the catalyst efficiency. The toluene conversion was 36--99% and the naphthalene conversion was 37%--93% at 700--900 °C. Finally, effects of atmosphere and pressure on catalytic reforming of lignin-derived tars over the developed catalyst

  20. Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

    Directory of Open Access Journals (Sweden)

    Carugo Oliviero

    2011-10-01

    Full Text Available Abstract Background Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. Results A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. Conclusions The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.

  1. Characterization of alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) in tar-balls collected from the East Coast of Peninsular Malaysia.

    Science.gov (United States)

    Chandru, Kuhan; Zakaria, Mohamad Pauzi; Anita, Sofia; Shahbazi, Azadeh; Sakari, Mahyar; Bahry, Pourya Shahpoury; Mohamed, Che Abd Rahim

    2008-05-01

    The East Coast of Peninsular Malaysia faces the South China Sea and is vulnerable to oil pollution because of intense petroleum production activities in the area. The South China Sea is also a favored route for supertankers carrying crude oil to the Far East. Consequently, oil spills can occur, causing pollution and contamination in the surrounding areas. Residual oil spills stranded on coastal beaches usually end up as tar-balls. Elucidating the sources of tar-balls using a molecular marker approach is essential in assessing environmental impacts and perhaps settling legal liabilities for affected parties. This study utilizes a multimodal molecular marker approach through the use of diagnostic ratios of alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) to determine the source, distribution and weathering of tar-balls. Hopane ratios (e.g., C29/C30, and summation C31-C35/C30 ratios) were used to identify the sources of tar-balls. The weathering effects were distinguished by using alkanes, namely the unresolved complex mixture (UCM) and low molecular weight/high molecular weight (L/H) ratios. Similarly, PAHs were also used for the determination of weathering processes undergone by the tar-balls. This multimodal molecular marker gave a very strong indication of the sources of tar-balls in this study. For example, 16 out of 17 samples originated from South East Asian Crude Oil (SEACO) with one sample from Merang, Terengganu originating from North Sea Oil (Troll). The TRME-2 sample may have come from a supertanker's ballast water discharge. The second possibility is that the tar-ball may have been transported via oceanographic currents. All 'weathered' sample characterizations were based on the presence of UCM and other ratios. The multimodal molecular marker approach applied in this study has enabled us to partially understand the transport behavior of tar-balls in the marine environment and has revealed insights into the weathering process of tar-balls.

  2. Visualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls

    OpenAIRE

    Sansen , Joris; Bourqui , Romain; Thebault , Patricia; Allali , Julien; Auber , David

    2015-01-01

    International audience; The challenge 1 of the BIOVIS 2015 design contest consists in designing an intuitive visual depiction of base pairs binding probabilities for secondary structure of ncRNA. Our representation depicts the potential nucleotide pairs binding using nested concave hulls over the computed MFE ncRNA secondary structure. Thus, it allows to identify regions with a high level of uncertainty in the MFE computation and the structures which seem to match to reality.

  3. Characterisation and catalytic upgrading of tars from coal-tyre hydropyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Mastral, A.M.; Murillo, R.; Callen, M.S.; Garcia, T. [Instituto de Carboquimica, Zaragoza (Spain)

    1999-07-01

    Tars from coal-tyre hydropyrolysis obtained in a swept fixed bed reactor were upgraded with catalysts. Upgraded oils were characterized, and naphtha, kerosene, gas oil, heavy gas oil and vacuum residue percentages were quantified. 7 refs., 3 tabs.

  4. Class I cultural resource overview for oil shale and tar sands areas in Colorado, Utah and Wyoming.

    Energy Technology Data Exchange (ETDEWEB)

    O' Rourke, D.; Kullen, D.; Gierek, L.; Wescott, K.; Greby, M.; Anast, G.; Nesta, M.; Walston, L.; Tate, R.; Azzarello, A.; Vinikour, B.; Van Lonkhuyzen, B.; Quinn, J.; Yuen, R.; Environmental Science Division

    2007-11-01

    In August 2005, the U.S. Congress enacted the Energy Policy Act of 2005, Public Law 109-58. In Section 369 of this Act, also known as the 'Oil Shale, Tar Sands, and Other Strategic Unconventional Fuels Act of 2005', Congress declared that oil shale and tar sands (and other unconventional fuels) are strategically important domestic energy resources that should be developed to reduce the nation's growing dependence on oil from politically and economically unstable foreign sources. The Bureau of Land Management (BLM) is developing a Programmatic Environmental Impact Statement (PEIS) to evaluate alternatives for establishing commercial oil shale and tar sands leasing programs in Colorado, Wyoming, and Utah. This PEIS evaluates the potential impacts of alternatives identifying BLM-administered lands as available for application for commercial leasing of oil shale resources within the three states and of tar sands resources within Utah. The scope of the analysis of the PEIS also includes an assessment of the potential effects of future commercial leasing. This Class I cultural resources study is in support of the Draft Oil Shale and Tar Sands Resource Management Plan Amendments to Address Land Use Allocations in Colorado, Utah, and Wyoming and Programmatic Environmental Impact Statement and is an attempt to synthesize archaeological data covering the most geologically prospective lands for oil shale and tar sands in Colorado, Utah, and Wyoming. This report is based solely on geographic information system (GIS) data held by the Colorado, Utah, and Wyoming State Historic Preservation Offices (SHPOs). The GIS data include the information that the BLM has provided to the SHPOs. The primary purpose of the Class I cultural resources overview is to provide information on the affected environment for the PEIS. Furthermore, this report provides recommendations to support planning decisions and the management of cultural resources that could be impacted by future

  5. Guideline for Sampling and Analysis of Tar and Particles in Biomass Producer Gases. Version 3.3

    Energy Technology Data Exchange (ETDEWEB)

    Neeft, J.P.A.; Knoef, H.A.M.; Zielke, U.; Sjoestroem, K.; Hasler, P.; Simell, P.A.; Dorrington, M.A.; Thomas, L.; Abatzoglou, N.; Deutch, S.; Greil, C.; Buffinga, G.J.; Brage, C.; Suomalainen, M.

    2002-07-01

    This Guideline provides a set of procedures for the measurement of organic contaminants and particles in producer gases from biomass gasifiers. The procedures are designed to cover different gasifier types (updraft or downdraft fixed bed or fluidised bed gasifiers), operating conditions (0 - 900C and 0.6-60 bars) and concentration ranges (1 mg/m{sub n}{sup 3} to 300 g/m{sub n}{sup 3}). The Guideline describes a modular sampling train, and a set of procedures, which include: planning and preparation of the sampling, sampling and post-sampling, analysis, calculations, error analysis and reporting. The modular sampling train consists of 4 modules. Module 1 is a preconditioning module for isokinetic sampling and gas cooling. Module 2 is a particle collection module including a heated filter. Module 3 is a tar collection module with a gas quench (optionally by circulating a liquid), impinger bottles and a backup adsorber. Module 4 is a volume-sampling module consisting of a pump, a rotameter, a gas flow meter and pressure and temperature indicators. The equipment and materials that are required for procuring this modular sampling train are given in the Guideline. The sampling procedures consist of a description for isokinetic sampling, a leakage test prior to sampling, the actual sampling and its duration, how the equipment is cleaned after the sampling, and how the samples are prepared and stored. Analysis of the samples is performed via three procedures. Prior to these procedures, the sample is prepared by Soxhlet extraction of the tars on the particle filter and by collection of all tars in one bulk solution. The first procedure describes the weighing of the particle filter to obtain the concentration of particles in the biomass producer gas. The bulk tar solution is used for two purposes: for determination of gravimetric tar and for analysis of individual compounds. The second procedure describes how to determine the gravimetric tar mass from the bulk solution. The

  6. Treatment of low-temperature tar-gas mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Schick, F

    1928-07-04

    Process for the treating and conversion of low-temperature tar-vapor and gas mixtures in the presence of metals or metal oxides as well as bodies of large surface, without previous condensation of the liquid material to be treated, characterized by the treatment taking place with a mixture of desulfurizing metals and metal oxides which, if necessary, are precipitated on carriers and large surface nonmetal cracking catalysts, such as active carbon and silica gel.

  7. Receiving demulsifying agent from the acid tar

    Energy Technology Data Exchange (ETDEWEB)

    Nikitina, A.A.; Belyaeva, A.S.; Kunakova, R.V. [FGBIHE ' Ufa State Academy of Economics and Services' , Ufa (Russian Federation); Movsumzade, E.M. [FGBIHE ' Ufa State Petroleum Technological Univ.' , Ufa (Russian Federation); Lapidus, A.L. [Russian Academy of Sciences, Moscow (Russian Federation). N.D. Zelinsky Institute of Organic Chemistry

    2012-07-01

    The processing of wastes of petrochemical production makes it possible to reduce the price of produced commodity of petroleum products substantially. Bitumen, fuel oils, tars and other mixture of heavy organic compounds are widely used in road construction, in paint and cable industries, manufacture of roofing materials, are used as boiler and furnace fuel, fuel for marine diesel engines, raw material for the production of modifying additives, fillers, surfaceactive substances, etc. (orig.)

  8. Tar DNA binding protein-43 (TDP-43 associates with stress granules: analysis of cultured cells and pathological brain tissue.

    Directory of Open Access Journals (Sweden)

    Liqun Liu-Yesucevitz

    2010-10-01

    Full Text Available Tar DNA Binding Protein-43 (TDP-43 is a principle component of inclusions in many cases of frontotemporal lobar degeneration (FTLD-U and amyotrophic lateral sclerosis (ALS. TDP-43 resides predominantly in the nucleus, but in affected areas of ALS and FTLD-U central nervous system, TDP-43 is aberrantly processed and forms cytoplasmic inclusions. The mechanisms governing TDP-43 inclusion formation are poorly understood. Increasing evidence indicates that TDP-43 regulates mRNA metabolism by interacting with mRNA binding proteins that are known to associate with RNA granules. Here we show that TDP-43 can be induced to form inclusions in cell culture and that most TDP-43 inclusions co-localize with SGs. SGs are cytoplasmic RNA granules that consist of mixed protein-RNA complexes. Under stressful conditions SGs are generated by the reversible aggregation of prion-like proteins, such as TIA-1, to regulate mRNA metabolism and protein translation. We also show that disease-linked mutations in TDP-43 increased TDP-43 inclusion formation in response to stressful stimuli. Biochemical studies demonstrated that the increased TDP-43 inclusion formation is associated with accumulation of TDP-43 detergent insoluble complexes. TDP-43 associates with SG by interacting with SG proteins, such as TIA-1, via direct protein-protein interactions, as well as RNA-dependent interactions. The signaling pathway that regulates SGs formation also modulates TDP-43 inclusion formation. We observed that inclusion formation mediated by WT or mutant TDP-43 can be suppressed by treatment with translational inhibitors that suppress or reverse SG formation. Finally, using Sudan black to quench endogenous autofluorescence, we also demonstrate that TDP-43 positive-inclusions in pathological CNS tissue co-localize with multiple protein markers of stress granules, including TIA-1 and eIF3. These data provide support for accumulating evidence that TDP-43 participates in the SG pathway.

  9. Brown carbon in tar balls from smoldering biomass combustion

    Science.gov (United States)

    R. K. Chakrabarty; H. Moosmuller; L.-W. A. Chen; K. Lewis; W. P. Arnott; C. Mazzoleni; M. K. Dubey; C. E. Wold; W. M. Hao; S. M. Kreidenweis

    2010-01-01

    We report the direct observation of laboratory production of spherical, carbonaceous particles - "tar balls" - from smoldering combustion of two commonly occurring dry mid-latitude fuels. Real-time measurements of spectrally varying absorption Angstrom coefficients (AAC) indicate that a class of light absorbing organic carbon (OC) with wavelength dependent...

  10. lncRNA Structure: Message to the Heart.

    Science.gov (United States)

    Fazal, Furqan M; Chang, Howard Y

    2016-10-06

    In this issue, Xue et al. (2016) describe the secondary structure of the heart-specific long non-coding RNA Braveheart, leading to the discovery of a short, asymmetric G-rich loop that controls cardiac lineage commitment by interacting with the transcription factor CNBP. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA

    OpenAIRE

    Dibrov, Sergey; McLean, Jaime; Hermann, Thomas

    2011-01-01

    An oligonucleotide representing a regulatory element of human thymidylate synthase mRNA has been crystallized as a dimer. The structure of the asymmetric dimer has been determined at 1.97 Å resolution.

  12. Radiocarbon dating of extinct fauna in the Americas recovered from tar pits

    International Nuclear Information System (INIS)

    Jull, A.J.T.; Iturralde-Vinent, M.; O'Malley, J.M.; MacPhee, R.D.E.; McDonald, H.G.; Martin, P.S.; Moody, J.; Rincon, A.

    2004-01-01

    We have obtained radiocarbon dates by accelerator mass spectrometry on bones of extinct large mammals from tar pits. Results on some samples of Glyptodon and Holmesina (extinct large mammals similar to armadillos) yielded ages of >25 and >21 ka, respectively. We also studied the radiocarbon ages of three different samples of bones from the extinct Cuban ground sloth, Parocnus bownii, which yielded dates ranging from 4960 ± 280 to 11 880 ± 420 yr BP. In order to remove the tar component pretreat the samples sufficiently to obtain reliable dates, we cleaned the samples by Soxhlet extraction in benzene. Resulting samples of collagenous material were often small

  13. RNA secondary structure diagrams for very large molecules: RNAfdl

    DEFF Research Database (Denmark)

    Hecker, Nikolai; Wiegels, Tim; Torda, Andrew E.

    2013-01-01

    There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10 3 bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments...

  14. Structure and Dynamics of the tRNA-like Structure Domain of Brome Mosaic Virus

    Science.gov (United States)

    Vieweger, Mario; Nesbitt, David

    2014-03-01

    Conformational switching is widely accepted as regulatory mechanism in gene expression in bacterial systems. More recently, similar regulation mechanisms are emerging for viral systems. One of the most abundant and best studied systems is the tRNA-like structure domain that is found in a number of plant viruses across eight genera. In this work, the folding dynamics of the tRNA-like structure domain of Brome Mosaic Virus are investigated using single-molecule Fluorescence Resonance Energy Transfer techniques. In particular, Burst fluorescence is applied to observe metal-ion induced folding in freely diffusing RNA constructs resembling the 3'-terminal 169nt of BMV RNA3. Histograms of EFRET probabilities reveal a complex equilibrium of three distinct populations. A step-wise kinetic model for TLS folding is developed in accord with the evolution of conformational populations and structural information in the literature. In this mechanism, formation of functional TLS domains from unfolded RNAs requires two consecutive steps; 1) hybridization of a long-range stem interaction followed by 2) formation of a 3' pseudoknot. This three-state equilibrium is well described by step-wise dissociation constants K1(328(30) μM) and K2(1092(183) μM) for [Mg2+] and K1(74(6) mM) and K2(243(52) mM) for [Na+]-induced folding. The kinetic model is validated by oligo competition with the STEM interaction. Implications of this conformational folding mechanism are discussed in regards to regulation of virus replication.

  15. Structure of Lipid Nanoparticles Containing siRNA or mRNA by Dynamic Nuclear Polarization-Enhanced NMR Spectroscopy.

    Science.gov (United States)

    Viger-Gravel, Jasmine; Schantz, Anna; Pinon, Arthur C; Rossini, Aaron J; Schantz, Staffan; Emsley, Lyndon

    2018-02-22

    Here, we show how dynamic nuclear polarization (DNP) NMR spectroscopy experiments permit the atomic level structural characterization of loaded and empty lipid nanoparticles (LNPs). The LNPs used here were synthesized by the microfluidic mixing technique and are composed of ionizable cationic lipid (DLin-MC3-DMA), a phospholipid (distearoylphosphatidylcholine, DSPC), cholesterol, and poly(ethylene glycol) (PEG) (dimyristoyl phosphatidyl ethanolamine (DMPE)-PEG 2000), as well as encapsulated cargoes that are either phosphorothioated siRNA (50 or 100%) or mRNA. We show that LNPs form physically stable complexes with bioactive drug siRNA for a period of 94 days. Relayed DNP experiments are performed to study 1 H- 1 H spin diffusion and to determine the spatial location of the various components of the LNP by studying the average enhancement factors as a function of polarization time. We observe a striking feature of LNPs in the presence and in the absence of encapsulating siRNA or mRNA by comparing our experimental results to numerical spin-diffusion modeling. We observe that LNPs form a layered structure, and we detect that DSPC and DMPE-PEG 2000 lipids form a surface rich layer in the presence (or absence) of the cargoes and that the cholesterol and ionizable cationic lipid are embedded in the core. Furthermore, relayed DNP 31 P solid-state NMR experiments allow the location of the cargo encapsulated in the LNPs to be determined. On the basis of the results, we propose a new structural model for the LNPs that features a homogeneous core with a tendency for layering of DSPC and DMPE-PEG at the surface.

  16. Evolution of the RNase P RNA structural domain in Leptospira spp.

    Science.gov (United States)

    Ravishankar, Vigneshwaran; Ahmed, Ahmed; Sivagnanam, Ulaganathan; Muthuraman, Krishnaraja; Karthikaichamy, Anbarasu; Wilson, Herald A; Devendran, Ajay; Hartskeerl, Rudy A; Raj, Stephen M L

    2014-12-01

    We have employed the RNase P RNA (RPR) gene, which is present as single copy in chromosome I of Leptospira spp. to investigate the phylogeny of structural domains present in the RNA subunit of the tRNA processing enzyme, RNase P. RPR gene sequences of 150 strains derived from NCBI database along with sequences determined from 8 reference strains were examined to fathom strain specific structural differences present in leptospiral RPR. Sequence variations in the RPR gene impacted on the configuration of loops, stems and bulges found in the RPR highlighting species and strain specific structural motifs. In vitro transcribed leptospiral RPR ribozymes are demonstrated to process pre-tRNA into mature tRNA in consonance with the positioning of Leptospira in the taxonomic domain of bacteria. RPR sequence datasets used to construct a phylogenetic tree exemplified the segregation of strains into their respective lineages with a (re)speciation of strain SH 9 to Leptospira borgpetersenii, strains Fiocruz LV 3954 and Fiocruz LV 4135 to Leptospira santarosai, strain CBC 613 to Leptospira kirschneri and strain HAI 1536 to Leptospira noguchii. Furthermore, it allowed characterization of an isolate P2653, presumptively characterized as either serovar Hebdomadis, Kremastos or Longnan to Leptospira weilii, serovar Longnan. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  17. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

    Science.gov (United States)

    Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

    2017-05-01

    Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  18. Modelling the structure of a ceRNA-theoretical, bipartite microRNA-mRNA interaction network regulating intestinal epithelial cellular pathways using R programming.

    Science.gov (United States)

    Robinson, J M; Henderson, W A

    2018-01-12

    We report a method using functional-molecular databases and network modelling to identify hypothetical mRNA-miRNA interaction networks regulating intestinal epithelial barrier function. The model forms a data-analysis component of our cell culture experiments, which produce RNA expression data from Nanostring Technologies nCounter ® system. The epithelial tight-junction (TJ) and actin cytoskeleton interact as molecular components of the intestinal epithelial barrier. Upstream regulation of TJ-cytoskeleton interaction is effected by the Rac/Rock/Rho signaling pathway and other associated pathways which may be activated or suppressed by extracellular signaling from growth factors, hormones, and immune receptors. Pathway activations affect epithelial homeostasis, contributing to degradation of the epithelial barrier associated with osmotic dysregulation, inflammation, and tumor development. The complexity underlying miRNA-mRNA interaction networks represents a roadblock for prediction and validation of competing-endogenous RNA network function. We developed a network model to identify hypothetical co-regulatory motifs in a miRNA-mRNA interaction network related to epithelial function. A mRNA-miRNA interaction list was generated using KEGG and miRWalk2.0 databases. R-code was developed to quantify and visualize inherent network structures. We identified a sub-network with a high number of shared, targeting miRNAs, of genes associated with cellular proliferation and cancer, including c-MYC and Cyclin D.

  19. Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility.

    Science.gov (United States)

    Leistra, Abigail N; Amador, Paul; Buvanendiran, Aishwarya; Moon-Walker, Alex; Contreras, Lydia M

    2017-12-15

    Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering. We then modularly recombine the selected substructures, differentially representing those of presumed high or low functional contribution, to build a library of 21 CsrB variants. Using fluorescent translational reporter assays, we demonstrate that the CsrB variants achieve a 5-fold gradient of control of well-characterized Csr network targets. Interestingly, results suggest that less conserved local structures within long, multisubstrate sRNAs may represent better targets for rational engineering than their well-conserved counterparts. Lastly, mapping the impact of sRNA variants on a signature Csr network phenotype indicates the potential of this approach for tuning the activity of global sRNA regulators in the context of metabolic engineering applications.

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

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

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

  1. Evolution of primary and secondary structures in 5S and 5.8S rRNA

    International Nuclear Information System (INIS)

    Curtiss, W.C.

    1986-01-01

    The secondary structure of Bombyx mori 5S rRNA was studied using the sing-strand specific S1 nuclease and the base pair specific cobra venom ribonuclease. The RNA was end-labeled with [ 32 P] at either the 5' or 3' end and sequenced using enzymatic digestion techniques. These enzymatic data coupled with thermodynamic structure prediction were used to generate a secondary structure for 5S rRNA. A computer algorithm has been implemented to aid in the comparison of a large set of homologous RNAs. Eukaryotic 5S rRNA sequences from thirty four diverse species were compared by (1) alignment or the sequences, (2) the positions of substitutions were located with respect to the aligned sequence and secondary structure, and (3) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. Eukaryotic 5S rRNA was found to have significant sequence variation throughout much of the molecule while maintaining a relatively constant secondary structure. A detailed analysis of the sequence and structure variability in each region of the molecule is presented

  2. Primary and secondary structure of U8 small nuclear RNA

    International Nuclear Information System (INIS)

    Reddy, R.; Henning, D.; Busch, H.

    1985-01-01

    U8 small nuclear RNA is a new, capped, 140 nucleotides long RNA species found in Novikoff hepatoma cells. Its sequence is: m3GpppAmUmCGUCAGGA GGUUAAUCCU UACCUGUCCC UCCUUUCGGA GGGCAGAUAG AAAAUGAUGA UUGGAGCUUG CAUGAUCUGC UGAUUAUAGC AUUUCCGUGU AAUCAGGACC UGACAACAUC CUGAUUGCUU CUAUCUGAUUOH. This RNA is present in approximately 25,000 copies/cell, and it is enriched in nucleolar preparations. Like U1, U2, U4/U6, and U5 RNAs, U8 RNA was also present as a ribonucleoprotein associated with the Sm antigen. The rat U8 RNA was highly homologous (greater than 90%) to a recently characterized 5.4 S RNA from mouse cells infected with spleen focus-forming virus. In addition to the U8 RNA, three other U small nuclear RNAs were found in anti-Sm antibody immunoprecipitates from labeled rat and HeLa cells. Each of these contained a m3GpppAm cap structure; their apparent chain lengths were 60, 130, and 65 nucleotides. These U small nuclear RNAs are designated U7, U9, and U10 RNAs, respectively

  3. ANALYSIS OF MEASURED AND MODELED SOLAR RADIATION AT THE TARS SOLAR HEATING PLANT IN DENMARK

    DEFF Research Database (Denmark)

    Tian, Zhiyong; Perers, Bengt; Furbo, Simon

    2017-01-01

    , such as solar radiation, inlet and outlet temperature for the solar collector field, flow rate and pressure, ambient temperature, Wind speed and wind direction were measured. Global horizontal radiation, direct normal irradiation (DNI) and total radiation on the tilted collector plane of the flat plate...... collector field have been measured in Tars solar heating plant. To determine the accuracy of modeled and measured solar radiation in Tars solar heating plant, monthly comparisons of measured and calculated radiation using 6 empirical models have been carried out. Comparisons of measured and modeled total......A novel combined solar heating plant with tracking parabolic trough collectors (PTC) and flat plate collectors (FPC) has been constructed and put into operation in Tars, 30 km north of Aalborg, Denmark in August 2015. To assess the operation performance of the plant, detailed parameters...

  4. NMR-study of dynamic structural transtions in RNA-molecules

    OpenAIRE

    Fürtig, Boris

    2007-01-01

    The following thesis is concerned with the elucidation of structural changes of RNA molecules during the time course of dynamic processes that are commonly denoted as folding reactions. In contrast to the field of protein folding, the concept of RNA folding comprises not only folding reactions itself but also refolding- or conformational switching- and assembly processes (see chapter III). The method in this thesis to monitor these diverse processes is high resolution liquid-state NMR spectro...

  5. Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA

    Directory of Open Access Journals (Sweden)

    Eric R. Gamache

    2017-04-01

    Full Text Available The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5′ terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT. To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1, a 1-nucleotide interhelical loop and an 8-bp stem (S2 that delineate two long, structured loops. Nucleotide substitutions that disrupt either pseudoknot stem greatly reduced helper-Ty1-mediated retrotransposition of a mini-Ty1, but only mutations in S2 destabilized mini-Ty1 RNA in cis and helper-Ty1 RNA in trans. Nested in different loops of the pseudoknot are two hairpins with complementary 7-nucleotide motifs at their apices. Nucleotide substitutions in either motif also reduced retrotransposition and destabilized mini- and helper-Ty1 RNA. Compensatory mutations that restore base-pairing in the S2 stem or between the hairpins rescued retrotransposition and RNA stability in cis and trans. These data inform a model whereby a Ty1 RNA kissing complex with two intermolecular kissing-loop interactions initiates dimerization and packaging.

  6. Crowdsourcing RNA structural alignments with an online computer game.

    Science.gov (United States)

    Waldispühl, Jérôme; Kam, Arthur; Gardner, Paul P

    2015-01-01

    The annotation and classification of ncRNAs is essential to decipher molecular mechanisms of gene regulation in normal and disease states. A database such as Rfam maintains alignments, consensus secondary structures, and corresponding annotations for RNA families. Its primary purpose is the automated, accurate annotation of non-coding RNAs in genomic sequences. However, the alignment of RNAs is computationally challenging, and the data stored in this database are often subject to improvements. Here, we design and evaluate Ribo, a human-computing game that aims to improve the accuracy of RNA alignments already stored in Rfam. We demonstrate the potential of our techniques and discuss the feasibility of large scale collaborative annotation and classification of RNA families.

  7. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    Science.gov (United States)

    Ellington, Roni; Wachira, James

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

  8. RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

    Science.gov (United States)

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems.

  9. Parallels between playbacks and Pleistocene tar seeps suggest sociality in an extinct sabretooth cat, Smilodon

    OpenAIRE

    Carbone, Chris; Maddox, Tom; Funston, Paul J.; Mills, Michael G.L.; Grether, Gregory F.; Van Valkenburgh, Blaire

    2008-01-01

    Inferences concerning the lives of extinct animals are difficult to obtain from the fossil record. Here we present a novel approach to the study of extinct carnivores, using a comparison between fossil records (n=3324) found in Late Pleistocene tar seeps at Rancho La Brea in North America and counts (n=4491) from playback experiments used to estimate carnivore abundance in Africa. Playbacks and tar seep deposits represent competitive, potentially dangerous encounters where multiple predators ...

  10. Non-Watson Crick base pairs might stabilize RNA structural motifs in ...

    Indian Academy of Sciences (India)

    Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural ...

  11. Traditional African Religions (TARs): on HIV/AIDS, health and ...

    African Journals Online (AJOL)

    This is because the moral guidance put forward by. African religions is underestimated; hence making HIV/AIDS more of a moral problem. Rethinking the dialogue with TARs, will help in setting appropriate means of enhancing health in a broad sense and living in human dignity in Africa. Mtafiti Mwafrika Vol. 15 2005: pp.

  12. Coal-tar-based pavement sealcoat and PAHs: implications for the environment, human health, and stormwater management.

    Science.gov (United States)

    Mahler, Barbara J; Metre, Peter C Van; Crane, Judy L; Watts, Alison W; Scoggins, Mateo; Williams, E Spencer

    2012-03-20

    Coal-tar-based sealcoat products, widely used in the central and eastern U.S. on parking lots, driveways, and even playgrounds, are typically 20-35% coal-tar pitch, a known human carcinogen that contains about 200 polycyclic aromatic hydrocarbon (PAH) compounds. Research continues to identify environmental compartments-including stormwater runoff, lake sediment, soil, house dust, and most recently, air-contaminated by PAHs from coal-tar-based sealcoat and to demonstrate potential risks to biological communities and human health. In many cases, the levels of contamination associated with sealed pavement are striking relative to levels near unsealed pavement: PAH concentrations in air over pavement with freshly applied coal-tar-based sealcoat, for example, were hundreds to thousands of times higher than those in air over unsealed pavement. Even a small amount of sealcoated pavement can be the dominant source of PAHs to sediment in stormwater-retention ponds; proper disposal of such PAH-contaminated sediment can be extremely costly. Several local governments, the District of Columbia, and the State of Washington have banned use of these products, and several national and regional hardware and home-improvement retailers have voluntarily ceased selling them.

  13. Coal-tar-based pavement sealcoat and PAHs: implications for the environment, human health, and stormwater management

    Science.gov (United States)

    Mahler, Barbara J.; Van Metre, Peter C.; Crane, Judy L.; Watts, Alison W.; Scoggins, Mateo; Williams, E. Spencer

    2012-01-01

    Coal-tar-based sealcoat products, widely used in the central and eastern U.S. on parking lots, driveways, and even playgrounds, are typically 20-35% coal-tar pitch, a known human carcinogen that contains about 200 polycyclic aromatic hydrocarbon (PAH) compounds. Research continues to identify environmental compartments—including stormwater runoff, lake sediment, soil, house dust, and most recently, air—contaminated by PAHs from coal-tar-based sealcoat and to demonstrate potential risks to biological communities and human health. In many cases, the levels of contamination associated with sealed pavement are striking relative to levels near unsealed pavement: PAH concentrations in air over pavement with freshly applied coal-tar-based sealcoat, for example, were hundreds to thousands of times higher than those in air over unsealed pavement. Even a small amount of sealcoated pavement can be the dominant source of PAHs to sediment in stormwater-retention ponds; proper disposal of such PAH-contaminated sediment can be extremely costly. Several local governments, the District of Columbia, and the State of Washington have banned use of these products, and several national and regional hardware and home-improvement retailers have voluntarily ceased selling them.

  14. Coal-tar pavement sealants might substantially increase children's PAH exposures

    Science.gov (United States)

    Williams, E. Spencer; Mahler, Barbara J.; Van Metre, Peter C.

    2012-01-01

    Dietary ingestion has been identified repeatedly as the primary route of human exposure to polycyclic aromatic hydrocarbons (PAHs), seven of which are classified as probable human carcinogens (B2 PAHs) by the U.S. EPA. Humans are exposed to PAHs through ingestion of cooked and uncooked foods, incidental ingestion of soil and dust, inhalation of ambient air, and absorption through skin. Although PAH sources are ubiquitous in the environment, one recently identified PAH source stands out: Coal-tar-based pavement sealant—a product applied to many parking lots, driveways, and even playgrounds primarily in the central, southern, and eastern U.S.—has PAH concentrations 100–1000 times greater than most other PAH sources. It was reported recently that PAH concentrations in house dust in residences adjacent to parking lots with coal-tar-based sealant were 25 times higher than in residences adjacent to unsealed asphalt parking lots.

  15. The Structure of the RNA m5C Methyltransferase YebU from Escherichia coli Reveals a C-terminal RNA-recruiting PUA Domain

    DEFF Research Database (Denmark)

    Hallberg, B. Martin; Ericsson, Ulrika B.; Johnson, Kenneth A

    2006-01-01

    potential that differ from other RNA-MTase structures, suggesting that YebU interacts with its RNA target in a different manner. Docking of YebU onto the 30 S subunit indicates that the PUA and MTase domains make several contacts with 16 S rRNA as well as with the ribosomal protein S12. The ribosomal...... protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU....... by X-ray crystallography, and we present a molecular model for how YebU specifically recognizes, binds and methylates its ribosomal substrate. The YebU protein has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other m(5)C RNA MTases including...

  16. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

    Directory of Open Access Journals (Sweden)

    Sharma Gaurav

    2011-04-01

    Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

  17. How do different cigarette design features influence the standard tar yields of popular cigarette brands sold in different countries?

    Science.gov (United States)

    O'Connor, R J; Hammond, D; McNeill, A; King, B; Kozlowski, L T; Giovino, G A; Cummings, K M

    2008-09-01

    To examine the associations among cigarette design features and tar yields of leading cigarette brands sold in the United States, Canada, Australia and the United Kingdom. Government reports and numbers listed on packs were used to obtain data on International Organization for Standardization (ISO)/Federal Trade Commission (FTC) yields for the tar of 172 cigarette varieties sold in the United States, Canada, Australia and the United Kingdom. We used standardised methods to measure the following 11 cigarette design parameters: filter ventilation, cigarette pressure drop, filter pressure drop, tobacco rod length, filter length, cigarette diameter, tipping paper length, tobacco weight, filter weight, rod density and filter density. Filter ventilation was found to be the predominant design feature accounting for the variations between brands in ISO/FTC tar yields in each of the four countries. After accounting for filter ventilation, design parameters such as overwrap length, tobacco weight and rod density played comparatively minor roles in determining tar yields. Variation in ISO/FTC tar yields are predicted by a limited set of cigarette design features, especially filter ventilation, suggesting that governments should consider mandatory disclosure of cigarette design parameters as part of comprehensive tobacco product regulations.

  18. RNA is an integral component of chromatin that contributes to its structural organization.

    Directory of Open Access Journals (Sweden)

    Antonio Rodríguez-Campos

    Full Text Available Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA(- and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with alpha-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.

  19. A combinatorial enumeration problem of RNA secondary structures

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... connection between Discrete Mathematics and Compu- tational Molecular Biology (Chen et al, 2005; Hofacker et ... in Computational Molecular Biology. An RNA molecule is described by its sequences of bases ... Here, a mathematical definition of secondary structure is given (Stein and Waterman 1978).

  20. Fresh tar (from biomass gasification) destruction with downstream catalysts: comparison of their intrinsic activity with a realistic kinetic model

    Energy Technology Data Exchange (ETDEWEB)

    Corella, J.; Narvaez, I.; Orio, A. [Complutense Univ. of Madrid (Spain). Dept. of Chemical Engineering

    1996-12-31

    A model for fresh tar destruction over catalysts placed downstream a biomass gasifier is presented. It includes the stoichio-metry and the calculation of the kinetic constants for the tar destruction. Catalysts studied include commercial Ni steam reforming catalysts and calcinated dolomites. Kinetic constants for tar destruction are calculated for several particle sizes, times- on-stream and temperatures of the catalyst and equivalence ratios in the gasifier. Such intrinsic kinetic constants allow a rigorous or scientific comparison of solids and conditions to be used in an advanced gasification process. (orig.) 4 refs.

  1. Fresh tar (from biomass gasification) destruction with downstream catalysts: comparison of their intrinsic activity with a realistic kinetic model

    Energy Technology Data Exchange (ETDEWEB)

    Corella, J; Narvaez, I; Orio, A [Complutense Univ. of Madrid (Spain). Dept. of Chemical Engineering

    1997-12-31

    A model for fresh tar destruction over catalysts placed downstream a biomass gasifier is presented. It includes the stoichio-metry and the calculation of the kinetic constants for the tar destruction. Catalysts studied include commercial Ni steam reforming catalysts and calcinated dolomites. K