Sample records for tar hairpin annealing

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

    PubMed Central

    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

  2. Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC

    PubMed Central

    Bazzi, Ali; Zargarian, Loussiné; Chaminade, Françoise; Boudier, Christian; De Rocquigny, Hughes; René, Brigitte; Mély, Yves; Fossé, Philippe; Mauffret, Olivier

    2011-01-01

    An essential step of the reverse transcription of the HIV-1 genome is the first strand transfer that requires the annealing of the TAR RNA hairpin to the cTAR DNA hairpin. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. Using nuclear magnetic resonance and gel retardation assays, we investigated the interaction between NC and the top half of the cTAR DNA (mini-cTAR). We show that NC(11-55) binds the TGG sequence in the lower stem that is destabilized by the adjacent internal loop. The 5′ thymine interacts with residues of the N-terminal zinc knuckle and the 3′ guanine is inserted in the hydrophobic plateau of the C-terminal zinc knuckle. The TGG sequence is preferred relative to the apical and internal loops containing unpaired guanines. Investigation of the DNA–protein contacts shows the major role of hydrophobic interactions involving nucleobases and deoxyribose sugars. A similar network of hydrophobic contacts is observed in the published NC:DNA complexes, whereas NC contacts ribose differently in NC:RNA complexes. We propose that the binding polarity of NC is related to these contacts that could be responsible for the preferential binding to single-stranded nucleic acids. PMID:21227929

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

    DOEpatents

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2010-10-12

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

  4. Non-Natural Linker Configuration in 2,6-Dipeptidyl-Anthraquinones Enhances the Inhibition of TAR RNA Binding/Annealing Activities by HIV-1 NC and Tat Proteins.

    PubMed

    Sosic, Alice; Saccone, Irene; Carraro, Caterina; Kenderdine, Thomas; Gamba, Elia; Caliendo, Giuseppe; Corvino, Angela; Di Vaio, Paola; Fiorino, Ferdinando; Magli, Elisa; Perissutti, Elisa; Santagada, Vincenzo; Severino, Beatrice; Spada, Valentina; Fabris, Dan; Frecentese, Francesco; Gatto, Barbara

    2018-06-12

    The HIV-1 nucleocapsid (NC) protein represents an excellent molecular target for the development of anti-retrovirals by virtue of its well-characterized chaperone activities, which play pivotal roles in essential steps of the viral life cycle. Our ongoing search for candidates able to impair NC binding/annealing activities led to the identification of peptidyl-anthraquinones as a promising class of nucleic acid ligands. Seeking to elucidate the inhibition determinants and increase the potency of this class of compounds, we have now explored the effects of chirality in the linker connecting the planar nucleus to the basic side chains. We show here that the non-natural linker configuration imparted unexpected TAR RNA targeting properties to the 2,6-peptidyl-anthraquinones and significantly enhanced their potency. Even if the new compounds were able to interact directly with the NC protein, they manifested a consistently higher affinity for the TAR RNA substrate and their TAR-binding properties mirrored their ability to interfere with NC-TAR interactions. Based on these findings, we propose that the viral Tat protein, sharing the same RNA substrate but acting in distinct phases of the viral life cycle, constitutes an additional druggable target for this class of peptidyl-anthraquinones. The inhibition of Tat-TAR interaction for the test compounds correlated again with their TAR-binding properties, while simultaneously failing to demonstrate any direct Tat-binding capabilities. These considerations highlighted the importance of TAR RNA in the elucidation of their inhibition mechanism, rather than direct protein inhibition. We have therefore identified anti-TAR compounds with dual in vitro inhibitory activity on different viral proteins, demonstrating that it is possible to develop multitarget compounds capable of interfering with processes mediated by the interactions of this essential RNA domain of HIV-1 genome with NC and Tat proteins.

  5. Grooved nanowires from self-assembling hairpin molecules for solar cells.

    PubMed

    Tevis, Ian D; Tsai, Wei-Wen; Palmer, Liam C; Aytun, Taner; Stupp, Samuel I

    2012-03-27

    One of the challenges facing bulk heterojunction organic solar cells is obtaining organized films during the phase separation of intimately mixed donor and acceptor components. We report here on the use of hairpin-shaped sexithiophene molecules to generate by self-assembly grooved nanowires as the donor component in bulk heterojunction solar cells. Photovoltaic devices were fabricated via spin-casting to produce by solvent evaporation a percolating network of self-assembled nanowires and fullerene acceptors. Thermal annealing was found to increase power conversion efficiencies by promoting domain growth while still maintaining this percolating network of nanostructures. The benefits of self-assembly and grooved nanowires were examined by building devices from a soluble sexithiophene derivative that does not form one-dimensional structures. In these systems, excessive phase separation caused by thermal annealing leads to the formation of defects and lower device efficiencies. We propose that the unique hairpin shape of the self-assembling molecules allows the nanowires as they form to interact well with the fullerenes in receptor-ligand type configurations at the heterojunction of the two domains, thus enhancing device efficiencies by 23%. © 2012 American Chemical Society

  6. Coal Tar and Coal-Tar Pitch

    Cancer.gov

    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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lowe, N.J.; Wortzman, M.S.; Breeding, J.

    1983-06-01

    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 tomore » 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.« less

  8. Hairpin vortices in turbulent boundary layers

    NASA Astrophysics Data System (ADS)

    Eitel-Amor, G.; Örlü, R.; Schlatter, P.; Flores, O.

    2015-02-01

    The present work presents a number of parallel and spatially developing simulations of boundary layers to address the question of whether hairpin vortices are a dominant feature of near-wall turbulence, and which role they play during transition. In the first part, the parent-offspring regeneration mechanism is investigated in parallel (temporal) simulations of a single hairpin vortex introduced in a mean shear flow corresponding to either turbulent channels or boundary layers (Reτ ≲ 590). The effect of a turbulent background superimposed on the mean flow is considered by using an eddy viscosity computed from resolved simulations. Tracking the vortical structure downstream, it is found that secondary hairpins are only created shortly after initialization, with all rotational structures decaying for later times. For hairpins in a clean (laminar) environment, the decay is relatively slow, while hairpins in weak turbulent environments (10% of νt) dissipate after a couple of eddy turnover times. In the second part, the role of hairpin vortices in laminar-turbulent transition is studied using simulations of spatial boundary layers tripped by hairpin vortices. These vortices are generated by means of specific volumetric forces representing an ejection event, creating a synthetic turbulent boundary layer initially dominated by hairpin-like vortices. These hairpins are advected towards the wake region of the boundary layer, while a sinusoidal instability of the streaks near the wall results in rapid development of a turbulent boundary layer. For Reθ > 400, the boundary layer is fully developed, with no evidence of hairpin vortices reaching into the wall region. The results from both the parallel and spatial simulations strongly suggest that the regeneration process is rather short-lived and may not sustain once a turbulent background is developed. From the transitional flow simulations, it is conjectured that the forest of hairpins reported in former direct numerical

  9. Hairpin exact coherent states in channel flow

    NASA Astrophysics Data System (ADS)

    Graham, Michael; Shekar, Ashwin

    2017-11-01

    Questions remain over the role of hairpin vortices in fully developed turbulent flows. Studies have shown that hairpins play a role in the dynamics away from the wall but the question still persists if they play any part in (near wall) fully developed turbulent dynamics. In addition, the robustness of the hairpin vortex regeneration mechanism is still under investigation. Recent studies have shown the existence of nonlinear traveling wave solutions to the Navier-Stokes equations, also known as exact coherent states (ECS), that capture many aspects of near-wall turbulent structures. Previously discovered ECS in channel flow have a quasi-streamwise vortex structure, with no indication of hairpin formation. Here we present a family of traveling wave solutions for channel flow that displays hairpin vortices. They have a streamwise vortex-streak structure near the wall with a spatially localized hairpin head near the channel centerline, attached to and sustained by the near wall structures. This family of solutions emerges through a transcritical bifurcation from a branch of traveling wave solutions with y and z reflectional symmetry. We also look into the instabilities that lead to the development of hairpins also explore its connection to turbulent dynamics.

  10. Low-tar and high-tar cigarettes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Holt, P.G.; Chalmer, J.E.; Roberts, L.M.

    Mice were exposed for 7 to 8 minutes on weekdays to fresh smoke from high-tar (HT) or low-tar (LT) cigarettes for varying periods of up to 36 weeks. Mice exposed to HT cigarettes exhibited more marked alterations in humoral immune responsiveness, hematological profiles, and pulmonary pathologic findings than those exposed to LT cigarettes. However, cell-mediated immune responsiveness to both bacterial and tumor-specific antigens was depressed similarly in animals exposed to HT or LT cigarettes. Furthermore, the growth rates of subcutaneously established tumors were enhanced similarly in the two groups, with respect to those in control animals.

  11. tRNA Shifts the G-quadruplex-Hairpin Conformational Equilibrium in RNA towards the Hairpin Conformer.

    PubMed

    Rode, Ambadas B; Endoh, Tamaki; Sugimoto, Naoki

    2016-11-07

    Non-coding RNAs play important roles in cellular homeostasis and are involved in many human diseases including cancer. Intermolecular RNA-RNA interactions are the basis for the diverse functions of many non-coding RNAs. Herein, we show how the presence of tRNA influences the equilibrium between hairpin and G-quadruplex conformations in the 5' untranslated regions of oncogenes and model sequences. Kinetic and equilibrium analyses of the hairpin to G-quadruplex conformational transition of purified RNA as well as during co-transcriptional folding indicate that tRNA significantly shifts the equilibrium toward the hairpin conformer. The enhancement of relative translation efficiency in a reporter gene assay is shown to be due to the tRNA-mediated shift in hairpin-G-quadruplex equilibrium of oncogenic mRNAs. Our findings suggest that tRNA is a possible therapeutic target in diseases in which RNA conformational equilibria is dysregulated. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Topical tar: Back to the future

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Paghdal, K.V.; Schwartz, R.A.

    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 clearingmore » 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.« less

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

    PubMed

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

    2018-05-07

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

  14. Evolution of hairpin vortices in a shear flow

    NASA Technical Reports Server (NTRS)

    Hon, T.-L.; Walker, J. D. A.

    1988-01-01

    Recent experimental studies suggest that the hairpin vortex plays an important (and perhaps dominant) role in the dynamics of turbulent flows near walls. In this study a numerical procedure is developed to allow the accurate computation of the trajectory of a 3-D vortex having a small core radius. For hairpin vortices which are convected in a shear flow above a wall, the calculated results show that a 2-D vortex containing a small 3-D disturbance distorts into a complex shape with subsidiary hairpin vortices forming outboard of the original hairpin vortex. As the vortex moves above the wall, it induces unsteady motion in the viscous flow near the wall: numerical solutions suggest that the boundary-layer flow near the wall will ultimately erupt in response to the motion of the hairpin vortex and in the process a secondary hairpin vortex will be created. The computer results agree with recent experimental investigations.

  15. How hairpin vortices emerge from exact invariant solutions

    NASA Astrophysics Data System (ADS)

    Schneider, Tobias M.; Farano, Mirko; de Palma, Pietro; Robinet, Jean-Christoph; Cherubini, Stefania

    2017-11-01

    Hairpin vortices are among the most commonly observed flow structures in wall-bounded shear flows. However, within the dynamical system approach to turbulence, those structures have not yet been described. They are not captured by known exact invariant solutions of the Navier-Stokes equations nor have other state-space structures supporting hairpins been identified. We show that hairpin structures are observed along an optimally growing trajectory leaving a well known exact traveling wave solution of plane Poiseuille flow. The perturbation triggering hairpins does not correspond to an unstable mode of the exact traveling wave but lies in the stable manifold where non-normality causes strong transient amplification.

  16. Ultrafast Unzipping of a Beta-Hairpin Peptide

    NASA Astrophysics Data System (ADS)

    Zinth, W.; Schrader, T. E.; Schreier, W. J.; Koller, F. O.; Cordes, T.; Babitzki, G.; Denschlag, R.; Tavan, P.; Löweneck, M.; Dong, Shou-Liang; Moroder, L.; Renner, C.

    Light induced switching of a beta-hairpin structure is investigated by femtosecond IR spectroscopy. While the unzipping process comprises ultrafast kinetics and is finished within 1 ns, the folding into the hairpin structure is a much slower process.

  17. Exploring TAR–RNA aptamer loop–loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance

    PubMed Central

    Lebars, Isabelle; Legrand, Pierre; Aimé, Ahissan; Pinaud, Noël; Fribourg, Sébastien; Di Primo, Carmelo

    2008-01-01

    In HIV-1, trans-activation of transcription of the viral genome is regulated by an imperfect hairpin, the trans-activating responsive (TAR) RNA element, located at the 5′ untranslated end of all viral transcripts. TAR acts as a binding site for viral and cellular proteins. In an attempt to identify RNA ligands that would interfere with the virus life-cycle by interacting with TAR, an in vitro selection was previously carried out. RNA hairpins that formed kissing-loop dimers with TAR were selected [Ducongé F. and Toulmé JJ (1999) RNA, 5:1605–1614]. We describe here the crystal structure of TAR bound to a high-affinity RNA aptamer. The two hairpins form a kissing complex and interact through six Watson–Crick base pairs. The complex adopts an overall conformation with an inter-helix angle of 28.1°, thus contrasting with previously reported solution and modelling studies. Structural analysis reveals that inter-backbone hydrogen bonds between ribose 2′ hydroxyl and phosphate oxygens at the stem-loop junctions can be formed. Thermal denaturation and surface plasmon resonance experiments with chemically modified 2′-O-methyl incorporated into both hairpins at key positions, clearly demonstrate the involvement of this intermolecular network of hydrogen bonds in complex stability. PMID:18996893

  18. Process for hydrogenation of hydrocarbon tars

    DOEpatents

    Dolbear, Geoffrey E.

    1978-07-18

    Hydrocarbon tars of high asphaltene content such as tars obtained from pyrolysis of coal are dissolved in a solvent formed from the hydrogenation of the coal tars, and the resultant mixture hydrogenated in the presence of a catalyst at a pressure from about 1500 to 5000 psig at a temperature from about 500.degree. F to about the critical temperature of the solvent to form a light hydrocarbon as a solvent for the tars. Hydrogen content is at least three times the amount of hydrogen consumed.

  19. On hairpin vortices as model of wall turbulence structure

    NASA Technical Reports Server (NTRS)

    Liu, N.-S.; Shamroth, S. J.; Mcdonald, H.

    1985-01-01

    A model of the hairpin vortex has been constructed and used in two distinct but related approaches. The first approach is kinematic in nature in which a synthesis procedure using hairpin vortices to provide a quantitative link between mean flow quantities and the statistical quantities of near wall turbulence has become developed. The second approach is dynamic in nature, and the evolution of an incipient 'representative' hairpin vortex as well as the distortion of a background laminar boundary layer flow, in which the hairpin vortex is immersed, has been simulated by numerical solution of the unsteady, three-dimensional Navier-Stokes equations.

  20. The hairpin resonator: A plasma density measuring technique revisited

    NASA Astrophysics Data System (ADS)

    Piejak, R. B.; Godyak, V. A.; Garner, R.; Alexandrovich, B. M.; Sternberg, N.

    2004-04-01

    A microwave resonator probe is a resonant structure from which the relative permittivity of the surrounding medium can be determined. Two types of microwave resonator probes (referred to here as hairpin probes) have been designed and built to determine the electron density in a low-pressure gas discharge. One type, a transmission probe, is a functional equivalent of the original microwave resonator probe introduced by R. L. Stenzel [Rev. Sci. Instrum. 47, 603 (1976)], modified to increase coupling to the hairpin structure and to minimize plasma perturbation. The second type, a reflection probe, differs from the transmission probe in that it requires only one coaxial feeder cable. A sheath correction, based on the fluid equations for collisionless ions in a cylindrical electron-free sheath, is presented here to account for the sheath that naturally forms about the hairpin structure immersed in plasma. The sheath correction extends the range of electron density that can be accurately measured with a particular wire separation of the hairpin structure. Experimental measurements using the hairpin probe appear to be highly reproducible. Comparisons with Langmuir probes show that the Langmuir probe determines an electron density that is 20-30% lower than the hairpin. Further comparisons, with both an interferometer and a Langmuir probe, show hairpin measurements to be in good agreement with the interferometer while Langmuir probe measurements again result in a lower electron density.

  1. Characterization of Bleomycin-Mediated Cleavage of a Hairpin DNA Library

    PubMed Central

    Segerman, Zachary J.; Roy, Basab; Hecht, Sidney M.

    2013-01-01

    A study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal free BLM. The ability of Fe(II)•BLM to effect cleavage on both the 3' and 5'-arms of the hairpin DNAs was characterized. The strongly bound DNAs were found to be efficient substrates for Fe•BLM A5-mediated hairpin DNA cleavage. Surprisingly, the most prevalent site of BLM-mediated cleavage was found to be the 5′-AT-3′ dinucleotide sequence. This dinucleotide sequence, and other sequences generally not cleaved well by BLM when examined using arbitrarily chosen DNA substrates, were apparent when examining the library of ten hairpin DNAs. In total, 132 sites of DNA cleavage were produced by exposure of the hairpin DNA library to Fe•BLM A5. The existence of multiple sites of cleavage on both the 3′- and 5′-arms of the hairpin DNAs suggested that some of these might be double-strand cleavage events. Accordingly, an assay was developed with which to test the propensity of the hairpin DNAs to undergo double-strand DNA damage. One hairpin DNA was characterized using this method, and gave results consistent with earlier reports of double-strand DNA cleavage, but with a sequence selectivity different from those reported previously. PMID:23834496

  2. Method for treatment of tar-bearing fuel gas

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Frauen, L.L.; Kasper, S.

    1986-01-07

    A process is described of producing a fuel gas which contains condensable tar vapor when it leaves a gasifier, the improvement wherein the tar-bearing gases are treated to remove tar therefrom. The process consists of: (a) continuously conducting hot fuel gas from a gasifier to and discharging it into a spray chamber where the hot tar-bearing gas is contacted with a fine spray of water thereby cooling the tar vapor and evaporating the water to produce a fog-like dispersion of tar in an atmosphere of fuel gas with the temperature in the spray chamber maintained above the dew point ofmore » water; (b) continuously transferring the fuel gas and the dispersion of tar and water to an electrostatic precipitator and precipitating therein at least most of the condensed tar as a liquid; (c) removing the liquid tar so precipitated and conducting at least most of it to a tar burner; (d) burning the tar with no more than the stoichiometric supply of oxygen provided by air to produce oxygen-free and tar-free hot combustion gases; (e) conducting the hot combustion gases directly into a mixer into which the fuel gas and water vapor flows from the precipitator, thereby adding to the fuel gas the sensible heat of the combustion gases; and (f) conducting the mixture so produced to a place of use as a hot fuel gas mixture.« less

  3. Tomographic PIV Study of Hairpin Vortices

    NASA Astrophysics Data System (ADS)

    Sabatino, Daniel; Rossmann, Tobias

    2014-11-01

    Tomographic PIV is used in a free surface water channel to quantify the flow behavior of hairpin vortices that are artificially generated in a laminar boundary layer. Direct injection from a 32:1 aspect ratio slot at low blowing ratios (0 . 1 < BR < 0 . 2) is used to generate an isolated hairpin vortex in a thick laminar boundary layer (485 < Reδ* < 600). Due to the large dynamic range of length and velocity scales (the resulting vortices have advection velocities 5X greater than their tangential velocities), a tailored optical arrangement and specialized post processing techniques are required to fully capture the small-scale behavior and long-time development of the flow field. Hairpin generation and evolution are presented using the λ2 criterion derived from the instantaneous, three-dimensional velocity field. The insight provided by the tomographic data is also compared to the conclusions drawn from 2D PIV and passive scalar visualizations. Finally, the three-dimensional behavior of the measured velocity field is correlated with that of a simultaneously imaged, passive scalar dye that marks the boundary of the injected fluid, allowing the examination of the entrainment behavior of the hairpin. Supported by the National Science Foundation under Grant CBET-1040236.

  4. On hairpin vortex generation from near-wall streamwise vortices

    NASA Astrophysics Data System (ADS)

    Wang, Yinshan; Huang, Weixi; Xu, Chunxiao

    2015-04-01

    The generation of a hairpin vortex from near-wall streamwise vortices is studied via the direct numerical simulation (DNS) of the streak transient growth in the minimal channel flow at . The streak profile is obtained by conditionally averaging the DNS data of the fully developed turbulent channel flow at the same Reynolds number. The near-wall streamwise vortices are produced by the transient growth of the streak which is initially subjected to the sinuous perturbation of the spanwise velocity. It is shown that the arch head of the hairpin vortex first grows from the downstream end of the stronger streamwise vortex and then connects with the weaker, opposite-signed streamwise vortex in their overlap region, forming a complete individual hairpin structure. The vorticity transport along the vortex lines indicates that the strength increase and the spatial expansion of the arch head are due to the stretching and the turning of the vorticity vector, respectively. The hairpin packets could be further produced from the generated individual hairpin vortex following the parent-offspring process.

  5. 40 CFR 721.10532 - Tar, brown coal.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Tar, brown coal. 721.10532 Section 721... Tar, brown coal. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as tar, brown coal (PMN P-12-167, CAS No. 101316-83-0) is subject to...

  6. 40 CFR 721.10532 - Tar, brown coal.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Tar, brown coal. 721.10532 Section 721... Tar, brown coal. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as tar, brown coal (PMN P-12-167, CAS No. 101316-83-0) is subject to...

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

    PubMed Central

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

    2001-01-01

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

  8. Free energy profile of RNA hairpins: a molecular dynamics simulation study.

    PubMed

    Deng, Nan-Jie; Cieplak, Piotr

    2010-02-17

    RNA hairpin loops are one of the most abundant secondary structure elements and participate in RNA folding and protein-RNA recognition. To characterize the free energy surface of RNA hairpin folding at an atomic level, we calculated the potential of mean force (PMF) as a function of the end-to-end distance, by using umbrella sampling simulations in explicit solvent. Two RNA hairpins containing tetraloop cUUCGg and cUUUUg are studied with AMBER ff99 and CHARMM27 force fields. Experimentally, the UUCG hairpin is known to be significantly more stable than UUUU. In this study, the calculations using AMBER force field give a qualitatively correct description for the folding of two RNA hairpins, as the calculated PMF confirms the global stability of the folded structures and the resulting relative folding free energy is in quantitative agreement with the experimental result. The hairpin stabilities are also correctly differentiated by the more rapid molecular mechanics-Poisson Boltzmann-surface area approach, but the relative free energy estimated from this method is overestimated. The free energy profile shows that the native state basin and the unfolded state plateau are separated by a wide shoulder region, which samples a variety of native-like structures with frayed terminal basepair. The calculated PMF lacks major barriers that are expected near the transition regions, and this is attributed to the limitation of the 1-D reaction coordinate. The PMF results are compared with other studies of small RNA hairpins using kinetics method and coarse grained models. The two RNA hairpins described by CHARMM27 are significantly more deformable than those represented by AMBER. Compared with the AMBER results, the CHARMM27 calculated DeltaG(fold) for the UUUU tetraloop is in better agreement with the experimental results. However, the CHARMM27 calculation does not confirm the global stability of the experimental UUCG structure; instead, the extended conformations are predicted

  9. Stabilization of RNA hairpins using non-nucleotide linkers and circularization.

    PubMed

    Kiliszek, Agnieszka; Blaszczyk, Leszek; Kierzek, Ryszard; Rypniewski, Wojciech

    2017-06-02

    An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem. One method involves stilbene diether or hexaethylene glycol linkers and circularization by T4 RNA ligase. Another method uses click chemistry to stitch the RNA ends with a triazole linker. Both techniques are efficient and easy to perform. They should be useful in making stable, biologically relevant RNA constructs for structural studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Treating tar sands formations with karsted zones

    DOEpatents

    Vinegar, Harold J.; Karanikas, John Michael

    2010-03-09

    Methods for treating a tar sands formation are described herein. The tar sands formation may have one or more karsted zones. Methods may include providing heat from one or more heaters to one or more karsted zones of the tar sands formation to mobilize fluids in the formation. At least some of the mobilized fluids may be produced from the formation.

  11. Development of Hairpin Vortices in Turbulent Spots and End-Wall Transition

    NASA Technical Reports Server (NTRS)

    Smith, Charles R.

    2007-01-01

    The end-stage phase of boundary layer transition is characterized by the development of hairpin-like vortices which evolve rapidly into patches of turbulent behavior. In general, the characteristics of the evolution form this hairpin stage to the turbulent stage is poorly understood, which has prompted the present experimental examination of hairpin vortex development and growth processes. Two topics of particular relevance to the workshop focus will be covered: 1) the growth of turbulent spots through the generatio and amalgamation of hairpin-like vortices, and 2) the development of hairpin vortices during transition in an end-wall junction flow. Brief summaries of these studies are described below. Using controlled generation of hairpin vortices by surface injection in a critical laminar boundary layer, detailed flow visualization studies have been done of the phases of growth of single hairpin vortices, from the initial hairgin generation, through the systematic generation of secondary hairpin-like flow structures, culminating in the evolution to a turbulent spot. The key to the growth process is strong vortex-surface interactions, which give rise to strong eruptive events adjacent to the surface, which results in the generation of subsequent hairpin vortex structures due to inviscid-viscuous interactions between the eruptive events and the free steam fluid. The general process of vortex-surface fluid interaction, coupled with subsequent interactions and amalgamation of the generated multiple hairpin-type vortices, is demonstrated as a physical mechanism for the growth and development of turbulent spots. When a boundary layer flow along a surface encounters a bluff body obstruction extending from the surface (such as cylinder or wing), the strong adverse pressure gradients generated by these types of flows result in the concentration of the impinging vorticity into a system of discrete vortices near the end-wall juncture of the obstruction, with the extensions

  12. Tar Management and Recycling in Biomass Gasification and Syngas Purification

    NASA Astrophysics Data System (ADS)

    McCaffrey, Zach

    Removal of tars is critical to the design and operation of biomass gasification systems as most syngas utilization processing equipment (e.g. internal combustion engines, gas turbines, fuel cells, and liquid fuel synthesis reactors) have a low tolerance for tar. Capturing and disposal of tar is expensive due to equipment costs, high hazardous waste disposal costs where direct uses cannot be found, and system energy losses incurred. Water scrubbing is an existing technique commonly used in gasification plants to remove contaminants and tar; however using water as the absorbent is non-ideal as tar compounds have low or no water solubility. Hydrophobic solvents can improve scrubber performance and this study evaluated tar solubility in selected solvents using slip-streams of untreated syngas from a laboratory fluidized bed reactor operated on almond composite feedstock using both air and steam gasification. Tar solubility was compared with Hansen's solubility theory to examine the extent to which the tar removal can be predicted. As collection of tar without utilization leads to a hazardous waste problem, the study investigated the effects of recycling tars back into the gasifier for destruction. Prior to experiments conducted on tar capture and recycle, characterizations of the air and steam gasification of the almond composite mix were made. This work aims to provide a better understanding of tar collection and solvent selection for wet scrubbers, and to provide information for designing improved tar management systems for biomass gasification.

  13. Method for filtering solvent and tar sand mixtures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kelterborn, J. C.; Stone, R. A.

    1985-09-03

    A method for filtering spent tar sands from a bitumen and organic solvent solution comprises separating the solution into two streams wherein the bulk of the coarser spent tar sand is in a first stream and has an average particle size of about 10 to about 100 mesh and the bulk of the finer spent tar sand is in a second stream; producing a filter cake by filtering the coarser spent tar sand from the first stream; and filtering the finer spent tar sand from the second stream with the filter cake. The method is particularly useful for filtering solutionsmore » of bitumen extracted from bitumen containing diatomite, spent diatomite and organic solvent.« less

  14. Final safety assessment of Coal Tar as used in cosmetics.

    PubMed

    2008-01-01

    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. Coal Tar is a nearly black, viscous liquid, heavier than water, with a naphthalene-like odor and a sharp burning taste, produced in cooking ovens as a by-product in the manufacture of coke. Crude Coal Tar is composed of 48% hydrocarbons, 42% carbon, and 10% water. 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. In short-term studies, mice fed a diet containing Coal Tar found it unpalatable, but no adverse effects were reported other than weight loss; rats injected with Coal Tar experienced malaise in one study and decreased water intake and increased liver weights in another; rabbits injected with Coal Tar residue experienced eating avoidance, respiratory difficulty, sneezing, and weight loss. In a subchronic neurotoxicity study using mice, a mixture of phenols, cresols, and xylenols at concentrations approximately equal to those expected in Coal Tar extracts produced regionally selective effects, with a rank order of corpus striatum > cerebellum > cerebral cortex. Coal Tar applied to the backs of guinea pigs increases epidermal thickness. Painting female rabbits with tar decreases the absolute and relative weights of the ovaries and decreased the number of interstitial cells in the ovary. Four therapeutic Coal Tar preparations used in the treatment of psoriasis were mutagenic in the Ames assay. Urine and blood from patients treated with Coal Tar

  15. Smokers' knowledge and understanding of advertised tar numbers: health policy implications.

    PubMed

    Cohen, J B

    1996-01-01

    This article examines health policy implications of providing smokers with numerical tar yield information in cigarette advertising. Results of a national probability telephone survey regarding smokers' knowledge and understanding of numerical tar yields and deliveries are reported. Few smokers knew the tar level of their own cigarettes (the exception being smokers of 1- to 5-mg tar cigarettes), and a majority could not correctly judge the relative tar levels of cigarettes. Smokers were unsure whether switching to lower-tar cigarettes would reduce their personal health risks. Many smokers relied on absolute numbers in making trade-offs between number of cigarettes smoked and their tar levels, thus confusion machine-rated tar-yields with actual amounts ingested. The wisdom of the present method of providing tar and nicotine numbers in ads and recommendations for modifying the test protocol are now under discussion. This research indicates that these tar numbers and their implications are poorly understood. The paper recommends revisions in tar ratings to make them more useful and a required statement on cigarette packages to more explicitly relate tar levels to major health risks.

  16. Identification and tracking of hairpin vortex auto-generation in turbulent wall-bounded flow

    NASA Astrophysics Data System (ADS)

    Huang, Yangzi; Green, Melissa

    2016-11-01

    Hairpin vortices have been widely accepted as component structures of turbulent boundary layers. Their properties (size, vorticity, energy) and dynamic phenomena (origin, growth, breakdown) have been shown to correlate to the complex, multi-scaled turbulent motions observed in both experiments and simulations. As established in the literature, the passage of a hairpin vortex creates a wall-normal ejection of fluid, which encounters the high-speed freestream resulting in near-wall shear and increased drag. A previously generated simulation of an isolated hairpin vortex is used to study the auto-generation of a secondary vortex structure. Eulerian methods such as the Q criterion and Γ2 function, as well as Lagrangian methods are used to visualize the three-dimensional hairpin vortices and the auto-generation process. The circulation development and wall-normal location of both primary and secondary hairpin heads are studied to determine if there is a correlation between the strength and height of the primary hairpin vortex with the secondary hairpin vortex auto-generation.

  17. MultiMiTar: a novel multi objective optimization based miRNA-target prediction method.

    PubMed

    Mitra, Ramkrishna; Bandyopadhyay, Sanghamitra

    2011-01-01

    Machine learning based miRNA-target prediction algorithms often fail to obtain a balanced prediction accuracy in terms of both sensitivity and specificity due to lack of the gold standard of negative examples, miRNA-targeting site context specific relevant features and efficient feature selection process. Moreover, all the sequence, structure and machine learning based algorithms are unable to distribute the true positive predictions preferentially at the top of the ranked list; hence the algorithms become unreliable to the biologists. In addition, these algorithms fail to obtain considerable combination of precision and recall for the target transcripts that are translationally repressed at protein level. In the proposed article, we introduce an efficient miRNA-target prediction system MultiMiTar, a Support Vector Machine (SVM) based classifier integrated with a multiobjective metaheuristic based feature selection technique. The robust performance of the proposed method is mainly the result of using high quality negative examples and selection of biologically relevant miRNA-targeting site context specific features. The features are selected by using a novel feature selection technique AMOSA-SVM, that integrates the multi objective optimization technique Archived Multi-Objective Simulated Annealing (AMOSA) and SVM. MultiMiTar is found to achieve much higher Matthew's correlation coefficient (MCC) of 0.583 and average class-wise accuracy (ACA) of 0.8 compared to the others target prediction methods for a completely independent test data set. The obtained MCC and ACA values of these algorithms range from -0.269 to 0.155 and 0.321 to 0.582, respectively. Moreover, it shows a more balanced result in terms of precision and sensitivity (recall) for the translationally repressed data set as compared to all the other existing methods. An important aspect is that the true positive predictions are distributed preferentially at the top of the ranked list that makes MultiMiTar

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

    PubMed

    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

  19. β-hairpin-mediated nucleation of polyglutamine amyloid formation

    PubMed Central

    Kar, Karunakar; Hoop, Cody L.; Drombosky, Kenneth W.; Baker, Matthew A.; Kodali, Ravindra; Arduini, Irene; van der Wel, Patrick C. A.; Horne, W. Seth; Wetzel, Ronald

    2013-01-01

    The conformational preferences of polyglutamine (polyQ) sequences are of major interest because of their central importance in the expanded CAG repeat diseases that include Huntington’s disease (HD). Here we explore the response of various biophysical parameters to the introduction of β-hairpin motifs within polyQ sequences. These motifs (trpzip, disulfide, D-Pro-Gly, Coulombic attraction, L-Pro-Gly) enhance formation rates and stabilities of amyloid fibrils with degrees of effectiveness well-correlated with their known abilities to enhance β-hairpin formation in other peptides. These changes led to decreases in the critical nucleus for amyloid formation from a value of n* = 4 for a simple, unbroken Q23 sequence to approximate unitary n* values for similar length polyQs containing β-hairpin motifs. At the same time, the morphologies, secondary structures, and bioactivities of the resulting fibrils were essentially unchanged from simple polyQ aggregates. In particular, the signature pattern of SSNMR 13C Gln resonances that appears to be unique to polyQ amyloid is replicated exactly in fibrils from a β-hairpin polyQ. Importantly, while β-hairpin motifs do produce enhancements in the equilibrium constant for nucleation in aggregation reactions, these Kn* values remain quite low (~ 10−10) and there is no evidence for significant embellishment of β-structure within the monomer ensemble. The results indicate an important role for β-turns in the nucleation mechanism and structure of polyQ amyloid and have implications for the nature of the toxic species in expanded CAG repeat diseases. PMID:23353826

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

    PubMed

    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.

  1. 7 CFR 3201.76 - Asphalt and tar removers.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Asphalt and tar removers. 3201.76 Section 3201.76... Designated Items § 3201.76 Asphalt and tar removers. (a) Definition. Cleaning agents designed to remove asphalt or tar from equipment, roads, or other surfaces. (b) Minimum biobased content. The Federal...

  2. 7 CFR 3201.76 - Asphalt and tar removers.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Asphalt and tar removers. 3201.76 Section 3201.76... Designated Items § 3201.76 Asphalt and tar removers. (a) Definition. Cleaning agents designed to remove asphalt or tar from equipment, roads, or other surfaces. (b) Minimum biobased content. The Federal...

  3. Smokers' knowledge and understanding of advertised tar numbers: health policy implications.

    PubMed Central

    Cohen, J B

    1996-01-01

    OBJECTIVES. This article examines health policy implications of providing smokers with numerical tar yield information in cigarette advertising. METHODS. Results of a national probability telephone survey regarding smokers' knowledge and understanding of numerical tar yields and deliveries are reported. RESULTS. Few smokers knew the tar level of their own cigarettes (the exception being smokers of 1- to 5-mg tar cigarettes), and a majority could not correctly judge the relative tar levels of cigarettes. Smokers were unsure whether switching to lower-tar cigarettes would reduce their personal health risks. Many smokers relied on absolute numbers in making trade-offs between number of cigarettes smoked and their tar levels, thus confusion machine-rated tar-yields with actual amounts ingested. CONCLUSIONS. The wisdom of the present method of providing tar and nicotine numbers in ads and recommendations for modifying the test protocol are now under discussion. This research indicates that these tar numbers and their implications are poorly understood. The paper recommends revisions in tar ratings to make them more useful and a required statement on cigarette packages to more explicitly relate tar levels to major health risks. PMID:8561236

  4. An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation

    PubMed Central

    Shi, Ke; Huang, Wai Mun; Aihara, Hideki

    2013-01-01

    Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting–rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions. PMID:23382649

  5. The Australian tar derby: the origins and fate of a low tar harm reduction programme

    PubMed Central

    King, W; Carter, S; Borland, R; Chapman, S; Gray, N

    2003-01-01

    Objective: To document the development of the low tar harm reduction programme in Australia, including tobacco industry responses. Data sources: Tobacco industry documents, retail tobacco journals, newspapers, medical journals, and Anti-Cancer Council of Victoria (ACCV) newsletters and archival records. Study selection: Documents on the strategies and knowledge bases of the ACCV, other Australian health authorities, and the tobacco industry. Results: The ACCV built a durable system for measuring and publicising the tar and nicotine yields of Australian cigarettes and influencing their development. The tobacco industry initially sought to block the development of this system but later appeared to cooperate with it, as is evidenced by the current market dominance of low tar brands. However, behind the scenes, the industry used its substantial knowledge advantage regarding compensatory smoking and its ability to re-engineer cigarettes to gain effective control of the system and subvert the ACCV's objectives. Conclusions: Replacement of the low tar programme with new means of minimising the harms from cigarette smoking should be a policy priority for the Australian government. This will require regulation, rather than further voluntary agreements, and stringent monitoring of successor programmes will be necessary. PMID:14645950

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

    PubMed Central

    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

  7. Modeling the mechanism of CLN025 beta-hairpin formation

    NASA Astrophysics Data System (ADS)

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

    2017-09-01

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

  8. Internal vs Fishhook Hairpin DNA: Unzipping Locations and Mechanisms in the α-Hemolysin Nanopore

    PubMed Central

    2015-01-01

    Studies on the interaction of hairpin DNA with the α-hemolysin (α-HL) nanopore have determined hairpin unzipping kinetics, thermodynamics, and sequence-dependent DNA/protein interactions. Missing from these results is a systematic study comparing the unzipping process for fishhook (one-tail) vs internal (two-tail) hairpins when they are electrophoretically driven from the cis to the trans side of α-HL via a 30-mer single-stranded tail. In the current studies, fishhook hairpins showed long unzipping times with one deep blockage current level. In contrast, the internal hairpins demonstrated relatively fast unzipping and a characteristic pulse-like current pattern. These differences were further explored with respect to stem length and sequence context. Further, a series of internal hairpins with asymmetric tails were studied, for which it was determined that a second tail longer than 12 nucleotides results in internal hairpin unzipping behavior, while tail lengths of 6 nucleotides behaved like fishhook hairpins. Interestingly, these studies were able to resolve a current difference of ∼6% between hairpin DNA immobilized in the nanopore waiting to unzip vs the translocating unzipped DNA, with the latter showing a deeper current blockage level. This demonstration of different currents for immobilized and translocating DNA has not been described previously. These results were interpreted as fishhook hairpins unzipping inside the vestibule, while the internal hairpins unzip outside the vestibule of α-HL. Lastly, we used this knowledge to study the unzipping of a long double-stranded DNA (>50 base pairs) outside the vestibule of α-HL. The conclusions drawn from these studies are anticipated to be beneficial in future application of nanopore analysis of nucleic acids. PMID:25333648

  9. Peptide Inhibitors of the Amyloidogenesis of IAPP: Verification of the Hairpin Binding Geometry Hypothesis

    PubMed Central

    Sivanesam, Kalkena; Shu, Irene; Huggins, Kelly N. L.; Tatarek-Nossol, Marianna; Kapurniotu, Aphrodite; Andersen, Niels H.

    2016-01-01

    Versions of a previously discovered β-hairpin peptide inhibitor of IAPP aggregation that are stabilized in that conformation, or even forced to remain in the hairpin conformation by a backbone cyclization constraint, display superior activity as inhibitors. The cyclized hairpin, cyclo-WW2, displays inhibitory activity at sub-stoichiometric concentrations relative to this amyloidogenic peptide. The hairpin binding hypothesis stands confirmed. PMID:27317951

  10. Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.

    PubMed

    Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J

    2014-12-31

    RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.

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

    PubMed

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

    2014-09-01

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

  12. Peptide Inhibitors of the amyloidogenesis of IAPP: verification of the hairpin-binding geometry hypothesis.

    PubMed

    Sivanesam, Kalkena; Shu, Irene; Huggins, Kelly N L; Tatarek-Nossol, Marianna; Kapurniotu, Aphrodite; Andersen, Niels H

    2016-08-01

    Versions of a previously discovered β-hairpin peptide inhibitor of IAPP aggregation that are stabilized in that conformation, or even forced to remain in the hairpin conformation by a backbone cyclization constraint, display superior activity as inhibitors. The cyclized hairpin, cyclo-WW2, displays inhibitory activity at substoichiometric concentrations relative to this amyloidogenic peptide. The hairpin-binding hypothesis stands confirmed. © 2016 Federation of European Biochemical Societies.

  13. Replacement of RNA hairpins by in vitro selected tetranucleotides.

    PubMed Central

    Dichtl, B; Pan, T; DiRenzo, A B; Uhlenbeck, O C

    1993-01-01

    An in vitro selection method based on the autolytic cleavage of yeast tRNA(Phe) by Pb2+ was applied to obtain tRNA derivatives with the anticodon hairpin replaced by four single-stranded nucleotides. Based on the rates of the site-specific cleavage by Pb2+ and the presence of a specific UV-induced crosslink, certain tetranucleotide sequences allow proper folding of the rest of the tRNA molecule, whereas others do not. One such successful tetramer sequence was also used to replace the acceptor stem of yeast tRNA(Phe) and the anticodon hairpin of E.coli tRNA(Phe) without disrupting folding. These experiments suggest that certain tetramers may be able to replace structurally nonessential hairpins in any RNA. Images PMID:7680121

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

    PubMed

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

    2013-05-23

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

  15. Transverse Aeolian Ridges (TARs) on Mars II: Distributions, orientations, and ages

    NASA Astrophysics Data System (ADS)

    Berman, Daniel C.; Balme, Matthew R.; Rafkin, Scot C. R.; Zimbelman, James R.

    2011-05-01

    Transverse Aeolian Ridges (TARs), 10 m scale, ripple-like aeolian bedforms with simple morphology, are widespread on Mars but it is unknown what role they play in Mars' wider sediment cycle. We present the results of a survey of all Mars Global Surveyor Narrow angle images in a pole-to-pole study area, 45° longitude wide. Following on from the classification scheme and preliminary surveys of Balme et al. (Balme, M.R., Berman, D.C., Bourke, M.C., Zimbelman, J.R. [2008a]. Geomorphology 101, 703-720) and Wilson and Zimbelman (Wilson, S.A., Zimbelman, J.R. [2004]. J. Geophys. Res. 109 (E10). doi: 10.1029/2004JE002247) we searched more than 10,000 images, and found that over 2000 reveal at least 5% areal cover by TARs. The mean TAR areal cover in the study area is about 7% (3% in the northern hemisphere and 11% in the southern hemisphere) but TARs are not homogenously distributed - they are concentrated in the mid-low latitudes and almost absent poleward of 35°N and 55°S. We found no clear correlation between TAR distribution and any of thermal inertia, kilometer-scale roughness, or elevation. We did find that TARs are less common at extremes of elevation. We found that TARs are most common near the equator (especially in the vicinity of Meridiani Planum, in which area they have a distinctive "barchan-like" morphology) and in large southern-hemisphere impact craters. TARs in the equatorial band are usually associated with outcrops of layered terrain or steep slopes, hence their relative absence in the northern hemisphere. TARs in the southern hemisphere are most commonly associated with low albedo, intercrater dune fields. We speculate that the mid-latitude mantling terrain (e.g., Mustard, J.F., Cooper, C.D., Rifkin, M.K. [2001]. Nature 412, 411-414; Kreslavsky, M.A., Head, J.W. [2002]. J. Geophys. Res. 29 (15). doi: 10.1029/2002GL015392) could also play a role in covering TARs or inhibiting saltation. We compared TAR distribution with general circulation model (GCM

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

    NASA Technical Reports Server (NTRS)

    Singer, Bart A.; Joslin, Ronald D.

    1995-01-01

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

  17. Atmospheric tar balls from biomass burning in Mexico

    NASA Astrophysics Data System (ADS)

    Adachi, K.; Buseck, P. R.

    2009-12-01

    Tar balls are spherical, organic aerosol particles that result from biofuel or biomass burning. They absorb sunlight and cause warming of the atmosphere. Although distinctive when viewed with a transmission electron microscope (TEM) because of their spherical shape, much remains to be determined about details of their compositions, occurrences, and generation. Here we aim to characterize the occurrences of tar balls using individual-particle analyses with a TEM and to study their formation in young biomass-burning smoke. The samples were collected using the U.S. Forest Service Twin Otter aircraft during the MILAGRO (Megacity Initiative: Local and Global Research Observations) campaign conducted in March 2006. We analyzed 84 TEM grid samples from ~30 biomass-burning events near Mexico City and over Yucatan. Sixty samples were from young smoke (less than an hour old), and others were from haze that mainly occurred from biomass burning. Tar balls have neither an evident nucleus nor are they normally attached to other particles. They are almost perfectly spherical on TEM grids, indicating that they were solid when collected. It appears as if tar balls consist of lower volatility organic matter than many other organic aerosol particles. On average, 9% by number of biomass-burning aerosol particles were tar balls in samples collected between a few minutes to an hour after emission. On the other hand, samples collected within a few minutes after emission included few or no tar balls. The occurrences and abundances of atmospheric tar balls are important when evaluating the effects of smoke on local and regional climate.

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

    PubMed

    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.

  19. Atmospheric Tar Balls: Particles from Biomass and Biofuel Burning

    NASA Technical Reports Server (NTRS)

    Posfai, Mihaly; Gelencser, Andras; Simonics, Renata; Arato, Krisztina; Li, Jia; Hobbs, Peter V.; Buseck, Peter R.

    2004-01-01

    Tar balls are amorphous, carbonaceous spherules that occur in the tropospheric aerosol as a result of biomass and biofuel burning. They form a distinct group of particles with diameters typically between 30 and 500 nm and readily identifiable with electron microscopy. Their lack of a turbostratic microstructure distinguishes them from soot, and their morphology and composition (approximately 90 mol% carbon) renders them distinct from other carbonaceous particles. Tar balls are particularly abundant in slightly aged (minutes to hours old) biomass smoke, indicating that they likely form by gas-to-particle conversion within smoke plumes. The material of tar balls is initially hygroscopic; however, the particles become largely insoluble as a result of free radical polymerization of their organic molecules. Consequently, tar balls are primarily externally mixed with other particle types, and they do not appreciably increase in size during aging. When tar balls coagulate with water-bearing particles, their material may partly dissolve and no longer be recognizable as distinct particles. Tar balls may contain organic compounds that absorb sunlight. They are an important, previously unrecognized type of carbonaceous (organic) atmospheric particle.

  20. Tar, nicotine, and carbon monoxide yields of some Nigerian cigarettes.

    PubMed Central

    Awotedu, A A; Higenbottam, T W; Onadeko, B O

    1983-01-01

    Fourteen cigarette brands manufactured in Nigeria in 1981 were analysed to determine the tar, nicotine, and carbon monoxide yields. Five of the brands belonged to the high and middle to high tar category (greater than 22 mg/cigarette) and nine to the middle tar (17-22 mg/cigarette) category. None of the cigarettes was in the low to middle and low tar (less than 17 mg/cigarette) category. The nicotine and carbon monoxide yields were similar to those of European cigarettes. Tobacco companies need to manufacture low tar cigarettes in the Third World as is the practice in the economically developed parts of the world. PMID:6619721

  1. Method and apparatus for hydrocarbon recovery from tar sands

    DOEpatents

    Westhoff, J.D.; Harak, A.E.

    1988-05-04

    A method and apparatus for utilizing tar sands having a broad range of bitumen content is disclosed. More particularly, tar sands are pyrolyzed in a cyclone retort with high temperature gases recycled from the cyclone retort to produce oil and hydrocarbon products. The spent tar sands are then burned at 2000/degree/F in a burner to remove residual char and produce a solid waste that is easily disposable. The process and apparatus have the advantages of being able to utilize tar sands having a broad range of bitumen content and the advantage of producing product gases that are free from combustion gases and thereby have a higher heating value. Another important advantage is rapid pyrolysis of the tar sands in the cyclone so as to effectively utilize smaller sized reactor vessels for reducing capitol and operating costs. 1 fig., 1 tab.

  2. Method and apparatus for hydrocarbon recovery from tar sands

    DOEpatents

    Westhoff, James D.; Harak, Arnold E.

    1989-01-01

    A method and apparatus for utilizing tar sands having a broad range of bitumen content is disclosed. More particularly, tar sands are pyrolyzed in a cyclone retort with high temperature gases recycled from the cyclone retort to produce oil and hydrocarbon products. The spent tar sands are then burned at 2000.degree. F. in a burner to remove residual char and produce a solid waste that is easily disposable. The process and apparatus have the advantages of being able to utilize tar sands having a broad range of bitumen content and the advantage of producing product gases that are free from combustion gases and thereby have a higher heating value. Another important advantage is rapid pyrolysis of the tar sands in the cyclone so as to effectively utilize smaller sized reactor vessels for reducing capitol and operating costs.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 whichmore » 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.« less

  4. Treating tar sands formations with dolomite

    DOEpatents

    Vinegar, Harold J.; Karanikas, John Michael

    2010-06-08

    Methods for treating a tar sands formation are described herein. The tar sands formation may include dolomite and hydrocarbons. Methods may include providing heat at less than the decomposition temperature of dolomite from one or more heaters to at least a portion of the formation. At least some of the hydrocarbon fluids are mobilized in the formation. At least some of the hydrocarbon fluids may be produced from the formation.

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

    PubMed

    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.

  6. Fractal-like Tar Ball Aggregates from Wildfire Smoke

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Girotto, Giulia; China, Swarup; Bhandari, Janarjan

    Tar balls are atmospheric particles abundant in slightly aged biomass burning smoke and have a significant, but highly uncertain, role on Earth's radiative balance. Tar balls are typically detected using electron microscopy; they are resistant to the electron beam, and generally, they are observed as individual spheres. Here, we report new observations of a significant fraction of tar ball aggregates (~27% by number) from samples collected in a plume of the Whitewater-Baldy Complex fire in New Mexico. The structure of these aggregates is fractal-like and follows a scale invariant power law similar to that of soot particles, despite the considerablymore » larger size and smaller number of monomers. We also present observations of tar ball aggregates from four other geographical locations, including from a remote high elevation site in the North Atlantic Ocean. Aggregation affects the particle optical properties and therefore, their climatic impact. We performed numerical simulations based on the observed morphology and estimated the effects of aggregation on the tar balls optical properties. We find that aggregation can enhance single scattering albedo by up to 41%.« less

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

    PubMed

    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

    PubMed Central

    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

  9. Sydney Tar Ponds Remediation: Experience to China

    ERIC Educational Resources Information Center

    Liu, Fan; Bryson, Ken A.

    2009-01-01

    The infamous "Sydney Tar Ponds" are well known as one of the largest toxic waste sites of Canada, due to almost 100 years of steelmaking in Sydney, a once beautiful and peaceful city located on the east side of Cape Breton Island, Nova Scotia. This article begins with a contextual overview of the Tar Ponds issue including a brief…

  10. Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein.

    PubMed

    Belfetmi, Anissa; Zargarian, Loussiné; Tisné, Carine; Sleiman, Dona; Morellet, Nelly; Lescop, Ewen; Maskri, Ouerdia; René, Brigitte; Mély, Yves; Fossé, Philippe; Mauffret, Olivier

    2016-04-01

    The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem-loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR-cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59. © 2016 Belfetmi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  11. A label-free DNA hairpin biosensor for colorimetric detection of target with suitable functional DNA partners.

    PubMed

    Nie, Ji; Zhang, De-Wen; Tie, Cai; Zhou, Ying-Lin; Zhang, Xin-Xiang

    2013-11-15

    The combination of aptamer and peroxidase-mimicking DNAzyme within a hairpin structure can form a functional DNA probe. The activities of both aptamer (as biorecognition element) and DNAzyme (as signal amplification element) are blocked via base pairing in the hairpin structure. The presence of target triggers the opening of the hairpin to form target/aptamer complex and releases G-quadruplex sequence which can generate amplified colorimetric signals. In this work, we elaborated a universal and simple procedure to design an efficient and sensitive hairpin probe with suitable functional DNA partners. A fill-in-the-blank process was developed for sequence design, and two key points including the pretreatment of the hairpin probe and the selection of suitable signal transducer sequence were proved to enhance the detection sensitivity. Cocaine was chosen as a model target for a proof of concept. A series of hairpins with different numbers of base pairs in the stem region were prepared. Hairpin-C10 with ten base pairs was screened out and a lowest detectable cocaine concentration of 5 μM by colorimetry was obtained. The proposed functional DNA hairpin showed good selectivity and satisfactory analysis in spiked biologic fluid. The whole "mix-and-measure" detection based on DNA hairpin without the need of immobilization and labeling was indicated to be time and labor saving. The strategy has potential to be transplanted into more smart hairpins toward other targets for general application in bioanalytical chemistry. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

    PubMed Central

    Belfetmi, Anissa; Zargarian, Loussiné; Tisné, Carine; Sleiman, Dona; Morellet, Nelly; Lescop, Ewen; Maskri, Ouerdia; René, Brigitte; Mély, Yves; Fossé, Philippe; Mauffret, Olivier

    2016-01-01

    The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem–loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR–cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59. PMID:26826129

  13. 48 CFR Appendix to Part 1252 - Tar Matrix

    Code of Federal Regulations, 2010 CFR

    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...

  14. Integrated Biomass Gasification with Catalytic Partial Oxidation for Selective Tar Conversion

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Lingzhi; Wei, Wei; Manke, Jeff

    Biomass gasification is a flexible and efficient way of utilizing widely available domestic renewable resources. Syngas from biomass has the potential for biofuels production, which will enhance energy security and environmental benefits. Additionally, with the successful development of low Btu fuel engines (e.g. GE Jenbacher engines), syngas from biomass can be efficiently used for power/heat co-generation. However, biomass gasification has not been widely commercialized because of a number of technical/economic issues related to gasifier design and syngas cleanup. Biomass gasification, due to its scale limitation, cannot afford to use pure oxygen as the gasification agent that used in coal gasification.more » Because, it uses air instead of oxygen, the biomass gasification temperature is much lower than well-understood coal gasification. The low temperature leads to a lot of tar formation and the tar can gum up the downstream equipment. Thus, the biomass gasification tar removal is a critical technology challenge for all types of biomass gasifiers. This USDA/DOE funded program (award number: DE-FG36-O8GO18085) aims to develop an advanced catalytic tar conversion system that can economically and efficiently convert tar into useful light gases (such as syngas) for downstream fuel synthesis or power generation. This program has been executed by GE Global Research in Irvine, CA, in collaboration with Professor Lanny Schmidt's group at the University of Minnesota (UoMn). Biomass gasification produces a raw syngas stream containing H2, CO, CO2, H2O, CH4 and other hydrocarbons, tars, char, and ash. Tars are defined as organic compounds that are condensable at room temperature and are assumed to be largely aromatic. Downstream units in biomass gasification such as gas engine, turbine or fuel synthesis reactors require stringent control in syngas quality, especially tar content to avoid plugging (gum) of downstream equipment. Tar- and ash-free syngas streams are a

  15. Macromolecular crowding impacts on the diffusion and conformation of DNA hairpins

    NASA Astrophysics Data System (ADS)

    Stiehl, Olivia; Weidner-Hertrampf, Kathrin; Weiss, Matthias

    2015-01-01

    Biochemical reactions in crowded fluids differ significantly from those in dilute solutions. Both, excluded-volume interactions with surrounding macromolecules ("crowders") and an enhanced rebinding of reaction partners due to crowding-induced viscoelasticity and subdiffusion have been hypothesized to shift chemical equilibria towards the associated state. We have explored the impact of both cues in an experimentally tunable system by monitoring the steady-state fraction of open DNA hairpins in crowded fluids with varying viscoelastic characteristics but similar occupied volume fractions. As a result, we observed an increased fraction of closed DNA hairpins in viscoelastic crowded fluids. Our observations compare favorably to a simple statistical model that considers both facets of crowding, while preferential interactions between crowders and DNA hairpins appear to have little influence.

  16. Banded TARs in Iapygia

    NASA Image and Video Library

    2014-09-10

    The tropics of Mars are commonly littered with small bright ripples that were somehow shaped by the wind. NASA Mars Reconnaissance Orbiter might provide a valuable clue to the formation of transverse aeolian ridges TARs elsewhere on Mars.

  17. Propensities of peptides containing the Asn-Gly segment to form β-turn and β-hairpin structures.

    PubMed

    Kang, Young Kee; Yoo, In Kee

    2016-09-01

    The propensities of peptides that contain the Asn-Gly segment to form β-turn and β-hairpin structures were explored using the density functional methods and the implicit solvation model in CH2 Cl2 and water. The populations of preferred β-turn structures varied depending on the sequence and solvent polarity. In solution, β-hairpin structures with βI' turn motifs were most preferred for the heptapeptides containing the Asn-Gly segment regardless of the sequence of the strands. These preferences in solution are consistent with the corresponding X-ray structures. The sequence, H-bond strengths, solvent polarity, and conformational flexibility appeared to interact to determine the preferred β-hairpin structure of each heptapeptide, although the β-turn segments played a role in promoting the formation of β-hairpin structures and the β-hairpin propensity varied. In the heptapeptides containing the Asn-Gly segment, the β-hairpin formation was enthalpically favored and entropically disfavored at 25°C in water. The calculated results for β-turns and β-hairpins containing the Asn-Gly segment imply that these structural preferences may be useful for the design of bioactive macrocyclic peptides containing β-hairpin mimics and the design of binding epitopes for protein-protein and protein-nucleic acid recognitions. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 653-664, 2016. © 2016 Wiley Periodicals, Inc.

  18. A 2',2'-disulfide-bridged dinucleotide conformationally locks RNA hairpins.

    PubMed

    Gauthier, Florian; Beltran, Frédéric; Biscans, Annabelle; Debart, Françoise; Dupouy, Christelle; Vasseur, Jean-Jacques

    2018-05-02

    The synthesis and the impact of a disulfide bridge between 2'-O-positions of two adjacent nucleotides in an RNA duplex and in the loop of RNA hairpins are reported. The incorporation of this 2',2'-disulfide (S-S) bridge enabled thermal and enzymatic stabilization of the hairpin depending on its position in the loop. The influence of the disulfide bridge on RNA folding was studied at the HIV Dimerization Initiation Site (DIS) as an RNA sequence model. We have shown that this S-S bridge locked the hairpin form, whereas the extended duplex form was generated after the reduction of the disulfide bond in the presence of tris(2-carboxyethyl)phosphine or glutathione. Thus, the S-S bridge can be useful for understanding RNA folding; an RNA molecular beacon locked by an S-S bridge was also investigated as a sensor for the detection of glutathione.

  19. Design of the hairpin ribozyme for targeting specific RNA sequences.

    PubMed

    Hampel, A; DeYoung, M B; Galasinski, S; Siwkowski, A

    1997-01-01

    The following steps should be taken when designing the hairpin ribozyme to cleave a specific target sequence: 1. Select a target sequence containing BN*GUC where B is C, G, or U. 2. Select the target sequence in areas least likely to have extensive interfering structure. 3. Design the conventional hairpin ribozyme as shown in Fig. 1, such that it can form a 4 bp helix 2 and helix 1 lengths up to 10 bp. 4. Synthesize this ribozyme from single-stranded DNA templates with a double-stranded T7 promoter. 5. Prepare a series of short substrates capable of forming a range of helix 1 lengths of 5-10 bp. 6. Identify these by direct RNA sequencing. 7. Assay the extent of cleavage of each substrate to identify the optimal length of helix 1. 8. Prepare the hairpin tetraloop ribozyme to determine if catalytic efficiency can be improved.

  20. Effects of a mutation on the folding mechanism of a beta-hairpin.

    PubMed

    Juraszek, Jarek; Bolhuis, Peter G

    2009-12-17

    The folding mechanism of a protein is determined by its primary sequence. Yet, how the mechanism is changed by a mutation is still poorly understood, even for basic secondary structures such as beta-hairpins. We perform an extensive simulation study of the effects of mutating the GB1 beta-hairpin into Trpzip4 (Y5W, F12W, V14W) on the folding mechanism. While Trpzip4 has a much more stable native state due to very strong hydrophobic interactions of the side chains, its folding rate does not differ significantly from the wild type beta-hairpin. We sample the free-energy landscapes of both hairpins with Replica Exchange Molecular Dynamics (REMD) and identify the four (meta)stable states (U, H, F, and N). Using Transition Path Sampling (TPS), we then harvest ensembles of unbiased pathways between the H and F states and between the F and N states to investigate the unbiased folding mechanisms. In both hairpins, the hydrophobic collapse (U-H) is followed by the middle hydrogen bond formation (H-F), and finally a closing of the strands in a zipper-like fashion (F-N). For the Trpzip4, the path ensembles indicate that the final F-N step is much more difficult than for GB1 and involves partial unfolding, rezipping of hydrogen bonds, and rearrangement of the Trp-14 side chain. For the rate-limiting (H-F) step, the path ensembles show that in GB1 desolvation and strand closure go hand in hand, while in Trpzip4 desolvation is decoupled from strand closure. Nevertheless, likelihood maximization shows that the reaction coordinate for both hairpins remains the interstrand distance. We conclude that the folding mechanism of both hairpins is a combination of hydrophobic collapse and zipping of hydrogen bonds but that the zipper mechanism is more visible in Trpzip4. A major difference between the two hairpins is that in the transition state of the rate-limiting step for Trpzip4 one tryptophan is exposed to the solvent due to steric hindrance, making the folding mechanism more complex

  1. A triplex ribozyme expression system based on a single hairpin ribozyme.

    PubMed

    Aquino-Jarquin, Guillermo; Benítez-Hess, María Luisa; DiPaolo, Joseph A; Alvarez-Salas, Luis M

    2008-09-01

    Triplex ribozyme (RZ) configurations allow for the individual activity of trans-acting RZs in multiple expression cassettes (multiplex), thereby increasing target cleavage relative to conventionally expressed RZs. Although hairpin RZs have been advantageously compared to hammerhead RZs, their longer size and structural features complicated triplex design. We present a triplex expression system based on a single hairpin RZ with transcleavage capability and simple engineering. The system was tested in vitro using cis- and trans-cleavage kinetic assays against a known target RNA from HPV-16 E6/E7 mRNA. Single and multiplex triplex RZ constructs were more efficient in cleaving the target than tandem-cloned hairpin RZs, suggesting that the release of individual RZs enhanced trans-cleavage kinetics. Multiplex systems constructed with two different hairpin RZs resulted in better trans-cleavage compared to standard double-RZ constructs. In addition, the triplex RZ performed cis- and trans-cleavage in cervical cancer cells. The use of triplex configurations with multiplex RZs permit differential targeting of the same or different RNA, thus improving potential use against unstable targets. This prototype will provide the basis for the development of future RZ-based therapies and technologies.

  2. Electronic Interactions of Michler's Ketone with DNA Bases in Synthetic Hairpins.

    PubMed

    Jalilov, Almaz S; Young, Ryan M; Eaton, Samuel W; Wasielewski, Michael R; Lewis, Frederick D

    2015-01-01

    The mechanism and dynamics of photoinduced electron transfer in two families of DNA hairpins possessing Michler's ketone linkers have been investigated by means of steady state and time-resolved transient absorption and emission spectroscopies. The excited state behavior of the diol linker employed in hairpin synthesis is similar to that of Michler's ketone in methanol solution. Hairpins possessing only a Michler's ketone linker undergo fast singlet state charge separation and charge recombination with an adjacent purine base, attributed to well-stacked ground state conformations, and intersystem crossing to the triplet state, attributed to poorly stacked ground state conformations. The failure of the triplet to undergo electron transfer reactions on the 7 ns time scale of our measurements is attributed to the low triplet energy and reduction potential of the twisted triplet state. Hairpins possessing both a Michler's ketone linker and a perylenediimide base surrogate separated by four base pairs undergo photoinduced hole transport from the diimide to Michler's ketone upon excitation of the diimide. The efficiency of hole transport is dependent upon the sequence of the intervening purine bases. © 2014 The American Society of Photobiology.

  3. 29 CFR 1910.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 6 2013-07-01 2013-07-01 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...

  4. 29 CFR 1910.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2010 CFR

    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...

  5. 29 CFR 1910.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 6 2011-07-01 2011-07-01 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...

  6. 29 CFR 1910.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 6 2012-07-01 2012-07-01 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...

  7. 29 CFR 1910.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 6 2014-07-01 2013-07-01 true 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...

  8. Coal tar-containing asphalt - resource or hazardous waste?

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Andersson-Skold, Y.; Andersson, K.; Lind, B.

    2007-09-30

    Coal tar was used in Sweden for the production of asphalt and for the drenching of stabilization gravel until 1973. The tar has high concentrations of polycyclic aromatic hydrocarbons (PAH), some of which may be strongly carcinogenic. Approximately 20 million tonnes of tar-containing asphalt is present in the public roads in Sweden. Used asphalt from rebuilding can be classified as hazardous waste according to the Swedish Waste Act. The cost of treating the material removed as hazardous waste can be very high due to the large amount that has to be treated, and the total environmental benefit is unclear. Themore » transport of used asphalt to landfill or combustion will affect other environmental targets. The present project, based on three case studies of road projects in Sweden, evaluates the consequences of four scenarios for handling the material: reuse, landfill, biological treatment, and incineration. The results show that reuse of the coal tar-containing materials in new road construction is the most favorable alternative in terms of cost, material use, land use, energy consumption, and air emissions.« less

  9. Competitive folding of anti-terminator/terminator hairpins monitored by single molecule FRET.

    PubMed

    Clerte, Caroline; Declerck, Nathalie; Margeat, Emmanuel

    2013-02-01

    The control of transcription termination by RNA-binding proteins that modulate RNA-structures is an important regulatory mechanism in bacteria. LicT and SacY from Bacillus subtilis prevent the premature arrest of transcription by binding to an anti-terminator RNA hairpin that overlaps an intrinsic terminator located in the 5'-mRNA leader region of the gene to be regulated. In order to investigate the molecular determinants of this anti-termination/termination balance, we have developed a fluorescence-based nucleic acids system that mimics the competition between the LicT or SacY anti-terminator targets and the overlapping terminators. Using Förster Resonance Energy Transfer on single diffusing RNA hairpins, we could monitor directly their opening or closing state, and thus investigate the effects on this equilibrium of the binding of anti-termination proteins or terminator-mimicking oligonucleotides. We show that the anti-terminator hairpins adopt spontaneously a closed structure and that their structural dynamics is mainly governed by the length of their basal stem. The induced stability of the anti-terminator hairpins determines both the affinity and specificity of the anti-termination protein binding. Finally, we show that stabilization of the anti-terminator hairpin, by an extended basal stem or anti-termination protein binding can efficiently counteract the competing effect of the terminator-mimic.

  10. Competitive folding of anti-terminator/terminator hairpins monitored by single molecule FRET

    PubMed Central

    Clerte, Caroline; Declerck, Nathalie; Margeat, Emmanuel

    2013-01-01

    The control of transcription termination by RNA-binding proteins that modulate RNA-structures is an important regulatory mechanism in bacteria. LicT and SacY from Bacillus subtilis prevent the premature arrest of transcription by binding to an anti-terminator RNA hairpin that overlaps an intrinsic terminator located in the 5′-mRNA leader region of the gene to be regulated. In order to investigate the molecular determinants of this anti-termination/termination balance, we have developed a fluorescence-based nucleic acids system that mimics the competition between the LicT or SacY anti-terminator targets and the overlapping terminators. Using Förster Resonance Energy Transfer on single diffusing RNA hairpins, we could monitor directly their opening or closing state, and thus investigate the effects on this equilibrium of the binding of anti-termination proteins or terminator-mimicking oligonucleotides. We show that the anti-terminator hairpins adopt spontaneously a closed structure and that their structural dynamics is mainly governed by the length of their basal stem. The induced stability of the anti-terminator hairpins determines both the affinity and specificity of the anti-termination protein binding. Finally, we show that stabilization of the anti-terminator hairpin, by an extended basal stem or anti-termination protein binding can efficiently counteract the competing effect of the terminator-mimic. PMID:23303779

  11. Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology

    PubMed Central

    Kouprina, Natalay; Larionov, Vladimir

    2016-01-01

    Transformation-associated recombination (TAR) cloning represents a unique tool for isolation and manipulation of large DNA molecules. The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. So far, TAR cloning is the only method available to selectively recover chromosomal segments up to 300 kb in length from complex and simple genomes. In addition, TAR cloning allows the assembly and cloning of entire microbe genomes up to several Mb as well as engineering of large metabolic pathways. In this review, we summarize applications of TAR cloning for functional/structural genomics and synthetic biology. PMID:27116033

  12. Asymmetric structure of five and six membered DNA hairpin loops

    NASA Technical Reports Server (NTRS)

    Baumann, U.; Chang, S.

    1995-01-01

    The tertiary structure of nucleic acid hairpins was elucidated by means of the accessibility of the single-strand-specific nuclease from mung bean. This molecular probe has proven especially useful in determining details of the structural arrangement of the nucleotides within a loop. In this study 3'-labeling is introduced to complement previously used 5'-labeling in order to assess and to exclude possible artifacts of the method. Both labeling procedures result in mutually consistent cleavage patterns. Therefore, methodological artifacts can be excluded and the potential of the nuclease as structural probe is increased. DNA hairpins with five and six membered loops reveal an asymmetric loop structure with a sharp bend of the phosphate-ribose backbone between the second and third nucleotide on the 3'-side of a loop. These hairpin structures differ from smaller loops with 3 or 4 members, which reveal this type of bend between the first and second 3' nucleotide, and resemble with respect to the asymmetry anticodon loops of tRNA.

  13. Study on the stability of the DNA hairpin d(ATCCAT-GTTA-TAGGAT) employing molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Wu, Sangwook

    2015-03-01

    DNA hairpin plays a critical role in the regulation of gene expression and DNA recombination. We studied the conformation of the DNA hairpin, d(ATCCAT-GTTA-TAGGAT) (PDB id:1AC7), employing molecular dynamics (MD) simulation. Despite the non-canonical Watson-Crick base pair (G:A) in the tetraloop (GTTA), MD simulation reveals that the conformation of the DNA hairpin is remarkably stable. In this study, we discuss about the physical/chemical origin of the stability of the DNA hairpin. Department of Biomedical Engineering, Korea University, Seoul 136-703, Korea.

  14. The potential use of tar sand bitumen as paving asphalt

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Petersen, J.C.

    1988-01-01

    In this paper several research reports describing the preparation of potential paving asphalts from tar sand bitumen are reviewed and the results of the studies compared. The tar sand asphalts described in the studies were prepared from 1) hot water-recovered bitumen from deposits near San Luis Obispo, California (Edna deposits), and deposits near Vernal and Sunnyside, Utah; and 2) bitumen recovered from the Northwest Asphalt Ridge deposits near Vernal, Utah, by both in situ steamflood and in situ combustion recovery processes. Important properties of the tar sand asphalts compare favorably with those of specification petroleum asphalts. Laboratory data suggest thatmore » some tar sand asphalts may have superior aging characteristics and produce more water-resistant paving mixtures than typical petroleum asphalts.« less

  15. Coal tar induces AHR-dependent skin barrier repair in atopic dermatitis

    PubMed Central

    van den Bogaard, Ellen H.; Bergboer, Judith G.M.; Vonk-Bergers, Mieke; van Vlijmen-Willems, Ivonne M.J.J.; Hato, Stanleyson V.; van der Valk, Pieter G.M.; Schröder, Jens Michael; Joosten, Irma; Zeeuwen, Patrick L.J.M.; Schalkwijk, Joost

    2013-01-01

    Topical application of coal tar is one of the oldest therapies for atopic dermatitis (AD), a T helper 2 (Th2) lymphocyte–mediated skin disease associated with loss-of-function mutations in the skin barrier gene, filaggrin (FLG). Despite its longstanding clinical use and efficacy, the molecular mechanism of coal tar therapy is unknown. Using organotypic skin models with primary keratinocytes from AD patients and controls, we found that coal tar activated the aryl hydrocarbon receptor (AHR), resulting in induction of epidermal differentiation. AHR knockdown by siRNA completely abrogated this effect. Coal tar restored filaggrin expression in FLG-haploinsufficient keratinocytes to wild-type levels, and counteracted Th2 cytokine–mediated downregulation of skin barrier proteins. In AD patients, coal tar completely restored expression of major skin barrier proteins, including filaggrin. Using organotypic skin models stimulated with Th2 cytokines IL-4 and IL-13, we found coal tar to diminish spongiosis, apoptosis, and CCL26 expression, all AD hallmarks. Coal tar interfered with Th2 cytokine signaling via dephosphorylation of STAT6, most likely due to AHR-regulated activation of the NRF2 antioxidative stress pathway. The therapeutic effect of AHR activation herein described opens a new avenue to reconsider AHR as a pharmacological target and could lead to the development of mechanism-based drugs for AD. PMID:23348739

  16. Coal tar induces AHR-dependent skin barrier repair in atopic dermatitis.

    PubMed

    van den Bogaard, Ellen H; Bergboer, Judith G M; Vonk-Bergers, Mieke; van Vlijmen-Willems, Ivonne M J J; Hato, Stanleyson V; van der Valk, Pieter G M; Schröder, Jens Michael; Joosten, Irma; Zeeuwen, Patrick L J M; Schalkwijk, Joost

    2013-02-01

    Topical application of coal tar is one of the oldest therapies for atopic dermatitis (AD), a T helper 2 (Th2) lymphocyte-mediated skin disease associated with loss-of-function mutations in the skin barrier gene, filaggrin (FLG). Despite its longstanding clinical use and efficacy, the molecular mechanism of coal tar therapy is unknown. Using organotypic skin models with primary keratinocytes from AD patients and controls, we found that coal tar activated the aryl hydrocarbon receptor (AHR), resulting in induction of epidermal differentiation. AHR knockdown by siRNA completely abrogated this effect. Coal tar restored filaggrin expression in FLG-haploinsufficient keratinocytes to wild-type levels, and counteracted Th2 cytokine-mediated downregulation of skin barrier proteins. In AD patients, coal tar completely restored expression of major skin barrier proteins, including filaggrin. Using organotypic skin models stimulated with Th2 cytokines IL-4 and IL-13, we found coal tar to diminish spongiosis, apoptosis, and CCL26 expression, all AD hallmarks. Coal tar interfered with Th2 cytokine signaling via dephosphorylation of STAT6, most likely due to AHR-regulated activation of the NRF2 antioxidative stress pathway. The therapeutic effect of AHR activation herein described opens a new avenue to reconsider AHR as a pharmacological target and could lead to the development of mechanism-based drugs for AD.

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

    PubMed

    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.

  18. Probing interaction of a fluorescent ligand with HIV TAR RNA

    NASA Astrophysics Data System (ADS)

    Qi, Liang; Zhang, Jing; He, Tian; Huo, Yuan; Zhang, Zhi-Qi

    2017-02-01

    Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.

  19. Thermocatalytic treatment of biomass tar model compounds via radio frequency.

    PubMed

    Anis, Samsudin; Zainal, Z A; Bakar, M Z A

    2013-05-01

    A new effective RF tar thermocatalytic treatment process with low energy intensive has been proposed to remove tar from biomass gasification. Toluene and naphthalene as biomass tar model compounds were removed via both thermal and catalytic treatment over a wide temperature range from 850 °C to 1200 °C and 450 °C to 900 °C, respectively at residence time of 0-0.7 s. Thermal characteristics of the new technique are also described in this paper. This study clearly clarified that toluene was much easier to be removed than naphthalene. Soot was found as the final product of thermal treatment of the tar model and completely removed during catalytic treatment. Radical reactions generated by RF non-thermal effect improve the tar removal. The study showed that Y-zeolite has better catalytic activity compared to dolomite on toluene and naphthalene removal due to its acidic nature and large surface area, even at lower reaction temperature of about 550 °C. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Assessment of tar pollution on the United Arab emirates beaches

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Abu-Hilal, A.H.; Khordagui, H.K.

    1993-01-01

    In light of the inadequate information concerning stranded tar on the southwest beaches of the Arabian Gulf and the Gulf of Oman, particularly following the massive oil releases during the Gulf War, the present investigation was designed to provide reference-integrated information on the nature, location, and levels of stranded tar balls on the beaches of the United Arab Emirates (UAE). The recorded levels appeared to be higher than expected or previously reported. The tar distribution pattern, in addition to the degree of weathering, indicates that the massive oil release during the Gulf War did not reach the UAE shorelines. Themore » highest reported levels of stranded tar ever recorded in the Arabian Gulf at Jabal Dhannah apparently originated from oil spills and tankers' ballast water at the main oil terminal at the Al-Ruwaiss oil refinery some 10 km to the east. The surprising, relatively high levels of stranded tar on the beaches of the Gulf of Oman were solely attributed to the heavy navigation traffic close to the shorelines. 19 refs., 2 figs., 3 tabs.« less

  1. DNA hairpins promote temperature controlled cargo encapsulation in a truncated octahedral nanocage structure family

    NASA Astrophysics Data System (ADS)

    Franch, Oskar; Iacovelli, Federico; Falconi, Mattia; Juul, Sissel; Ottaviani, Alessio; Benvenuti, Claudia; Biocca, Silvia; Ho, Yi-Ping; Knudsen, Birgitta R.; Desideri, Alessandro

    2016-07-01

    In the present study we investigate the mechanism behind temperature controlled cargo uptake using a truncated octahedral DNA cage scaffold functionalized with one, two, three or four hairpin forming DNA strands inserted in one corner of the structure. This investigation was inspired by our previous demonstration of temperature controlled reversible encapsulation of the cargo enzyme, horseradish peroxidase, in the cage with four hairpin forming strands. However, in this previous study the mechanism of cargo uptake was not directly addressed (Juul, et al., Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage, ACS Nano, 2013, 7, 9724-9734). In the present study we use a combination of molecular dynamics simulations and in vitro analyses to unravel the mechanism of cargo uptake in hairpin containing DNA cages. We find that two hairpin forming strands are necessary and sufficient to facilitate efficient cargo uptake, which argues against a full opening-closing of one corner of the structure being responsible for encapsulation. Molecular dynamics simulations were carried out to evaluate the atomistic motions responsible for encapsulation and showed that the two hairpin forming strands facilitated extension of at least one of the face surfaces of the cage scaffold, allowing entrance of the cargo protein into the cavity of the structure. Hence, the presented data demonstrate that cargo uptake does not involve a full opening of the structure. Rather, the uptake mechanism represents a feature of increased flexibility integrated in this nanocage structure upon the addition of at least two hairpin-forming strands.In the present study we investigate the mechanism behind temperature controlled cargo uptake using a truncated octahedral DNA cage scaffold functionalized with one, two, three or four hairpin forming DNA strands inserted in one corner of the structure. This investigation was inspired by our previous

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

    PubMed

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

    2005-08-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nurhadi, N., E-mail: nurhadi@tekmira.esdm.go.id; Diniyati, Dahlia; Efendi, M. Ade Andriansyah

    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 mostmore » 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.« less

  4. Groundwater contamination by organic bases derived from coal-tar wastes

    USGS Publications Warehouse

    Pereira, W.E.; Rostad, C.E.; Garbarino, J.R.; Hult, M.F.

    1983-01-01

    A fluid sample from a shallow aquifer contaminated by coal-tar wastes was analyzed for organic bases. The sample consisted of a mixture of aqueous and oily-tar phases. The phases were separated by centrifugation and filtration. Organic bases were isolated from each phase by pH adjustment and solvent extraction. Organic bases in the oily-tar phase were further purified by neutral-alumina, micro-column adsorption chromatography. Separation and identification of the organic bases in each phase were achieved by using capillary gas chromatography-mass spectrometry-computer (GC-MS-COM) and probe distillation-high resolution mass spectrometry (PD-HRMS) techniques. Organic bases present in the aqueous phase included primary aromatic amines (such as aniline, alkylated anilines, and naphthylamines) as well as azaarenes (such as alkylated pyridines, quinolines, acridine, and benzoquinolines). The oily-tar phase contained acridine, benzacridines, dibenzacridines, and numerous other azaarenes, the elemental compositions of which were determined by PD-HRMS. Azaarenes in the oily-tar phase, varying in size from 6 to 12 rings, are reported for the first time. The origin and environmental significance of these compounds are discussed. ?? 1983.

  5. Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study.

    PubMed

    Shao, Qiang; Yang, Lijiang; Gao, Yi Qin

    2011-12-21

    Our previous study showed that for the tested polypeptides which have similar β-hairpin structures but different sequences, their folding free energy pathways are dominantly determined by the turn conformational propensity. In this study, we study how the turn conformational propensity affects the structure of hairpins. The folding of two mutants of GB1p peptide (GB1m2 and GB1m3), which have the optimized turn sequence ((6)DDATK(11)T → (6)NPATG(11)K) with native structures unsolved, were simulated using integrated tempering sampling molecular dynamics simulations and the predicted stable structures were compared to wild-type GB1p. It was observed that the turn optimization of GB1p generates a more favored 5-residue type I(') turn in addition to the 6-residue type I turn in wild-type GB1p. As a result two distinctly different hairpin structures are formed corresponding to the "misfolded" (M) and the "folded" (F) states. M state is a one-residue-shifted asymmetric β-hairpin structure whereas F state has the similar symmetric hairpin structure as wild-type GB1p. The formation of the favored type I(') turn has a small free energy barrier and leads to the shifted β-hairpin structure, following the modified "zipping" model. The presence of disfavored type I turn structure makes the folding of a β-hairpin consistent with the "hydrophobic-core-centric" model. On the other hand, the folding simulations on other two GB1p mutants (GB1r1 and GBr2), which have the position of the hydrophobic core cluster further away from the turn compared to wild-type GB1p, showed that moving the hydrophobic core cluster away from the turn region destabilizes but does not change the hairpin structure. Therefore, the present study showed that the turn conformational propensity is a key factor in affecting not only the folding pathways but also the stable structure of β-hairpins, and the turn conformational change induced by the turn optimization leads to significant changes of β-hairpin

  6. Investigation of RNA Hairpin Loop Folding with Time-Resolved Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Stancik, Aaron Lee

    Ribonucleic acids (RNAs) are a group of functional biopolymers central to the molecular underpinnings of life. To complete the many processes they mediate, RNAs must fold into precise three-dimensional structures. Hairpin loops are the most ubiquitous and basic structural elements present in all folded RNAs, and are the foundation upon which all complex tertiary structures are built. A hairpin loop forms when a single stranded RNA molecule folds back on itself creating a helical stem of paired bases capped by a loop. This work investigates the formation of UNCG hairpin loops with the sequence 5'-GC(UNCG)GC-3' (N = A, U, G, or C) using both equilibrium infrared (IR) and time-resolved IR spectroscopy. Equilibrium IR melting data were used to determine thermodynamic parameters. Melting temperatures ranged from 50 to 60°C, and enthalpies of unfolding were on the order of 100 kJ/mol. In the time-resolved work, temperature jumps of up to 20°C at 2.5°C increments were obtained with transient relaxation kinetics spanning nanoseconds to hundreds of microseconds. The relaxation kinetics for all of the oligomers studied were fit to first or second order exponentials. Multiple vibrational transitions were probed on each oligomer for fully folded and partially denatured structures. In the time-resolved limit, in contrast to equilibrium melting, RNA does not fold according to two-state behavior. These results are some of the first to show that RNA hairpins fold according to a rugged energy landscape, which contradicts their relatively simple nature. In addition, this work has proven that time-resolved IR spectroscopy is a powerful and novel tool for investigating the earliest events of RNA folding, the formation of the hairpin loop.

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

    PubMed

    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.

  8. β-Hairpin-Mediated Formation of Structurally Distinct Multimers of Neurotoxic Prion Peptides

    PubMed Central

    Gill, Andrew C.

    2014-01-01

    Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109–122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109–122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109–122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106–126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new

  9. Effect of water addition in a microwave assisted thermal cracking of biomass tar gasification

    NASA Astrophysics Data System (ADS)

    Warsita, A.; Surya, I.

    2018-02-01

    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 for removing tar from producer gas. A question arises as to the possibility of enhancing the removal mechanism by adding water into the reactor. Thermal treatment with a various amount of water was added at temperatures in the range of 800-1200°C. The tar removal efficiency obtained 96.32% at the optimum temperature of 1200°C at the 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.

  10. Exploring the free energy landscape of a model β-hairpin peptide and its isoform.

    PubMed

    Narayanan, Chitra; Dias, Cristiano L

    2014-10-01

    Secondary structural transitions from α-helix to β-sheet conformations are observed in several misfolding diseases including Alzheimer's and Parkinson's. Determining factors contributing favorably to the formation of each of these secondary structures is therefore essential to better understand these disease states. β-hairpin peptides form basic components of anti-parallel β-sheets and are suitable model systems for characterizing the fundamental forces stabilizing β-sheets in fibrillar structures. In this study, we explore the free energy landscape of the model β-hairpin peptide GB1 and its E2 isoform that preferentially adopts α-helical conformations at ambient conditions. Umbrella sampling simulations using all-atom models and explicit solvent are performed over a large range of end-to-end distances. Our results show the strong preference of GB1 and the E2 isoform for β-hairpin and α-helical conformations, respectively, consistent with previous studies. We show that the unfolded states of GB1 are largely populated by misfolded β-hairpin structures which differ from each other in the position of the β-turn. We discuss the energetic factors contributing favorably to the formation of α-helix and β-hairpin conformations in these peptides and highlight the energetic role of hydrogen bonds and non-bonded interactions. © 2014 Wiley Periodicals, Inc.

  11. The TAR effect: when the ones who dislike become the ones who are disliked.

    PubMed

    Gawronski, Bertram; Walther, Eva

    2008-09-01

    Four studies tested whether a source's evaluations of other individuals can recursively transfer to the source, such that people who like others acquire a positive valence, whereas people who dislike others acquire a negative valence (Transfer of Attitudes Recursively; TAR). Experiment 1 provides first evidence for TAR effects, showing recursive transfers of evaluations regardless of whether participants did or did not have prior knowledge about the (dis)liking source. Experiment 2 shows that previously but not subsequently acquired knowledge about targets that were (dis)liked by a source overrode TAR effects in a manner consistent with cognitive balance. Finally, Experiments 3 and 4 demonstrate that TAR effects are mediated by higher order propositional inferences (in contrast to lower order associative processes), in that TAR effects on implicit attitude measures were fully mediated by TAR effects on explicit attitude measures. Commonalities and differences between the TAR effect and previously established phenomena are discussed.

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

    PubMed

    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 < 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. Copyright 2009 Elsevier Ltd. All rights reserved.

  13. Ground-water contamination by organic bases derived from coal-tar wastes

    USGS Publications Warehouse

    Pereira, Wilfred E.; Rostad, Colleen E.; Garbarino, John R.; Hult, Marc F.

    1983-01-01

    A fluid sample from a shallow aquifer contaminated by coal-tar wastes was analyzed for organic bases. The sample consisted of a mixture of aqueous and oily-tar phases. The phases were separated by centrifugation and filtration. Organic bases were isolated from each phase by pH adjustment and solvent extraction. Organic bases in the oily-tar phase were further purified by neutral-alumina, micro-column adsorption chromatography. Separation and identification of the organic bases in each phase were achieved by using capillary gas chromatography-mass spectrometry-computer (GC-MS-COM) and probe distillation-high resolution mass spectrometry (PD-HRMS) techniques. Organic bases present in the aqueous phase included primary aromatic amines (such as aniline, alkylated anilines, and naphthylamines) as well as azaarenes (such as alkylated pyridines, quinolines, acridine, and benzoquinolines). The oily-tar phase contained acridine, benzacridines, dibenzacridines, and numerous other azaarenes, the elemental compositions of which were determined by PD-HRMS. Azaarenes in the oily-tar phase, varying in size from 6 to 12 rings, are reported for the first time. The origin and environmental significance of these compounds are discussed.

  14. DNA Hairpins Containing the Cytidine Analog Pyrrolo-dC: Structural, Thermodynamic, and Spectroscopic Studies

    PubMed Central

    Zhang, Xu; Wadkins, Randy M.

    2009-01-01

    Structures formed by single-strand DNA have become increasingly interesting because of their roles in a number of biological processes, particularly transcription and its regulation. Of particular importance is the fact that antitumor drugs such as Actinomycin D can selectively bind DNA hairpins over fully paired, double-strand DNA. A new fluorescent base analog, pyrrolo-deoxycytidine (PdC), can now be routinely incorporated into single-strand DNA. The fluorescence of PdC is particularly useful for studying the formation of single-strand DNA in regions of double-strand DNA. The fluorescence is quenched when PdC is paired with a complementary guanine residue, and thus is greatly enhanced upon formation of single-strand DNA. Hence, any process that results in melting or opening of DNA strands produces an increase in the fluorescence intensity of this base analog. In this study we measured the structural effects of incorporating PdC into DNA hairpins, and the effect of this incorporation on the binding of the hairpins by a fluorescent analog of the drug Actinomycin D. Two hairpin DNAs were used: one with PdC in the stem (basepaired) and one with PdC in the loop (unpaired). The thermal stability, 7-aminoactinomycin D binding, and three-dimensional structures of PdC incorporated into these DNA hairpins were all quite similar as compared to the hairpins containing an unmodified dC residue. Fluorescence lifetime measurements indicate that two lifetimes are present in PdC, and that the increase in fluorescence of the unpaired PdC residue compared to the basepaired PdC is due to an increase in the contribution of the longer lifetime to the average fluorescence lifetime. Our data indicate that PdC can be used effectively to differentiate paired and unpaired bases in DNA hairpin secondary structures, and should be similarly applicable for related structures such as cruciforms and quadruplexes. Further, our data indicate that PdC can act as a fluorescence resonance energy

  15. DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies.

    PubMed

    Zhang, Xu; Wadkins, Randy M

    2009-03-04

    Structures formed by single-strand DNA have become increasingly interesting because of their roles in a number of biological processes, particularly transcription and its regulation. Of particular importance is the fact that antitumor drugs such as Actinomycin D can selectively bind DNA hairpins over fully paired, double-strand DNA. A new fluorescent base analog, pyrrolo-deoxycytidine (PdC), can now be routinely incorporated into single-strand DNA. The fluorescence of PdC is particularly useful for studying the formation of single-strand DNA in regions of double-strand DNA. The fluorescence is quenched when PdC is paired with a complementary guanine residue, and thus is greatly enhanced upon formation of single-strand DNA. Hence, any process that results in melting or opening of DNA strands produces an increase in the fluorescence intensity of this base analog. In this study we measured the structural effects of incorporating PdC into DNA hairpins, and the effect of this incorporation on the binding of the hairpins by a fluorescent analog of the drug Actinomycin D. Two hairpin DNAs were used: one with PdC in the stem (basepaired) and one with PdC in the loop (unpaired). The thermal stability, 7-aminoactinomycin D binding, and three-dimensional structures of PdC incorporated into these DNA hairpins were all quite similar as compared to the hairpins containing an unmodified dC residue. Fluorescence lifetime measurements indicate that two lifetimes are present in PdC, and that the increase in fluorescence of the unpaired PdC residue compared to the basepaired PdC is due to an increase in the contribution of the longer lifetime to the average fluorescence lifetime. Our data indicate that PdC can be used effectively to differentiate paired and unpaired bases in DNA hairpin secondary structures, and should be similarly applicable for related structures such as cruciforms and quadruplexes. Further, our data indicate that PdC can act as a fluorescence resonance energy

  16. Role of TAR RNA splicing in translational regulation of simian immunodeficiency virus from rhesus macaques.

    PubMed Central

    Viglianti, G A; Rubinstein, E P; Graves, K L

    1992-01-01

    The untranslated leader sequences of rhesus macaque simian immunodeficiency virus mRNAs form a stable secondary structure, TAR. This structure can be modified by RNA splicing. In this study, the role of TAR splicing in virus replication was investigated. The proportion of viral RNAs containing a spliced TAR structure is high early after infection and decreases at later times. Moreover, proviruses containing mutations which prevent TAR splicing are significantly delayed in replication. These mutant viruses require approximately 20 days to achieve half-maximal virus production, in contrast to wild-type viruses, which require approximately 8 days. We attribute this delay to the inefficient translation of unspliced-TAR-containing mRNAs. The molecular basis for this translational effect was examined in in vitro assays. We found that spliced-TAR-containing mRNAs were translated up to 8.5 times more efficiently than were similar mRNAs containing an unspliced TAR leader. Furthermore, these spliced-TAR-containing mRNAs were more efficiently associated with ribosomes. We postulate that the level of TAR splicing provides a balance for the optimal expression of both viral proteins and genomic RNA and therefore ultimately controls the production of infectious virions. Images PMID:1629957

  17. Selected constituents in the smoke of domestic low tar cigarettes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Griest, W. H.; Quincy, R. B.; Guerin, M. R.

    Thirty-two brands of domestic commercial low tar and nicotine cigarettes were analyzed for their production of tar, nicotine, nitrogen oxides (as nitric oxide), hydrogen cyanide, acrolein, carbon monoxide and carbon dioxide under standard analytical smoking conditions. Results are compared with published data for certain brands.

  18. Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy.

    PubMed

    Wu, Ling; McElheny, Dan; Setnicka, Vladimír; Hilario, Jovencio; Keiderling, Timothy A

    2012-01-01

    Model β-hairpin peptides based on variations in the turn sequence of Cochran's tryptophan zipper peptide, SWTWENGKWTWK, were studied using electronic circular dichroism (ECD), fluorescence, and infrared (IR) spectroscopies. The trpzip2 Asn-Gly turn sequence was substituted with Thr-Gly, Aib-Gly, (D)Pro-Gly, and Gly-Asn (trpzip1) to study the impact of turn stability on β-hairpin formation. Stability and conformational changes of these hairpins were monitored by thermodynamic analyses of the temperature variation of both FTIR (amide I') and ECD spectral intensities. These changes were fit to a two-state model which yielded different T(m) values, representing the folding/unfolding process, for hairpins with different β-turns. Different β-turns show systematic contributions to hairpin structure formation, and their inclusion in hairpin design can modify the folding pathways. Aib-Gly or (D)Pro-Gly sequences stabilize the turn resulting in residual Trp-Trp interaction at high temperatures, but at the same time the β-structure (cross strand H-bonds) can become less stable due to constraints of the turn, as seen for (D)Pro-Gly. The structure of the Aib-Gly turn containing hairpin was determined by NMR and was shown to be like trpzip2 (Asn-Gly turn) as regards turn and strand geometries, but to differ from trpzip1 (Gly-Asn turn). The Munoz and Eaton statistical mechanically derived multistate model, tested as an alternate point of view, represented contributions from H-bonds and hydrophobic interactions as well as conformational change as interdependent. Use of different spectral methods that vary in dependence on these physical interactions along with the structural variations provided insight to the complex folding pathways of these small, well-folded peptides. Copyright © 2011 Wiley Periodicals, Inc.

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

    NASA Astrophysics Data System (ADS)

    Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus

    2015-12-01

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

  20. The contribution of low tar cigarettes to environmental tobacco smoke

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chortyk, O.T.; Schlotzhauer, W.S.

    A series of low tar cigarettes (LTC) were smoked and the quantities of condensable mainstream (inhaled) and sidestream (between puffs) smoke compounds were determined and compared to those produced by a high tar, nonfilter cigarette. It was found that the LTC produced large quantities of sidestream smoke condensates, about equal to the high tar cigarette, and contained very high levels of toxic or cocarcinogenic phenols. On an equal weight basis, the LTC emitted more of these hazardous compounds into sidestream and environmental tobacco smoke. Higher smoke yields of a flavor additive and a sugar degradation product indicated addition of suchmore » compounds during the manufacture of LTC. It was concluded that, compared to a high tar cigarette, smoking LTC may be better for the smoker, but not for the nearby nonsmoker. Information should be developed to allow smokers to choose LTC that produce lower levels of hazardous compounds in their environmentally emitted sidestream smoke.« less

  1. Creating fluid injectivity in tar sands formations

    DOEpatents

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

    2012-06-05

    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 including mobilized hydrocarbons are produced from the portion.

  2. Creating fluid injectivity in tar sands formations

    DOEpatents

    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.

  3. Effect of the reflectional symmetry on the coherent hole transport across DNA hairpins

    NASA Astrophysics Data System (ADS)

    Zarea, Mehdi; Berlin, Yuri; Ratner, Mark A.

    2017-03-01

    The coherent hole transfer in three types of DNA hairpins containing strands with adenine (A) and guanine (G) nucleobases has been studied. The investigated hairpins involve An+1GGAn, AnGAGAn, or (AG)2nA strands that connect the hole donor and hole acceptor located on opposite ends of hairpins. The positive charge transfer from the photo-excited donor to the acceptor is shown to be slower for An+1GGAn in comparison with AnGAGAn and (AG)2nA sequences. We have revealed that this is due to the reflectional symmetry of the last two sequences with respect to the axis passing through the middle base. As has been demonstrated, the symmetry of the sequence structure manifests itself in the reflectional symmetry of the energy eigenstates. In addition, it has been shown that (AG)2nA is the only symmetric sequence with a zero energy state in the middle of the LUMO tight-binding energy band. Based on our theoretical findings, we predict that the hairpin with this sequence should have the fastest coherent hole transfer rate among the class of base sequences studied.

  4. 21 CFR 740.18 - Coal tar hair dyes posing a risk of cancer.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 7 2012-04-01 2012-04-01 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...

  5. Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpins

    NASA Astrophysics Data System (ADS)

    Bui, Hieu; Garg, Sudhanshu; Miao, Vincent; Song, Tianqi; Mokhtar, Reem; Reif, John

    2017-01-01

    DNA self-assembly has been employed non-conventionally to construct nanoscale structures and dynamic nanoscale machines. The technique of hybridization chain reactions by triggered self-assembly has been shown to form various interesting nanoscale structures ranging from simple linear DNA oligomers to dendritic DNA structures. Inspired by earlier triggered self-assembly works, we present a system for controlled self-assembly of linear cascade DNA hybridization chain reactions using nine distinct DNA hairpins. NUPACK is employed to assist in designing DNA sequences and Matlab has been used to simulate DNA hairpin interactions. Gel electrophoresis and ensemble fluorescence reaction kinetics data indicate strong evidence of linear cascade DNA hybridization chain reactions. The half-time completion of the proposed linear cascade reactions indicates a linear dependency on the number of hairpins.

  6. Unfolding and folding internal friction of β-hairpins is smaller than that of α-helices.

    PubMed

    Schulz, Julius C F; Miettinen, Markus S; Netz, R R

    2015-04-02

    By the forced unfolding of polyglutamine and polyalanine homopeptides in competing α-helix and β-hairpin secondary structures, we disentangle equilibrium free energetics from nonequilibrium dissipative effects. We find that α-helices are characterized by larger friction or dissipation upon unfolding, regardless of whether they are free energetically preferred over β-hairpins or not. Our analysis, based on MD simulations for atomistic peptide models with explicit water, suggests that this difference is related to the internal friction and mostly caused by the different number of intrapeptide hydrogen bonds in the α-helix and β-hairpin states.

  7. Understanding the stability of pyrolysis tars from biomass in a view point of free radicals.

    PubMed

    He, Wenjing; Liu, Qingya; Shi, Lei; Liu, Zhenyu; Ci, Donghui; Lievens, Caroline; Guo, Xiaofen; Liu, Muxin

    2014-03-01

    Fast pyrolysis of biomass has attracted increasing attention worldwide to produce bio-tars that can be upgraded into liquid fuels and chemicals. However, the bio-tars are usually poor in quality and stability and are difficult to be upgraded. To better understand the nature of the bio-tars, this work reveals radical concentration of tars derived from pyrolysis of two kinds of biomass. The tars were obtained by condensing the pyrolysis volatiles in 3s. It shows that the tars contain large amounts of radicals, at a level of 10(16)spins/g, and are able to generate more radicals at temperatures of 573K or higher, reaching a level of 10(19)spins/g at 673K in less than 30min. The radical generation in the tar samples is attributed to the formation of THF insoluble matters (coke), which also contain radicals. The radical concentrations of the aqueous liquids obtained in pyrolysis are also studied. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. A nonenzymatic DNA nanomachine for biomolecular detection by target recycling of hairpin DNA cascade amplification.

    PubMed

    Zheng, Jiao; Li, Ningxing; Li, Chunrong; Wang, Xinxin; Liu, Yucheng; Mao, Guobin; Ji, Xinghu; He, Zhike

    2018-06-01

    Synthetic enzyme-free DNA nanomachine performs quasi-mechanical movements in response to external intervention, suggesting the promise of constructing sensitive and specific biosensors. Herein, a smart DNA nanomachine biosensor for biomolecule (such as nucleic acid, thrombin and adenosine) detection is developed by target-assisted enzyme-free hairpin DNA cascade amplifier. The whole DNA nanomachine system is constructed on gold nanoparticle which decorated with hundreds of locked hairpin substrate strands serving as DNA tracks, and the DNA nanomachine could be activated by target molecule toehold-mediated exchange on gold nanoparticle surface, resulted in the fluorescence recovery of fluorophore. The process is repeated so that each copy of the target can open multiplex fluorophore-labeled hairpin substrate strands, resulted in amplification of the fluorescence signal. Compared with the conventional biosensors of catalytic hairpin assembly (CHA) without substrate in solution, the DNA nanomachine could generate 2-3 orders of magnitude higher fluorescence signal. Furthermore, the DNA nanomachine could be used for nucleic acid, thrombin and adenosine highly sensitive specific detection based on isothermal, and homogeneous hairpin DNA cascade signal amplification in both buffer and a complicated biomatrix, and this kind of DNA nanomachine could be efficiently applied in the field of biomedical analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Catalytic Tar Reduction for Assistance in Thermal Conversion of Space Waste for Energy Production

    NASA Technical Reports Server (NTRS)

    Caraccio, Anne Joan; Devor, Robert William; Hintze, Paul E.; Muscatello, Anthony C.; Nur, Mononita

    2014-01-01

    The Trash to Gas (TtG) project investigates technologies for converting waste generated during spaceflight into various resources. One of these technologies was gasification, which employed a downdraft reactor designed and manufactured at NASA's Kennedy Space Center (KSC) for the conversion of simulated space trash to carbon dioxide. The carbon dioxide would then be converted to methane for propulsion and water for life support systems. A minor byproduct of gasification includes large hydrocarbons, also known as tars. Tars are unwanted byproducts that add contamination to the product stream, clog the reactor and cause complications in analysis instrumentation. The objective of this research was to perform reduction studies of a mock tar using select catalysts and choose the most effective for primary treatment within the KSC downdraft gasification reactor. Because the KSC reactor is operated at temperatures below typical gasification reactors, this study evaluates catalyst performance below recommended catalytic operating temperatures. The tar reduction experimentation was observed by passing a model tar vapor stream over the catalysts at similar conditions to that of the KSC reactor. Reduction in tar was determined using gas chromatography. Tar reduction efficiency and catalyst performances were evaluated at different temperatures.

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

    PubMed

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

    2017-01-01

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

  11. Coal-tar-based pavement sealants—a potent source of PAHs

    USGS Publications Warehouse

    Mahler, Barbara J.; Van Metre, Peter C.

    2017-01-01

    P avement sealants are applied to the asphalt pavement of many parking lots, driveways, and even playgrounds in North America (Figure 1), where, when first applied, they render the pavement glossy black and looking like new. Sealant products used commercially in the central, eastern, and northern United States typically are coal-tarbased, whereas those used in the western United States typically are asphalt-based. Although the products look similar, they are chemically different. Coal-tarbased pavement sealants typically are 25-35 percent (by weight) coal tar or coal-tar pitch, materials that are known human carcinogens and that contain high concentrations of polycyclic aromatic hydrocarbons (PAHs) and related chemicals (unless otherwise noted, all Figure 1. Pavement sealant is commonly used to seal parking lots, playgrounds, and driveways throughout the United States. Sealants used in the central, northern, eastern, and southern United States typically contain coal tar or coal-tar pitch, both of which are known human carcinogens. Photos by the U.S. Geological Survey. data in this article are from Mahler et al. 2012 and references therein).

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  13. Metal catalysts for steam reforming of tar derived from the gasification of lignocellulosic biomass.

    PubMed

    Li, Dalin; Tamura, Masazumi; Nakagawa, Yoshinao; Tomishige, Keiichi

    2015-02-01

    Biomass gasification is one of the most important technologies for the conversion of biomass to electricity, fuels, and chemicals. The main obstacle preventing the commercial application of this technology is the presence of tar in the product gas. Catalytic reforming of tar appears a promising approach to remove tar and supported metal catalysts are among the most effective catalysts. Nevertheless, improvement of catalytic performances including activity, stability, resistance to coke deposition and aggregation of metal particles, as well as catalyst regenerability is greatly needed. This review focuses on the design and catalysis of supported metal catalysts for the removal of tar in the gasification of biomass. The recent development of metal catalysts including Rh, Ni, Co, and their alloys for steam reforming of biomass tar and tar model compounds is introduced. The role of metal species, support materials, promoters, and their interfaces is described. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Wet scrubbing of biomass producer gas tars using vegetable oil

    NASA Astrophysics Data System (ADS)

    Bhoi, Prakashbhai Ramabhai

    The overall aims of this research study were to generate novel design data and to develop an equilibrium stage-based thermodynamic model of a vegetable oil based wet scrubbing system for the removal of model tar compounds (benzene, toluene and ethylbenzene) found in biomass producer gas. The specific objectives were to design, fabricate and evaluate a vegetable oil based wet scrubbing system and to optimize the design and operating variables; i.e., packed bed height, vegetable oil type, solvent temperature, and solvent flow rate. The experimental wet packed bed scrubbing system includes a liquid distributor specifically designed to distribute a high viscous vegetable oil uniformly and a mixing section, which was designed to generate a desired concentration of tar compounds in a simulated air stream. A method and calibration protocol of gas chromatography/mass spectroscopy was developed to quantify tar compounds. Experimental data were analyzed statistically using analysis of variance (ANOVA) procedure. Statistical analysis showed that both soybean and canola oils are potential solvents, providing comparable removal efficiency of tar compounds. The experimental height equivalent to a theoretical plate (HETP) was determined as 0.11 m for vegetable oil based scrubbing system. Packed bed height and solvent temperature had highly significant effect (p0.05) effect on the removal of model tar compounds. The packing specific constants, Ch and CP,0, for the Billet and Schultes pressure drop correlation were determined as 2.52 and 2.93, respectively. The equilibrium stage based thermodynamic model predicted the removal efficiency of model tar compounds in the range of 1-6%, 1-4% and 1-2% of experimental data for benzene, toluene and ethylbenzene, respectively, for the solvent temperature of 30° C. The NRTL-PR property model and UNIFAC for estimating binary interaction parameters are recommended for modeling absorption of tar compounds in vegetable oils. Bench scale

  15. Transmembrane Segments Form Tertiary Hairpins in the Folding Vestibule of the Ribosome.

    PubMed Central

    Tu, LiWei; Khanna, Pooja; Deutsch, Carol

    2013-01-01

    Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100 Å of tunnel from the peptidyltransferase center to the exit port. Proximal to the exit port is a ‘folding vestibule’ that permits the nascent peptide to compact and explore conformational space for potential tertiary folding partners. The latter occurs for cytosolic subdomains, but has not yet been shown for transmembrane segments. We now demonstrate, using an accessibility assay and an improved, intramolecular crosslinking assay, that the helical transmembrane S3b-S4 hairpin (‘paddle’) of a voltage-gated potassium (Kv) channel, a critical region of the Kv voltage sensor, forms in the vestibule. S3-S4 hairpin interactions are detected at an early stage of Kv biogenesis. Moreover, this vestibule hairpin is consistent with a closed-state conformation of the Kv channel in the plasma membrane. PMID:24055377

  16. Acid Tar Lagoons: Management and Recovery

    NASA Astrophysics Data System (ADS)

    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

  17. Porous Carbon Nanofibers from Electrospun Biomass Tar/Polyacrylonitrile/Silver Hybrids as Antimicrobial Materials.

    PubMed

    Song, Kunlin; Wu, Qinglin; Zhang, Zhen; Ren, Suxia; Lei, Tingzhou; Negulescu, Ioan I; Zhang, Quanguo

    2015-07-15

    A novel route to fabricate low-cost porous carbon nanofibers (CNFs) using biomass tar, polyacrylonitrile (PAN), and silver nanoparticles has been demonstrated through electrospinning and subsequent stabilization and carbonization processes. The continuous electrospun nanofibers had average diameters ranging from 392 to 903 nm. The addition of biomass tar resulted in increased fiber diameters, reduced thermal stabilities, and slowed cyclization reactions of PAN in the as-spun nanofibers. After stabilization and carbonization, the resultant CNFs showed more uniformly sized and reduced average diameters (226-507 nm) compared to as-spun nanofibers. The CNFs exhibited high specific surface area (>400 m(2)/g) and microporosity, attributed to the combined effects of phase separations of the tar and PAN and thermal decompositions of tar components. These pore characteristics increased the exposures and contacts of silver nanoparticles to the bacteria including Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli, leading to excellent antimicrobial performances of as-spun nanofibers and CNFs. A new strategy is thus provided for utilizing biomass tar as a low-cost precursor to prepare functional CNFs and reduce environmental pollutions associated with direct disposal of tar as an industrial waste.

  18. Estimating tar and nicotine exposure: human smoking versus machine generated smoke yields.

    PubMed

    St Charles, F K; Kabbani, A A; Borgerding, M F

    2010-02-01

    Determine human smoked (HS) cigarette yields of tar and nicotine for smokers using their own brand in their everyday environment. A robust, filter analysis method was used to estimate the tar and nicotine yields for 784 subjects. Seventeen brands were chosen to represent a wide range of styles: 85 and 100 mm lengths; menthol and non-menthol; 17, 23, and 25 mm circumference; with tar yields [Federal Trade Commission (FTC) method] ranging from 1 to 18 mg. Tar bands chosen corresponded to yields of 1-3 mg, 4-6 mg, 7-12 mg, and 13+ mg. A significant difference (p<0.0001) in HS yields of tar and nicotine between tar bands was found. Machine-smoked yields were reasonable predictors of the HS yields for groups of subjects, but the relationship was neither exact nor linear. Neither the FTC, the Massachusetts (MA) nor the Canadian Intensive (CI) machine-smoking methods accurately reflect the HS yields across all brands. The FTC method was closest for the 7-12 mg and 13+ mg products and the MA method was closest for the 1-3mg products. The HS yields for the 4-6 mg products were approximately midway between the FTC and the MA yields. HS nicotine yields corresponded well with published urinary and plasma nicotine biomarker studies. 2009 Elsevier Inc. All rights reserved.

  19. On the application of a hairpin vortex model of wall turbulence to trailing edge noise prediction

    NASA Technical Reports Server (NTRS)

    Liu, N. S.; Shamroth, S. J.

    1985-01-01

    The goal is to develop a technique via a hairpin vortex model of the turbulent boundary layer, which would lead to the estimation of the aerodynamic input for use in trailing edge noise prediction theories. The work described represents an initial step in reaching this goal. The hairpin vortex is considered as the underlying structure of the wall turbulence and the turbulent boundary layer is viewed as an ensemble of typical hairpin vortices of different sizes. A synthesis technique is examined which links the mean flow and various turbulence quantities via these typical vortices. The distribution of turbulence quantities among vortices of different scales follows directly from the probability distribution needed to give the measured mean flow vorticity. The main features of individual representative hairpin vortices are discussed in detail and a preliminary assessment of the synthesis approach is made.

  20. Characterization of the stereochemical selectivity of beta-hairpin formation by molecular dynamics simulations.

    PubMed

    Soto, Patricia; Zangi, Ronen

    2005-01-27

    The stability of secondary structure motifs found in proteins is influenced by the choice of the configuration of the chiral centers present in the amino acid residues (i.e., D vs L). Experimental studies showed that the structural properties of the tetrapeptide (L)V(L)P(L)A(L)L (all-L) are drastically altered upon mutating the L-proline and the L-alanine by their d-enantiomers [J. Am. Chem. Soc. 1996, 118, 6975]. The all-L diastereomer is unstructured, experiencing little or no beta-hairpin formation, while the (L)V(D)P(D)A(L)L peptide exhibits a substantial population of beta-hairpin conformation. In this study, we perform molecular dynamics simulations to investigate the folding propensity of these two model peptides. The results confirm the experimental findings, namely, that the presence of d-amino acids in the loop region strongly induces beta-hairpin formation (a population increase from about 1.5% to 50% is observed). The major factor determining the different behavior is found to be the large difference in energy between the two diastereomers, approximately 22 kJ/mol, when they adopt a beta-hairpin structure. The higher energy observed for the all-L peptide is a consequence of none-ideal hydrogen bond formation and of steric repulsions. The results suggest that selective incorporation of D-amino acids in proteins can be used to enhance certain secondary structure elements. The kinetic behavior of the folding process observed in the simulations is also investigated. We find that the decay rate of the folded structure fits to a biexponential function, suggesting that the folding/unfolding process of a beta-hairpin is governed by two different mechanisms.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Huang, Wai Mun; DaGloria, Jeanne; Fox, Heather

    2012-09-05

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

  2. 29 CFR 1926.1102 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 8 2014-07-01 2014-07-01 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...

  3. 29 CFR 1926.1102 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 8 2011-07-01 2011-07-01 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...

  4. 29 CFR 1926.1102 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 8 2012-07-01 2012-07-01 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...

  5. 29 CFR 1926.1102 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2010 CFR

    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...

  6. Minimization and Optimization of Designed β-Hairpin Folds

    PubMed Central

    Andersen, Niels H.; Olsen, Katherine A.; Fesinmeyer, R. Matthew; Tan, Xu; Hudson, F. Michael; Eidenschink, Lisa A.; Farazi, Shabnam R.

    2011-01-01

    Mimimized β hairpins have provided additional data on the geometric preferences of Trp interactions in TW-loop-WT motifs. This motif imparts significant fold stability to peptides as short as 8 residues. High-resolution NMR structures of a 16- (KKWTWNPATGKWTWQE, ΔGU298 ≥ +7 kJ/mol) and 12-residue (KTWNPATGKWTE, ΔGU298 = +5.05 kJ/mol) hairpin reveal a common turn geometry and edge-to-face (EtF) packing motif and a cation-π interaction between Lys1 and the Trp residue nearest the C-terminus. The magnitude of a CD exciton couplet (due to the two Trp residues) and the chemical shifts of a Trp Hε3 site (shifted upfield by 2.4 ppm due to the EtF stacking geometry) provided near-identical measures of folding. CD melts of representative peptides with the –TW-loop-WT- motif provided the thermodynamic parameters for folding, which reflect enthalpically driven folding at laboratory temperatures with a small ΔCp for unfolding (+420 JK−1/mol). In the case of Asx-Pro-Xaa-Thr-Gly-Xaa loops, mutations established that the two most important residues in this class of direction-reversing loops are Asx and Gly: mutation to alanine is destabilizing by about 6 and 2 kJ/mol, respectively. All indicators of structuring are retained in a minimized 8-residue construct (Ac-WNPATGKW-NH2) with the fold stability reduced to ΔGU278 = −0.7 kJ/mol. NMR and CD comparisons indicate that -TWXNGKWT- (X = S, I) sequences also forms the same hairpin-stabilizing W/W interaction. PMID:16669679

  7. Task 3.9 -- Catalytic tar cracking. Semi-annual report, January 1--June 30, 1995

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Young, B.C.; Timpe, R.C.

    1995-12-31

    Tar produced in the gasification of coal is deleterious to the operation of downstream equipment including fuel cells, gas turbines, hot-gas stream cleanup filters, and pressure swing adsorption systems. Catalytic cracking of tars to smaller hydrocarbons can be an effective means to remove these tars from gas streams and, in the process, generate useful products, e.g., methane gas, which is crucial to the operation of molten carbonate fuel cells. The objectives of this project are to investigate whether gasification tars can be cracked by synthetic nickel-substituted micamontmorillonite, zeolite, or dolomite material; and whether the tars can be cracked selectively bymore » these catalysts to produce a desired liquid and/or gas stream. Results to date are presented in the cited papers.« less

  8. Microwave-induced cracking of pyrolytic tars coupled to microwave pyrolysis for syngas production.

    PubMed

    Beneroso, D; Bermúdez, J M; Montes-Morán, M A; Arenillas, A; Menéndez, J A

    2016-10-01

    Herein a new process is proposed to produce a syngas-rich gas fraction (>80vol% H2+CO) from biowaste based on microwave heating within two differentiated steps in order to avoid tars production. The first step consists of the microwave pyrolysis of biowaste induced by a char-based susceptor at 400-800°C; tars, char and syngas-rich gas fractions being produced. The tars are then fed into the second step where a portion of the char from the first step is used as a bed material in a 0.3:1wt% ratio. This bed is heated up by microwaves up to 800°C, allowing thermal cracking of tars and additional syngas (>90vol% H2+CO) being then produced. This new concept arises as an alternative technology to the gasification of biowastes for producing syngas with no need for catalysts or gasifying reagents to minimise tars production. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Relation Between PAHs and Coal-Tar-Based Pavement Sealant in Urban Environments (Invited)

    NASA Astrophysics Data System (ADS)

    Mahler, B. J.; van Metre, P. C.

    2010-12-01

    Since 2003, coal-tar-based sealant products have come under increased scrutiny as a source of PAHs in urban environments. Sealant (or sealcoat) is the black, shiny substance often applied to asphalt pavement, in particular parking lots and driveways, for esthetic and maintenance purposes. Coal-tar-based sealant, one of the two primary pavement sealant types on the market, typically is 20-35 percent coal-tar pitch, a known carcinogen that is more than 50 percent polycyclic aromatic hydrocarbons (PAHs). The PAH content of the coal-tar-based sealant product is about 1,000 times that of a similar, asphalt-based product, on average. This difference is reflected in regional differences in sealant use and PAH concentrations in pavement dust. In the central and eastern U.S., where the coal-tar-based formulation is prevalent, ΣPAH in mobile particles from sealed pavement have been shown to be about 1,000 times higher than in the western U.S., where the asphalt-based formulation is prevalent (the median ΣPAH concentrations are 2,200 mg/kg in the central and eastern U.S. and 2.1 mg/kg in the western U.S.). Source apportionment modeling indicates that, in the central and eastern U.S., particles from sealed pavement are contributing the majority of the PAHs in recently deposited (post-1990) lake sediment, with implications for ecological health, and that coal-tar-based sealant is the primary cause of upward trends in PAHs in U.S. urban lakes. From the standpoint of human health, research indicates that mobile particles from parking lots with coal-tar-based sealant are tracked indoors, resulting in elevated PAH concentrations in house dust. Coal-tar-based sealcoat being applied to an asphalt parking lot at the University of Texas Pickle Research Center.

  10. 29 CFR 1915.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 7 2014-07-01 2014-07-01 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...

  11. 29 CFR 1915.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 7 2011-07-01 2011-07-01 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...

  12. 29 CFR 1915.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 7 2013-07-01 2013-07-01 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...

  13. 29 CFR 1915.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 7 2012-07-01 2012-07-01 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...

  14. 29 CFR 1915.1002 - Coal tar pitch volatiles; interpretation of term.

    Code of Federal Regulations, 2010 CFR

    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...

  15. Detailed microscopic unfolding pathways of an α-helix and a β-hairpin: direct observation and molecular dynamics.

    PubMed

    Jas, Gouri S; Hegefeld, Wendy A; Middaugh, C Russell; Johnson, Carey K; Kuczera, Krzysztof

    2014-07-03

    We present a combined experimental and computational study of unfolding pathways of a model 21-residue α-helical heteropeptide (W1H5-21) and a 16-residue β-hairpin (GB41-56). Experimentally, we measured fluorescence energy transfer efficiency as a function of temperature, employing natural tryptophans as donors and dansylated lysines as acceptors. Secondary structural analysis was performed with circular dichroism and Fourier transform infrared spectroscopy. Our studies present markedly different unfolding pathways of the two elementary secondary structural elements. During thermal denaturation, the helical peptide exhibits an initial decrease in length, followed by an increase, while the hairpin undergoes a systematic increase in length. In the complementary computational part of the project, we performed microsecond length replica-exchange molecular dynamics simulations of the peptides in explicit solvent, yielding a detailed microscopic picture of the unfolding processes. For the α-helical peptide, we found a large heterogeneous population of intermediates that are primarily frayed single helices or helix-turn-helix motifs. Unfolding starts at the termini and proceeds through a stable helical region in the interior of the peptide but shifted off-center toward the C-terminus. The simulations explain the experimentally observed non-monotonic variation of helix length with temperature as due primarily to the presence of frayed-end single-helix intermediate structures. For the β-hairpin peptide, our simulations indicate that folding is initiated at the turn, followed by formation of the hairpin in zipper-like fashion, with Cα···Cα contacts propagating from the turn to termini and hairpin hydrogen bonds forming in parallel with these contacts. In the early stages of hairpin formation, the hydrophobic side-chain contacts are only partly populated. Intermediate structures with low numbers of β-hairpin hydrogen bonds have very low populations. This is in

  16. The universality of β-hairpin misfolding indicated by molecular dynamics simulations.

    PubMed

    Shao, Qiang; Wang, Jinan; Shi, Jiye; Zhu, Weiliang

    2013-10-28

    Previous molecular dynamics simulations showed that besides the experimentally measured folded structures, several β-structured polypeptides could also have misfolded "out-of-register" structures. Through the enhanced sampling molecular dynamics simulations on a series of polypeptides using either implicit or explicit solvent model, the present study systematically investigated the universality of β-hairpin misfolding and its determinants. It was observed that the misfolding could take place for almost all polypeptides under study, especially in the presence of weak side chain hydrophobicity. Moreover, the observed misfolded structures for various polypeptides share the following common features: (1) the turn length in misfolded structure is one-residue shorter than that in folded structure; (2) the hydrophobic side chains on the two strands are pointed to the opposite directions instead of packing in the same direction to form hydrophobic core cluster in the folded structure; and (3) the misfolded structure is one-residue-shifted asymmetric β-hairpin structure. The detailed analysis suggested that the misfolding of β-hairpin is the result of the competition between the formation of the alterable turn configurations and the inter-strand hydrophobic interactions. These predictions are desired to be tested by experiments.

  17. The universality of β-hairpin misfolding indicated by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shao, Qiang; Wang, Jinan; Shi, Jiye; Zhu, Weiliang

    2013-10-01

    Previous molecular dynamics simulations showed that besides the experimentally measured folded structures, several β-structured polypeptides could also have misfolded "out-of-register" structures. Through the enhanced sampling molecular dynamics simulations on a series of polypeptides using either implicit or explicit solvent model, the present study systematically investigated the universality of β-hairpin misfolding and its determinants. It was observed that the misfolding could take place for almost all polypeptides under study, especially in the presence of weak side chain hydrophobicity. Moreover, the observed misfolded structures for various polypeptides share the following common features: (1) the turn length in misfolded structure is one-residue shorter than that in folded structure; (2) the hydrophobic side chains on the two strands are pointed to the opposite directions instead of packing in the same direction to form hydrophobic core cluster in the folded structure; and (3) the misfolded structure is one-residue-shifted asymmetric β-hairpin structure. The detailed analysis suggested that the misfolding of β-hairpin is the result of the competition between the formation of the alterable turn configurations and the inter-strand hydrophobic interactions. These predictions are desired to be tested by experiments.

  18. Aviation Turbine Fuels from Tar Sands Bitumen and Heavy Oils. Part 1. Process Analysis.

    DTIC Science & Technology

    1984-09-01

    Uinta Basin .......................too.... 11 b . Asphalt Ridge ........................ 13 c.* Tar Sand Triangle ..... to .. .. . .. .. . 15 e...Estimated ............**..* 7 3 CHARACTERISTICS OF UTAH’S MAJOR TAR SANDS ....... 12 4 UINTA BASIN DEPOSITS ................... *........ 13 *.5 UINTA ...7 UINTA BASIN , UTAH PROPERTIES -SUNNYSIDE ........ 20 8 UINTA BASIN , UTAH PROPERTIES -P. R. SPRINGS . 22 r9 ESTIMATED CALIFORNIA TAR SAND DISTRIBUTION

  19. Hairpin Folding of HIV gp41 Abrogates Lipid Mixing Function at Physiologic pH and Inhibits Lipid Mixing by Exposed gp41 Constructs†

    PubMed Central

    Sackett, Kelly; Nethercott, Matthew J.; Shai, Yechiel; Weliky, David P.

    2009-01-01

    Conformational changes in the HIV gp41 protein are directly correlated with fusion between the HIV and target cell plasma membranes which is the initial step of infection. Key gp41 fusion conformations include an early extended conformation termed pre-hairpin which contains exposed regions and a final low energy conformation termed hairpin which has compact six-helix bundle structure. Current fusion models debate the roles of hairpin and pre-hairpin conformations in the process of membrane merger. In the present work, gp41 constructs have been engineered which correspond to fusion relevant parts of both pre-hairpin and hairpin conformations, and have been analyzed for their ability to induce lipid mixing between membrane vesicles. The data correlate membrane fusion function with the pre-hairpin conformation and suggest that one of the roles of the final hairpin conformation is sequestration of membrane perturbing gp41 regions with consequent loss of the membrane disruption induced earlier by the pre-hairpin structure. To our knowledge, this is the first biophysical study to delineate the membrane fusion potential of gp41 constructs modeling key fusion conformations. PMID:19222185

  20. Binding of DNA hairpins to an assembler-strand as part of a primordial translation device

    NASA Astrophysics Data System (ADS)

    Baumann, Ulrich

    1987-09-01

    A crucial event in the process leading to the origin of life is the emergence of a simple translation device. To approach experimental realization of this device the binding ability of short DNA hairpins to complementary oligonucleotides fixed on a solid support was investigated. The binding is achieved by base pairing between the loop nucleotides of the hairpins containing different numbers of adenosine residues and oligothymidylates covalently linked to cellulose. The loop has to consist of at least five nucleotides to achieve binding. The exact number of established base pairs was determined in two ways. First, the elution temperatures of hairpins and those of oligoadenylates which had the length of the loop were compared. Secondly, the architecture of the loop was analyzed by means of the single-strand-specific nuclease from mung bean acting as structural probe. Onlyn-2 of n loop nucleotides of a hairpin are able to form base pairs. Therefore, a strong evidence for the formation of a triplet of base pairs between primeval tRNA and mRNA sufficient to stabilize the complex enzyme-free is given.

  1. Identification of sources of tar balls deposited along the Southwest Caspian Coast, Iran using fingerprinting techniques.

    PubMed

    Shirneshan, Golshan; Bakhtiari, Alireza Riyahi; Memariani, Mahmoud

    2016-10-15

    In 2012, a significant number of tar balls occurred along the Southwest coasts of the Caspian Sea (Iran). Several oil fields of Turkmenistan, Azerbaijan and Iran might be sources of oil spills and lead to the formation of these tar balls. For source identification, 6 tar ball samples were collected from the Southwest beaches of the Caspian Sea and subjected to fingerprint analysis based on the distribution of the source-specific biomarkers of pentacyclic tri-terpanes and steranes. Comparing the diagenic ratios revealed that the tar balls were chemically similar and originated from the same source. Results of double ratio plots (e.g., C29/C30 versus ∑C31-C35/C30 and C28 αββ/(C27 αββ+C29 αββ) versus C29 αββ/(C27 αββ+C28 αββ)) in the tar balls and oils from Iran, Turkmenistan and Azerbaijan indicated that the tar balls might be the result of spills from Turkmenistan oil. Moreover, principle component analysis (PCA) using biomarker ratios on the tar balls and 20 crude oil samples from different wells of Azerbaijan, Iran and Turkmenistan oils showed that the tar balls collected at the Southwest beaches are highly similar to the Turkmenistan oil but one of the Azerbaijan oils (from Bahar field oils) was found to be also slightly close to the tar balls. The weathering characterizations based on the presence of UCM (unresolved complex mixture) and low/high molecular weight ratios (L/H) of alkanes and PAHs indicated the tar ball samples have been significantly influenced by natural weathering processes such as evaporation, photo-degradation and biodegradation. This is the first study of its kind in Iran to use fingerprinting for source identification of tar balls. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2016-01-01

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

  3. Coal-tar-based pavement sealcoat—Potential concerns for human health and aquatic life

    USGS Publications Warehouse

    Mahler, Barbara J.; Woodside, Michael D.; Van Metre, Peter C.

    2016-04-20

    Aquatic Life Concerns—Runoff from coal-tar-sealcoated pavement, even runoff collected more than 3 months after sealcoat application, is acutely toxic to fathead minnows and water fleas, two species commonly used to assess toxicity to aquatic life. Exposure to even highly diluted runoff from coal-tar-sealcoated pavement can cause DNA damage and impair DNA repair. These findings demonstrate that coal-tar-sealcoat runoff can remain a risk to aquatic life for months after application.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wicakso, Doni Rahmat; Chemical Engineering Department, Faculty of Engineering, Gadjah Mada University, Jalan Grafika No. 2 Bulaksumur, Yogyakarta, 55281; Sutijan

    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 evaporatedmore » 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.« less

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    Cheng, Zihao; Campbell, Robert E.

    2007-02-01

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

  7. Beta-hairpin formation in aqueous solution and in the presence of trifluoroethanol: a (1)H and (13)C nuclear magnetic resonance conformational study of designed peptides.

    PubMed

    Santiveri, Clara M; Pantoja-Uceda, David; Rico, Manuel; Jiménez, M Angeles

    2005-10-15

    In order to check our current knowledge on the principles involved in beta-hairpin formation, we have modified the sequence of a 3:5 beta-hairpin forming peptide with two different purposes, first to increase the stability of the formed 3:5 beta-hairpin, and second to convert the 3:5 beta-hairpin into a 2:2 beta-hairpin. The conformational behavior of the designed peptides was investigated in aqueous solution and in 30% trifluoroethanol (TFE) by analysis of the following nuclear magnetic resonance (NMR) parameters: nuclear Overhauser effect (NOE) data, and C(alpha)H, (13)C(alpha), and (13)C(beta) conformational shifts. From the differences in the ability to adopt beta-hairpin structures in these peptides, we have arrived to the following conclusions: (i) beta-Hairpin population increases with the statistical propensity of residues to occupy each turn position. (ii) The loop length, and in turn, the beta-hairpin type, can be modified as a function of the type of turn favored by the loop sequence. These two conclusions reinforce previous results about the importance of beta-turn sequence in beta-hairpin folding. (iii) Side-chain packing on each face of the beta-sheet may play a major role in beta-hairpin stability; hence simplified analysis in terms of isolated pair interactions and intrinsic beta-sheet propensities is insufficient. (iv) Contributions to beta-hairpin stability of turn and strand sequences are not completely independent. (v) The burial of hydrophobic surface upon beta-hairpin formation that, in turn, depends on side-chain packing also contributes to beta-hairpin stability. (vi) As previously observed, TFE stabilizes beta-hairpin structures, but the extent of the contribution of different factors to beta-hairpin formation is sometimes different in aqueous solution and in 30% TFE. (c) 2005 Wiley Periodicals, Inc. Biopolymers 79: 150-162, 2005.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jack L. Arbiser; Baskaran Govindarajan; Traci E. Battle

    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 endothelialmore » 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.« less

  9. Reduced tar, nicotine, and carbon monoxide exposure while smoking ultralow- but not low-yield cigarettes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Benowitz, N.L.; Jacob, P. III; Yu, L.

    An unresolved public health issue is whether some modern cigarettes are less hazardous than other and whether patients who cannot stop smoking should be advised to switch to lower-yield cigarettes. The authors studied tar (estimated by urine mutagenicity), nicotine, and carbon monoxide exposure in habitual smokers switched from their usual brand to high- (15 mg of tar), low- (5 mg of tar), or ultralow-yield (1 mg of tar) cigarettes. There were no differences in exposure comparing high- or low-yield cigarettes, but tar and nicotine exposures were reduced by 49% and 56%, respectively, and carbon monoxide exposure by 36% while smokingmore » ultralow-yield cigarettes. Similarly, in 248 subjects smoking their self-selected brand, nicotine intake, estimated by blood concentrations of its metabolite continine, was 40% lower in those who smoked ultralow but no different in those smoking higher yields of cigarettes. The data indicate that ultralow-yield cigarettes do deliver substantial doses of tar, nicotine, and carbon monoxide, but that exposure are considerably less than for other cigarettes.« less

  10. Pollutant sensitivity of the endangered Tar River Spinymussel as assessed by single chemical and effluent toxicity tests

    USGS Publications Warehouse

    Augspurger, Thomas P.; Wang, Ning; Kunz, James L.; Ingersoll, Christopher G.

    2014-01-01

    The federally endangered Tar River spinymussel (Elliptio steinstansana) is endemic to the Tar River and Neuse River systems in North Carolina. The extent to which water quality limits Tar River spinymussels’ recovery is important to establish, and one aspect of that is understanding the species’ pollutant sensitivity. The primary objectives of this study were to 1) develop captive propagation and culture methods for Tar River spinymussels; 2) determine the pollutant sensitivity of captively propagated Tar River spinymussels; 3) examine the utility of the non-endangered yellow lance (Elliptio lanceolata), yellow lampmussel (Lampsilis cariosa) and notched rainbow (Villosa constricta) as surrogates for the Tar River spinymussels’ chemical sensitivity; 4) develop a 7-d method for conducting effluent toxicity tests starting with newly transformed mussels; 5) assess the toxicity of municipal wastewater effluents discharged into the Tar River spinymussels’ current and historic habitat; and, 6) evaluate the protection afforded by existing effluent toxicity test requirements.

  11. Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

    NASA Astrophysics Data System (ADS)

    Verma, Abhinav; Wenzel, Wolfgang

    2008-03-01

    Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500cycles corresponding to 7.4×107 energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04Å to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5Å bRMSD from native.

  12. Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations.

    PubMed

    Verma, Abhinav; Wenzel, Wolfgang

    2008-03-14

    Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500 cycles corresponding to 7.4 x 10(7) energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04 A to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5 A bRMSD from native.

  13. Effects of human chromosome 12 on interactions between Tat and TAR of human immunodeficiency virus type 1.

    PubMed Central

    Alonso, A; Cujec, T P; Peterlin, B M

    1994-01-01

    Rates of transcriptions of the human immunodeficiency virus are greatly increased by the viral trans activator Tat. In vitro, Tat binds to the 5' bulge of the trans-activation response (TAR) RNA stem-loop, which is present in all viral transcripts. In human cells, the central loop in TAR and its cellular RNA-binding proteins are also critical for the function of Tat. Previously, we demonstrated that in rodent cells (CHO cells), but not in those which contain the human chromosome 12 (CHO12 cells), Tat-TAR interactions are compromised. In this study, we examined the roles of the bulge and loop in TAR in Tat trans activation in these cells. Whereas low levels of trans activation depended solely on interactions between Tat and the bulge in CHO cells, high levels of trans activation depended also on interactions between Tat and the loop in CHO12 cells. Since the TAR loop binding proteins in these two cell lines were identical and different from their human counterpart, the human chromosome 12 does not encode TAR loop binding proteins. In vivo binding competition studies with TAR decoys confirmed that the binding of Tat to TAR is more efficient in CHO12 cells. Thus, the protein(s) encoded on human chromosome 12 helps to tether Tat to TAR via its loop, which results in high levels of trans activation. Images PMID:8083988

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

    PubMed

    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.

  15. Impact of genetic variants on haematopoiesis in patients with thrombocytopenia absent radii (TAR) syndrome.

    PubMed

    Manukjan, Georgi; Bösing, Hendrik; Schmugge, Markus; Strauß, Gabriele; Schulze, Harald

    2017-11-01

    Thrombocytopenia absent radii (TAR) syndrome is clearly defined by the combination of radial aplasia and reduced platelet counts. The genetics of TAR syndrome has recently been resolved and comprises a microdeletion on Chromosome 1 including the RBM8A gene and a single nucleotide polymorphism (SNP) either at the 5' untranslated region (5'UTR) or within the first intron of RBM8A. Although phenotypically readily diagnosed after birth, the genetic determination of particular SNPs in TAR syndrome harbours valuable information to evaluate disease severity and treatment decisions. Here, we present clinical data in a cohort of 38 patients and observed that platelet counts in individuals with 5'UTR SNP are significantly lower compared to patients bearing the SNP in intron 1. Moreover, elevated haemoglobin values could only be assessed in patients with 5'UTR SNP whereas white blood cell count is unaffected, indicating that frequently observed anaemia in TAR patients could also be SNP-dependent whereas leucocytosis does not correlate with genetic background. However, this report on a large cohort provides an overview of important haematological characteristics in TAR patients, facilitating evaluation of the various traits in this disease and indicating the importance of genetic validation for TAR syndrome. © 2017 John Wiley & Sons Ltd.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan

    2015-04-03

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

  17. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation

    PubMed Central

    Roden, Christine; Gaillard, Jonathan; Kanoria, Shaveta; Rennie, William; Barish, Syndi; Cheng, Jijun; Pan, Wen; Liu, Jun; Cotsapas, Chris; Ding, Ye; Lu, Jun

    2017-01-01

    Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36 ± 3 nt is optimal for pri-miRNA processing. We identify two bulge-depleted regions on the miRNA stem, located ∼16–21 nt and ∼28–32 nt from the base of the stem, that are less tolerant of unpaired bases. We further show that the CNNC primary sequence motif selectively enhances the processing of optimal-length hairpins. We predict that a small but significant fraction of human single-nucleotide polymorphisms (SNPs) alter pri-miRNA processing, and confirm several predictions experimentally including a disease-causing mutation. Our study enhances the rules governing mammalian pri-miRNA processing and suggests a diverse impact of human genetic variation on miRNA biogenesis. PMID:28087842

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

    PubMed

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

    2011-03-01

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

  19. Technology for the production of Zero Q.I pitch from coal tar

    NASA Astrophysics Data System (ADS)

    Karthik, K.; Kumar, K. Rajesh; Rao, C. V. Nageswara; Kumar, B. Vinod; Murty, J. V. S.

    2013-06-01

    Zero Quinoline Insolubles (Q.I) pitch is a special type of pitch obtained from pre-treatment of coal tar, which is converted into pitch. This is used for impregnation of electrodes for improving the strength, electrical properties and also used as a pre-cursor for Mesophase pitch for producing Mesophase pitch based carbon fibers, carbon foam, and Meso carbon micro beads. This paper discusses the technology of Q.I separation from Coal Tar by using decantation of Coal Tar mixed with Heavy Creosote Oil (HC Oil) at different temperatures. By this method we were able to produce the Zero Q.I pitch with a Q.I value of 0.1%.

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

    DOEpatents

    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.

  1. Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin.

    PubMed

    Jimenez-Cruz, Camilo A; Garcia, Angel E

    2014-04-14

    Equilibrium thermodynamics of a short beta-hairpin are studied using unbiased all-atom replica exchange molecular dynamics simulations in explicit solvent. An exploratory analysis of the free energy landscape of the system is provided in terms of various structural characteristics, for both the folded and unfolded ensembles. We find that the favorable interactions between the ends introduced by the tryptophan cap, along with the flexibility of the turn region, explain the remarkable stability of the folded state. Charging of the N termini results in effective roughening of the free energy landscape and stabilization of non-native contacts. Folding-unfolding dynamics are further discussed using a set of 2413 independent molecular dynamics simulations, 2 ns to 20 ns long, at the melting temperature of the beta-hairpin. A novel method for the construction of Markov models consisting of an iterative refinement of the discretization in reduced dimensionality is presented and used to generate a detailed kinetic network of the system. The hairpin is found to fold heterogeneously on sub-microsecond timescales, with the relative position of the tryptophan side chains driving the selection of the specific pathway.

  2. Analysis of a DNA simulation model through hairpin melting experiments.

    PubMed

    Linak, Margaret C; Dorfman, Kevin D

    2010-09-28

    We compare the predictions of a two-bead Brownian dynamics simulation model to melting experiments of DNA hairpins with complementary AT or GC stems and noninteracting loops in buffer A. This system emphasizes the role of stacking and hydrogen bonding energies, which are characteristics of DNA, rather than backbone bending, stiffness, and excluded volume interactions, which are generic characteristics of semiflexible polymers. By comparing high throughput data on the open-close transition of various DNA hairpins to the corresponding simulation data, we (1) establish a suitable metric to compare the simulations to experiments, (2) find a conversion between the simulation and experimental temperatures, and (3) point out several limitations of the model, including the lack of G-quartets and cross stacking effects. Our approach and experimental data can be used to validate similar coarse-grained simulation models.

  3. Exosomes from HIV-1-infected Cells Stimulate Production of Pro-inflammatory Cytokines through Trans-activating Response (TAR) RNA*

    PubMed Central

    Sampey, Gavin C.; Saifuddin, Mohammed; Schwab, Angela; Barclay, Robert; Punya, Shreya; Chung, Myung-Chul; Hakami, Ramin M.; Asad Zadeh, Mohammad; Lepene, Benjamin; Klase, Zachary A.; El-Hage, Nazira; Young, Mary; Iordanskiy, Sergey; Kashanchi, Fatah

    2016-01-01

    HIV-1 infection results in a chronic illness because long-term highly active antiretroviral therapy can lower viral titers to an undetectable level. However, discontinuation of therapy rapidly increases virus burden. Moreover, patients under highly active antiretroviral therapy frequently develop various metabolic disorders, neurocognitive abnormalities, and cardiovascular diseases. We have previously shown that exosomes containing trans-activating response (TAR) element RNA enhance susceptibility of undifferentiated naive cells to HIV-1 infection. This study indicates that exosomes from HIV-1-infected primary cells are highly abundant with TAR RNA as detected by RT-real time PCR. Interestingly, up to a million copies of TAR RNA/μl were also detected in the serum from HIV-1-infected humanized mice suggesting that TAR RNA may be stable in vivo. Incubation of exosomes from HIV-1-infected cells with primary macrophages resulted in a dramatic increase of proinflammatory cytokines, IL-6 and TNF-β, indicating that exosomes containing TAR RNA could play a direct role in control of cytokine gene expression. The intact TAR molecule was able to bind to PKR and TLR3 effectively, whereas the 5′ and 3′ stems (TAR microRNAs) bound best to TLR7 and -8 and none to PKR. Binding of TAR to PKR did not result in its phosphorylation, and therefore, TAR may be a dominant negative decoy molecule in cells. The TLR binding through either TAR RNA or TAR microRNA potentially can activate the NF-κB pathway and regulate cytokine expression. Collectively, these results imply that exosomes containing TAR RNA could directly affect the proinflammatory cytokine gene expression and may explain a possible mechanism of inflammation observed in HIV-1-infected patients under cART. PMID:26553869

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Thermal Cracking of Tars in a Continuously Fed Reactor with Steam

    DTIC Science & Technology

    2011-05-01

    Fluidized Bed using biomass 8 Tars  Mixture of organic components present in gasification product gas with high molecular weight hydrocarbons [MW...Disable sulfur removal systems FoulingPlugging [Ref. 3: Biomass Gasification – Tar and Particles in Product Gases Sampling and Analysis”, European...P., and Nussbaumer T., “Gas Cleaning Requirements for Internal Combustion Engine Applications of Fixed Bed Biomass Gasification ”, Biomass and

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

    PubMed

    Caetano-Anollés, G; Gresshoff, P M

    1996-06-01

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

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

    PubMed

    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. The Auxin Biosynthetic TRYPTOPHAN AMINOTRANSFERASE RELATED TaTAR2.1-3A Increases Grain Yield of Wheat.

    PubMed

    Shao, An; Ma, Wenying; Zhao, Xueqiang; Hu, Mengyun; He, Xue; Teng, Wan; Li, Hui; Tong, Yiping

    2017-08-01

    Controlling the major auxin biosynthetic pathway to manipulate auxin content could be a target for genetic engineering of crops with desired traits, but little progress had been made because low or high auxin contents often cause developmental inhibition. Here, we performed a genome-wide analysis of bread wheat ( Triticum aestivum ) to identify the Tryptophan Aminotransferase of Arabidopsis1/Tryptophan Aminotransferase-Related (TAA1/TAR) genes that function in the tryptophan-dependent pathway of auxin biosynthesis. Sequence mining together with gene cloning identified 15 TaTAR genes, among which 12 and three genes were phylogenetically close to Arabidopsis ( Arabidopsis thaliana ) AtTAR2 and AtTAR3, respectively. TaTAR2.1 had the most abundant transcripts in the TaTAR2 genes and was expressed mainly in roots and up-regulated by low nitrogen (N) availability. Knockdown of TaTAR2.1 caused vegetative and reproductive deficiencies and impaired lateral root (LR) growth under both high- and low-N conditions. Overexpressing TaTAR2.1-3A in wheat enhanced LR branching, plant height, spike number, grain yield, and aerial N accumulation under different N supply levels. In addition, overexpressing TaTAR2.1-3A in Arabidopsis elevated auxin accumulation in the primary root tip, LR tip, LR primordia, and cotyledon and hypocotyl and increased primary root length, visible LR number, and shoot fresh weight under high- and low-N conditions. Our results indicate that TaTAR2.1 is critical for wheat growth and also shows potential for genetic engineering to reach the aim of improving the grain yield of wheat. © 2017 American Society of Plant Biologists. All Rights Reserved.

  9. Use of mineral oil Fleet enema for the removal of a large tar burn: a case report.

    PubMed

    Carta, Tricia; Gawaziuk, Justin; Liu, Song; Logsetty, Sarvesh

    2015-03-01

    Extensive hot tar burns are relatively uncommon. Management of these burns provides a significant clinical challenge especially with respect to tar removal involving a large total body surface area (TBSA), without causing further tissue injury. We report a case of an over 40-year old male construction worker who was removing a malfunctioning cap from broken valve. This resulted in tar spraying over the anterior surface of his body including legs, feet, chest, abdomen, arms, face and oral cavity (80% TBSA covered in tar resulting in a 50% TBSA burn injury). Initially, petrolatum-based, double antibiotic ointment was used to remove the tar, based on our previous experience with small tar burns. However, this was time-consuming and ineffective. The tar was easily removed with mineral oil without irritation. In order to meet the demand for quantity of mineral oil, the pharmacy suggested using mineral oil Fleet enema (C.B. Fleet Company, Inc., Lynchburg, Virginia, USA). The squeezable bottle and catheter tip facilitated administration of oil into the patient's construction boots and under clothing that was adhered to the patient's skin. Tar removal requires an effective, non-toxic and non-irritating agent. Mineral oil is such an agent. For patients that may present with a large surface area tar burn, using mineral oil Fleet enema is a viable option that facilitates application into difficult areas. Grant Support: The Firefighters' Burn Fund (Manitoba) supported this project. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

  10. Method of identifying hairpin DNA probes by partial fold analysis

    DOEpatents

    Miller, Benjamin L [Penfield, NY; Strohsahl, Christopher M [Saugerties, NY

    2009-10-06

    Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  11. Method of identifying hairpin DNA probes by partial fold analysis

    DOEpatents

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2008-10-28

    Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  12. Partitioning studies of coal-tar constituents in a two-phase contaminated ground-water system

    USGS Publications Warehouse

    Rostad, C.E.; Pereira, W.E.; Hult, M.F.

    1985-01-01

    Organic compounds derived from coal-tar wastes in a contaminated aquifer in St. Louis Park, Minnesota, were identified, and their partition coefficients between the tar phase and aqueous phase were determined and compared with the corresponding n-octanol/water partition coefficients. Coal tar contains numerous polycyclic aromatic compounds, many of which are suspected carcinogens or mutagens. Groundwater contamination by these toxic compounds may pose an environmental health hazard in nearby public water-supply wells. Fluid samples from this aquifer developed two phases upon settling: an upper aqueous phase, and a lower oily-tar phase. After separating the phases, polycyclic aromatic compounds in each phase were isolated using complexation with N-methyl-2-pyrrolidone and identified by fused-silica capillary gas chromatography/mass spectrometry. Thirty-one of the polycyclic aromatic compounds were chosen for further study from four different classes: 12 polycyclic aromatic hydrocarbons, 10 nitrogen heterocycles, 5 sulfur heterocycles, and 4 oxygen heterocycles. Within each compound class, the tar/water partition coefficients of these compounds were reasonably comparable with the respective n-octanol/water partition coefficient.

  13. Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions.

    PubMed Central

    Earnshaw, D J; Gait, M J

    1998-01-01

    The hairpin ribozyme is a small catalytic RNA that achieves an active configuration by docking of its two helical domains in an antiparallel fashion. Both docking and subsequent cleavage are dependent on the presence of divalent metal ions, such as magnesium, but there is no evidence to date for direct participation of such ions in the chemical cleavage step. We show that aminoglycoside antibiotics inhibit cleavage of the hairpin ribozyme in the presence of metal ions with the most effective being 5-epi-sisomicin and neomycin B. In contrast, in the absence of metal ions, a number of aminoglycoside antibiotics at 10 mM concentration promote hairpin cleavage with rates only 13-20-fold lower than the magnesium-dependent reaction. We show that neomycin B competes with metal ions by ion replacement with the postively charged amino groups of the antibiotic. In addition, we show that the polyamine spermine at 10 mM promotes efficient hairpin cleavage with rates similar to the magnesium-dependent reaction. Low concentrations of either spermine or the shorter polyamine spermidine synergize with 5 mM magnesium ions to boost cleavage rates considerably. In contrast, at 500 microM magnesium ions, 4 mM spermine, but not spermidine, boosts the cleavage rate. The results have significance both in understanding the role of ions in hairpin ribozyme cleavage and in potential therapeutic applications in mammalian cells. PMID:9837982

  14. A photographic method for estimating wear of coal tar sealcoat from parking lots

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mateo Scoggins; Tom Ennis; Nathan Parker

    2009-07-01

    Coal-tar-based sealcoat has been recognized as an important source of PAHs to the environment through wear and transport via stormwater runoff. Sealcoat removal rates have not been measured or even estimated in the literature due to the complex array of physical and chemical process involved. A photographic study was conducted that incorporates all sources of wear using 10 coal tar-sealed parking lots in Austin, Texas, with sealcoat age ranging from 0 to 5 years. Randomly located photographs from each parking lot were analyzed digitally to quantify black sealed areas versus lighter colored unsealed areas at the pixel level. The resultsmore » indicate that coal tar sealcoat wears off of the driving areas of parking lots at a rate of approximately 4.7% per year, and from the parking areas of the lots at a rate of approximately 1.4% per year. The overall annual loss of sealcoat was calculated at 2.4%. This results in an annual delivery to the environment of 0.51 g of PAHs per m{sup 2} of coal tar-sealed parking lot. These values provide a more robust and much higher estimate of loading of PAHs from coal tar sealcoated parking lots when compared to other available measures. 20 refs., 6 figs.« less

  15. Morphology of transverse aeolian ridges (TARs) on Mars from a large sample: Further evidence of a megaripple origin?

    NASA Astrophysics Data System (ADS)

    Hugenholtz, Chris H.; Barchyn, Thomas E.; Boulding, Adam

    2017-04-01

    Using HiRISE digital terrain models (DTMs), we developed a large morphological dataset to examine the three-dimensional shape, size, and scaling of Martian transverse aeolian ridges (TARs). Considerable debate exists on the characteristic morphology of TARs and the origins of these enigmatic bedforms. Some researchers suggest polygenesis or multiple classes of similar bedforms. Reliably characterizing the morphology of TARs is an essential prerequisite to developing and evaluating process-based models of TAR genesis and unraveling aeolian processes on the surface of Mars. We present measurements of TAR morphology from a large, DTM-derived dataset (n = 2295). We focused on TARs with 'simple' morphologies in order enable more defensible discretization. Histograms and cumulative log-frequency plots of morphometric parameters (length, width, height, elongation ratio, and wavelength) indicate the sample represents a continuum of bedforms from a single population. A typical TAR from our dataset is 88.5 m long (longest planview axis), 17.3 m wide (shortest planview axis), 1.3 m tall, and has a wavelength of 25.8 m. Combined with these data, the bulk of evidence presented to date suggests that interpreting TARs as megaripples is the most viable working hypothesis.

  16. TarPmiR: a new approach for microRNA target site prediction.

    PubMed

    Ding, Jun; Li, Xiaoman; Hu, Haiyan

    2016-09-15

    The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (crosslinking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods. Applying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2% of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision. The TarPmiR software is freely available at http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/ CONTACTS: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Modeling the impact of bubbling bed hydrodynamics on tar yield and its fluctuations during biomass fast pyrolysis

    DOE PAGES

    Xiong, Qingang; Ramirez, Emilio; Pannala, Sreekanth; ...

    2015-10-09

    The impact of bubbling bed hydrodynamics on temporal variations in the exit tar yield for biomass fast pyrolysis was investigated using computational simulations of an experimental laboratory-scale reactor. A multi-fluid computational fluid dynamics model was employed to simulate the differential conservation equations in the reactor, and this was combined with a multi-component, multi-step pyrolysis kinetics scheme for biomass to account for chemical reactions. The predicted mean tar yields at the reactor exit appear to match corresponding experimental observations. Parametric studies predicted that increasing the fluidization velocity should improve the mean tar yield but increase its temporal variations. Increases in themore » mean tar yield coincide with reducing the diameter of sand particles or increasing the initial sand bed height. However, trends in tar yield variability are more complex than the trends in mean yield. The standard deviation in tar yield reaches a maximum with changes in sand particle size. As a result, the standard deviation in tar yield increases with the increases in initial bed height in freely bubbling state, while reaches a maximum in slugging state.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pittelkow, M.R.; Perry, H.O.; Muller, S.A.

    1981-08-01

    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 whenmore » 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.« less

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

    USGS Publications Warehouse

    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. Combined High-Speed 3D Scalar and Velocity Reconstruction of Hairpin Vortex

    NASA Astrophysics Data System (ADS)

    Sabatino, Daniel; Rossmann, Tobias; Zhu, Xuanyu; Thorsen, Mary

    2017-11-01

    The combination of 3D scanning stereoscopic particle image velocimetry (PIV) and 3D Planar Laser Induced Fluorescence (PLIF) is used to create high-speed three-dimensional reconstructions of the scalar and velocity fields of a developing hairpin vortex. The complete description of the regenerating hairpin vortex is needed as transitional boundary layers and turbulent spots are both comprised of and influenced by these vortices. A new high-speed, high power, laser-based imaging system is used which enables both high-speed 3D scanning stereo PIV and PLIF measurements. The experimental system uses a 250 Hz scanning mirror, two high-speed cameras with a 10 kHz frame rate, and a 40 kHz pulsed laser. Individual stereoscopic PIV images and scalar PLIF images are then reconstructed into time-resolved volumetric velocity and scalar data. The results from the volumetric velocity and scalar fields are compared to previous low-speed tomographic PIV data and scalar visualizations to determine the accuracy and fidelity of the high-speed diagnostics. Comparisons between the velocity and scalar field during hairpin development and regeneration are also discussed. Supported by the National Science Foundation under Grant CBET-1531475, Lafayette College,and the McCutcheon Foundation.

  2. Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs

    PubMed Central

    Morita, Teppei; Nishino, Ryo; Aiba, Hiroji

    2017-01-01

    Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of seven or more T residues at the 3′ end, as noted in previous studies. Here, we have studied the role of the terminator hairpin in the biogenesis of sRNAs focusing on SgrS and RyhB in Escherichia coli. We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the poly(U) tail is shortened. The transcripts with shortened poly(U) tails no longer bind to Hfq and lose the ability to repress the target mRNAs. The shortened transcripts are generated in an in vitro transcription system with purified RNA polymerase, indicating that the generation of shortened transcripts is caused by premature transcription termination. We conclude that the terminator structure of sRNA genes is optimized to generate functional sRNAs. Thus, the Rho-independent terminators of sRNA genes possess two common features: a long T residue stretch that is a prerequisite for generation of functional sRNAs and a moderate strength of hairpin structure that ensures the termination at the seventh or longer position within the consecutive T stretch. The modulation of the termination position at the Rho-independent terminators is critical for biosynthesis of functional sRNAs. PMID:28606943

  3. Iron(II) supramolecular helicates interfere with the HIV-1 Tat–TAR RNA interaction critical for viral replication

    PubMed Central

    Malina, Jaroslav; Hannon, Michael J.; Brabec, Viktor

    2016-01-01

    The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat–TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates. PMID:27405089

  4. Iron(II) supramolecular helicates interfere with the HIV-1 Tat-TAR RNA interaction critical for viral replication.

    PubMed

    Malina, Jaroslav; Hannon, Michael J; Brabec, Viktor

    2016-07-12

    The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat-TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates.

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

    PubMed

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

    2016-04-01

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

  6. The free energy landscape for hairpin folding in explicit water

    NASA Astrophysics Data System (ADS)

    Zhou, Ruhong; Berne, Bruce J.; Germain, Robert

    2001-12-01

    The folding free energy landscape of the C-terminal hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and OPLSAA force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The β hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.

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

    PubMed

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

    2017-03-15

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mise, Takeshi; Matsunami, Hideyuki; Samatey, Fadel A.

    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 weremore » 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.« less

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

    USGS Publications Warehouse

    Yang, Y.; Mahler, B.J.; Van Metre, P.C.; Ligouis, B.; Werth, C.J.

    2010-01-01

    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 (Cr2O7) oxidation and chemo-thermal oxidation at 375??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 Cr2O7 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 Cr2O7 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 Cr2O7 oxidation or CTO-375, and caution is advised when interpreting BC measurements made with these methods. ?? 2010 Elsevier Ltd.

  10. A comparison of physicochemical methods for the remediation of porous medium systems contaminated with tar

    NASA Astrophysics Data System (ADS)

    Hauswirth, Scott C.; Miller, Cass T.

    2014-10-01

    The remediation of former manufactured gas plant (FMGP) sites contaminated with tar DNAPLs (dense non-aqueous phase liquids) presents a significant challenge. The tars are viscous mixtures of thousands of individual compounds, including known and suspected carcinogens. This work investigates the use of combinations of mobilization, solubilization, and chemical oxidation approaches to remove and degrade tars and tar components in porous medium systems. Column experiments were conducted using several flushing solutions, including an alkaline-polymer (AP) solution containing NaOH and xanthan gum (XG), a surfactant-polymer (SP) solution containing Triton X-100 surfactant (TX100) and XG, an alkaline-surfactant-polymer (ASP) solution containing NaOH, TX100, and XG, and base-activated sodium persulfate both with and without added TX100. The effectiveness of the flushing solutions was assessed based on both removal of polycyclic aromatic hydrocarbon (PAH) mass and on the reduction of dissolved-phase PAH concentrations. SP flushes of 6.6 to 20.9 PV removed over 99% of residual PAH mass and reduced dissolved-phase concentrations by up to two orders of magnitude. ASP flushing efficiently removed 95-96% of residual PAH mass within about 2 PV, and significantly reduced dissolved-phase concentrations of several low molar mass compounds, including naphthalene, acenaphthene, fluorene, and phenanthrene. AP flushing removed a large portion of the residual tar (77%), but was considerably less effective than SP and ASP in terms of the effect on dissolved PAH concentrations. Persulfate was shown to oxidize tar components, primarily those with low molar mass, however, the overall degradation was relatively low (30-50% in columns with low initial tar saturations), and the impact on dissolved-phase concentrations was minimal.

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs.

    PubMed

    Morita, Teppei; Nishino, Ryo; Aiba, Hiroji

    2017-09-01

    Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of seven or more T residues at the 3' end, as noted in previous studies. Here, we have studied the role of the terminator hairpin in the biogenesis of sRNAs focusing on SgrS and RyhB in Escherichia coli. We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the poly(U) tail is shortened. The transcripts with shortened poly(U) tails no longer bind to Hfq and lose the ability to repress the target mRNAs. The shortened transcripts are generated in an in vitro transcription system with purified RNA polymerase, indicating that the generation of shortened transcripts is caused by premature transcription termination. We conclude that the terminator structure of sRNA genes is optimized to generate functional sRNAs. Thus, the Rho-independent terminators of sRNA genes possess two common features: a long T residue stretch that is a prerequisite for generation of functional sRNAs and a moderate strength of hairpin structure that ensures the termination at the seventh or longer position within the consecutive T stretch. The modulation of the termination position at the Rho-independent terminators is critical for biosynthesis of functional sRNAs. © 2017 Morita et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  15. Optical, Physical and Chemical Properties of Tar Balls Observed During the Yosemite Aerosol Characterization Study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hand, Jenny L.; Malm, W. C.; Laskin, Alexander

    2005-11-09

    The Yosemite Aerosol Characterization Study of summer 2002 (YACS) occurred during an active fire season in the western U. S., and provided an opportunity to investigate many unresolved issues related to the radiative effects of biomass burning aerosols. Single particle analysis was performed on field collected aerosol samples using an array of electron microscopy techniques. Amorphous carbon spheres, or “tar balls”, were present in samples collected during episodes of high particle light scattering coefficients that occurred during the peak of a smoke/haze event. The highest concentrations of light-absorbing carbon from a dual-wavelength aethalometer (λ = 370 and 880 nm) occurredmore » during periods when the particles were predominantly tar balls, indicating they do absorb light in the UV and near-IR range of the solar spectrum. Closure experiments of mass concentrations and light scattering coefficients during periods dominated by tar balls did not require any distinct assumptions of organic carbon molecular weight correction factors, density, or refractive index compared to periods dominated by other types of organic carbon aerosols. Measurements of the hygroscopic behavior of tar balls using an environmental SEM indicate that tar balls do not exhibit deliquescence, but do uptake some water at high (~83 %) relative humidity. The ability of tar balls to efficiently scatter and absorb light, and to absorb water has important implications for their role in regional haze and climate fence.« less

  16. Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

    PubMed

    Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

    2008-08-07

    A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

  17. Comparative evaluation of topical calcipotriol versus coal tar and salicylic acid ointment in chronic plaque psoriasis.

    PubMed

    Singh, Preeti; Gupta, Surabhi; Abidi, Afroz; Krishna, Arvind

    2013-08-01

    Calcipotriol is a newer topical treatment option available for plaque psoriasis and coal tar being one of the oldest treatment and still in use. To evaluate and compare the differences in terms of efficacy, safety and relapse with Calcipotriol 0.005% (50 mcg/gm) and 6% coal tar and 3% salicylic ointment in patients with Plaque psoriasis. SETTING and Study conducted on 60 patients of plaque psoriasis, who attended the skin OPD in our hospital. The patients with mild to moderate plaque psoriasis were selected. 60 patients were enrolled for the study after obtaining informed consent. Subjects were asked to apply Calcipotriol 0.005% (50 mcg/gm) (Heximar Win care) twice a day on the right side plaques and on left side plaques, Petroleum jelly (Vaseline) in the morning and 6% coal tar and 3% salicylic ointment (Protar® Percos) at nighttime. PASI score was used to assess the reponse to therapy at 2nd, 4th, 6th and 8th week. After treatment subjects were observed for 6 weeks for any relapse. It was done by paired t-test and independent sample t-test. The results showed that statistically significant difference was seen in the mean percentage reduction of PASI score between both the groups, at all the assessment visits, 2, 4, 6, and 8 weeks, the mean percentage reduction at 2 weeks for calcipotriol being 21±12.06 and for coal tar being 13.44±11.19 (P=0.000), at 4 weeks for calcipotriol was 40±16.71 and for coal tar 25±99 (P=0.000), at 6 weeks for calcipotriol was 53.99+-22.43 and for coal tar 41±21.23 (P=0.002), at 8 weeks for calcipotriol was 62.73±24.04 and for coal tar was 51.53±23.27 (P=0.11). Relapse was seen in 5/60 (8.3%) of patients on calcipotriol treated side and 9/60 (15%) of patients with coal tar treated side. Thus it can be concluded that calcipotriol cream is more efficacious when compared with coal tar and does have a quick response. It is well tolerated and acceptable cosmetically.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    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.more » 4 figures, 6 tables.« less

  19. Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA

    PubMed Central

    BRADRICK, THOMAS D.; MARINO, JOHN P.

    2004-01-01

    Replication of human immunodeficiency virus type 1 (HIV-1) is regulated in part through an interaction between the virally encoded trans-activator protein Tat and the trans-activator responsive region (TAR) of the viral RNA genome. Because TAR is highly conserved and its interaction with Tat is required for efficient viral replication, it has received much attention as an antiviral drug target. Here, we report a 2-aminopurine (2-AP) fluorescence-based assay for evaluating potential TAR inhibitors. Through selective incorporation of 2-AP within the bulge (C23 or U24) of a truncated form of the TAR sequence (Δ TAR-ap23 and Δ TAR-ap24), binding of argininamide, a 24-residue arginine-rich peptide derived from Tat, and Neomycin has been characterized using steady-state fluorescence. Binding of argininamide to the 2-AP ΔTAR constructs results in a four- to 11-fold increase in fluorescence intensity, thus providing a sensitive reporter of that interaction (KD ~ 1 mM). Similarly, binding of the Tat peptide results in an initial 14-fold increase in fluorescence (KD ~ 25 nM), but is then followed by a slight decrease that is attributed to an additional, lower-affinity association(s). Using the ΔTAR-ap23 and TAR-ap24 constructs, two classes of Neomycin binding sites are detected; the first molecule of antibiotic binds as a noncompetitive inhibitor of Tat/argininamide (KD ~ 200 nM), whereas the second, more weakly bound molecule(s) becomes associated in a presumably nonspecific manner (KD ~ 4 μM). Taken together, the results demonstrate that the 2-AP fluorescence-detected binding assays provide accurate and general methods for quantitatively assessing TAR interactions. PMID:15273324

  20. Stepwise nanoassembly of a single hairpin probe and its biosensing.

    PubMed

    Xu, Jianguo; Zheng, Tingting; Le, Jingqing; Jia, Lee

    2018-09-01

    Herein, we describe a novel trigger-induced DNA nanoassembly method using only one loop-stem shaped hairpin probe (HP) that consists of three different functional regions as a single building unit. The Region I is designed complementary to the trigger, while the Region II and Region III are projected to complementary with each other. When hybridized with the trigger, a toehold mediated strand displacement (TMSD) occurred on the strand of Region I, leading to the release of Region III for further hybridization with the Region II on another HP molecule and in turn inducing a stepwise growth of HP with the aid of polymerase. Unlike the conventional assembly approaches that rely on the sophisticated sequence design and complex operation, the single-HP nanoassembly is easy and fast. Moreover, because many HPs are opened during the assembly process, we exemplified the nanoassembly strategy by re-designing a new labeled hairpin probe to analyze the Kras oncogene with a high sensitivity and specificity. The present study demonstrated a novel promising DNA nanoassembly strategy for biological applications. Copyright © 2018 Elsevier B.V. All rights reserved.

  1. Pyrolysis of aseptic packages (tetrapak) in a laboratory screw type reactor and secondary thermal/catalytic tar decomposition.

    PubMed

    Haydary, J; Susa, D; Dudáš, J

    2013-05-01

    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 H2, CO, CH4, CO2 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Free energy landscapes of a highly structured β-hairpin peptide and its single mutant

    NASA Astrophysics Data System (ADS)

    Kim, Eunae; Yang, Changwon; Jang, Soonmin; Pak, Youngshang

    2008-10-01

    We investigated the free energy landscapes of a highly structured β-hairpin peptide (MBH12) and a less structured peptide with a single mutation of Tyr6 to Asp6 (MBH10). For the free energy mapping, starting from an extended conformation, the replica exchange molecular dynamic simulations for two β-hairpins were performed using a modified version of an all-atom force field employing an implicit solvation (param99MOD5/GBSA). With the present simulation approach, we demonstrated that detailed stability changes associated with the sequence modification from MBH12 to MBH10 are quantitatively well predicted at the all-atom level.

  3. Identification of amino acids that promote specific and rigid TAR RNA-tat protein complex formation.

    PubMed

    Edwards, Thomas E; Robinson, Bruce H; Sigurdsson, Snorri Th

    2005-03-01

    The Tat protein and the transactivation responsive (TAR) RNA form an essential complex in the HIV lifecycle, and mutations in the basic region of the Tat protein alter this RNA-protein molecular recognition. Here, EPR spectroscopy was used to identify amino acids, flanking an essential arginine of the Tat protein, which contribute to specific and rigid TAR-Tat complex formation by monitoring changes in the mobility of nitroxide spin-labeled TAR RNA nucleotides upon binding. Arginine to lysine N-terminal mutations did not affect TAR RNA interfacial dynamics. In contrast, C-terminal point mutations, R56 in particular, affected the mobility of nucleotides U23 and U38, which are involved in a base-triple interaction in the complex. This report highlights the role of dynamics in specific molecular complex formation and demonstrates the ability of EPR spectroscopy to study interfacial dynamics of macromolecular complexes.

  4. Machine-smoking studies of cigarette filter color to estimate tar yield by visual assessment and through the use of a colorimeter.

    PubMed

    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.

  5. The free energy landscape for beta hairpin folding in explicit water.

    PubMed

    Zhou, R; Berne, B J; Germain, R

    2001-12-18

    The folding free energy landscape of the C-terminal beta hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and OPLSAA force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the beta strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The beta hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.

  6. The free energy landscape for β hairpin folding in explicit water

    PubMed Central

    Zhou, Ruhong; Berne, Bruce J.; Germain, Robert

    2001-01-01

    The folding free energy landscape of the C-terminal β hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and oplsaa force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the β strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The β hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature. PMID:11752441

  7. A case-control study of asphalt and tar exposure and lung cancer in minorities.

    PubMed

    McClean, Michael D; Kelsey, Karl T; Sison, Jennette D; Quesenberry, Charles P; Wrensch, Margaret R; Wiencke, John K

    2011-11-01

    Considerable controversy surrounds the carcinogenic potential of asphalt and tar. Since minority individuals may have had relatively high historical exposures, we investigated asphalt and tar exposure and lung cancer risk among African Americans and Latino Americans. We conducted a case-control study of lung cancer among African Americans and Latino Americans in the San Francisco Bay area (422 cases, 894 controls). A questionnaire was used to obtain detailed work histories and exposure information. Self-reported exposure to asphalt and tar as well as other factors (e.g., smoking, automobile exhaust, and asbestos) were evaluated as predictors of lung cancer risk. Potential effect modification by cytochrome P450 (CYP) 1A1 was also explored. Self-reported duration of exposure to asphalt and tar was associated with a statistically significant excess risk of lung cancer in the overall population (OR: 1.11, 95% CI: 1.01-1.22), evaluating risk per year of exposure. Years of exposure to automobile exhaust (OR: 1.02, 95% CI: 1.00-1.05) and asbestos (OR: 1.04, 95% CI: 1.02-1.06) were also associated with statistically significant elevations in risk. In Latino Americans, the lung cancer risks associated with polycyclic aromatic hydrocarbon-related exposures were consistently higher in the CYP1A1 wild-type subjects as compared to the variant genotype subjects, and the interaction was statistically significant for smoking and the CYP1A1 M2 polymorphism (P-value(interaction) = 0.02). These data are consistent with the literature suggesting that exposure to asphalt and tar may increase risk of lung cancer. However, it was not possible to separate the effects and asphalt and tar in this study. Copyright © 2011 Wiley Periodicals, Inc.

  8. A Case-Control Study of Asphalt and Tar Exposure and Lung Cancer in Minorities

    PubMed Central

    McClean, Michael D.; Kelsey, Karl T.; Sison, Jennette D; Quesenberry, Charles P; Wrensch, Margaret R; Wiencke, John K.

    2011-01-01

    Objectives Considerable controversy surrounds the carcinogenic potential of asphalt and tar. Since minority individuals may have had relatively high historical exposures, we investigated asphalt and tar exposure and lung cancer risk among African Americans and Latino Americans. Methods We conducted a case-control study of lung cancer among African Americans and Latino Americans in the San Francisco Bay area (422 cases, 894 controls). A questionnaire was used to obtain detailed work histories and exposure information. Self-reported exposure to asphalt and tar as well as other factors (eg. smoking, automobile exhaust, and asbestos) were evaluated as predictors of lung cancer risk. Potential effect modification by cytochrome P450 (CYP) 1A1 was also explored. Results Self-reported duration of exposure to asphalt and tar was associated with a statistically significant excess risk of lung cancer in the overall population (OR: 1.11, 95%CI: 1.01–1.22), evaluating risk per year of exposure. Years of exposure to automobile exhaust (OR: 1.02, 95%CI: 1.00–1.05) and asbestos (OR: 1.04, 95%CI: 1.02–1.06) were also associated with statistically significant elevations in risk. In Latino Americans, the lung cancer risks associated with polycyclic aromatic hydrocarbon-related exposures were consistently higher in the CYP1A1 wildtype subjects as compared to the variant genotype subjects, and the interaction was statistically significant for smoking and the CYP1A1 M2 polymorphism (p-valueinteraction=0.02). Conclusions These data are consistent with the literature suggesting that exposure to asphalt and tar may increase risk of lung cancer. However, it was not possible to separate the effects and asphalt and tar in this study. PMID:21882217

  9. The linear relationship between cigarette tar and nicotine yields: regulatory implications for smoke constituent ratios.

    PubMed

    St Charles, F K; Cook, C J; Clayton, P M

    2011-02-01

    Cigarette smoke analyte yields are often expressed as ratios relative to tar or nicotine yields, usually to compare different products or to estimate human uptake of smoke in relation to nicotine uptake measurements. The method, however, can lead to distorted interpretations, especially in the case of ratios from ultra-low tar yield cigarettes. In brief, as tar yields decrease below the 5–6 mg per cigarette range, the tar-to-nicotine ratio (TNR) decreases rapidly in a non-linear fashion. If, however, the nicotine yield, rather than the ratio, is plotted versus the tar yield, the non-linearity disappears and a straight line is obtained, with a slight positive intercept for nicotine on the ordinate. Unlike the ratio, the slope appears to depend only on the concentration of the nicotine in the blend and does not appear to vary with smoking parameters such as puff volume, puff interval or length smoked or with cigarette design parameters such as length, circumference or the amount of filtration or filter ventilation. Therefore, such a slope is analogous to the TNR although, unlike that ratio, it is invariant. Even more simply, the concentration of the nicotine in the blend, at least for American blend-style cigarettes, provides a similar index.

  10. Design-Based Peptidomimetic Ligand Discovery to Target HIV TAR RNA Using Comparative Analysis of Different Docking Methods.

    PubMed

    Fu, Junjie; Xia, Amy; Dai, Yao; Qi, Xin

    2016-01-01

    Discovering molecules capable of binding to HIV trans-activation responsive region (TAR) RNA thereby disrupting its interaction with Tat protein is an attractive strategy for developing novel antiviral drugs. Computational docking is considered as a useful tool for predicting binding affinity and conducting virtual screening. Although great progress in predicting protein-ligand interactions has been achieved in the past few decades, modeling RNA-ligand interactions is still largely unexplored due to the highly flexible nature of RNA. In this work, we performed molecular docking study with HIV TAR RNA using previously identified cyclic peptide L22 and its analogues with varying affinities toward HIV-1 TAR RNA. Furthermore, sarcosine scan was conducted to generate derivatives of CGP64222, a peptide-peptoid hybrid with inhibitory activity on Tat/TAR RNA interaction. Each compound was docked using CDOCKER, Surflex-Dock and FlexiDock to compare the effectiveness of each method. It was found that FlexiDock energy values correlated well with the experimental Kd values and could be used to predict the affinity of the ligands toward HIV-1 TAR RNA with a superior accuracy. Our results based on comparative analysis of different docking methods in RNA-ligand modeling will facilitate the structure-based discovery of HIV TAR RNA ligands for antiviral therapy.

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

    PubMed

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

    2003-02-01

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

  12. Hairpin assembly circuit-based fluorescence cooperative amplification strategy for enzyme-free and label-free detection of small molecule.

    PubMed

    Feng, Chunjing; Zhu, Jing; Sun, Jiewei; Jiang, Wei; Wang, Lei

    2015-10-01

    Here, we developed an enzyme-free, label-free, and sensitive fluorescence cooperative amplification strategy based on a hairpin assembly circuit which coupled catalytic hairpin assembly (CHA) with hybridization chain reaction (HCR) for small molecule adenosine. A double-strand DNA probe with aptamer-catalysis strand (Apt-C) and inhibit strand (Inh) was designed for adenosine recognition and signal transduction which was named as Apt-C/Inh. Hairpins H1 and H2 were employed for constructing the CHA, and hairpins H3 and H4 for the HCR. Through the binding of adenosine and the Apt-C, the Inh was released from the Apt-C/Inh. Then the free Apt-C initiated the CHA through successively opening H1 and H2, generating H1/H2 complex and recyclable Apt-C. Next, the released Apt-C entered another CHA cycle, and the H1/H2 complex further initiated the HCR of H3 and H4 which induced the formation of the concatemers of H3/H4 complex. Such a process brought the two ends of hairpins H3 into close proximity, yielding numerous integrated G-quadruplexes which were initially sequestered in the stem and two terminals of H3. Finally, N-methyl mesoporphyrin IX (NMM) was added to generate an enhanced fluorescence signal. In the proposed strategy, driven only by the energy from hybridization, one target could trigger multiple HCR events via CHA-based target-cycle, leading to a remarkable enzyme-free amplification for adenosine. The detection limit could achieve as low as 9.7 × 10(-7) mol L(-1). Furthermore, G-quadruplexes were applied to construct label-free hairpin assembly circuit, which made it more simple and cost-effective. The satisfactory recoveries were obtained when detecting adenosine in spiked human serum and urine samples, demonstrating the feasibility of this detection strategy in biological samples. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2013-05-15

    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 (δ¹³C) 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Ubiquitous tar balls with a California-source signature on the shorelines of Prince William Sound, Alaska

    USGS Publications Warehouse

    Kvenvolden, K.A.; Hostettler, F.D.; Carlson, P.R.; Rapp, J.B.; Threlkeld, C.N.; Warden, A.

    1995-01-01

    Although the shorelines of Prince William Sound still bear traces of the 1989 Exxon Valdez oil spill, most of the flattened tar balls that can be found today on these shorelines are not residues of Exxon Valdez oil. Instead, the carbon-isotopic and hydrocarbon-biomarker signatures of 61 tar ball samples, collected from shorelines throughout the northern and western parts of the sound, are all remarkably similar and have characteristics consistent with those of oil products that originated from the Monterey Formation source rocks of California. The carbon-isotopic compositions of the tar balls are all closely grouped (??13CPDB = -23.7 ?? 0.2???), within the range found in crude oils from those rocks, but are distinct from isotopic compositions of 28 samples of residues from the Exxon Valdez oil spill (??13CPDB = -29.4 ?? 0.1???). Likewise, values for selected biomarker ratios in the tar balls are all similar but distinct from values of residues from the 1989 oil spill. Carbon-isotopic and biomarker signatures generally relate the tar balls to oil products used in Alaska before ???1970 for construction and pavements. How these tar balls with such similar geochemical characteristics became so widely dispersed throughout the northern and western parts of the sound is not known with certainty, but the great 1964 Alaska earthquake was undoubtedly an important trigger, causing spills from ruptured storage facilities of California-sourced asphalt and fuel oil into Prince William Sound.

  15. Microplastic and tar pollution on three Canary Islands beaches: An annual study.

    PubMed

    Herrera, A; Asensio, M; Martínez, I; Santana, A; Packard, T; Gómez, M

    2018-04-01

    Marine debris accumulation was analyzed from three exposed beaches of the Canary Islands (Lambra, Famara and Las Canteras). Large microplastics (1-5mm), mesoplastics (5-25mm) and tar pollution were assessed twice a month for a year. There was great spatial and temporal variability in the Canary Island coastal pollution. Seasonal patterns differed at each location, marine debris concentration depended mainly of local-scale wind and wave conditions. The most polluted beach was Lambra, a remote beach infrequently visited. The types of debris found were mainly preproduction resin pellets, plastic fragments and tar, evidencing that pollution was not of local origin, but it cames from the open sea. The levels of pollution were similar to those of highly industrialized and contaminated regions. This study corroborates that the Canary Islands are an area of accumulation of microplastics and tar rafted from the North Atlantic Ocean by the southward flowing Canary Current. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Numerical simulation of vortex pyrolysis reactors for condensable tar production from biomass

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Miller, R.S.; Bellan, J.

    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 frommore » 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.« less

  17. Understanding the fate and transport of petroleum hydrocarbons from coal tar within gasholders.

    PubMed

    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.

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

    PubMed

    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.

  19. The role of plastic β-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Duan, Yong

    2004-12-01

    In this study, the thermal stability of a designed α/β protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (α helix and β hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix.

  20. The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein.

    PubMed

    Lei, Hongxing; Duan, Yong

    2004-12-15

    In this study, the thermal stability of a designed alpha/beta protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (alpha helix and beta hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix. (c) 2004 American Institute of Physics

  1. Human immunodeficiency virus type 1 LTR TATA and TAR region sequences required for transcriptional regulation.

    PubMed Central

    Garcia, J A; Harrich, D; Soultanakis, E; Wu, F; Mitsuyasu, R; Gaynor, R B

    1989-01-01

    The human immunodeficiency virus (HIV) type 1 LTR is regulated at the transcriptional level by both cellular and viral proteins. Using HeLa cell extracts, multiple regions of the HIV LTR were found to serve as binding sites for cellular proteins. An untranslated region binding protein UBP-1 has been purified and fractions containing this protein bind to both the TAR and TATA regions. To investigate the role of cellular proteins binding to both the TATA and TAR regions and their potential interaction with other HIV DNA binding proteins, oligonucleotide-directed mutagenesis of both these regions was performed followed by DNase I footprinting and transient expression assays. In the TATA region, two direct repeats TC/AAGC/AT/AGCTGC surround the TATA sequence. Mutagenesis of both of these direct repeats or of the TATA sequence interrupted binding over the TATA region on the coding strand, but only a mutation of the TATA sequence affected in vivo assays for tat-activation. In addition to TAR serving as the site of binding of cellular proteins, RNA transcribed from TAR is capable of forming a stable stem-loop structure. To determine the relative importance of DNA binding proteins as compared to secondary structure, oligonucleotide-directed mutations in the TAR region were studied. Local mutations that disrupted either the stem or loop structure were defective in gene expression. However, compensatory mutations which restored base pairing in the stem resulted in complete tat-activation. This indicated a significant role for the stem-loop structure in HIV gene expression. To determine the role of TAR binding proteins, mutations were constructed which extensively changed the primary structure of the TAR region, yet left stem base pairing, stem energy and the loop sequence intact. These mutations resulted in decreased protein binding to TAR DNA and defects in tat-activation, and revealed factor binding specifically to the loop DNA sequence. Further mutagenesis which inverted

  2. Upgrading producer gas quality from rubber wood gasification in a radio frequency tar thermocatalytic treatment reactor.

    PubMed

    Anis, Samsudin; Zainal, Z A

    2013-12-01

    This study focused on improving the producer gas quality using radio frequency (RF) tar thermocatalytic treatment reactor. The producer gas containing tar, particles and water was directly passed at a particular flow rate into the RF reactor at various temperatures for catalytic and thermal treatments. Thermal treatment generates higher heating value of 5.76 MJ Nm(-3) at 1200°C. Catalytic treatments using both dolomite and Y-zeolite provide high tar and particles conversion efficiencies of about 97% on average. The result also showed that light poly-aromatic hydrocarbons especially naphthalene and aromatic compounds particularly benzene and toluene were still found even at higher reaction temperatures. Low energy intensive RF tar thermocatalytic treatment was found to be effective for upgrading the producer gas quality to meet the end user requirements and increasing its energy content. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry

    PubMed Central

    Walker, Peter

    2017-01-01

    Abstract The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. PMID:28108663

  4. Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.

    PubMed

    Shi, Xuesong; Walker, Peter; Harbury, Pehr B; Herschlag, Daniel

    2017-05-05

    The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Hairpin vortices in the outer and near wall regions of the canonical turbulent boundary layer

    NASA Astrophysics Data System (ADS)

    Wallace, James; Wu, Xiaohua; Moin, Parviz

    2016-11-01

    While the dominance of hairpin vortices and their significance for transport processes in the transitional and early turbulent regions of the canonical turbulent boundary layer has been widely accepted, opinion is divided about the developed flow downstream. Here we investigate the representative vortical structures in the outer and near wall regions for the momentum thickness Reynolds number, Reθ , of up to 3000 using the DNS database described in. This boundary layer grows spatially from a laminar state at Reθ = 80 beneath a freestream of continuous and nearly isotropic turbulence decaying from an intensity of 3 to 0.8%. The vortical structures are visualized with the swirling strength, λci. In the outer region hairpin vortices appear and are advected over distances corresponding to about 300 - 400 in Reθ within the fully turbulent region, demonstrating that they are not remnants of transitional structures. The near wall vortical structures are more difficult to visualize and require careful tuning of the swirling strength and making invisible the flow above the near wall region of the flow. The hairpins in this region occur in intermittent clusters that have features remarkably similar to transitional turbulent spots.

  6. SULFUR TOLERANT CATALYSTS FOR BIOMASS TAR REMOVAL - PHASE I

    EPA Science Inventory

    In this Small Business Innovation Research (SBIR) project, NexTech Materials proposes a catalytic reforming approach to remove waste tar from gasified biomass on nickel-based catalysts. Biomass gasification is a potential renewable route to producing electricity, liquid fue...

  7. Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice

    PubMed Central

    Ou-Yang, Fangqian; Luo, Qing-Jun; Zhang, Yue; Richardson, Casey R.; Jiang, Yingwen; Rock, Christopher D.

    2013-01-01

    microRNAs (miRNAs) are a class of small RNAs (sRNAs) of ~21 nucleotides (nt) in length processed from foldback hairpins by DICER-LIKE1 (DCL1) or DCL4. They regulate the expression of target mRNAs by base pairing through RNA-Induced Silencing Complex (RISC). In the RISC, ARGONAUTE1 (AGO1) is the key protein that cleaves miRNA targets at position ten of a miRNA:target duplex. The authenticity of many annotated rice miRNA hairpins is under debate because of their homology to repeat sequences. Some of them, like miR1884b, have been removed from the current release of miRBase based on incomplete information. In this study, we investigated the association of transposable element (TE)-derived miRNAs with typical miRNA pathways (DCL1/4- and AGO1-dependent) using publicly available deep sequencing datasets. Seven miRNA hairpins with 13 unique sRNAs were specifically enriched in AGO1 immunoprecipitation samples and relatively reduced in DCL1/4 knockdown genotypes. Interestingly, these species are ~21-nt long, instead of 24-nt as annotated in miRBase and the literature. Their expression profiles meet current criteria for functional annotation of miRNAs. In addition, diagnostic cleavage tags were found in degradome datasets for predicted target mRNAs. Most of these miRNA hairpins share significant homology with miniature inverted-repeat transposable elements (MITEs), one type of abundant DNA transposons in rice. Finally, the root-specific production of a 24 nt miRNA-like sRNA was confirmed by RNA blot for a novel EST that maps to the 3'-UTR of a candidate pseudogene showing extensive sequence homology to miR1884b hairpin. Our data are consistent with the hypothesis that TEs can serve as a driving force for the evolution of some MIRNAs, where co-opting of DICER-LIKE1/4 processing and integration into AGO1 could exapt transcribed TE-associated hairpins into typical miRNA pathways. PMID:23420033

  8. Influence of the presence of PAHs and coal tar on naphthalene sorption in soils

    NASA Astrophysics Data System (ADS)

    Bayard, Rémy; Barna, Ligia; Mahjoub, Borhane; Gourdon, Rémy

    2000-11-01

    The mobility of the most water-soluble polynuclear aromatic hydrocarbons (PAHs) such as naphthalene in contaminated soils from manufactured gas plant (MGP) sites or other similar sites is influenced not only by the naturally occurring soil organic matter (SOM) but also, and in many cases mostly, by the nature and concentration of coal tar xenobiotic organic matter (XOM) and other PAH molecules present in the medium under various physical states. The objective of the present study was to quantify the effects of these factors using batch experiments, in order to simulate naphthalene transport in soil-tar-water systems using column experiments. Naphthalene sorption was studied in the presence of (i) solid coal tar particles, (ii) phenanthrene supplied as pure crystals, in the aqueous solution or already sorbed onto the soil, (iii) fluoranthene as pure crystals, and (iv) an aqueous solution of organic molecules extracted from a liquid tar. All experiments were conducted under abiotic conditions using short naphthalene/sorbent contact times of 24-60 h. Although these tests do not reflect true equilibrium conditions which usually take more time to establish, they were used to segregate relatively rapid sorption phenomena ("pseudo equilibrium") from slow sorption and other aging phenomena. For longer contact times, published data have shown that experimental biases due to progressive changes in the characteristics of the soil and the solution may drastically modify the affinity of the solutes for the soil. Slow diffusion in the microporosity and in dense organic phases may also become significant over the long term, along with some irreversible aging phenomena which have not been addressed in this work. Results showed that PAHs had no effect on naphthalene sorption when present in the aqueous solution or as pure crystals, due to their low solubility in water. Adsorbed phenanthrene was found to reduce naphthalene adsorption only when present at relatively high

  9. Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

    PubMed

    Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

    2009-12-31

    To systematically construct a low-dimensional free-energy landscape of RNA systems from a classical molecular dynamics simulation, various versions of the principal component analysis (PCA) are compared: the cPCA using the Cartesian coordinates of all atoms, the dPCA using the sine/cosine-transformed six backbone dihedral angles as well as the glycosidic torsional angle chi and the pseudorotational angle P, the aPCA which ignores the circularity of the 6 + 2 dihedral angles of the RNA, and the dPCA(etatheta), which approximates the 6 backbone dihedral angles by 2 pseudotorsional angles eta and theta. As representative examples, a 10-nucleotide UUCG hairpin and the 36-nucleotide segment SL1 of the Psi site of HIV-1 are studied by classical molecular dynamics simulation, using the Amber all-atom force field and explicit solvent. It is shown that the conformational heterogeneity of the RNA hairpins can only be resolved by an angular PCA such as the dPCA but not by the cPCA using Cartesian coordinates. Apart from possible artifacts due to the coupling of overall and internal motion, this is because the details of hydrogen bonding and stacking interactions but also of global structural rearrangements of the RNA are better discriminated by dihedral angles. In line with recent experiments, it is found that the free energy landscape of RNA hairpins is quite rugged and contains various metastable conformational states which may serve as an intermediate for unfolding.

  10. Quantitative evaluation of first, second, and third generation hairpin systems reveals the limit of mammalian vector-based RNAi

    PubMed Central

    Watanabe, Colin; Cuellar, Trinna L.; Haley, Benjamin

    2016-01-01

    ABSTRACT Incorporating miRNA-like features into vector-based hairpin scaffolds has been shown to augment small RNA processing and RNAi efficiency. Therefore, defining an optimal, native hairpin context may obviate a need for hairpin-specific targeting design schemes, which confound the movement of functional siRNAs into shRNA/artificial miRNA backbones, or large-scale screens to identify efficacious sequences. Thus, we used quantitative cell-based assays to compare separate third generation artificial miRNA systems, miR-E (based on miR-30a) and miR-3G (based on miR-16-2 and first described in this study) to widely-adopted, first and second generation formats in both Pol-II and Pol-III expression vector contexts. Despite their unique structures and strandedness, and in contrast to first and second-generation RNAi triggers, the third generation formats operated with remarkable similarity to one another, and strong silencing was observed with a significant fraction of the evaluated target sequences within either promoter context. By pairing an established siRNA design algorithm with the third generation vectors we could readily identify targeting sequences that matched or exceeded the potency of those discovered through large-scale sensor-based assays. We find that third generation hairpin systems enable the maximal level of siRNA function, likely through enhanced processing and accumulation of precisely-defined guide RNAs. Therefore, we predict future gains in RNAi potency will come from improved hairpin expression and identification of optimal siRNA-intrinsic silencing properties rather than further modification of these scaffolds. Consequently, third generation systems should be the primary format for vector-based RNAi studies; miR-3G is advantageous due to its small expression cassette and simplified, cost-efficient cloning scheme. PMID:26786363

  11. A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins.

    PubMed

    Cochran, A G; Tong, R T; Starovasnik, M A; Park, E J; McDowell, R S; Theaker, J E; Skelton, N J

    2001-01-31

    Phage display of peptide libraries has become a powerful tool for the evolution of novel ligands that bind virtually any protein target. However, the rules governing conformational preferences in natural peptides are poorly understood, and consequently, structure-activity relationships in these molecules can be difficult to define. In an effort to simplify this process, we have investigated the structural stability of 10-residue, disulfide-constrained beta-hairpins and assessed their suitability as scaffolds for beta-turn display. Using disulfide formation as a probe, relative free energies of folding were measured for 19 peptides that differ at a one strand position. A tryptophan substitution promotes folding to a remarkable degree. NMR analysis confirms that the measured energies correlate well with the degree of beta-hairpin structure in the disulfide-cyclized peptides. Reexamination of a subset of the strand substitutions in peptides with different turn sequences reveals linear free energy relationships, indicating that turns and strand-strand interactions make independent, additive contributions to hairpin stability. Significantly, the tryptophan strand substitution is highly stabilizing with all turns tested, and peptides that display model turns or the less stable C'-C' ' turn of CD4 on this tryptophan "stem" are highly structured beta-hairpins in water. Thus, we have developed a small, structured beta-turn scaffold, containing only natural L-amino acids, that may be used to display peptide libraries of limited conformational diversity on phage.

  12. 33 CFR 165.927 - Safety Zone; St. Louis River, Duluth/Interlake Tar Remediation Site, Duluth, MN.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Safety Zone; St. Louis River, Duluth/Interlake Tar Remediation Site, Duluth, MN. 165.927 Section 165.927 Navigation and Navigable... Coast Guard District § 165.927 Safety Zone; St. Louis River, Duluth/Interlake Tar Remediation Site...

  13. PAH volatilization following application of coal-tar-based pavement sealant

    USGS Publications Warehouse

    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.

  14. Supercritical-Fluid Extraction of Oil From Tar Sands

    NASA Technical Reports Server (NTRS)

    Compton, L. E.

    1982-01-01

    New supercritical solvent mixtures have been laboratory-tested for extraction of oil from tar sands. Mixture is circulated through sand at high pressure and at a temperature above critical point, dissolving organic matter into the compressed gas. Extract is recovered from sand residues. Low-temperature super-critical solvents reduce energy consumption and waste-disposal problems.

  15. The search for a source rock for the giant Tar Sand triangle accumulation, southeastern Utah

    USGS Publications Warehouse

    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

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

    PubMed

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

    2018-06-14

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

  17. Hairpin DNA probe with 5'-TCC/CCC-3' overhangs for the creation of silver nanoclusters and miRNA assay.

    PubMed

    Xia, Xiaodong; Hao, Yuanqiang; Hu, Shengqiang; Wang, Jianxiu

    2014-01-15

    A facile strategy for the assay of target miRNA using fluorescent silver nanoclusters (AgNCs) has been described. Due to the preferable interaction between cytosine residues and Ag(+), a short cytosine-rich oligonucleotide (ODN) with only six bases 5'-TCCCCC-3' served as an efficient scaffold for the creation of the AgNCs. The AgNCs displayed a bright red emission when excited at 545nm. Such ODN base-stabilized AgNCs have been exploited for miRNA sensing. Overhangs of TCC at the 5' end (5'-TCC) and CCC at the 3' end (CCC-3') (denoted as 5'-TCC/CCC-3') appended to the hairpin ODN probe which also contains recognition sequences for target miRNA were included. Interestingly, the AgNCs/hairpin ODN probe showed similar spectral properties as that templated by 5'-TCCCCC-3'. The formation of the hairpin ODN probe/miRNA duplex separated the 5'-TCC/CCC-3' overhangs, thus disturbing the optical property or structure of the AgNCs. As a result, fluorescence quenching of the AgNCs/hairpin ODN probe was obtained, which allows for facile determination of target miRNA. The proposed method is simple and cost-effective, holding great promise for clinical applications. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction.

    PubMed

    Ronsard, Larance; Ganguli, Nilanjana; Singh, Vivek K; Mohankumar, Kumaravel; Rai, Tripti; Sridharan, Subhashree; Pajaniradje, Sankar; Kumar, Binod; Rai, Devesh; Chaudhuri, Suhnrita; Coumar, Mohane S; Ramachandran, Vishnampettai G; Banerjea, Akhil C

    2017-01-01

    HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans -activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans -activation response (TAR) RNA. In this study, HIV-1 infected patients ( n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities. Molecular dynamics simulation data verified that the variants with this mutation had a higher binding affinity for TAR than both the wild-type Tat and other variants that lacked Ser46Phe and Ser61Arg. Other mutations in Tat conferred varying affinities for TAR interaction leading to differential transactivation abilities. This is the first report from North India with a clinical validation of CD4 counts to demonstrate the influence of Tat genetic variations affecting the stability of Tat and its interaction with TAR. This study highlights the co-evolution pattern of Tat and predominant nucleotides for Tat activity, facilitating the identification of genetic determinants for the attenuation of viral gene expression.

  19. Kinetics of hairpin ribozyme cleavage in yeast.

    PubMed Central

    Donahue, C P; Fedor, M J

    1997-01-01

    Hairpin ribozymes catalyze a self-cleavage reaction that provides a simple model for quantitative analyses of intracellular mechanisms of RNA catalysis. Decay rates of chimeric mRNAs containing self-cleaving ribozymes give a direct measure of intracellular cleavage kinetics in yeast. Intracellular ribozyme-mediated cleavage occurs at similar rates and shows similar inhibition by ribozyme mutations as ribozyme-mediated reactions in vitro, but only when ribozymes are located in a favorable mRNA sequence context. The impact of cleavage on mRNA abundance is shown to depend directly on intrinsic mRNA stability. Surprisingly, cleavage products are no more labile than uncleaved mRNAs despite the loss of terminal cap structures or poly (A). PMID:9292496

  20. Method of producing drive fluid in situ in tar sands formations

    DOEpatents

    Mudunuri, Ramesh Raju; Jaiswal, Namit; Vinegar, Harold J.; Karanikas, John Michael

    2010-03-23

    Methods of treating a tar sands formation are described herein. Methods for treating a tar sands may include providing heat to at least part of a hydrocarbon layer in the formation from one or more heaters located in the formation. The heat may be allowed to transfer from the heaters to at least a portion of the formation such that a drive fluid is produced in situ in the formation. The drive fluid may move at least some mobilized, visbroken, and/or pyrolyzed hydrocarbons from a first portion of the formation to a second portion of the formation. At least some of the mobilized, visbroken, and/or pyrolyzed hydrocarbons may be produced from the formation.

  1. Marketing 'less harmful, low-tar' cigarettes is a key strategy of the industry to counter tobacco control in China.

    PubMed

    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.

  2. Relationship between cigarette format and mouth-level exposure to tar and nicotine in smokers of Russian king-size cigarettes.

    PubMed

    Ashley, Madeleine; Dixon, Mike; Prasad, Krishna

    2014-10-01

    Differences in length and circumference of cigarettes may influence smoker behaviour and exposure to smoke constituents. Superslim king-size (KSSS) cigarettes (17mm circumference versus 25mm circumference of conventional king-size [KS] cigarettes), have gained popularity in several countries, including Russia. Some smoke constituents are lower in machine-smoked KSSS versus KS cigarettes, but few data exist on actual exposure in smokers. We investigated mouth-level exposure (MLE) to tar and nicotine in Russian smokers of KSSS versus KS cigarettes and measured smoke constituents under machine-smoking conditions. MLE to tar was similar for smokers of 1mg ISO tar yield products, but lower for smokers of 4mg and 7mg KSSS versus KS cigarettes. MLE to nicotine was lower in smokers of 4mg KSSS versus KS cigarettes, but not for other tar bands. No gender differences were observed for nicotine or tar MLE. Under International Organization for Standardization, Health Canada Intense and Massachusetts regimes, KSSS cigarettes tended to yield less carbon monoxide, acetaldehyde, nitric oxide, acrylonitrile, benzene, 1,3-butadiene and tobacco-specific nitrosamines, but more formaldehyde, than KS cigarettes. In summary, differences in MLE were observed between cigarette formats, but not systematically across pack tar bands. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  3. The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure

    PubMed Central

    Tobé, Sylvia; Heams, Thomas; Vergne, Jacques; Hervé, Guy; Maurel, Marie-Christine

    2005-01-01

    The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 ± 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 ± 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms. PMID:15870387

  4. [Energetics of complex formation of the DNA hairpin structure d(GCGAAGC) with aromatic ligands].

    PubMed

    Kostiukov, V V

    2011-01-01

    The energy contributions of various physical interactions to the total Gibbs energy of complex formation of the biologically important DNA hairpin d(GCGAAGC) with aromatic antitumor antibiotics daunomycin and novantron and the mutagens ethidium and proflavine have been calculated. It has been shown that the relatively small value of the total energy of binding of the ligands to the hairpin is the sum of components great in absolute value and different in sign. The contributions of van der Waals interactions and both intra- and intermolecular hydrogen bonds and bonds with aqueous environment have been studied. According to the calculations, the hydrophobic and van der Waals components are energetically favorable in complex formation of the ligands with the DNA pairpin d(GCGAAGC), whereas the electrostatic (with consideration of hydrogen bonds) and entropic components are unfavorable.

  5. An Arrayed Genome-Scale Lentiviral-Enabled Short Hairpin RNA Screen Identifies Lethal and Rescuer Gene Candidates

    PubMed Central

    Bhinder, Bhavneet; Antczak, Christophe; Ramirez, Christina N.; Shum, David; Liu-Sullivan, Nancy; Radu, Constantin; Frattini, Mark G.

    2013-01-01

    Abstract RNA interference technology is becoming an integral tool for target discovery and validation.; With perhaps the exception of only few studies published using arrayed short hairpin RNA (shRNA) libraries, most of the reports have been either against pooled siRNA or shRNA, or arrayed siRNA libraries. For this purpose, we have developed a workflow and performed an arrayed genome-scale shRNA lethality screen against the TRC1 library in HeLa cells. The resulting targets would be a valuable resource of candidates toward a better understanding of cellular homeostasis. Using a high-stringency hit nomination method encompassing criteria of at least three active hairpins per gene and filtered for potential off-target effects (OTEs), referred to as the Bhinder–Djaballah analysis method, we identified 1,252 lethal and 6 rescuer gene candidates, knockdown of which resulted in severe cell death or enhanced growth, respectively. Cross referencing individual hairpins with the TRC1 validated clone database, 239 of the 1,252 candidates were deemed independently validated with at least three validated clones. Through our systematic OTE analysis, we have identified 31 microRNAs (miRNAs) in lethal and 2 in rescuer genes; all having a seed heptamer mimic in the corresponding shRNA hairpins and likely cause of the OTE observed in our screen, perhaps unraveling a previously unknown plausible essentiality of these miRNAs in cellular viability. Taken together, we report on a methodology for performing large-scale arrayed shRNA screens, a comprehensive analysis method to nominate high-confidence hits, and a performance assessment of the TRC1 library highlighting the intracellular inefficiencies of shRNA processing in general. PMID:23198867

  6. Can a continuum solvent model reproduce the free energy landscape of a -hairpin folding in water?

    NASA Astrophysics Data System (ADS)

    Zhou, Ruhong; Berne, Bruce J.

    2002-10-01

    The folding free energy landscape of the C-terminal -hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the -hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native -strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this -hairpin. Furthermore, the -hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and 80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields.

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

    PubMed

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

    2018-03-01

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

  8. Identification and characterization of a HeLa nuclear protein that specifically binds to the trans-activation-response (TAR) element of human immunodeficiency virus.

    PubMed Central

    Marciniak, R A; Garcia-Blanco, M A; Sharp, P A

    1990-01-01

    Human immunodeficiency virus type 1 RNAs contain a sequence, trans-activation-response (TAR) element, which is required for tat protein-mediated trans-activation of viral gene expression. We have identified a nuclear protein from extracts of HeLa cells that binds to the TAR element RNA in a sequence-specific manner. The binding of this 68-kDa polypeptide was detected by UV cross-linking proteins to TAR element RNA transcribed in vitro. Competition experiments were performed by using a partially purified preparation of the protein to quantify the relative binding affinities of TAR element RNA mutants. The binding affinity of the TAR mutants paralleled the reported ability of those mutants to support tat trans-activation in vivo. We propose that this cellular protein moderates TAR activity in vivo. Images PMID:2333305

  9. Pyrolysis characteristics and kinetics of acid tar waste from crude benzol refining: A thermogravimetry-mass spectrometry analysis.

    PubMed

    Chihobo, Chido H; Chowdhury, Arindrajit; Kuipa, Pardon K; Simbi, David J

    2016-12-01

    Pyrolysis is an attractive thermochemical conversion technology that may be utilised as a safe disposal option for acid tar waste. The kinetics of acid tar pyrolysis were investigated using thermogravimetry coupled with mass spectrometry under a nitrogen atmosphere at different heating rates of 10, 15 and 20 K min -1 The thermogravimetric analysis shows three major reaction peaks centred around 178 °C, 258 °C, and 336 °C corresponding to the successive degradation of water soluble lower molecular mass sulphonic acids, sulphonated high molecular mass hydrocarbons, and high molecular mass hydrocarbons. The kinetic parameters were evaluated using the iso-conversional Kissinger-Akahira-Sunose method. A variation in the activation energy with conversion revealed that the pyrolysis of the acid tar waste progresses through complex multi-step kinetics. Mass spectrometry results revealed a predominance of gases such as hydrogen, methane and carbon monoxide, implying that the pyrolysis of acid tar waste is potentially an energy source. Thus the pyrolysis of acid tar waste may present a viable option for its environmental treatment. There are however, some limitations imposed by the co-evolution of corrosive gaseous components for which appropriate considerations must be provided in both pyrolysis reactor design and selection of construction materials. © The Author(s) 2016.

  10. Annealing study of poly(etheretherketone)

    NASA Technical Reports Server (NTRS)

    Cebe, Peggy

    1988-01-01

    Annealing of PEEK has been studied for two materials cold-crystallized from the rubbery amorphous state. The first material is a low molecular weight PEEK; the second is commercially available neat resin. Differential scanning calorimetry was used to monitor the melting behavior of annealed samples. The effect of thermal history on melting behavior is very complex and depends upon annealing temperature, residence time at the annealing temperature, and subsequent scanning rate. Thermal stability of both materials is improved by annealing, and for an annealing temperature near the melting point, the polymer can be stabilized against reorganization during the scan. Variations of density, degree of crystallinity, and X-ray long period were studied as a function of annealing temperature for the commercial material.

  11. Social-cognitive remediation in schizophrenia: generalization of effects of the Training of Affect Recognition (TAR).

    PubMed

    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.

  12. Double-hairpin molecular-beacon-based amplification detection for gene diagnosis linked to cancer.

    PubMed

    Xu, Huo; Zhang, Rongbo; Li, Feng; Zhou, Yingying; Peng, Ting; Wang, Xuedong; Shen, Zhifa

    2016-09-01

    A powerful double-hairpin molecular beacon (DHMB) was developed for cancer-related KRAS gene detection based on the one-to-two stoichiometry. During target DNA detection, DHMB can execute signal transduction even if no any exogenous element is involved. Unlike the conventional molecular beacon based on the one-to-one interaction, one target DNA not only hybridizes with one DHMB and opens its hairpin but also promotes the interaction between two DHMBs, causing the separation of two fluorophores from quenchers. This leads to an enhanced fluorescence signal. As a result, the target KRAS gene is able to be detected within a wide dynamic range from 0.05 to 200 nM with the detection limit of 50 pM, indicating a dramatic improvement compared with traditional molecular beacons. Moreover, the point mutations existing in target DNAs can be easily screened. The potential application for target species in real samples was indicated by the analysis of PCR amplicons of DNAs from the DNA extracted from SW620 cell. Besides becoming a promising candidate probe for molecular biology research and clinical diagnosis of genetic diseases, the DHMB is expected to provide a significant insight into the design of DNA probe-based homogenous sensing systems. Graphical Abstract A powerful double-hairpin molecular beacon (DHMB) was developed for cancer-related gene KRAS detection based on the one-to-two stoichiometry. Without the help of any exogenous probe, the point mutation is easily screened, and the target DNA can be quantified down to 50 pM, indicating a dramatic improvement compared with traditional molecular beacons.

  13. Recent progress of quantum annealing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Suzuki, Sei

    2015-03-10

    We review the recent progress of quantum annealing. Quantum annealing was proposed as a method to solve generic optimization problems. Recently a Canadian company has drawn a great deal of attention, as it has commercialized a quantum computer based on quantum annealing. Although the performance of quantum annealing is not sufficiently understood, it is likely that quantum annealing will be a practical method both on a conventional computer and on a quantum computer.

  14. In situ heat treatment of a tar sands formation after drive process treatment

    DOEpatents

    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.

  15. Micelle-Triggered β-Hairpin to α-Helix Transition in a 14-Residue Peptide from a Choline-Binding Repeat of the Pneumococcal Autolysin LytA

    PubMed Central

    Zamora-Carreras, Héctor; Maestro, Beatriz; Strandberg, Erik; Ulrich, Anne S; Sanz, Jesús M; Jiménez, M Ángeles

    2015-01-01

    Choline-binding modules (CBMs) have a ββ-solenoid structure composed of choline-binding repeats (CBR), which consist of a β-hairpin followed by a short linker. To find minimal peptides that are able to maintain the CBR native structure and to evaluate their remaining choline-binding ability, we have analysed the third β-hairpin of the CBM from the pneumococcal LytA autolysin. Circular dichroism and NMR data reveal that this peptide forms a highly stable native-like β-hairpin both in aqueous solution and in the presence of trifluoroethanol, but, strikingly, the peptide structure is a stable amphipathic α-helix in both zwitterionic (dodecylphosphocholine) and anionic (sodium dodecylsulfate) detergent micelles, as well as in small unilamellar vesicles. This β-hairpin to α-helix conversion is reversible. Given that the β-hairpin and α-helix differ greatly in the distribution of hydrophobic and hydrophilic side chains, we propose that the amphipathicity is a requirement for a peptide structure to interact and to be stable in micelles or lipid vesicles. To our knowledge, this “chameleonic” behaviour is the only described case of a micelle-induced structural transition between two ordered peptide structures. PMID:25917218

  16. Cigarettes, lung cancer, and coronary heart disease: the effects of inhalation and tar yield.

    PubMed

    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.

  17. Properties of gasification-derived char and its utilization for catalytic tar reforming

    NASA Astrophysics Data System (ADS)

    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

  18. Characterization of alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) in tar-balls collected from the East Coast of Peninsular Malaysia.

    PubMed

    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.

  19. Exploring the chemical composition of pelagic tar collected in the North Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Green, H. S.; Reddy, C. M.; Valentine, D. L.; Aeppli, C.; Swarthout, B.; Sharpless, C.; Joyce, P.; Meyer, A. W.; Fuller, S. A.; Gosselin, K.

    2016-12-01

    Pelagic tarballs have been linked to multiple sources and their abundances follow notable historical and geographic trends. An overwhelming number of studies point to operational discharges (cargo washing) as the main source of pelagic tar. In a recent review article, Warnock et al. (2015) summarized that the abundance of tar balls has decreased over the last 30 years. The decreasing trend of tarballs has been attributed to the MARPOL 73/78 Annex I legislation, which was created from conventions held in 1973 and again in 1978 to respond to several tanker accidents and other pollution-related inputs. Two of the studies supporting the "MARPOL 73/78 effect" were based on the historical record of tarballs collected in the North Atlantic Ocean by the Sea Education Association (SEA; Woods Hole, MA). To supplement the SEA record, we performed a series of geochemical analyses on 100 of the SEA samples collected from 1988 to 2014. Bulk and gas chromatographic (GC) analyses revealed that the samples were highly variable. For example, the amount of material that could be dissolved in organic solvent but not measured by gas chromatography (referred to as the % GC amenable, a proxy on the distribution of compound classes that compose the tar) ranged from 10 to 80%, although skewed to values less than 40%. Another parameter, based on the GC data, was the perecentage of the resolved relative to the unresolved signal spanned from 0.1 to 1.8. Nine of the sampes would not dissolve in organic solvents and appear to be soot or coal. This study has an operation limitation as we choose to only examine samples > 1 cm (relative to samples smaller than 1mm). Our approach was based on the assumption that these samples were the most unlikely to be weathered and hence retain the genetic features of the initially released tar. While this study does not have the capacity to test confidently the MARPOL 73/78 effect, it does show that pelagic tars are highly variable, which in turn, have

  20. Membrane curvature and the Tol-Pal complex determine polar localization of the chemoreceptor Tar in E. coli.

    PubMed

    Saaki, Terrens N V; Strahl, Henrik; Hamoen, Leendert W

    2018-02-20

    Chemoreceptors are localized at the cell poles of Escherichia coli and other rod-shaped bacteria. Over the years different mechanisms have been put forward to explain this polar localization; from stochastic clustering, membrane curvature driven localization, interactions with the Tol-Pal complex, to nucleoid exclusion. To evaluate these mechanisms, we monitored the cellular localization of the aspartate chemoreceptor Tar in different deletion mutants. We did not find any indication for either stochastic cluster formation or nucleoid exclusion. However, the presence of a functional Tol-Pal complex appeared to be essential to retain Tar at cell poles. Interestingly, Tar still accumulated at midcell in tol and in pal deletion mutants. In these mutants, the protein appears to gather at the base of division septa, a region characterised by strong membrane curvature. Chemoreceptors, like Tar, form trimer-of-dimers that bend the cell membrane due to a rigid tripod structure. The curvature approaches the curvature of the cell membrane generated during cell division, and localization of chemoreceptor tripods at curved membrane areas is therefore energetically favourable as it lowers membrane tension. Indeed, when we introduced mutations in Tar that abolish the rigid tripod structure, the protein was no longer able to accumulate at midcell or cell poles. These findings favour a model where chemoreceptor localization in E. coli is driven by strong membrane curvature and association with the Tol-Pal complex. Importance Bacteria have exquisite mechanisms to sense and to adapt to the environment they live in. One such mechanism involves the chemotaxis signal transduction pathway, in which chemoreceptors specifically bind certain attracting or repelling molecules and transduce the signals to the cell. In different rod-shaped bacteria, these chemoreceptors localize specifically to cell poles. Here, we examined the polar localization of the aspartate chemoreceptor Tar in E. coli

  1. Class I cultural resource overview for oil shale and tar sands areas in Colorado, Utah and Wyoming.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    O'Rourke, D.; Kullen, D.; Gierek, L.

    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 sandsmore » 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 oil shale

  2. Tar-free fuel gas production from high temperature pyrolysis of sewage sludge

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Leguan; Xiao, Bo; Hu, Zhiquan

    2014-01-15

    Highlights: • High temperature pyrolysis of sewage sludge was efficient for producing tar-free fuel gas. • Complete tar removal and volatile matter release were at elevated temperature of 1300 °C. • Sewage sludge was converted to residual solid with high ash content. • 72.60% of energy conversion efficiency for gas production in high temperature pyrolysis. • Investment and costing for tar cleaning were reduced. - Abstract: Pyrolysis of sewage sludge was studied in a free-fall reactor at 1000–1400 °C. The results showed that the volatile matter in the sludge could be completely released to gaseous product at 1300 °C. Themore » high temperature was in favor of H{sub 2} and CO in the produced gas. However, the low heating value (LHV) of the gas decreased from 15.68 MJ/N m{sup 3} to 9.10 MJ/N m{sup 3} with temperature increasing from 1000 °C to 1400 °C. The obtained residual solid was characterized by high ash content. The energy balance indicated that the most heating value in the sludge was in the gaseous product.« less

  3. Forced-Unfolding and Force-Quench Refolding of RNA Hairpins

    PubMed Central

    Hyeon, Changbong; Thirumalai, D.

    2006-01-01

    Nanomanipulation of individual RNA molecules, using laser optical tweezers, has made it possible to infer the major features of their energy landscape. Time-dependent mechanical unfolding trajectories, measured at a constant stretching force (fS) of simple RNA structures (hairpins and three-helix junctions) sandwiched between RNA/DNA hybrid handles show that they unfold in a reversible all-or-none manner. To provide a molecular interpretation of the experiments we use a general coarse-grained off-lattice Gō-like model, in which each nucleotide is represented using three interaction sites. Using the coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of fS and the loading rate (rf). The simulations and theoretical analysis have been done both with and without the handles that are explicitly modeled by semiflexible polymer chains. The mechanisms and timescales for denaturation by temperature jump and mechanical unfolding are vastly different. The directed perturbation of the native state by fS results in a sequential unfolding of the hairpin starting from their ends, whereas thermal denaturation occurs stochastically. From the dependence of the unfolding rates on rf and fS we show that the position of the unfolding transition state is not a constant but moves dramatically as either rf or fS is changed. The transition-state movements are interpreted by adopting the Hammond postulate for forced-unfolding. Forced-unfolding simulations of RNA, with handles attached to the two ends, show that the value of the unfolding force increases (especially at high pulling speeds) as the length of the handles increases. The pathways for refolding of RNA from stretched initial conformation, upon quenching fS to the quench force fQ, are highly heterogeneous. The refolding times, upon force-quench, are at least an order-of-magnitude greater than those obtained by temperature-quench. The long fQ-dependent refolding times starting from fully stretched

  4. Brown carbon in tar balls from smoldering biomass combustion

    Treesearch

    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...

  5. Scalable effective-temperature reduction for quantum annealers via nested quantum annealing correction

    NASA Astrophysics Data System (ADS)

    Vinci, Walter; Lidar, Daniel A.

    2018-02-01

    Nested quantum annealing correction (NQAC) is an error-correcting scheme for quantum annealing that allows for the encoding of a logical qubit into an arbitrarily large number of physical qubits. The encoding replaces each logical qubit by a complete graph of degree C . The nesting level C represents the distance of the error-correcting code and controls the amount of protection against thermal and control errors. Theoretical mean-field analyses and empirical data obtained with a D-Wave Two quantum annealer (supporting up to 512 qubits) showed that NQAC has the potential to achieve a scalable effective-temperature reduction, Teff˜C-η , with 0 <η ≤2 . We confirm that this scaling is preserved when NQAC is tested on a D-Wave 2000Q device (supporting up to 2048 qubits). In addition, we show that NQAC can also be used in sampling problems to lower the effective-temperature of a quantum annealer. Such effective-temperature reduction is relevant for machine-learning applications. Since we demonstrate that NQAC achieves error correction via a reduction of the effective-temperature of the quantum annealing device, our results address the problem of the "temperature scaling law for quantum annealers," which requires the temperature of quantum annealers to be reduced as problems of larger sizes are attempted to be solved.

  6. Radiocarbon dating of extinct fauna in the Americas recovered from tar pits

    NASA Astrophysics Data System (ADS)

    Jull, A. J. T.; Iturralde-Vinent, M.; O'Malley, J. M.; MacPhee, R. D. E.; McDonald, H. G.; Martin, P. S.; Moody, J.; Rincón, A.

    2004-08-01

    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.

  7. Controlling and assessing pressure conditions during treatment of tar sands formations

    DOEpatents

    Zhang, Etuan; Beer, Gary Lee

    2015-11-10

    A method for treating a tar sands formation includes providing heat to at least part of a hydrocarbon layer in the tar sands formation from a plurality of heaters located in the formation. Heat is allowed to transfer from the heaters to at least a portion of the formation. A pressure in the portion of the formation is controlled such that the pressure remains below a fracture pressure of the formation overburden while allowing the portion of the formation to heat to a selected average temperature of at least about 280.degree. C. and at most about 300.degree. C. The pressure in the portion of the formation is reduced to a selected pressure after the portion of the formation reaches the selected average temperature.

  8. Characterizing Peptide β-HAIRPIN Loops via Cold Ion Spectroscopy of Model Compounds

    NASA Astrophysics Data System (ADS)

    Lawler, John T.; DeBlase, Andrew F.; Harrilal, Christopher P.; Fischer, Joshua L.; McLuckey, Scott A.; Zwier, Timothy S.

    2017-06-01

    The introduction of non-native D-amino acids into peptides is known to reduce conformational entropy in peptides. D-proline has been shown to promote the formation of β-hairpin loops when paired with Gly, providing a framework for building these loops with different lengths of anti-parallel beta-sheet. This study seeks to characterize and compare the conformational preferences of a model protonated pentapeptide containing DPG, [YAP^{D}GA+H]^{+}, with its L-Pro counterpart via conformation specific cold ion spectroscopy as a foundation for future consideration of larger beta-hairpin models. The UV spectrum of YAP^{D}GA of the Tyr chromophore is beautifully sharp, but contains a complicated set of transitions that could arise from the presence of more than one conformer. To assess this possibility, we recorded non-conformation specific IR "gain" spectra in the hydride stretch region. The IR spectrum so obtained displays a set of five strong IR transitions that bear a close resemblance to those found in one of the conformers of its close analog, [YAP^{D}AA+H]^{+}, signaling that a single conformer dominates the population. Two transitions at 3392 and 3464 cm-1 are slightly shifted versions of the C10 and C14 hydrogen bonds found in one of the conformers of [YAP^{D}AA+H]^{+}, and are characteristic of formation of a β-hairpin loop. Notably, in [YAP^{D}GA+H]^{+}, there is at most a minor second conformer with a free carboxylic acid OH, appearing weakly in the IR "gain" spectrum. As expected, the UV spectrum of YAP^{L}GA is more congested, which suggests the presence of multiple conformers. Further investigation into this peptide will reveal the conformational preferences of the L-pro containing molecule. Preliminary data affirms that D-proline containing peptides show reduced conformational states when compared to their natural counterparts.

  9. Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA

    DOE PAGES

    Meagher, Robert J.; Priye, Aashish; Light, Yooli K.; ...

    2018-03-27

    Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer-dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer-dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMPmore » or RT-LAMP assays. In this study, we examine the impact of primer-dimers and hairpins on previously-published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter to predict the probability of non-specific amplification associated with LAMP primers.« less

  10. Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Meagher, Robert J.; Priye, Aashish; Light, Yooli K.

    Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer-dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer-dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMPmore » or RT-LAMP assays. In this study, we examine the impact of primer-dimers and hairpins on previously-published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter to predict the probability of non-specific amplification associated with LAMP primers.« less

  11. Circular permutation of a WW domain: Folding still occurs after excising the turn of the folding-nucleating hairpin

    PubMed Central

    Kier, Brandon L.; Anderson, Jordan M.; Andersen, Niels H.

    2014-01-01

    A hyperstable Pin1 WW domain has been circularly permuted via excision of the fold-nucleating turn; it still folds to form the native three-strand sheet and hydrophobic core features. Multiprobe folding dynamics studies of the normal and circularly permuted sequences, as well as their constituent hairpin fragments and comparable-length β-strand-loop-β-strand models, indicate 2-state folding for all topologies. N-terminal hairpin formation is the fold nucleating event for the wild-type sequence; the slower folding circular permutant has a more distributed folding transition state. PMID:24350581

  12. Alteration of hairpin ribozyme specificity utilizing PCR.

    PubMed

    DeGrandis, P; Hampel, A; Galasinski, S; Borneman, J; Siwkowski, A; Altschuler, M

    1994-12-01

    We have developed a method by which a researcher can quickly alter the specificity of a trans hairpin ribozyme. Utilizing this PCR method, two oligonucleotides, and any target vector, new ribozyme template sequences can be generated without the synthesis of longer oligonucleotides. We have produced templates with altered specificity for both standard and modified (larger) ribozymes. After transcription, these ribozymes show specific cleavage activity with the new substrate beta-glucuronidase (GUS), and no activity against the original substrate (HIV-1, 5' leader sequence). Utilizing this technique, it is also possible to produce an inactive ribozyme that can be used as an antisense control. Applications of this procedure would provide a rapid and economical system for the assessment of trans ribozyme activity.

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

    NASA Astrophysics Data System (ADS)

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

    1993-04-01

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

  14. Characteristics of PAH tar oil contaminated soils-Black particles, resins and implications for treatment strategies.

    PubMed

    Trellu, Clément; Miltner, Anja; Gallo, Rosita; Huguenot, David; van Hullebusch, Eric D; Esposito, Giovanni; Oturan, Mehmet A; Kästner, Matthias

    2017-04-05

    Tar oil contamination is a major environmental concern due to health impacts of polycyclic aromatic hydrocarbons (PAH) and the difficulty of reaching acceptable remediation end-points. Six tar oil-contaminated soils with different industrial histories were compared to investigate contamination characteristics by black particles. Here we provide a simple method tested on 6 soils to visualize and identify large amounts of black particles (BP) as either solid aggregates of resinified and weathered tar oil or various wood/coke/coal-like materials derived from the contamination history. These materials contain 2-10 times higher PAH concentrations than the average soil and were dominantly found in the sand fraction containing 42-86% of the total PAH. The PAH contamination in the different granulometric fractions was directly proportional to the respective total organic carbon content, since the PAH were associated to the carbonaceous particulate materials. Significantly lower (bio)availability of PAH associated to these carbonaceous phases is widely recognized, thus limiting the efficiency of remediation techniques. We provide a conceptual model of the limited mass transfer of PAH from resinated tar oil phases to the water phase and emphasize the options to physically separate BP based on their lower bulk density and slower settling velocity. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Aspects of tar sands development in Nigeria

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Adewusi, V.A.

    1992-07-01

    Development of Nigerian massive reserves of crude bitumen and associated heavy oil is imminent in view of the impacts that the huge importation of these materials and their products have on the nation's economy, coupled with the depleting reserves of Nigeria and highlights the appropriate production technology options and their environmental implications. The utilization potentials of these resources are also enumerated, as well as the government's role in achieving accelerated, long-term tar sands development in the country.

  16. Shock, Post-Shock Annealing, and Post-Annealing Shock in Ureilites

    NASA Technical Reports Server (NTRS)

    Rubin, Alan E.

    2006-01-01

    The thermal and shock histories of ureilites can be divided into four periods: 1) formation, 2) initial shock, 3) post-shock annealing, and 4) post-annealing shock. Period 1 occurred approx.4.55 Ga ago when ureilites formed by melting chondritic material. Impact events during period 2 caused silicate darkening, undulose to mosaic extinction in olivines, and the formation of diamond, lonsdaleite, and chaoite from indigenous carbonaceous material. Alkali-rich fine-grained silicates may have been introduced by impact injection into ureilites during this period. About 57% of the ureilites were unchanged after period 2. During period 3 events, impact-induced annealing caused previously mosaicized olivine grains to become aggregates of small unstrained crystals. Some ureilites experienced reduction as FeO at the edges of olivine grains reacted with C from the matrix. Annealing may also be responsible for coarsening of graphite in a few ureilites, forming euhedral-appearing, idioblastic crystals. Orthopyroxene in Meteorite Hills (MET) 78008 may have formed from pigeonite by annealing during this period. The Rb-Sr internal isochron age of approx.4.0 Ga for MET 78008 probably dates the annealing event. At this late date, impacts are the only viable heat source. About 36% of ureilites experienced period 3 events, but remained unchanged afterwards. During period 4, approx.7% of the ureilites were shocked again, as is evident in the polymict breccia, Elephant Moraine (EET) 83309. This rock contains annealed mosaicized olivine aggregates composed of small individual olivine crystals that exhibit undulose extinction. Ureilites may have formed by impact-melting chondritic material on a primitive body with heterogeneous O isotopes. Plagioclase was preferentially lost from the system due to its low impedance to shock compression. Brief melting and rapid burial minimized the escape of planetary-type noble gases from the ureilitic melts. Incomplete separation of metal from silicates

  17. Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide

    NASA Astrophysics Data System (ADS)

    Diana, Donatella; De Rosa, Lucia; Palmieri, Maddalena; Russomanno, Anna; Russo, Luigi; La Rosa, Carmelo; Milardi, Danilo; Colombo, Giorgio; D'Andrea, Luca D.; Fattorusso, Roberto

    2015-11-01

    HPLW, a designed VEGF (Vascular Endothelium Growth Factor) receptor-binding peptide, assumes a well folded β-hairpin conformation in water and is able to induce angiogenesis in vivo. In this study, we investigated at atomic resolution the thermal folding/unfolding pathway of HPLW by means of an original multi-technique approach combining DSC, NMR, MD and mutagenesis analyses. In particular, careful NMR investigation of the single proton melting temperatures together with DSC analysis accurately delineate the peptide folding mechanism, which is corroborated by computational folding/unfolding simulations. The HPLW folding process consists of two main events, which are successive but do not superimpose. The first folding step initiates at 320 K upon the hydrophobic collapse of the Trp5 and Trp13 side-chains which stabilizes the concurrent β-turn formation, whose COi-HNi + 3 hydrogen bond (Asp10 → Arg7) appears particularly stable. At 316 K, once the β-turn is completely formed, the two β-strands pair, very likely starting by Trp5 and Trp13, which thus play a key role also in the final step of the β-hairpin folding. Overall, here we describe a multi-state hierarchical folding pathway of a highly structured β-hairpin, which can be classified as a broken-zipper mechanism.

  18. Remediation of Coal Tar by STAR: Self-Sustaining Propagation Across Clean Gaps

    NASA Astrophysics Data System (ADS)

    Gerhard, J.; Brown, J.; Torero, J. L.; Grant, G.

    2016-12-01

    Self-sustaining Treatment for Active Remediation (STAR) is an emerging remediation technique which utilizes a subsurface smouldering reaction to destroy non-aqueous phase liquids (NAPL) in situ. The reaction is self-sustaining in that, once ignited, the destructive smouldering front will propagate outwards using only the energy embedded in the contaminant. However, it is known that coal tar can occur as both a continuous pool as well as in distinct seams separated by clean intervals. This study evaluated the hypothesis that the smouldering reaction can cross or `jump' clean gaps by transferring enough heat through the gap to re-ignite the reaction in the contaminated region beyond. Column and 2D box experiments were performed at two scales to determine the maximum clean gap which could be jumped vertically and horizontally. Once the maximum gap had been determined, sensitivity to various in situ and engineering control parameters were explored including: coal tar layer thickness, soil permeability, moisture content, NAPL saturation, and air injection flowrate. High resolution thermocouples informed the progress of the reaction, continuous gas emissions analysis revealed when the reaction was active and dormant, and detailed excavation mapped the extent of remediation and whether gaps were successfully jumped. The work demonstrated that substantial clean gaps, approaching the limit of the laboratory scale, can be jumped by the smouldering reaction using convective heat transfer. Also observed in some cases was the mobilization of pre-heated coal tar into the clean gaps and the reaction's ability to propagate through and destroy coal tar both adjacent to and within the gaps. This work is providing new insights into the robust nature of the technology for in situ applications, and indicating how extreme the heterogeneity has to be before the reaction is interrupted and a new ignition location would be required.

  19. Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact.

    PubMed

    Ray-Soni, Ananya; Mooney, Rachel A; Landick, Robert

    2017-10-31

    In bacteria, intrinsic termination signals cause disassembly of the highly stable elongating transcription complex (EC) over windows of two to three nucleotides after kilobases of RNA synthesis. Intrinsic termination is caused by the formation of a nascent RNA hairpin adjacent to a weak RNA-DNA hybrid within RNA polymerase (RNAP). Although the contributions of RNA and DNA sequences to termination are largely understood, the roles of conformational changes in RNAP are less well described. The polymorphous trigger loop (TL), which folds into the trigger helices to promote nucleotide addition, also is proposed to drive termination by folding into the trigger helices and contacting the terminator hairpin after invasion of the hairpin in the RNAP main cleft [Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E (2007) Mol Cell 28:991-1001]. To investigate the contribution of the TL to intrinsic termination, we developed a kinetic assay that distinguishes effects of TL alterations on the rate at which ECs terminate from effects of the TL on the nucleotide addition rate that indirectly affect termination efficiency by altering the time window in which termination can occur. We confirmed that the TL stimulates termination rate, but found that stabilizing either the folded or unfolded TL conformation decreased termination rate. We propose that conformational fluctuations of the TL (TL dynamics), not TL-hairpin contact, aid termination by increasing EC conformational diversity and thus access to favorable termination pathways. We also report that the TL and the TL sequence insertion (SI3) increase overall termination efficiency by stimulating pausing, which increases the flux of ECs into the termination pathway. Published under the PNAS license.

  20. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?

    PubMed Central

    Zhou, Ruhong; Berne, Bruce J.

    2002-01-01

    The folding free energy landscape of the C-terminal β-hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the β-hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native β-strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this β-hairpin. Furthermore, the β-hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and ≈80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields. PMID:12242327

  1. Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

    PubMed

    Zhou, Ruhong; Berne, Bruce J

    2002-10-01

    The folding free energy landscape of the C-terminal beta-hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the beta-hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native beta-strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this beta-hairpin. Furthermore, the beta-hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and approximately equal 80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields.

  2. Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact

    PubMed Central

    Ray-Soni, Ananya; Mooney, Rachel A.; Landick, Robert

    2017-01-01

    In bacteria, intrinsic termination signals cause disassembly of the highly stable elongating transcription complex (EC) over windows of two to three nucleotides after kilobases of RNA synthesis. Intrinsic termination is caused by the formation of a nascent RNA hairpin adjacent to a weak RNA−DNA hybrid within RNA polymerase (RNAP). Although the contributions of RNA and DNA sequences to termination are largely understood, the roles of conformational changes in RNAP are less well described. The polymorphous trigger loop (TL), which folds into the trigger helices to promote nucleotide addition, also is proposed to drive termination by folding into the trigger helices and contacting the terminator hairpin after invasion of the hairpin in the RNAP main cleft [Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E (2007) Mol Cell 28:991–1001]. To investigate the contribution of the TL to intrinsic termination, we developed a kinetic assay that distinguishes effects of TL alterations on the rate at which ECs terminate from effects of the TL on the nucleotide addition rate that indirectly affect termination efficiency by altering the time window in which termination can occur. We confirmed that the TL stimulates termination rate, but found that stabilizing either the folded or unfolded TL conformation decreased termination rate. We propose that conformational fluctuations of the TL (TL dynamics), not TL-hairpin contact, aid termination by increasing EC conformational diversity and thus access to favorable termination pathways. We also report that the TL and the TL sequence insertion (SI3) increase overall termination efficiency by stimulating pausing, which increases the flux of ECs into the termination pathway. PMID:29078293

  3. Coal-Tar-Based Pavement Sealcoat and PAHs: Implications for the Environment, Human Health, and Stormwater Management

    PubMed Central

    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. PMID:22296333

  4. Coal-tar-based pavement sealcoat and PAHs: implications for the environment, human health, and stormwater management

    USGS Publications Warehouse

    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.

  5. Coal-tar-based pavement sealcoat and PAHs: implications for the environment, human health, and stormwater management.

    PubMed

    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.

  6. Tar Creek study, Sargent oil field, Santa Clara County, California

    USGS Publications Warehouse

    Wagner, David L.; Fedasko, Bill; Carnahan, J.R.; Brunetti, Ross; Magoon, Leslie B.; Lillis, Paul G.; Lorenson, T.D.; Stanley, Richard G.

    2002-01-01

    Field work in the Tar Creek area of Sargent oil field was performed June 26 to 28, 2000. The Santa Clara County study area is located in Sections, 30, 31, and 32, Township 11 South, Range 4 East, M.D.B&M; and in Sections 25 and 36, Township 11 South, Range 3 East, M.D.B.&M., north and south of Tar Creek, west of Highway 101. The work was a cooperative effort of the California Department of Conservation's Division of Oil, Gas, and Geothermal Resources (DOGGR), California Geological Survey (CGS), and the United States Geological Survey (USGS). The purpose of the project was to map the stratigraphy and geologic structure (David Wagner, CGS); sample oil for age dating (Les Magoon, USGS); and search for undocumented wells plus conduct a GPS survey of the area (Bill Fedasko, J.P. Carnahan, and Ross Brunetti, DOGGR)

  7. Coal-tar pavement sealants might substantially increase children's PAH exposures

    USGS Publications Warehouse

    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.

  8. Citizen science identifies the effects of nitrogen dioxide and other environmental drivers on tar spot of sycamore.

    PubMed

    Gosling, Laura; Ashmore, Mike; Sparks, Tim; Bell, Nigel

    2016-07-01

    Elevated sulphur dioxide (SO2) concentrations were the major cause of the absence of symptoms of tar spot (Rhytisma acerinum) of sycamore (Acer pseudoplatanus), in urban areas in the 1970s. The subsequent large decline in SO2 concentrations has not always been accompanied by increased tar spot symptoms, for reasons that have remained unresolved. We used a large citizen science survey, providing over 1000 records across England, to test two competing hypotheses proposed in earlier studies. We were able to demonstrate the validity of both hypotheses; tar spot symptoms were reduced where there were fewer fallen leaves as a source of inoculum, and elevated nitrogen dioxide concentrations reduced tar spot symptoms above a threshold concentration of about 20 μg m(-3). Symptom severity was also lower at sites with higher temperature and lower rainfall. Our findings demonstrate the power of citizen science to resolve competing hypotheses about the impacts of air pollution and other environmental drivers. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Effect of cavitation on the properties of coal-tar pitch as studied by gas-liquid chromatography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    M.I. Baikenov; T.B. Omarbekov; S.K. Amerkhanova

    2008-02-15

    The applicability of the cavitation-wave effect to coal-tar pitch processing is considered. The results of the GLC analysis of the test material before and after rotor-pulsation cavitation treatment are given. The organic matter of coal-tar pitch was found to degrade upon cavitation; as a result of this, the yields of light and medium fractions considerably increased. 5 refs., 2 figs., 4 tabs.

  10. Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits▿

    PubMed Central

    Kim, Jong-Shik; Crowley, David E.

    2007-01-01

    Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation. PMID:17416692

  11. Athermal Annealing of Silicon

    NASA Astrophysics Data System (ADS)

    Fischer, R. P.; Grun, J.; Ting, A.; Felix, C.; Peckerar, M.; Fatemi, M.; Manka, C. K.

    1999-11-01

    Current semiconductor annealing methods are based on thermal processes which are accompanied by diffusion that degrades the definition of device features or causes other problems. This will be a serious obstacle for the production of next-generation ultra-high density, low power semiconductor devices. Experiments underway at NRL utilize a new annealing method which is much faster than thermal annealing and does not depend upon thermal energy (J. Grun, et al)., Phys. Rev. Letters 78, 1584 (1997).. A 10 J, 30 nsec, 1.053 nm wavelength laser pulse is focussed to approximately 1 mm diameter on a silicon sample. Acoustic and shock waves propagate from the impact region, which deposit mechanical energy into the material and anneal the silicon. Experimental results will be presented on annealing neutron-transmutation-doped (NTD) and ion implanted silicon samples with impurity concentrations from 1 × 10^15-3 × 10^20/cm^3.

  12. Effects of varying marijuana potency on deposition of tar and delta9-THC in the lung during smoking.

    PubMed

    Matthias, P; Tashkin, D P; Marques-Magallanes, J A; Wilkins, J N; Simmons, M S

    1997-12-01

    To determine whether smoking more, compared to less, potent marijuana (MJ) cigarettes to a desired level of intoxication ("high") reduces pulmonary exposure to noxious smoke components, in 10 habitual smokers of MJ, we measured respiratory delivery and deposition of tar and delta9-tetrahydrocannabinol (THC), carboxyhemoglobin (COHb) boost, smoking topography, including cumulative puff volume (CPV) and breathholding time, change in heart rate (deltaHR) and "high" during ad lib smoking of 0, 1.77, and 3.95% MJ cigarettes on 3 separate days. At each session, subjects had access to only a single MJ cigarette. On average, smoking topography and COHb boost did not differ across the different strengths of MJ, while THC delivery, as well as HR, were significantly greater (p < 0.01) and tar deposition significantly less (p < 0.03) for 3.95% than 1.77% MJ. Although individual adaptations in smoking topography for 3.95% compared to 1.77% MJ were highly variable, three subjects with the lowest 3.95% MJ:1.77% MJ ratios for CPV also displayed the lowest 3.95% MJ:1.77% MJ ratios for tar deposition. In vitro studies using a standardized smoking technique revealed a mean 25% lower tar yield from 3.95% than 1.77% MJ (p < 0.05), but no difference between 1.77% and 0% marijuana. Under the conditions of this study, we conclude that tar delivery is reduced relative to THC content in a minority of subjects, and this reduction appears to be due to a reduced intake of smoke (decreased CPV) and/or a reduced tar yield from the stronger MJ preparation.

  13. Label-free technology for the amplified detection of microRNA based on the allosteric hairpin DNA switch and hybridization chain reaction.

    PubMed

    Cai, Sheng; Cao, Zhijuan; Lau, Choiwan; Lu, Jianzhong

    2014-11-21

    By using the allosteric hairpin DNA switch, a novel assay for the detection of microRNA (miRNA) let-7a via a hybridization chain reaction (HCR) was introduced. Briefly, the hairpin DNA switch probe is a single-stranded DNA consisting of a streptavidin (SA) aptamer sequence, a target binding sequence and a certain sequence that acts as a trigger of the HCR. In the presence of target let-7a, the hairpin DNA switch would open and expose the stem region sequences, where a part of this sequence acts as initiator sequence strands for the HCR and triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers, another part is the SA aptamer sequence which activates its binding affinity to SA on SA-coated magnetic particles. The hybridization event could be sensitively detected via an instantaneous derivatization reaction between a special chemiluminescence (CL) reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotides within the target, the hairpin DNA switch probe, and HCR helices to form an unstable CL intermediate for the generation of light. Our results show that the coupling of the hairpin DNA switch probe and the HCR for the amplified detection of let-7a achieves a better performance (e.g. wide linear response range: 0.1-1000 fmol, low detection limit: 0.1 fmol, and high specificity). Furthermore, this approach could be easily applied to the detection of let-7a in human lung cells, and extended to detect other types of miRNA and proteins such as PDGF based on aptamers. We believe such advancements will represent a significant step towards improved diagnostics and more personalized medical treatment.

  14. The influence of sequence context and length on the kinetics of DNA duplex formation from complementary hairpins possessing (CNG) repeats.

    PubMed

    Paiva, Anthony M; Sheardy, Richard D

    2005-04-20

    The formation of unusual structures during DNA replication has been invoked for gene expansion in genomes possessing triplet repeat sequences, CNG, where N = A, C, G, or T. In particular, it has been suggested that the daughter strand of the leading strand partially dissociates from the parent strand and forms a hairpin. The equilibrium between the fully duplexed parent:daugter species and the parent:hairpin species is dependent upon their relative stabilities and the rates of reannealing of the daughter strand back to the parent. These stabilities and rates are ultimately influenced by the sequence context of the DNA and its length. Previous work has demonstrated that longer strands are more stable than shorter strands and that the identity of N also influences the thermal stability [Paiva, A. M.; Sheardy, R. D. Biochemistry 2004, 43, 14218-14227]. Here, we show that the rate of duplex formation from complementary hairpins is also sequence context and length dependent. In particular, longer duplexes have higher activation energies than shorter duplexes of the same sequence context. Further, [(CCG):(GGC)] duplexes have lower activation energies than corresponding [(CAG):(GTC)] duplexes of the same length. Hence, hairpins formed from long CNG sequences are more thermodynamically stable and have slower kinetics for reannealing to their complement than shorter analogues. Gene expansion can now be explained in terms of thermodynamics and kinetics.

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

    PubMed

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

    2013-04-15

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

  16. PAHs underfoot: Contaminated dust from coal-tar sealcoated pavement is widespread in the United States

    USGS Publications Warehouse

    Van Metre, P.C.; Mahler, B.J.; Wilson, J.T.

    2009-01-01

    We reported in 2005 that runoff from parking lots treated with coal-tar-based sealcoat was a major source of polycyclic aromatic hydrocarbons (PAHs) to streams in Austin, Texas. Here we present new data from nine U. S. cities that show nationwide patterns in concentrations of PAHs associated with sealcoat Dust was swept from parking lots in six cities in the central and eastern U. S., where coal-tar-based sealcoat dominates use, and three cities in the western U. S., where asphalt-based sealcoat dominates use. For six central and eastern cities, median ?? PAH concentrations in dust from sealcoated and unsealcoated pavement are 2200 and 27 mg/kg, respectively. For three western cities, median ?? PAH concentrations in dust from sealcoated and unsealcoated pavement are similar and very low (2. 1 and 0. 8 mg/kg, respectively). Lakes in the central and eastern cities where pavement was sampled have bottom sediments with higher PAH concentrations than do those in the western cities relative to degree of urbanization. Bottom-sediment PAH assemblages are similar to those of sealcoated pavement dust regionally, implicating coal-tar-based sealcoat as a PAH source to the central and eastern lakes. Concentrations of benzo[a]pyrene in dust from coal-tar sealcoated pavement and adjacent soils greatly exceed generic soil screening levels, suggesting that research on human-health risk is warranted.

  17. Uptake of pyrene in a breast-fed child of a mother treated with coal tar.

    PubMed

    Scheepers, Paul T J; van Houtum, Jeanette L M; Anzion, Rob B M; Harder, Rianne; Bos, Rob P; van der Valk, Pieter G M

    2009-01-01

    A woman was treated for atopic dermatitis with coal tar containing ointments. Coal tar containing ointments contain genotoxic polycyclic aromatic hydrocarbons. Over a period of 50 days the accumulated dose of different coal tar containing ointments treatments corresponded to 993 mg of pyrene and 464 mg of benz[a]pyrene. During this treatment she gave breast milk to her 3-month-old daughter. Analysis of urine samples from the breast-fed child showed elevated levels of urinary excretion of a metabolite of pyrene (1-hydroxypyrene, 1-OHP). These levels were in the same range as urinary excretion levels of this metabolite observed in the mother's urine. As no pyrene was observed in breast milk at a limit of determination of 0.0035 micromol/L, transfer of pyrene from mother to child via breast milk is not likely. Also, a low level of 1-hydroxypyrene observed in the mother's milk did not account for the observed urinary excretion levels in the child. It must therefore be assumed that pyrene was transferred from mother to child via another route, presumably direct skin-to-skin or skin-to-mouth contact. Dermatologists should inform their patients who receive treatment with coal tar containing ointments of the risk of transfer of polycyclic aromatic hydrocarbons by skin-to-skin or skin-to-mouth contact.

  18. Tar removal during the fluidized bed gasification of plastic waste.

    PubMed

    Arena, Umberto; Zaccariello, Lucio; Mastellone, Maria Laura

    2009-02-01

    A recycled polyethylene was fed in a pilot plant bubbling fluidized bed gasifier, having an internal diameter of 0.381 m and a maximum feeding capacity of 90 kg/h. The experimental runs were carried out under various operating conditions: the bed temperature was kept at about 850 degrees C, the equivalence ratio varied between 0.2 and 0.35, the amount of bed material was between 131 and 215 kg, the fluidizing velocity was between 0.5 and 0.7 m/s, quartz sand and olivine were used as bed material, and air and steam were used as fluidizing reactants. The results confirm that the tar removal treatments applied inside the gasifier (primary methods) can eliminate or strongly reduce the need for a further downstream cleanup of the syngas. In particular, the utilization of a natural olivine as an in situ tar reduction agent remarkably improves the quality of the product gas, in terms of both high hydrogen volumetric fraction and larger syngas yield.

  19. PeaTAR1B: Characterization of a Second Type 1 Tyramine Receptor of the American Cockroach, Periplaneta americana

    PubMed Central

    Balfanz, Sabine

    2017-01-01

    The catecholamines norepinephrine and epinephrine regulate important physiological functions in vertebrates. In insects; these neuroactive substances are functionally replaced by the phenolamines octopamine and tyramine. Phenolamines activate specific guanine nucleotide-binding (G) protein-coupled receptors (GPCRs). Type 1 tyramine receptors are better activated by tyramine than by octopamine. In contrast; type 2 tyramine receptors are almost exclusively activated by tyramine. Functionally; activation of type 1 tyramine receptors leads to a decrease in the intracellular concentration of cAMP ([cAMP]i) whereas type 2 tyramine receptors can mediate Ca2+ signals or both Ca2+ signals and effects on [cAMP]i. Here; we report that the American cockroach (Periplaneta americana) expresses a second type 1 tyramine receptor (PeaTAR1B) in addition to PeaTAR1A (previously called PeaTYR1). When heterologously expressed in flpTM cells; activation of PeaTAR1B by tyramine leads to a concentration-dependent decrease in [cAMP]i. Its activity can be blocked by a series of established antagonists. The functional characterization of two type 1 tyramine receptors from P. americana; PeaTAR1A and PeaTAR1B; which respond to tyramine by changing cAMP levels; is a major step towards understanding the actions of tyramine in cockroach physiology and behavior; particularly in comparison to the effects of octopamine. PMID:29084141

  20. PeaTAR1B: Characterization of a Second Type 1 Tyramine Receptor of the American Cockroach, Periplaneta americana.

    PubMed

    Blenau, Wolfgang; Balfanz, Sabine; Baumann, Arnd

    2017-10-30

    The catecholamines norepinephrine and epinephrine regulate important physiological functions in vertebrates. In insects; these neuroactive substances are functionally replaced by the phenolamines octopamine and tyramine. Phenolamines activate specific guanine nucleotide-binding (G) protein-coupled receptors (GPCRs). Type 1 tyramine receptors are better activated by tyramine than by octopamine. In contrast; type 2 tyramine receptors are almost exclusively activated by tyramine. Functionally; activation of type 1 tyramine receptors leads to a decrease in the intracellular concentration of cAMP ([cAMP] i ) whereas type 2 tyramine receptors can mediate Ca 2+ signals or both Ca 2+ signals and effects on [cAMP] i . Here; we report that the American cockroach ( Periplaneta americana ) expresses a second type 1 tyramine receptor (PeaTAR1B) in addition to PeaTAR1A (previously called PeaTYR1). When heterologously expressed in flpTM cells; activation of PeaTAR1B by tyramine leads to a concentration-dependent decrease in [cAMP] i . Its activity can be blocked by a series of established antagonists. The functional characterization of two type 1 tyramine receptors from P. americana ; PeaTAR1A and PeaTAR1B; which respond to tyramine by changing cAMP levels; is a major step towards understanding the actions of tyramine in cockroach physiology and behavior; particularly in comparison to the effects of octopamine.

  1. Aviation Turbine Fuels from Tar Sands Bitumen and Heavy Oils. Part 2. Laboratory Sample Production.

    DTIC Science & Technology

    1987-07-01

    tar sand bitumen from West Central Kentucky; and Sunnyside tar sand bitumen from the Uinta Basin , Utah. Each of the feedstocks had unique...fuel and about 50 volume percent heavy gas oil (600-1000°F). The Westken bitumen was overall the heaviest of the four feedstocks evaluated. K factors...was 40 weight percent and about 20 weight percent in the total crude. 3. San Ardo Heavy oil The San Ardo field is located in the Coastal basin of the

  2. Genetically Encoded Catalytic Hairpin Assembly for Sensitive RNA Imaging in Live Cells.

    PubMed

    Mudiyanselage, Aruni P K K Karunanayake; Yu, Qikun; Leon-Duque, Mark A; Zhao, Bin; Wu, Rigumula; You, Mingxu

    2018-06-26

    DNA and RNA nanotechnology has been used for the development of dynamic molecular devices. In particular, programmable enzyme-free nucleic acid circuits, such as catalytic hairpin assembly, have been demonstrated as useful tools for bioanalysis and to scale up system complexity to an extent beyond current cellular genetic circuits. However, the intracellular functions of most synthetic nucleic acid circuits have been hindered by challenges in the biological delivery and degradation. On the other hand, genetically encoded and transcribed RNA circuits emerge as alternative powerful tools for long-term embedded cellular analysis and regulation. Herein, we reported a genetically encoded RNA-based catalytic hairpin assembly circuit for sensitive RNA imaging inside living cells. The split version of Broccoli, a fluorogenic RNA aptamer, was used as the reporter. One target RNA can catalytically trigger the fluorescence from tens-to-hundreds of Broccoli. As a result, target RNAs can be sensitively detected. We have further engineered our circuit to allow easy programming to image various target RNA sequences. This design principle opens the arena for developing a large variety of genetically encoded RNA circuits for cellular applications.

  3. Heating tar sands formations to visbreaking temperatures

    DOEpatents

    Karanikas, John Michael [Houston, TX; Colmenares, Tulio Rafael [Houston, TX; Zhang, Etuan [Houston, TX; Marino, Marian [Houston, TX; Roes, Augustinus Wilhelmus Maria [Houston, TX; Ryan, Robert Charles [Houston, TX; Beer, Gary Lee [Houston, TX; Dombrowski, Robert James [Houston, TX; Jaiswal, Namit [Houston, TX

    2009-12-22

    Methods for treating a tar sands formation are described herein. Methods may include heating at least a section of a hydrocarbon layer in the formation from a plurality of heaters located in the formation. The heat may be controlled so that at least a majority of the section reaches an average temperature of between 200.degree. C. and 240.degree. C., which results in visbreaking of at least some hydrocarbons in the section. At least some visbroken hydrocarbon fluids may be produced from the formation.

  4. Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids

    PubMed Central

    2015-01-01

    Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a detection limit of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon also benefits from the hairpin-free amplification strategy and zero-background, excellent thermostability from 20 °C to 50 °C, as well as good resistance to complex environments. In particular, based on the huge difference between the breathing rate of a single base pair and two adjacent base pairs, Ebeacon also shows high selectivity toward base mutations, such as substitution, insertion, and deletion and, therefore, is an efficient nucleic acid detection method, comparable to most reported enzyme-free strategies. PMID:26505212

  5. Structure-activity relationships of β-hairpin mimics as modulators of amyloid β-peptide aggregation.

    PubMed

    Tonali, Nicolo; Kaffy, Julia; Soulier, Jean-Louis; Gelmi, Maria Luisa; Erba, Emanuela; Taverna, Myriam; van Heijenoort, Carine; Ha-Duong, Tap; Ongeri, Sandrine

    2018-05-18

    Aggregation of amyloid proteins is currently involved in more than 20 serious human diseases that are actually untreated, such as Alzheimer's disease (AD). Despite many efforts made to target the amyloid cascade in AD, finding an aggregation inhibiting compound and especially modulating early oligomerization remains a relevant and challenging strategy. We report herein the first examples of small and non-peptide mimics of acyclic beta-hairpins, showing an ability to delay the fibrillization of amyloid-β (Aβ 1-42 ) peptide and deeply modify its early oligomerization process. Modifications providing better druggability properties such as increased hydrophilicity and reduced peptidic character were performed. We also demonstrate that an appropriate balance between flexibility and stability of the β-hairpin must be reached to adapt to the different shape of the various aggregated forms of the amyloid peptide. This strategy can be investigated to target other challenging amyloid proteins. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  6. Evidence that a sequence similar to TAR is important for induction of the JC virus late promoter by human immunodeficiency virus type 1 Tat.

    PubMed Central

    Chowdhury, M; Taylor, J P; Chang, C F; Rappaport, J; Khalili, K

    1992-01-01

    A specific RNA sequence located in the leader of all human immunodeficiency virus type 1 (HIV-1) mRNAs termed the transactivation response element, or TAR, is a primary target for induction of HIV-1 long terminal repeat activity by the HIV-1-derived trans-regulatory protein, Tat. Human neurotropic virus, JC virus (JCV), a causative agent of the degenerative demyelinating disease progressive multifocal leukoencephalopathy, contains sequences in the 5' end of the late RNA species with an extensive homology to HIV-1 TAR. In this study, we examined the possible role of the JCV-derived TAR-homologous sequence in Tat-mediated activation of the JCV late promoter (Tada et al., Proc. Natl. Acad. Sci. USA 87:3479-3483, 1990). Results from site-directed mutagenesis revealed that critical G residues required for the function of HIV-1 TAR that are conserved in the JCV TAR homolog play an important role in Tat activation of the JCV promoter. In addition, in vivo competition studies suggest that shared regulatory components mediate Tat activation of the JCV late and HIV-1 long terminal repeat promoters. Furthermore, we showed that the JCV-derived TAR sequence behaves in the same way as HIV-1 TAR in response to two distinct Tat mutants, one of which that has no ability to bind to HIV-1 TAR and another that lacks transcriptional activity on a responsive promoter. These results suggest that the TAR homolog of the JCV late promoter is responsive to HIV-1 Tat induction and thus may participate in the overall activation of the JCV late promoter mediated by this transactivation. Images PMID:1331525

  7. Integrating DNA structure switch with branched hairpins for the detection of uracil-DNA glycosylase activity and inhibitor screening.

    PubMed

    Zhu, Jing; Hao, Qijie; Liu, Yi; Guo, Zhaohui; Rustam, Buayxigul; Jiang, Wei

    2018-03-01

    The detection of uracil-DNA glycosylase (UDG) activity is pivotal for its biochemical studies and the development of drugs for UDG-related diseases. Here, we explored an integrated DNA structure switch for high sensitive detection of UDG activity. The DNA structure switch containing two branched hairpins was employed to recognize UDG enzyme and generate fluorescent signal. Under the action of UDG, one branched hairpin was impelled folding into a close conformation after the excision of the single uracil. This reconfigured hairpin could immediately initiate the polymerization/nicking amplification reaction of another branched hairpin accompanying with the release of numerous G-quadruplexes (G4s). In the absence of UDG, the DNA structure switch kept its original configuration, and thus the subsequent polymerization/nicking reaction was inhibited, resulting in the release of few G4 strands. In this work, Thioflavin T was used as signal reporter to target G4s. By integrating the DNA structure switch, the quick response and high sensitivity for UDG determination was achieved and a low detection limit of 0.0001U/mL was obtained, which was superior to the most fluorescent methods for UDG assay. The repeatability of the as-proposed strategy was demonstrated under the concentration of 0.02U/mL and 0.002U/mL, the relative standard deviation obtained from 5 successive samples were 1.7% and 2.8%, respectively. The integrated DNA structure switch strategy proposed here has the potential application for the study of mechanism and function of UDG enzyme and the screening the inhibitors as potential drugs and biochemical tools. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Analysis of hairpin RNA transgene-induced gene silencing in Fusarium oxysporum

    PubMed Central

    2013-01-01

    Background Hairpin RNA (hpRNA) transgenes can be effective at inducing RNA silencing and have been exploited as a powerful tool for gene function analysis in many organisms. However, in fungi, expression of hairpin RNA transcripts can induce post-transcriptional gene silencing, but in some species can also lead to transcriptional gene silencing, suggesting a more complex interplay of the two pathways at least in some fungi. Because many fungal species are important pathogens, RNA silencing is a powerful technique to understand gene function, particularly when gene knockouts are difficult to obtain. We investigated whether the plant pathogenic fungus Fusarium oxysporum possesses a functional gene silencing machinery and whether hairpin RNA transcripts can be employed to effectively induce gene silencing. Results Here we show that, in the phytopathogenic fungus F. oxysporum, hpRNA transgenes targeting either a β-glucuronidase (Gus) reporter transgene (hpGus) or the endogenous gene Frp1 (hpFrp) did not induce significant silencing of the target genes. Expression analysis suggested that the hpRNA transgenes are prone to transcriptional inactivation, resulting in low levels of hpRNA and siRNA production. However, the hpGus RNA can be efficiently transcribed by promoters acquired either by recombination with a pre-existing, actively transcribed Gus transgene or by fortuitous integration near an endogenous gene promoter allowing siRNA production. These siRNAs effectively induced silencing of a target Gus transgene, which in turn appeared to also induce secondary siRNA production. Furthermore, our results suggested that hpRNA transcripts without poly(A) tails are efficiently processed into siRNAs to induce gene silencing. A convergent promoter transgene, designed to express poly(A)-minus sense and antisense Gus RNAs, without an inverted-repeat DNA structure, induced consistent Gus silencing in F. oxysporum. Conclusions These results indicate that F. oxysporum possesses

  9. Comparative carcinogenic potencies of particulates from diesel engine exhausts, coke oven emissions, roofing tar aerosols and cigarette smoke.

    PubMed Central

    Albert, R E

    1983-01-01

    Mammalian cell mutagenesis, transformation and skin tumorigenesis assays show similar results in comparing the potencies of diesel, coke oven, roofing tar and cigarette smoke particulates. These assay results are reasonably consistent with the comparative carcinogenic potencies of coke oven and roofing tar emissions as determined by epidemiological studies. The bacterial mutagenesis assay tends to show disproportionately high potencies, particularly with diesel particulates. Results to date encourage the approach to the assessment for carcinogenic risks from diesel emissions based on the use of epidemiological data on cancer induced by coke oven emissions, roofing tar particulates and cigarette smoke with the comparative potencies of these materials determined by in vivo and in vitro bioassays. PMID:6186481

  10. Norbornene-constrained cyclic peptides with hairpin architecture: design, synthesis, conformation, and membrane ion transport.

    PubMed

    Ranganathan, D; Haridas, V; Kurur, S; Nagaraj, R; Bikshapathy, E; Kunwar, A C; Sarma, A V; Vairamani, M

    2000-01-28

    A novel family of hairpin cyclic peptides has been designed on the basis of the use of norbornene units as the bridging ligands. The design is flexible with respect to the choice of an amino acid, the ring size, and the nature of the second bridging ligand as illustrated here with the preparation of a large number of norborneno cyclic peptides containing a variety of amino acids in ring sizes varying from 12- to 29-membered, with the choice of the second bridging ligand being a rigid norbornene (11, 13a,b), an adamantane unit (7a,b and 8), or a flexible cystine residue (4a,b and 10). The presence of built-in handles (as protected COOH groups) permits the attachment of a variety of subunits as shown here with the ligation of Leu-Leu, Val-Val, or Aib-Aib pendants in 4b, 7b, and 13b, respectively. This novel class of constrained cyclic peptides are demonstrated to adopt beta-sheet- or hairpin-like conformation as shown by (1)H NMR and CD spectra. Membrane ion-transport studies have shown that the norborneno cyclic peptides 4b and 7b containing Leu-Leu or Val-Val pendants symmetrically placed on the exterior of the ring show high efficiency and selectivity in the transport of specifically monovalent cations. This property can be attributed to the hairpin-like architecture induced by the norbornene unit since the bis-adamantano peptide 15 containing two pairs of Leu-Leu pendants on the exterior is able to transport both monovalent (Na(+), K(+)) and divalent (Mg(2+)/Ca(2+)) cations.

  11. PAHs underfoot: contaminated dust from coal-tar sealcoated pavement is widespread in the United States

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peter C. Van Metre; Barbara J. Mahler; Jennifer T. Wilson

    We reported in 2005 that runoff from parking lots treated with coal-tar-based sealcoat was a major source of polycyclic aromatic hydrocarbons (PAHs) to streams in Austin, Texas. Here we present new data from nine U.S. cities that show nationwide patterns in concentrations of {Sigma}PAHs associated with sealcoat. Dust was swept from parking lots in six cities in the central and eastern U.S., where coal-tar-based sealcoat dominates use, and three cities in the western U.S., where asphalt-based sealcoat dominates use. For six central and eastern cities, median SPAH concentrations in dust from sealcoated and unsealcoated pavement are 2200 and 27 mg/kg,more » respectively. For three western cities, median SPAH concentrations in dust from sealcoated and unsealcoated pavement are similar and very low (2.1 and 0.8 mg/kg, respectively). Lakes in the central and eastern cities where pavement was sampled have bottom sediments with higher PAH concentrations than do those in the western cities relative to degree of urbanization. Bottom-sediment PAH assemblages are similar to those of sealcoated pavement dust regionally, implicating coal-tar-based sealcoat as a PAH source to the central and eastern lakes. Concentrations of benzo(a)pyrene in dust from coal-tar sealcoated pavement and adjacent soils greatly exceed generic soil screening levels, suggesting that research on human-health risk is warranted. 30 refs., 4 figs., 2 tabs.« less

  12. Fluorescent aptasensor for detection of four tetracycline veterinary drugs in milk based on catalytic hairpin assembly reaction and displacement of G-quadruplex.

    PubMed

    Zhou, Chen; Zou, Haimin; Sun, Chengjun; Ren, Dongxia; Xiong, Wei; Li, Yongxin

    2018-05-01

    Based on a novel signal amplification strategy by catalytic hairpin assembly and displacement of G-quadruplex DNA, an enzyme-free, non-label fluorescent aptasensing approach was established for sensitive detection of four tetracycline veterinary drugs in milk. The network consisted of a pair of partially complementary DNA hairpins (HP1 and HP2). The DNA aptamer of four tetracycline veterinary drugs was located at the sticky end of the HP1. The ring region of HP1 rich in G and C could form a stable G-quadruplex structure, which could emit specific fluorescence signal after binding with the fluorescent dye and N-methylmesoporphyrin IX (NMM). When presented in the system, the target analytes would be repeatedly used to trigger a recycling procedure between the hairpins, generating numerous HP1-HP2 duplex complexes and displacing G-quadruplex DNA. Thus, the sensitive detection of target analytes was achieved in a wide linear range (0-1000 μg/L) with the detection limit of 4.6 μg/L. Moreover, this proposed method showed high discrimination efficiency towards target analytes against other common mismatched veterinary drugs, and could be successfully applied to the analysis of milk samples. Graphical abstract Schematic of target analyte detection based on catalytic hairpin assembly reaction and displacement of G-quadruplex.

  13. Analytical Determination of Nicotine and Tar Levels in Various Dokha and Shisha Tobacco Products.

    PubMed

    Mahboub, Bassam; Mohammad, Ayesha Begum; Nahlé, Ayssar; Vats, Mayank; Al Assaf, Omar; Al-Zarooni, Hamdan

    2018-05-10

    In the Middle East, there is no precise data and literature on tobacco-based products, such as dokha and shisha. The proposed study aims to quantify the levels of nicotine and tar in different kinds of dokha and shisha products that are sold in the local marketplace. The amount of nicotine in dokha and shisha products can be quantitatively determined using a combination of the "kissling" and "silicotungstic acid" method proposed by Robert M. Chapin. The tar residue from the smoke sample was collected on a glass wool placed before the stopcock (tap) of a separatory funnel as the smoke passes through the inlet of an electronically controlled vacuum pump. The nicotine levels in dokha and shisha samples ranged from 23.83 to 52.80 mg/g and 0.80 to 20.52 mg/g, respectively. The nicotine level varies between different tobacco products. It varies from 0.5 to 19.5 mg/g in cigarettes, from 10.3 to 23.1 mg/g in snuff tobacco, from 11 to 18 mg/g in electronic cigarettes and from 2.9 to 16.6 mg/g in chewing tobacco. The tar levels in the dokha and shisha samples ranged from 21.6 to 45.02 mg/g and 1.68 to 11.87 mg/g, respectively. Smokers are at a high risk of getting lung cancer, chronic obstructive pulmonary disease, emphysema and coronary artery disease owing to the high levels of nicotine and tar present in dokha and shisha tobacco products. These findings contradict the widespread belief among teenagers that dokha and shisha tobacco products are safer alternatives to cigarettes.

  14. Selected constituents in the smokes of foreign commercial cigaretts: tar, nicotine, carbon monoxide, and carbon dioxide

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    The tar, nicotine, carbon monoxide, and carbon dioxide contents of the smokes of 220 brands of foreign commercial cigarettes are reported. In some instances, filter cigarettes of certain brands were found to deliver as much or more smoke constituents than their nonfilter counterparts. Also, data indicated that there can be a great variation in the tar, nicotine, or carbon monoxide content of the smoke of samples of a given brand of cigarettes, depending on the nation in which they are purchased. 24 tables.

  15. The Size of the Internal Loop in DNA Hairpins Influences Their Targeting with Partially Complementary Strands

    PubMed Central

    2015-01-01

    Targeting of noncanonical DNA structures, such as hairpin loops, may have significant diagnostic and therapeutic potential. Oligonucleotides can be used for binding to mRNA, forming a DNA/RNA hybrid duplex that inhibits translation. This kind of modulation of gene expression is called the antisense approach. In order to determine the best strategy to target a common structural motif in mRNA, we have designed a set of stem-loop DNA molecules with sequence: d(GCGCTnGTAAT5GTTACTnGCGC), where n = 1, 3, or 5, “T5” is an end loop of five thymines. We used a combination of calorimetric and spectroscopy techniques to determine the thermodynamics for the reaction of a set of hairpins containing internal loops with their respective partially complementary strands. Our aim was to determine if internal- and end-loops are promising regions for targeting with their corresponding complementary strands. Indeed, all targeting reactions were accompanied by negative changes in free energy, indicating that reactions proceed spontaneously. Further investigation showed that these negative free energy terms result from a net balance of unfavorable entropy and favorable enthalpy contributions. In particular, unfolding of hairpins and duplexes is accompanied by positive changes in heat capacity, which may be a result of exposure of hydrophobic groups to the solvent. This study provides a new method for the targeting of mRNA in order to control gene expression. PMID:25486129

  16. Quantum Spin Glasses, Annealing and Computation

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Bikas K.; Inoue, Jun-ichi; Tamura, Ryo; Tanaka, Shu

    2017-05-01

    List of tables; List of figures, Preface; 1. Introduction; Part I. Quantum Spin Glass, Annealing and Computation: 2. Classical spin models from ferromagnetic spin systems to spin glasses; 3. Simulated annealing; 4. Quantum spin glass; 5. Quantum dynamics; 6. Quantum annealing; Part II. Additional Notes: 7. Notes on adiabatic quantum computers; 8. Quantum information and quenching dynamics; 9. A brief historical note on the studies of quantum glass, annealing and computation.

  17. Polycyclic aromatic hydrocarbon (PAHs) and hopanes in stranded tar-balls on the coasts of Peninsular Malaysia: applications of biomarkers for identifying sources of oil pollution.

    PubMed

    Zakaria, M P; Okuda, T; Takada, H

    2001-12-01

    Malaysian coasts are subjected to various threats of petroleum pollution including routine and accidental oil spill from tankers, spillage of crude oils from inland and off-shore oil fields, and run-off from land-based human activities. Due to its strategic location, the Straits of Malacca serves as a major shipping lane. This paper expands the utility of biomarker compounds, hopanes, in identifying the source of tar-balls stranded on Malaysian coasts. 20 tar-ball samples collected from the east and west coast were analyzed for hopanes and polycyclic aromatic hydrocarbons (PAHs). Four of the 13 tar-ball samples collected from the west coast of Peninsular Malaysia were identified as the Middle East crude oil (MECO) based on their biomarker signatures, suggesting tanker-derived sources significantly contributing the petroleum pollution in the Straits of Malacca. The tar-balls found on the east coast seem to originate from the offshore oil platforms in the South China Sea. The presence of South East Asian crude oil (SEACO) tar-balls on the west coast carry several plausible explanations. Some of the tar-balls could have been transported via sea currents from the east coast. The tankers carrying SEACO to other countries could have accidentally spilt the oil as well. Furthermore, discharge of tank washings and ballast water from the tankers were suggested based on the abundance in higher molecular weight n-alkanes and the absence of unresolved complex mixture (UCM) in the tar-ball samples. The other possibilities are that the tar-balls may have been originated from the Sumatran oil fields and spillage of domestic oil from oil refineries in Port Dickson and Malacca. The results of PAHs analysis suggest that all the tar-ball samples have undergone various extent of weathering through evaporation, dissolution and photooxidation.

  18. High-mobility group 1/2 proteins are essential for initiating rolling-circle-type DNA replication at a parvovirus hairpin origin.

    PubMed

    Cotmore, S F; Tattersall, P

    1998-11-01

    Rolling-circle replication is initiated by a replicon-encoded endonuclease which introduces a single-strand nick into specific origin sequences, becoming covalently attached to the 5' end of the DNA at the nick and providing a 3' hydroxyl to prime unidirectional, leading-strand synthesis. Parvoviruses, such as minute virus of mice (MVM), have adapted this mechanism to amplify their linear single-stranded genomes by using hairpin telomeres which sequentially unfold and refold to shuttle the replication fork back and forth along the genome, creating a continuous, multimeric DNA strand. The viral initiator protein, NS1, then excises individual genomes from this continuum by nicking and reinitiating synthesis at specific origins present within the hairpin sequences. Using in vitro assays to study ATP-dependent initiation within the right-hand (5') MVM hairpin, we have characterized a HeLa cell factor which is absolutely required to allow NS1 to nick this origin. Unlike parvovirus initiation factor (PIF), the cellular complex which activates NS1 endonuclease activity at the left-hand (3') viral origin, the host factor which activates the right-hand hairpin elutes from phosphocellulose in high salt, has a molecular mass of around 25 kDa, and appears to bind preferentially to structured DNA, suggesting that it might be a member of the high-mobility group 1/2 (HMG1/2) protein family. This prediction was confirmed by showing that purified calf thymus HMG1 and recombinant human HMG1 or murine HMG2 could each substitute for the HeLa factor, activating the NS1 endonuclease in an origin-specific nicking reaction.

  19. On the origin of the decrease in stability of the DNA hairpin d(GCGAAGC) on complexation with aromatic drugs.

    PubMed

    Kostjukov, V V; Lantushenko, A O; Davies, D B; Evstigneev, M P

    2007-08-01

    Molecular dynamics simulations of drug-DNA complexes have been carried out in order to explain the experimentally observed decrease in thermal stability of the DNA hairpin d(GCGAAGC) on binding the aromatic drug molecules, daunomycin, ethidium bromide, novantrone and proflavine. This complexation behavior is in contrast to the stabilizing effect of the same aromatic drug molecules on DNA duplexes. Analysis of the energy parameters and the hydration properties of the complexes shows that the main factor correlating with the decrease in melting temperatures of the drug-hairpin complexes is the number of water bridges, with a reduction of at least 40% on ligand binding.

  20. Heating tar sands formations while controlling pressure

    DOEpatents

    Stegemeier, George Leo [Houston, TX; Beer, Gary Lee [Houston, TX; Zhang, Etuan [Houston, TX

    2010-01-12

    Methods for treating a tar sands formation are described herein. Methods may include heating at least a section of a hydrocarbon layer in the formation from a plurality of heaters located in the formation. A pressure in the majority of the section may be maintained below a fracture pressure of the formation. The pressure in the majority of the section may be reduced to a selected pressure after the average temperature reaches a temperature that is above 240.degree. C. and is at or below pyrolysis temperatures of hydrocarbons in the section. At least some hydrocarbon fluids may be produced from the formation.

  1. DOE`s annealing prototype demonstration projects

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Warren, J.; Nakos, J.; Rochau, G.

    1997-02-01

    One of the challenges U.S. utilities face in addressing technical issues associated with the aging of nuclear power plants is the long-term effect of plant operation on reactor pressure vessels (RPVs). As a nuclear plant operates, its RPV is exposed to neutrons. For certain plants, this neutron exposure can cause embrittlement of some of the RPV welds which can shorten the useful life of the RPV. This RPV embrittlement issue has the potential to affect the continued operation of a number of operating U.S. pressurized water reactor (PWR) plants. However, RPV material properties affected by long-term irradiation are recoverable throughmore » a thermal annealing treatment of the RPV. Although a dozen Russian-designed RPVs and several U.S. military vessels have been successfully annealed, U.S. utilities have stated that a successful annealing demonstration of a U.S. RPV is a prerequisite for annealing a licensed U.S. nuclear power plant. In May 1995, the Department of Energy`s Sandia National Laboratories awarded two cost-shared contracts to evaluate the feasibility of annealing U.S. licensed plants by conducting an anneal of an installed RPV using two different heating technologies. The contracts were awarded to the American Society of Mechanical Engineers (ASME) Center for Research and Technology Development (CRTD) and MPR Associates (MPR). The ASME team completed its annealing prototype demonstration in July 1996, using an indirect gas furnace at the uncompleted Public Service of Indiana`s Marble Hill nuclear power plant. The MPR team`s annealing prototype demonstration was scheduled to be completed in early 1997, using a direct heat electrical furnace at the uncompleted Consumers Power Company`s nuclear power plant at Midland, Michigan. This paper describes the Department`s annealing prototype demonstration goals and objectives; the tasks, deliverables, and results to date for each annealing prototype demonstration; and the remaining annealing technology

  2. General acid-base catalysis mediated by nucleobases in the hairpin ribozyme

    PubMed Central

    Kath-Schorr, Stephanie; Wilson, Timothy J.; Li, Nan-Sheng; Lu, Jun; Piccirilli, Joseph A.; Lilley, David M. J.

    2012-01-01

    The catalytic mechanism by which the hairpin ribozyme accelerates cleavage or ligation of the phosphodiester backbone of RNA has been incompletely understood. There is experimental evidence for an important role for an adenine (A38) and a guanine (G8), and it has been proposed that these act in general acid-base catalysis. In this work we show that a large reduction in cleavage rate on substitution of A38 by purine (A38P) can be reversed by replacement of the 5′-oxygen atom at the scissile phosphate by sulfur (5′-PS), which is a much better leaving group. This is consistent with A38 acting as the general acid in the unmodified ribozyme. The rate of cleavage of the 5′-PS substrate by the A38P ribozyme increases with pH log-linearly, indicative of a requirement for a deprotonated base with a relatively high pKa. On substitution of G8 by diaminopurine, the 5′-PS substrate cleavage rate at first increases with pH and then remains at a plateau, exhibiting an apparent pKa consistent with this nucleotide acting in general base catalysis. Alternative explanations for the pH dependence of hairpin ribozyme reactivity are discussed, from which we conclude that general acid-base catalysis by A38 and G8 is the simplest and most probable explanation consistent with all the experimental data. PMID:22958171

  3. Cancer risk from incidental ingestion exposures to PAHs associated with coal-tar-sealed pavement

    USGS Publications Warehouse

    Williams, E. Spencer; Mahler, Barbara J.; Van Metre, Peter C.

    2012-01-01

    Recent (2009-10) studies documented significantly higher concentrations of polycyclic aromatic hydrocarbons (PAHs) in settled house dust in living spaces and soil adjacent to parking lots sealed with coal-tar-based products. To date, no studies have examined the potential human health effects of PAHs from these products in dust and soil. Here we present the results of an analysis of potential cancer risk associated with incidental ingestion exposures to PAHs in settings near coal-tar-sealed pavement. Exposures to benzo[a]pyrene equivalents were characterized across five scenarios. The central tendency estimate of excess cancer risk resulting from lifetime exposures to soil and dust from nondietary ingestion in these settings exceeded 1 × 10–4, as determined using deterministic and probabilistic methods. Soil was the primary driver of risk, but according to probabilistic calculations, reasonable maximum exposure to affected house dust in the first 6 years of life was sufficient to generate an estimated excess lifetime cancer risk of 6 × 10–5. Our results indicate that the presence of coal-tar-based pavement sealants is associated with significant increases in estimated excess lifetime cancer risk for nearby residents. Much of this calculated excess risk arises from exposures to PAHs in early childhood (i.e., 0–6 years of age).

  4. Comprehensive GC²/MS for the monitoring of aromatic tar oil constituents during biodegradation in a historically contaminated soil.

    PubMed

    Vasilieva, Viktoriya; Scherr, Kerstin E; Edelmann, Eva; Hasinger, Marion; Loibner, Andreas P

    2012-02-20

    The constituents of tar oil comprise a wide range of physico-chemically heterogeneous pollutants of environmental concern. Besides the sixteen polycyclic aromatic hydrocarbons defined as priority pollutants by the US-EPA (EPA-PAHs), a wide range of substituted (NSO-PAC) and alkylated (alkyl-PAC) aromatic tar oil compounds are gaining increased attention for their toxic, carcinogenic, mutagenic and/or teratogenic properties. Investigations on tar oil biodegradation in soil are in part hampered by the absence of an efficient analytical tool for the simultaneous analysis of this wide range of compounds with dissimilar analytical properties. Therefore, the present study sets out to explore the applicability of comprehensive two-dimensional gas chromatography (GC²/MS) for the simultaneous measurement of compounds with differing polarity or that are co-eluting in one-dimensional systems. Aerobic tar oil biodegradation in a historically contaminated soil was analyzed over 56 days in lab-scale bioslurry tests. Forty-three aromatic compounds were identified with GC²/MS in one single analysis. The number of alkyl chains on a molecule was found to prime over alkyl chain length in hampering compound biodegradation. In most cases, substitution of carbon with nitrogen and oxygen was related to increased compound degradation in comparison to unalkylated and sulphur- or unsubstituted PAH with a similar ring number.The obtained results indicate that GC²/MS can be employed for the rapid assessment of a large variety of structurally heterogeneous environmental contaminants. Its application can contribute to facilitate site assessment, development and control of microbial cleanup technologies for tar oil contaminated sites. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. An NMR (Nuclear Magnetic Resonance) Investigation of the Chemical Association and Molecular Dynamics in Asphalt Ridge Tar Sand Ore and Bitumen

    DOE R&D Accomplishments Database

    Netzel, D. A.; Coover, P. T.

    1987-09-01

    Preliminary studies on tar sand bitumen given in this report have shown that the reassociation of tar sand bitumen to its original molecular configuration after thermal stressing is a first-order process requiring nearly a week to establish equilibrium. Studies were also conducted on the dissolution of tar sand bitumen in solvents of varying polarity. At a high-weight fraction of solute to solvent the apparent molecular weight of the bitumen molecules was greater than that of the original bitumen when dissolved in chloroform-d{sub 1} and benzene-d{sub 6}. This increase in the apparent molecular weight may be due to micellar formation or a weak solute-solvent molecular complex. Upon further dilution with any of the solvents studied, the apparent molecular weight of the tar sand bitumen decreased because of reduced van der Waals forces of interaction and/or hydrogen bonding. To define the exact nature of the interactions, it will be necessary to have viscosity measurements of the solutions.

  6. Changes in tar yields and cigarette design in samples of Chinese cigarettes, 2009 and 2012

    PubMed Central

    Schneller, Liane M.; Zwierzchowski, Benjamin A.; Caruso, Rosalie V.; Li, Qiang; Yuan, Jiang; Fong, Geoffrey T.; O'Connor, Richard J.

    2015-01-01

    BACKGROUND China is home to both the greatest number of smokers and the greatest number of smoking-related deaths. An active and growing market of cigarettes marketed as “light” or “low tar” may keep health-concerned smokers from quitting, wrongly believing that such brands are less harmful. OBJECTIVE This study sought to observe changes in cigarette design characteristics and reported tar, nicotine and carbon monoxide (TNCO) levels in a sample of cigarette brands obtained in seven Chinese cities from 2009 and 2012. METHODS Cigarettes were purchased and shipped to Roswell Park Cancer Institute, where 91 pairs of packs were selected for physical cigarette design characteristic testing and recording of TNCO values. Data analysis was conducted using SPSS, and was initially characterized using descriptive statistics, correlations and generalized estimating equations to observe changes in brand varieties over time. FINDINGS Reported TNCO values on packs saw mean tar, nicotine and CO levels decrease from 2009 to 2012 by 7.9%, 4.5% and 6.0%, respectively. Ventilation was the only cigarette design feature that significantly changed over time (p < 0.001), with an increase of 31.7%. Significant predictors of tar and CO yields overall were ventilation and per-cigarette tobacco weight, while for nicotine tobacco moisture was also an independent predictor of yield. CONCLUSION The use of ventilation to decrease TNCO emissions is misleading smokers to believe that they are smoking a “light/low” tar cigarette that is healthier, and is potentially forestalling the quitting behaviors that would begin to reduce the health burden of tobacco in China, and so should be prohibited. PMID:25352560

  7. Association of daily tar and nicotine intake with incident myocardial infarction: Results from the population-based MONICA/KORA Augsburg Cohort Study 1984 - 2002

    PubMed Central

    2011-01-01

    Background Cigarette smoking has been shown to be one of the most important risk factors for cardiovascular diseases. However, little is known about cumulative effects of daily tar and nicotine intake on the risk of incident myocardial infarction (MI) so far. To bridge this gap, we conducted an analysis in a large prospective study from Southern Germany investigating associations of daily tar and nicotine intake with an incident MI event. Methods The study was based on 4,099 men and 4,197 women participating in two population-based MONICA Augsburg surveys between 1984 and 1990 and followed up within the KORA framework until 2002. During a mean follow-up of 13.3 years, a number of 307 men and 80 women developed an incident MI event. Relative risks were calculated as hazard ratios (HRs) estimated by Cox proportional hazards models adjusted for cardiovascular risk factors. Results In the present study, male regular smokers consumed on average more cigarettes per day than female regular smokers (20 versus 15) and had a higher tar and nicotine intake per day. In men, the MI risk compared to never-smokers increased with higher tar intake: HRs were 2.24 (95% CI 1.40-3.56) for 1-129 mg/day, 2.12 (95% CI 1.37-3.29) for 130-259 mg/day and 3.01 (95% CI 2.08-4.36) for ≥ 260 mg/day. In women, the corresponding associations were comparable but more pronounced for high tar intake (HR 4.67, 95% CI 1.76-12.40). Similar associations were observed for nicotine intake. Conclusions The present study based on a large population-based sample adds important evidence of cumulative effects of tar and nicotine intake on the risk of incident MI. Even low or medium tar and nicotine intake revealed substantial risk increases as compared to never-smokers. Therefore, reduction of tar and nicotine contents in cigarettes cannot be seen as a suitable public health policy in preventing myocardial infarction. PMID:21542909

  8. Analysis of pure tar substances (polycyclic aromatic hydrocarbons) in the gas stream using ultraviolet visible (UV-Vis) spectroscopy and multivariate curve resolution (MCR).

    PubMed

    Weide, Tobias; Guschin, Viktor; Becker, Wolfgang; Koelle, Sabine; Maier, Simon; Seidelt, Stephan

    2015-01-01

    The analysis of tar, mostly characterized as polycyclic aromatic hydrocarbons (PAHs), describes a topic that has been researched for years. An online analysis of tar in the gas stream in particular is needed to characterize the tar conversion or formation in the biomass gasification process. The online analysis in the gas is carried out with ultraviolet-visible (UV-Vis) spectroscopy (190-720 nm). This online analysis is performed with a measuring cell developed by the Fraunhofer Institute for Chemical Technology (ICT). To this day, online tar measurements using UV-Vis spectroscopy have not been carried out in detail. Therefore, PAHs are analyzed as follows. The measurements are split into different steps. The first step to prove the online method is to vaporize single tar substances. These experiments show that a qualitative analysis of PAHs in the gas stream with the used measurement setup is possible. Furthermore, it is shown that the method provides very exact results, so that a differentiation of various PAHs is possible. The next step is to vaporize a PAH mixture. This step consists of vaporizing five pure substances almost simultaneously. The interpretation of the resulting data is made using a chemometric interpretation method, the multivariate curve resolution (MCR). The verification of the calculated results is the main aim of this experiment. It has been shown that the tar mixture can be analyzed qualitatively and quantitatively (in arbitrary units) in detail using the MCR. Finally it is the main goal of this paper to show the first steps in the applicability of the UV-Vis spectroscopy and the measurement setup on online tar analysis in view of characterizing the biomass gasification process. Due to that, the gasification plant (at the laboratory scale), developed and constructed by the Fraunhofer ICT, has been used to vaporize these substances. Using this gasification plant for the experiments enables the usage of the measurement setup also for the

  9. Methotrexate iontophoresis versus coal tar ointment in palmoplantar psoriasis: A pilot study.

    PubMed

    Haseena, K; George, Sandhya; Riyaz, Najeeba; Sasidharanpillai, Sarita; Puthussery, Paul V

    2017-01-01

    Palmoplantar psoriasis is often disabling and refractory to conventional therapy. Systemic drugs are indicated in its severe form, but side effects are a concern with their use. Methotrexate is one such systemic drug which is effective and cheap. To reduce systemic toxicity, methotrexate has been tried topically but results have been inconsistent due to poor drug penetration into the skin by passive diffusion. Iontophoresis may enhance its absorption and efficacy. To evaluate the efficacy and safety of topical methotrexate iontophoresis in comparison with coal tar ointment in the treatment of palmoplantar psoriasis. Thirty-one patients with palmar and/or plantar psoriasis were selected for the study and 28 patients completed it. The side having more severe involvement was treated while the other palm/sole served as a control. Iontophoresis using methotrexate solution was carried out on the study palm/sole with the injectable preparation of methotrexate (50 mg/2 ml) once a week for the first 4 weeks and subsequently every two weeks, for a total of six sittings. The control palm/sole was treated with coal tar ointment on other days. Erythema, scaling, induration and fissuring scores were noted in both groups before and after treatment. Both study and control groups showed decreases in scores but the reduction was more in the study group, the difference being statistically significant. Drawbacks of our study include the small sample size and the lack of follow-up. The study and control arms were not exactly matched and the study was not blinded. Methotrexate iontophoresis was safe and more effective than coal tar ointmentin palmoplantarpsoriasis.

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

    PubMed

    Straus, Rita N; Jockusch, Rebecca A

    2017-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Straus, Rita N.; Jockusch, Rebecca A.

    2017-02-01

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

  12. Relationship of respiratory symptoms and pulmonary function to tar, nicotine, and carbon monoxide yield of cigarettes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Krzyzanowski, M.; Sherrill, D.L.; Paoletti, P.

    The data from consecutive surveys of the Tucson Epidemiologic Study (1981-1988) were used to evaluate the relationship in cigarette smokers of respiratory symptoms and pulmonary function to tar, nicotine, and carbon monoxide (CO) yields of the cigarette. There were 690 subjects who reported smoking regularly in at least one survey, over age 15. After adjustment for intensity and duration of smoking and for depth of inhalation, the risk of chronic phlegm, cough, and dyspnea were not related to the tar and nicotine yields. In 414 subjects with pulmonary function tested in at least one of the three surveys the spirometricmore » indices used were significantly related to the daily dose of tar, nicotine, and CO (product of the cigarette yield and daily number of cigarettes smoked). The effects were more pronounced for past than for current doses. However, the differentiation of pulmonary function due to various yields of cigarettes was small in comparison to the difference in pulmonary function between smokers and nonsmokers.« less

  13. Adsorption of nicotine and tar from the mainstream smoke of cigarettes by oxidized carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chen, Zhigang; Zhang, Lisha; Tang, Yiwen; Jia, Zhijie

    2006-02-01

    The adsorption of nicotine and tar from the mainstream smoke (MS) by the filter tips filled respectively with oxidized carbon nanotubes (O-CNTs), activated carbon and zeolite (NaY) has been investigated. O-CNTs show exceptional removal efficiency and their adsorption mechanism is investigated. Capillary condensation of some ingredients from MS in the inner hole of O-CNTs is observed and may be the primary reason for their superior removal efficiency. The effect of O-CNTs mass on the removal efficiencies is also studied and the results show that about 20-30 mg O-CNTs per cigarette can effectively remove most of nicotine and tar.

  14. Meta-analysis of lung cancer in asphalt roofing and paving workers with external adjustment for confounding by coal tar

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fayerweather, W.E.

    2007-07-01

    The study's objectives were to update Partanen's and Boffetta's 1994 meta-analysis of lung cancer among roofing and paving asphalt workers and explore the role of coal tar in explaining the statistical heterogeneity among these studies. Information retrieval strategies and eligibility criteria were defined for identifying the epidemiologic studies to be included in the analysis. The relative risk ratio (RR) for lung cancer was selected as the effect measure of interest. Coal tar bias factors were developed and used to externally adjust each eligible study's published RR for confounding by coal tar. The meta-Relative Risk (meta-RR) and its variance were estimatedmore » by general variance-based methods. Heterogeneity of the RRs was assessed by heterogeneity chi-square and I{sup 2} tests. The results from this update were similar to those in Partanen's and Boffetta's original meta-analysis. Although the meta-RRs for the roofers and the pavers were no longer statistically significantly different from one another, significant heterogeneity remained within each of the coal tar-adjusted sectors. Meta-analysis of non-experimental epidemiologic studies is subject to significant uncertainties as is externally correcting studies for confounding. Given these uncertainties, the specific quantitative estimates in this (or any similar) analysis must be viewed with caution. Nevertheless, this analysis provides support for the hypothesis proposed by several major reviewers that confounding by coal tar-related PAH exposures may explain most or all of the lung cancer risks found in the epidemiologic literature on asphalt roofing and paving workers.« less

  15. Deformation and annealing response of TD-nickel chromium

    NASA Technical Reports Server (NTRS)

    Kane, R. D.; Ebert, L. J.

    1975-01-01

    The recrystallization and grain growth processes occurring in TD-NiCr were examined with respect to deformation severity, annealing time, and temperature. Results indicated that two different annealing responses of TD-NiCr are possible, depending on the initial state and processing history prior to annealing. As-received sheet showed a dramatic increase in grain size with decreasing annealing temperature, whereas sheet prior-annealed at 1316 C for 1 hr exhibited very little variation with subsequent annealing temperature.

  16. 48 CFR 1201.301-70 - Amendment of (TAR) 48 CFR chapter 12.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Amendment of (TAR) 48 CFR chapter 12. 1201.301-70 Section 1201.301-70 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION GENERAL FEDERAL ACQUISITION REGULATIONS SYSTEM Agency Acquisition Regulations 1201.301-70...

  17. 48 CFR 1201.301-70 - Amendment of (TAR) 48 CFR chapter 12.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false Amendment of (TAR) 48 CFR chapter 12. 1201.301-70 Section 1201.301-70 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION GENERAL FEDERAL ACQUISITION REGULATIONS SYSTEM Agency Acquisition Regulations 1201.301-70...

  18. 48 CFR 1201.301-70 - Amendment of (TAR) 48 CFR chapter 12.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false Amendment of (TAR) 48 CFR chapter 12. 1201.301-70 Section 1201.301-70 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION GENERAL FEDERAL ACQUISITION REGULATIONS SYSTEM Agency Acquisition Regulations 1201.301-70...

  19. 48 CFR 1201.301-70 - Amendment of (TAR) 48 CFR chapter 12.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false Amendment of (TAR) 48 CFR chapter 12. 1201.301-70 Section 1201.301-70 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION GENERAL FEDERAL ACQUISITION REGULATIONS SYSTEM Agency Acquisition Regulations 1201.301-70...

  20. Ultrasensitive detection of nucleic acids by template enhanced hybridization followed by rolling circle amplification and catalytic hairpin assembly.

    PubMed

    Song, Weiling; Zhang, Qiao; Sun, Wenbo

    2015-02-11

    An ultrasensitive protocol for fluorescent detection of DNA is designed by combining the template enhanced hybridization process (TEHP) with Rolling Circle Amplification (RCA) and Catalytic Hairpin Assembly (CHA), showing a remarkable amplification efficiency.

  1. Design of miniature type parallel coupled microstrip hairpin filter in UHF range

    NASA Astrophysics Data System (ADS)

    Hasan, Adib Belhaj; Rahman, Maj Tarikur; Kahhar, Azizul; Trina, Tasnim; Saha, Pran Kanai

    2017-12-01

    A microstrip parallel coupled line bandpass filter is designed in UHF range and the filter size is reduced by microstrip hairpin structure. The FR4 substrate is used as base material of the filter. The filter is analyzed by both ADS and CST design studio in the frequency range of 500 MHz to 650 MHz. The Bandwidth is found 13.27% with a center frequency 570 MHz. Simulation from both ADS and CST shows a very good agreement of performance of the filter.

  2. Oxygenated Interface on Biomass Burn Tar Balls Determined bySingle Particle Scanning Transmission X-ray Microscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tivanski, A.V.; Hopkins, R.J.; Tyliszczak, T.

    2007-06-21

    Carbonaceous particles originating from biomass burning canaccount for a large fraction of organic aerosols in a local environment.Presently, their composition, physical and chemical properties, as wellas their environmental effects are largely unknown. Tar balls, a distincttype of highly spherical carbonaceous biomass burn particles, have beenobserved in a number of field campaigns. The Yosemite AerosolCharacterization Study that took place in summer 2002 occurred during anactive fire season in the western United States; tar balls collectedduring this field campaign are described in this article. Scanningtransmission X-ray microscopy and near-edge X-ray absorption finestructure spectroscopy are used to determine the shape, structure, andsize-dependent chemicalmore » composition of ~;150 individual sphericalparticles ranging in size from 0.15 to 1.2mu m.The elemental compositionof tar balls is ~;55 percent atomic carbon and ~;45 percent atomicoxygen. Oxygen is present primarily as carboxylic carbonyls andoxygen-substituted alkyl (O-alkyl-C) functional groups, followed bymoderate amounts of ketonic carbonyls. The observed chemical composition,density, and carbon functional groups are distinctly different from sootor black carbon and more closely resemble high molecular weight polymerichumic-like substances, which could account for their reported opticalproperties. A detailed examination of the carboxylic carbonyl andO-alkyl-C functional groups as a function of particle size reveals a thinoxygenated interface layer. The high oxygen content, as well as thepresence of water-soluble carboxylic carbonyl groups, could account forthe reported hygroscopic properties of tar balls. The presence of theoxygenated layer is attributed to atmospheric processing of biomass burnparticles.« less

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

    PubMed

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

    2014-10-10

    Bordetella pertussis, causative agent of whooping cough, produces an adenylate cyclase toxin (CyaA) that is an important virulence factor. In the host cell, the adenylate cyclase domain of CyaA (CyaA-ACD) is activated upon association with calmodulin (CaM), an EF-hand protein comprised of N- and C-lobes (N-CaM and C-CaM, respectively) connected by a flexible tether. Maximal CyaA-ACD activation is achieved through its binding to both lobes of intact CaM, but the structural mechanisms remain unclear. No high-resolution structure of the intact CaM/CyaA-ACD complex is available, but crystal structures of isolated C-CaM bound to CyaA-ACD shed light on the molecular mechanism by which this lobe activates the toxin. Previous studies using molecular modeling, biochemical, and biophysical experiments demonstrate that CyaA-ACD's β-hairpin participates in site-specific interactions with N-CaM. In this study, we utilize nuclear magnetic resonance (NMR) spectroscopy to probe the molecular association between intact CaM and CyaA-ACD. Our results indicate binding of CyaA-ACD to CaM induces large conformational perturbations mapping to C-CaM, while substantially smaller structural changes are localized primarily to helices I, II, and IV, and the metal-binding sites in N-CaM. Site-specific mutations in CyaA-ACD's β-hairpin structurally modulate N-CaM, resulting in conformational perturbations in metal binding sites I and II, while no significant structural modifications are observed in C-CaM. Moreover, dynamic light scattering (DLS) analysis reveals that mutation of the β-hairpin results in a decreased hydrodynamic radius (Rh) and reduced thermal stability in the mutant complex. Taken together, our data provide new structural insights into the β-hairpin's role in stabilizing interactions between CyaA-ACD and N-CaM. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual Chromosomes.

    PubMed

    Giehr, Pascal; Walter, Jörn

    2018-01-01

    The accurate and quantitative detection of 5-methylcytosine is of great importance in the field of epigenetics. The method of choice is usually bisulfite sequencing because of the high resolution and the possibility to combine it with next generation sequencing. Nevertheless, also this method has its limitations. Following the bisulfite treatment DNA strands are no longer complementary such that in a subsequent PCR amplification the DNA methylation patterns information of only one of the two DNA strand is preserved. Several years ago Hairpin Bisulfite sequencing was developed as a method to obtain the pattern information on complementary DNA strands. The method requires fragmentation (usually by enzymatic cleavage) of genomic DNA followed by a covalent linking of both DNA strands through ligation of a short DNA hairpin oligonucleotide to both strands. The ligated covalently linked dsDNA products are then subjected to a conventional bisulfite treatment during which all unmodified cytosines are converted to uracils. During the treatment the DNA is denatured forming noncomplementary ssDNA circles. These circles serve as a template for a locus specific PCR to amplify chromosomal patterns of the region of interest. As a result one ends up with a linearized product, which contains the methylation information of both complementary DNA strands.

  5. An N-terminal glycine-rich sequence contributes to retrovirus trimer of hairpins stability

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wilson, Kirilee A.; Maerz, Anne L.; Baer, Severine

    2007-08-10

    Retroviral transmembrane proteins (TMs) contain a glycine-rich segment linking the N-terminal fusion peptide and coiled coil core. Previously, we reported that the glycine-rich segment (Met-326-Ser-337) of the human T-cell leukemia virus type 1 (HTLV-1) TM, gp21, is a determinant of membrane fusion function [K.A. Wilson, S. Baer, A.L. Maerz, M. Alizon, P. Poumbourios, The conserved glycine-rich segment linking the N-terminal fusion peptide to the coiled coil of human T-cell leukemia virus type 1 transmembrane glycoprotein gp21 is a determinant of membrane fusion function, J. Virol. 79 (2005) 4533-4539]. Here we show that the reduced fusion activity of an I334A mutantmore » correlated with a decrease in stability of the gp21 trimer of hairpins conformation, in the context of a maltose-binding protein-gp21 chimera. The stabilizing influence of Ile-334 required the C-terminal membrane-proximal sequence Trp-431-Ser-436. Proline substitution of four of five Gly residues altered gp21 trimer of hairpins stability. Our data indicate that flexibility within and hydrophobic interactions mediated by this region are determinants of gp21 stability and membrane fusion function.« less

  6. Streamflow, Water Quality, and Metal Loads from Chat Leachate and Mine Outflow into Tar Creek, Ottawa County, Oklahoma, 2005

    USGS Publications Warehouse

    Cope, Caleb C.; Becker, Mark F.; Andrews, William J.; DeHay, Kelli

    2008-01-01

    Picher mining district is an abandoned lead and zinc mining area located in Ottawa County, northeastern Oklahoma. During the first half of the 20th century, the area was a primary producer of lead and zinc in the United States. Large accumulations of mine tailings, locally referred to as chat, produce leachate containing cadmium, iron, lead, and zinc that enter drainages within the mining area. Metals also seep to local ground water and streams from unplugged shafts, vent holes, seeps, and abandoned mine dewatering wells. Streamflow measurements were made and water-quality samples were collected and analyzed from two locations in Picher mining district from August 16 to August 29 following a rain event beginning on August 14, 2005, to determine likely concentrations and loads of metals from tailings and mine outflows in the part of Picher mining district near Tar Creek. Locations selected for sampling included a tailings pile with an adjacent mill pond, referred to as the Western location, and a segment of Tar Creek from above the confluence with Lytle Creek to below Douthat bridge, referred to as Tar Creek Study Segment. Measured streamflow was less than 0.01 cubic foot per second at the Western location, with streamflow only being measurable at that site on August 16, 2005. Measured streamflows ranged from <0.01 to 2.62 cubic feet per second at Tar Creek Study Segment. One water-quality sample was collected from runoff at the Western location. Total metals concentrations in that sample were 95.3 micrograms per liter cadmium, 182 micrograms per liter iron, 170 micrograms per liter lead, 1,760 micrograms per liter zinc. Total mean metals concentrations in 29 water-quality samples collected from Tar Creek Study Segment from August 16-29, 2005, were 21.8 micrograms per liter cadmium, 7,924 micrograms per liter iron, 7.68 micrograms per liter lead, and 14,548 micrograms per liter zinc. No metals loading values were calculated for the Western location. Metals loading

  7. Hairpin structures with conserved sequence motifs determine the 3' ends of non-polyadenylated invertebrate iridovirus transcripts.

    PubMed

    İnce, İkbal Agah; Pijlman, Gorben P; Vlak, Just M; van Oers, Monique M

    2017-11-01

    Previously, we observed that the transcripts of Invertebrate iridescent virus 6 (IIV6) are not polyadenylated, in line with the absence of canonical poly(A) motifs (AATAAA) downstream of the open reading frames (ORFs) in the genome. Here, we determined the 3' ends of the transcripts of fifty-four IIV6 virion protein genes in infected Drosophila Schneider 2 (S2) cells. By using ligation-based amplification of cDNA ends (LACE) it was shown that the IIV6 mRNAs often ended with a CAUUA motif. In silico analysis showed that the 3'-untranslated regions of IIV6 genes have the ability to form hairpin structures (22-56 nt in length) and that for about half of all IIV6 genes these 3' sequences contained complementary TAATG and CATTA motifs. We also show that a hairpin in the 3' flanking region with conserved sequence motifs is a conserved feature in invertebrate-infecting iridoviruses (genus Iridovirus and Chloriridovirus). Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Population Annealing Monte Carlo for Frustrated Systems

    NASA Astrophysics Data System (ADS)

    Amey, Christopher; Machta, Jonathan

    Population annealing is a sequential Monte Carlo algorithm that efficiently simulates equilibrium systems with rough free energy landscapes such as spin glasses and glassy fluids. A large population of configurations is initially thermalized at high temperature and then cooled to low temperature according to an annealing schedule. The population is kept in thermal equilibrium at every annealing step via resampling configurations according to their Boltzmann weights. Population annealing is comparable to parallel tempering in terms of efficiency, but has several distinct and useful features. In this talk I will give an introduction to population annealing and present recent progress in understanding its equilibration properties and optimizing it for spin glasses. Results from large-scale population annealing simulations for the Ising spin glass in 3D and 4D will be presented. NSF Grant DMR-1507506.

  9. Yields of tar, nicotine, and carbon monoxide in the sidestream smoke from 15 brands of Canadian cigarettes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rickert, W.S.; Robinson, J.C.; Collishaw, N.

    Sidestream smoke yields for 15 brands of cigarettes were determined under conditions where mainstream yields were approximately equal to those used for determining the values which appear on packages of Canadian cigarettes. Sidestream yields of tar, nicotine, and carbon monoxide were much higher than mainstream yields for all brands tested. The average sidestream-to-mainstream ratios for the 15 brands were 3.5, 6.6, and 6.8 for tar, nicotine, and carbon monoxide, respectively. The highest yields of sidestream were obtained from the brands with the lowest mainstream yields.

  10. The impact of steam and current density on carbon formation from biomass gasification tar on Ni/YSZ, and Ni/CGO solid oxide fuel cell anodes

    NASA Astrophysics Data System (ADS)

    Mermelstein, Joshua; Millan, Marcos; Brandon, Nigel

    The combination of solid oxide fuel cells (SOFCs) and biomass gasification has the potential to become an attractive technology for the production of clean renewable energy. However the impact of tars, formed during biomass gasification, on the performance and durability of SOFC anodes has not been well established experimentally. This paper reports an experimental study on the mitigation of carbon formation arising from the exposure of the commonly used Ni/YSZ (yttria stabilized zirconia) and Ni/CGO (gadolinium-doped ceria) SOFC anodes to biomass gasification tars. Carbon formation and cell degradation was reduced through means of steam reforming of the tar over the nickel anode, and partial oxidation of benzene model tar via the transport of oxygen ions to the anode while operating the fuel cell under load. Thermodynamic calculations suggest that a threshold current density of 365 mA cm -2 was required to suppress carbon formation in dry conditions, which was consistent with the results of experiments conducted in this study. The importance of both anode microstructure and composition towards carbon deposition was seen in the comparison of Ni/YSZ and Ni/CGO anodes exposed to the biomass gasification tar. Under steam concentrations greater than the thermodynamic threshold for carbon deposition, Ni/YSZ anodes still exhibited cell degradation, as shown by increased polarization resistances, and carbon formation was seen using SEM imaging. Ni/CGO anodes were found to be more resilient to carbon formation than Ni/YSZ anodes, and displayed increased performance after each subsequent exposure to tar, likely due to continued reforming of condensed tar on the anode.

  11. The hairpin region of Ndc80 is important for the kinetochore recruitment of Mph1/MPS1 in fission yeast.

    PubMed

    Chmielewska, Aldona Ewa; Tang, Ngang Heok; Toda, Takashi

    2016-01-01

    The establishment of proper kinetochore-microtubule attachments facilitates faithful chromosome segregation. Incorrect attachments activate the spindle assembly checkpoint (SAC), which blocks anaphase onset via recruitment of a cohort of SAC components (Mph1/MPS1, Mad1, Mad2, Mad3/BubR1, Bub1 and Bub3) to kinetochores. KNL1, a component of the outer kinetochore KMN network (KNL1/Mis12 complex/Ndc80 complex), acts as a platform for Bub1 and Bub3 localization upon its phosphorylation by Mph1/MPS1. The Ndc80 protein, a major microtubule-binding site, is critical for MPS1 localization to the kinetochores in mammalian cells. Here we characterized the newly isolated mutant ndc80-AK01 in fission yeast, which contains a single point mutation within the hairpin region. This hairpin connects the preceding calponin-homology domain with the coiled-coil region. ndc80-AK01 was hypersensitive to microtubule depolymerizing reagents with no apparent growth defects without drugs. Subsequent analyses indicated that ndc80-AK01 is defective in SAC signaling, as mutant cells proceeded into lethal cell division in the absence of microtubules. Under mitotic arrest conditions, all SAC components (Ark1/Aurora B, Mph1, Bub1, Bub3, Mad3, Mad2 and Mad1) did not localize to the kinetochore. Further genetic analyses indicated that the Ndc80 hairpin region might act as a platform for the kinetochore recruitment of Mph1, which is one of the most upstream SAC components in the hierarchy. Intriguingly, artificial tethering of Mph1 to the kinetochore fully restored checkpoint signaling in ndc80-AK01 cells, further substantiating the notion that Ndc80 is a kinetochore platform for Mph1. The hairpin region of Ndc80, therefore, plays a critical role in kinetochore recruitment of Mph1.

  12. Development of 2, 7-Diamino-1, 8-Naphthyridine (DANP) Anchored Hairpin Primers for RT-PCR Detection of Chikungunya Virus Infection.

    PubMed

    Chen, Huixin; Parimelalagan, Mariya; Takei, Fumie; Hapuarachchi, Hapuarachchige Chanditha; Koay, Evelyn Siew-Chuan; Ng, Lee Ching; Ho, Phui San; Nakatani, Kazuhiko; Chu, Justin Jang Hann

    2016-08-01

    A molecular diagnostic platform with DANP-anchored hairpin primer was developed and evaluated for the rapid and cost-effective detection of Chikungunya virus (CHIKV) with high sensitivity and specificity. The molecule 2, 7-diamino-1, 8-naphthyridine (DANP) binds to a cytosine-bulge and emits fluorescence at 450 nm when it is excited by 400 nm light. Thus, by measuring the decline in fluorescence emitted from DANP-primer complexes after PCR reaction, we could monitor the PCR progress. By adapting this property of DANP, we have previously developed the first generation DANP-coupled hairpin RT-PCR assay. In the current study, we improved the assay performance by conjugating the DANP molecule covalently onto the hairpin primer to fix the DANP/primer ratio at 1:1; and adjusting the excitation emission wavelength to 365/430 nm to minimize the background signal and a 'turn-on' system is achieved. After optimizing the PCR cycle number to 30, we not only shortened the total assay turnaround time to 60 minutes, but also further reduced the background fluorescence. The detection limit of our assay was 0.001 PFU per reaction. The DANP-anchored hairpin primer, targeting nsP2 gene of CHIKV genome, is highly specific to CHIKV, having no cross-reactivity to a panel of other RNA viruses tested. In conclusion, we report here a molecular diagnostic assay that is sensitive, specific, rapid and cost effective for CHIKV detection and can be performed where no real time PCR instrumentation is required. Our results from patient samples indicated 93.62% sensitivity and 100% specificity of this method, ensuring that it can be a useful tool for rapid detection of CHIKV for outbreaks in many parts of the world.

  13. Development of 2, 7-Diamino-1, 8-Naphthyridine (DANP) Anchored Hairpin Primers for RT-PCR Detection of Chikungunya Virus Infection

    PubMed Central

    Chen, Huixin; Parimelalagan, Mariya; Takei, Fumie; Hapuarachchi, Hapuarachchige Chanditha; Koay, Evelyn Siew-Chuan; Ng, Lee Ching; Ho, Phui San; Nakatani, Kazuhiko; Chu, Justin Jang Hann

    2016-01-01

    A molecular diagnostic platform with DANP-anchored hairpin primer was developed and evaluated for the rapid and cost-effective detection of Chikungunya virus (CHIKV) with high sensitivity and specificity. The molecule 2, 7-diamino-1, 8-naphthyridine (DANP) binds to a cytosine-bulge and emits fluorescence at 450 nm when it is excited by 400 nm light. Thus, by measuring the decline in fluorescence emitted from DANP—primer complexes after PCR reaction, we could monitor the PCR progress. By adapting this property of DANP, we have previously developed the first generation DANP-coupled hairpin RT-PCR assay. In the current study, we improved the assay performance by conjugating the DANP molecule covalently onto the hairpin primer to fix the DANP/primer ratio at 1:1; and adjusting the excitation emission wavelength to 365/430 nm to minimize the background signal and a ‘turn-on’ system is achieved. After optimizing the PCR cycle number to 30, we not only shortened the total assay turnaround time to 60 minutes, but also further reduced the background fluorescence. The detection limit of our assay was 0.001 PFU per reaction. The DANP-anchored hairpin primer, targeting nsP2 gene of CHIKV genome, is highly specific to CHIKV, having no cross-reactivity to a panel of other RNA viruses tested. In conclusion, we report here a molecular diagnostic assay that is sensitive, specific, rapid and cost effective for CHIKV detection and can be performed where no real time PCR instrumentation is required. Our results from patient samples indicated 93.62% sensitivity and 100% specificity of this method, ensuring that it can be a useful tool for rapid detection of CHIKV for outbreaks in many parts of the world. PMID:27571201

  14. The hairpin region of Ndc80 is important for the kinetochore recruitment of Mph1/MPS1 in fission yeast

    PubMed Central

    Chmielewska, Aldona Ewa; Tang, Ngang Heok; Toda, Takashi

    2016-01-01

    ABSTRACT The establishment of proper kinetochore-microtubule attachments facilitates faithful chromosome segregation. Incorrect attachments activate the spindle assembly checkpoint (SAC), which blocks anaphase onset via recruitment of a cohort of SAC components (Mph1/MPS1, Mad1, Mad2, Mad3/BubR1, Bub1 and Bub3) to kinetochores. KNL1, a component of the outer kinetochore KMN network (KNL1/Mis12 complex/Ndc80 complex), acts as a platform for Bub1 and Bub3 localization upon its phosphorylation by Mph1/MPS1. The Ndc80 protein, a major microtubule-binding site, is critical for MPS1 localization to the kinetochores in mammalian cells. Here we characterized the newly isolated mutant ndc80-AK01 in fission yeast, which contains a single point mutation within the hairpin region. This hairpin connects the preceding calponin-homology domain with the coiled-coil region. ndc80-AK01 was hypersensitive to microtubule depolymerizing reagents with no apparent growth defects without drugs. Subsequent analyses indicated that ndc80-AK01 is defective in SAC signaling, as mutant cells proceeded into lethal cell division in the absence of microtubules. Under mitotic arrest conditions, all SAC components (Ark1/Aurora B, Mph1, Bub1, Bub3, Mad3, Mad2 and Mad1) did not localize to the kinetochore. Further genetic analyses indicated that the Ndc80 hairpin region might act as a platform for the kinetochore recruitment of Mph1, which is one of the most upstream SAC components in the hierarchy. Intriguingly, artificial tethering of Mph1 to the kinetochore fully restored checkpoint signaling in ndc80-AK01 cells, further substantiating the notion that Ndc80 is a kinetochore platform for Mph1. The hairpin region of Ndc80, therefore, plays a critical role in kinetochore recruitment of Mph1. PMID:26900649

  15. The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface.

    PubMed

    Lorieau, Justin L; Louis, John M; Bax, Ad

    2010-06-22

    All but five of the N-terminal 23 residues of the HA2 domain of the influenza virus glycoprotein hemagglutinin (HA) are strictly conserved across all 16 serotypes of HA genes. The structure and function of this HA2 fusion peptide (HAfp) continues to be the focus of extensive biophysical, computational, and functional analysis, but most of these analyses are of peptides that do not include the strictly conserved residues Trp(21)-Tyr(22)-Gly(23). The heteronuclear triple resonance NMR study reported here of full length HAfp of sero subtype H1, solubilized in dodecylphosphatidyl choline, reveals a remarkably tight helical hairpin structure, with its N-terminal alpha-helix (Gly(1)-Gly(12)) packed tightly against its second alpha-helix (Trp(14)-Gly(23)), with six of the seven conserved Gly residues at the interhelical interface. The seventh conserved Gly residue in position 13 adopts a positive angle, enabling the hairpin turn that links the two helices. The structure is stabilized by multiple interhelical C(alpha)H to C=O hydrogen bonds, characterized by strong interhelical H(N)-H(alpha) and H(alpha)-H(alpha) NOE contacts. Many of the previously identified mutations that make HA2 nonfusogenic are also incompatible with the tight antiparallel hairpin arrangement of the HAfp helices.(15)N relaxation analysis indicates the structure to be highly ordered on the nanosecond time scale, and NOE analysis indicates HAfp is located at the water-lipid interface, with its hydrophobic surface facing the lipid environment, and the Gly-rich side of the helix-helix interface exposed to solvent.

  16. Investigating the role of chain and linker length on the catalytic activity of an H 2 production catalyst containing a β-hairpin peptide

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Reback, Matthew L.; Ginovska, Bojana; Buchko, Garry W.

    Building on our recent report of an active H2 production catalyst [Ni(PPh2NProp-peptide)2]2+ (Prop=para-phenylpropionic acid, peptide (R10)=WIpPRWTGPR-NH2, p=D-proline, and P2N=1-aza-3,6-diphosphacycloheptane) that contains structured -hairpin peptides, here we investigate how H2 production is effected by: (1) the length of the hairpin (eight or ten residues) and (2) limiting the flexibility between the peptide and the core complex by altering the length of the linker: para-phenylpropionic acid (three carbons) or para-benzoic acid (one carbon). Reduction of the peptide chain length from ten to eight residues increases or maintains the catalytic current for H2 production for all complexes, suggesting a non-productive steric interaction atmore » longer peptide lengths. While the structure of the hairpin appears largely intact for the complexes, NMR data are consistent with differences in dynamic behavior which may contribute to the observed differences in catalytic activity. Molecular dynamics simulations demonstrate that complexes with a one-carbon linker have the desired effect of restricting the motion of the hairpin relative to the complex; however, the catalytic currents are significantly reduced compared to complexes containing a three-carbon linker as a result of the electron withdrawing nature of the -COOH group. These results demonstrate the complexity and interrelated nature of the outer coordination sphere on catalysis.« less

  17. Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water.

    PubMed

    Daidone, Isabella; Amadei, Andrea; Di Nola, Alfredo

    2005-05-15

    The folding of the amyloidogenic H1 peptide MKHMAGAAAAGAVV taken from the syrian hamster prion protein is explored in explicit aqueous solution at 300 K using long time scale all-atom molecular dynamics simulations for a total simulation time of 1.1 mus. The system, initially modeled as an alpha-helix, preferentially adopts a beta-hairpin structure and several unfolding/refolding events are observed, yielding a very short average beta-hairpin folding time of approximately 200 ns. The long time scale accessed by our simulations and the reversibility of the folding allow to properly explore the configurational space of the peptide in solution. The free energy profile, as a function of the principal components (essential eigenvectors) of motion, describing the main conformational transitions, shows the characteristic features of a funneled landscape, with a downhill surface toward the beta-hairpin folded basin. However, the analysis of the peptide thermodynamic stability, reveals that the beta-hairpin in solution is rather unstable. These results are in good agreement with several experimental evidences, according to which the isolated H1 peptide adopts very rapidly in water beta-sheet structure, leading to amyloid fibril precipitates [Nguyen et al., Biochemistry 1995;34:4186-4192; Inouye et al., J Struct Biol 1998;122:247-255]. Moreover, in this article we also characterize the diffusion behavior in conformational space, investigating its relations with folding/unfolding conditions. Copyright 2005 Wiley-Liss, Inc.

  18. Structural effects of extracellular loop mutations in CFTR helical hairpins.

    PubMed

    Chang, Yuan-Heng; Stone, Tracy A; Chin, Stephanie; Glibowicka, Mira; Bear, Christine E; Deber, Charles M

    2018-05-01

    Missense mutations constitute 40% of 2000 cystic fibrosis-phenotypic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) database, yet the precise mechanism as to how a point mutation can render the entire 1480-residue CFTR protein dysfunctional is not well-understood. Here we investigate the structural effects of two CF-phenotypic mutations - glutamic acid to glycine at position 217 (E217G) and glutamine to arginine at position 220 (Q220R) - in the extracellular (ECL2) loop region of human CFTR using helical hairpin constructs derived from transmembrane (TM) helices 3 and 4 of the first membrane domain. We systematically replaced the wild type (WT) residues E217 and Q220 with the subset of missense mutations that could arise through a single nucleotide change in their respective codons. Circular dichroism spectra of E217G revealed that a significant increase in helicity vs. WT arises in the membrane-mimetic environment of sodium dodecylsulfate (SDS) micelles, while this mutant showed a similar gel shift to WT on SDS-PAGE gels. In contrast, the CF-mutant Q220R showed similar helicity but an increased gel shift vs. WT. These structural variations are compared with the maturation levels of the corresponding mutant full-length CFTRs, which we found are reduced to approx. 50% for E217G and 30% for Q220R vs. WT. The overall results with CFTR hairpins illustrate the range of impacts that single mutations can evoke in intramolecular protein-protein and/or protein-lipid interactions - and the levels to which corresponding mutations in full-length CFTR may be flagged by quality control mechanisms during biosynthesis. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Local Resistance Profiling of Ultra Shallow Junction Annealed with Combination of Spike Lamp and Laser Annealing Processes using Scanning Spreading Resistance Microscope

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Abo, Satoshi; Nishikawa, Kazuhisa; Ushigome, Naoya

    2011-01-07

    Local resistance profiles of ultra shallow boron and arsenic implanted into silicon with energies of 2.0 and 4.0 keV and doses of 2.0x10{sup 15} and 1.0x10{sup 15} ions/cm{sup 2} activated by a combination of conventional spike lamp and laser annealing processes were measured by scanning spreading resistance microscope (SSRM) with a depth resolution of less than 10 nm. The lowest local resistance at the low resistance region in 2.0 keV boron implanted silicon with 1050 deg. C spike lamp annealing followed by 0.35 kW/mm{sup 2} laser annealing was half of that without laser annealing. The lowest local resistance at themore » low resistance region in the arsenic implanted silicon activated by 1050 deg. C spike lamp annealing followed by 0.39 kW/mm{sup 2} laser annealing was 74% lower than that followed by 0.36 kW/mm{sup 2} laser annealing. The lowest local resistances at the low resistance regions in the arsenic implanted silicon with 0.36 and 0.39 kW/mm{sup 2} laser annealing followed by 1050 deg. C spike lamp annealing were 41 and 33% lower than those with spike lamp annealing followed by laser annealing. Laser annealing followed by spike lamp annealing could suppress the diffusion of the impurities and was suitable for making the ultra shallow and low resistance regions.« less

  20. Pulsed Laser Annealing of Carbon

    NASA Astrophysics Data System (ADS)

    Abrahamson, Joseph P.

    This dissertation investigates laser heating of carbon materials. The carbon industry has been annealing carbon via traditional furnace heating since at least 1800, when Sir Humphry Davy produced an electric arc with carbon electrodes made from carbonized wood. Much knowledge has been accumulated about carbon since then and carbon materials have become instrumental both scientifically and technologically. However, to this day the kinetics of annealing are not known due to the slow heating and cooling rates of furnaces. Additionally, consensus has yet to be reached on the cause of nongraphitizability. Annealing trajectories with respect to time at temperature are observed from a commercial carbon black (R250), model graphitizable carbon (anthracene coke) and a model nongraphitizable carbon (sucrose char) via rapid laser heating. Materials were heated with 1064 nm and 10.6 im laser radiation from a Q-switched Nd:YAG laser and a continuous wave CO2 laser, respectively. A pulse generator was used reduce the CO2 laser pulse width and provide high temporal control. Time-temperature-histories with nanosecond temporal resolution and temperature reproducibility within tens of degrees Celsius were determined by spectrally resolving the laser induced incandescence signal and applying multiwavelength pyrometry. The Nd:YAG laser fluences include: 25, 50, 100, 200, 300, and 550 mJ/cm2. The maximum observed temperature ranged from 2,400 °C to the C2 sublimation temperature of 4,180 °C. The CO2 laser was used to collect a series of isothermal (1,200 and 2,600 °C) heat treatments versus time (100 milliseconds to 30 seconds). Laser heated samples are compared to furnace annealing at 1,200 and 2,600 °C for 1 hour. The material transformation trajectory of Nd:YAG laser heated carbon is different than traditional furnace heating. The traditional furnace annealing pathway is followed for CO2 laser heating as based upon equivalent end structures. The nanostructure of sucrose char

  1. Detection of Nucleic Acids in Complex Samples via Magnetic Microbead-assisted Catalyzed Hairpin Assembly and "DD-A" FRET.

    PubMed

    Fang, Hongmei; Xie, Nuli; Ou, Min; Huang, Jin; Li, Wenshan; Wang, Qing; Liu, Jianbo; Yang, Xiaohai; Wang, Kemin

    2018-05-21

    Nucleic acids, as one kind of significant biomarkers, have attracted tremendous attention and exhibited immense value in fundamental studies and clinical applications. In this work, we developed a fluorescent assay for detecting nucleic acids in complex samples based on magnetic microbead (MMB)-assisted catalyzed hairpin assembly (CHA) and donor donor-acceptor fluorescence resonance energy transfer ("DD-A" FRET) signaling mechanism. Three types of DNA hairpin probes were employed in this system, including Capture, H1 (double FAM-labelled probe as FRET donor) and H2 (TAMRA-labelled probe as FRET acceptor). Firstly, the Captures immobilized on MMBs bound to targets in complex samples, and the sequences in Captures that could trigger catalyzed hairpin assembly (CHA) were exposed. Then, target-enriched MMBs complexes were separated and resuspended in the reaction buffer containing H1 and H2. As a result, numerous H1-H2 duplexes were formed during CHA process, inducing an obvious FRET signal. In contrast, CHA could not be trigger and the FRET signal was weak while target was absent. With the aid of magnetic separation and "DD-A" FRET, it was demonstrated to effectively eliminate errors from background interference. Importantly, this strategy realized amplified detection in buffer, with detection limits of microRNA as low as 34 pM. Furthermore, this method was successfully applied to detect microRNA-21 in serum and cell culture media. The results showed that our method has the potential for biomedical research and clinical application.

  2. Studying the Processes Contributed to the Hairpin Turn of Hurricane Joaquin with WRF numerical simulations and TCI-2015 observations

    NASA Astrophysics Data System (ADS)

    Pu, Z.; Yu, Y.

    2016-12-01

    The prediction of Hurricane Joaquin's hairpin clockwise during 1 and 2 October 2015 presents a forecasting challenge during real-time numerical weather prediction, as tracks of several major numerical weather prediction models differ from each other. To investigate the large-scale environment and hurricane inner-core structures related to the hairpin turn of Joaquin, a series of high-resolution mesoscale numerical simulations of Hurricane Joaquin had been performed with an advanced research version of the Weather Research and Forecasting (WRF) model. The outcomes were compared with the observations obtained from the US Office of Naval Research's Tropical Cyclone Intensity (TCI) Experiment during 2015 hurricane season. Specifically, five groups of sensitivity experiments with different cumulus, boundary layer, and microphysical schemes as well as different initial and boundary conditions and initial times in WRF simulations had been performed. It is found that the choice of the cumulus parameterization scheme plays a significant role in reproducing reasonable track forecast during Joaquin's hairpin turn. The mid-level environmental steering flows can be the reason that leads to different tracks in the simulations with different cumulus schemes. In addition, differences in the distribution and amounts of the latent heating over the inner-core region are associated with discrepancies in the simulated intensity among different experiments. Detailed simulation results, comparison with TCI-2015 observations, and comprehensive diagnoses will be presented.

  3. Pattern Laser Annealing by a Pulsed Laser

    NASA Astrophysics Data System (ADS)

    Komiya, Yoshio; Hoh, Koichiro; Murakami, Koichi; Takahashi, Tetsuo; Tarui, Yasuo

    1981-10-01

    Preliminary experiments with contact-type pattern laser annealing were made for local polycrystallization of a-Si, local evaporation of a-Si and local formation of Ni-Si alloy. These experiments showed that the mask patterns can be replicated as annealed regions with a resolution of a few microns on substrates. To overcome shortcomings due to the contact type pattern annealing, a projection type reduction pattern laser annealing system is proposed for resistless low temperature pattern forming processes.

  4. Establishment of conditional vectors for hairpin siRNA knockdowns

    PubMed Central

    Matsukura, Shiro; Jones, Peter A.; Takai, Daiya

    2003-01-01

    Small interference RNA (siRNA) is an emerging methodology in reverse genetics. Here we report the development of a new tetracycline-inducible vector-based siRNA system, which uses a tetracycline-responsive derivative of the U6 promoter and the tetracycline repressor for conditional in vivo transcription of short hairpin RNA. This method prevents potential lethality immediately after transfection of a vector when the targeted gene is indispensable, or the phenotype of the knockdown is lethal or results in a growth abnormality. We show that the controlled knockdown of DNA methyltransferase 1 (DNMT1) in human cancer resulted in growth arrest. Removal of the inducer, doxycycline, from treated cells led to re-expression of the targeted gene. Thus the method allows for a highly controlled approach to gene knockdown. PMID:12888529

  5. Bilaterally cleft lip, limb defects, and haematological manifestations: Roberts syndrome versus TAR syndrome.

    PubMed

    Urban, M; Opitz, C; Bommer, C; Enders, H; Tinschert, S; Witkowski, R

    1998-09-23

    We report on a 13-year-old patient followed since birth. He is the only offspring of young, non-consanguineous German parents. His mother has an isolated left cleft of lip and a cleft palate. At birth, our patient presented with bilaterally cleft lip/cleft palate, phocomelia of upper limbs with normal hands, and mild symmetrical deficiencies of the long bones of the lower limbs. Haematological evaluation demonstrated a leukaemoid reaction during a urinary tract infection as well as intermittent thrombocytopenia and episodes of marked eosinophilia during the first two years of life. Intellectual development has been normal. Comparison with two similar cases from the literature suggests a non-random phenotypic overlap of Roberts syndrome (MIM 268300) and TAR syndrome (MIM 274000). Such clinical constellations may be key observations to understand the genetic relationship of Roberts syndrome and TAR syndrome in future phenotype-genotype correlations.

  6. Reduced annealing temperatures in silicon solar cells

    NASA Technical Reports Server (NTRS)

    Weinberg, I.; Swartz, C. K.

    1981-01-01

    Cells irradiated to a fluence of 5x10,000,000,000,000/square cm showed short circuit current on annealing at 200 C, with complete annealing occurring at 275 C. Cells irradiated to 100,000,000,000,000/square cm showed a reduction in annealing temperature from the usual 500 to 300 C. Annealing kinetic studies yield an activation energy of (1.5 + or - 2) eV for the low fluence, low temperature anneal. Comparison with activation energies previously obtained indicate that the presently obtained activation energy is consistent with the presence of either the divacancy or the carbon interstitial carbon substitutional pair, a result which agrees with the conclusion based on defect behavior in boron-doped silicon.

  7. AAV delivery of tumor necrosis factor-α short hairpin RNA attenuates cold-induced pulmonary hypertension and pulmonary arterial remodeling.

    PubMed

    Crosswhite, Patrick; Chen, Kai; Sun, Zhongjie

    2014-11-01

    Cold temperatures are associated with increased mortality and morbidity of cardiovascular and pulmonary disease. Cold exposure causes lung inflammation, pulmonary hypertension (PH), and right ventricle hypertrophy, but there is no effective therapy because of unknown mechanism. Here, we investigated whether RNA interference silencing of tumor necrosis factor (TNF)-α decreases cold-induced macrophage infiltration, PH, and pulmonary arterial (PA) remodeling. We found for the first time that continuous cold exposure (5.0°C) increased TNF-α expression and macrophage infiltration in the lungs and PAs right before elevation of right ventricle systolic pressure. The in vivo RNA interference silencing of TNF-α was achieved by intravenous delivery of recombinant AAV-2 carrying TNF-α short hairpin small-interfering RNA 24 hours before cold exposure. Cold exposure for 8 weeks significantly increased right ventricle pressure compared with the warm controls (40.19±4.9 versus 22.9±1.1 mm Hg), indicating that cold exposure caused PH. Cold exposure increased TNF-α, interleukin-6, and phosphodiesterase-1C protein expression in the lungs and PAs and increased lung macrophage infiltration. Notably, TNF-α short hairpin small-interfering RNA prevented the cold-induced increases in TNF-α, interleukin-6, and phosphodiesterase-1C protein expression, abolished lung macrophage infiltration, and attenuated PH (26.28±1.6 mm Hg), PA remodeling, and right ventricle hypertrophy. PA smooth muscle cells isolated from cold-exposed animals showed increased intracellular superoxide levels and cell proliferation along with decreased intracellular cGMP. These cold-induced changes were prevented by TNF-α short hairpin small-interfering RNA. In conclusions, upregulation of TNF-α played a critical role in the pathogenesis of cold-induced PH by promoting pulmonary macrophage infiltration and inflammation. AAV delivery of TNF-α short hairpin small-interfering RNA may be an effective

  8. Thermal stability, structural features, and B-to-Z transition in DNA tetraloop hairpins as determined by optical spectroscopy in d(CG)(3)T(4)(CG)(3) and d(CG)(3)A(4)(CG)(3) oligodeoxynucleotides.

    PubMed

    Hernández, Belén; Baumruk, Vladimir; Gouyette, Catherine; Ghomi, Mahmoud

    2005-05-01

    NMR and CD data have previously shown the formation of the T(4) tetraloop hairpin in aqueous solutions, as well as the possibility of the B-to-Z transition in its stem in high salt concentration conditions. It has been shown that the stem B-to-Z transition in T(4) hairpins leads to S (south)- to N (north)-type conformational changes in the loop sugars, as well as anti to syn orientations in the loop bases. In this article, we have compared by means of UV absorption, CD, Raman, and Fourier transform infrared (FTIR), the thermodynamic and structural properties of the T(4) and A(4) tetraloop hairpins formed in 5'-d(CGCGCG-TTTT-CGCGCG)-3' and 5'-d(CGCGCG-AAAA-CGCGCG)-3', respectively. In presence of 5M NaClO(4), a complete B-to-Z transition of the stems is first proved by CD spectra. UV melting profiles are consistent with a higher thermal stability of the T(4) hairpin compared to the A(4) hairpin. Order-to-disorder transition of both hairpins has also been analyzed by means of Raman spectra recorded as a function of temperature. A clear Z-to-B transition of the stem has been confirmed in the T(4) hairpin, and not in the A(4) hairpin. With a right-handed stem, Raman and FTIR spectra have confirmed the C2'-endo/anti conformation for all the T(4) loop nucleosides. With a left-handed stem, a part of the T(4) loop sugars adopt a N-type (C3'-endo) conformation, and the C3'-endo/syn conformation seems to be the preferred one for the dA residues involved in the A(4) tetraloop.

  9. Rapid Annealing Of Amorphous Hydrogenated Carbon

    NASA Technical Reports Server (NTRS)

    Alterovitz, Samuel A.; Pouch, John J.; Warner, Joseph D.

    1989-01-01

    Report describes experiments to determine effects of rapid annealing on films of amorphous hydrogenated carbon. Study represents first efforts to provide information for applications of a-C:H films where rapid thermal processing required. Major finding, annealing causes abrupt increase in absorption and concomitant decrease in optical band gap. Most of change occurs during first 20 s, continues during longer annealing times. Extend of change increases with annealing temperature. Researchers hypothesize abrupt initial change caused by loss of hydrogen, while gradual subsequent change due to polymerization of remaining carbon into crystallites or sheets of graphite. Optical band gaps of unannealed specimens on silicon substrates lower than those of specimens on quartz substrates.

  10. Coherent Coupled Qubits for Quantum Annealing

    NASA Astrophysics Data System (ADS)

    Weber, Steven J.; Samach, Gabriel O.; Hover, David; Gustavsson, Simon; Kim, David K.; Melville, Alexander; Rosenberg, Danna; Sears, Adam P.; Yan, Fei; Yoder, Jonilyn L.; Oliver, William D.; Kerman, Andrew J.

    2017-07-01

    Quantum annealing is an optimization technique which potentially leverages quantum tunneling to enhance computational performance. Existing quantum annealers use superconducting flux qubits with short coherence times limited primarily by the use of large persistent currents Ip. Here, we examine an alternative approach using qubits with smaller Ip and longer coherence times. We demonstrate tunable coupling, a basic building block for quantum annealing, between two flux qubits with small (approximately 50-nA) persistent currents. Furthermore, we characterize qubit coherence as a function of coupler setting and investigate the effect of flux noise in the coupler loop on qubit coherence. Our results provide insight into the available design space for next-generation quantum annealers with improved coherence.

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

    PubMed

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

    2003-05-09

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

  12. Epoxy-borax-coal tar composition for a radiation protective, burn resistant drum liner and centrifugal casting method

    DOEpatents

    Taylor, Robert S.; Boyer, Norman W.

    1980-01-01

    A boron containing burn resistant, low level radiation protection material useful, for example, as a liner for radioactive waste disposal and storage, a component for neutron absorber, and a shield for a neutron source. The material is basically composed of Borax in the range of 25-50%, coal tar in the range of 25-37.5%, with the remainder being an epoxy resin mix. A preferred composition is 50% Borax, 25% coal tar and 25% epoxy resin. The material is not susceptible to burning and is about 1/5 the cost of existing radiation protection material utilized in similar applications.

  13. Epoxy-borax-coal tar composition for a radiation protective, burn resistant drum liner and centrifugal casting method

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Boyer, N.W.; Taylor, R.S.

    1980-10-28

    A boron containing burn resistant, low level radiation protection material useful, for example, as a liner for radioactive waste disposal and storage, a component for neutron absorber, and a shield for a neutron source. The material is basically composed of borax in the range of 25-50%, coal tar in the range of 25-37.5%, with the remainder being an epoxy resin mix. A preferred composition is 50% borax, 25% coal tar and 25% epoxy resin. The material is not susceptible to burning and is about 1/5 the cost of existing radiation protection material utilized in similar applications.

  14. Performance of Quantum Annealers on Hard Scheduling Problems

    NASA Astrophysics Data System (ADS)

    Pokharel, Bibek; Venturelli, Davide; Rieffel, Eleanor

    Quantum annealers have been employed to attack a variety of optimization problems. We compared the performance of the current D-Wave 2X quantum annealer to that of the previous generation D-Wave Two quantum annealer on scheduling-type planning problems. Further, we compared the effect of different anneal times, embeddings of the logical problem, and different settings of the ferromagnetic coupling JF across the logical vertex-model on the performance of the D-Wave 2X quantum annealer. Our results show that at the best settings, the scaling of expected anneal time to solution for D-WAVE 2X is better than that of the DWave Two, but still inferior to that of state of the art classical solvers on these problems. We discuss the implication of our results for the design and programming of future quantum annealers. Supported by NASA Ames Research Center.

  15. A designed beta-hairpin forming peptide undergoes a consecutive stepwise process for self-assembly into nanofibrils.

    PubMed

    Wang, Chong; Sha, Yinlin

    2010-04-01

    We used a de novo designed, beta-hairpin forming T1 peptide as a model to investigate the kinetics of peptide fibrogenesis by a combination of light scattering (LS), circular dichroism (CD), fluorescence, and atomic force microscopy (AFM). The results demonstrate that the T1 fibrogenesis undergoes a consecutive stepwise process, with a high degree of cooperation, presenting sigmoidal time-courses of the peptide aggregation, the subsequent conformational conversion of the backbone, and the peptide sidechains' rearrangement. We suggest that the conformational conversion was initiated after the peptide aggregates reach a dimensional size threshold, which could be a key step in the formation of beta-structural nuclei that catalyze the subsequent reactions. Furthermore, besides triggering the peptide aggregation, the interactions between the peptide sidechains predominately facilitate the regular alignment of the peptide molecules and the formation of a well-defined suprastructure. This work provides an insight of the hierarchical self-assembly of beta-hairpin forming peptides. It is helpful for designing beta-structural peptides for self-assembly into nanowires, which would have potential applications in the construction of nano-materials.

  16. Constitutive Expression of Short Hairpin RNA in Vivo Triggers Buildup of Mature Hairpin Molecules

    PubMed Central

    Ahn, M.; Witting, S.R.; Ruiz, R.; Saxena, R.

    2011-01-01

    Abstract RNA interference (RNAi) has become the cornerstone technology for studying gene function in mammalian cells. In addition, it is a promising therapeutic treatment for multiple human diseases. Virus-mediated constitutive expression of short hairpin RNA (shRNA) has the potential to provide a permanent source of silencing molecules to tissues, and it is being devised as a strategy for the treatment of liver conditions such as hepatitis B and hepatitis C virus infection. Unintended interaction between silencing molecules and cellular components, leading to toxic effects, has been described in vitro. Despite the enormous interest in using the RNAi technology for in vivo applications, little is known about the safety of constitutively expressing shRNA for multiple weeks. Here we report the effects of in vivo shRNA expression, using helper-dependent adenoviral vectors. We show that gene-specific knockdown is maintained for at least 6 weeks after injection of 1 × 1011 viral particles. Nonetheless, accumulation of mature shRNA molecules was observed up to weeks 3 and 4, and then declined gradually, suggesting the buildup of mature shRNA molecules induced cell death with concomitant loss of viral DNA and shRNA expression. No evidence of well-characterized innate immunity activation (such as interferon production) or saturation of the exportin-5 pathway was observed. Overall, our data suggest constitutive expression of shRNA results in accumulation of mature shRNA molecules, inducing cellular toxicity at late time points, despite the presence of gene silencing. PMID:21780944

  17. DNA sequence selectivity of hairpin polyamide turn units

    PubMed Central

    Farkas, Michelle E.; Li, Benjamin C.; Dose, Christian; Dervan, Peter B.

    2011-01-01

    A class of hairpin polyamides linked by 3,4-diaminobutyric acid, resulting in a β-amine residue at the turn unit, showed improved binding affinities relative to their α-amino-γ-turn analogs for particular sequences. We incorporated β-amino-γ-turns in six-ring polyamides and determined whether there are any sequence preferences under the turn unit by quantitative footprinting titrations. Although there was an energetic penalty for G·C and C·G base pairs, we found little preference for T·A over A·T at the β-amino-γ-turn position. Fluorine and hydroxyl substituted α-amino-γ-turns were synthesized for comparison. Their binding affinities and specificities in the context of six-ring polyamides demonstrated overall diminished affinity and no additional specificity at the turn position. We anticipate that this study will be a baseline for further investigation of the turn subunit as a recognition element for the DNA minor groove. PMID:19349175

  18. Temperature Scaling Law for Quantum Annealing Optimizers.

    PubMed

    Albash, Tameem; Martin-Mayor, Victor; Hen, Itay

    2017-09-15

    Physical implementations of quantum annealing unavoidably operate at finite temperatures. We point to a fundamental limitation of fixed finite temperature quantum annealers that prevents them from functioning as competitive scalable optimizers and show that to serve as optimizers annealer temperatures must be appropriately scaled down with problem size. We derive a temperature scaling law dictating that temperature must drop at the very least in a logarithmic manner but also possibly as a power law with problem size. We corroborate our results by experiment and simulations and discuss the implications of these to practical annealers.

  19. The region preceding the C-terminal NWETF pentapeptide modulates baseline activity and aspartate inhibition of Escherichia coli Tar.

    PubMed

    Lai, Run-Zhi; Bormans, Arjan F; Draheim, Roger R; Wright, Gus A; Manson, Michael D

    2008-12-16

    The Tar chemoreceptor-CheA-CheW ternary complex of Escherichia coli is a transmembrane allosteric enzyme in which binding of ligands to the periplasmic domain modulates the activity of CheA kinase. Kinase activity is also affected by reversible methylation of four glutamyl residues in the cytoplasmic domain of the receptor. E. coli Tar contains 553 residues. Residues 549-553 comprise the NWETF pentapeptide that binds the CheR methyltransferase and CheB methylesterase. The crystal structure of the similar Tsr chemoreceptor predicts that residues 263-289 and 490-515 of Tar form the most membrane-proximal portion of the extended CD1-CD2 four-helix bundle of the cytoplasmic domain. The last methylation site, Glu-491, is in the C19 heptad, and the N22-19 and C22-19 heptads are present in all classes of bacterial transmembrane chemoreceptors. Residues 516-548 probably serve as a flexible tether for the NWETF pentapeptide. Here, we present a mutational analysis of residues 505-548. The more of this region that is deleted, the less sensitive Tar is to inhibition by aspartate. Tar deleted from residue 505 through the NWETF sequence stimulates CheA in vitro but is not inhibited by aspartate. Thus, interaction of the last two heptads (C21 and C22) of CD2 with the first two heptads (N22 and N21) of CD1 must be important for transmitting an inhibitory signal from the HAMP domain to the four-helix bundle. The R514A, K523A, R529A, R540A, and R542A substitutions, singly or together, increase the level of activation of CheA in vitro, whereas the R505A substitution decreases the level of CheA stimulation by 40% and lowers the aspartate K(i) 7-fold. The R505E substitution completely abolishes stimulation of CheA in vitro. Glu-505 may interact electrostatically with Asp-273 to destabilize the "on" signaling state by loosening the four-helix bundle.

  20. Coal-tar-based sealcoated pavement: a major PAH source to urban stream sediments.

    PubMed

    Witter, Amy E; Nguyen, Minh H; Baidar, Sunil; Sak, Peter B

    2014-02-01

    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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. PAHs underfoot: contaminated dust from coal-tar sealcoated pavement is widespread in the United States.

    PubMed

    Van Metre, Peter C; Mahler, Barbara J; Wilson, Jennifer T

    2009-01-01

    We reported in 2005 that runoff from parking lots treated with coal-tar-based sealcoat was a major source of polycyclic aromatic hydrocarbons (PAHs) to streams in Austin, Texas. Here we present new data from nine U.S. cities that show nationwide patterns in concentrations of PAHs associated with sealcoat. Dust was swept from parking lots in six cities in the central and eastern U.S., where coal-tar-based sealcoat dominates use, and three cities in the western U.S., where asphalt-based sealcoat dominates use. For six central and eastern cities, median SigmaPAH concentrations in dust from sealcoated and unsealcoated pavement are 2200 and 27 mg/kg, respectively. For three western cities, median SigmaPAH concentrations in dust from sealcoated and unsealcoated pavement are similar and very low (2.1 and 0.8 mg/kg, respectively). Lakes in the central and eastern cities where pavement was sampled have bottom sediments with higher PAH concentrations than do those in the western cities relative to degree of urbanization. Bottom-sediment PAH assemblages are similar to those of sealcoated pavement dust regionally, implicating coal-tar-based sealcoat as a PAH source to the central and eastern lakes. Concentrations of benzo[a]pyrene in dustfrom coal-tarsealcoated pavement and adjacent soils greatly exceed generic soil screening levels, suggesting that research on human-health risk is warranted.

  2. Boosting quantum annealer performance via sample persistence

    NASA Astrophysics Data System (ADS)

    Karimi, Hamed; Rosenberg, Gili

    2017-07-01

    We propose a novel method for reducing the number of variables in quadratic unconstrained binary optimization problems, using a quantum annealer (or any sampler) to fix the value of a large portion of the variables to values that have a high probability of being optimal. The resulting problems are usually much easier for the quantum annealer to solve, due to their being smaller and consisting of disconnected components. This approach significantly increases the success rate and number of observations of the best known energy value in samples obtained from the quantum annealer, when compared with calling the quantum annealer without using it, even when using fewer annealing cycles. Use of the method results in a considerable improvement in success metrics even for problems with high-precision couplers and biases, which are more challenging for the quantum annealer to solve. The results are further enhanced by applying the method iteratively and combining it with classical pre-processing. We present results for both Chimera graph-structured problems and embedded problems from a real-world application.

  3. Coal-tar-based pavement sealcoat, polycyclic aromatic Hydrocarbons (PAHs), and environmental health

    USGS Publications Warehouse

    Mahler, B.J.; Van Metre, P.C.

    2011-01-01

    Studies by the U.S. Geological Survey (USGS) have identified coal-tar-based sealcoat-the black, viscous liquid sprayed or painted on asphalt pavement such as parking lots-as a major source of polycyclic aromatic hydrocarbon (PAH) contamination in urban areas for large parts of the Nation. Several PAHs are suspected human carcinogens and are toxic to aquatic life.

  4. Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Signal Amplification

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Youyu; Tang, Zhiwen; Wang, Jun

    2010-08-01

    A novel DNA detection platform based on a hairpin-DNA switch, nanoparticles, and enzyme signal amplification for ultrasensitive detection of DNA hybridization has been developed in this work. In this DNA assay, a “stem-loop” DNA probe dually labeled with a thiol at its 5’ end and a biotin at its 3’ end, respectively, was used. This probe was immobilized on the gold nanoparticles (AuNPs) anchored by a protein, globulin, on a 96-well microplate. In the absence of target DNA, the immobilized probe with the stem-loop structure shields the biotin from being approached by a bulky horseradish peroxidase linked-avidin (avidin-HRP) conjugate duemore » to the steric hindrance. However, in the presence of target DNA, the hybridization between the hairpin DNA probe and the target DNA causes significant conformational change of the probe, which forces biotin away from the surface of AuNPs. As a result, the biotin becomes accessible by the avidin-HRP, and the target hybridization event can be sensitively detected via the HRP catalyzed substrate 3, 3', 5, 5'-tetramethylbenzidine using spectrophometric method. Some experimental parameters governing the performance of the assay have been optimized. At optimal conditions, this DNA assay can detect DNA at the concentration of femtomolar level by means of a signal amplification strategy based on the combination of enzymes and nanoparticles. This approach also has shown excellent specificity to distinguish single-base mismatches of DNA targets because of the intrinsic high selectivity of the hairpin DNA probe.« less

  5. A novel nonenzymatic cascade amplification for ultrasensitive photoelectrochemical DNA sensing based on target driven to initiate cyclic assembly of hairpins.

    PubMed

    Wen, Guangming; Dong, Wenxia; Liu, Bin; Li, Zhongping; Fan, Lifang

    2018-05-29

    A novel cascade photoelectrochemical (PEC) signal amplification biosensing tactics was developed for DNA detection based on a target-driven DNA association to induce cyclic hairpin assembly. In the circulatory system there are two ssDNA (A and B) and two hairpins (C and D). The hybridization of these ssDNA led to the formation of an A-target-B structure. The close proximity of their toehold and branch-migration regions was able to induce the cyclic hairpin assembly. Afterwards, the assembly result further causes the separation of a double-stranded probe DNA (Q:F) to switch the PEC signal via toehold-mediated strand replacement. As such, the signal stranded DNA-CdS QDs (F) as the signal tag was released in the presence of the target DNA. The signal DNA-CdS QDs was then coated to F-doped tin oxide (FTO) electrode leading to the "signal-on" PEC signal. The designed biosensing strategy showed a low detection limit of 21.3 pM for target DNA and a broad linear range from 50 pM to 100 nM. This signal amplification PEC sensing method exhibited a potential application to detect protein molecules, RNA or metal ions via changing the sequence of A and B recognition. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.

    PubMed

    Kundu, Sangeeta

    2018-02-01

    The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.

  7. Streak instability and generation of hairpin-vortices by a slotted jet in channel crossflow: Experiments and linear stability analysis

    NASA Astrophysics Data System (ADS)

    Philip, Jimmy; Karp, Michael; Cohen, Jacob

    2016-01-01

    Streaks and hairpin-vortices are experimentally generated in a laminar plane Poiseuille crossflow by injecting a continuous jet through a streamwise slot normal to the crossflow, with air as the working media. Small disturbances form stable streaks, however, higher disturbances cause the formation of streaks which undergo instability leading to the generation of hairpin vortices. Particular emphasis is placed on the flow conditions close to the generation of hairpin-vortices. Measurements are carried out in the cases of natural and phase-locked disturbance employing smoke visualisation, particle image velocimetry, and hot-wire anemometry, which include, the dominant frequency, wavelength, and the disturbance shape (or eigenfunctions) associated with the coherent part of the velocity field. A linear stability analysis for both one- and two-dimensional base-flows is carried out to understand the mechanism of instability and good agreement of wavelength and eigenfunctions are obtained when compared to the experimental data, and a slight under-prediction of the growth-rates by the linear stability analysis consistent with the final nonlinear stages in transitional flows. Furthermore, an energy analysis for both the temporal and spatial stability analysis revels the dominance of the symmetric varicose mode, again, in agreement with the experiments, which is found to be governed by the balance of the wallnormal shear and dissipative effects rather than the spanwise shear. In all cases the anti-symmetric sinuous modes governed by the spanwise shear are found to be damped both in analysis and in our experiments.

  8. Analysis and optimization of population annealing

    NASA Astrophysics Data System (ADS)

    Amey, Christopher; Machta, Jonathan

    2018-03-01

    Population annealing is an easily parallelizable sequential Monte Carlo algorithm that is well suited for simulating the equilibrium properties of systems with rough free-energy landscapes. In this work we seek to understand and improve the performance of population annealing. We derive several useful relations between quantities that describe the performance of population annealing and use these relations to suggest methods to optimize the algorithm. These optimization methods were tested by performing large-scale simulations of the three-dimensional (3D) Edwards-Anderson (Ising) spin glass and measuring several observables. The optimization methods were found to substantially decrease the amount of computational work necessary as compared to previously used, unoptimized versions of population annealing. We also obtain more accurate values of several important observables for the 3D Edwards-Anderson model.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

    The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural studies. PMID:24723920

  11. Annealed importance sampling with constant cooling rate

    NASA Astrophysics Data System (ADS)

    Giovannelli, Edoardo; Cardini, Gianni; Gellini, Cristina; Pietraperzia, Giangaetano; Chelli, Riccardo

    2015-02-01

    Annealed importance sampling is a simulation method devised by Neal [Stat. Comput. 11, 125 (2001)] to assign weights to configurations generated by simulated annealing trajectories. In particular, the equilibrium average of a generic physical quantity can be computed by a weighted average exploiting weights and estimates of this quantity associated to the final configurations of the annealed trajectories. Here, we review annealed importance sampling from the perspective of nonequilibrium path-ensemble averages [G. E. Crooks, Phys. Rev. E 61, 2361 (2000)]. The equivalence of Neal's and Crooks' treatments highlights the generality of the method, which goes beyond the mere thermal-based protocols. Furthermore, we show that a temperature schedule based on a constant cooling rate outperforms stepwise cooling schedules and that, for a given elapsed computer time, performances of annealed importance sampling are, in general, improved by increasing the number of intermediate temperatures.

  12. Computational Multiqubit Tunnelling in Programmable Quantum Annealers

    DTIC Science & Technology

    2016-08-25

    ARTICLE Received 3 Jun 2015 | Accepted 26 Nov 2015 | Published 7 Jan 2016 Computational multiqubit tunnelling in programmable quantum annealers...state itself. Quantum tunnelling has been hypothesized as an advantageous physical resource for optimization in quantum annealing. However, computational ...qubit tunnelling plays a computational role in a currently available programmable quantum annealer. We devise a probe for tunnelling, a computational

  13. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.

    PubMed

    Vlachos, Ioannis S; Paraskevopoulou, Maria D; Karagkouni, Dimitra; Georgakilas, Georgios; Vergoulis, Thanasis; Kanellos, Ilias; Anastasopoulos, Ioannis-Laertis; Maniou, Sofia; Karathanou, Konstantina; Kalfakakou, Despina; Fevgas, Athanasios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G

    2015-01-01

    microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw next-generation sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. A novel DANP-coupled hairpin RT-PCR for rapid detection of Chikungunya virus.

    PubMed

    Chen, Huixin; Takei, Fumie; Koay, Evelyn Siew-Chuan; Nakatani, Kazuhiko; Chu, Justin Jang Hann

    2013-03-01

    Chikungunya has re-emerged as an important arboviral infection of global health significance. Because of lack of a vaccine and effective treatment, rapid diagnosis plays an important role in early clinical management of patients. In this study, we have developed a novel molecular diagnostic platform that ensures a rapid and cost-effective one-step RT-PCR assay, with high sensitivity and specificity, for the early detection of the Chikungunya virus (CHIKV). It uses 2,7-diamino-1,8-naphthyridine derivative (DANP)-labeled cytosine-bulge hairpin primers to amplify the nsP2 region of the CHIKV genome, followed by measurement of the fluorescence emitted from DANP-primer complexes after PCRs. The detection limit of our assay was 0.01 plaque-forming units per reaction of CHIKV. Furthermore, the HP-nsP2 primers were highly specific in detecting CHIKV, without any cross-reactivity with the panel of RNA viruses validated in this study. The feasibility of the DANP-coupled hairpin RT-PCR for clinical diagnosis was evaluated using clinical serum samples from CHIKV-infected patients, and the specificity and sensitivity were 100% (95% CI, 80.0% to 100%) and 95.5% (95% CI, 75.1% to 99.8%), respectively. These findings confirmed its potential as a point-of-care clinical molecular diagnostic assay for CHIKV in acute-phase patient serum samples. Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  15. Electrically contacted enzyme based on dual hairpin DNA structure and its application for amplified detection of Hg2+.

    PubMed

    Wang, Guangfeng; Huang, Hao; Zhang, Xiaojun; Wang, Lun

    2012-05-15

    In the present study, based on a dual hairpin DNA structure, a novel system of electrically contacted enzyme and its signal amplification for ultrasensitive detection of Hg(2+) was demonstrated. In the presence of Hg(2+), with the interaction of thymine-Hg(2+)-thymine (T-Hg(2+)-T), DNA sequence dully labeled with ferrocene (Fc) at 5' end and horseradish peroxidase (HRP) at 3' end, hybridized to the capture probe and formed the dual hairpin structure on the electrode. Fc unit acts as a relay that electrically contacts HRP with the electrode and activates the bioelectrocatalyzed reduction of H(2)O(2). And based on the bioelectrocatalyzed signal amplification of the presented system, Hg(2+) could be quantitatively detected in the range of 10(-10)-10(-6)M with a low detection limit of 52 pM. And it also demonstrated excellent selectivity against other interferential metal ions. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Crystal growth and annealing method and apparatus

    DOEpatents

    Gianoulakis, Steven E.; Sparrow, Robert

    2001-01-01

    A method and apparatus for producing crystals that minimizes birefringence even at large crystal sizes, and is suitable for production of CaF.sub.2 crystals. The method of the present invention comprises annealing a crystal by maintaining a minimal temperature gradient in the crystal while slowly reducing the bulk temperature of the crystal. An apparatus according to the present invention includes a thermal control system added to a crystal growth and annealing apparatus, wherein the thermal control system allows a temperature gradient during crystal growth but minimizes the temperature gradient during crystal annealing. An embodiment of the present invention comprises a secondary heater incorporated into a conventional crystal growth and annealing apparatus. The secondary heater supplies heat to minimize the temperature gradients in the crystal during the annealing process. The secondary heater can mount near the bottom of the crucible to effectively maintain appropriate temperature gradients.

  17. In vitro resolution of the dimer bridge of the minute virus of mice (MVM) genome supports the modified rolling hairpin model for MVM replication.

    PubMed

    Liu, Q; Yong, C B; Astell, C R

    1994-06-01

    Previous characterization of the terminal sequences of the minute virus of mice (MVM) genome demonstrated that the right hand palindrome contains two sequences, each the inverted complement of the other. However, the left hand palindrome was shown to exist as a unique sequence [Astell et al., J. Virol. 54: 179-185 (1985)]. The modified rolling hairpin (MRH) model for MVM replication provided an explanation of how the right hand palindrome could undergo hairpin transfer to generate two sequences, while the left end palindrome within the dimer bridge could undergo asymmetric resolution and retain the unique left end sequence. This report describes in vitro resolution of the wild-type dimer bridge sequence of MVM using recombinant (baculovirus) expressed NS-1 and a replication extract from LA9 cells. The resolution products are consistent with those predicted by the MRH model, providing support for this replication mechanism. In addition, mutant dimer bridge clones were constructed and used in the resolution assay. The mutant structures included removal of the asymmetry in the hairpin stem, inversion of the sequence at the initiating nick site, and a 2-bp deletion within one stem of the dimer bridge. In all cases, the mutant dimer bridge structures are resolved; however, the resolution pattern observed with the mutant dimer bridge compared with the wild-type dimer bridge is shifted toward symmetrical resolution. These results suggest that sequences within the left hand hairpin (and hence dimer bridge sequence) are responsible for asymmetric resolution and conservation of the unique sequence within the left hand palindrome of the MVM genome.

  18. Quenched-in defects in flashlamp-annealed silicon

    NASA Technical Reports Server (NTRS)

    Borenstein, J. T.; Jones, J. T.; Corbett, J. W.; Oehrlein, G. S.; Kleinhenz, R. L.

    1986-01-01

    Deep levels introduced in boron-doped silicon by heat-pulse annealing with a tungsten-halogen flashlamp are investigated using deep-level transient spectroscopy. Two majority-carrier trapping levels in the band gap, at Ev + 0.32 eV and at Ev + 0.45 eV, are observed. These results are compared to those obtained by furnace-quenching and laser-annealing studies. Both the position in the gap and the annealing kinetics of the hole trap at Ev + 0.45 eV suggest that this center is due to an interstitial iron impurity in the lattice. The deep levels are not consistently observed in all flashlamp-annealed Si crystals utilized.

  19. Effect of stabilization annealing on SCC susceptibility of β-annealed Ti-6Al-4V alloy in 0.6 M NaCl solution

    NASA Astrophysics Data System (ADS)

    Jeong, Daeho; Park, Jiho; Ahn, Soojin; Sung, Hyokyung; Kwon, Yongnam; Kim, Sangshik

    2018-01-01

    The effect of stabilization annealing on the stress corrosion cracking (SCC) susceptibility of β-annealed Ti-6Al-4V (Ti64) alloy was examined in an aqueous 0.6 M NaCl solution under various applied potentials of +0.1, -0.05 and -0.1 V vs Ecorr, respectively, at a strain rate of 10 -6 s -1. The stabilization annealing substantially improved the resistance to SCC of β-annealed Ti64 alloy in 0.6 M NaCl solution under cathodic applied potentials, while the effect was marginal under an anodic applied potential. It was also noted that the areal fraction between ductile and brittle fracture of β-annealed Ti64 specimens, which were slow strain rate tested in 0.6 M NaCl solution, varied with stabilization annealing and applied potentials. The effect of stabilization annealing on the SCC behavior of β-annealed Ti64 alloy in SCC-causing environment was discussed based on the micrographic and fractographic observation.

  20. Short hairpin RNA interference therapy for ischemic heart disease.

    PubMed

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

    2008-09-30

    During hypoxia, upregulation of hypoxia inducible factor-1 alpha transcriptional factor can activate several downstream angiogenic genes. However, hypoxia inducible factor-1 alpha is naturally degraded by prolyl hydroxylase-2 (PHD2) protein. Here we hypothesize that short hairpin RNA (shRNA) interference therapy targeting PHD2 can be used for treatment of myocardial ischemia and this process can be followed noninvasively by molecular imaging. PHD2 was cloned from mouse embryonic stem cells by comparing the homolog gene in human and rat. The best candidate shRNA sequence for inhibiting PHD2 was inserted into the pSuper vector driven by the H1 promoter followed by a separate hypoxia response element-incorporated promoter driving a firefly luciferase reporter gene. This construct was used to transfect mouse C2C12 myoblast cell line for in vitro confirmation. Compared with the control short hairpin scramble (shScramble) as control, inhibition of PHD2 increased levels of hypoxia inducible factor-1 alpha protein and several downstream angiogenic genes by >30% (P<0.01). Afterward, shRNA targeting PHD2 (shPHD2) plasmid was injected intramyocardially following ligation of left anterior descending artery in mice. Animals were randomized into shPHD2 experimental group (n=25) versus shScramble control group (n=20). Bioluminescence imaging detected plasmid-mediated transgene expression for 4 to 5 weeks. Echocardiography showed the shPHD2 group had improved fractional shortening compared with the shScramble group at Week 4 (33.7%+/-1.9% versus 28.4%+/-2.8%; P<0.05). Postmortem analysis showed increased presence of small capillaries and venules in the infarcted zones by CD31 staining. Finally, Western blot analysis of explanted hearts also confirmed that animals treated with shPHD2 had significantly higher levels of hypoxia inducible factor-1 alpha protein. This is the first study to image the biological role of shRNA therapy for improving cardiac function. Inhibition of PHD2 by

  1. Hydrogels constructed via self-assembly of beta-hairpin molecules

    NASA Astrophysics Data System (ADS)

    Ozbas, Bulent

    There is a recent and growing interest in hydrogel materials that are formed via peptide self-assembly for tissue engineering applications. Peptide based materials are excellent candidates for diverse applications in biomedical field due to their responsive behavior and complex self-assembled structures. However, there is very limited information on the self-assembly and resultant network and mechanical properties of these types of hydrogels. The main goal of this dissertation is to investigate the self-assembly mechanism and viscoelastic properties of hydrogels that can be altered by changing solution conditions as well as the primary structure of the peptide. These hydrogels are formed via intramolecular folding and consequent self-assembly of 20 amino acid long beta-hairpin peptide molecules (Max1). The peptide molecules are locally amphiphilic with two linear strands of alternating hydrophobic valine and hydrophilic lysine amino acids connected with a Dproline-LProline turn sequence. Circular dichroism and FTIR spectroscopy show that at physiological conditions peptides are unfolded in the absence of salt. By raising the ionic strength of the solution electrostatic interactions between charged lysines are screened and the peptide arms are forced into a beta-sheet secondary structure stabilized by the turn sequence. These folded molecules intermolecularly assemble via hydrophobic collapse and hydrogen bonding into a three dimensional network. Folding and self-assembly of these molecules can also be triggered by increasing temperature and/or pH of the peptide solution. In addition, the random-coil to beta-sheet transition of the beta-hairpin peptides is pH and, with proper changes in the peptide sequence, thermally reversible. Rheological measurements demonstrate that the resultant supramolecular structure forms an elastic material, whose structure, and thus modulus, can be tuned by magnitude of the stimulus. Hydrogels recover their initial viscoelastic

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

    PubMed

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

    2017-03-01

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

  3. Lack of effect of menthol level and type on smokers' estimated mouth level exposures to tar and nicotine and perceived sensory characteristics of cigarette smoke.

    PubMed

    Ashley, Madeleine; Dixon, Mike; Sisodiya, Ajit; Prasad, Krishna

    2012-08-01

    Menthol can reduce sensory irritation and it has been hypothesised that this could result in smokers of mentholated cigarettes taking larger puffs and deeper post-puff inhalations thereby obtaining higher exposures to smoke constituents than smokers of non-mentholated cigarettes. The aim of our study was to use part-filter analysis methodology to assess the effects of cigarette menthol loading on regular and occasional smokers of mentholated cigarettes. We measured mouth level exposure to tar and nicotine and investigated the effects of mentholation on smokers' sensory perceptions such as cooling and irritation. Test cigarettes were produced containing no menthol and different loadings of synthetic and natural l-menthol at 1 and 4mg ISO tar yields. A target of 100 smokers of menthol cigarettes and 100 smokers who predominantly smoked non-menthol cigarettes from both 1 and 4mg ISO tar yield categories were recruited in Poland and Japan. Each subject was required to smoke the test cigarette types of their usual ISO tar yield. There were positive relationships between menthol loading and the perceived 'strength of menthol taste' and 'cooling' effect. However, we did not see marked menthol-induced reductions in perceived irritation or menthol-induced increases in mouth level exposure to tar and nicotine. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Molecular Dynamics of β-Hairpin Models of Epigenetic Recognition Motifs

    PubMed Central

    Zheng, Xiange; Wu, Chuanjie; Ponder, Jay W.; Marshall, Garland R.

    2012-01-01

    The conformations and stabilities of the β-hairpin model peptides of Waters1,2 have been experimentally characterized as a function of lysine ε-methylation. These models were developed to explore molecular recognition of known epigenetic recognition motifs. This system offered an opportunity to computationally examine the role of cation-π interactions, desolvation of the ε-methylated ammonium groups, and aromatic/aromatic interactions on the observed differences in NMR spectra. AMOEBA, a second-generation force field4, was chosen as it includes both multipole electrostatics and polarizability thought to be essential to accurately characterize such interactions. Independent parameterization of ε-methylated amines was required from which aqueous solvation free energies were estimated and shown to agree with literature values. Molecular dynamics simulations (100 ns) using the derived parameters with model peptides, such as Ac-R-W-V-W-V-N-G-Orn-K(Me)n -I-L-Q-NH2, where n = 0, 1, 2, or 3, were conducted in explicit solvent. Distances between the centers of the indole rings of the two-tryptophan residues, 2 and 4, and the ε-methylated ammonium group on Lys-9 as well as the distance between the N- and C-termini were monitored to estimate the strength and orientation of the cation-π and aromatic/aromatic interactions. In agreement with the experimental data, the stability of the β-hairpin increased significantly with lysine ε-methylation. The ability of MD simulations to reproduce the observed NOEs for the four peptides was further estimated for the monopole-based force fields, AMBER, CHARMM, and OPLSAA. AMOEBA correctly predicted over 80% of the observed NOEs for all four peptides, while the three-monopole force fields were 40–50% predictive in only two cases and approximately 10% in the other ten examples. Preliminary analysis suggests that the decreased cost of desolvation of the substituted ammonium group significantly compensated for the reduced cation

  5. Super-secondary structure peptidomimetics: design and synthesis of an α-α hairpin analogue

    PubMed Central

    Nevola, Laura; Rodriguez, Johanna M.; Thompson, Sam; Hamilton, Andrew D.

    2015-01-01

    The α-α helix motif presents key recognition domains in protein-protein and protein-oligonucleotide binding, and is one of the most common super-secondary structures. Herein we describe the design, synthesis and structural characterization of an α-α hairpin analogue based on a tetra-coordinated Pd(II) bis-(iminoisoquinoline) complex as a template for the display of two α-helix mimics. This approach is exemplified by the attachment of two biphenyl peptidomimetics to reproduce the side-chains of the i and i+4 residues of two helices. PMID:26052191

  6. Efficient fabrication of carbon nanotube micro tip arrays by tailoring cross-stacked carbon nanotube sheets.

    PubMed

    Wei, Yang; Liu, Peng; Zhu, Feng; Jiang, Kaili; Li, Qunqing; Fan, Shoushan

    2012-04-11

    Carbon nanotube (CNT) micro tip arrays with hairpin structures on patterned silicon wafers were efficiently fabricated by tailoring the cross-stacked CNT sheet with laser. A blade-like structure was formed at the laser-cut edges of the CNT sheet. CNT field emitters, pulled out from the end of the hairpin by an adhesive tape, can provide 150 μA intrinsic emission currents with low beam noise. The nice field emission is ascribed to the Joule-heating-induced desorption of the emitter surface by the hairpin structure, the high temperature annealing effect, and the surface morphology. The CNT emitters with hairpin structures will greatly promote the applications of CNTs in vacuum electronic devices and hold the promises to be used as the hot tips for thermochemical nanolithography. More CNT-based structures and devices can be fabricated on a large scale by this versatile method. © 2012 American Chemical Society

  7. Ranking methodology for determining the relative favorability for commercial development of US tar-sand deposits

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Aamodt, P.L.; Freiwald, J.G.

    1983-03-01

    As a part of the DOE's program to stimulate petroleum production from unconventional sources, the Los Alamos National Laboratory has developed a methodology to compare and rank tar sand deposits, based on their suitability for commercial development. Major categories influencing favorability were identified and evaluated to determine their individual and collective impacts. To facilitate their evaluation, deposit characteristics, extraction technologies, environmental controls, and institutional constraints were broken down into their elements. The elements were assessed singly and in interactive groups to determine their influence on favorability for commercial development. A numerical value was assigned each element to signify its estimatedmore » importance relative to the other elements. Eight tar sand deposits were evaluated using only one major category, deposit characteristics. This initial, and only partial favorability assessment, was solely a test of the methodology, and it was considered successful. Because only one of the four major categories was used for this initial favorability ranking, and also because the available deposit characteristic data were barely adequate for the test, these first results should be used only as an example of how the methodology is to be applied when more complete data are available. The eight deposits and their relative favorability rankings for commercial development, based only on the deposit characteristics, are Sunnyside, Utah; Asphalt Ridge, Utah; Edna, California; Santa Rosa, New Mexico; Tar Sand Triangle, Utah; PR Spring, Utah; Uvalde, Texas; and circle cliffs, Utah.« less

  8. Dynamics of hairpin vortices and polymer-induced turbulent drag reduction.

    PubMed

    Kim, Kyoungyoun; Adrian, Ronald J; Balachandar, S; Sureshkumar, R

    2008-04-04

    It has been known for over six decades that the dissolution of minute amounts of high molecular weight polymers in wall-bounded turbulent flows results in a dramatic reduction in turbulent skin friction by up to 70%. First principles simulations of turbulent flow of model polymer solutions can predict the drag reduction (DR) phenomenon. However, the essential dynamical interactions between the coherent structures present in turbulent flows and polymer conformation field that lead to DR are poorly understood. We examine this connection via dynamical simulations that track the evolution of hairpin vortices, i.e., counter-rotating pairs of quasistreamwise vortices whose nonlinear autogeneration and growth, decay and breakup are centrally important to turbulence stress production. The results show that the autogeneration of new vortices is suppressed by the polymer stresses, thereby decreasing the turbulent drag.

  9. Selective molecular annealing: in situ small angle X-ray scattering study of microwave-assisted annealing of block copolymers.

    PubMed

    Toolan, Daniel T W; Adlington, Kevin; Isakova, Anna; Kalamiotis, Alexis; Mokarian-Tabari, Parvaneh; Dimitrakis, Georgios; Dodds, Christopher; Arnold, Thomas; Terrill, Nick J; Bras, Wim; Hermida Merino, Daniel; Topham, Paul D; Irvine, Derek J; Howse, Jonathan R

    2017-08-09

    Microwave annealing has emerged as an alternative to traditional thermal annealing approaches for optimising block copolymer self-assembly. A novel sample environment enabling small angle X-ray scattering to be performed in situ during microwave annealing is demonstrated, which has enabled, for the first time, the direct study of the effects of microwave annealing upon the self-assembly behavior of a model, commercial triblock copolymer system [polystyrene-block-poly(ethylene-co-butylene)-block-polystyrene]. Results show that the block copolymer is a poor microwave absorber, resulting in no change in the block copolymer morphology upon application of microwave energy. The block copolymer species may only indirectly interact with the microwave energy when a small molecule microwave-interactive species [diethylene glycol dibenzoate (DEGDB)] is incorporated directly into the polymer matrix. Then significant morphological development is observed at DEGDB loadings ≥6 wt%. Through spatial localisation of the microwave-interactive species, we demonstrate targeted annealing of specific regions of a multi-component system, opening routes for the development of "smart" manufacturing methodologies.

  10. Annealing of Solar Cells and Other Thin Film Devices

    NASA Technical Reports Server (NTRS)

    Escobar, Hector; Kuhlman, Franz; Dils, D. W.; Lush, G. B.; Mackey, Willie R. (Technical Monitor)

    2001-01-01

    Annealing is a key step in most semiconductor fabrication processes, especially for thin films where annealing enhances performance by healing defects and increasing grain sizes. We have employed a new annealing oven for the annealing of CdTe-based solar cells and have been using this system in an attempt to grow US on top of CdTe by annealing in the presence of H2S gas. Preliminary results of this process on CdTe solar cells and other thin-film devices will be presented.

  11. Implications of Use of Coal-Tar-Based Pavement Sealcoat on Urban Water Quality

    NASA Astrophysics Data System (ADS)

    Van Metre, P. C.

    2015-12-01

    Coal-tar-based (CT) sealcoat is used to protect and improve the appearance of asphalt pavement of driveways and parking lots primarily in the central and eastern U.S. and in Canada. CT sealcoat typically is 20 to 35% crude coal tar or coal-tar pitch and contains from 50,000 to 100,000 mg/kg polycyclic aromatic hydrocarbons (PAH), about 1,000 times more than asphalt-based (AS) sealcoat or asphalt itself. Tires and snowplows abrade the friable sealcoat surface into fine particles—median total PAH concentrations in dust from CT-sealcoated pavement are 2,200 mg/kg compared to a median concentration of 11 mg/kg for dust from unsealed pavement. Use of CT sealcoat has several implications for urban streams and lakes. Source apportionment modeling has indicated that, in regions where CT sealcoat is prevalent, particles from sealcoated pavement are contributing the majority of the PAHs to recently deposited lake sediment, often resulting in sediment concentrations above toxicity thresholds based on effects-based sediment quality guidelines. Acute 2-day laboratory toxicity testing of simulated runoff from CT-sealcoated pavement to a cladoceran (Ceriodaphnia dubia) and fathead minnows (Pimephales promelas) demonstrated that toxicity continues for samples collected for weeks or months following sealcoat application and that toxicity is enhanced by exposure to UV light. Using the fish-liver cell line RTL-W1, runoff collected as much as 36 days following CT-sealcoat application has been demonstrated to cause DNA damage and impair DNA repair capacity. These results demonstrate that CT runoff is a potential hazard to aquatic ecosystems and that exposure to sunlight can enhance toxicity and genetic damage. Recent research has provided direct evidence that restricting use of CT sealcoat in a watershed can lead to a substantial reduction in PAH concentrations in receiving water bodies.

  12. Final report on the safety assessment of Juniperus communis Extract, Juniperus oxycedrus Extract, Juniperus oxycedrus Tar, Juniperus phoenicea extract, and Juniperus virginiana Extract.

    PubMed

    2001-01-01

    The common juniper is a tree that grows in Europe, Asia, and North America. The ripe fruit of Juniperus communis and Juniperus oxycedrus is alcohol extracted to produce Juniperus Communis Extract and Juniperus Oxycedrus Extract, respectively. Juniperus Oxycedrus Tar is the volatile oil from the wood of J. oxycedrus. Juniperus Phoenicea Extract comes from the gum of Juniperus phoenicea, and Juniperus Virginiana Extract is extracted from the wood of Juniperus virginiana. Although Juniperus Oxycedrus Tar is produced as a by-product of distillation, no information was available on the manufacturing process for any of the Extracts. Oils derived from these varieties of juniper are used solely as fragrance ingredients; they are commonly produced using steam distillation of the source material, but it is not known if that procedure is used to produce extracts. One report does state that the chemical composition of Juniper Communis Oil and Juniperus Communis Extract is similar, each containing a wide variety of terpenoids and aromatic compounds, with the occasional aliphatic alcohols and aldehydes, and, more rarely, alkanes. The principle component of Juniperus Oxycedrus Tar is cadinene, a sesquiterpene, but cresol and guaiacol are also found. No data were available, however, indicating the extent to which there would be variations in composition that may occur as a result of extraction differences or any other factor such as plant growth conditions. Information on the composition of the other ingredients was not available. All of the Extracts function as biological additives in cosmetic formulations, and Juniperus Oxycedrus Tar is used as a hair-conditioning agent and a fragrance component. Most of the available safety test data are from studies using oils derived from the various varieties of juniper. Because of the expected similarity in composition to the extract, these data were considered. Acute studies using animals show little toxicity of the oil or tar. The oils

  13. Tar yields from low-temperature carbonization of coal facies from the Powder River Basin, Wyoming, USA

    USGS Publications Warehouse

    Stanton, Ronald W.; Warwick, Peter D.; Swanson, Sharon M.

    2005-01-01

    Tar yields from low-temperature carbonization correlate with the amount of crypto-eugelinite in samples selected to represent petrographically distinct coal facies of the Wyodak-Anderson coal zone. Tar yields from Fischer Assay range from <1 to 11 wt.% on a dry basis and correspond (r = 0.72) to crypto-eugelinite contents of the coal that range from 15 to 60 vol.%. Core and highwall samples were obtained from active surface mines in the Gillette field, Powder River Basin, Wyoming. Because the rank of the samples is essentially the same, differences in low-temperature carbonization yields are interpreted from compositional differences, particularly the crypto-eugelinite content. In the Wyodak-Anderson coal zone, crypto-eugelinite probably was derived from degraded humic matter which absorbed decomposition products from algae, fungi, bacteria, and liptinitic plant parts (materials possibly high in hydrogen). Previous modeling of the distribution of crypto-eugelinite in the discontinuous Wyodak-Anderson coal zone indicated that tar yields should be greater from coal composing the upper part and interior areas than from coal composing the lower parts and margins of the individual coal bodies. It is possible that hydrocarbon yields from natural coalification processes would be similar to yields obtained from laboratory pyrolysis. If so, the amount of crypto-eugelinite may also be an important characteristic when evaluating coal as source rock for migrated hydrocarbons.

  14. Antitumor and antiangiogenic activities of anti-vascular endothelial growth factor hairpin ribozyme in human hepatocellular carcinoma cell cultures and xenografts.

    PubMed

    Li, Li-Hua; Guo, Zi-Jian; Yan, Ling-Ling; Yang, Ji-Cheng; Xie, Yu-Feng; Sheng, Wei-Hua; Huang, Zhao-Hui; Wang, Xue-Hao

    2007-12-21

    To study the effectiveness and mechanisms of anti- human vascular endothelial growth factor (hVEGF) hairpin ribozyme on angiogenesis, oncogenicity and tumor growth in a hepatocarcinoma cell line and a xenografted model. The artificial anti-hVEGF hairpin ribozyme was transfected into hepatocarcinoma cell line SMMC-7,721 and, subsequently, polymerase chain reaction (PCR) and reverse transcription polymerase chain reaction (RT-PCR) were performed to confirm the ribozyme gene integration and transcription. To determine the effects of ribozyme ,VEGF expression was detected by semiquantitative RT-PCR and enzyme liked immunosorbent assay (ELISA). MTT assay was carried out to measure the cell proliferation. Furthermore,the transfected and control cells were inoculated into nude mice respectively, the growth of cells in nude mice and angiogenesis were observed. VEGF expression was down-regulated sharply by ribozyme in transfected SMMC-7,721 cells and xenografted tumor. Compared to the control group, the transfected cells grew slower in cell cultures and xenografts, and the xenograft formation was delayed as well. In addition, the microvessel density of the xenografted tumor was obviously declined in the transfected group. As demonstrated by microscopy,reduction of VEGF production induced by ribozyme resulted in a significantly higher cell differentiation and less proliferation vigor in xenografted tumor. Anti-hVEGF hairpin ribozyme can effectively inhibit VEGF expression and growth of hepatocarcinoma in vitro and in vivo. VEGF is functionally related to cell proliferation, differentiation and tumori-genesis in hepatocarcinoma.

  15. Radiation damage annealing mechanisms and possible low temperature annealing in silicon solar cells

    NASA Technical Reports Server (NTRS)

    Weinberg, I.; Swartz, C. K.

    1980-01-01

    Deep level transient spectroscopy and the Shockley-Read-Hall recombination theory are used to identify the defect responsible for reverse annealing in 2 ohm-cm n+/p silicon solar cells. This defect, with energy level at Ev + 0.30 eV, has been tentatively identified as a boron-oxygen-vacancy complex. It has been also determined by calculation that the removal of this defect could result in significant annealing at temperatures as low as 200 C for 2 ohm-cm and lower resistivity cells.

  16. Periodic annealing of radiation damage in GaAs solar cells

    NASA Technical Reports Server (NTRS)

    Loo, R. Y.; Knechtli, R. C.; Kamath, G. S.

    1980-01-01

    Continuous annealing of GaAs solar cells is compared with periodic annealing to determine their relative effectiveness in minimizing proton radiation damage. It is concluded that continuous annealing of the cells in space at 150 C can effectively reduce the proton radiation damage to the GaAs solar cells. Periodic annealing is most effective if it can be initiated at relatively low fluences (approximating continuous annealing), especially if low temperatures of less than 200 C are to be used. If annealing is started only after the fluence of the damaging protons has accumulated to a high value 10 to the 11th power sq/pcm), effective annealing is still possible at relatively high temperatures. Finally, since electron radiation damage anneals even more easily than proton radiation damage, substantial improvements in GaAs solar cell life can be achieved by incorporating the proper annealing capabilities in solar panels for practical space missions where both electron and proton radiation damage have to be minimized.

  17. Error suppression and correction for quantum annealing

    NASA Astrophysics Data System (ADS)

    Lidar, Daniel

    While adiabatic quantum computing and quantum annealing enjoy a certain degree of inherent robustness against excitations and control errors, there is no escaping the need for error correction or suppression. In this talk I will give an overview of our work on the development of such error correction and suppression methods. We have experimentally tested one such method combining encoding, energy penalties and decoding, on a D-Wave Two processor, with encouraging results. Mean field theory shows that this can be explained in terms of a softening of the closing of the gap due to the energy penalty, resulting in protection against excitations that occur near the quantum critical point. Decoding recovers population from excited states and enhances the success probability of quantum annealing. Moreover, we have demonstrated that using repetition codes with increasing code distance can lower the effective temperature of the annealer. References: K.L. Pudenz, T. Albash, D.A. Lidar, ``Error corrected quantum annealing with hundreds of qubits'', Nature Commun. 5, 3243 (2014). K.L. Pudenz, T. Albash, D.A. Lidar, ``Quantum annealing correction for random Ising problems'', Phys. Rev. A. 91, 042302 (2015). S. Matsuura, H. Nishimori, T. Albash, D.A. Lidar, ``Mean Field Analysis of Quantum Annealing Correction''. arXiv:1510.07709. W. Vinci et al., in preparation.

  18. Effect of Transport and Aging Processes on Metal Speciation in Iron Oxyhydroxide Aggregates, Tar Creek Superfund Site, Oklahoma

    NASA Astrophysics Data System (ADS)

    Estes, E. R.; Schaider, L. A.; Shine, J. P.; Brabander, D. J.

    2010-12-01

    Following the cessation of mining activity in the late 20th century, Tar Creek Superfund Site was left highly contaminated by Pb, Zn, and Cd. Tar Creek, which flows through the site and into the Neosho River, has been studied extensively because of its potential to transport metals from the mining site to downstream communities. Previous research identified aggregated iron oxyhydroxide material, which forms when mine seepage mixes with Tar Creek surface water, as a major transport vector of metals. Frequent flooding in Tar Creek deposits aggregates on downstream floodplains, where wetting and drying processes alter the speciation of iron and other metals. This study seeks to better quantify those changes and to determine how transport and aging affects the human and ecological health risk. Sequential extractions of aggregate samples collected from the creek demonstrate that Fe is present in both amorphous (10-35% of Fe extracted) and more crystalline (8-23% of Fe extracted) phases. Substantial portions of heavy metals sorb to amorphous iron oxyhydroxide phases (accounting for 10-30% of Pb and Zn extracted) but are not associated with more crystalline iron oxide phases (representing only 1% or less of the Pb and Zn extracted). Samples have a high organic matter content (18-25% mass loss on ignition), but only Fe was significantly extracted by the oxidizing step targeting organic matter (1-2% of Pb and Zn extracted, but 10-26% of Fe extracted). The majority of metals were extracted by the soluble or residual steps. If metals and organic matter inhibit transformation of amorphous iron oxyhydroxide material to nano and crystalline iron oxides, then a steady-state volume of amorphous iron oxyhydroxide material with a high total sorption capacity may exist within Tar Creek, enhancing the metal flux accommodated by this transport mechanism. Once transported downstream and deposited on floodplains, however, it is hypothesized that repeated changes in soil matrix

  19. The chimeric VirA-tar receptor protein is locked into a highly responsive state.

    PubMed Central

    Turk, S C; van Lange, R P; Sonneveld, E; Hooykaas, P J

    1993-01-01

    The wild-type VirA protein is known to be responsive not only to phenolic compounds but also to sugars via the ChvE protein (G. A. Cangelosi, R. G. Ankenbauer, and E. W. Nester, Proc. Natl. Acad. Sci. USA 87:6708-6712, 1990, and N. Shimoda, A. Toyoda-Yamamoto, J. Nagamine, S. Usami, M. Katayama, Y. Sakagami, and Y. Machida, Proc. Natl. Acad. Sci. USA 87:6684-6688, 1990). It is shown here that the mutant VirA(Ser-44, Arg-45) protein and the chimeric VirA-Tar protein are no longer responsive to sugars and the ChvE protein. However, whereas the chimeric VirA-Tar protein was found to be locked in a highly responsive state, the VirA(Ser-44, Arg-45) mutant protein appeared to be locked in a low responsive state. This difference turned out to be important for tumorigenicity of the host strains in virulence assays on Kalanchoë daigremontiana. Images PMID:8366057

  20. Injection-site vein loss and soft tissue abscesses associated with black tar heroin injection: A cross-sectional study of two distinct populations in USA.

    PubMed

    Summers, Phillip J; Struve, Isabelle A; Wilkes, Michael S; Rees, Vaughan W

    2017-01-01

    Injection-site vein loss and skin abscesses impose significant morbidity on people who inject drugs (PWID). The two common forms of street heroin available in the USA include black tar and powder heroin. Little research has investigated these different forms of heroin and their potential implications for health outcomes. A multiple-choice survey was administered to a sample of 145 participants seeking services at reduction facilities in both Sacramento, CA and greater Boston, MA, USA. Multivariate regression models for reporting one or more abscesses in one year, injection-site veins lost in six months, and soft tissue injection. Participants in Sacramento exclusively used black tar (99%), while those in Boston used powder heroin (96%). Those who used black tar heroin lost more injection-site veins (β=2.34, 95% CI: 0.66-4.03) and were more likely to report abscesses (AOR=7.68, 95% CI: 3.01-19.60). Soft tissue injection was also associated with abscesses (AOR=4.68, 95% CI: 1.84-11.93). Consistent venous access (AOR: 0.088, 95% CI: 0.011-0.74) and losing more injection sites (AOR: 1.22, 95% CI: 1.03-1.45) were associated with soft tissue injection. Use of black tar heroin is associated with more frequent abscesses and more extensive vein loss. Poor venous access predisposes people who inject drugs to soft tissue injection, which may constitute a causal pathway between black tar heroin injection and abscess formation. The mechanisms by which black tar heroin contributes to vein loss and abscess formation must be further elucidated in order to develop actionable interventions for maintaining vein health and decreasing the abscess burden. Potential interventions include increased access to clean injection equipment and education, supervised injection facilities, opioid substitution therapy, and supply chain interventions targeting cutting agents. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Potential impacts to perennial springs from tar sand mining, processing, and disposal on the Tavaputs Plateau, Utah, USA.

    PubMed

    Johnson, William P; Frederick, Logan E; Millington, Mallory R; Vala, David; Reese, Barbara K; Freedman, Dina R; Stenten, Christina J; Trauscht, Jacob S; Tingey, Christopher E; Kip Solomon, D; Fernandez, Diego P; Bowen, Gabriel J

    2015-11-01

    Similar to fracking, the development of tar sand mining in the U.S. has moved faster than understanding of potential water quality impacts. Potential water quality impacts of tar sand mining, processing, and disposal to springs in canyons incised approximately 200 m into the Tavaputs Plateau, at the Uinta Basin southern rim, Utah, USA, were evaluated by hydrogeochemical sampling to determine potential sources of recharge, and chemical thermodynamic estimations to determine potential changes in transfer of bitumen compounds to water. Because the ridgetops in an area of the Tavaputs Plateau named PR Spring are starting to be developed for their tar sand resource, there is concern for potential hydrologic connection between these ridgetops and perennial springs in adjacent canyons on which depend ranching families, livestock, wildlife and recreationalists. Samples were collected from perennial springs to examine possible progression with elevation of parameters such as temperature, specific conductance, pH, dissolved oxygen, isotopic tracers of phase change, water-rock interaction, and age since recharge. The groundwater age dates indicate that the springs are recharged locally. The progression of hydrogeochemical parameters with elevation, in combination with the relatively short groundwater residence times, indicate that the recharge zone for these springs includes the surrounding ridges, and thereby suggests a hydrologic connection between the mining, processing, disposal area and the springs. Estimations based on chemical thermodynamic approaches indicate that bitumen compounds will have greatly enhanced solubility in water that comes into contact with the residual bitumen-solvent mixture in disposed tailings relative to water that currently comes into contact with natural tar. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Spatial confinement induces hairpins in nicked circular DNA

    PubMed Central

    Japaridze, Aleksandre; Orlandini, Enzo; Smith, Kathleen Beth; Gmür, Lucas; Valle, Francesco; Micheletti, Cristian

    2017-01-01

    Abstract In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent–tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions. PMID:28201616

  3. Do increases in cigarette prices lead to increases in sales of cigarettes with high tar and nicotine yields?

    PubMed

    Farrelly, Matthew C; Loomis, Brett R; Mann, Nathan H

    2007-10-01

    We used scanner data on cigarette prices and sales collected from supermarkets across the United States from 1994 to 2004 to test the hypothesis that cigarette prices are positively correlated with sales of cigarettes with higher tar and nicotine content. During this period the average inflation-adjusted price for menthol cigarettes increased 55.8%. Price elasticities from multivariate regression models suggest that this price increase led to an increase of 1.73% in sales-weighted average tar yields and a 1.28% increase in sales-weighted average nicotine yields for menthol cigarettes. The 50.5% price increase of nonmenthol varieties over the same period yielded an estimated increase of 1% in tar per cigarette but no statistically significant increase in nicotine yields. An ordered probit model of the impact of cigarette prices on cigarette strength (ultra-light, light, full flavor, unfiltered) offers an explanation: As cigarette prices increase, the probability that stronger cigarette types will be sold increases. This effect is larger for menthol than for nonmenthol cigarettes. Our results are consistent with earlier population-based cross-sectional and longitudinal studies showing that higher cigarette prices and taxes are associated with increasing consumption of higher-yield cigarettes by smokers.

  4. [The application of non-annealing thermoluminescent dosimetry (TLD)].

    PubMed

    Wu, J M; Chen, C S; Lan, R H

    1993-06-01

    Conventional use of Thermoluminescence (TL) in radiation dosimetry is very time-consuming. It requires repeating the procedures of preheating and annealing. In an attempt to simplify these procedures, we conducted an experiment of non-annealing TL dosimetry. This article reports the experiment's results. We adopted Lithium Fluoride (LiF) chip (TLD-100) in polystyrene under the exposure of Co-60, and the result was taken by HAR-SHAW-4000 TL reading system. The TL response was analyzed, including linearity, reproducibility and fading test. Because non-annealing TL response was greatly influenced by residual electron, TLD calibration curves were separated into two parts: (1) high dose region (HDR, 50-1500 cGy); (2) low dose region (LDR, 0-50 cGy). When TL dosimeters were exposed to a single high does (about 500 cGy), the HDR could be reproduced within 3% and fit a good linearity. For LDR, we had to give up the tail of glow curve in the high temperature region. We could then get good linearity and reproducibility. Furthermore, fading of non-annealing was apparently larger than annealing. We could control the fading of non-annealing was apparently larger than annealing. We could control the fading influence within 1% by taking the TL reading one hour after exposure. On the other hand, a combination of photon and electron exposure was also performed by non-annealing TL dosimetry. The results were compatible with Co-60 exposure in the same system.

  5. Precision Laser Annealing of Focal Plane Arrays

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bender, Daniel A.; DeRose, Christopher; Starbuck, Andrew Lea

    2015-09-01

    We present results from laser annealing experiments in Si using a passively Q-switched Nd:YAG microlaser. Exposure with laser at fluence values above the damage threshold of commercially available photodiodes results in electrical damage (as measured by an increase in photodiode dark current). We show that increasing the laser fluence to values in excess of the damage threshold can result in annealing of a damage site and a reduction in detector dark current by as much as 100x in some cases. A still further increase in fluence results in irreparable damage. Thus we demonstrate the presence of a laser annealing windowmore » over which performance of damaged detectors can be at least partially reconstituted. Moreover dark current reduction is observed over the entire operating range of the diode indicating that device performance has been improved for all values of reverse bias voltage. Additionally, we will present results of laser annealing in Si waveguides. By exposing a small (<10 um) length of a Si waveguide to an annealing laser pulse, the longitudinal phase of light acquired in propagating through the waveguide can be modified with high precision, <15 milliradian per laser pulse. Phase tuning by 180 degrees is exhibited with multiple exposures to one arm of a Mach-Zehnder interferometer at fluence values below the morphological damage threshold of an etched Si waveguide. No reduction in optical transmission at 1550 nm was found after 220 annealing laser shots. Modeling results for laser annealing in Si are also presented.« less

  6. Identifying the source of tar balls deposited along the beaches of Goa in 2013 and comparing with historical data collected along the West Coast of India.

    PubMed

    Suneel, V; Vethamony, P; Naik, B G; Krishna, M S; Jadhav, Lakshmikant

    2015-09-15

    Deposition of oil residues, also known as tar balls, is a seasonal phenomenon, and it occurs only in the southwest monsoon season along the west coast of India. This has become a serious environmental issue, as Goa is a global tourist destination. The present work aims at identifying the source oil of the tar balls that consistently depositing along the Goa coast using multi-marker fingerprint technique. In this context, the tar ball samples collected in May 2013 from 9 beaches of Goa coast and crude oils from different oil fields and grounded ship were subject to multi-marker analyses such as n-alkanes, pentacyclic terpanes, regular steranes, compound specific isotope analysis (CSIA) and principle component analysis (PCA). The n-alkane weathering index shows that samples have been weathered to various degrees, and the status of weathering is moderate. Since the international tanker route passes closer to the west coast of India (WCI), it is generally presumed that tanker wash is the source of the tar balls. We found that 2010/2011 tar balls are as tanker wash, but the present study demonstrates that the Bombay High (BH) oil fields can also contribute to oil contamination (tar balls) along ≈ 650 km stretch of the WCI, running from Gujarat in the north to Goa in the south. The simulated trajectories show that all the particles released in April traveled in the southeast direction, and by May, they reached the Goa coast with the influence of circulation of Indian monsoon system. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    PubMed

    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.

  8. 21 CFR 740.18 - Coal tar hair dyes posing a risk of cancer.

    Code of Federal Regulations, 2010 CFR

    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... posing a risk of cancer. (a) The principal display panel of the label and any labeling accompanying a... your skin and has been determined to cause cancer in laboratory animals. (b) Hair dyes containing any...

  9. 21 CFR 740.18 - Coal tar hair dyes posing a risk of cancer.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Coal tar hair dyes posing a risk of cancer. 740.18... posing a risk of cancer. (a) The principal display panel of the label and any labeling accompanying a... your skin and has been determined to cause cancer in laboratory animals. (b) Hair dyes containing any...

  10. 21 CFR 740.18 - Coal tar hair dyes posing a risk of cancer.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Coal tar hair dyes posing a risk of cancer. 740.18... posing a risk of cancer. (a) The principal display panel of the label and any labeling accompanying a... your skin and has been determined to cause cancer in laboratory animals. (b) Hair dyes containing any...

  11. 21 CFR 740.18 - Coal tar hair dyes posing a risk of cancer.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Coal tar hair dyes posing a risk of cancer. 740.18... posing a risk of cancer. (a) The principal display panel of the label and any labeling accompanying a... your skin and has been determined to cause cancer in laboratory animals. (b) Hair dyes containing any...

  12. Single-Molecule Mechanical (Un)folding of RNA Hairpins: Effects of Single A-U to A∙C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting.

    PubMed

    Yang, Lixia; Zhong, Zhensheng; Tong, Cailing; Jia, Huan; Liu, Yiran; Chen, Gang

    2018-06-08

    A wobble A∙C pair can be protonated at near physiological pH to form a more stable wobble A+∙C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A∙C mismatch on the top (near the loop, U22C), middle (U25C) and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A∙C pair substitution, and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (~2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (~1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.

  13. Annealing Reduces Free Volumes In Thermoplastics

    NASA Technical Reports Server (NTRS)

    Singh, Jag J.; St. Clair, Terry L.

    1988-01-01

    Investigation conducted to determine free volumes and water-absorption characteristics of two types of thermoplastic polymide as functions of annealing histories. Reductions reach asymptotic values after several annealing cycles. High-temperature thermoplastics excellent candidates for use in aerospace applications. Graphite-fiber composites containing thermoplastic matrices have wide applicability.

  14. AmTAR2: Functional characterization of a honeybee tyramine receptor stimulating adenylyl cyclase activity.

    PubMed

    Reim, Tina; Balfanz, Sabine; Baumann, Arnd; Blenau, Wolfgang; Thamm, Markus; Scheiner, Ricarda

    2017-01-01

    The biogenic monoamines norepinephrine and epinephrine regulate important physiological functions in vertebrates. Insects such as honeybees do not synthesize these neuroactive substances. Instead, they employ octopamine and tyramine for comparable physiological functions. These biogenic amines activate specific guanine nucleotide-binding (G) protein-coupled receptors (GPCRs). Based on pharmacological data obtained on heterologously expressed receptors, α- and β-adrenergic-like octopamine receptors are better activated by octopamine than by tyramine. Conversely, GPCRs forming the type 1 tyramine receptor clade (synonymous to octopamine/tyramine receptors) are better activated by tyramine than by octopamine. More recently, receptors were characterized which are almost exclusively activated by tyramine, thus forming an independent type 2 tyramine receptor clade. Functionally, type 1 tyramine receptors inhibit adenylyl cyclase activity, leading to a decrease in intracellular cAMP concentration ([cAMP] i ). Type 2 tyramine receptors can mediate Ca 2+ signals or both Ca 2+ signals and effects on [cAMP] i . We here provide evidence that the honeybee tyramine receptor 2 (AmTAR2), when heterologously expressed in flpTM cells, exclusively causes an increase in [cAMP] i . The receptor displays a pronounced preference for tyramine over octopamine. Its activity can be blocked by a series of established antagonists, of which mianserin and yohimbine are most efficient. The functional characterization of two tyramine receptors from the honeybee, AmTAR1 (previously named AmTYR1) and AmTAR2, which respond to tyramine by changing cAMP levels in opposite direction, is an important step towards understanding the actions of tyramine in honeybee behavior and physiology, particularly in comparison to the effects of octopamine. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Laboratory studies to characterize the efficacy of sand capping a coal tar-contaminated sediment.

    PubMed

    Hyun, Seunghun; Jafvert, Chad T; Lee, Linda S; Rao, P Suresh C

    2006-06-01

    Placement of a microbial active sand cap on a coal tar-contaminated river sediment has been suggested as a cost effective remediation strategy. This approach assumes that the flux of contaminants from the sediment is sufficiently balanced by oxygen and nutrient fluxes into the sand layer such that microbial activity will reduce contaminant concentrations within the new benthic zone and reduce the contaminant flux to the water column. The dynamics of such a system were evaluated using batch and column studies with microbial communities from tar-contaminated sediment under different aeration and nutrient inputs. In a 30-d batch degradation study on aqueous extracts of coal tar sediment, oxygen and nutrient concentrations were found to be key parameters controlling the degradation rates of polycyclic aromatic hydrocarbons (PAHs). For the five PAHs monitored (naphthalene, fluorene, phenanthrene, anthracene, and pyrene), degradation rates were inversely proportional to molecular size. For the column studies, where three columns were packed with a 20-cm sand layer on the top of a 5 cm of sediment layer, flow was established to sand layers with (1) aerated water, (2) N(2) sparged water, or (3) HgCl(2)-sterilized N(2) sparged water. After steady-state conditions, PAH concentrations in effluents were the lowest in the aerated column, except for pyrene, whose concentration was invariant with all effluents. These laboratory scale studies support that if sufficient aeration can be achieved in the field through either active and passive means, the resulting microbially active sand layer can improve the water quality of the benthic zone and reduce the flux of many, but not all, PAHs to the water column.

  16. Quantum annealing correction with minor embedding

    NASA Astrophysics Data System (ADS)

    Vinci, Walter; Albash, Tameem; Paz-Silva, Gerardo; Hen, Itay; Lidar, Daniel A.

    2015-10-01

    Quantum annealing provides a promising route for the development of quantum optimization devices, but the usefulness of such devices will be limited in part by the range of implementable problems as dictated by hardware constraints. To overcome constraints imposed by restricted connectivity between qubits, a larger set of interactions can be approximated using minor embedding techniques whereby several physical qubits are used to represent a single logical qubit. However, minor embedding introduces new types of errors due to its approximate nature. We introduce and study quantum annealing correction schemes designed to improve the performance of quantum annealers in conjunction with minor embedding, thus leading to a hybrid scheme defined over an encoded graph. We argue that this scheme can be efficiently decoded using an energy minimization technique provided the density of errors does not exceed the per-site percolation threshold of the encoded graph. We test the hybrid scheme using a D-Wave Two processor on problems for which the encoded graph is a two-level grid and the Ising model is known to be NP-hard. The problems we consider are frustrated Ising model problem instances with "planted" (a priori known) solutions. Applied in conjunction with optimized energy penalties and decoding techniques, we find that this approach enables the quantum annealer to solve minor embedded instances with significantly higher success probability than it would without error correction. Our work demonstrates that quantum annealing correction can and should be used to improve the robustness of quantum annealing not only for natively embeddable problems but also when minor embedding is used to extend the connectivity of physical devices.

  17. Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method.

    PubMed

    Harada, Ryuhei; Kitao, Akio

    2011-07-14

    The folding process for a β-hairpin miniprotein, chignolin, was investigated by free energy landscape (FEL) calculations using the recently proposed multiscale free energy landscape calculation method (MSFEL). First, coarse-grained molecular dynamics simulations searched a broad conformational space, then multiple independent, all-atom molecular dynamics simulations with explicit solvent determined the detailed local FEL using massively distributed computing. The combination of the two models enabled efficient calculation of the free energy landscapes. The MSFEL analysis showed that chignolin has an intermediate state as well as a misfolded state. The folding process is initiated by the formation of a β-hairpin turn, followed by the formation of contacts in the hydrophobic core between Tyr2 and Trp9. Furthermore, mutation of Tyr2 shifts the population to the misfolded conformation. The results indicate that the hydrophobic core plays an important role in stabilizing the native state of chignolin. © 2011 American Chemical Society

  18. Chemical characterization of the smokes of selected US commercial cigarettes: tar, nicotine, carbon monoxide, oxides of nitrogen, hydrogen cyanide, and acrolein. [32 brands

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jenkins, R.A.; White, S.K.; Griest, W.H.

    Thirty-two brands of US commercial cigarettes were analyzed for their deliveries of tar, nicotine, CO, CO/sub 2/, HCN, NO/sub x/, and acrolein under standard smoking conditions. Per cigarette and per puff deliveries were calculated. The sample suite contained filtered and non-filtered varieties, and relatively popular high, low, and medium tar delivery cigarettes. The range of deliveries of these constituents was considerable. Statistical analysis indicated that the deliveries of nicotine, CO, NO/sub x/, and HCN could usually be estimated to within 50% of their actual delivery if the tar delivery was known. However, brand to brand variation in the constituent ratiosmore » was sufficient so as to preclude the exact calculation of the delivery of one component from that of another.« less

  19. Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR

    PubMed Central

    Miner, Brooks E.; Stöger, Reinhard J.; Burden, Alice F.; Laird, Charles D.; Hansen, R. Scott

    2004-01-01

    PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular ‘batch-stamps’ that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes. PMID:15459281

  20. The effects of higher cigarette prices on tar and nicotine consumption in a cohort of adult smokers.

    PubMed

    Farrelly, M C; Nimsch, C T; Hyland, A; Cummings, M

    2004-01-01

    The objective of this paper is to estimate the demand for tar and nicotine in cigarettes as a function of cigarette prices in a cohort of cigarette 11,966 smokers followed for 5 years. Data for the analysis come from a longitudinal telephone survey of 11,966 smokers who were interviewed in 1988 and 1993 as part of the Community Intervention Trial for Smoking Cessation (COMMIT). Separate models are estimated for three age groups to account for differences in levels of addiction and brand loyalty across age. We found that smokers respond to higher cigarette prices by reducing the number of cigarettes smoked per day but also by switching to cigarettes that are higher in tar and nicotine per cigarette. Copyright 2003 John Wiley & Sons, Ltd.

  1. Deformation and annealing response of TD-nickel chromium sheet

    NASA Technical Reports Server (NTRS)

    Kane, R. D.; Ebert, L. J.

    1973-01-01

    The deformation and annealing response of TD-nickel chromium (TD-NiCr) 0.1 inch thick sheet was examined using various cold-rolling and annealing treatments. Upon annealing (above 816 C (1500 F), the as-received material was converted from an initially ultra-fine grain size (average grain dimension 0.51 micron) to a large grain structure. Increases in grain size by a factor of 100 to 200 were observed for this transformation. However, in those material states where the large grain transformation was absent, a fine grain recrystallized structure formed upon annealing (above 732 C (1350 F)). The deformation and annealing response of TD-NiCr sheet was evaluated with respect to the processing related variables as mode and severity of deformation and annealing temperature. Results indicate that the large grain transformation, classical primary recrystallization occurs. Using selected materials produced during the deformation and annealing study, the elevated temperature tensile properties of TD-NiCr sheet were examined in the temperature range 593 C (1100 F) to 1093 C (2000 F). It was observed that the elevated temperature tensile properties of TD-NiCr sheet could be optimized by the stabilization of a large grain size in this material using the cold working and/or annealing treatments developed during the present investigation.

  2. Production from multiple zones of a tar sands formation

    DOEpatents

    Karanikas, John Michael; Vinegar, Harold J

    2013-02-26

    A method for treating a tar sands formation includes providing heat to at least part of a hydrocarbon layer in the formation from a plurality of heaters located in the formation. The heat is allowed to transfer from the heaters to at least a portion of the formation. Fluids are produced from the formation through at least one production well that is located in at least two zones in the formation. The first zone has an initial permeability of at least 1 darcy. The second zone has an initial of at most 0.1 darcy. The two zones are separated by a substantially impermeable barrier.

  3. Solution structure of a modified 2′,5′-linked RNA hairpin involved in an equilibrium with duplex

    PubMed Central

    Plevnik, Miha; Gdaniec, Zofia; Plavec, Janez

    2005-01-01

    The isomerization of phosphodiester functionality of nucleic acids from 3′,5′- to a less common 2′,5′-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conformational propensities for compact or more extended structures. The present study highlights the subtle balance of non-covalent forces at play in structural equilibrium of 2′,5′-linked RNA analogue, 3′-O-(2-methoxyethyl) substituted dodecamer *CG*CGAA*U*U*CG*CG, 3′-MOE-2′,5′-RNA, where all cytosines and uracils are methylated at C5. The NMR and UV spectroscopic studies have shown that 3′-MOE-2′,5′-RNA adopts both hairpin and duplex secondary structures, which are involved in a dynamic exchange that is slow on the NMR timescale and exhibits strand and salt concentration as well as pH dependence. Unusual effect of pH over a narrow physiological range is observed for imino proton resonances with exchange broadening observed at lower pH and relatively sharp lines observed at higher pH. The solution structure of 3′-MOE-2′,5′-RNA hairpin displays a unique and well-defined loop, which is stabilized by Watson–Crick A5·*U8 base pair and by n → π* stacking interactions of O4′ lone-pair electrons of A6 and *U8 with aromatic rings of A5 and *U7, respectively. In contrast, the stem region of 3′-MOE-2′,5′-RNA hairpin is more flexible. Our data highlight the important feature of backbone modifications that can have pronounced effects on interstrand association of nucleic acids. PMID:15788747

  4. Responsive hairpin DNA aptamer switch to program the strand displacement reaction for the enhanced electrochemical assay of ATP.

    PubMed

    Wang, Li; Fang, Li; Liu, Shufeng

    2015-09-07

    A responsive hairpin DNA aptamer switch was ingeniously designed for enzyme-free, sensitive and selective electrochemical detection of ATP. It takes full advantage of the target-triggered liberation effect of the toehold region and the concomitant proximity effect with the branch-migration region to execute the toehold-mediated strand displacement reaction on the electrode surface.

  5. Microstructural evolution during thermal annealing of ice-Ih

    NASA Astrophysics Data System (ADS)

    Hidas, Károly; Tommasi, Andréa; Mainprice, David; Chauve, Thomas; Barou, Fabrice; Montagnat, Maurine

    2017-06-01

    We studied the evolution of the microstructure of ice-Ih during static recrystallization by stepwise annealing experiments. We alternated thermal annealing and electron backscatter diffraction (EBSD) analyses on polycrystalline columnar ice pre-deformed in uniaxial compression at temperature of -7 °C to macroscopic strains of 3.0-5.2. Annealing experiments were carried out at -5 °C and -2 °C up to a maximum of 3.25 days, typically in 5-6 steps. EBSD crystal orientation maps obtained after each annealing step permit the description of microstructural changes. Decrease in average intragranular misorientation at the sample scale and modification of the misorientation across subgrain boundaries provide evidence for recovery from the earliest stages of annealing. This initial evolution is similar for all studied samples irrespective of their initial strain or annealing temperature. After an incubation period ≥1.5 h, recovery is accompanied by recrystallization (nucleation and grain boundary migration). Grain growth proceeds at the expense of domains with high intragranular misorientations, consuming first the most misorientated parts of primary grains. Grain growth kinetics fits the parabolic growth law with grain growth exponents in the range of 2.4-4.0. Deformation-induced tilt boundaries and kink bands may slow down grain boundary migration. They are stable features during early stages of static recrystallization, only erased by normal growth, which starts after >24 h of annealing.

  6. Improvement on the electrical characteristics of Pd/HfO2/6H-SiC MIS capacitors using post deposition annealing and post metallization annealing

    NASA Astrophysics Data System (ADS)

    Esakky, Papanasam; Kailath, Binsu J.

    2017-08-01

    HfO2 as a gate dielectric enables high electric field operation of SiC MIS structure and as gas sensor HfO2/SiC capacitors offer higher sensitivity than SiO2/SiC capacitors. The issue of higher density of oxygen vacancies and associated higher leakage current necessitates better passivation of HfO2/SiC interface. Effect of post deposition annealing in N2O plasma and post metallization annealing in forming gas on the structural and electrical characteristics of Pd/HfO2/SiC MIS capacitors are reported in this work. N2O plasma annealing suppresses crystallization during high temperature annealing thereby improving the thermal stability and plasma annealing followed by rapid thermal annealing in N2 result in formation of Hf silicate at the HfO2/SiC interface resulting in order of magnitude lower density of interface states and gate leakage current. Post metallization annealing in forming gas for 40 min reduces interface state density by two orders while gate leakage current density is reduced by thrice. Post deposition annealing in N2O plasma and post metallization annealing in forming gas are observed to be effective passivation techniques improving the electrical characteristics of HfO2/SiC capacitors.

  7. You're standing on it! Coal-tar-based pavement sealcoat and environmental and human health

    USGS Publications Warehouse

    Mahler, Barbara J.; Van Metre, Peter C.

    2013-01-01

    Results from a new study by researchers from Baylor University and the USGS indicate that living adjacent to a coal-tar-sealed pavement is associated with significant increases in estimated excess lifetime cancer risk, and that much of the increased risk occurs during early childhood.

  8. Quantum annealing of the traveling-salesman problem.

    PubMed

    Martonák, Roman; Santoro, Giuseppe E; Tosatti, Erio

    2004-11-01

    We propose a path-integral Monte Carlo quantum annealing scheme for the symmetric traveling-salesman problem, based on a highly constrained Ising-like representation, and we compare its performance against standard thermal simulated annealing. The Monte Carlo moves implemented are standard, and consist in restructuring a tour by exchanging two links (two-opt moves). The quantum annealing scheme, even with a drastically simple form of kinetic energy, appears definitely superior to the classical one, when tested on a 1002-city instance of the standard TSPLIB.

  9. Deformation and annealing study of Nicraly

    NASA Technical Reports Server (NTRS)

    Trela, D. M.; Ebert, L. J.

    1975-01-01

    Extensive experiments were carried out on the ODS alloy Nicraly, (an alloy prepared by mechanical alloying and consolidating a powder blend consisting of 16% chromium, 4% aluminum, 2-3% yttria, balance nickel), in efforts to develop methods of controlling the grain size and grain shape of the material. The experiments fell into two general categories: variations in the annealing parameters using the as-extruded material as it was received, and various thermomechanical processing schedules (various combinations of cold work and annealing). Success was achieved in gaining grain size and grain shape control by annealing of the as-extruded material. By proper selection of annealing temperature and cooling rates, the grain size of the as-received material was increased almost two orders of magnitude (from an average grain dimension of 0.023 mm to 1.668 mm) while the aspect ratio was increased by some 50% (from 20:1 to 30:1). No success was achieved in gaining significant control of the grain size and shape of the material by thermo-mechanical processing.

  10. Deterministic quantum annealing expectation-maximization algorithm

    NASA Astrophysics Data System (ADS)

    Miyahara, Hideyuki; Tsumura, Koji; Sughiyama, Yuki

    2017-11-01

    Maximum likelihood estimation (MLE) is one of the most important methods in machine learning, and the expectation-maximization (EM) algorithm is often used to obtain maximum likelihood estimates. However, EM heavily depends on initial configurations and fails to find the global optimum. On the other hand, in the field of physics, quantum annealing (QA) was proposed as a novel optimization approach. Motivated by QA, we propose a quantum annealing extension of EM, which we call the deterministic quantum annealing expectation-maximization (DQAEM) algorithm. We also discuss its advantage in terms of the path integral formulation. Furthermore, by employing numerical simulations, we illustrate how DQAEM works in MLE and show that DQAEM moderate the problem of local optima in EM.

  11. A randomized, investigator-masked clinical evaluation of the efficacy and safety of clobetasol propionate 0.05% shampoo and tar blend 1% shampoo in the treatment of moderate to severe scalp psoriasis.

    PubMed

    Griffiths, Christopher E M; Finlay, Andrew Y; Fleming, Colin J; Barker, Jonathan N W N; Mizzi, Fabienne; Arsonnaud, Stéphanie

    2006-01-01

    The clinical benefit of currently available tar blend shampoos for the treatment of scalp psoriasis is restricted due to their limited efficacy, low cosmetic appeal and potential for carcinogenicity. This 4-week multicentre, randomized, parallel-group, investigator-masked study included 162 subjects and aimed to compare the efficacy, safety and cosmetic acceptability of clobetasol propionate 0.05% shampoo versus a currently marketed tar blend 1% shampoo in subjects with moderate to severe scalp psoriasis. Clobetasol propionate shampoo was superior to tar blend shampoo with respect to all efficacy variables tested (p<0.001): Total and Global Severity Score; erythema; plaque thickening; desquamation; pruritus; total scalp area involved; and the subject's global assessment of clinical improvement. Both treatments were safe and well-tolerated. Furthermore, more subjects indicated that clobetasol propionate shampoo was more cosmetically acceptable than tar blend shampoo. Clobetasol propionate 0.05% shampoo is a good alternative to tar blend shampoo in the treatment of moderate to severe scalp psoriasis.

  12. TAR-independent transactivation by Tat in cells derived from the CNS: a novel mechanism of HIV-1 gene regulation.

    PubMed Central

    Taylor, J P; Pomerantz, R; Bagasra, O; Chowdhury, M; Rappaport, J; Khalili, K; Amini, S

    1992-01-01

    The Tat protein of human immunodeficiency virus type 1 (HIV-1) is essential for productive infection and is a potential target for antiviral therapy. Tat, a potent activator of HIV-1 gene expression, serves to greatly increase the rate of transcription directed by the viral promoter. This induction, which seems to be an important component in the progression of acquired immune deficiency syndrome (AIDS), may be due to increased transcriptional initiation, increased transcriptional elongation, or a combination of these processes. Much attention has been focused on the interaction of Tat with a specific RNA target termed TAR (transactivation responsive) which is present in the leader sequence of all HIV-1 mRNAs. This interaction is believed to be an important component of the mechanism of transactivation. In this report we demonstrate that in certain CNS-derived cells Tat is capable of activating HIV-1 through a TAR-independent pathway. A Tat-responsive element is found upstream within the viral promoter that in glial-derived cell lines allows transactivation in the absence of TAR. Deletion mapping and hybrid promoter constructs demonstrate that the newly identified Tat-responsive element corresponds to a sequence within the viral long terminal repeat (LTR) previously identified as the HIV-1 enhancer, or NF-kappa B domain. DNA band-shift analysis reveals NF-kappa B binding activity in glial cells that differs from that present in T lymphoid cells. Further, we observe that TAR-deleted mutants of HIV-1 demonstrate normal late gene expression in glial cells as evidenced by syncytia formation and production of viral p24 antigen.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:1505523

  13. Simulated annealing with probabilistic analysis for solving traveling salesman problems

    NASA Astrophysics Data System (ADS)

    Hong, Pei-Yee; Lim, Yai-Fung; Ramli, Razamin; Khalid, Ruzelan

    2013-09-01

    Simulated Annealing (SA) is a widely used meta-heuristic that was inspired from the annealing process of recrystallization of metals. Therefore, the efficiency of SA is highly affected by the annealing schedule. As a result, in this paper, we presented an empirical work to provide a comparable annealing schedule to solve symmetric traveling salesman problems (TSP). Randomized complete block design is also used in this study. The results show that different parameters do affect the efficiency of SA and thus, we propose the best found annealing schedule based on the Post Hoc test. SA was tested on seven selected benchmarked problems of symmetric TSP with the proposed annealing schedule. The performance of SA was evaluated empirically alongside with benchmark solutions and simple analysis to validate the quality of solutions. Computational results show that the proposed annealing schedule provides a good quality of solution.

  14. G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.

    PubMed

    Kaplan, Oktay I; Berber, Burak; Hekim, Nezih; Doluca, Osman

    2016-11-02

    Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Short hairpin RNA interference therapy for ischemic heart disease

    PubMed Central

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

    2013-01-01

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

  16. Burst annealing of high temperature GaAs solar cells

    NASA Technical Reports Server (NTRS)

    Brothers, P. R.; Horne, W. E.

    1991-01-01

    One of the major limitations of solar cells in space power systems is their vulnerability to radiation damage. One solution to this problem is to periodically heat the cells to anneal the radiation damage. Annealing was demonstrated with silicon cells. The obstacle to annealing of GaAs cells was their susceptibility to thermal damage at the temperatures required to completely anneal the radiation damage. GaAs cells with high temperature contacts and encapsulation were developed. The cells tested are designed for concentrator use at 30 suns AMO. The circular active area is 2.5 mm in diameter for an area of 0.05 sq cm. Typical one sun AMO efficiency of these cells is over 18 percent. The cells were demonstrated to be resistant to damage after thermal excursions in excess of 600 C. This high temperature tolerance should allow these cells to survive the annealing of radiation damage. A limited set of experiments were devised to investigate the feasibility of annealing these high temperature cells. The effect of repeated cycles of electron and proton irradiation was tested. The damage mechanisms were analyzed. Limitations in annealing recovery suggested improvements in cell design for more complete recovery. These preliminary experiments also indicate the need for further study to isolate damage mechanisms. The primary objective of the experiments was to demonstrate and quantify the annealing behavior of high temperature GaAs cells. Secondary objectives were to measure the radiation degradation and to determine the effect of repeated irradiation and anneal cycles.

  17. Yeast Pif1 Accelerates Annealing of Complementary DNA Strands

    PubMed Central

    2015-01-01

    Pif1 is a helicase involved in the maintenance of nuclear and mitochondrial genomes in eukaryotes. Here we report a new activity of Saccharomyces cerevisiae Pif1, annealing of complementary DNA strands. We identified preferred substrates for annealing as those that generate a duplex product with a single-stranded overhang relative to a blunt end duplex. Importantly, we show that Pif1 can anneal DNA in the presence of ATP and Mg2+. Pif1-mediated annealing also occurs in the presence of single-stranded DNA binding proteins. Additionally, we show that partial duplex substrates with 3′-single-stranded overhangs such as those generated during double-strand break repair can be annealed by Pif1. PMID:25393406

  18. Yeast Pif1 accelerates annealing of complementary DNA strands.

    PubMed

    Ramanagoudr-Bhojappa, Ramanagouda; Byrd, Alicia K; Dahl, Christopher; Raney, Kevin D

    2014-12-09

    Pif1 is a helicase involved in the maintenance of nuclear and mitochondrial genomes in eukaryotes. Here we report a new activity of Saccharomyces cerevisiae Pif1, annealing of complementary DNA strands. We identified preferred substrates for annealing as those that generate a duplex product with a single-stranded overhang relative to a blunt end duplex. Importantly, we show that Pif1 can anneal DNA in the presence of ATP and Mg(2+). Pif1-mediated annealing also occurs in the presence of single-stranded DNA binding proteins. Additionally, we show that partial duplex substrates with 3'-single-stranded overhangs such as those generated during double-strand break repair can be annealed by Pif1.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23605042

  20. Improved perovskite phototransistor prepared using multi-step annealing method

    NASA Astrophysics Data System (ADS)

    Cao, Mingxuan; Zhang, Yating; Yu, Yu; Yao, Jianquan

    2018-02-01

    Organic-inorganic hybrid perovskites with good intrinsic physical properties have received substantial interest for solar cell and optoelectronic applications. However, perovskite film always suffers from a low carrier mobility due to its structural imperfection including sharp grain boundaries and pinholes, restricting their device performance and application potential. Here we demonstrate a straightforward strategy based on multi-step annealing process to improve the performance of perovskite photodetector. Annealing temperature and duration greatly affects the surface morphology and optoelectrical properties of perovskites which determines the device property of phototransistor. The perovskite films treated with multi-step annealing method tend to form highly uniform, well-crystallized and high surface coverage perovskite film, which exhibit stronger ultraviolet-visible absorption and photoluminescence spectrum compare to the perovskites prepared by conventional one-step annealing process. The field-effect mobilities of perovskite photodetector treated by one-step direct annealing method shows mobility as 0.121 (0.062) cm2V-1s-1 for holes (electrons), which increases to 1.01 (0.54) cm2V-1s-1 for that treated with muti-step slow annealing method. Moreover, the perovskite phototransistors exhibit a fast photoresponse speed of 78 μs. In general, this work focuses on the influence of annealing methods on perovskite phototransistor, instead of obtains best parameters of it. These findings prove that Multi-step annealing methods is feasible to prepared high performance based photodetector.

  1. Rebound of a coal tar creosote plume following partial source zone treatment with permanganate.

    PubMed

    Thomson, N R; Fraser, M J; Lamarche, C; Barker, J F; Forsey, S P

    2008-11-14

    The long-term management of dissolved plumes originating from a coal tar creosote source is a technical challenge. For some sites stabilization of the source may be the best practical solution to decrease the contaminant mass loading to the plume and associated off-site migration. At the bench-scale, the deposition of manganese oxides, a permanganate reaction byproduct, has been shown to cause pore plugging and the formation of a manganese oxide layer adjacent to the non-aqueous phase liquid creosote which reduces post-treatment mass transfer and hence mass loading from the source. The objective of this study was to investigate the potential of partial permanganate treatment to reduce the ability of a coal tar creosote source zone to generate a multi-component plume at the pilot-scale over both the short-term (weeks to months) and the long-term (years) at a site where there is >10 years of comprehensive synoptic plume baseline data available. A series of preliminary bench-scale experiments were conducted to support this pilot-scale investigation. The results from the bench-scale experiments indicated that if sufficient mass removal of the reactive compounds is achieved then the effective solubility, aqueous concentration and rate of mass removal of the more abundant non-reactive coal tar creosote compounds such as biphenyl and dibenzofuran can be increased. Manganese oxide formation and deposition caused an order-of-magnitude decrease in hydraulic conductivity. Approximately 125 kg of permanganate were delivered into the pilot-scale source zone over 35 days, and based on mass balance estimates <10% of the initial reactive coal tar creosote mass in the source zone was oxidized. Mass discharge estimated at a down-gradient fence line indicated >35% reduction for all monitored compounds except for biphenyl, dibenzofuran and fluoranthene 150 days after treatment, which is consistent with the bench-scale experimental results. Pre- and post-treatment soil core data

  2. Evaluation of ocular irritancy of coal-tar dyes used in cosmetics employing reconstructed human cornea-like epithelium and short time exposure tests.

    PubMed

    Lee, Miri; Nam, Ki Taek; Kim, Jungah; Lim, Song E; Yeon, Sang Hyeon; Lee, Buhyun; Lee, Joo Young; Lim, Kyung-Min

    2017-10-01

    Coal-tar dyes in cosmetics may elicit adverse effects in the skin and eyes. Countries, like the US, have banned the use of coal-tar dyes in cosmetics for the eye area due to the potential for ocular irritation. We evaluated the eye irritation potential of 15 coal-tar dyes permitted as cosmetic ingredients in reconstructed human cornea-like epithelium (RhCEs [EpiOcular™ and MCTT HCE™]) tests and the short time exposure (STE) test. Eosin YS, phloxine B, tetrachlorotetrabromofluorescein, and tetrabromofluorescein were identified as irritants in RhCEs; dibromofluorescein and uranine yielded discrepant results. STE enabled further classification in accordance with the UN Globally Harmonized System of Classification and Labelling of Chemicals, as follows: eosin YS as Cat 2; phloxine B, Cat 1; and tetrachlorotetrabromofluorescein and tetrabromofluorescein, Cat 1/2. STE indicated dibromofluorescein (irritant in EpiOcular™) and uranine (irritant in MCTT HCE™) as No Cat, resulting in the classification of "No prediction can be made." based on bottom-up approach with each model. These results demonstrated that in vitro eye irritation tests can be utilized to evaluate the potential ocular irritancy of cosmetic ingredients and provide significant evidence with which to determine whether precautions should be given for the use of coal-tar dyes in cosmetics or other substances applied to the eye area. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. High-temperature annealing of graphite: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Petersen, Andrew; Gillette, Victor

    2018-05-01

    A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

  4. Smokers' sensory beliefs mediate the relation between smoking a light/low tar cigarette and perceptions of harm.

    PubMed

    Elton-Marshall, Tara; Fong, Geoffrey T; Yong, Hua-Hie; Borland, Ron; Xu, Steve Shaowei; Quah, Anne C K; Feng, Guoze; Jiang, Yuan

    2015-11-01

    The sensory belief that 'light/low tar' cigarettes are smoother can also influence the belief that 'light/low tar' cigarettes are less harmful. However, the 'light' concept is one of several factors influencing beliefs. No studies have examined the impact of the sensory belief about one's own brand of cigarettes on perceptions of harm. The current study examines whether a smoker's sensory belief that their brand is smoother is associated with the belief that their brand is less harmful and whether sensory beliefs mediate the relation between smoking a 'light/low tar' cigarette and relative perceptions of harm among smokers in China. Data are from 5209 smokers who were recruited using a stratified multistage sampling design and participated in Wave 3 of the International Tobacco Control (ITC) China Survey, a face-to-face survey of adult smokers and non-smokers in seven cities. Smokers who agreed that their brand of cigarettes was smoother were significantly more likely to say that their brand of cigarettes was less harmful (p<0.001, OR=6.86, 95% CI 5.64 to 8.33). Mediational analyses using the bootstrapping procedure indicated that both the direct effect of 'light/low tar' cigarette smokers on the belief that their cigarettes are less harmful (b=0.24, bootstrapped bias corrected 95% CI 0.13 to 0.34, p<0.001) and the indirect effect via their belief that their cigarettes are smoother were significant (b=0.32, bootstrapped bias-corrected 95% CI 0.28 to 0.37, p<0.001), suggesting that the mediation was partial. These results demonstrate the importance of implementing tobacco control policies that address the impact that cigarette design and marketing can have in capitalising on the smoker's natural associations between smoother sensations and lowered perceptions of harm. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  5. Optimization Via Open System Quantum Annealing

    DTIC Science & Technology

    2016-01-07

    Daniel A. Lidar. Experimental signature of programmable quantum annealing, Nature Communications , (06 2013): 0. doi: 10.1038/ncomms3067 T. F...Demonstrated error correction effectiveness. • Demonstrated quantum annealing correction on antiferromagnetic chains, with substantial fidelity gains...Rev. A 91, 022309 (2015). 3. A. Kalev and I. Hen, “ Fidelity -optimized quantum state estimation”, New Journal of Physics 17 092008 (2015). 4. I

  6. Benefits of Intercritical Annealing in Quenching and Partitioning Steel

    NASA Astrophysics Data System (ADS)

    Wang, X.; Liu, L.; Liu, R. D.; Huang, M. X.

    2018-03-01

    Compared to the quenching and partitioning (Q&P) steel produced by full austenization annealing, the Q&P steel produced by the intercritical annealing shows a similar ultimate tensile stress but a larger tensile ductility. This property is attributable to the higher volume fraction and the better mechanical stability of the retained austenite after the intercritical annealing. Moreover, intercritical annealing produces more ferrite and fewer martensite phases in the microstructure, making an additional contribution to a higher work hardening rate and therefore a better tensile ductility.

  7. Tar sand extraction by steam stimulation and steam drive: measurement of physical properties

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Linberg, W.R.

    The measurement of the following thermophysical properties of Utah tar sands is in progress: thermal conductivity, specific heat relative permeability, and viscosity (of the recovered bitumen). During the report period (October 1, 1978 to November 1, 1979), experimental procedures have been developed and a basic data set has been measured. Additionally, standard core analysis has been performed for four drill sites in the Asphalt Ridge, Utah area.

  8. [Effects of different annealing conditions on the photoluminescence of nanoporous alumina film].

    PubMed

    Xie, Ning; Ma, Kai-Di; Shen, Yi-Fan; Wang, Qian

    2013-12-01

    The nanoporous alumina films were prepared by two-step anodic oxidation in 0.5 mol L-1 oxalic acid electrolyte at 40 V. Photoluminescence (PL) of nanoporous alumina films was investigated under different annealing atmosphere and different temperature. The authors got three results about the PL measurements. In the same annealing atmosphere, when the annealling temperature T< or =600 degreeC, the intensity of the PL peak increases with elevated annealing temperature and reaches a maximum value at 500 degreeC, but the intensity decreases with a further increase in the annealing temperature, and the PL peak intensity of samples increases with the increase in the annealing temperature when the annealling temperature T> or =800 degreeC. In the different annealling atmosphere, the change in the photoluminescence peak position for nanoporous alumina films with the increase in the annealing temperature is different: With the increase in the annealling temperature, the PL peak position for the samples annealed in air atmosphere is blue shifted, while the PL peak position for the samples annealed in vacuum atmosphere will not change. The PL spectra of nanoporous alumina films annealed at 1100 degreeC in air atmosphere can be de-convoluted by three Gaussian components at an excitation wavelength of 350 nm, with bands centered at 387, 410 and 439 nm, respectively. These results suggest that there might be three luminescence centers for the PL of annealed alumina films. At the same annealling temperature, the PL peak intensity of samples annealed in air atmosphere is stronger than that annealed in the vacuum. Based on the experimental results and the X-ray dispersive energy spectrum (EDS) combined with infrared reflect spectra, the luminescence mechanisms of nanoporous alumina films are discussed. There are three luminescence centers in the annealed nanoporous alumina films, which originate from the F center, F+ center and the center associated with the oxalic impurities. The

  9. A novel electrochemical cytosensor for selective and highly sensitive detection of cancer cells using binding-induced dual catalytic hairpin assembly.

    PubMed

    Zhang, Ye; Luo, Shihua; Situ, Bo; Chai, Zhixin; Li, Bo; Liu, Jumei; Zheng, Lei

    2018-04-15

    Rare cancer cells in body fluid could be useful biomarkers for noninvasive diagnosis of cancer. However, detection of these rare cells is currently challenging. In this work, a binding-induced dual catalytic hairpin assembly (DCHA) electrochemical cytosensor was developed for highly selective and sensitive detection of cancer cells. The fuel probe, released by hybridization between the capture probe and catalytic hairpin assembly (CHA) products of target cell-responsive reaction, initiated dual CHA recycling, leading to multiple CHA products. Furthermore, the hybridization between fuel probe and capture probe decreased non-specific CHA products, improving the signal-to-noise ratio and detection sensitivity. Under the optimal conditions, the developed cytosensor was able to detect cells down to 30 cells mL -1 (S/N = 3) with a linear range from 50 to 100,000 cells mL -1 and was capable of distinguishing target cells from normal cells in clinical blood samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. LiDAR-Derived Flood-Inundation Maps for Real-Time Flood-Mapping Applications, Tar River Basin, North Carolina

    USGS Publications Warehouse

    Bales, Jerad D.; Wagner, Chad R.; Tighe, Kirsten C.; Terziotti, Silvia

    2007-01-01

    Flood-inundation maps were created for selected streamgage sites in the North Carolina Tar River basin. Light detection and ranging (LiDAR) data with a vertical accuracy of about 20 centimeters, provided by the Floodplain Mapping Information System of the North Carolina Floodplain Mapping Program, were processed to produce topographic data for the inundation maps. Bare-earth mass point LiDAR data were reprocessed into a digital elevation model with regularly spaced 1.5-meter by 1.5-meter cells. A tool was developed as part of this project to connect flow paths, or streams, that were inappropriately disconnected in the digital elevation model by such features as a bridge or road crossing. The Hydraulic Engineering Center-River Analysis System (HEC-RAS) model, developed by the U.S. Army Corps of Engineers, was used for hydraulic modeling at each of the study sites. Eleven individual hydraulic models were developed for the Tar River basin sites. Seven models were developed for reaches with a single gage, and four models were developed for reaches of the Tar River main stem that receive flow from major gaged tributaries, or reaches in which multiple gages were near one another. Combined, the Tar River hydraulic models included 272 kilometers of streams in the basin, including about 162 kilometers on the Tar River main stem. The hydraulic models were calibrated to the most current stage-discharge relations at 11 long-term streamgages where rating curves were available. Medium- to high-flow discharge measurements were made at some of the sites without rating curves, and high-water marks from Hurricanes Fran and Floyd were available for high-stage calibration. Simulated rating curves matched measured curves over the full range of flows. Differences between measured and simulated water levels for a specified flow were no more than 0.44 meter and typically were less. The calibrated models were used to generate a set of water-surface profiles for each of the 11 modeled

  11. Characterisation of dense non-aqueous phase liquids of coal tar using comprehensive two-dimensional gas chromatography coupled with time of flight mass spectrometry.

    NASA Astrophysics Data System (ADS)

    Gauchotte-Lindsay, Caroline; McGregor, Laura; Richards, Phil; Kerr, Stephanie; Glenn, Aliyssa; Thomas, Russell; Kalin, Robert

    2013-04-01

    Comprehensive two-dimensional gas chromatography (GCxGC) is a recently developed analytical technique in which two capillary columns with different stationary phases are placed in series enabling planar resolution of the analytes. The resolution power of GCxGC is one order of magnitude higher than that of one dimension gas chromatography. Because of its high resolution capacity, the use of GCxGC for complex environmental samples such as crude oils, petroleum derivatives and polychlorinated biphenyls mixtures has rapidly grown in recent years. We developed a one-step method for the forensic analysis of coal tar dense non-aqueous phase liquids (DNAPLs) from former manufactured gas plant (FMGP) sites. Coal tar is the by-product of the gasification of coal for heating and lighting and it is composed of thousands of organic and inorganic compounds. Before the boom of natural gases and oils, most towns and cities had one or several manufactured gas plants that have, in many cases, left a devastating environmental print due to coal tar contamination. The fate of coal tar DNAPLs, which can persist in the environment for more than a hundred years, is therefore of crucial interest. The presented analytical method consists of a unique clean-up/ extraction stage by pressurized liquid extraction and a single analysis of its organic chemical composition using GCxGC coupled with time of flight mass spectrometry (TOFMS). The chemical fingerprinting is further improved by derivatisation by N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) of the tar compounds containing -OH functions such as alcohols and carboxylic acids. We present here how, using the logical order of elution in GCxGC-TOFMS system, 1) the identification of never before observed -OH containing compounds is possible and 2) the isomeric selectivity of an oxidation reaction on a DNAPL sample can be revealed. Using samples collected at various FMGP sites, we demonstrate how this GCxGC method enables the simultaneous

  12. films on silicon at different annealing temperatures

    NASA Astrophysics Data System (ADS)

    Zhao, Yan; Zhou, Chunlan; Zhang, Xiang; Zhang, Peng; Dou, Yanan; Wang, Wenjing; Cao, Xingzhong; Wang, Baoyi; Tang, Yehua; Zhou, Su

    2013-03-01

    Thermal atomic layer-deposited (ALD) aluminum oxide (Al2O3) acquires high negative fixed charge density ( Q f) and sufficiently low interface trap density after annealing, which enables excellent surface passivation for crystalline silicon. Q f can be controlled by varying the annealing temperatures. In this study, the effect of the annealing temperature of thermal ALD Al2O3 films on p-type Czochralski silicon wafers was investigated. Corona charging measurements revealed that the Q f obtained at 300°C did not significantly affect passivation. The interface-trapping density markedly increased at high annealing temperature (>600°C) and degraded the surface passivation even at a high Q f. Negatively charged or neutral vacancies were found in the samples annealed at 300°C, 500°C, and 750°C using positron annihilation techniques. The Al defect density in the bulk film and the vacancy density near the SiO x /Si interface region decreased with increased temperature. Measurement results of Q f proved that the Al vacancy of the bulk film may not be related to Q f. The defect density in the SiO x region affected the chemical passivation, but other factors may dominantly influence chemical passivation at 750°C.

  13. False promises: the tobacco industry, "low tar" cigarettes, and older smokers.

    PubMed

    Cataldo, Janine K; Malone, Ruth E

    2008-09-01

    To investigate the role of the tobacco industry in marketing to and sustaining tobacco addiction among older smokers and aging baby boomers, We performed archival searches of electronic archives of internal tobacco company documents using a snowball sampling approach. Analysis was done using iterative and comparative review of documents, classification by themes, and a hermeneutic interpretive approach to develop a case study. Based on extensive marketing research, tobacco companies aggressively targeted older smokers and sought to prevent them from quitting. Innovative marketing approaches were used. "Low tar" cigarettes were developed in response to the health concerns of older smokers, despite industry knowledge that such products had no health advantage and did not help smokers quit. Tobacco industry activities influence the context of cessation for older smokers in several ways. Through marketing "low tar" or "light" cigarettes to older smokers "at risk" of quitting, the industry contributes to the illusion that such cigarettes are safer, although "light" cigarettes may make it harder for addicted smokers to quit. Through targeted mailings of coupons and incentives, the industry discourages older smokers from quitting. Through rhetoric aimed at convincing addicted smokers that they alone are responsible for their smoking, the industry contributes to self-blame, a documented barrier to cessation. Educating practitioners, older smokers, and families about the tobacco industry's influence may decrease the tendency to "blame the victim," thereby enhancing the likelihood of older adults receiving tobacco addiction treatment. Comprehensive tobacco control measures must include a focus on older smokers.

  14. Annealed CVD molybdenum thin film surface

    DOEpatents

    Carver, Gary E.; Seraphin, Bernhard O.

    1984-01-01

    Molybdenum thin films deposited by pyrolytic decomposition of Mo(CO).sub.6 attain, after anneal in a reducing atmosphere at temperatures greater than 700.degree. C., infrared reflectance values greater than reflectance of supersmooth bulk molybdenum. Black molybdenum films deposited under oxidizing conditions and annealed, when covered with an anti-reflecting coating, approach the ideal solar collector characteristic of visible light absorber and infrared energy reflector.

  15. Preparation and Thermal Characterization of Annealed Gold Coated Porous Silicon

    PubMed Central

    Behzad, Kasra; Mat Yunus, Wan Mahmood; Talib, Zainal Abidin; Zakaria, Azmi; Bahrami, Afarin

    2012-01-01

    Porous silicon (PSi) layers were formed on a p-type Si wafer. Six samples were anodised electrically with a 30 mA/cm2 fixed current density for different etching times. The samples were coated with a 50–60 nm gold layer and annealed at different temperatures under Ar flow. The morphology of the layers, before and after annealing, formed by this method was investigated by scanning electron microscopy (SEM). Photoacoustic spectroscopy (PAS) measurements were carried out to measure the thermal diffusivity (TD) of the PSi and Au/PSi samples. For the Au/PSi samples, the thermal diffusivity was measured before and after annealing to study the effect of annealing. Also to study the aging effect, a comparison was made between freshly annealed samples and samples 30 days after annealing. PMID:28817037

  16. Preparation and Thermal Characterization of Annealed Gold Coated Porous Silicon.

    PubMed

    Behzad, Kasra; Mat Yunus, Wan Mahmood; Talib, Zainal Abidin; Zakaria, Azmi; Bahrami, Afarin

    2012-01-16

    Porous silicon (PSi) layers were formed on a p-type Si wafer. Six samples were anodised electrically with a 30 mA/cm² fixed current density for different etching times. The samples were coated with a 50-60 nm gold layer and annealed at different temperatures under Ar flow. The morphology of the layers, before and after annealing, formed by this method was investigated by scanning electron microscopy (SEM). Photoacoustic spectroscopy (PAS) measurements were carried out to measure the thermal diffusivity (TD) of the PSi and Au/PSi samples. For the Au/PSi samples, the thermal diffusivity was measured before and after annealing to study the effect of annealing. Also to study the aging effect, a comparison was made between freshly annealed samples and samples 30 days after annealing.

  17. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]^{+} and [YGPAA+H]^{+} Ions: a Stereochemical "twist" on the β-HAIRPIN Turn

    NASA Astrophysics Data System (ADS)

    DeBlase, Andrew F.; Harrilal, Christopher P.; Lawler, John T.; Burke, Nicole L.; McLuckey, Scott A.; Zwier, Timothy S.

    2017-06-01

    Incorporation of the unnatural D-proline (^{D}P) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of β-hairpin loops because natural sequences are often unstructured in solution. Using conformation-specific IR and UV spectroscopy of cold (10 K) gas-phase ions, we probe the inherent conformational preferences of the ^{D}P and ^{L}P diastereomers in the protonated peptide [YAPAA+H]^{+}, where only intramolecular interactions are possible. Consistent with the solution phase studies, one of the conformers of [YADPAA+H]^{+} is folded into a charge-stabilized β-hairpin turn. However, a second predominant conformer family containing two sequential γ-turns is also identified, with similar energetic stability. A single conformational isomer of the ^{L}P diastereomer, [YALPAA+H]^{+}, is found and assigned to a structure that is not the anticipated "mirror image" β-turn. Instead, the ^{L}P stereo center promotes a cis alanine-proline amide bond. The assigned structures contain clues that the preference of the ^{D}P diastereomer to support a trans-amide bond and the proclivity of ^{L}P for a cis-amide bond is sterically driven and can be reversed by substituting glycine for alanine in position 2, forming [YGLPAA+H]^{+}. These results provide a basis for understanding the residue-specific and stereo-specific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of β-hairpin formation.

  18. Mineralization Of PAHs In Coal-Tar Impacted Aquifer Sediments And Associated Microbial Community Structure Investigated With FISH

    EPA Science Inventory

    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-detect...

  19. Effect of Annealing Processes on Cu-Zr Alloy Film for Copper Metallization

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Li, Fu-yin; Tang, Bin-han

    2017-12-01

    The effect of two different annealing processes on the microstructure and barrier-forming ability of Cu-Zr alloy films has been investigated. Cu-Zr alloy films were deposited directly onto SiO2/Si substrates via direct current magnetron sputtering and subsequently annealed by the vacuum annealing process (VAP) or rapid annealing process under argon atmosphere at temperatures 350°C, 450°C, and 550°C. Then, the microstructure, interface characteristics, and electrical properties of the samples were measured. After annealing, the samples showed a preferential (111) crystal orientation, independent of the annealing process. After two annealing methods, Zr aggregated at the Cu-Zr/SiO2 interface and no serious interdiffusion occurred between Cu and Si. The leakage current measurements revealed that the samples annealed by VAP show a higher reliability. According to the results, the vacuum annealing has better barrier performance than the rapid annealing when used for the fabrication of Cu-based interconnects.

  20. Population annealing simulations of a binary hard-sphere mixture

    NASA Astrophysics Data System (ADS)

    Callaham, Jared; Machta, Jonathan

    2017-06-01

    Population annealing is a sequential Monte Carlo scheme well suited to simulating equilibrium states of systems with rough free energy landscapes. Here we use population annealing to study a binary mixture of hard spheres. Population annealing is a parallel version of simulated annealing with an extra resampling step that ensures that a population of replicas of the system represents the equilibrium ensemble at every packing fraction in an annealing schedule. The algorithm and its equilibration properties are described, and results are presented for a glass-forming fluid composed of a 50/50 mixture of hard spheres with diameter ratio of 1.4:1. For this system, we obtain precise results for the equation of state in the glassy regime up to packing fractions φ ≈0.60 and study deviations from the Boublik-Mansoori-Carnahan-Starling-Leland equation of state. For higher packing fractions, the algorithm falls out of equilibrium and a free volume fit predicts jamming at packing fraction φ ≈0.667 . We conclude that population annealing is an effective tool for studying equilibrium glassy fluids and the jamming transition.