WorldWideScience

Sample records for stable hairpin structure

  1. Structure of a Stable G-Hairpin

    Czech Academy of Sciences Publication Activity Database

    Gajarský, M.; Zivkovic, M.L.; Stadlbauer, Petr; Pagano, B.; Fiala, R.; Amato, J.; Tomáška, L´.; Šponer, Jiří; Plavec, J.; Trantírek, L.

    2017-01-01

    Roč. 139, č. 10 (2017), s. 3591-3594 ISSN 0002-7863 R&D Projects: GA ČR GA13-28310S; GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : g-quadruplex structures * human telomeric dna * single-stranded- dna * g-triplex Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 13.858, year: 2016

  2. Structural modeling of DNA mini-hairpin molecules with various loop sequences

    Science.gov (United States)

    Nakamura, Shugo; Hirose, Hitoshi; Ikeguchi, Mitsunori; Shimizu, Kentaro

    1999-07-01

    We modeled the structures of DNA fragments dGC(GNA)GC (N = A, G, T, and C), which are known to form mini-hairpins, and dGC(GAC)GC and dGC(GAG)GC, which are known not to form mini-hairpins, by using global optimization of conformational energy. For all of the fragments, we obtained mini-hairpins which had similar backbone structures and positions of bases. The conformational energy differences between the energy-optimized structures were small. Our results suggest that the optimized energy values are not sufficient to discriminate which fragments form thermo-stable mini-hairpins and which do not.

  3. Folding of single-stranded DNA quadruplexes containing an autonomously stable mini-hairpin loop.

    Science.gov (United States)

    Balkwill, Graham D; Garner, Thomas P; Searle, Mark S

    2009-05-01

    The single-stranded DNA quadruplex motif TG(3)-L(1)-G(3)-L(2)-G(3)-L(3)-G(3)T (where L(1), L(2) and L(3) are the three loop sequences) was used as a template for probing the effects of the loop sequences on stability and folding topology. An autonomously stable mini-hairpin sequence (ACGTAGT) was inserted into the central loop (L(2)) of different sequences with intrinsic propensities to form either parallel or anti-parallel structures. Single nucleotides (T) at positions L(1) and L(3) strongly favour the formation of a parallel structure with the L(2) hairpin insert affecting stability in the same way as a T(7) loop. However, in the context of an anti-parallel quadruplex with T(3) loops in positions L(1) and L(3), the mini-hairpin in the central loop forms a stable structure which enhances the T(m) of the quadruplex by approximately 10 degrees C when compared with the T(7) insert. The CD and UV melting data show that base pairing interactions within the ACGTAGT hairpin loop sequence, when accommodated as a diagonal loop in an anti-parallel structure, can enhance stability and lead to novel quadruplex structures, adding complexity to the folding landscape and expanding the potential repertoire of sequences that are able to regulate gene expression in vivo.

  4. Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing.

    OpenAIRE

    Hirao, I; Nishimura, Y; Tagawa, Y; Watanabe, K; Miura, K

    1992-01-01

    A small DNA fragment having a characteristic sequence d(GCGAAAGC) has been shown to form an extraordinarily stable mini-hairpin structure and to have an unusually rapid mobility in polyacrylamide gel electrophoresis, even when containing 7M urea. Here, we have studied the stability of the various sequence variants of d(GCGAAAGC) and the corresponding RNA fragments. Many such sequence variants form stable mini-hairpins in a similar manner to the d(GCGAAAGC) sequence. The RNA fragment, r(GCGAAA...

  5. Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop.

    Science.gov (United States)

    Balkwill, Graham D; Garner, Thomas P; Williams, Huw E L; Searle, Mark S

    2009-02-06

    We describe the NMR structural characterisation of a bimolecular anti-parallel DNA quadruplex d(G(3)ACGTAGTG(3))(2) containing an autonomously stable mini-hairpin motif inserted within the diagonal loop. A folding topology is identified that is different from that observed for the analogous d(G(3)T(4)G(3))(2) dimer with the two structures differing in the relative orientation of the diagonal loops. This appears to reflect specific base stacking interactions at the quadruplex-duplex interface that are not present in the structure with the T(4)-loop sequence. A truncated version of the bimolecular quadruplex d(G(2)ACGTAGTG(2))(2), with only two core G-tetrads, is less stable and forms a heterogeneous mixture of three 2-fold symmetric quadruplexes with different loop arrangements. We demonstrate that the nature of the loop sequence, its ability to form autonomously stable structure, the relative stabilities of the hairpin loop and core quadruplex, and the ability to form favourable stacking interactions between these two motifs are important factors in controlling DNA G-quadruplex topology.

  6. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA...... structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

  7. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic......-DNA and DNA-DNA duplexes can be formed with these target hairpins, even when the melting temperatures for the resulting duplexes are up to 50 degrees C lower than that of the hairpin target. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary...

  8. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides.

    Directory of Open Access Journals (Sweden)

    Andrew C Gill

    Full Text Available 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

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

    Science.gov (United States)

    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

  10. Short hairpin-loop-structured oligodeoxynucleotides reduce HSV-1 replication

    Directory of Open Access Journals (Sweden)

    Heinrich Jochen

    2009-04-01

    Full Text Available Abstract The Herpes simplex virus (HSV is known as an infectious agent and widespread in the human population. The symptoms of HSV infections can range from mild to life threatening, especially in immune-compromised individuals. HSV infections are commonly treated with the guanosine analogue Aciclovir, but reports of resistance are increasing. Efforts are made to establish single-stranded antisense oligodeoxynucleotides (as and small interfering ribonucleic acids (siRNAs for antiviral treatment. Recently, another class of short interfering nucleic acids, partially double-stranded hairpin loop-structured 54 mer oligodeoxynucleotides (ODNs, was shown to allow hydrolysis of HIV RNA by binding to the viral RNA. This leads to a substrate for the viral RNase H. To assess the potential of such ODNs for inhibition of HSV-1 replication, five partially double-stranded ODNs were designed based on the sequences of known siRNAs against HSV-1 with antiviral activity. Three of them are directed against early and two against leaky late genes. Primary human lung fibroblasts, MRC-5, and African green monkey kidney cells, Vero, were transfected with ODNs and subsequently infected. The effect on HSV-1 replication was determined by analyzing the virus titer in cell culture supernatants by quantitative PCR and plaque assays. An inhibitory effect was observed with all five selected ODNs, with two cases showing statistical significance in both cell types. The observed effect was sequence-specific and dose dependent. In one case the ODN was more efficient than a previously described siRNA directed against the same target site in the mRNA of UL5, a component of the helicase/primase complex. HSV-1 virions and ODNs can be applied simultaneously without transfection reagent, but at a 50-fold higher concentration to Vero cells with similar efficiencies. The results underline the potential of partially double-stranded hairpin loop-structured ODNs as antiviral agents.

  11. Hairpin packet structure of a turbulent boundary layer in inclined wall-normal/spanwise planes

    Science.gov (United States)

    Lee, Jae Hwa; Sung, Hyung Jin

    2009-11-01

    Turbulent coherent structures associated with hairpin packet motions have been scrutinized using the instantaneous flow fields obtained from the direct numerical simulation (DNS) of a turbulent boundary layer (TBL). The Reynolds number based on the momentum thickness was varied in the range Reθ=890˜2560. This study focused on the hairpin packet motions in inclined wall-normal/spanwise planes. The hairpin vortex signature associated with the hairpin leg components in the vertical inclined plane consists of a counter-rotating vortex pair, upward and downward motions and a stagnation point induced by the Q2 and Q4 events. These hairpin signatures were observed in the instantaneous flow field, in the two-point correlations and in the conditionally averaged flow fields, respectively. We considered three inclined planes (45^o, 90^o, and 135^o) to investigate the spatial characteristics of the hairpin packet motions in the log and wake regions. The statistical flow fields showed that significantly different flow patterns are induced by the intersections of the three inclined planes with the hairpin packet motions.

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

    DEFF Research Database (Denmark)

    Franch, Oskar; Iacovelli, Federico; Falconi, Mattia

    2016-01-01

    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...

  13. How hairpin vortices emerge from exact invariant solutions

    Science.gov (United States)

    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.

  14. Hairpins under tension: RNA versus DNA.

    Science.gov (United States)

    Bercy, Mathilde; Bockelmann, Ulrich

    2015-11-16

    We use optical tweezers to control the folding and unfolding of individual DNA and RNA hairpins by force. Four hairpin molecules are studied in comparison: two DNA and two RNA ones. We observe that the conformational dynamics is slower for the RNA hairpins than for their DNA counterparts. Our results indicate that structures made of RNA are dynamically more stable. This difference might contribute to the fact that DNA and RNA play fundamentally different biological roles in spite of chemical similarity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Short-hairpin RNA-mediated stable silencing of Grb2 impairs cell growth and DNA synthesis

    International Nuclear Information System (INIS)

    Di Fulvio, Mauricio; Henkels, Karen M.; Gomez-Cambronero, Julian

    2007-01-01

    Grb2 is an SH2-SH3 protein adaptor responsible for linking growth factor receptors with intracellular signaling cascades. To study the role of Grb2 in cell growth, we have generated a new COS7 cell line (COS7 shGrb2 ), based on RNAi technology, as null mutations in mammalian Grb2 genes are lethal in early development. This novel cell line continuously expresses a short hairpin RNA that targets endogenous Grb2. Stable COS7 shGrb2 cells had the shGrb2 integrated into the genomic DNA and carried on SiL construct (made refractory to the shRNA-mediated interference), but not with an SH2-deficient mutant (R86K). Thus, a viable knock-down and rescue protocol has demonstrated that Grb2 is crucial for cell proliferation

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

    Science.gov (United States)

    Zargarian, Loussiné; Kanevsky, Igor; Bazzi, Ali; Boynard, Jonathan; Chaminade, Françoise; Fossé, Philippe; Mauffret, Olivier

    2009-01-01

    First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop–loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR). We show that the upper stem located between the apical and the internal loops is stable, but that the lower stem of mini-cTAR is unstable. The residues of the internal loop undergo slow motions at the NMR time-scale that are consistent with conformational exchange phenomena. In contrast, residues of the apical loop undergo fast motions. The lower stem is destabilized by the slow interconversion processes in the internal loop, and thus the internal loop is responsible for asymmetric destabilization of mini-cTAR. These findings are consistent with the functions of cTAR in first strand transfer: its apical loop is suitably exposed to interact with the apical loop of TAR RNA and its lower stem is significantly destabilized to facilitate the subsequent action of the nucleocapsid protein which promotes the annealing reaction. PMID:19417069

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

    OpenAIRE

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

    2009-01-01

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

  18. Structural characterization of a six-nucleotide RNA hairpin loop found in Escherichia coli, r(UUAAGU).

    Science.gov (United States)

    Zhang, H; Fountain, M A; Krugh, T R

    2001-08-21

    The binding region of the Escherichia coli S2 ribosomal protein contains a conserved UUAAGU hairpin loop. The structure of the hairpin formed by the oligomer r(GCGU4U5A6A7G8U9CGCA), which has an r(UUAAGU) hairpin loop, was determined by NMR and molecular modeling techniques as part of a study aimed at characterizing the structure and thermodynamics of RNA hairpin loops. Thermodynamic data obtained from melting curves for this RNA oligomer show that it forms a hairpin in solution with the following parameters: DeltaH degrees = -42.8 +/- 2.2 kcal/mol, DeltaS degrees = -127.6 +/- 6.5 eu, and DeltaG degrees (37) = -3.3 +/- 0.2 kcal/mol. Two-dimensional NOESY WATERGATE spectra show an NOE between U imino protons, which suggests that U4 and U9 form a hydrogen bonded U.U pair. The U5(H2') proton shows NOEs to both the A6(H8) proton and the A7(H8) proton, which is consistent with formation of a "U" turn between nucleotides U5 and A6. An NOE between the A7(H2) proton and the U9(H4') proton shows the proximity of the A7 base to the U9 sugar, which is consistent with the structure determined for the six-nucleotide loop. In addition to having a hydrogen-bonded U.U pair as the first mismatch and a U turn, the r(UUAAGU) loop has the G8 base protruding into the solvent. The solution structure of the r(UUAAGU) loop is essentially identical to the structure of an identical loop found in the crystal structure of the 30S ribosomal subunit where the guanine in the loop is involved in tertiary interactions with RNA bases from adjacent regions [Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V. (2000) Nature 407, 327-339]. The similarity of the solution and solid-state structures of this hairpin loop suggests that formation of this hairpin may facilitate folding of 16S RNA.

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

    Science.gov (United States)

    White, Neil A; Hoogstraten, Charles G

    2017-09-01

    The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Correlations between structure, material properties and bioproperties in self-assembled beta-hairpin peptide hydrogels.

    Science.gov (United States)

    Hule, Rohan A; Nagarkar, Radhika P; Altunbas, Aysegul; Ramay, Hassna R; Branco, Monica C; Schneider, Joel P; Pochan, Darrin J

    2008-01-01

    A de novo designed beta-hairpin peptide (MAX8), capable of undergoing intramolecular folding and consequent intermolecular self-assembly into a cytocompatible hydrogel, has been studied. A combination of small angle neutron scattering (SANS) and cryogenic-transmission electron microscopy (cryo-TEM) have been used to quantitatively investigate the MAX8 nanofibrillar hydrogel network morphology. A change in the peptide concentration from 0.5 to 2 wt% resulted in a denser fibrillar network as revealed via SANS by a change in the high q (q = (4 pi/lambda) x sin (theta/2), where lambda = wavelength of incident neutrons and theta = scattering angle) mass fractal exponent from 2.5 to 3 and by a decrease in the measured correlation length from 23 to 16 A. A slope of -4 in the USANS regime indicates well-defined gel microporosity, an important characteristic for cellular substrate applications. These changes, both at the network as well as the individual fibril lengthscales, can be directly visualized in situ by cryo-TEM. Fibrillar nanostructures and network properties are directly related to bulk hydrogel stiffness via oscillatory rheology. Preliminary cell viability and anchorage studies at varying hydrogel stiffness confirm cell adhesion at early stages of cell culture within the window of stiffness investigated. Knowledge of the precise structure spanning length scales from the nanoscale up to the microscale can help in the formation of future, specific structure-bioproperty relationships when studying in vitro and in vivo behavior of these new peptide scaffolds.

  1. Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides.

    Science.gov (United States)

    Oparin, Peter B; Mineev, Konstantin S; Dunaevsky, Yakov E; Arseniev, Alexander S; Belozersky, Mikhail A; Grishin, Eugene V; Egorov, Tsezi A; Vassilevski, Alexander A

    2012-08-15

    A new peptide trypsin inhibitor named BWI-2c was obtained from buckwheat (Fagopyrum esculentum) seeds by sequential affinity, ion exchange and reversed-phase chromatography. The peptide was sequenced and found to contain 41 amino acid residues, with four cysteine residues involved in two intramolecular disulfide bonds. Recombinant BWI-2c identical to the natural peptide was produced in Escherichia coli in a form of a cleavable fusion with thioredoxin. The 3D (three-dimensional) structure of the peptide in solution was determined by NMR spectroscopy, revealing two antiparallel α-helices stapled by disulfide bonds. Together with VhTI, a trypsin inhibitor from veronica (Veronica hederifolia), BWI-2c represents a new family of protease inhibitors with an unusual α-helical hairpin fold. The linker sequence between the helices represents the so-called trypsin inhibitory loop responsible for direct binding to the active site of the enzyme that cleaves BWI-2c at the functionally important residue Arg(19). The inhibition constant was determined for BWI-2c against trypsin (1.7×10(-1)0 M), and the peptide was tested on other enzymes, including those from various insect digestive systems, revealing high selectivity to trypsin-like proteases. Structural similarity shared by BWI-2c, VhTI and several other plant defence peptides leads to the acknowledgement of a new widespread family of plant peptides termed α-hairpinins.

  2. Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains.

    Science.gov (United States)

    Nguyen, Thanh H; Ballmann, Mónika Z; Do, Huyen T; Truong, Hai N; Benkő, Mária; Harrach, Balázs; van Raaij, Mark J

    2016-06-22

    Most adenoviruses recognize their host cells via an interaction of their fibre head domains with a primary receptor. The structural framework of adenovirus fibre heads is conserved between the different adenovirus genera for which crystal structures have been determined (Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus), but genus-specific differences have also been observed. The only known siadenovirus fibre head structure, that of turkey adenovirus 3 (TAdV-3), revealed a twisted beta-sandwich resembling the reovirus fibre head architecture more than that of other adenovirus fibre heads, plus a unique beta-hairpin embracing a neighbouring monomer. The TAdV-3 fibre head was shown to bind sialyllactose. Raptor adenovirus 1 (RAdV-1) fibre head was expressed, crystallized and its structure was solved and refined at 1.5 Å resolution. The structure could be solved by molecular replacement using the TAdV-3 fibre head structure as a search model, despite them sharing a sequence identity of only 19 %. Versions of both the RAdV-1 and TAdV-3 fibre heads with their beta-hairpin arm deleted were prepared and their stabilities were compared with the non-mutated proteins by a thermal unfolding assay. The structure of the RAdV-1 fibre head contains the same twisted ABCJ-GHID beta-sandwich and beta-hairpin arm as the TAdV-3 fibre head. However, while the predicted electro-potential surface charge of the TAdV-3 fibre head is mainly positive, the RAdV-1 fibre head shows positively and negatively charged patches and does not appear to bind sialyllactose. Deletion of the beta-hairpin arm does not affect the structure of the raptor adenovirus 1 fibre head and only affects the stability of the RAdV-1 and TAdV-3 fibre heads slightly. The high-resolution structure of RAdV-1 fibre head is the second known structure of a siadenovirus fibre head domain. The structure shows that the siadenovirus fibre head structure is conserved, but differences in the predicted surface charge

  3. Correlations between structure, material properties and bioproperties in self-assembled β-hairpin peptide hydrogels

    Science.gov (United States)

    Hule, Rohan A.; Nagarkar, Radhika P.; Altunbas, Aysegul; Ramay, Hassna R.; Branco, Monica C.; Schneider, Joel P.; Pochan, Darrin J.

    2009-01-01

    A de novo designed β-hairpin peptide (MAX8), capable of undergoing intramolecular folding and consequent intermolecular self-assembly into a cytocompatible hydrogel, has been studied. A combination of small angle neutron scattering (SANS) and cryogenic-transmission electron microscopy (cryo-TEM) have been used to quantitatively investigate the MAX8 nanofibrillar hydrogel network morphology. A change in the peptide concentration from 0.5 to 2 wt% resulted in a denser fibrillar network as revealed via SANS by a change in the high q (q = (4π/λ) × sin (θ/2), where λ = wavelength of incident neutrons and θ = scattering angle) mass fractal exponent from 2.5 to 3 and by a decrease in the measured correlation length from 23 to 16 A. Å slope of −4 in the USANS regime indicates well-defined gel microporosity, an important characteristic for cellular substrate applications. These changes, both at the network as well as the individual fibril lengthscales, can be directly visualized in situ by cryo-TEM. Fibrillar nanostructures and network properties are directly related to bulk hydrogel stiffness via oscillatory rheology. Preliminary cell viability and anchorage studies at varying hydrogel stiffness confirm cell adhesion at early stages of cell culture within the window of stiffness investigated. Knowledge of the precise structure spanning length scales from the nanoscale up to the microscale can help in the formation of future, specific structure-bioproperty relationships when studying in vitro and in vivo behavior of these new peptide scaffolds. PMID:19048999

  4. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2007-01-01

    -18 to extend perpendicular to the beta-hairpin plane. This bend was driven by a highly persistent hydrogen-bond between the polar peptide side-chain of TYR7 and the unshielded backbone carbonyl oxygen atom of GLY17. The H-bond formation relieves the unfavorable free energy of insertion of polar groups......All atom molecular dynamics simulations of the 18-residue beta-hairpin antimicrobial peptide protegrin-1 (PG-1, RGGRLCYCRRRFCVCVGR-NH(2)) in a fully hydrated dilauroylphosphatidylcholine (DLPC) lipid bilayer have been implemented. The goal of the reported work is to investigate the structure......-550]), and to delineate specific peptide-membrane interactions which are responsible for the peptide's membrane binding properties. A novel, previously unknown, "kick" shaped conformation of the peptide was detected, where a bend at the C-terminal beta-strand of the peptide caused the peptide backbone at residues 16...

  5. Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms

    DEFF Research Database (Denmark)

    Galli, Andrea; Lai, Alessia; Corvasce, Stefano

    2008-01-01

    throughout the genome, leading to viral recombination. Some recombination hotspots have been identified and found to correlate with RNA structure or sequence features. The aim of this study was to evaluate the presence of recombination hotspots in the pol gene of HIV-1 and to assess their correlation......Recombination is recognized as a primary force in human immunodeficiency virus type 1 (HIV-1) evolution, increasing viral diversity through reshuffling of genomic portions. The strand-switching activity of reverse transcriptase is required to complete HIV-1 replication and can occur randomly...... with the underlying RNA structure. Analysis of the recombination pattern and breakpoint distribution in a group of unique recombinant forms (URFs) detected two recombination hotspots in the pol region. Two stable and conserved hairpins were consistently predicted corresponding to the identified hotspots using six...

  6. Vibrational spectral simulation for peptides of mixed secondary structure: Method comparisons with the Trpzip model hairpin

    Czech Academy of Sciences Publication Activity Database

    Bouř, Petr; Keiderling, T. A.

    2005-01-01

    Roč. 109, - (2005), 23687-23697 ISSN 1089-5647 R&D Projects: GA AV ČR(CZ) IAA4055104 Grant - others:NSF(US) CHE03-16014 Institutional research plan: CEZ:AV0Z40550506 Keywords : VCD * trpzin model hairpin * peptides Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.679, year: 2003

  7. Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer.

    Science.gov (United States)

    Miller, Matthew T; Tuske, Steve; Das, Kalyan; DeStefano, Jeffrey J; Arnold, Eddy

    2016-01-01

    The development of a modified DNA aptamer that binds HIV-1 reverse transcriptase (RT) with ultra-high affinity has enabled the X-ray structure determination of an HIV-1 RT-DNA complex to 2.3 Å resolution without the need for an antibody Fab fragment or RT-DNA cross-linking. The 38-mer hairpin-DNA aptamer has a 15 base-pair duplex, a three-deoxythymidine hairpin loop, and a five-nucleotide 5'-overhang. The aptamer binds RT in a template-primer configuration with the 3'-end positioned at the polymerase active site and has 2'-O-methyl modifications at the second and fourth duplex template nucleotides that interact with the p66 fingers and palm subdomains. This structure represents the highest resolution RT-nucleic acid structure to date. The RT-aptamer complex is catalytically active and can serve as a platform for studying fundamental RT mechanisms and for development of anti-HIV inhibitors through fragment screening and other approaches. Additionally, the structure allows for a detailed look at a unique aptamer design and provides the molecular basis for its remarkably high affinity for RT. © 2015 The Protein Society.

  8. Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII

    Science.gov (United States)

    Lebars, Isabelle; Yoshizawa, Satoko; Stenholm, Anne R.; Guittet, Eric; Douthwaite, Stephen; Fourmy, Dominique

    2003-01-01

    The bacterial rRNA methyltransferase RlmAII (formerly TlrB) contributes to resistance against tylosin-like 16-membered ring macrolide antibiotics. RlmAII was originally discovered in the tylosin-producer Streptomyces fradiae, and members of this subclass of methyltransferases have subsequently been found in other Gram-positive bacteria, including Streptococcus pneumoniae. In all cases, RlmAII methylates 23S rRNA at nucleotide G748, which is situated in a stem–loop (hairpin 35) at the macrolide binding site of the ribosome. The conformation of hairpin 35 recognized by RlmAII is shown here by NMR spectroscopy to resemble the anticodon loop of tRNA. The loop folds independently of the rest of the 23S rRNA, and is stabilized by a non-canonical G–A pair and a U-turn motif, rendering G748 accessible. Binding of S.pneumoniae RlmAII induces changes in NMR signals at specific nucleotides that are involved in the methyltransferase–RNA interaction. The conformation of hairpin 35 that interacts with RlmAII is radically different from the structure this hairpin adopts within the 50S subunit. This indicates that the hairpin undergoes major structural rearrangement upon interaction with ribosomal proteins during 50S assembly. PMID:12514124

  9. Ultrafast Unzipping of a Beta-Hairpin Peptide

    NARCIS (Netherlands)

    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.; Corkum, Paul; Jonas, David M.; Miller, R.J. Dwayne; Weiner, Andrew M.

    2007-01-01

    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.

  10. The hairpin structure of the 6F11F22F2 fragment from human fibronectin enhances gelatin binding

    Science.gov (United States)

    Pickford, Andrew R.; Smith, Steven P.; Staunton, David; Boyd, Jonathan; Campbell, Iain D.

    2001-01-01

    The solution structure of the 6F11F22F2 fragment from the gelatin-binding region of fibronectin has been determined (Protein Data Bank entry codes 1e88 and 1e8b). The structure reveals an extensive hydrophobic interface between the non-contiguous 6F1 and 2F2 modules. The buried surface area between 6F1 and 2F2 (∼870 Å2) is the largest intermodule interface seen in fibronectin to date. The dissection of 6F11F22F2 into the 6F11F2 pair and 2F2 results in near-complete loss of gelatin-binding activity. The hairpin topology of 6F11F22F2 may facilitate intramolecular contact between the matrix assembly regions flanking the gelatin-binding domain. This is the first high-resolution study to reveal a compact, globular arrangement of modules in fibronectin. This arrangement is not consistent with the view that fibronectin is simply a linear ‘string of beads’. PMID:11285216

  11. Determination of low-energy structures of a small RNA hairpin using ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110 067, India. *Corresponding author (Fax, 011-26741586; Email, praban07@gmail.com). The energy landscape of RNA is known to be extremely rugged, and hence finding low-energy structures starting.

  12. Determination of low-energy structures of a small RNA hairpin using ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... ensemble. However, here we have used only the potential energy in the acceptance/rejection part of the MC scheme, since no thermodynamic quantity was calculated from the simulation. The simulations were used to get low-energy structures only. To ensure that temperature of a bin does not increase to a ...

  13. Structure of acid-stable carmine.

    Science.gov (United States)

    Sugimoto, Naoki; Kawasaki, Yoko; Sato, Kyoko; Aoki, Hiromitsu; Ichi, Takahito; Koda, Takatoshi; Yamazaki, Takeshi; Maitani, Tamio

    2002-02-01

    Acid-stable carmine has recently been distributed in the U.S. market because of its good acid stability, but it is not permitted in Japan. We analyzed and determined the structure of the major pigment in acid-stable carmine, in order to establish an analytical method for it. Carminic acid was transformed into a different type of pigment, named acid-stable carmine, through amination when heated in ammonia solution. The features of the structure were clarified using a model compound, purpurin, in which the orientation of hydroxyl groups on the A ring of the anthraquinone skeleton is the same as that of carminic acid. By spectroscopic means and the synthesis of acid-stable carmine and purpurin derivatives, the structure of the major pigment in acid-stable carmine was established as 4-aminocarminic acid, a novel compound.

  14. Target-induced structure switching of hairpin aptamers for label-free and sensitive fluorescent detection of ATP via exonuclease-catalyzed target recycling amplification.

    Science.gov (United States)

    Xu, Yunying; Xu, Jin; Xiang, Yun; Yuan, Ruo; Chai, Yaqin

    2014-01-15

    In this work, we described the development of a new label-free, simple and sensitive fluorescent ATP sensing platform based on exonuclease III (Exo III)-catalyzed target recycling (ECTR) amplification and SYBR Green I indicator. The hairpin aptamer probes underwent conformational structure switching and re-configuration in the presence of ATP, which led to catalytic cleavage of the re-configured aptamers by Exo III to release ATP and to initiate the ECTR process. Such ECTR process resulted in the digestion of a significant number of the hairpin aptamer probes, leading to much less intercalation of SYBR Green I to the hairpin stems and drastic suppression of the fluorescence emission for sensitive ATP detection down to the low nanomolar level. Due to the highly specific affinity bindings between aptamers and ATP, the developed method exhibited excellent selectivity toward ATP against other analogous molecules. Besides, our ATP sensing approach used un-modified aptamer probes and could be performed in a "mix-and-detect" fashion in homogenous solutions. All these distinct advantages of the developed method thus made it hold great potential for the development of simple and robust sensing strategies for the detection of other small molecules. © 2013 Elsevier B.V. All rights reserved.

  15. Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation.

    Directory of Open Access Journals (Sweden)

    Matthias Sipiczki

    Full Text Available Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution.

  16. Disulfide-stabilized Helical Hairpin Structure and Activity of a Novel Antifungal Peptide EcAMP1 from Seeds of Barnyard Grass (Echinochloa crus-galli)*

    Science.gov (United States)

    Nolde, Svetlana B.; Vassilevski, Alexander A.; Rogozhin, Eugene A.; Barinov, Nikolay A.; Balashova, Tamara A.; Samsonova, Olga V.; Baranov, Yuri V.; Feofanov, Alexey V.; Egorov, Tsezi A.; Arseniev, Alexander S.; Grishin, Eugene V.

    2011-01-01

    This study presents purification, activity characterization, and 1H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold. PMID:21561864

  17. Disulfide-stabilized helical hairpin structure and activity of a novel antifungal peptide EcAMP1 from seeds of barnyard grass (Echinochloa crus-galli).

    Science.gov (United States)

    Nolde, Svetlana B; Vassilevski, Alexander A; Rogozhin, Eugene A; Barinov, Nikolay A; Balashova, Tamara A; Samsonova, Olga V; Baranov, Yuri V; Feofanov, Alexey V; Egorov, Tsezi A; Arseniev, Alexander S; Grishin, Eugene V

    2011-07-15

    This study presents purification, activity characterization, and (1)H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold.

  18. Design and Simulation of Microstrip Hairpin Bandpass Filter with Open Stub and Defected Ground Structure (DGS) at X-Band Frequency

    Science.gov (United States)

    Hariyadi, T.; Mulyasari, S.; Mukhidin

    2018-02-01

    In this paper we have designed and simulated a Band Pass Filter (BPF) at X-band frequency. This filter is designed for X-band weather radar application with 9500 MHz center frequency and bandwidth -3 dB is 120 MHz. The filter design was performed using a hairpin microstrip combined with an open stub and defected ground structure (DGS). The substrate used is Rogers RT5880 with a dielectric constant of 2.2 and a thickness of 1.575 mm. Based on the simulation results, it is found that the filter works on frequency 9,44 - 9,56 GHz with insertion loss value at pass band is -1,57 dB.

  19. Effect of hairpin loop structure on reactivity, sequence preference and adduct orientation of a DNA-interactive pyrrolo[2,1-c][1,4]benzodiazepine (PBD) antitumour agent.

    Science.gov (United States)

    Thurston, David E; Vassoler, Higia; Jackson, Paul J M; James, Colin H; Rahman, Khondaker M

    2015-04-07

    The pyrrolobenzodiazepines (PBDs) are a family of covalent-binding DNA-interactive minor-groove binding agents with a thermodynamic preference for binding to 5'-Pu-G-Pu-3' sequences (Pu = Purine) but a kinetic preference for 5'-Py-G-Py-3' (Py = Pyrimidine). Using HPLC/MS methodology and a range of designed hairpin-forming oligonucleotides, the kinetics of reaction of a C8-bis-pyrrole pyrrolobenzodiazepine (PBD) conjugate (GWL-78, 2) with sixteen isomeric oligonucleotides has been evaluated, each containing a single PBD binding site in one of two locations. The PBD-binding base-pair triplets were designed to include every possible combination of A and T bases adjacent to the covalently-reacting guanine, with the set of hairpins consisting of isomeric pairs containing the same sequence in the hairpin stem but with either hexaethylene glycol (HEG) or TTT loops. The PBD 2 reacted most rapidly with TGT and TGA sequences, with the possibility that adducts might form in both the 3'- and 5'-directions with some sequences according to modelling studies. A faster reaction rate was observed for all hairpins containing the HEG loop except one (Seq 10) when the PBD binding triplets were located either near the loop or adjacent to the 5'-end. Modelling studies have suggested that this difference in reactivity could be due to the structural flexibility of the HEG loop allowing both A-ring-3' and A-ring-5' adducts to form, while a TTT loop should favour only A-ring-5' adducts due to steric considerations. These findings contrast with the results reported by Nguyen and Wilson for the interaction of non-covalent DNA-binding molecules with DNA hairpins, where the loop structure was found to have little effect on interaction in the main stem of the hairpin.

  20. Cisplatin Targeting of Bacterial Ribosomal RNA Hairpins

    Directory of Open Access Journals (Sweden)

    Gayani N. P. Dedduwa-Mudalige

    2015-09-01

    Full Text Available Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human.

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

    Directory of Open Access Journals (Sweden)

    Gregory Upert

    2012-01-01

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

  2. Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal β-Hairpin in the Absence of N-Terminal Proline

    Directory of Open Access Journals (Sweden)

    Christelle Folio

    2017-11-01

    Full Text Available Feline immunodeficiency virus (FIV is a member of the Retroviridae family. It is the causative agent of an acquired immunodeficiency syndrome (AIDS in cats and wild felines. Its capsid protein (CA drives the assembly of the viral particle, which is a critical step in the viral replication cycle. Here, the first atomic structure of full-length FIV CA to 1.67 Å resolution is determined. The crystallized protein exhibits an original tetrameric assembly, composed of dimers which are stabilized by an intermolecular disulfide bridge induced by the crystallogenesis conditions. The FIV CA displays a standard α-helical CA topology with two domains, separated by a linker shorter than other retroviral CAs. The β-hairpin motif at its amino terminal end, which interacts with nucleotides in HIV-1, is unusually long in FIV CA. Interestingly, this functional β-motif is formed in this construct in the absence of the conserved N-terminal proline. The FIV CA exhibits a cis Arg–Pro bond in the CypA-binding loop, which is absent in known structures of lentiviral CAs. This structure represents the first tri-dimensional structure of a functional, full-length FIV CA.

  3. Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal β-Hairpin in the Absence of N-Terminal Proline.

    Science.gov (United States)

    Folio, Christelle; Sierra, Natalia; Dujardin, Marie; Alvarez, Guzman; Guillon, Christophe

    2017-11-09

    Feline immunodeficiency virus (FIV) is a member of the Retroviridae family. It is the causative agent of an acquired immunodeficiency syndrome (AIDS) in cats and wild felines. Its capsid protein (CA) drives the assembly of the viral particle, which is a critical step in the viral replication cycle. Here, the first atomic structure of full-length FIV CA to 1.67 Å resolution is determined. The crystallized protein exhibits an original tetrameric assembly, composed of dimers which are stabilized by an intermolecular disulfide bridge induced by the crystallogenesis conditions. The FIV CA displays a standard α-helical CA topology with two domains, separated by a linker shorter than other retroviral CAs. The β-hairpin motif at its amino terminal end, which interacts with nucleotides in HIV-1, is unusually long in FIV CA. Interestingly, this functional β-motif is formed in this construct in the absence of the conserved N-terminal proline. The FIV CA exhibits a cis Arg-Pro bond in the CypA-binding loop, which is absent in known structures of lentiviral CAs. This structure represents the first tri-dimensional structure of a functional, full-length FIV CA.

  4. How structurally stable are global socioeconomic systems?

    Science.gov (United States)

    Saavedra, Serguei; Rohr, Rudolf P; Gilarranz, Luis J; Bascompte, Jordi

    2014-11-06

    The stability analysis of socioeconomic systems has been centred on answering whether small perturbations when a system is in a given quantitative state will push the system permanently to a different quantitative state. However, typically the quantitative state of socioeconomic systems is subject to constant change. Therefore, a key stability question that has been under-investigated is how strongly the conditions of a system itself can change before the system moves to a qualitatively different behaviour, i.e. how structurally stable the systems is. Here, we introduce a framework to investigate the structural stability of socioeconomic systems formed by a network of interactions among agents competing for resources. We measure the structural stability of the system as the range of conditions in the distribution and availability of resources compatible with the qualitative behaviour in which all the constituent agents can be self-sustained across time. To illustrate our framework, we study an empirical representation of the global socioeconomic system formed by countries sharing and competing for multinational companies used as proxy for resources. We demonstrate that the structural stability of the system is inversely associated with the level of competition and the level of heterogeneity in the distribution of resources. Importantly, we show that the qualitative behaviour of the observed global socioeconomic system is highly sensitive to changes in the distribution of resources. We believe that this work provides a methodological basis to develop sustainable strategies for socioeconomic systems subject to constantly changing conditions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  5. Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation.

    Science.gov (United States)

    Swadling, Jacob B; Ishii, Kunihiko; Tahara, Tahei; Kitao, Akio

    2018-01-31

    Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.

  6. DFT computations of the lattice constant, stable atomic structure and ...

    African Journals Online (AJOL)

    This paper presents the most stable atomic structure and lattice constant of Fullerenes (C60). FHI-aims DFT code was used to predict the stable structure and the computational lattice constant of C60. These were compared with known experimental structures and lattice constants of C60. The results obtained showed that ...

  7. Functional conservation of the pre-sensor one beta-finger hairpin (PS1-hp) structures in mini-chromosome maintenance proteins of Saccharomyces cerevisiae and archaea.

    Science.gov (United States)

    Ramey, Christopher J; Sclafani, Robert A

    2014-05-28

    Mini-chromosome maintenance (MCM) proteins form complexes that are required for DNA replication and are highly conserved throughout evolution. The replicative helicase of eukaryotic organisms is composed of the six paralogs MCM2-7, which form a heterohexameric ring structure. In contrast, the structure of the archaean replicative MCM helicase is a single Mcm protein that forms a homohexameric complex. Atomic structures of archaeal MCMs have identified multiple beta-finger structures in Mcm proteins whose in vivo function is unknown. In the present study, we have investigated the physiological role of the pre-sensor 1 beta-hairpin (PS1-hp) beta-fingers of Saccharomyces cerevisiae Mcm4p and Mcm5p in DNA replication initiation and elongation in vivo. The PS1-hp beta-finger mutant of Mcm5p (mcm5-HAT K506A::URA3) has a growth defect at both 18° and 37°. Mutation of the Mcm4p PS1-hp beta-finger (mcm4-HA K658A::TRP1) does not have a growth defect, indicating different functional contributions of the PS1-hp beta-finger structures of different MCM helicase subunits. Both Mcm4p and Mcm5p PS1-hp beta-finger mutants can coimmunoprecipitate Mcm2p, indicating the formation of the hexameric MCM helicase complex. Both PS1-hp beta-finger mutants have a plasmid loss phenotype that is suppressible by origin dosage, indicating a defective replication initiation. Surprisingly, a defect in the binding of PS1-hp MCM mutants to origins of DNA replication was not found by chromatin immunoprecipitation, suggesting a novel interpretation in which the defect is in a subsequent step of DNA strand separation by the MCM helicase. The double mutant mcm4-HA K658A::TRP1 mcm5-HAT K506A::URA3 is lethal, displaying a terminal MCM mutant phenotype of large budded cells. Copyright © 2014 Ramey and Sclafani.

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

    Science.gov (United States)

    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

  9. Structural Changes of Zn(IIbleomycin Complexes When Bound to DNA Hairpins Containing the 5′-GT-3′ and 5′-GC-3′ Binding Sites, Studied through NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Shelby E. Follett

    2017-12-01

    Full Text Available We have previously investigated the diverse levels of disruption caused by Zn(IIBLMs with different C-termini to DNA hairpins containing 5′-GC-3′ and 5′-GT-3′ binding sites. The results of this investigation indicated that both the DNA-binding site and the bleomycin C-termini have an impact on the final conformation of the aforementioned hairpins in the drug-target complexes, as suggested by the different sets of intramolecular NOEs displayed by both oligonucleotides when bound to each Zn(IIBLM. The NMR signals elicited by 1H nuclei in the oligonucleotide bases and sugar moieties were also affected differently (shifted upfield or downfield in various patterns depending on the BLM C-termini and the binding site in the oligonucleotides. The overall conclusion derived from the precedent research is that the spatial conformation of target DNA segments in DNA-Zn(IIBLM complexes could be forged by interactions between drug and DNA that are guided by the DNA binding site and the BLM C-termini. The present study focuses on the structural alterations exhibited by Zn(IIbleomycin-A2, -B2, -A5 and Zn(IIpeplomycin molecules upon binding to the previously studied hairpins. Our main goal is to determine if different spatial conformations of the drugs in their DNA-bound forms are found in drug-DNA complexes that differ in the oligonucleotide binding site and BLM C-termini. Evidence that suggest that each Zn(IIbleomycin is structurally affected depending these two factors, as indicated by different sets of intramolecular NOE connectivities between drug protons and diverse patterns of shifting of their 1H-NMR signals, is provided.

  10. High precision and stable structures for particle detectors

    CERN Document Server

    Da Mota Silva, S; Hauviller, Claude

    1999-01-01

    The central detectors used in High Energy Physics Experiments require the use of light and stable structures capable of supporting delicate and precise radiation detection elements. These structures need to be highly stable under environmental conditions where external vibrations, high radiation levels, temperature and humidity gradients should be taken into account. Their main design drivers are high dimension and dynamic stability, high stiffness to mass ratio and large radiation length. For most applications, these constraints lead us to choose Carbon Fiber Reinforced Plastics ( CFRP) as structural element. The construction of light and stable structures with CFRP for these applications can be achieved by careful design engineering and further confirmation at the prototyping phase. However, the experimental environment can influence their characteristics and behavior. In this case, theuse of adaptive structures could become a solution for this problem. We are studying structures in CFRP with bonded piezoel...

  11. Dynamics and control of twisting bi-stable structures

    Science.gov (United States)

    Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.

    2018-02-01

    Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states

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

    Science.gov (United States)

    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.

  13. Design of a new hairpin DNAzyme: The activity controlled by TMPyP ...

    African Journals Online (AJOL)

    The catalytic activity of the 10-23 hairpin DNAzyme decreased and even inactivated due to the enhanced stability of G-quadruplex structure by TMPyP4 molecules. This DNAzyme is controllable to cleavage substrate and has some potential significance in gene therapy. Key words: 10-23 DNAzyme, hairpin DNAzyme, ...

  14. Recent developments in low cost stable structures for space

    International Nuclear Information System (INIS)

    Thompson, T.C.; Grastataro, C.; Smith, B.G.

    1994-01-01

    The Los Alamos National Laboratory (LANL) in partnership with Composite Optics Incorporated (COI) is advancing the development of low cost, lightweight, composite technology for use in spacecraft and stable structures. The use of advanced composites is well developed, but the application of an all-composite tracker structure has never been achieved. This paper investigates the application of composite technology to the design and fabrication of an all-composite spacecraft bus for small satellites, using technology directly applicable to central tracking in a high luminosity environment. The satellite program Fast On-Orbit Recording of Transient Events (FORTE) is the second in a series of satellites to be launched into orbit for the US Department of Energy (DOE). This paper will discuss recent developments in the area of low cost composites, used for either spacecraft or ultra stable applications in high energy physics (HEP) detectors. The use of advanced composites is a relatively new development in the area of HEP. The Superconducting Super Collider (SSC) spawned a new generation of Trackers which made extensive use of graphite fiber reinforced plastic (GFRP) composite systems. LANL has designed a structure employing new fabrication technology. This concept will lower the cost of composite structures to a point that they may now compete with conventional materials. This paper will discuss the design, analysis and proposed fabrication of a small satellite structure. Central tracking structures using advanced materials capable of operating in an adverse environment typical of that found in a high luminosity collider could use identical concepts

  15. Modeling the mechanism of CLN025 beta-hairpin formation

    Science.gov (United States)

    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.

  16. Lentiviral delivery of short hairpin RNAs

    Science.gov (United States)

    Manjunath, N; Haoquan, Wu; Sandesh, Subramanya; Premlata, Shankar

    2009-01-01

    In less than a decade after discovery, RNA interference-mediated gene silencing is already being tested as potential therapy in clinical trials for a number of diseases. Lentiviral vectors provide a means to express short hairpin RNA (shRNA) to induce stable and long-term gene silencing in both dividing and non-dividing cells and thus, are being intensively investigated for this purpose. However, induction of long-term shRNA expression can also cause toxicities by inducing off target effects and interference with the endogenous micro RNA (miRNA) pathway that regulates cellular gene expression. Recently, several advances have been made in the shRNA vector design to mimic cellular miRNA processing and to express multiplex siRNAs in a tightly regulated and reversible manner to overcome toxicities. In this review we describe some of these advances, focusing on the progress made in the development of lentiviral shRNA delivery strategies to combat viral infections. PMID:19341774

  17. Highly stable thin film transistors using multilayer channel structure

    KAUST Repository

    Nayak, Pradipta K.

    2015-03-09

    We report highly stable gate-bias stress performance of thin film transistors (TFTs) using zinc oxide (ZnO)/hafnium oxide (HfO2) multilayer structure as the channel layer. Positive and negative gate-bias stress stability of the TFTs was measured at room temperature and at 60°C. A tremendous improvement in gate-bias stress stability was obtained in case of the TFT with multiple layers of ZnO embedded between HfO2 layers compared to the TFT with a single layer of ZnO as the semiconductor. The ultra-thin HfO2 layers act as passivation layers, which prevent the adsorption of oxygen and water molecules in the ZnO layer and hence significantly improve the gate-bias stress stability of ZnO TFTs.

  18. Structure of stable degeneration of K3 surfaces into pairs of rational elliptic surfaces

    OpenAIRE

    Kimura, Yusuke

    2018-01-01

    F-theory/heterotic duality is formulated in the stable degeneration limit of a K3 fibration on the F-theory side. In this note, we analyze the structure of the stable degeneration limit. We discuss whether stable degeneration exists for pairs of rational elliptic surfaces. We demonstrate that, when two rational elliptic surfaces have an identical complex structure, stable degeneration always exists. We provide an equation that systematically describes the stable degeneration of a K3 surface i...

  19. Stable structural color patterns displayed on transparent insect wings.

    Science.gov (United States)

    Shevtsova, Ekaterina; Hansson, Christer; Janzen, Daniel H; Kjærandsen, Jostein

    2011-01-11

    Color patterns play central roles in the behavior of insects, and are important traits for taxonomic studies. Here we report striking and stable structural color patterns--wing interference patterns (WIPs)--in the transparent wings of small Hymenoptera and Diptera, patterns that have been largely overlooked by biologists. These extremely thin wings reflect vivid color patterns caused by thin film interference. The visibility of these patterns is affected by the way the insects display their wings against various backgrounds with different light properties. The specific color sequence displayed lacks pure red and matches the color vision of most insects, strongly suggesting that the biological significance of WIPs lies in visual signaling. Taxon-specific color patterns are formed by uneven membrane thickness, pigmentation, venation, and hair placement. The optically refracted pattern is also stabilized by microstructures of the wing such as membrane corrugations and spherical cell structures that reinforce the pattern and make it essentially noniridescent over a large range of light incidences. WIPs can be applied to map the micromorphology of wings through direct observation and are useful in several fields of biology. We demonstrate their usefulness as identification patterns to solve cases of cryptic species complexes in tiny parasitic wasps, and indicate their potentials for research on the genetic control of wing development through direct links between the transregulatory wing landscape and interference patterns we observe in Drosophila model species. Some species display sexually dimorphic WIPs, suggesting sexual selection as one of the driving forces for their evolution.

  20. Different Fluorophore Labeling Strategies and Designs Affect Millisecond Kinetics of DNA Hairpins

    Directory of Open Access Journals (Sweden)

    Andreas Hartmann

    2014-09-01

    Full Text Available Changes in molecular conformations are one of the major driving forces of complex biological processes. Many studies based on single-molecule techniques have shed light on conformational dynamics and contributed to a better understanding of living matter. In particular, single-molecule FRET experiments have revealed unprecedented information at various time scales varying from milliseconds to seconds. The choice and the attachment of fluorophores is a pivotal requirement for single-molecule FRET experiments. One particularly well-studied millisecond conformational change is the opening and closing of DNA hairpin structures. In this study, we addressed the influence of base- and terminal-labeled fluorophores as well as the fluorophore DNA interactions on the extracted kinetic information of the DNA hairpin. Gibbs free energies varied from ∆G0 = −3.6 kJ/mol to ∆G0 = −0.2 kJ/mol for the identical DNA hairpin modifying only the labeling scheme and design of the DNA sample. In general, the base-labeled DNA hairpin is significantly destabilized compared to the terminal-labeled DNA hairpin and fluorophore DNA interactions additionally stabilize the closed state of the DNA hairpin. Careful controls and variations of fluorophore attachment chemistry are essential for a mostly undisturbed measurement of the underlying energy landscape of biomolecules.

  1. A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.

    Science.gov (United States)

    Lee, Jeong Hyun; Andrabi, Raiees; Su, Ching-Yao; Yasmeen, Anila; Julien, Jean-Philippe; Kong, Leopold; Wu, Nicholas C; McBride, Ryan; Sok, Devin; Pauthner, Matthias; Cottrell, Christopher A; Nieusma, Travis; Blattner, Claudia; Paulson, James C; Klasse, Per Johan; Wilson, Ian A; Burton, Dennis R; Ward, Andrew B

    2017-04-18

    Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature. Somatic hypermutation in the other CDRs of PGT145 were crucially involved in stabilizing the structure of the HCDR3, similar to bovine antibodies, to aid in recognition of a cluster of conserved basic residues hypothesized to facilitate trimer disassembly during viral entry. Overall, the findings exemplify the creative solutions that the human immune system can evolve to recognize a conserved motif buried under a canopy of glycans. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  2. Short Hairpin RNA (shRNA): Design, Delivery, and Assessment of Gene Knockdown

    Science.gov (United States)

    Moore, Chris B.; Guthrie, Elizabeth H.; Huang, Max Tze-Han; Taxman, Debra J.

    2013-01-01

    Shortly after the cellular mechanism of RNA interference (RNAi) was first described, scientists began using this powerful technique to study gene function. This included designing better methods for the successful delivery of small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) into mammalian cells. While the simplest method for RNAi is the cytosolic delivery of siRNA oligonucleotides, this technique is limited to cells capable of transfection and is primarily utilized during transient in vitro studies. The introduction of shRNA into mammalian cells through infection with viral vectors allows for stable integration of shRNA and long-term knockdown of the targeted gene; however, several challenges exist with the implementation of this technology. Here we describe some well-tested protocols which should increase the chances of successful design, delivery, and assessment of gene knockdown by shRNA. We provide suggestions for designing shRNA targets and controls, a protocol for sequencing through the secondary structure of the shRNA hairpin structure, and protocols for packaging and delivery of shRNA lentiviral particles. Using real-time PCR and functional assays we demonstrate the successful knockdown of ASC, an inflammatory adaptor molecule. These studies demonstrate the practicality of including two shRNAs with different efficacies of knockdown to provide an additional level of control and to verify dose dependency of functional effects. Along with the methods described here, as new techniques and algorithms are designed in the future, shRNA is likely to include further promising application and continue to be a critical component of gene discovery. PMID:20387148

  3. Thermally-Stable High Strain Deployable Structures, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation is for the development of a thermally-stable composite made of carbon fibers and elastomeric resin. This combination of materials will allow...

  4. An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.

    Directory of Open Access Journals (Sweden)

    Ke Shi

    Full Text Available 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.

  5. Hairpin formation within the enhancer region of the human enkephalin gene

    Energy Technology Data Exchange (ETDEWEB)

    McMurray, C.T.; Douglass, J.O. (Oregon Health Sciences Univ., Portland (United States)); Wilson, W.D. (Georgia State Univ., Atlanta (United States))

    1991-01-15

    The 3{prime},5{prime}-cyclic adenosine monophosphate (cAMP)-inducible enhancer of the human enkephaline gene is located within an imperfect palindrom of 23 base pairs. The authors have found that a 23-base-pair oligonucleotide duplex containing the enhancer undergoes a reversible conformational transition from the duplex to two individual hairpin structures each formed from one strand of the duplex. Each individual hairpin forms with mismatched base pairs, one containing two GT pairs and the other containing two AC pairs. The conformational transition is stabilized by proton transfer to the hairpin containing AC mismatched pairs. The unique physical and thermodynamic properties of the enkephalin enhancer DNA suggest a model in which DNA secondary structure within the enhancer region plays and active role incAMP-inducible activation of the human enkephalin gene via formation of cruciform structures.

  6. Mechanism of membrane permeation induced by synthetic β-hairpin peptides.

    Science.gov (United States)

    Gupta, Kshitij; Jang, Hyunbum; Harlen, Kevin; Puri, Anu; Nussinov, Ruth; Schneider, Joel P; Blumenthal, Robert

    2013-11-05

    We have investigated the membrane destabilizing properties of synthetic amphiphilic cationic peptides, MAX1 and MAX35, which have the propensity to form β-hairpin structures under certain conditions, and a control non-β-hairpin-forming peptide MAX8V16E. All three peptides bind to liposomes containing a mixture of zwitterionic POPC and negatively charged POPS lipids as determined by Zeta potential measurements. Circular dichroism measurements indicated folding of MAX1 and MAX35 in the presence of the POPC/POPS liposomes, whereas no such folding was observed with MAX8V16E. There was no binding or folding of these peptides to liposomes containing only POPC. MAX1 and MAX35 induced release of contents from negatively charged liposomes, whereas MAX8V16E failed to promote solute release under identical conditions. Thus, MAX1 and MAX35 bind to, and fold at the surface of negatively charged liposomes adopting a lytic conformation. We ruled out leaky fusion as a mechanism of release by including 2 mol % PEG-PE in the liposomes, which inhibits aggregation/fusion but not folding of MAX or MAX-induced leakage. Using a concentration-dependent quenching probe (calcein), we determined that MAX-induced leakage of liposome contents was an all-or-none process. At MAX1 concentrations, which cause release of ~50% of the liposomes that contain small (R(h) peptides are relatively more stable than MAX8V16E barrels in the bilayer, suggesting that barrels of this size are responsible for the peptides lytic action. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  7. Design and function of triplex hairpin ribozymes.

    Science.gov (United States)

    Aquino-Jarquin, Guillermo; Rojas-Hernández, Ramiro; Alvarez-Salas, Luis Marat

    2010-01-01

    Triplex ribozymes allow for the individual activity of multiple trans-acting ribozymes producing higher target cleavage relative to tandem-expressed RZs. A triplex expression system based on a single hairpin ribozyme for the multiple expression (multiplex) vectors can be engineered to target RNAs with single or multiple antisense-accessible sites. System construction relies on triplex expression modules consisting of hairpin ribozyme cassettes flanked by ribozymes lacking catalytic domains. Multiplex vectors can be generated with single or multiple specificity by tandem cloning of triplex expression modules. Triplex ribozymes are initially tested in vitro using cis- and trans-cleavage assays against radioactive-labeled targets. In addition, triplex ribozymes are tested for cis and trans cleavage in vivo by transfection in cultured cells followed by ribonuclease protection assays (RPAs) and RT-PCR. The use of triplex configurations with multiplex ribozymes will provide the basis for the development of future RZ-based therapies and technologies.

  8. Size estimation of complexes consisting of hairpin DNAs bound to an assembler-strand. [Abstract only

    Science.gov (United States)

    Baumann, Ulrich

    1994-01-01

    In connection with a model of a primitive translation based entirely on nucleic acids the structural requirements and interactions of small nucleic acids were studied. As shown previously hairpins bind to a complementary single-strand by base pairs of their loop nucleotides if the loop contains at least five nucleotides (Baumann et al 1987). Here, the question is approached to which degree a single-strand, the assembler-strand, is occupied with hairpin molecules. A gapless occupation would allow the close proximity necessary for the assumed peptide bond formation by hairpins bearing an amino acid at their 3'-end. Oligo(dC)(sub n), n = 12, 15, 18, and the investigated hairpins form complexes which are detectable under nondenaturing electrophoretic conditions. The size range is estimated to be 3-4 hairpin molecules to one assembler molecule when oligo(dC)(sub n), n = 15, 18, is used. Due to the limitation of the method, dependence of the migration velocity on the shape which is unique and thus limits the use of marker nucleic acids, and due to the uncertainty if the ends of the assembler form base pairs, a gapless occupation of the assembler is conceivable but not proven.

  9. Hygro-Thermal Transient Analysis for Highly Stable Structures

    CERN Document Server

    Da Mota Silva, S; Hauviller, Claude; Kanoute, P; Ribeiro, R

    1999-01-01

    This paper presents the results obtained with the simulations of a sandwich rectangular plate made of carbon/epoxy composite when subjected to temperature and humidity cycles. Fickian diffusion process, moisture transport along the interfaces and damage caused by slipping and debonding between the components of the microscopic structure are considered. The application of the design methodology to a real structure is shown.

  10. Active structural control with stable fuzzy PID techniques

    CERN Document Server

    Yu, Wen

    2016-01-01

    This book presents a detailed discussion of intelligent techniques to measure the displacement of buildings when they are subjected to vibration. It shows how these techniques are used to control active devices that can reduce vibration 60–80% more effectively than widely used passive anti-seismic systems. After introducing various structural control devices and building-modeling and active structural control methods, the authors propose offset cancellation and high-pass filtering techniques to solve some common problems of building-displacement measurement using accelerometers. The most popular control algorithms in industrial settings, PD/PID controllers, are then analyzed and then combined with fuzzy compensation. The stability of this combination is proven with standard weight-training algorithms. These conditions provide explicit methods for selecting PD/PID controllers. Finally, fuzzy-logic and sliding-mode control are applied to the control of wind-induced vibration. The methods described are support...

  11. An Energy stable Monolithic Eulerian Fluid-Structure Numerical Scheme *

    OpenAIRE

    Pironneau , Olivier

    2017-01-01

    The conservation laws of continuum mechanic written in an Eulerian frame make no difference between fluids and solids except in the expression of the stress tensors, usually with Newton's hypothesis for the fluids and Helmholtz potentials of energy for hyperelastic solids. By taking the velocities as unknown , monolithic methods for fluid structure interactions (FSI) are built. In this article such a formulation is analyzed when the fluid is compressible and the fluid is incompressible. The i...

  12. Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

    Science.gov (United States)

    Sachtler, Wolfgang M. H.; Huang, Yin-Yan

    1998-01-01

    Methods for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physisorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics.

  13. Numerically stable fluid–structure interactions between compressible flow and solid structures

    KAUST Repository

    Grétarsson, Jón Tómas

    2011-04-01

    We propose a novel method to implicitly two-way couple Eulerian compressible flow to volumetric Lagrangian solids. The method works for both deformable and rigid solids and for arbitrary equations of state. The method exploits the formulation of [11] which solves compressible fluid in a semi-implicit manner, solving for the advection part explicitly and then correcting the intermediate state to time tn+1 using an implicit pressure, obtained by solving a modified Poisson system. Similar to previous fluid-structure interaction methods, we apply pressure forces to the solid and enforce a velocity boundary condition on the fluid in order to satisfy a no-slip constraint. Unlike previous methods, however, we apply these coupled interactions implicitly by adding the constraint to the pressure system and combining it with any implicit solid forces in order to obtain a strongly coupled, symmetric indefinite system (similar to [17], which only handles incompressible flow). We also show that, under a few reasonable assumptions, this system can be made symmetric positive-definite by following the methodology of [16]. Because our method handles the fluid-structure interactions implicitly, we avoid introducing any new time step restrictions and obtain stable results even for high density-to-mass ratios, where explicit methods struggle or fail. We exactly conserve momentum and kinetic energy (thermal fluid-structure interactions are not considered) at the fluid-structure interface, and hence naturally handle highly non-linear phenomenon such as shocks, contacts and rarefactions. © 2011 Elsevier Inc.

  14. Exquisite allele discrimination by toehold hairpin primers

    Science.gov (United States)

    Byrom, Michelle; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.

    2014-01-01

    The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer. PMID:24990378

  15. An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets.

    Science.gov (United States)

    Lee, Su Jin; Hyun, Soonsil; Kieft, Jeffrey S; Yu, Jaehoon

    2009-02-18

    The hairpin RNA motif is one of the most frequently observed secondary structures and is often targeted by therapeutic agents. An amphiphilic peptide with seven lysine and eight leucine residues and its derivatives were designed for use as ligands against RNA hairpin motifs. We hypothesized that variations in both the hydrophobic leucine-rich and hydrophilic lysine-rich spheres of these amphiphilic peptides would create extra attractive interactions with hairpin RNA targets. A series of alanine-scanned peptides were probed to identify the most influential lysine residues in the hydrophilic sphere. The binding affinities of these modified peptides with several hairpins, such as RRE, TAR from HIV, a short hairpin from IRES of HCV, and a hairpin from the 16S A-site stem from rRNA, were determined. Since the hairpin from IRES of HCV was the most susceptible to the initial series of alanine-scanned peptides, studies investigating how further variations in the peptides effect binding employed the IRES hairpin. Next, the important Lys residues were substituted by shorter chain amines, such as ornithine, to place the peptide deeper into the hairpin groove. In a few cases, a 70-fold improved binding was observed for peptides that contained the specifically located shorter amine side chains. To further explore changes in binding affinities brought about by alterations in the hydrophobic sphere, tryptophan residues were introduced in place of leucine. A few peptides with tryptophan in specific positions also displayed 70-fold improved binding affinities. Finally, double mutant peptides incorporating both specifically located shorter amine side chains in the hydrophilic region and tryptophan residues in the hydrophobic region were synthesized. The binding affinities of peptides containing the simple double modification were observed to be 80 times lower, and their binding specificities were increased 40-fold. The results of this effort provide important information about

  16. Spatial variations in food web structures with alternative stable states: evidence from stable isotope analysis in a large eutrophic lake

    Science.gov (United States)

    Li, Yunkai; Zhang, Yuying; Xu, Jun; Zhang, Shuo

    2017-05-01

    Food web structures are well known to vary widely among ecosystems. Moreover, many food web studies of lakes have generally attempted to characterize the overall food web structure and have largely ignored internal spatial and environmental variations. In this study, we hypothesize that there is a high degree of spatial heterogeneity within an ecosystem and such heterogeneity may lead to strong variations in environmental conditions and resource availability, in turn resulting in different trophic pathways. Stable carbon and nitrogen isotopes were employed for the whole food web to describe the structure of the food web in different sub-basins within Taihu Lake. This lake is a large eutrophic freshwater lake that has been intensively managed and highly influenced by human activities for more than 50 years. The results show significant isotopic differences between basins with different environmental characteristics. Such differences likely result from isotopic baseline differences combining with a shift in food web structure. Both are related to local spatial heterogeneity in nutrient loading in waters. Such variation should be explicitly considered in future food web studies and ecosystem-based management in this lake ecosystem.

  17. Regional Comparisons of Oceanic Food Web Structure Using Stable Isotopes

    Science.gov (United States)

    Choy, A.; Drazen, J.; Popp, B. N.; Robison, B. H.

    2016-02-01

    Food chain length, or the number of trophic steps between primary producers and apex predators within an ecosystem, is a key determinant of ecosystem structure, including overall efficiency, stability, and productivity. Here, we quantitatively estimate food chain length for three pelagic ecosystems characterized by distinct biogeochemical and oceanographic regimes: the Northern California Current (NCC), the North Pacific Subtropical Gyre (NPSG), and the Gulf of California (GoC). From each region, ecologically equivalent organisms were selected from each of four successive trophic steps, including zooplankton (primary consumers), zooplanktivores (secondary consumers), piscivores (tertiary consumers), and higher order predators. Bulk tissue δ15N values of the organisms from all four trophic steps spanned ranges of approximately 9.8‰ (NCC), 1.4‰ (NPSG), and 2.1‰ (GoC). Regional variations in nitrogen biogeochemistry, however, can alter isotopic baselines and food web dynamics, ultimately complicating bulk isotope measurements across regions. Thus, we apply amino acid nitrogen isotope measurements to quantitatively measure and compare food chain length across consumers from the three regions, accounting for biogeochemical disparities in isotopic baseline. Implications for ecosystem production and efficiency are discussed, including the potential for these different ecosystems to withstand environmental change, including shifting oxygen levels and surface productivity.

  18. On hairpin vortices in a transitional boundary layer

    Directory of Open Access Journals (Sweden)

    Uruba Václav

    2012-04-01

    Full Text Available In the presented paper the results of experiments on transitional boundary layer are presented. The boundary layer was generated on smooth flat wall with zero pressure gradient forming one side of the channel of rectangular cross section. The hairpin vortices, packets of hairpin vortices, turbulent spots and calmed regions were experimentally investigated using time-resolved PIV technique.

  19. TGP, an extremely stable, non-aggregating fluorescent protein created by structure-guided surface engineering

    OpenAIRE

    Close, Devin W.; Don Paul, Craig; Langan, Patricia S.; Wilce, Matthew C.J.; Traore, Daouda A.K.; Halfmann, Randal; Rocha, Reginaldo C.; Waldo, Geoffery S.; Payne, Riley J.; Rucker, Joseph B.; Prescott, Mark; Bradbury, Andrew R.M.

    2015-01-01

    In this paper we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP....

  20. Structure of stable degeneration of K3 surfaces into pairs of rational elliptic surfaces

    Science.gov (United States)

    Kimura, Yusuke

    2018-03-01

    F-theory/heterotic duality is formulated in the stable degeneration limit of a K3 fibration on the F-theory side. In this note, we analyze the structure of the stable degeneration limit. We discuss whether stable degeneration exists for pairs of rational elliptic surfaces. We demonstrate that, when two rational elliptic surfaces have an identical complex structure, stable degeneration always exists. We provide an equation that systematically describes the stable degeneration of a K3 surface into a pair of isomorphic rational elliptic surfaces. When two rational elliptic surfaces have different complex structures, whether their sum glued along a smooth fiber admits deformation to a K3 surface can be determined by studying the structure of the K3 lattice. We investigate the lattice theoretic condition to determine whether a deformation to a K3 surface exists for pairs of extremal rational elliptic surfaces. In addition, we discuss the configurations of singular fibers under stable degeneration. The sum of two isomorphic rational elliptic surfaces glued together admits a deformation to a K3 surface, the singular fibers of which are twice that of the rational elliptic surface. For special situations, singular fibers of the resulting K3 surface collide and they are enhanced to a fiber of another type. Some K3 surfaces become attractive in these situations. We determine the complex structures and the Weierstrass forms of these attractive K3 surfaces. We also deduce the gauge groups in F-theory compactifications on these attractive K3 surfaces times a K3. E 6, E 7, E 8, SU(5), and SO(10) gauge groups arise in these compactifications.

  1. Novel stable structure of Li3PS4 predicted by evolutionary algorithm under high-pressure

    Directory of Open Access Journals (Sweden)

    S. Iikubo

    2018-01-01

    Full Text Available By combining theoretical predictions and in-situ X-ray diffraction under high pressure, we found a novel stable crystal structure of Li3PS4 under high pressures. At ambient pressure, Li3PS4 shows successive structural transitions from γ-type to β-type and from β-type to α type with increasing temperature, as is well established. In this study, an evolutionary algorithm successfully predicted the γ-type crystal structure at ambient pressure and further predicted a possible stable δ-type crystal structures under high pressure. The stability of the obtained structures is examined in terms of both static and dynamic stability by first-principles calculations. In situ X-ray diffraction using a synchrotron radiation revealed that the high-pressure phase is the predicted δ-Li3PS4 phase.

  2. Stabilization of a β-hairpin in monomeric Alzheimer's amyloid-β peptide inhibits amyloid formation

    Science.gov (United States)

    Hoyer, Wolfgang; Grönwall, Caroline; Jonsson, Andreas; Ståhl, Stefan; Härd, Torleif

    2008-01-01

    According to the amyloid hypothesis, the pathogenesis of Alzheimer's disease is triggered by the oligomerization and aggregation of the amyloid-β (Aβ) peptide into protein plaques. Formation of the potentially toxic oligomeric and fibrillar Aβ assemblies is accompanied by a conformational change toward a high content of β-structure. Here, we report the solution structure of Aβ(1–40) in complex with the phage-display selected affibody protein ZAβ3, a binding protein of nanomolar affinity. Bound Aβ(1–40) features a β-hairpin comprising residues 17–36, providing the first high-resolution structure of Aβ in β conformation. The positions of the secondary structure elements strongly resemble those observed for fibrillar Aβ. ZAβ3 stabilizes the β-sheet by extending it intermolecularly and by burying both of the mostly nonpolar faces of the Aβ hairpin within a large hydrophobic tunnel-like cavity. Consequently, ZAβ3 acts as a stoichiometric inhibitor of Aβ fibrillation. The selected Aβ conformation allows us to suggest a structural mechanism for amyloid formation based on soluble oligomeric hairpin intermediates. PMID:18375754

  3. Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme

    Science.gov (United States)

    Bezem, Maria T.; Baumann, Anne; Skjærven, Lars; Meyer, Romain; Kursula, Petri; Martinez, Aurora; Flydal, Marte I.

    2016-01-01

    Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of catecholamine neurotransmitters. TH is a highly complex enzyme at mechanistic, structural, and regulatory levels, and the preparation of kinetically and conformationally stable enzyme for structural characterization has been challenging. Here, we report on improved protocols for purification of recombinant human TH isoform 1 (TH1), which provide large amounts of pure, stable, active TH1 with an intact N-terminus. TH1 purified through fusion with a His-tagged maltose-binding protein on amylose resin was representative of the iron-bound functional enzyme, showing high activity and stabilization by the natural feedback inhibitor dopamine. TH1 purified through fusion with a His-tagged ZZ domain on TALON is remarkably stable, as it was partially inhibited by resin-derived cobalt. This more stable enzyme preparation provided high-quality small-angle X-ray scattering (SAXS) data and reliable structural models of full-length tetrameric TH1. The SAXS-derived model reveals an elongated conformation (Dmax = 20 nm) for TH1, different arrangement of the catalytic domains compared with the crystal structure of truncated forms, and an N-terminal region with an unstructured tail that hosts the phosphorylation sites and a separated Ala-rich helical motif that may have a role in regulation of TH by interacting with binding partners. PMID:27462005

  4. Short hairpin RNA expression for enhancing the resistance of ...

    African Journals Online (AJOL)

    Short hairpin RNA expression for enhancing the resistance of Bombyx mori (Bm) to nucleopolyhedrovirus in vitro and in vivo. Roy Bhaskar, Fang Zhou, Shuang Liang, Wan-Fu Yue, Yan-shan Niu, Yun- gen Miao ...

  5. Efficacy Analysis of Combinatorial siRNAs against HIV Derived from One Double Hairpin RNA Precursor.

    Science.gov (United States)

    Liu, Chang; Liang, Zhipin; Kong, Xiaohong

    2017-01-01

    Combinatorial small interfering RNA duplexes (siRNAs) have the potential to be a gene therapy against HIV-1, and some studies have reported that transient combinatorial siRNA expression represses HIV replication, but the effects of long-term siRNA expression on HIV replication have not been studied in detail. In this study, HIV-1 replication under the influence of stable combinatorial siRNA expression from a single RNA transcript was analyzed. First, a series of cassettes encoding short hairpin RNA (shRNA)/long hairpin RNA (lhRNA)/double long hairpins (dlhRNA) was constructed and subjected to an analysis of inhibitory efficacy. Next, an optimized dlhRNA encoding cassette was selected and inserted into lentiviral delivery vector FG12. Transient dlhRNA expression reduced replication of HIV-1 in TZM-bl cells and CD4+ T cells successfully. HIV-1 susceptible TZM-bl cells were transducted with the dlhRNA expressing lentiviral vector and sorted by fluorescence-activated cell sorting to obtain stable dlhRNA expressing cells. The generation of four anti-HIV siRNAs in these dlhRNA expressing cells was verified by stem-loop RT-PCR assay. dlhRNA expression did not activate a non-specific interferon response. The dlhRNA expressing cells were also challenged with HIV-1 NL4-3, which revealed that stable expression of combinatorial siRNAs repressed HIV-1 replication for 8 days, after which HIV-1 overcame the inhibitory effect of siRNA expression by expressing mutant versions of RNAi targets. The results of this evaluation of the long-term inhibitory effects of combinatorial siRNAs against HIV-1 provide a reference for researchers who utilize combinatorial RNA interference against HIV-1 or other error-prone viruses.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Hang; Ma, Wen [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Han, Wei [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

    2015-12-28

    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 {sup 3}J(H{sub N}H{sub C{sub α}})-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.

  7. Embodied memory: effective and stable perception by combining optic flow and image structure.

    Science.gov (United States)

    Pan, Jing Samantha; Bingham, Ned; Bingham, Geoffrey P

    2013-12-01

    Visual perception studies typically focus either on optic flow structure or image structure, but not on the combination and interaction of these two sources of information. Each offers unique strengths in contrast to the other's weaknesses. Optic flow yields intrinsically powerful information about 3D structure, but is ephemeral. It ceases when motion stops. Image structure is less powerful in specifying 3D structure, but is stable. It remains when motion stops. Optic flow and image structure are intrinsically related in vision because the optic flow carries one image to the next. This relation is especially important in the context of progressive occlusion, in which optic flow provides information about the location of targets hidden in subsequent image structure. In four experiments, we investigated the role of image structure in "embodied memory" in contrast to memory that is only in the head. We found that either optic flow (Experiment 1) or image structure (Experiment 2) alone were relatively ineffective, whereas the combination was effective and, in contrast to conditions requiring reliance on memory-in-the-head, much more stable over extended time (Experiments 2 through 4). Limits well documented for visual short memory (that is, memory-in-the-head) were strongly exceeded by embodied memory. The findings support J. J. Gibson's (1979/1986, The Ecological Approach to Visual Perception, Boston, MA, Houghton Mifflin) insights about progressive occlusion and the embodied nature of perception and memory.

  8. Prediction of Stable Ruthenium Silicides from First-Principles Calculations: Stoichiometries, Crystal Structures, and Physical Properties.

    Science.gov (United States)

    Zhang, Chuanzhao; Kuang, Xiaoyu; Jin, Yuanyuan; Lu, Cheng; Zhou, Dawei; Li, Peifang; Bao, Gang; Hermann, Andreas

    2015-12-09

    We present results of an unbiased structure search for stable ruthenium silicide compounds with various stoichiometries, using a recently developed technique that combines particle swarm optimization algorithms with first-principles calculations. Two experimentally observed structures of ruthenium silicides, RuSi (space group P2(1)3) and Ru2Si3 (space group Pbcn), are successfully reproduced under ambient pressure conditions. In addition, a stable RuSi2 compound with β-FeSi2 structure type (space group Cmca) was found. The calculations of the formation enthalpy, elastic constants, and phonon dispersions demonstrate the Cmca-RuSi2 compound is energetically, mechanically, and dynamically stable. The analysis of electronic band structures and densities of state reveals that the Cmca-RuSi2 phase is a semiconductor with a direct band gap of 0.480 eV and is stabilized by strong covalent bonding between Ru and neighboring Si atoms. On the basis of the Mulliken overlap population analysis, the Vickers hardness of the Cmca structure RuSi2 is estimated to be 28.0 GPa, indicating its ultra-incompressible nature.

  9. Spatial confinement induces hairpins in nicked circular DNA

    Science.gov (United States)

    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

  10. On the a priori possibility of the formation of hexameric mini-hairpin d(GCGAGC) in solution

    Science.gov (United States)

    Rubin, Yu. V.; Belous, L. F.; Evstigneev, M. P.

    2012-11-01

    Combined high-level (M05-2x, M06-2x functionals of DFT method) and semi-empirical structural and energetic analyses have confirmed the a priori possibility for the formation of the shortest ever known hexameric hairpin d(GCGAGC) with GA loop in aqueous solution. The origin of stabilisation comes from intramolecular H-bonding and hydrophobic interactions and, to lesser extent, from intramolecular van der Waals and electrostatic forces. This result provides a basis for seeking of such mini-hairpins in experiment.

  11. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  12. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    International Nuclear Information System (INIS)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database

  13. Dipolar Quinoidal Acene Analogues as Stable Isoelectronic Structures of Pentacene and Nonacene

    KAUST Repository

    Shi, Xueliang

    2015-10-08

    Quinoidal thia-acene analogues, as the respective isoelectronic structures of pentacene and nonacene, were synthesized and an unusual 1,2-sulfur migration was observed during the Friedel-Crafts alkylation reaction. The analogues display a closed-shell quinoidal structure in the ground state with a distinctive dipolar character. In contrast to their acene isoelectronic structures, both compounds are stable because of the existence of more aromatic sextet rings, a dipolar character, and kinetic blocking. They exhibit unique packing in single crystals resulting from balanced dipole-dipole and [C-H⋯π]/[C-H⋯S] interactions.

  14. ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins

    Directory of Open Access Journals (Sweden)

    Tempel Sébastien

    2012-09-01

    Full Text Available Abstract Background Inverted repeat genes encode precursor RNAs characterized by hairpin structures. These RNA hairpins are then metabolized by biosynthetic pathways to produce functional small RNAs. In eukaryotic genomes, short non-autonomous transposable elements can have similar size and hairpin structures as non-coding precursor RNAs. This resemblance leads to problems annotating small RNAs. Results We mapped all microRNA precursors from miRBASE to several genomes and studied the repetition and dispersion of the corresponding loci. We then searched for repetitive elements overlapping these loci. We developed an automatic method called ncRNAclassifier to classify pre-ncRNAs according to their relationship with transposable elements (TEs. We showed that there is a correlation between the number of scattered occurrences of ncRNA precursor candidates and the presence of TEs. We applied ncRNAclassifier on six chordate genomes and report our findings. Among the 1,426 human and 721 mouse pre-miRNAs of miRBase, we identified 235 and 68 mis-annotated pre-miRNAs respectively corresponding completely to TEs. Conclusions We provide a tool enabling the identification of repetitive elements in precursor ncRNA sequences. ncRNAclassifier is available at http://EvryRNA.ibisc.univ-evry.fr.

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

    Directory of Open Access Journals (Sweden)

    Das Atze T

    2012-07-01

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

  16. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate

    Science.gov (United States)

    Tan, Elliot; Wilson, Timothy J.; Nahas, Michelle K.; Clegg, Robert M.; Lilley, David M. J.; Ha, Taekjip

    2003-01-01

    The natural form of the hairpin ribozyme comprises two major structural elements: a four-way RNA junction and two internal loops carried by adjacent arms of the junction. The ribozyme folds into its active conformation by an intimate association between the loops, and the efficiency of this process is greatly enhanced by the presence of the junction. We have used single-molecule spectroscopy to show that the natural form fluctuates among three distinct states: the folded state and two additional, rapidly interconverting states (proximal and distal) that are inherited from the junction. The proximal state juxtaposes the two loop elements, thereby increasing the probability of their interaction and thus accelerating folding by nearly three orders of magnitude and allowing the ribozyme to fold rapidly in physiological conditions. Therefore, the hairpin ribozyme exploits the dynamics of the junction to facilitate the formation of the active site from its other elements. Dynamic interplay between structural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other functional RNA molecules. PMID:12883002

  17. Stable algorithm for the computation of the electromagnetic field distribution of eigenmodes of periodic diffraction structures.

    Science.gov (United States)

    Bezus, Evgeni A; Doskolovich, Leonid L

    2012-11-01

    In the present work, a stable algorithm for the calculation of the electromagnetic field distributions of the eigenmodes of one-dimensional diffraction gratings is presented. The proposed approach is based on the method for the computation of the propagation constants of Bloch waves of such structures previously presented by Cao et al.[J. Opt. Soc. Am. A 19, 335 (2002)] and uses a modified S-matrix algorithm to ensure numerical stability.

  18. Muon-Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution.

    Science.gov (United States)

    Goli, Mohammad; Shahbazian, Shant

    2016-02-12

    Isotope substitutions are usually conceived to play a marginal role on the structure and bonding pattern of molecules. However, a recent study [Angew. Chem. Int. Ed. 2014, 53, 13706-13709; Angew. Chem. 2014, 126, 13925-13929] further demonstrates that upon replacing a proton with a positively charged muon, as the lightest radioisotope of hydrogen, radical changes in the nature of the structure and bonding of certain species may take place. The present report is a primary attempt to introduce another example of structural transformation on the basis of the malonaldehyde system. Accordingly, upon replacing the proton between the two oxygen atoms of malonaldehyde with the positively charged muon a serious structural transformation is observed. By using the ab initio nuclear-electronic orbital non-Born-Oppenheimer procedure, the nuclear configuration of the muon-substituted species is derived. The resulting nuclear configuration is much more similar to the transition state of the proton transfer in malonaldehyde rather than to the stable configuration of malonaldehyde. The comparison of the "atoms in molecules" (AIM) structure of the muon-substituted malonaldehyde and the AIM structure of the stable and the transition-state configurations of malonaldehyde also unequivocally demonstrates substantial similarities of the muon-substituted malonaldehyde to the transition state. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Structure and Dynamics of Thin Ionomer Films: a Key to A Stable Fuel Cell Membrane.

    Science.gov (United States)

    Perahia, Dvora

    2000-03-01

    The technology for solid polymeric electrolytic membranes for a fuel cells, calls for the thinnest film which is electrochemically stable. At present, none supported polymeric solid state fuel cell membranes, thinner than 50 microns, fail mechanically during fuel cell operation. When approaching the thin film limits, interfacial effects become significant to structure dynamics and consequently, the stability of the membranes. Our work focuses on understanding the interfacial effects on thin per-fluorinated ionomer films, including interfacial effects on the thin films themselves and nanotubes-thin film complexes, mimicking the catalyst-ionomer complexes. In particular we investigated the dynamics and structure in 500 angstrom and less, films made by several perfluorinated ionomers, cast on a solid support. Both the films and their parent solutions were investigated with the goal of resolving the factors that affect the stability in the ultra thin regime. AFM/STM and X-ray and neutron reflectivity were used to investigate the thin films and small angle neutron scattering was utilized to the study of the solutions. Films were both spin-coated and self assembles from solutions on a model oxidized single crystal silicon wafer, treated with HF. When coated from molecular solutions, the films tend to dewet on a time scale of minutes to hours. With increasing concentrations, above the critical micellar concentration of the ionomers in water/alcohol, stable films on the order of 200-500 angstroms were formed. While self-assembled films were found to be stable at temperatures close to Tg of the ionomer, spin-coated ones partially dewet. The surface structure obtained, exhibit periodicity on different length scales, depending on the concentration of the polymer in the solution from which the film was assembled. In the ultra dilute regime, micelles were detected at the solid interface. Films formed from dilute solutions exhibit fractal nature with a fractal dimension varying

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  2. scid cells efficiently integrate hairpin and linear DNA substrates.

    Science.gov (United States)

    Staunton, J E; Weaver, D T

    1994-01-01

    The scid mouse mutation affects V(D)J rearrangement and double-strand break repair. scid V(D)J rearrangement is characterized by defective coding joint formation which prevents the development of mature B and T cells. Hairpin DNA has been implicated in the formation of V(D)J coding joints. We found scid cells to be proficient in hairpin processing in the context of DNA integration. In addition, we found that the scid defect did not impair integration of linear DNA via nonhomologous recombination. Therefore, hairpin processing and integration of DNA into the genome are distinct from hypersensitivity to ionizing radiation and the defect in V(D)J recombination. Images PMID:8196630

  3. Stable Encoding of Task Structure Coexists With Flexible Coding of Task Events in Sensorimotor Striatum

    Science.gov (United States)

    Kubota, Yasuo; Liu, Jun; Hu, Dan; DeCoteau, William E.; Eden, Uri T.; Smith, Anne C.

    2009-01-01

    The sensorimotor striatum, as part of the brain's habit circuitry, has been suggested to store fixed action values as a result of stimulus-response learning and has been contrasted with a more flexible system that conditionally assigns values to behaviors. The stability of neural activity in the sensorimotor striatum is thought to underlie not only normal habits but also addiction and clinical syndromes characterized by behavioral fixity. By recording in the sensorimotor striatum of mice, we asked whether neuronal activity acquired during procedural learning would be stable even if the sensory stimuli triggering the habitual behavior were altered. Contrary to expectation, both fixed and flexible activity patterns appeared. One, representing the global structure of the acquired behavior, was stable across changes in task cuing. The second, a fine-grain representation of task events, adjusted rapidly. Such dual forms of representation may be critical to allow motor and cognitive flexibility despite habitual performance. PMID:19625536

  4. TGP, an extremely stable, non-aggregating fluorescent protein created by structure-guided surface engineering

    Science.gov (United States)

    Close, Devin W.; Don Paul, Craig; Langan, Patricia S.; Wilce, Matthew C.J.; Traore, Daouda A.K.; Halfmann, Randal; Rocha, Reginaldo C.; Waldo, Geoffery S.; Payne, Riley J.; Rucker, Joseph B.; Prescott, Mark; Bradbury, Andrew R.M.

    2014-01-01

    In this paper we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction of high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization. PMID:25287913

  5. Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering.

    Science.gov (United States)

    Close, Devin W; Paul, Craig Don; Langan, Patricia S; Wilce, Matthew C J; Traore, Daouda A K; Halfmann, Randal; Rocha, Reginaldo C; Waldo, Geoffery S; Payne, Riley J; Rucker, Joseph B; Prescott, Mark; Bradbury, Andrew R M

    2015-07-01

    In this article, we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction of high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization. © 2014 Wiley Periodicals, Inc.

  6. The search for the most stable structures of silicon-carbon monolayer compounds.

    Science.gov (United States)

    Li, Pengfei; Zhou, Rulong; Zeng, Xiao Cheng

    2014-10-21

    The most stable structures of two-dimensional (2D) silicon-carbon monolayer compounds with different stoichiometric compositions (i.e., Si : C ratio = 2 : 3, 1 : 3 and 1 : 4) are predicted for the first time based on the particle-swarm optimization (PSO) technique combined with density functional theory optimization. Although the 2D Si-C monolayer compounds considered here are rich in carbon, many of the low-energy metastable and the lowest-energy silicon-carbon structures are not graphene (carbon monolayer) like. Phonon-spectrum calculations and ab initio molecular dynamics simulations were also performed to confirm the dynamical stability of the predicted most stable 2D silicon-carbon structures as well their thermal stability at elevated temperature. The computed electronic band structures show that all three predicted silicon-carbon compounds are semiconductors with direct or indirect bandgaps. Importantly, their bandgaps are predicted to be close to those of bulk silicon or bulk germanium. If confirmed in the laboratory, these 2D silicon-carbon compounds with different stoichiometric compositions may be exploited for future applications in nanoelectronic devices.

  7. Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus.

    Science.gov (United States)

    Dror, Adi; Kanteev, Margarita; Kagan, Irit; Gihaz, Shalev; Shahar, Anat; Fishman, Ayelet

    2015-11-01

    Enzymatic production of biodiesel by transesterification of triglycerides and alcohol, catalyzed by lipases, offers an environmentally friendly and efficient alternative to the chemically catalyzed process while using low-grade feedstocks. Methanol is utilized frequently as the alcohol in the reaction due to its reactivity and low cost. However, one of the major drawbacks of the enzymatic system is the presence of high methanol concentrations which leads to methanol-induced unfolding and inactivation of the biocatalyst. Therefore, a methanol-stable lipase is of great interest for the biodiesel industry. In this study, protein engineering was applied to substitute charged surface residues with hydrophobic ones to enhance the stability in methanol of a lipase from Geobacillus stearothermophilus T6. We identified a methanol-stable variant, R374W, and combined it with a variant found previously, H86Y/A269T. The triple mutant, H86Y/A269T/R374W, had a half-life value at 70 % methanol of 324 min which reflects an 87-fold enhanced stability compared to the wild type together with elevated thermostability in buffer and in 50 % methanol. This variant also exhibited an improved biodiesel yield from waste chicken oil compared to commercial Lipolase 100L® and Novozyme® CALB. Crystal structures of the wild type and the methanol-stable variants provided insights regarding structure-stability correlations. The most prominent features were the extensive formation of new hydrogen bonds between surface residues directly or mediated by structural water molecules and the stabilization of Zn and Ca binding sites. Mutation sites were also characterized by lower B-factor values calculated from the X-ray structures indicating improved rigidity.

  8. Structurally stable gel bead containing entrapped enzyme and method for manufacture thereof

    Science.gov (United States)

    Woodward, J.

    1998-12-08

    This research provides a structurally stable gel bead containing an entrapped enzyme and a method for its manufacture. The enzyme is covalently cross-linked to gelatin in the presence of glutaraldehyde prior to the formation of the gel bead, to prevent leakage of the enzyme. Propylene glycol alginate is then added to the mixture. Once the gel beads are formed, they are then soaked in glutaraldehyde, which imparts structural stability to the gel beads. This method can be used with many types of enzymes, such as proteases, carbohydrases, proteases, ligases, isomerases, oxidoreductases, and specialty enzymes. These and other enzymes can be immobilized in the gel beads and utilized in a number of enzymatic processes. Exogenously added ions are not required to maintain the structural stability of these gel beads. 7 figs.

  9. Rich stoichiometries of stable Ca-Bi system: Structure prediction and superconductivity

    Science.gov (United States)

    Dong, Xu; Fan, Changzeng

    2015-03-01

    Using a variable-composition ab initio evolutionary algorithm implemented in the USPEX code, we have performed a systematic search for stable compounds in the Ca-Bi system at different pressures. In addition to the well-known tI12-Ca2Bi and oS12-CaBi2, a few more structures were found by our calculations, among which phase transitions were also predicted in Ca2Bi (tI12 --> oI12 --> hP6), Ca3Bi2 (hP5 --> mC20 --> aP5) and CaBi (tI2 --> tI8), as well as a new phase (Ca3Bi) with a cF4 structure. All the newly predicted structures can be both dynamically and thermodynamically stable with increasing pressure. The superconductive properties of cF4-CaBi3, tI2-CaBi and cF4-Ca3Bi were studied and the superconducting critical temperature Tc can be as high as 5.16, 2.27 and 5.25 K, respectively. Different superconductivity behaviors with pressure increasing have been observed by further investigations.

  10. Entropy stable high order discontinuous Galerkin methods for ideal compressible MHD on structured meshes

    Science.gov (United States)

    Liu, Yong; Shu, Chi-Wang; Zhang, Mengping

    2018-02-01

    We present a discontinuous Galerkin (DG) scheme with suitable quadrature rules [15] for ideal compressible magnetohydrodynamic (MHD) equations on structural meshes. The semi-discrete scheme is analyzed to be entropy stable by using the symmetrizable version of the equations as introduced by Godunov [32], the entropy stable DG framework with suitable quadrature rules [15], the entropy conservative flux in [14] inside each cell and the entropy dissipative approximate Godunov type numerical flux at cell interfaces to make the scheme entropy stable. The main difficulty in the generalization of the results in [15] is the appearance of the non-conservative "source terms" added in the modified MHD model introduced by Godunov [32], which do not exist in the general hyperbolic system studied in [15]. Special care must be taken to discretize these "source terms" adequately so that the resulting DG scheme satisfies entropy stability. Total variation diminishing / bounded (TVD/TVB) limiters and bound-preserving limiters are applied to control spurious oscillations. We demonstrate the accuracy and robustness of this new scheme on standard MHD examples.

  11. Use of systematics in the interpretation of nuclear structure far from the beta-stable region

    International Nuclear Information System (INIS)

    Wood, J.L.

    1979-01-01

    The use of systematics in the interpretation of nuclear structure far from the beta-stable region is discussed. In particular, a set of rules for the use of systematics is presented together with some experimental criteria that need to be fulfilled for radioactive decay scheme studies in order that all states up to a given spin-parity and energy are located. Illustrative examples are taken from the region 180 < A < 210, with particular emphasis on the odd-mass Au and Hg nuclei. 6 figures

  12. Stable isotopes provide insight into population structure and segregation in eastern North Atlantic sperm whales

    DEFF Research Database (Denmark)

    Borrell, Asunción; Velásquez Vacca, Adriana; Pinela, Ana M.

    2013-01-01

    highly mobile, shows indication of structuring in the eastern North Atlantic, an ocean basin in which a single population is believed to occur. To do so, we examined stable isotope values in sequential growth layer groups of teeth from individuals sampled in Denmark and NW Spain. In each layer we...... measured oxygen-isotope ratios (delta O-18) in the inorganic component (hydroxyapatite), and nitrogen and carbon isotope ratios (delta N-15: delta C-13) in the organic component (primarily collagenous). We found significant differences between Denmark and NW Spain in delta N-15 and delta O-18 values...

  13. Structure-Guided Redesign Increases the Propensity of HIV Env To Generate Highly Stable Soluble Trimers.

    Science.gov (United States)

    Guenaga, Javier; Dubrovskaya, Viktoriya; de Val, Natalia; Sharma, Shailendra K; Carrette, Barbara; Ward, Andrew B; Wyatt, Richard T

    2015-12-30

    Due to high viral diversity, an effective HIV-1 vaccine will likely require Envs derived from multiple subtypes to generate broadly neutralizing antibodies (bNAbs). Soluble Env mimics, like the native flexibly linked (NFL) and SOSIP trimers, derived from the subtype A BG505 Env, form homogeneous, stable native-like trimers. However, other Env sequences, such as JRFL and 16055 from subtypes B and C, do so to a lesser degree. The high-resolution BG505 SOSIP crystal structures permit the identification and redesign of Env elements involved in trimer stability. Here, we identified structure trimer-derived (TD) residues that increased the propensity of the subtype B JRFL and subtype C 16055 Env sequences to form well-ordered, homogenous, and highly stable soluble trimers. The generation of these spike mimics no longer required antibody-based selection, positive or negative. Using the redesigned subtype B and C trimer representatives as respective foundations, we further stabilized the NFL TD trimers by engineering an intraprotomer disulfide linkage in the prebridging sheet, I201C-A433C (CC), that locks the gp120 in the receptor nontriggered state. We demonstrated that this disulfide pair prevented CD4 induced-conformational rearrangements in NFL trimers derived from the prototypic subtype A, B, and C representatives. Coupling the TD-based design with the engineered disulfide linkage, CC, increased the propensity of Env to form soluble highly stable spike mimics that are resistant to CD4-induced changes. These advances will allow testing of the hypothesis that such stabilized immunogens will more efficiently elicit neutralizing antibodies in small-animal models and primates. HIV-1 displays unprecedented global diversity circulating in the human population. Since the envelope glycoprotein (Env) is the target of neutralizing antibodies, Env-based vaccine candidates that address such diversity are needed. Soluble well-ordered Env mimics, typified by NFL and SOSIP trimers

  14. The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition

    NARCIS (Netherlands)

    Das, Devashish; Folkers, Gert; van Dijk, Marc; Jaspers, Nicolaas G.J.; Hoeijmakers, Jan H.J.; Kaptein, Robert; Boelens, Rolf

    2012-01-01

    Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first

  15. Whirlwinds and hairpins in the atmospheric surface layer

    NARCIS (Netherlands)

    Oncley, Steven P.; Hartogensis, O.K.; Tong, Chenning

    2016-01-01

    Vortices in the atmospheric surface layer are characterized using observations at unprecedented resolution from a fixed array of 31 turbulence sensors. During the day, these vortices likely are dust devils, though no visual observations are available for confirmation. At night, hairpin vortices

  16. Design of extended short hairpin RNAs for HIV-1 inhibition

    NARCIS (Netherlands)

    Liu, Ying Poi; Haasnoot, Joost; Berkhout, Ben

    2007-01-01

    RNA interference (RNAi) targeted towards viral mRNAs is widely used to block virus replication in mammalian cells. The specific antiviral RNAi response can be induced via transfection of synthetic small interfering RNAs (siRNAs) or via intracellular expression of short hairpin RNAs (shRNAs). For

  17. Trophic structure in a seabird host-parasite food web: insights from stable isotope analyses.

    Directory of Open Access Journals (Sweden)

    Elena Gómez-Díaz

    2010-05-01

    Full Text Available Ecological studies on food webs rarely include parasites, partly due to the complexity and dimensionality of host-parasite interaction networks. Multiple co-occurring parasites can show different feeding strategies and thus lead to complex and cryptic trophic relationships, which are often difficult to disentangle by traditional methods. We analyzed stable isotope ratios of C ((13C/(12C, delta(13C and N ((15N/(14N, delta(15N of host and ectoparasite tissues to investigate trophic structure in 4 co-occurring ectoparasites: three lice and one flea species, on two closely related and spatially segregated seabird hosts (Calonectris shearwaters. delta(13C isotopic signatures confirmed feathers as the main food resource for the three lice species and blood for the flea species. All ectoparasite species showed a significant enrichment in delta(15N relatively to the host tissue consumed (discrimination factors ranged from 2 to 5 per thousand depending on the species. Isotopic differences were consistent across multiple host-ectoparasite locations, despite of some geographic variability in baseline isotopic levels. Our findings illustrate the influence of both ectoparasite and host trophic ecology in the isotopic structuring of the Calonectris ectoparasite community. This study highlights the potential of stable isotope analyses in disentangling the nature and complexity of trophic relationships in symbiotic systems.

  18. Ultra-Stable Zero-CTE HoneySiC and H2CMN Mirror Support Structures, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA MSFC, GSFC and JPL are interested in Ultra-Stable Mirror Support Structures for Exoplanet Missions. Telescopes with Apertures of 4-meters or larger and using an...

  19. Ultra-Stable Zero-CTE HoneySiC and H2CMN Mirror Support Structures, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA MSFC, GSFC and JPL are interested in Ultra-Stable Mirror Support Structures for Exoplanet Missions. Telescopes with Apertures of 4-meters or larger and using an...

  20. Morphology, molecular structure, and stable carbon isotopic composition of black carbon (BC) in urban topsoils.

    Science.gov (United States)

    Zong, Yutong; Xiao, Qing; Lu, Shenggao

    2018-02-01

    Urban soils contain significant amounts of black carbon (BC) from biomass and fossil fuel combustion and regard to be a pool of BC. BC in urban soils has multiple effects on environmental processes in urban system, such as global climate change, air quality, and public health. Urban topsoil samples (0-10 cm) were collected from Anshan, Liaoning Province, northeast China, which is one of the most important old steel industrial bases in China. The BC in urban topsoils was extracted using the density method. Their chemical composition, morphology, molecular structure, and stable carbon isotopic composition were examined using elemental analysis, scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and stable carbon isotope (δ 13 C). Elemental analysis shows that carbon content in the BC of studied soils ranged from 64.5 to 78.4%, with the average more than 70%. The O/C atomic ratio of BC is on average 0.18. The BC particle displays different morphology, including porous spherical, irregular porous fragmentary, and blocky shapes. The porous spherical BC particles has atomic molar O/C ratio determined by SEM-EDS ranging from 0.04 to 0.37. XRD indicates that BC exists in mainly combining with mineral phases hematite (Fe 2 O 3 ), kaolinite (Al 2 Si 2 O 5 (OH) 4 ), quartz (SiO 2 ), and calcite (CaCO 3 ). The FTIR spectra of BC particles show major bands at approximately 3400 cm -1 (O-H), 2920 cm -1 (C = H), 1600 cm -1 (C = C), 1230 cm -1 (C = O), and 1070 cm -1 (C = O). The stable carbon isotope (δ 13 C) of BC ranges from -24.48 to -23.18‰ with the average of -23.79 ± 0.39‰. The concentration of BC in the industrial area is significantly (p fuel combustion. Results indicated that a combination of atomic O/C ratio, porous structure, and stable carbon isotopic (δ 13 C) of BC could reflect effectively the origin of BC

  1. Human Ku70 protein binds hairpin RNA and double stranded DNA through two different sites.

    Science.gov (United States)

    Anisenko, Andrey N; Knyazhanskaya, Ekaterina S; Zatsepin, Timofey S; Gottikh, Marina B

    2017-01-01

    Human protein Ku usually functions in the cell as a complex of two subunits, Ku70 and Ku80. The Ku heterodimer plays a key role in the non-homologous end joining DNA repair pathway by specifically recognizing the DNA ends at the site of the lesion. The binding of the Ku heterodimer to DNA has been well-studied, and its interactions with RNA have been also described. However, Ku70 subunit is known to have independent DNA binding capability, which is less characterized. RNA binding properties of Ku70 have not been yet specially studied. We have prepared recombinant full-length Ku70 and a set of its truncated mutants in E. coli, and studied their interactions with nucleic acids of various structures: linear single- and double-stranded DNA and RNA, as well as closed circular DNA and hairpin RNA. Ku70 has demonstrated a high affinity binding to double stranded DNA and hairpin RNA with a certain structure only. Interestingly, in contrast to the Ku heterodimer, Ku70 is found to interact with closed circular DNA. We also show for the first time that Ku70 employs two different sites for DNA and RNA binding. The double-stranded DNA is recognized by the C-terminal part of Ku70 including SAP domain as it has been earlier demonstrated, whereas hairpin RNA binding is provided by amino acids 251-438. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  2. Effect of surface texture and structure on the development of stable fluvial armors

    Science.gov (United States)

    Bertin, Stephane; Friedrich, Heide

    2018-04-01

    Stable fluvial armors are found in river systems under conditions of partial sediment transport and limited sediment supply, a common occurrence in nature. Stable armoring is also readily recreated in experimental flumes. Initially, this bed stabilizing phenomenon was examined for different flow discharges and solely related to surface coarsening and bedload transport reduction. The models developed suggest a specific armor composition (i.e., texture) dependent on the parent bed material and formative discharge. Following developments in topographic remote sensing, recent research suggests that armor structure is an important control on bed stability and roughness. In this paper, replicated flume runs during which digital elevation models (DEMs) were collected from both exposed and flooded gravel beds are used to interpret armoring manifestations and to assess their replicability. A range of methodologies was used for the analysis, providing information on (i) surface grain size and orientation, (ii) bed-elevation distributions, (iii) the spatial coherence of the elevations at the grain-scale, (iv) surface slope and aspect, (v) grain imbrication and (vi) the spatial variability in DEM properties. The bed-surface topography was found to be more responsive than bed-material size to changes in flow strength. Our experimental results also provide convincing evidence that gravel-beds' response to water-work during parallel degradation is unique (i.e., replicable) given the formative parameters. Based on this finding, relationships between the armors' properties and formative parameters are proposed, and are supported by adding extensive data from previous research.

  3. Determination of Trophic Structure in Selected Freshwater Ecosystems by using Stable Isotope Analysis.

    Science.gov (United States)

    Zainordin, 'Amila Faqhira; Ab Hamid, Suhaila

    2017-07-01

    Stable isotope analysis has been used extensively to establish trophic relationships in many ecosystems. Present study utilised stable isotope signatures of carbon and nitrogen to identify trophic structure of aquatic food web in river and rice field ecosystems in Perak, northern peninsular Malaysia. The mean δ 13 C values of all producers ranged from -35.29 ± 0.21 to -26.00 ± 0.050‰. The greatest δ 15 N values noted was in zenarchopterid fish with 9.68 ± 0.020‰. The δ 15 N values of aquatic insects ranged between 2.59 ± 0.107 in Elmidae (Coleoptera) and 8.11 ± 0.022‰ in Nepidae (Hemiptera). Correspondingly, with all the δ 13 C and δ 15 N values recorded, it can be deduced that there are four trophic levels existed in the freshwater ecosystems which started with the producer (plants), followed by primary consumer (aquatic insects and non-predatory fish), secondary consumer (invertebrate predators) and lastly tertiary consumer (vertebrate predators).

  4. The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4

    International Nuclear Information System (INIS)

    Shen, Peter S.; Enderlein, Dirk; Nelson, Christian D.S.; Carter, Weston S.; Kawano, Masaaki; Xing Li; Swenson, Robert D.; Olson, Norman H.; Baker, Timothy S.; Cheng, R. Holland; Atwood, Walter J.; Johne, Reimar; Belnap, David M.

    2011-01-01

    Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.

  5. Statistical scale of hairpin packets in the later stage of bypass transition induced by cylinder wake

    Science.gov (United States)

    Tang, Z. Q.; Jiang, N.

    2012-08-01

    The hairpin packet's structure and its statistical scale in the later stage of bypass transition induced by a cylinder wake are investigated by time-resolved particle image velocimetry from the side and top view, respectively. Linear stochastic estimation is used to achieve the conditionally averaged velocity fields. For the side view case, the conditionally averaged structure consists of a series of swirling motions located along a line inclining at a large angle (18°) from the wall and a low-speed region occupied by the cylinder wake appearing right above them. In the ( x, z)-plane at the wall-normal height y/δ = 0.2, the dominant structures are shown to be the large-scale regions of low momentum elongated almost over 3δ along the streamwise. The low-speed regions are consistently bordered by small-scale counter-rotating vortice pairs organized in the streamwise with a statistical spanwise width of 0.55δ. The results suggest that in the later part of the transitional zone, the upward induction of the cylinder wake enhances both the wall-normal and spanwise extent of the hairpin packets.

  6. Stable anilinyl radicals coordinated to nickel: X-ray crystal structure and characterization.

    Science.gov (United States)

    Kochem, Amélie; Gellon, Gisèle; Leconte, Nicolas; Baptiste, Benoit; Philouze, Christian; Jarjayes, Olivier; Orio, Maylis; Thomas, Fabrice

    2013-12-02

    Two anilinosalen and a mixed phenol-anilinosalen ligands involving sterically hindered anilines moieties were synthesized. Their nickel(II) complexes 1, 2, and 3 were prepared and characterized. They could be readily one-electron oxidized (E(1/2)=-0.30, -0.26 and 0.10 V vs. Fc(+)/Fc, respectively) into anilinyl radicals species [1](+), [2](+), and [3](+), respectively. The radical complexes are extremely stable and were isolated as single crystals. X-ray crystallographic structures reveal that the changes in bond length resulting from oxidation do not exceed 0.02 Å within the ligand framework in the symmetrical [1](+) and [2](+). No quinoid bond pattern was present. In contrast, larger structural rearrangements were evidenced for the unsymmetrical [3](+), with shortening of one C(ortho)-C(meta) bond. Radical species [1](+) and [2](+) exhibit a strong absorption band at around 6000 cm(-1) (class III mixed valence compounds). This band is significantly less intense than [3](+), consistent with a rather localized anilinyl radical character, and thus a classification of this species as class II mixed-valence compound. Magnetic and electronic properties, as well as structural parameters, have been computed by DFT methods. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Highly active and stable oxaloacetate decarboxylase Na⁺ pump complex for structural analysis.

    Science.gov (United States)

    Inoue, Michio; Li, Xiaodan

    2015-11-01

    The oxaloacetate decarboxylase primary Na(+) pump (Oad) produces energy for the surviving of some pathogenic bacteria under anaerobic conditions. Oad composes of three subunits: Oad-α, a biotinylated soluble subunit and catalyzes the decarboxylation of oxaloacetate; Oad-β, a transmembrane subunit and functions as a Na(+) pump; and Oad-γ, a single transmembrane α-helical anchor subunit and assembles Oad-α/β/γ complex. The molecular mechanism of Oad complex coupling the exothermic decarboxylation to generate the Na(+) electrochemical gradient remains unsolved. Our biophysical and biochemical studies suggested that the stoichiometry of Oad complex from Vibrio cholerae composed of α, β, γ in 4:2:2 stoichiometry not that of 4:4:4. The high-resolution structure determination of the Oad complex would reveal the energetic transformation mechanism from the catalytical soluble α subunit to membrane β subunit. Sufficient amount stable, conformational homogenous and active Oad complex with the right stoichiometry is the prerequisite for structural analysis. Here we report an easy and reproducible protocol to obtain high quantity and quality Oad complex protein for structural analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. A versatile approach to multiple gene RNA interference using microRNA-based short hairpin RNAs

    Directory of Open Access Journals (Sweden)

    Kivork Christine

    2007-10-01

    Full Text Available Abstract Background Effective and stable knockdown of multiple gene targets by RNA interference is often necessary to overcome isoform redundancy, but it remains a technical challenge when working with intractable cell systems. Results We have developed a flexible platform using RNA polymerase II promoter-driven expression of microRNA-like short hairpin RNAs which permits robust depletion of multiple target genes from a single transcript. Recombination-based subcloning permits expression of multi-shRNA transcripts from a comprehensive range of plasmid or viral vectors. Retroviral delivery of transcripts targeting isoforms of cAMP-dependent protein kinase in the RAW264.7 murine macrophage cell line emphasizes the utility of this approach and provides insight to cAMP-dependent transcription. Conclusion We demonstrate functional consequences of depleting multiple endogenous target genes using miR-shRNAs, and highlight the versatility of the described vector platform for multiple target gene knockdown in mammalian cells.

  9. P element temperature-specific transposition: a model for possible regulation of mobile elements activity by pre-mRNA secondary structure.

    Science.gov (United States)

    Gultyaev, A; Redchuk, T; Korolova, A; Kozeretska, I

    2014-01-01

    P element is a DNA transposon, known to spread in genome using transposase activity. Its activity is tissue-specific and normally observed at high temperatures within 24 degrees C to 29 degrees C. Here, we present a predicted RNA secondary structure domain of P element pre-mRNA which could potentially regulate the temperature sensitivity of the P element activity. In canonical P elements, the structure is a small hairpin with double-helical part interrupted by a symmetric loop and a mismatch. In M type P elements, the A.A mismatch is substituted by an A-U base pair, stabilizing the structure. The hairpin structure covers the region involving the IVS-3 5' splice site and both pseudo-splice sites F1 and F2. While the IVS-3 and F1 binding sites of U1 snRNA are located in the double-stranded part of the structure, the F2 site is exposed in the hairpin loop. The formation of this structure may interfere with landing of U1 snRNA on IVS-3 site, while F2 is positioned for the interaction. Alignment of P element sequences supports the proposed existence of the hairpin, showing high similarity for this region. The hairpin structure, stable at low temperatures, may prevent correct IVS-3 splicing. Conversely, temperature-induced destabilization of the hairpin structure may result in the splicing at the proper IVS-3 splice site. Taking into account the increasing amount of data demonstrating the important influence of RNA folding on phenotypes determined by alternative splicing a model for possible regulation of the activity of mobile elements by pre-mRNA secondary structure seems intriguing.

  10. Aedes aegypti has spatially structured and seasonally stable populations in Yogyakarta, Indonesia.

    Science.gov (United States)

    Rašić, Gordana; Endersby-Harshman, Nancy; Tantowijoyo, Warsito; Goundar, Anjali; White, Vanessa; Yang, Qiong; Filipović, Igor; Johnson, Petrina; Hoffmann, Ary A; Arguni, Eggi

    2015-12-01

    Dengue fever, the most prevalent global arboviral disease, represents an important public health problem in Indonesia. Control of dengue relies on the control of its main vector, the mosquito Aedes aegypti, yet nothing is known about the population history and genetic structure of this insect in Indonesia. Our aim was to assess the spatio-temporal population genetic structure of Ae. aegypti in Yogyakarta, a densely populated region on Java with common dengue outbreaks. We used multiple marker systems (microsatellites, nuclear and mitochondrial genome-wide single nucleotide polymorphisms generated via Restriction-site Associated DNA sequencing) to analyze 979 Ae. aegypti individuals collected from the Yogyakarta city and the surrounding hamlets during the wet season in 2011 and the following dry season in 2012. We employed individual- and group-based approaches for inferring genetic structure. We found that Ae. aegypti in Yogyakarta has spatially structured and seasonally stable populations. The spatial structuring was significant for the nuclear and mitochondrial markers, while the temporal structuring was non-significant. Nuclear markers identified three main genetic clusters, showing that hamlets have greater genetic isolation from each other and from the inner city sites. However, one hamlet experienced unrestricted mosquito interbreeding with the inner city, forming a single genetic cluster. Genetic distance was poorly correlated with the spatial distance among mosquito samples, suggesting stronger influence of human-assisted gene flow than active mosquito movement on spatial genetic structure. A star-shaped mitochondrial haplotype network and a significant R(2) test statistic (R(2) = 0.0187, P = 0.001) support the hypothesis that Ae. aegypti in Yogyakarta originated from a small or homogeneous source and has undergone a relatively recent demographic expansion. We report the first insights into the spatio-temporal genetic structure and the underlying

  11. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines

    Directory of Open Access Journals (Sweden)

    Tatjana P Kristensen

    2014-03-01

    Full Text Available 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

  12. A Fundamental Approach to Developing Aluminium based Bulk Amorphous Alloys based on Stable Liquid Metal Structures and Electronic Equilibrium - 154041

    Science.gov (United States)

    2017-03-28

    AFRL-AFOSR-JP-TR-2017-0027 A Fundamental Approach to Developing Aluminium -based Bulk Amorphous Alloys based on Stable Liquid-Metal Structures and...to 16 Dec 2016 4.  TITLE AND SUBTITLE A Fundamental Approach to Developing Aluminium -based Bulk Amorphous Alloys based on Stable Liquid-Metal...Air Force Research Laboratory for accurately predicting compositions of new amorphous alloys specifically based on aluminium with properties superior

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

    International Nuclear Information System (INIS)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping; Ye, Lihong; Zhang, Xiaodong

    2015-01-01

    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 its 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China); Ye, Lihong [State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071 (China); Zhang, Xiaodong, E-mail: zhangxd@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China)

    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 its 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.

  15. Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding

    Directory of Open Access Journals (Sweden)

    Brewster Aaron S

    2010-08-01

    Full Text Available Abstract Background The mini-chromosome maintenance protein (MCM complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. While the eukaryotic complex consists of six homologous proteins (MCM2-7, the archaeon Sulfolobus solfataricus has only one MCM protein (ssoMCM, six subunits of which form a homohexamer. We have recently reported a 4.35Å crystal structure of the near full-length ssoMCM. The structure reveals a total of four β-hairpins per subunit, three of which are located within the main channel or side channels of the ssoMCM hexamer model generated based on the symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM structure. The fourth β-hairpin, however, is located on the exterior of the hexamer, near the exit of the putative side channels and next to the ATP binding pocket. Results In order to better understand this hairpin's role in DNA binding and helicase activity, we performed a detailed mutational and biochemical analysis of nine residues on this exterior β-hairpin (EXT-hp. We examined the activities of the mutants related to their helicase function, including hexamerization, ATPase, DNA binding and helicase activities. The assays showed that some of the residues on this EXT-hp play a role for DNA binding as well as for helicase activity. Conclusions These results implicate several current theories regarding helicase activity by this critical hexameric enzyme. As the data suggest that EXT-hp is involved in DNA binding, the results reported here imply that the EXT-hp located near the exterior exit of the side channels may play a role in contacting DNA substrate in a manner that affects DNA unwinding.

  16. β-Hairpin of Islet Amyloid Polypeptide Bound to an Aggregation Inhibitor

    Science.gov (United States)

    Mirecka, Ewa A.; Feuerstein, Sophie; Gremer, Lothar; Schröder, Gunnar F.; Stoldt, Matthias; Willbold, Dieter; Hoyer, Wolfgang

    2016-01-01

    In type 2 diabetes, the formation of islet amyloid consisting of islet amyloid polypeptide (IAPP) is associated with reduction in β-cell mass and contributes to the failure of islet cell transplantation. Rational design of inhibitors of IAPP amyloid formation has therapeutic potential, but is hampered by the lack of structural information on inhibitor complexes of the conformationally flexible, aggregation-prone IAPP. Here we characterize a β-hairpin conformation of IAPP in complex with the engineered binding protein β-wrapin HI18. The β-strands correspond to two amyloidogenic motifs, 12-LANFLVH-18 and 22-NFGAILS-28, which are connected by a turn established around Ser-20. Besides backbone hydrogen bonding, the IAPP:HI18 interaction surface is dominated by non-polar contacts involving hydrophobic side chains of the IAPP β-strands. Apart from monomers, HI18 binds oligomers and fibrils and inhibits IAPP aggregation and toxicity at low substoichiometric concentrations. The IAPP β-hairpin can serve as a molecular recognition motif enabling control of IAPP aggregation. PMID:27641459

  17. Structure of stable binary neutron star merger remnants: Role of initial spin

    Science.gov (United States)

    Kastaun, W.; Ciolfi, R.; Endrizzi, A.; Giacomazzo, B.

    2017-08-01

    We present general relativistic numerical simulations of binary neutron star (BNS) mergers with different initial spin configurations. We focus on models with stars of mass 1.4 M⊙ each, which employ the equation of state (EOS) by Shen, Horowitz, and Teige, and which result in stable NSs as merger remnants. For comparison, we consider two irrotational equal mass (M =1.35 M⊙) and unequal mass (M =1.29 , 1.42 M⊙ ) BNS models using the APR4 EOS, which result in a supramassive merger remnant. We present visualizations of the fluid flow and temperature distribution and find a strong impact of the spin on vortex structure and nonaxisymmetric deformation. We compute the radial mass distribution and the rotation profile in the equatorial plane using recently developed measures independent of spatial gauge, revealing slowly rotating cores that can be well approximated by the cores of spherical stars. We also study the influence of the spin on the inspiral phase and the gravitational wave (GW) signal. Using a newly developed analysis method, we further show that gravitational waveforms from BNS mergers can exhibit one or more phase jumps after merger, which occur together with minima of the strain amplitude. We provide a natural explanation in terms of the remnant's quadrupole moment, and show that cancellation effects due to phase jumps can have a strong impact on the GW power spectrum. Finally, we discuss the impact of the spin on the amount of ejected matter.

  18. Exploration of stable compounds, crystal structures, and superconductivity in the Be-H system

    Directory of Open Access Journals (Sweden)

    Shuyin Yu

    2014-10-01

    Full Text Available Using first-principles variable-composition evolutionary methodology, we explored the high-pressure structures of beryllium hydrides between 0 and 400 GPa. We found that BeH2 remains the only stable compound in this pressure range. The pressure-induced transformations are predicted as I b a m → P 3 ̄ m 1 → R 3 ̄ m → C m c m → P 4 / n m m , which occur at 24, 139, 204 and 349 GPa, respectively. P 3 ̄ m 1 and R 3 ̄ m structures are layered polytypes based on close packings of H atoms with Be atoms filling all octahedral voids in alternating layers. Cmcm and P4/nmm contain two-dimensional triangular networks with each layer forming a kinked slab in the ab-plane. P 3 ̄ m 1 and R 3 ̄ m are semiconductors while Cmcm and P4/nmm are metallic. We have explored superconductivity of both metal phases, and found large electron-phonon coupling parameters of λ = 0.63 for Cmcm with a Tc of 32.1-44.1 K at 250 GPa and λ = 0.65 for P4/nmm with a Tc of 46.1-62.4 K at 400 GPa. The dependence of Tc on pressure indicates that Tc initially increases to a maximum of 45.1 K for Cmcm at 275 GPa and 97.0 K for P4/nmm at 365 GPa, and then decreases with increasing pressure for both phases.

  19. Structure of stable binary neutron star merger remnants: A case study

    Science.gov (United States)

    Kastaun, W.; Ciolfi, R.; Giacomazzo, B.

    2016-08-01

    In this work, we study the merger of two neutron stars with a gravitational mass of 1.4 M⊙ each, employing the Shen-Horowitz-Teige equation of state. This equation of state is a corner case, allowing the formation of a stable neutron star with the given total baryonic mass of 3.03 M⊙. We investigate in unprecedented detail the structure of the remnant, in particular the mass distribution, the thermal structure, and the rotation profile. We also compute fluid trajectories both inside the remnant and those relevant for the formation of the disk. We find a peanut-shaped fluid flow inside the remnant following a strong m =2 perturbation. Moreover, the flow is locally compressive, causing the appearance of dynamic hot spots. Further, we introduce new diagnostic measures that are easy to implement in numeric simulations and that allow one to quantify mass and compactness of merger remnants in a well-defined way. As in previous studies of supra- and hypermassive stars, we find a remnant with a slowly rotating core and an outer envelope rotating at nearly Keplerian velocity. We compute a Tolman-Oppenheimer-Volkoff star model which agrees well with that of the remnant in the core, while the latter possesses extensive outer layers rotating close to Kepler velocity. Finally, we extract the gravitational wave signal and discuss the detectability with modern observatories. This study has implications for the interpretation of gravitational wave detections from the postmerger phase and is relevant for short gamma-ray burst models.

  20. Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-Hairpin.

    Directory of Open Access Journals (Sweden)

    2005-06-01

    Full Text Available The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity cinRO((N + nm log n, where N is the size of the output patterns and (n x m is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1 The method recovers states previously obtained by visually analyzing free energy surfaces. (2 It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3 The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the

  1. DNA-based stable isotope probing: a link between community structure and function

    Czech Academy of Sciences Publication Activity Database

    Uhlík, Ondřej; Ječná, K.; Leigh, M. B.; Macková, Martina; Macek, Tomáš

    2009-01-01

    Roč. 407, č. 12 (2009), s. 3611-3619 ISSN 0048-9697 Grant - others:GA MŠk(CZ) 2B08031 Program:2B Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA-based stable isotope probing * microbial diversity * bioremediation Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.905, year: 2009

  2. A chemically stable electrolyte with a novel sandwiched structure for proton-conducting solid oxide fuel cells (SOFCs)

    KAUST Repository

    Bi, Lei

    2013-11-01

    A chemically stable electrolyte structure was developed for proton-conducting SOFCs by using two layers of stable BaZr0.7Pr 0.1Y0.2O3 -δ to sandwich a highly-conductive but unstable BaCe0.8Y0.2O 3 -δ electrolyte layer. The sandwiched electrolyte structure showed good chemical stability in both CO2 and H2O atmosphere, indicating that the BZPY layers effectively protect the inner BCY electrolyte, while the BCY electrolyte alone decomposed completely under the same conditions. Fuel cell prototypes fabricated with the sandwiched electrolyte achieved a relatively high performance of 185 mW cm- 2 at 700 C, with a high electrolyte film conductivity of 4 × 10- 3 S cm- 1 at 600 C. © 2013 Elsevier B.V.

  3. Closed Pore Structured NiCo2O4-Coated Nickel Foams for Stable and Effective Oil/Water Separation.

    Science.gov (United States)

    Li, Yan; Zheng, Xi; Yan, Zhanheng; Tian, Dongliang; Ma, Jianmin; Zhang, Xiaofang; Jiang, Lei

    2017-08-30

    To solve the serious problem caused by oily wastewater pollution, unique interface designs, for example, membranes with superwetting properties such as superhydrophobicity/superoleophilicity and superhydrophilicity/underwater superoleophobicity, provide a good way to achieve oil/water separation. Here, inspired by the liquid storage property of the honeycomb structure, we propose a strategy to fabricate NiCo 2 O 4 -coated nickel foams for stable and efficient oil/water separation. NiCo 2 O 4 with a closed-pore structure was formed by assembling nanoflakes with a micro/nanoscale hierarchical structure. Compared with nickel foam coated by NiCo 2 O 4 with an open-pore structure (NiCo 2 O 4 nanowires), the enclosed nanostructure of NiCo 2 O 4 nanoflakes can firmly hold water for a more stable superhydrophilic/underwater superoleophobic interface. As a consequence, the NiCo 2 O 4 -nanoflake-coated nickel foam has a larger oil breakthrough pressure than the NiCo 2 O 4 -nanowire-coated nickel foam because of a slightly larger oil advancing angle and a lower underwater oil adhesion force, which makes it more stable and efficient for oil/water separation. Moreover, the NiCo 2 O 4 -coated nickel foams have excellent chemical and mechanical stability, and they are reusable for oil-water separation. This work will be beneficial for the design and development of stable underwater superoleophobic self-cleaning materials and related device applications, such as oil/water separation.

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

    Science.gov (United States)

    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.

  5. Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study

    Science.gov (United States)

    Pathak, Arup K.; Bandyopadhyay, Tusar

    2017-04-01

    Oral polio vaccine is considered to be the most thermolabile of all the common childhood vaccines. Despite heavy water (D2O) having been known for a long time to stabilise attenuated viral RNA against thermodegradation, the molecular underpinnings of its mechanism of action are still lacking. Whereas, understanding the basis of D2O action is an important step that might reform the way other thermolabile drugs are stored and could possibly minimize the cold chain problem. Here using a combination of parallel tempering and well-tempered metadynamics simulation in light water (H2O) and in D2O, we have fully described the free energy surface associated with the folding/unfolding of a RNA hairpin containing a non-canonical basepair motif, which is conserved within the 3'-untranslated region of poliovirus-like enteroviruses. Simulations reveal that in heavy water (D2O) there is a considerable increase of the stability of the folded basin as monitored through an intramolecular hydrogen bond (HB), size, shape, and flexibility of RNA structures. This translates into a higher melting temperature in D2O by 41 K when compared with light water (H2O). We have explored the hydration dynamics of the RNA, hydration shell around the RNA surface, and spatial dependence of RNA-solvent collective HB dynamics in the two water systems. Simulation in heavy water clearly showed that D2O strengthens the HB network in the solvent, lengthens inter-residue water-bridge lifetime, and weakens dynamical coupling of the hairpin to its solvation environment, which enhances the rigidity of solvent exposed sites of the native configurations. The results might suggest that like other added osmoprotectants, D2O can act as a thermostabilizer when used as a solvent.

  6. Finding the Stable Structures of WxN1-x with an ab-initio High-Throughput Approach

    Science.gov (United States)

    2014-03-13

    properties must be energetically stable against decomposition into other compounds. This stability can only be found after the determination of the...polarized. However, in every structure the self-consistent magnetic moment was negligible, and the final calculations were all done assuming no moment. The...of NaCl) we looked at all 255 combinations. We found 34 unique structures, including NbO itself, CsCl, S3U4, ReO3,[59] cubic perovskite (with formula

  7. Virus-derived transgenes expressing hairpin RNA give immunity to Tobacco mosaic virus and Cucumber mosaic virus

    Directory of Open Access Journals (Sweden)

    Liu Yong

    2011-01-01

    Full Text Available Abstract Background An effective method for obtaining resistant transgenic plants is to induce RNA silencing by expressing virus-derived dsRNA in plants and this method has been successfully implemented for the generation of different plant lines resistant to many plant viruses. Results Inverted repeats of the partial Tobacco mosaic virus (TMV movement protein (MP gene and the partial Cucumber mosaic virus (CMV replication protein (Rep gene were introduced into the plant expression vector and the recombinant plasmids were transformed into Agrobacterium tumefaciens. Agrobacterium-mediated transformation was carried out and three transgenic tobacco lines (MP16-17-3, MP16-17-29 and MP16-17-58 immune to TMV infection and three transgenic tobacco lines (Rep15-1-1, Rep15-1-7 and Rep15-1-32 immune to CMV infection were obtained. Virus inoculation assays showed that the resistance of these transgenic plants could inherit and keep stable in T4 progeny. The low temperature (15℃ did not influence the resistance of transgenic plants. There was no significant correlation between the resistance and the copy number of the transgene. CMV infection could not break the resistance to TMV in the transgenic tobacco plants expressing TMV hairpin MP RNA. Conclusions We have demonstrated that transgenic tobacco plants expressed partial TMV movement gene and partial CMV replicase gene in the form of an intermolecular intron-hairpin RNA exhibited complete resistance to TMV or CMV infection.

  8. HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis

    Directory of Open Access Journals (Sweden)

    Ming-an Sun

    2015-01-01

    Full Text Available The emerging genome-wide hairpin bisulfite sequencing (hairpin-BS-Seq technique enables the determination of the methylation pattern for DNA double strands simultaneously. Compared with traditional bisulfite sequencing (BS-Seq techniques, hairpin-BS-Seq can determine methylation fidelity and increase mapping efficiency. However, no computational tool has been designed for the analysis of hairpin-BS-Seq data yet. Here we present HBS-tools, a set of command line based tools for the preprocessing, mapping, methylation calling, and summarizing of genome-wide hairpin-BS-Seq data. It accepts paired-end hairpin-BS-Seq reads to recover the original (pre-bisulfite-converted sequences using global alignment and then calls the methylation statuses for cytosines on both DNA strands after mapping the original sequences to the reference genome. After applying to hairpin-BS-Seq datasets, we found that HBS-tools have a reduced mapping time and improved mapping efficiency compared with state-of-the-art mapping tools. The HBS-tools source scripts, along with user guide and testing data, are freely available for download.

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

    Directory of Open Access Journals (Sweden)

    Fangquan Wang

    2016-05-01

    Full Text Available Rice black-streaked dwarf virus (RBSDV belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21–24 nt small interfering RNA (siRNA. By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species.

  10. Detailed study of DNA hairpin dynamics using single-molecule fluorescence assisted by DNA origami.

    Science.gov (United States)

    Tsukanov, Roman; Tomov, Toma E; Masoud, Rula; Drory, Hagai; Plavner, Noa; Liber, Miran; Nir, Eyal

    2013-10-10

    The dynamics of two DNA hairpins (5'-TCGCCT-A31-AGGCGA-3' and 5'-TCGCCG-A31-CGGCGA-3') were studied using immobilization-based and diffusion-based single-molecule fluorescence techniques. The techniques enabled separated and detailed investigation of the states and of the transition reactions. Only two states, open and closed, were identified from analysis of the FRET histograms; metastable states with lifetimes longer than the technique resolution (0.3 ms) were not observed. The opening and closing reaction rates were determined directly from the FRET time trajectories, and the Gibbs free energies of these states and of the transition state were calculated using the Kramer theory. The rates, which are undoubtedly of transitions between the fully closed and the fully open states and ranged from 2 to 90 s(-1), were lower (∼10-fold) than the rates previously determined from fluorescence correlation spectroscopy. The heights of the barriers for closing were almost identical for the two hairpins. The barrier for opening the hairpin with the stronger stem was higher (4.3 kJ/mol) than that for the hairpin with the weaker stem, in very good agreement with the difference in stability calculated by the nearest-neighbor method. The barrier for closing the hairpin decreased (∼8 kJ/mol) and the barrier for opening increased (∼4 kJ/mol) with increasing NaCl concentration (10-100 mM), indicating that higher ionic strength stabilizes the folded state with respect to the transition state and stabilizes the transition state relative to the unfolded state. The very good agreements in the dynamics measured for free hairpins, for hairpins anchored to origami, and for hairpins anchored to the coverslip and the very good agreement between the two single-molecule techniques demonstrate that neither the origami nor the coverslip influence the hairpin dynamics, supporting a previous demonstration that origami can serve as a platform for biophysical investigations.

  11. The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE

    Directory of Open Access Journals (Sweden)

    Lavrov Dennis V

    2009-12-01

    Full Text Available Abstract Background The mitochondrial (mt genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida and compare it with mtDNA of other sponges. Results Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.

  12. Stable feature selection for clinical prediction: exploiting ICD tree structure using Tree-Lasso.

    Science.gov (United States)

    Kamkar, Iman; Gupta, Sunil Kumar; Phung, Dinh; Venkatesh, Svetha

    2015-02-01

    Modern healthcare is getting reshaped by growing Electronic Medical Records (EMR). Recently, these records have been shown of great value towards building clinical prediction models. In EMR data, patients' diseases and hospital interventions are captured through a set of diagnoses and procedures codes. These codes are usually represented in a tree form (e.g. ICD-10 tree) and the codes within a tree branch may be highly correlated. These codes can be used as features to build a prediction model and an appropriate feature selection can inform a clinician about important risk factors for a disease. Traditional feature selection methods (e.g. Information Gain, T-test, etc.) consider each variable independently and usually end up having a long feature list. Recently, Lasso and related l1-penalty based feature selection methods have become popular due to their joint feature selection property. However, Lasso is known to have problems of selecting one feature of many correlated features randomly. This hinders the clinicians to arrive at a stable feature set, which is crucial for clinical decision making process. In this paper, we solve this problem by using a recently proposed Tree-Lasso model. Since, the stability behavior of Tree-Lasso is not well understood, we study the stability behavior of Tree-Lasso and compare it with other feature selection methods. Using a synthetic and two real-world datasets (Cancer and Acute Myocardial Infarction), we show that Tree-Lasso based feature selection is significantly more stable than Lasso and comparable to other methods e.g. Information Gain, ReliefF and T-test. We further show that, using different types of classifiers such as logistic regression, naive Bayes, support vector machines, decision trees and Random Forest, the classification performance of Tree-Lasso is comparable to Lasso and better than other methods. Our result has implications in identifying stable risk factors for many healthcare problems and therefore can

  13. Sonochemical synthesis, structure and magnetic properties of air-stable Fe3O4/Au nanoparticles

    International Nuclear Information System (INIS)

    Wu Wei; He Quanguo; Chen Hong; Tang Jianxin; Nie Libo

    2007-01-01

    Air-stable nanoparticles of Fe 3 O 4 /Au were prepared via sonolysis of a solution mixture of hydrogen tetrachloroaureate(III) trihydrate (HAuCl 4 ) and (3-aminopropyl)triethoxysilane (APTES)-coated Fe 3 O 4 nanoparticles with further drop-addition of sodium citrate. The Fe 3 O 4 /Au nanoparticles were characterized by x-ray powder diffraction (XRD), ultraviolet-visible spectroscopy (UV-vis), scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDS), transmission electron microscopy (TEM), x-ray photoelectron spectroscopy (XPS) and superconducting quantum interference device (SQUID) magnetometry. Nanoparticles of Fe 3 O 4 /Au obtained under appropriate conditions possess a very high saturation magnetization of about 63 emu g -1 and their average diameter is about 30 nm

  14. Benthic Food Web Structure across the Canadian Arctic Ocean: Insights from stable isotopes and the IP25 biomarker

    Science.gov (United States)

    Friscourt, N.; Archambault, P.; Masse, G.; Nozais, C.

    2016-02-01

    In recent decades, the Arctic Ocean has undergone unprecedented changes, such as an increase in the surface temperature and a reduction of sea ice cover. These changes may cause variations in the intensity and spatial distribution of primary production and the nature of pelagic-benthic coupling. This could affect the amount and quality of organic matter that settles onto the seafloor, and the benthic communities that feed upon it. The objectives of this study were i) to describe the trophic structure and resilience of regional benthic food webs using stable carbon and nitrogen isotope analyses and ii) to evaluate the significance of ice algae in the diet of benthic communities using the sea ice proxy IP25. The study area extends from the North Water Polynya to the Chukchi Sea across five geographic regions (North Water Polynya, Canadian Archipelago, Amundsen Gulf, Beaufort Sea and Chukchi Sea) based on environmental factors. To reach these objectives, we collected particulate organic matter (POM), sediments and zoobenthic samples from July to October 2014 aboard the CCGS Amundsen. Stable isotope and IP25 data, the trophic structure within regions and comparison between regions will be presented. Potential impacts of climate change and human activities on benthic ecosystems in the Arctic are still difficult to assess because of the lack of baseline data. The baseline data once provided will enable us to make further predictions on how these changes may affect benthic food web structure.

  15. Soil structure stability and distribution of carbon in water-stable aggregates in different tilled and fertilized Haplic Luvisol

    Directory of Open Access Journals (Sweden)

    Vladimír Šimanský

    2012-01-01

    Full Text Available The influence of tillage and fertilization on soil structure stability and the distribution of carbon in water-stable aggregates of loamy Haplic Luvisol were studied. Soil samples from the locality of Dolná Malanta (experimental station of SUA Nitra were collected (in 2007–2009 from a depth of 0–0.2 m in two tillage variants: (1. conventional tillage, 2. minimal tillage and three treatments of fertilization: (1. without fertilization, 2. crop residues and NPK fertilizers, 3. NPK fertilizers. The minimal tillage system has a positive effect on both the aggregation processes and sequestration of carbon in size fractions of water-stable aggregates, as well as ploughing of crop residues together with NPK fertilizers. On the other hand, application of only NPK fertilizers had a negative effect on SOM content. Under the minimal tillage system and in treatment with crop residues together with NPK fertilizers, what has been observed is a statistically significant increase in the total organic carbon contents by increasing size fractions of water-stable aggregates. Organic carbon did not influence the aggregation processes with dependence on tillage systems. Under conventional tillage as well as in treatment with ploughing crop residues with NPK fertilizers, a very important effect on aggregation had bivalent cations Ca2+ and Mg2+.

  16. Natural abundance heteronuclear NMR studies of the T3 mini-loop hairpin in the terminal repeat of the adenoassociated virus 2.

    Science.gov (United States)

    Chou, S H; Tseng, Y Y; Chu, B Y

    2000-05-01

    A DNA hairpin containing a T3 loop, as occurs in the terminal repeat of a popular gene therapy vector (Adenoassociated Virus 2, AAV2), has been extensively studied using homo- and heteronuclear NMR experiments. Almost complete assignment of the proton and carbon resonances, including H5'(Pro-S) and H5'(Pro-R) protons, has been accomplished at natural abundance. NOESY spectra in H2O and D2O have revealed many unusual NOEs, which, when combined with the epsilon, beta, gamma, and chi torsion angles determined from heteronuclear 1H-13C, 1H-31P, and 13C-31P coupling constants, have allowed for a more detailed picture of the T3 mini-loop hairpin. The three loop thymidines are all unpaired, yet are highly structured when bracketed by a 5'-GC...GC-3' stem sequence. The structure determined in this manuscript is considerably different from several other structures reported so far. Contrary to an RNA oligomer with a central U3 sequence that has the tendency to form a duplex with three U*U mismatches, the d(GAAGC-TTT-GCTTC) sequence exists mostly as a hairpin under millimolar NMR conditions. Since T3 triloop was found to be an essential element for the site-specific non-homologous integration of the AAV2 virus, and modification of the T3 loop residue abolishes such capability, the structure we report here may be of biological significance.

  17. DNA-based stable isotope probing: a link between community structure and function

    International Nuclear Information System (INIS)

    Uhlik, Ondrej; Jecna, Katerina; Leigh, Mary Beth; Mackova, Martina; Macek, Tomas

    2009-01-01

    DNA-based molecular techniques permit the comprehensive determination of microbial diversity but generally do not reveal the relationship between the identity and the function of microorganisms. The first direct molecular technique to enable the linkage of phylogeny with function is DNA-based stable isotope probing (DNA-SIP). Applying this method first helped describe the utilization of simple compounds, such as methane, methanol or glucose and has since been used to detect microbial communities active in the utilization of a wide variety of compounds, including various xenobiotics. The principle of the method lies in providing 13C-labeled substrate to a microbial community and subsequent analyses of the 13C-DNA isolated from the community. Isopycnic centrifugation permits separating 13C-labeled DNA of organisms that utilized the substrate from 12C-DNA of the inactive majority. As the whole metagenome of active populations is isolated, its follow-up analysis provides successful taxonomic identification as well as the potential for functional gene analyses. Because of its power, DNA-SIP has become one of the leading techniques of microbial ecology research. But from other point of view, it is a labor-intensive method that requires careful attention to detail during each experimental step in order to avoid misinterpretation of results.

  18. Conjugated organic framework with three-dimensionally ordered stable structure and delocalized π clouds

    Science.gov (United States)

    Guo, Jia; Xu, Yanhong; Jin, Shangbin; Chen, Long; Kaji, Toshihiko; Honsho, Yoshihito; Addicoat, Matthew A.; Kim, Jangbae; Saeki, Akinori; Ihee, Hyotcherl; Seki, Shu; Irle, Stephan; Hiramoto, Masahiro; Gao, Jia; Jiang, Donglin

    2013-01-01

    Covalent organic frameworks are a class of crystalline organic porous materials that can utilize π–π-stacking interactions as a driving force for the crystallization of polygonal sheets to form layered frameworks and ordered pores. However, typical examples are chemically unstable and lack intrasheet π-conjugation, thereby significantly limiting their applications. Here we report a chemically stable, electronically conjugated organic framework with topologically designed wire frameworks and open nanochannels, in which the π conjugation-spans the two-dimensional sheets. Our framework permits inborn periodic ordering of conjugated chains in all three dimensions and exhibits a striking combination of properties: chemical stability, extended π-delocalization, ability to host guest molecules and hole mobility. We show that the π-conjugated organic framework is useful for high on-off ratio photoswitches and photovoltaic cells. Therefore, this strategy may constitute a step towards realizing ordered semiconducting porous materials for innovations based on two-dimensionally extended π systems. PMID:24220603

  19. Complexity Results and the Growths of Hairpin Completions of Regular Languages (Extended Abstract)

    Science.gov (United States)

    Diekert, Volker; Kopecki, Steffen

    The hairpin completion is a natural operation on formal languages which has been inspired by molecular phenomena in biology and by DNA-computing. In 2009 we presented in [6] a (polynomial time) decision algorithm to decide regularity of the hairpin completion. In this paper we provide four new results: 1.) We show that the decision problem is NL-complete. 2.) There is a polynomial time decision algorithm which runs in time O(n8), this improves [6], which provided O(n^{20}). 3.) For the one-sided case (which is closer to DNA computing) the time is O(n2), only. 4.) The hairpin completion is unambiguous linear context-free. This result allows to compute the growth (generating function) of the hairpin completion and to compare it with the growth of the underlying regular language.

  20. Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

    Science.gov (United States)

    Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

    2017-05-10

    Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Mutation in the β-hairpin of the Bordetella pertussis adenylate cyclase toxin modulates N-lobe conformation in calmodulin

    International Nuclear Information System (INIS)

    Springer, Tzvia I.; Goebel, Erich; Hariraju, Dinesh; Finley, Natosha L.

    2014-01-01

    Highlights: • Bordetella pertussis adenylate cyclase toxin modulates bi-lobal structure of CaM. • The structure and stability of the complex rely on intermolecular associations. • A novel mode of CaM-dependent activation of the adenylate cyclase toxin is proposed. - Abstract: 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 (R h ) and reduced thermal stability in the mutant complex. Taken together

  2. Mutation in the β-hairpin of the Bordetella pertussis adenylate cyclase toxin modulates N-lobe conformation in calmodulin

    Energy Technology Data Exchange (ETDEWEB)

    Springer, Tzvia I.; Goebel, Erich; Hariraju, Dinesh [Department of Microbiology, Miami University, Oxford, OH 45056 (United States); Finley, Natosha L., E-mail: finleynl@miamioh.edu [Department of Microbiology, Miami University, Oxford, OH 45056 (United States); Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 (United States)

    2014-10-10

    Highlights: • Bordetella pertussis adenylate cyclase toxin modulates bi-lobal structure of CaM. • The structure and stability of the complex rely on intermolecular associations. • A novel mode of CaM-dependent activation of the adenylate cyclase toxin is proposed. - Abstract: 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 (R{sub h}) and reduced thermal stability in the mutant complex. Taken

  3. A hypoplastic constitutive model for clays with meta-stable structure

    Czech Academy of Sciences Publication Activity Database

    Mašín, David

    2007-01-01

    Roč. 44, č. 3 (2007), s. 363-375 ISSN 0008-3674 R&D Projects: GA AV ČR(CZ) IAA200710605 Institutional research plan: CEZ:AV0Z20710524 Keywords : constitutive relations * hypoplasticity * clays * structure of soils Subject RIV: JM - Building Engineering Impact factor: 0.542, year: 2007

  4. Structurally stable design of output regulation for a class of nonlinear systems

    Czech Academy of Sciences Publication Activity Database

    Villanueva-Novelo, C.; Čelikovský, Sergej; Castillo-Toledo, B.

    2001-01-01

    Roč. 37, č. 5 (2001), s. 517-561 ISSN 0023-5954 R&D Projects: GA ČR GA102/99/1368 Institutional research plan: AV0Z1075907 Keywords : nonlinear systems * structural stability * output regulation Subject RIV: BC - Control Systems Theory Impact factor: 0.316, year: 2001

  5. Atomic-scale structure and properties of highly stable antiphase boundary defects in Fe3O4.

    Science.gov (United States)

    McKenna, Keith P; Hofer, Florian; Gilks, Daniel; Lazarov, Vlado K; Chen, Chunlin; Wang, Zhongchang; Ikuhara, Yuichi

    2014-12-10

    The complex and intriguing properties of the ferrimagnetic half metal magnetite (Fe 3 O 4 ) are of continuing fundamental interest as well as being important for practical applications in spintronics, magnetism, catalysis and medicine. There is considerable speculation concerning the role of the ubiquitous antiphase boundary (APB) defects in magnetite, however, direct information on their structure and properties has remained challenging to obtain. Here we combine predictive first principles modelling with high-resolution transmission electron microscopy to unambiguously determine the three-dimensional structure of APBs in magnetite. We demonstrate that APB defects on the {110} planes are unusually stable and induce antiferromagnetic coupling between adjacent domains providing an explanation for the magnetoresistance and reduced spin polarization often observed. We also demonstrate how the high stability of the {110} APB defects is connected to the existence of a metastable bulk phase of Fe 3 O 4 , which could be stabilized by strain in films or nanostructures.

  6. Structural changes, market concentration and vertical integration: would they lead to more stable markets

    International Nuclear Information System (INIS)

    Tahmassebi, H.

    1991-01-01

    This communication is concerned with three major developments that are likely to have significant impact on the future structure of world oil markets: oil company mergers and acquisitions, shift of exploration and production activity from the United States to overseas, and joint venture agreements between producing countries and oil companies aimed at further downstream integration by OPEC. The last two developments are likely to contribute substantially to price and market stability in the future

  7. Biological Applications of Designed Hairpin Peptides: As Antimicrobials and as Inhibitors of Amyloidogenesis

    Science.gov (United States)

    Sivanesam, Kalkena

    More than 40 diseases have been associated with the misfolding of peptides (or proteins) that form fibrils with a very specific morphology. These peptides classified as amyloidogenic peptides have been implicated in the development of Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, Hungtinton's Disease etc. To date, these diseases have no cure, only therapies that can ameliorate the symptoms to a degree. Inhibition of the amyloidogenesis of these peptides has been proposed as a possible treatment option. While small molecules have been heavily tested as inhibitors of amyloidogenesis, peptides have emerged as potential inhibitors. In this work, the ability of a set of designed hairpin peptides to inhibit the amyloidogenesis of two different systems, alpha-synuclein (implicated in Parkinson's Disease) and human amylin (implicated in Type II Diabetes) is tested. Using circular dichroism and thioflavin T fluorescence, the ability of these peptides to inhibit amyloidogenesis is tested. The binding loci of these inhibitors to alpha-synuclein are also explored. The use of peptides as antimicrobials on the other hand is not a novel concept. However, most antimicrobial peptides, both natural and designed, rely heavily on covalent stabilizations in order to maintain secondary structure. In this study, non-covalent stabilizations are applied to a couple of natural as well as designed antimicrobials in order to study the effects of secondary structure stabilization on biological activity.

  8. Stable isotope evidence of long-term changes in North Sea food web structure

    DEFF Research Database (Denmark)

    Richardson, Katherine; Christensen, Jens Tang

    2008-01-01

    coast. Porpoises collected after ~1960 had significantly lower d15N than porpoises collected earlier. This change in d15N implies that fundamental changes in food web structure in, or nutrient availability to, the North Sea have taken place over the last ~150 yr and that most of the change occurred over...... reported here may be a reflection of a change in the isotope signature of nitrogen entering the food web. Regardless of its underlying cause, the recorded change in isotopic signature in harbour porpoises is noteworthy as it represents the first fisheries-independent documentation of a long-term temporal...

  9. Bacterioplankton communities of Crater Lake, OR: Dynamic changes with euphotic zone food web structure and stable deep water populations

    Science.gov (United States)

    Urbach, E.; Vergin, K.L.; Larson, G.L.; Giovannoni, S.J.

    2007-01-01

    The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by ??-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting. ?? 2007 Springer Science+Business Media B.V.

  10. Pyridine and phosphonate containing ligands for stable lanthanide complexation. An experimental and theoretical study to assess the solution structure.

    Science.gov (United States)

    Mato-Iglesias, Marta; Balogh, Edina; Platas-Iglesias, Carlos; Tóth, Eva; de Blas, Andrés; Rodríguez Blas, Teresa

    2006-12-07

    We report an experimental and theoretical study of the stability and solution structure of lanthanide complexes with two novel ligands containing pyridine units and phosphonate pendant arms on either ethane-1,2-diamine (L2) or cyclohexane-1,2-diamine (L3) backbones. Potentiometric studies have been carried out to determine the protonation constants of the ligands and the stability constants of the complexes with Gd(III) and the endogenous metal ions Zn(II) and Cu(II). While the stability constant of the GdL2 complex is too high to be determined by direct pH-potentiometric titrations, the cyclohexyl derivative GdL3 has a lower and assessable stability (log K(GdL3)=17.62). Due to the presence of the phosphonate groups, various protonated species can be detected up to pH approximately 8 for both ligands and all metal ions studied. The molecular clusters [Ln(L)(H2O)](3-).19H2O (Ln=La, Nd, Ho or Lu; L=L2 or L3) were characterized by theoretical calculations at the HF level. Our calculations provide two minimum energy geometries where the ligand adopts different conformations: twist-wrap (tw), in which the ligand wraps around the metal ion by twisting the pyridyl units relative to each other, and twist-fold (tf), where the slight twisting of the pyridyl units is accompanied by an overall folding of the two pyridine units towards one of the phosphonate groups. The relative free energies of the tw and tf conformations of [Ln(L)(H2O)]3- (L=L2, L3) complexes calculated in aqueous solution (C-PCM) by using the B3LYP model indicate that the tw form is the most stable one along the whole lanthanide series for the complexes of L3, while for those of L2 only the Gd(III) complex is more stable in the tf conformation by ca. 0.5 kcal mol-1. 1H NMR studies of the Eu(III) complex of L3 show the initial formation of the tf complex in aqueous solution, which slowly converts to the thermodynamically stable tw form. The structures calculated for the Nd(III) complexes are in reasonably

  11. Global population structure of the stable fly (Stomoxys calcitrans) inferred by mitochondrial and nuclear sequence data.

    Science.gov (United States)

    Dsouli-Aymes, N; Michaux, J; De Stordeur, E; Couloux, A; Veuille, M; Duvallet, G

    2011-03-01

    Stomoxys calcitrans (Diptera: Muscidae: Stomoxyini), a synanthropic fly with a worldwide distribution, is recognized to have an important medical and veterinary impact. We conducted a phylogeographic analysis based on several populations from five major zoogeographic regions of the world in order to analyse population genetic structure of S. calcitrans and to trace its global dispersion. Results from mitochondrial (COI, Cyt-b and ND1-16S) and nuclear (ITS2) DNA show a substantial differentiation of Oriental populations (first lineage) from the Afrotropical, Palearctic, Nearctic, Neotropical and Oceanian populations (second lineage). The divergence time analyses suggest the separation between the two lineages approximately in mid-Pleistocene. Oriental populations are isolated and would not have participated in the colonization of other regions, unlike the Afrotropical one which seems to be the source of S. calcitrans dispersion towards other regions. Demographic analyses indicate that Oriental, Afrotropical and Palearctic regions have undergone a population expansion during late Pleistocene-early Holocene. The expansion time of this cosmopolitan species could have been influenced by continental human expansions and by animal domestication. Copyright © 2010 Elsevier B.V. All rights reserved.

  12. Peculiarities of the fundamental mode structure in stable-resonator lasers upon spatially inhomogeneous amplification

    International Nuclear Information System (INIS)

    Gorbunkov, Mikhail V; Kostryukov, P V; Telegin, L S; Tunkin, V G; Yakovlev, D V

    2007-01-01

    The structure of the fundamental mode of a laser is calculated by the iteration Fox-Li method in the case of inhomogeneous unsaturated amplification produced by axially symmetric longitudinal pumping. The calculation is performed for different parameters g 1 and g 2 of the resonator within the entire stability region. It is shown that in the case of inhomogeneous amplification, the fundamental mode considerably deviates from the Gaussian mode of an empty resonator only in the so-called critical configurations of the resonator, when the quantity [arccos(g 1 g 2 ) 1/2 ]/π is zero or takes a number of values expressed by irreducible fractions m/n. For the Fresnel number N F = 9, configurations with m/n = 1/2, 2/5, 3/8, 1/3, 3/10, 1/4, 1/5, 1/6, 1/8, and 1/10 are pronounced. As N F increases, the number of critical configurations increases. The expansion in a system of Laguerre-Gaussian beams shows that the fundamental mode in critical configurations is formed by a set of beams with certain radial indices p phased in the active medium. (resonators. modes)

  13. The structure of mAG, a monomeric mutant of the green fluorescent protein Azami-Green, reveals the structural basis of its stable green emission

    International Nuclear Information System (INIS)

    Ebisawa, Tatsuki; Yamamura, Akihiro; Kameda, Yasuhiro; Hayakawa, Kou; Nagata, Koji; Tanokura, Masaru

    2010-01-01

    The crystal structure of a monomeric mutant of Azami-Green (mAG) from G. fascicularis was determined at 2.2 Å resolution. Monomeric Azami-Green (mAG) from the stony coral Galaxea fascicularis is the first known monomeric green-emitting fluorescent protein that is not a variant of Aequorea victoria green fluorescent protein (avGFP). These two green fluorescent proteins are only 27% identical in their amino-acid sequences. mAG is more similar in its amino-acid sequence to four fluorescent proteins: Dendra2 (a green-to-red irreversibly photoconverting fluorescent protein), Dronpa (a bright-and-dark reversibly photoswitchable fluorescent protein), KikG (a tetrameric green-emitting fluorescent protein) and Kaede (another green-to-red irreversibly photoconverting fluorescent protein). To reveal the structural basis of stable green emission by mAG, the 2.2 Å crystal structure of mAG has been determined and compared with the crystal structures of avGFP, Dronpa, Dendra2, Kaede and KikG. The structural comparison revealed that the chromophore formed by Gln62-Tyr63-Gly64 (QYG) and the fixing of the conformation of the imidazole ring of His193 by hydrogen bonds and van der Waals contacts involving His193, Arg66 and Thr69 are likely to be required for the stable green emission of mAG. The crystal structure of mAG will contribute to the design and development of new monomeric fluorescent proteins with faster maturation, brighter fluorescence, improved photostability, new colours and other preferable properties as alternatives to avGFP and its variants

  14. Synthesis, structure and topological analysis of glycine templated highly stable cadmium sulfate framework: A New Lewis Acid catalyst

    Science.gov (United States)

    Paul, Avijit Kumar

    2018-04-01

    One new open-framework two-dimensional layer, [Cd(NH3CH2COO)(SO4)], I, has been synthesized using amino acid as templating agent. Single crystal structural analysis shows that the compound crystallizes in monoclinic cell with non-centrosymmetric space group P21, a = 4.9513(1) Å, b = 7.9763(2) Å, c = 8.0967(2) Å, β = 105.917(1)° and V = 307.504(12) Å3. The compound has connectivity between the Cd-centers and the sulfate units forming a two-dimensional layer structure. Sulfate unit is coordinated to metal center with η3, μ4 mode possessing a coordination free oxygen atom. The zwitterionic form of glycine molecule is present in the structure bridging with two metal centers through μ2-mode by carboxylate oxygens. The topological analysis reveals that the two-dimensional network is formed with a novel 4- and 6-connected binodal net of (32,42,52)(34,44,54,63) topology. Although one end of the glycine molecule is free from coordination, the structure is highly stable up to 350 °C. Strong N-H⋯ O hydrogen bonding interactions play an important role in the stabilization and formation of three-dimensional supramolecular structure. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicates good catalytic behavior. The present study illustrates the usefulness of the amino acid for the structure building in less studied sulfate based framework materials as well as designing of new heterogeneous catalysts for the broad application. The compound has also been characterized through elemental analysis, PXRD, IR, SEM and TG-DT studies.

  15. The effect of temperature on generic stable periodic structures in the parameter space of dissipative relativistic standard map

    Science.gov (United States)

    Horstmann, Ana C. C.; Albuquerque, Holokx A.; Manchein, Cesar

    2017-05-01

    In this work, we have characterized changes in the dynamics of a two-dimensional relativistic standard map in the presence of dissipation and specially when it is submitted to thermal effects modeled by a Gaussian noise reservoir. By the addition of thermal noise in the dissipative relativistic standard map (DRSM) it is possible to suppress typical stable periodic structures (SPSs) embedded in the chaotic domains of parameter space for large enough temperature strengths. Smaller SPSs are first affected by thermal effects, starting from their borders, as a function of temperature. To estimate the necessary temperature strength capable to destroy those SPSs we use the largest Lyapunov exponent to obtain the critical temperature (TC) diagrams. For critical temperatures the chaotic behavior takes place with the suppression of periodic motion, although the temperature strengths considered in this work are not so large to convert the deterministic features of the underlying system into a stochastic ones.

  16. Stable isotopes indicate population structuring in the southwest Atlantic population of right whales (Eubalaena australis.

    Directory of Open Access Journals (Sweden)

    Morgana Vighi

    Full Text Available From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina and another off central Argentina (Peninsula Valdés. This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n=72 and from contemporary and more recent strandings occurring in central Argentina (n=53. Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas.

  17. Stable isotopes indicate population structuring in the southwest Atlantic population of right whales (Eubalaena australis).

    Science.gov (United States)

    Vighi, Morgana; Borrell, Asunción; Crespo, Enrique A; Oliveira, Larissa R; Simões-Lopes, Paulo C; Flores, Paulo A C; García, Néstor A; Aguilar, Alex; Aguilar, Alejandro

    2014-01-01

    From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina) and another off central Argentina (Peninsula Valdés). This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n=72) and from contemporary and more recent strandings occurring in central Argentina (n=53). Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas.

  18. Optimum Design of Novel UWB Multilayer Microstrip Hairpin Filters with Harmonic Suppression and Impedance Matching

    Directory of Open Access Journals (Sweden)

    Homayoon Oraizi

    2012-01-01

    Full Text Available Optimum design of a novel ultra-wideband multilayer microstrip hairpin filter is presented, providing for harmonic suppression and impedance matching between source and load impedances. The theory of N-coupled transmission lines is employed to obtain an equivalent circuit for development of a design procedure based on the method of least squares. A prototype model of proposed two-layer filter of order 5 is fabricated for 3.1–10.6 GHz. The dimensions of designed filter are 23 mm × 7 mm. The insertion loss in the passband varies from 0.3 dB to 3 dB (in the worst case at the edge of passband and in the stopband is about 30 dB up to 20 GHz. Its group delay in the UWB region is about 0.5 ns. Close agreement among the filter frequency responses as obtained by the proposed method, full-wave computer simulation softwares, and measurement data verify the effectiveness of the proposed filter structure and design methods.

  19. Efficient production of superior dumbbell-shaped DNA minimal vectors for small hairpin RNA expression.

    Science.gov (United States)

    Yu, Han; Jiang, Xiaoou; Tan, Kar Tong; Hang, Liting; Patzel, Volker

    2015-10-15

    Genetic therapy holds great promise for the treatment of inherited or acquired genetic diseases; however, its breakthrough is hampered by the lack of suitable gene delivery systems. Dumbbell-shaped DNA minimal vectors represent an attractive, safe alternative to the commonly used viral vectors which are fraught with risk, but dumbbell generation appears to be costly and time-consuming. We developed a new PCR-based method for dumbbell production which comprises only two steps. First, PCR amplification of the therapeutic expression cassette using chemically modified primers to form a ready-to-ligate DNA structure; and second, a highly efficient intramolecular ligation reaction. Compared with conventional strategies, the new method produces dumbbell vector/span>s more rapidly, with higher yields and purity, and at lower costs. In addition, such produced small hairpin RNA expressing dumbbells triggered superior target gene knockdown compared with conventionally produced dumbbells or plasmids. Our novel method is suitable for large-scale dumbbell production and can facilitate clinical applications of this vector system. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Efficient production of superior dumbbell-shaped DNA minimal vectors for small hairpin RNA expression

    Science.gov (United States)

    Yu, Han; Jiang, Xiaoou; Tan, Kar Tong; Hang, Liting; Patzel, Volker

    2015-01-01

    Genetic therapy holds great promise for the treatment of inherited or acquired genetic diseases; however, its breakthrough is hampered by the lack of suitable gene delivery systems. Dumbbell-shaped DNA minimal vectors represent an attractive, safe alternative to the commonly used viral vectors which are fraught with risk, but dumbbell generation appears to be costly and time-consuming. We developed a new PCR-based method for dumbbell production which comprises only two steps. First, PCR amplification of the therapeutic expression cassette using chemically modified primers to form a ready-to-ligate DNA structure; and second, a highly efficient intramolecular ligation reaction. Compared with conventional strategies, the new method produces dumbbell vectors more rapidly, with higher yields and purity, and at lower costs. In addition, such produced small hairpin RNA expressing dumbbells triggered superior target gene knockdown compared with conventionally produced dumbbells or plasmids. Our novel method is suitable for large-scale dumbbell production and can facilitate clinical applications of this vector system. PMID:26068470

  1. The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer

    Science.gov (United States)

    Sanchez, Jacint G.; Okreglicka, Katarzyna; Chandrasekaran, Viswanathan; Welker, Jordan M.; Sundquist, Wesley I.; Pornillos, Owen

    2014-01-01

    Tripartite motif (TRIM) proteins make up a large family of coiled-coil-containing RING E3 ligases that function in many cellular processes, particularly innate antiviral response pathways. Both dimerization and higher-order assembly are important elements of TRIM protein function, but the atomic details of TRIM tertiary and quaternary structure have not been fully understood. Here, we present crystallographic and biochemical analyses of the TRIM coiled-coil and show that TRIM proteins dimerize by forming interdigitating antiparallel helical hairpins that position the N-terminal catalytic RING domains at opposite ends of the dimer and the C-terminal substrate-binding domains at the center. The dimer core comprises an antiparallel coiled-coil with a distinctive, symmetric pattern of flanking heptad and central hendecad repeats that appear to be conserved across the entire TRIM family. Our studies reveal how the coiled-coil organizes TRIM25 to polyubiquitylate the RIG-I/viral RNA recognition complex and how dimers of the TRIM5α protein are arranged within hexagonal arrays that recognize the HIV-1 capsid lattice and restrict retroviral replication. PMID:24550273

  2. Effect of DNA hairpin loops on the twist of planar DNA origami tiles.

    Science.gov (United States)

    Li, Zhe; Wang, Lei; Yan, Hao; Liu, Yan

    2012-01-31

    The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D) DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved. © 2011 American Chemical Society

  3. Stable phase CdS nanoparticles for optoelectronics: a study on surface morphology, structural and optical characterization

    Directory of Open Access Journals (Sweden)

    Kumar Suresh

    2016-06-01

    Full Text Available This work presents a study on the surface morphology, structure and optical behavior of stable phase cadmium sulphide (CdS nanoparticles synthesized via co-precipitation technique. Scanning electron microscopy (SEM analysis has been employed to study a cluster formation in the aggregated nanoparticles. An image analysis approach using ImageJ has been used to measure the size of nanoparticles from the SEM micrographs. Fourier transform infrared spectroscopic (FT-IR analysis identified absorption peaks of Cd–S stretching along with moisture content. X-ray diffraction (XRD analysis showed that CdS nanoparticles crystallized in wurtzite structure with a preferential orientation along (0 0 2 plane. The particle size, microstrain and lattice constants have been evaluated using XRD data. The lattice parameters of these nanoparticles were found to be shorter than the bulk value which led to lattice contraction. The optical absorption study showed a blue shift in the fundamental absorption edge indicating a quantum size effect.

  4. Impact of forest harvesting on trophic structure of eastern Canadian Boreal Shield lakes: insights from stable isotope analyses.

    Directory of Open Access Journals (Sweden)

    Patricia Glaz

    Full Text Available Perturbations on ecosystems can have profound immediate effects and can, accordingly, greatly alter the natural community. Land-use such as forestry activities in the Canadian Boreal region have increased in the last decades, raising concerns about their potential impact on aquatic ecosystems. The objective of this study was to evaluate the impact of forest harvesting on trophic structure in eastern Canadian Boreal Shield lakes. We measured carbon and nitrogen stable isotopes values for aquatic primary producers, terrestrial detritus, benthic macroinvertebrates, zooplankton and brook trout (Salvelinus fontinalis over a three-year period in eight eastern Boreal Shield lakes. Four lakes were studied before, one and two years after forest harvesting (perturbed lakes and compared with four undisturbed reference lakes (unperturbed lakes sampled at the same time. Stable isotope mixing models showed leaf-litter to be the main food source for benthic primary consumers in both perturbed and unperturbed lakes, suggesting no logging impact on allochthonous subsidies to the littoral food web. Brook trout derived their food mainly from benthic predatory macroinvertebrates in unperturbed lakes. However, in perturbed lakes one year after harvesting, zooplankton appeared to be the main contributor to brook trout diet. This change in brook trout diet was mitigated two years after harvesting. Size-related diet shift were also observed for brook trout, indicating a diet shift related to size. Our study suggests that carbon from terrestrial habitat may be a significant contribution to the food web of oligotrophic Canadian Boreal Shield lakes. Forest harvesting did not have an impact on the diet of benthic primary consumers. On the other hand, brook trout diet composition was affected by logging with greater zooplankton contribution in perturbed lakes, possibly induced by darker-colored environment in these lakes one year after logging.

  5. Impact of forest harvesting on trophic structure of eastern Canadian Boreal Shield lakes: insights from stable isotope analyses.

    Science.gov (United States)

    Glaz, Patricia; Sirois, Pascal; Archambault, Philippe; Nozais, Christian

    2014-01-01

    Perturbations on ecosystems can have profound immediate effects and can, accordingly, greatly alter the natural community. Land-use such as forestry activities in the Canadian Boreal region have increased in the last decades, raising concerns about their potential impact on aquatic ecosystems. The objective of this study was to evaluate the impact of forest harvesting on trophic structure in eastern Canadian Boreal Shield lakes. We measured carbon and nitrogen stable isotopes values for aquatic primary producers, terrestrial detritus, benthic macroinvertebrates, zooplankton and brook trout (Salvelinus fontinalis) over a three-year period in eight eastern Boreal Shield lakes. Four lakes were studied before, one and two years after forest harvesting (perturbed lakes) and compared with four undisturbed reference lakes (unperturbed lakes) sampled at the same time. Stable isotope mixing models showed leaf-litter to be the main food source for benthic primary consumers in both perturbed and unperturbed lakes, suggesting no logging impact on allochthonous subsidies to the littoral food web. Brook trout derived their food mainly from benthic predatory macroinvertebrates in unperturbed lakes. However, in perturbed lakes one year after harvesting, zooplankton appeared to be the main contributor to brook trout diet. This change in brook trout diet was mitigated two years after harvesting. Size-related diet shift were also observed for brook trout, indicating a diet shift related to size. Our study suggests that carbon from terrestrial habitat may be a significant contribution to the food web of oligotrophic Canadian Boreal Shield lakes. Forest harvesting did not have an impact on the diet of benthic primary consumers. On the other hand, brook trout diet composition was affected by logging with greater zooplankton contribution in perturbed lakes, possibly induced by darker-colored environment in these lakes one year after logging.

  6. Population-Level Metrics of Trophic Structure Based on Stable Isotopes and Their Application to Invasion Ecology

    Science.gov (United States)

    Jackson, Michelle C.; Donohue, Ian; Jackson, Andrew L.; Britton, J. Robert; Harper, David M.; Grey, Jonathan

    2012-01-01

    Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications. PMID:22363724

  7. Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes

    International Nuclear Information System (INIS)

    Mossa, A; Manosas, M; Forns, N; Huguet, J M; Ritort, F

    2009-01-01

    We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force dependent Kramers–Bell rates. To test the theory we have designed a specific DNA hairpin sequence that shows two-state cooperative folding under mechanical tension and carried out pulling experiments using optical tweezers. We show how we can determine the parameters that characterize the molecular free energy landscape of such sequences from rupture force kinetic studies. Finally we combine such kinetic studies with experimental investigations of the Crooks fluctuation relation to derive the free energy of formation of the hairpin at zero force

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

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Wai Mun; DaGloria, Jeanne; Fox, Heather; Ruan, Qiurong; Tillou, John; Shi, Ke; Aihara, Hideki; Aron, John; Casjens, Sherwood (Utah); (UMM)

    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 encodes 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.

  9. Trophic structure of mesopelagic fishes in the Gulf of Mexico revealed by gut content and stable isotope analyses

    Science.gov (United States)

    McClain-Counts, Jennifer P.; Demopoulos, Amanda W.J.; Ross, Steve W.

    2017-01-01

    Mesopelagic fishes represent an important component of the marine food web due to their global distributions, high abundances and ability to transport organic material throughout a large part of the water column. This study combined stable isotope (SIAs) and gut content analyses (GCAs) to characterize the trophic structure of mesopelagic fishes in the North-Central Gulf of Mexico. Additionally, this study examined whether mesopelagic fishes utilized chemosynthetic energy from cold seeps. Specimens were collected (9–25 August 2007) over three deep (>1,000 m) cold seeps at discrete depths (surface to 1,503 m) over the diurnal cycle. GCA classified 31 species (five families) of mesopelagic fishes into five feeding guilds: piscivores, large crustacean consumers, copepod consumers, generalists and mixed zooplanktivores. However, these guilds were less clearly defined based on stable isotope mixing model (MixSIAR) results, suggesting diets may be more mixed over longer time periods (weeks–months) and across co-occurring species. Copepods were likely important for the majority of mesopelagic fishes, consistent with GCA (this study) and previous literature. MixSIAR results also identified non-crustacean prey items, including salps and pteropods, as potentially important prey items for mesopelagic fishes, including those fishes not analysed in GCA (Sternoptyx spp. and Melamphaidae). Salps and other soft-bodied species are often missed in GCAs. Mesopelagic fishes had δ13C results consistent with particulate organic matter serving as the baseline organic carbon source, fueling up to three trophic levels. Fishes that undergo diel vertical migration were depleted in 15N relative to weak migrators, consistent with depth-specific isotope trends in sources and consumers, and assimilation of 15N-depleted organic matter in surface waters. Linear correlations between fish size and δ15N values suggested ontogenetic changes in fish diets for several species. While there was

  10. Étude expérimentale de structures stables en turbulence bidimensionnelle, comparaison avec une théorie de mécanique statistique

    OpenAIRE

    DENOIX , Marie-Alice

    1992-01-01

    We create two-dimensional flows within a thin layer of mercury, horizontal and subjected to a vertical uniform magnetic field. The fluid is set in motion by injecting electrical currents. We are interested in the inertial organization into stable structures of two-dimensional turbulence. With the experimental conditions in two areas of initial vorticity, we get axisymmetric structures, elliptical, or eccentric. We study these structures using visualizations and also measurements by potential ...

  11. Function and anatomy of plant siRNA pools derived from hairpin transgenes

    Directory of Open Access Journals (Sweden)

    Lee Kevin AW

    2007-11-01

    Full Text Available Abstract Background RNA interference results in specific gene silencing by small-interfering RNAs (siRNAs. Synthetic siRNAs provide a powerful tool for manipulating gene expression but high cost suggests that novel siRNA production methods are desirable. Strong evolutionary conservation of siRNA structure suggested that siRNAs will retain cross-species function and that transgenic plants expressing heterologous siRNAs might serve as useful siRNA bioreactors. Here we report a detailed evaluation of the above proposition and present evidence regarding structural features of siRNAs extracted from plants. Results Testing the gene silencing capacity of plant-derived siRNAs in mammalian cells proved to be very challenging and required partial siRNA purification and design of a highly sensitive assay. Using the above assay we found that plant-derived siRNAs are ineffective for gene silencing in mammalian cells. Plant-derived siRNAs are almost exclusively double-stranded and most likely comprise a mixture of bona fide siRNAs and aberrant partially complementary duplexes. We also provide indirect evidence that plant-derived siRNAs may contain a hitherto undetected physiological modification, distinct from 3' terminal 2-O-methylation. Conclusion siRNAs produced from plant hairpin transgenes and extracted from plants are ineffective for gene silencing in mammalian cells. Thus our findings establish that a previous claim that transgenic plants offer a cost-effective, scalable and sustainable source of siRNAs is unwarranted. Our results also indicate that the presence of aberrant siRNA duplexes and possibly a plant-specific siRNA modification, compromises the gene silencing capacity of plant-derived siRNAs in mammalian cells.

  12. DNA triplex structures in neurodegenerative disorder, Friedreich's ...

    Indian Academy of Sciences (India)

    canonical B-DNA structure or 'unusual' DNA structure. The unusual DNA structures like DNA-hairpin, cruciform, Z-DNA, triplex and tetraplex are represented as hotspots of chromosomal breaks, homologous recombination and gross ...

  13. Structurally Deformed MoS2 for Electrochemically Stable, Thermally Resistant, and Highly Efficient Hydrogen Evolution Reaction.

    Science.gov (United States)

    Chen, Yen-Chang; Lu, Ang-Yu; Lu, Ping; Yang, Xiulin; Jiang, Chang-Ming; Mariano, Marina; Kaehr, Bryan; Lin, Oliver; Taylor, André; Sharp, Ian D; Li, Lain-Jong; Chou, Stanley S; Tung, Vincent

    2017-11-01

    The emerging molybdenum disulfide (MoS 2 ) offers intriguing possibilities for realizing a transformative new catalyst for driving the hydrogen evolution reaction (HER). However, the trade-off between catalytic activity and long-term stability represents a formidable challenge and has not been extensively addressed. This study reports that metastable and temperature-sensitive chemically exfoliated MoS 2 (ce-MoS 2 ) can be made into electrochemically stable (5000 cycles), and thermally robust (300 °C) while maintaining synthetic scalability and excellent catalytic activity through physical-transformation into 3D structurally deformed nanostructures. The dimensional transition enabled by a high throughput electrohydrodynamic process provides highly accessible, and electrochemically active surface area and facilitates efficient transport across various interfaces. Meanwhile, the hierarchically strained morphology is found to improve electronic coupling between active sites and current collecting substrates without the need for selective engineering the electronically heterogeneous interfaces. Specifically, the synergistic combination of high strain load stemmed from capillarity-induced-self-crumpling and sulfur (S) vacancies intrinsic to chemical exfoliation enables simultaneous modulation of active site density and intrinsic HER activity regardless of continuous operation or elevated temperature. These results provide new insights into how catalytic activity, electrochemical-, and thermal stability can be concurrently enhanced through the physical transformation that is reminiscent of nature, in which properties of biological materials emerge from evolved dimensional transitions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Structural, physiological, and stable carbon isotopic evidence that the enigmatic Paleozoic fossil Prototaxites formed from rolled liverwort mats.

    Science.gov (United States)

    Graham, Linda E; Cook, Martha E; Hanson, David T; Pigg, Kathleen B; Graham, James M

    2010-02-01

    New structural, nutritional, and stable carbon isotope data may resolve a long-standing mystery-the biological affinities of the fossil Prototaxites, the largest organism on land during the Late Silurian to Late Devonian (420-370 Ma). The tree trunk-shaped specimens, of varying dimensions but consistent tubular anatomy, first formed prior to vascular plant dominance. Hence, Prototaxites has been proposed to represent giant algae, fungi, or lichens, despite incompatible biochemical and anatomical observations. Our comparative analyses instead indicate that Prototaxites formed from partially degraded, wind-, gravity-, or water-rolled mats of mixotrophic liverworts having fungal and cyanobacterial associates, much like the modern liverwort genus Marchantia. We propose that the fossil body is largely derived from abundant, highly degradation-resistant, tubular rhizoids of marchantioid liverworts, intermixed with tubular microbial elements. Our concept explains previously puzzling fossil features and is consistent with evidence for liverworts and microbial associates in Ordovician-Devonian deposits, extensive ancient and modern marchantioid mats, and modern associations of liverworts with cyanobacteria and diverse types of fungi. Our interpretation indicates that liverworts were important components of Devonian ecosystems, that some macrofossils and microfossils previously attributed to "nematophytes" actually represent remains of ancient liverworts, and that mixotrophy and microbial associations were features of early land plants.

  15. Structurally Deformed MoS2 for Electrochemically Stable, Thermally Resistant, and Highly Efficient Hydrogen Evolution Reaction

    KAUST Repository

    Chen, Yen-Chang

    2017-10-12

    The emerging molybdenum disulfide (MoS2) offers intriguing possibilities for realizing a transformative new catalyst for driving the hydrogen evolution reaction (HER). However, the trade-off between catalytic activity and long-term stability represents a formidable challenge and has not been extensively addressed. This study reports that metastable and temperature-sensitive chemically exfoliated MoS2 (ce-MoS2) can be made into electrochemically stable (5000 cycles), and thermally robust (300 °C) while maintaining synthetic scalability and excellent catalytic activity through physical-transformation into 3D structurally deformed nanostructures. The dimensional transition enabled by a high throughput electrohydrodynamic process provides highly accessible, and electrochemically active surface area and facilitates efficient transport across various interfaces. Meanwhile, the hierarchically strained morphology is found to improve electronic coupling between active sites and current collecting substrates without the need for selective engineering the electronically heterogeneous interfaces. Specifically, the synergistic combination of high strain load stemmed from capillarity-induced-self-crumpling and sulfur (S) vacancies intrinsic to chemical exfoliation enables simultaneous modulation of active site density and intrinsic HER activity regardless of continuous operation or elevated temperature. These results provide new insights into how catalytic activity, electrochemical-, and thermal stability can be concurrently enhanced through the physical transformation that is reminiscent of nature, in which properties of biological materials emerge from evolved dimensional transitions.

  16. Highly transparent, stable, and superhydrophobic coatings based on gradient structure design and fast regeneration from physical damage

    Science.gov (United States)

    Chen, Zao; Liu, Xiaojiang; Wang, Yan; Li, Jun; Guan, Zisheng

    2015-12-01

    Optical transparency, mechanical flexibility, and fast regeneration are important factors to expand the application of superhydrophobic surfaces. Herein, we fabricated highly transparent, stable, and superhydrophobic coatings through a novel gradient structure design by versatile dip-coating of silica colloid particles (SCPs) and diethoxydimethysiliane cross-linked silica nanoparticles (DDS-SNPs) on polyethylene terephthalate (PET) film and glass, followed by the modification of octadecyltrichlorosiliane (OTCS). When the DDS concentration reached 5 wt%, the modified SCPs/DDS-SNPs coating exhibited a water contact angle (WCA) of 153° and a sliding angle (SA) superhydrophobic coating on PET film and glass was increased by 2.7% and 1% in the visible wavelength, respectively. This superhydrophobic coating also showed good robustness and stability against water dropping impact, ultrasonic damage, and acid solution. Moreover, the superhydrophobic PET film after physical damage can quickly regain the superhydrophobicity by one-step spray regenerative solution of dodecyltrichlorosilane (DTCS) modified silica nanoparticles at room temperature. The demonstrated method for the preparation and regeneration of superhydrophobic coating is available for different substrates and large-scale production at room temperature.

  17. Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

    Directory of Open Access Journals (Sweden)

    Cody Springer Sheik

    2015-05-01

    Full Text Available Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

  18. Stable isotopes

    International Nuclear Information System (INIS)

    Evans, D.K.

    1986-01-01

    Seventy-five percent of the world's stable isotope supply comes from one producer, Oak Ridge Nuclear Laboratory (ORNL) in the US. Canadian concern is that foreign needs will be met only after domestic needs, thus creating a shortage of stable isotopes in Canada. This article describes the present situation in Canada (availability and cost) of stable isotopes, the isotope enrichment techniques, and related research programs at Chalk River Nuclear Laboratories (CRNL)

  19. Induction of RNAi Responses by Short Left-Handed Hairpin RNAi Triggers.

    Science.gov (United States)

    Hagopian, Jonathan C; Hamil, Alexander S; van den Berg, Arjen; Meade, Bryan R; Eguchi, Akiko; Palm-Apergi, Caroline; Dowdy, Steven F

    2017-10-01

    Small double-stranded, left-handed hairpin (LHP) RNAs containing a 5'-guide-loop-passenger-3' structure induce RNAi responses by a poorly understood mechanism. To explore LHPs, we synthesized fully 2'-modified LHP RNAs targeting multiple genes and found all to induce robust RNAi responses. Deletion of the loop and nucleotides at the 5'-end of the equivalent passenger strand resulted in a smaller LHP that still induced strong RNAi responses. Surprisingly, progressive deletion of up to 10 nucleotides from the 3'-end of the guide strand resulted in a 32mer LHP capable of inducing robust RNAi responses. However, further guide strand deletion inhibited LHP activity, thereby defining the minimal length guide targeting length to 13 nucleotides. To dissect LHP processing, we examined LHP species that coimmunoprecipitated with Argonaute 2 (Ago2), the catalytic core of RNA-induced silencing complex, and found that the Ago2-associated processed LHP species was of a length that correlated with Ago2 cleavage of the passenger strand. Placement of a blocking 2'-OMe blocking modification at the LHP predicted Ago2 cleavage site resulted in an intact LHP loaded into Ago2 and no RNAi response. Taken together, these data argue that in the absence of a substantial loop, this novel class of small LHP RNAs enters the RNAi pathway by a Dicer-independent mechanism that involves Ago2 cleavage and results in an extended guide strand. This work establishes LHPs as an alternative RNAi trigger that can be produced from a single synthesis for potential use as an RNAi therapeutic.

  20. Targeting of human interleukin-12B by small hairpin RNAs in xenografted psoriatic skin

    Directory of Open Access Journals (Sweden)

    Jakobsen Maria

    2011-02-01

    Full Text Available Abstract Background Psoriasis is a chronic inflammatory skin disorder that shows as erythematous and scaly lesions. The pathogenesis of psoriasis is driven by a dysregulation of the immune system which leads to an altered cytokine production. Proinflammatory cytokines that are up-regulated in psoriasis include tumor necrosis factor alpha (TNFα, interleukin-12 (IL-12, and IL-23 for which monoclonal antibodies have already been approved for clinical use. We have previously documented the therapeutic applicability of targeting TNFα mRNA for RNA interference-mediated down-regulation by anti-TNFα small hairpin RNAs (shRNAs delivered by lentiviral vectors to xenografted psoriatic skin. The present report aims at targeting mRNA encoding the shared p40 subunit (IL-12B of IL-12 and IL-23 by cellular transduction with lentiviral vectors encoding anti-IL12B shRNAs. Methods Effective anti-IL12B shRNAs are identified among a panel of shRNAs by potency measurements in cultured cells. The efficiency and persistency of lentiviral gene delivery to xenografted human skin are investigated by bioluminescence analysis of skin treated with lentiviral vectors encoding the luciferase gene. shRNA-expressing lentiviral vectors are intradermally injected in xenografted psoriatic skin and the effects of the treatment evaluated by clinical psoriasis scoring, by measurements of epidermal thickness, and IL-12B mRNA levels. Results Potent and persistent transgene expression following a single intradermal injection of lentiviral vectors in xenografted human skin is reported. Stable IL-12B mRNA knockdown and reduced epidermal thickness are achieved three weeks after treatment of xenografted psoriatic skin with lentivirus-encoded anti-IL12B shRNAs. These findings mimick the results obtained with anti-TNFα shRNAs but, in contrast to anti-TNFα treatment, anti-IL12B shRNAs do not ameliorate the psoriatic phenotype as evaluated by semi-quantitative clinical scoring and by

  1. Hairpin-like fluorescent probe for imaging of NF-κB transcription factor activity.

    Science.gov (United States)

    Metelev, Valeri; Zhang, Surong; Tabatadze, David; Bogdanov, Alexei

    2011-04-20

    Three oligodeoxyribonucleotides (ODN) covalently labeled with near-infrared (NIR) fluorochromes were synthesized and characterized with a goal of comparing in vitro a hairpin-based and a duplex-based FRET probe designed for the detection of human recombinant NF-κB p50/p65 heterodimer binding to DNA. Using deoxyguanosine phosphoramidite with a phosphorus-linked aminoethylene (diethylene glycol) hydrophilic linker, we synthesized ODNs with internucleoside reactive sites. The hairpin loop amino linker was modified with IRDye 800CW (FRET acceptor), and the 3'-end was modified with Cy5.5 (FRET donor) using a dithio-linker. To obtain a duplex probe, we conjugated Cy5.5 and 800CW to complementary strands at the distance of ten base pairs in the resultant duplex. No quenching of dyes was observed in either probe. The FRET efficiency was higher in the duplex (71%) than in the hairpin (56%) due to a more favorable distance between the donor and the acceptor. However, the hairpin design allowed more precise ratiometric measurement of fluorescence intensity changes as a result of NF-κB p50/p65 binding to the probe. We determined that as a result of binding there was a statistically significant increase of fluorescence intensity of Cy5.5 (donor) due to a decrease of FRET if normalized by 800CW intensity measured independently of FRET. We conclude that the hairpin based probe design allows for the synthesis of a dual fluorescence imaging probe that renders signal changes that are simple to interpret and stoichiometrically correct for detecting transcription factor-DNA interactions.

  2. Evolution of the bi-stable wake of a square-back automotive shape

    Science.gov (United States)

    Pavia, Giancarlo; Passmore, Martin; Sardu, Costantino

    2018-01-01

    Square-back shapes are popular in the automotive market for their high level of practicality. These geometries, however, are usually characterised by high drag and their wake dynamics present aspects, such as the coexistence of a long-time bi-stable behaviour and short-time global fluctuating modes that are not fully understood. In the present paper, the unsteady behaviour of the wake of a generic square-back car geometry is characterised with an emphasis on identifying the causal relationship between the different dynamic modes in the wake. The study is experimental, consisting of balance, pressure, and stereoscopic PIV measurements. Applying wavelet and cross-wavelet transforms to the balance data, a quasi-steady correlation is demonstrated between the forces and bi-stable modes. This is investigated by applying proper orthogonal decomposition to the pressure and velocity data sets and a new structure is proposed for each bi-stable state, consisting of a hairpin vortex that originates from one of the two model's vertical trailing edges and bends towards the opposite side as it merges into a single streamwise vortex downstream. The wake pumping motion is also identified and for the first time linked with the motion of the bi-stable vortical structure in the streamwise direction, resulting in out-of-phase pressure variations between the two vertical halves of the model base. A phase-averaged low-order model is also proposed that provides a comprehensive description of the mechanisms of the switch between the bi-stable states. It is demonstrated that, during the switch, the wake becomes laterally symmetric and, at this point, the level of interaction between the recirculating structures and the base reaches a minimum, yielding, for this geometry, a 7% reduction of the base drag compared to the time-averaged result.

  3. Stable and High OSNR Compound Linear-Cavity Single-Longitudinal-Mode Erbium-Doped Silica Fiber Laser Based on an Asymmetric Four-Cavity Structure

    International Nuclear Information System (INIS)

    Feng Ting; Yan Feng-Ping; Li Qi; Peng Wan-Jing; Feng Su-Chun; Wen Xiao-Dong; Tan Si-Yu; Liu Peng

    2012-01-01

    We propose a stable and high optical signal-to-noise ratio (OSNR) compound linear-cavity single-longitudinal-mode (SLM) erbium-doped silica fiber laser. It consists of three uniform fiber Bragg gratings (FBGs) and two fiber couplers to form a simple asymmetric four-cavity structure to select the longitudinal mode. The stable SLM operation at the wavelength of 1544.053 nm with a 3 dB bandwidth of 0.014 nm and an OSNR of ∼60 dB was verified experimentally. Under laboratory conditions, a power fluctuation performance of less than 0.05 dB for 5 h and wavelength variation of less than 0.01 nm for about 150 min is demonstrated. Finally, the characteristic of laser output power as a function of pump power is investigated. The proposed system provides a simple and cost-effective approach to realize a stable SLM fiber laser

  4. Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

    Science.gov (United States)

    Liu, Yang; Reeves, Dara; Kropachev, Konstantin; Cai, Yuqin; Ding, Shuang; Kolbanovskiy, Marina; Kolbanovskiy, Alexander; Bolton, Judith L.; Broyde, Suse; Van Houten, Bennett; Geacintov, Nicholas E.

    2011-01-01

    Nucleotide excision repair (NER) is an important prokaryotic and eukaryotic defense mechanism that removes a large variety of structurally distinct lesions in cellular DNA. While the proteins involved are completely different, the mode of action of these two repair systems is similar, involving a cut-and-patch mechanism in which an oligonucleotide sequence containing the lesion is excised. The prokaryotic and eukaryotic NER damage-recognition factors have common structural features of β-hairpin intrusion between the two DNA strands at the site of the lesion. In the present study, we explored the hypothesis that this common β-hairpin intrusion motif is mirrored in parallel NER incision efficiencies in the two systems. We have utilized human HeLa cell extracts and the prokaryotic UvrABC proteins to determine their relative NER incision efficiencies. We report here comparisons of relative NER efficiencies with a set of stereoisomeric DNA lesions derived from metabolites of benzo[a]pyrene and equine estrogens in different sequence contexts, utilizing 21 samples. We found a general qualitative trend towards similar relative NER incision efficiencies for ~ 65% of these substrates; the other cases deviate mostly by ~ 30% or less from a perfect correlation, although several more distant outliers are also evident. This resemblance is consistent with the hypothesis that lesion recognition through β-hairpin insertion, a common feature of the two systems, is facilitated by local thermodynamic destabilization induced by the lesions in both cases. In the case of the UvrABC system, varying the nature of the UvrC endonuclease, while maintaining the same UvrA/B proteins, can markedly affect the relative incision efficiencies. These observations suggest that, in addition to recognition involving the initial modified duplexes, downstream events involving UvrC can also play a role in distinguishing and processing different lesions in prokaryotic NER. PMID:21741328

  5. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]^{+} and [YGPAA+H]^{+} Ions: a Stereochemical "twist" on the β-HAIRPIN Turn

    Science.gov (United States)

    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.

  6. 2,6,10-Tris(dialkylamino)-trioxatriangulenium Ions. Synthesis, Structure, and Properties of Exceptionally Stable Carbenium Ions

    DEFF Research Database (Denmark)

    Laursen, Bo W.; Krebs, Frederik C; Nielsen, Merete F.

    1998-01-01

    is expressed as the pK(R+) value, which is determined in strongly basic nonaqueous solution on-the basis of a new acidity function C-. The pK(R+) value of 5a is measured to be 19.7, which is 10 orders of magnitude higher than the values found for the most stable carbenium ions previously reported...

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

    Science.gov (United States)

    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.

  8. 2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage

    International Nuclear Information System (INIS)

    El-Yazbi, Amira F.; Loppnow, Glen R.

    2012-01-01

    Highlights: ► Molecular beacon with 2AP bases detects DNA damage in a simple mix-and-read assay. ► Molecular beacons with 2AP bases detect damage at a 17.2 nM limit of detection. ► The 2AP molecular beacon is linear over a 0–3.5 μM concentration range for damage. - Abstract: Nucleic acid exposure to radiation and chemical insults leads to damage and disease. Thus, detection and understanding DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we develop a fluorescence sensor of 2-aminopurine (2AP), a fluorescent analogue of adenine, incorporated in the loop of a hairpin probe for the quantification of ultraviolet (UV) C-induced nucleic acid damage. Our results show that the selectivity of the 2AP hairpin probe to UV-induced nucleic acid damage is comparable to molecular beacon (MB) probes of DNA damage. The calibration curve for the 2AP hairpin probe shows good linearity (R 2 = 0.98) with a limit of detection of 17.2 nM. This probe is a simple, fast and economic fluorescence sensor for the quantification of UV-induced damage in DNA.

  9. DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

    Science.gov (United States)

    Smith, G. K.; Jie, J.; Fox, G. E.; Gao, X.

    1995-01-01

    DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

  10. Acousto-optical and SAW propagation characteristics of temperature stable multilayered structures based on LiNbO3 and diamond

    International Nuclear Information System (INIS)

    Shandilya, Swati; Sreenivas, K; Gupta, Vinay

    2008-01-01

    Theoretical studies on the surface acoustic wave (SAW) properties of c-axis oriented LiNbO 3 /IDT/diamond and diamond/IDT/128 0 rotated Y-X cut LiNbO 3 multilayered structures have been considered. Both layered structures exhibit a positive temperature coefficient of delay (TCD) characteristic, and a zero TCD device is obtained after integrating with an over-layer of either tellurium dioxide (TeO 2 ) or silicon dioxide (SiO 2 ). The presence of a TeO 2 over-layer enhanced the electromechanical coupling coefficients of both multilayered structures, which acts as a better temperature compensation layer than SiO 2 . The temperature stable TeO 2 /LiNbO 3 /IDT/diamond layered structure exhibits good electromechanical coefficient and higher phase velocity for SAW device applications. On the other hand, a high acousto-optical (AO) figure of merit (30-37) x 10 -15 s 3 kg -1 has been obtained for the temperature stable SiO 2 /diamond/IDT/LiNbO 3 layered structure indicating a promising device structure for AO applications

  11. Stable structures of Al510–800 clusters and lowest energy sequence of truncated octahedral Al clusters up to 10,000 atoms

    International Nuclear Information System (INIS)

    Wu, Xia; He, Chengdong

    2012-01-01

    Highlights: ► The stable structures of Al 510–800 clusters are obtained with the NP-B potential. ► Al 510–800 clusters adopt truncated octahedral (TO) growth pattern based on complete TOs at Al 405 , Al 586 , and Al 711 . ► The lowest energy sequence of complete TOs up to the size 10,000 is proposed. -- Abstract: The stable structures of Al 510–800 clusters are obtained using dynamic lattice searching with constructed cores (DLSc) method by the NP-B potential. According to the structural growth rule, octahedra and truncated octahedra (TO) configurations are adopted as the inner cores in DLSc method. The results show that in the optimized structures two complete TO structures are found at Al 586 and Al 711 . Furthermore, Al 510–800 clusters adopt TO growth pattern on complete TOs at Al 405 , Al 586 , and Al 711 , and the configurations of the surface atoms are investigated. On the other hand, Al clusters with complete TO motifs are studied up to the size 10,000 by the geometrical construction method. The structural characteristics of complete TOs are denoted by the term “family”, and the growth sequence of Al clusters is investigated. The lowest energy sequence of complete TOs is proposed.

  12. Stable isotope studies

    International Nuclear Information System (INIS)

    Ishida, T.

    1992-01-01

    The research has been in four general areas: (1) correlation of isotope effects with molecular forces and molecular structures, (2) correlation of zero-point energy and its isotope effects with molecular structure and molecular forces, (3) vapor pressure isotope effects, and (4) fractionation of stable isotopes. 73 refs, 38 figs, 29 tabs

  13. Conformational dynamics of DNA hairpins at millisecond resolution obtained from analysis of single-molecule FRET histograms.

    Science.gov (United States)

    Tsukanov, Roman; Tomov, Toma E; Berger, Yaron; Liber, Miran; Nir, Eyal

    2013-12-19

    Here we provide high resolution study of DNA hairpin dynamics achieved by probability distribution analysis (PDA) of diffusion-based single-molecule Förster resonance energy transfer (sm-FRET) histograms. The opening and closing rates of three hairpins both free and attached to DNA origami were determined. The agreement with rates previously obtained using the total internal reflection (TIRF) technique and between free hairpins and hairpins attached to origami validated the PDA and demonstrated that the origami had no influence on the hairpin dynamics. From comparison of rates of four DNA hairpins, differing only in stem sequence, and from comparison with rates calculated using nearest-neighbor method and standard transition state theory, we conclude that the unfolding reaction resembles that of melting of DNA duplex with a corresponding sequence and that the folding reaction depends on counterion concentration and not on stem sequence. Our validation and demonstration of the PDA method will encourage its implementation in future high-resolution dynamic studies of freely diffusing biomolecules.

  14. Application of Nitrogen and Carbon Stable Isotopes (δ15N and δ13C) to Quantify Food Chain Length and Trophic Structure

    OpenAIRE

    Perkins, Matthew J.; McDonald, Robbie A.; van Veen, F. J. Frank; Kelly, Simon D.; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ(15)N) and carbon (δ(13)C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ(15)N, and carbon range (CR) using δ(13)C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of kn...

  15. Synthesis and characterization of highly efficient and stable Pr6O11/Ag3PO4/Pt ternary hybrid structure

    International Nuclear Information System (INIS)

    Deng, Jiatao; Liu, Lin; Niu, Tongjun; Sun, Xiaosong

    2017-01-01

    Highlights: • Visible-light-driven Pr 6 O 11 /Ag 3 PO 4 /Pt photocatalysts were prepared. • Pr 6 O 11 /Ag 3 PO 4 /Pt showed highly efficient and stable photocatalystic activity. • The photocatalytic mechanism of Pr 6 O 11 /Ag 3 PO 4 /Pt composite was given. - Abstract: Ag 3 PO 4 is an excellent photocatalyst with high efficiency and quantum yield, but suffers from the fast recombination of photogenerated electron-hole pairs and photo-corrosion. Hereby, the highly efficient and stable visible-light-driven Pr 6 O 11 /Ag 3 PO 4 /Pt photocatalyst were prepared via a three-step wet chemical approach. The as-prepared Pr 6 O 11 /Ag 3 PO 4 /Pt composite was characterized by X-ray diffraction, US-vis diffuse reflectance spectroscopy, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, photoluminescence spectra and transient photocurrent as well. Comparing with single Pr 6 O 11 or Ag 3 PO 4 , the prepared Pr 6 O 11 /Ag 3 PO 4 /Pt composite exhibited much higher photocatalytic activity and stability for the degradation of Rhodamine B under visible light irradiation (>420 nm). The enhanced photocatalytic performance of Pr 6 O 11 /Ag 3 PO 4 /Pt composite has been attributed to the efficient separation of photo-generated electron-hole pairs through a scheme system composed of Pr 6 O 11, Ag 3 PO 4 and Pt.

  16. Highly stable new organic-inorganic perovskite (CH₃NH₃)₂PdBr₄: synthesis, structure and physical properties.

    Science.gov (United States)

    Liu, Xixia; Huang, Tang Jiao; Zhang, Liuyang; Tang, Baoshan; Zhang, Nengduo; Shi, Diwen; Gong, Hao

    2018-01-11

    Lead halide perovskite has attracted striking attention recently due to their appealing properties. However, toxicity and stability are two main factors restricting its application. In this work, we experimentally synthesized less toxic and highly stable Pd-based hybrid perovskite after exploring different experimental conditions. This new hybrid organic-inorganic perovskite (CH₃NH₃)₂PdBr₄ was found to be an orthorhombic crystal (Cmce, Z=4) with lattice parameters a=8.00 Å, b=7.99 Å, c= 18.89 Å. The Cmce symmetry and lattices parameters were confirmed using Pawley refinement. The atoms positions were testified based on DFT calculation. This perovskite compound was determined to be a p-type semiconductor, with a resistivity of 102.9 kΩ*cm, a carrier concentration of 3.4 ×1012 /cm³ and a mobility of 23.4 cm² /(V*S). Interestingly, XRD and UV-vis measurements indicated that the phase of this new perovskite was maintained with an optical gap of 1.91 eV after leaving in air with a high humidity of 60% for 4 days, and unchanged for months in N₂ ambiance, much more stable than most existing organic-inorganic perovskites. The synthesis and various characterizations of this work further the understanding of this (CH₃NH₃)₂PdBr₄ organic-inorganic hybrid perovskite material. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1994-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets, with a few more additions - with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers - exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the foree of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc. (orig.)

  18. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1993-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets. with a few more additions -- with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers-exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the forte of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc

  19. Crystal structure of Δ(185-243)ApoA-I suggests a mechanistic framework for the protein adaptation to the changing lipid load in good cholesterol: from flatland to sphereland via double belt, belt buckle, double hairpin and trefoil/tetrafoil.

    Science.gov (United States)

    Gursky, Olga

    2013-01-09

    Apolipoprotein A-I (apoA-I) is the major protein of plasma high-density lipoproteins (HDLs), macromolecular assemblies of proteins and lipids that remove cell cholesterol and protect against atherosclerosis. HDL heterogeneity, large size (7.7-12 nm), and ability to exchange proteins have prevented high-resolution structural analysis. Low-resolution studies showed that two apoA-I molecules form an antiparallel α-helical "double belt" around an HDL particle. The atomic-resolution structure of the C-terminal truncated lipid-free Δ(185-243)apoA-I, determined recently by Mei and Atkinson, provides unprecedented new insights into HDL structure-function. It allows us to propose a molecular mechanism for the adaptation of the full-length protein to increasing lipid load during cholesterol transport. ApoA-I conformations on small, midsize, and large HDLs are proposed based on the tandem α-helical repeats and the crystal structure of Δ(185-243)apoA-I and are validated by comparison with extensive biophysical data reported by many groups. In our models, the central half of the double belt ("constant" segment 66-184) is structurally conserved while the N- and C-terminal half ("variable" segments 1-65 and 185-243) rearranges upon HDL growth. This includes incremental unhinging of the N-terminal bundle around two flexible regions containing G39 and G65 to elongate the belt, along with concerted swing motion of the double belt around G65-P66 and G185-G186 hinges that are aligned on various-size particles, to confer two-dimensional surface curvature to spherical HDLs. The proposed conformational ensemble integrates and improves several existing HDL models. It helps provide a structural framework necessary to understand functional interactions with over 60 other HDL-associated proteins and, ultimately, improve the cardioprotective function of HDL. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Crystal Structure of Δ(185–243)apoA-I Suggests a Mechanistic Framework for the Protein Adaptation to the Changing Lipid Load in Good Cholesterol: From Flatland to Sphereland via Double Belt, Belt-Buckle, Double Hairpin and Trefoil/Tetrafoil

    Science.gov (United States)

    Gursky, Olga

    2012-01-01

    ApoA-I is the major protein of plasma high-density lipoproteins (HDL), macromolecular assemblies of proteins and lipids that remove cell cholesterol and protect against atherosclerosis. HDL heterogeneity, large size (7.7–12 nm) and ability to exchange proteins have prevented high-resolution structural analysis. Low-resolution studies showed that two apoA-I molecules form an antiparallel α-helical “double belt” around an HDL particle. Atomic-resolution structure of the C-terminal truncated lipid-free Δ(185–243)apoA-I, determined recently by Mei and Atkinson, provides unprecedented new insights into HDL structure-function. It allows us to propose a molecular mechanism for the adaptation of the full-length protein to increasing lipid load during cholesterol transport. ApoA-I conformations on the small, mid-size and large HDL are proposed based on the tandem α-helical repeats and the crystal structure of Δ(185–243)apoA-I, and are validated by comparison with extensive biophysical data reported by many groups. In our models, the central half of the double belt (“constant” segment 66–184) is structurally conserved while the N- and C-terminal half (“variable” segments 1–65 and 185–243) re-arranges upon HDL growth. This includes incremental unhinging of the N-terminal bundle around two flexible regions containing G39 and G65 to elongate the belt, along with concerted swing motion of the double belt around G65-P66 and G185–G186 hinges that are aligned on various-size particles, to confer 2D surface curvature to spherical HDL. The proposed conformational ensemble integrates and improves several existing HDL models. It helps provide a structural framework necessary to understand functional interactions with over 60 other HDL-associated proteins and, ultimately, improve cardioprotective function of HDL. PMID:23041415

  1. A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA

    Directory of Open Access Journals (Sweden)

    Robert J Scarborough

    2014-01-01

    Full Text Available Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.

  2. Robust RNAi-mediated resistance to infection of seven potyvirids in soybean expressing an intron hairpin NIb RNA.

    Science.gov (United States)

    Yang, Xiangdong; Niu, Lu; Zhang, Wei; He, Hongli; Yang, Jing; Xing, Guojie; Guo, Dongquan; Du, Qian; Qian, Xueyan; Yao, Yao; Li, Qiyun; Dong, Yingshan

    2017-10-01

    Viral pathogens, such as soybean mosaic virus (SMV), are a major constraint in soybean production and often cause significant yield loss and quality deterioration. Engineering resistance by RNAi-mediated gene silencing is a powerful strategy for controlling viral diseases. In this study, a 248-bp inverted repeat of the replicase (nuclear inclusion b, NIb) gene was isolated from the SMV SC3 strain, driven by the leaf-specific rbcS2 promoter from Phaseolus vulgaris, and introduced into soybean. The transgenic lines had significantly lower average disease indices (ranging from 2.14 to 12.35) than did the non-transformed (NT) control plants in three consecutive generations, exhibiting a stable and significantly enhanced resistance to the SMV SC3 strain under field conditions. Furthermore, seed mottling did not occur in transgenic seeds, whereas the NT plants produced ~90% mottled seeds. Virus resistance spectrum screening showed that the greenhouse-grown transgenic lines exhibited robust resistance to five SMV strains (SC3, SC7, SC15, SC18, and a recombinant SMV), bean common mosaic virus, and watermelon mosaic virus. Nevertheless, no significantly enhanced resistance to bean pod mottle virus (BPMV, Comovirus) was observed in the transgenic lines relative to their NT counterparts. Consistent with the results of resistance evaluation, the accumulation of each potyvirid (but not of BPMV) was significantly inhibited in the transgenic plants relative to the NT controls as confirmed by quantitative real-time (qRT-PCR) and double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). These results demonstrate that robust RNAi-mediated resistance to multiple potyvirids in soybean was conferred by expressing an intron hairpin SMV NIb RNA.

  3. Buckling control of morphing composite airfoil structure using multi-stable laminate by piezoelectric sensors/actuators

    Science.gov (United States)

    Zareie, Shahin; Zabihollah, Abolghassem; Azizi, Aydin

    2011-04-01

    In the present work, an unsymmetric laminated plate with surface bonded piezoelectric sensors, and actuators has been considered. Piezoelectric sensor were used to monitor the load and deformation bifurcation occurs. Monitoring the shape and load of a morphing structure is essential to ascertain that the structure is properly deployed and it is not loaded excessively ,thus, preventing structural to failure. A piezoceramic actuator is used to provide activation load and to force the structure to change its stability state from one to another. A non-linear finite element model based on the layerwise displacement theory considering the electro-mechanical coupling effects of piezoelectric elements has been developed for simulation purposes. A control mechanism is also employed to actively control the shape of the structure. It is observed that, utilizing multistable composite to design a morphing structure may significantly reduce the energy required for changing the shape. Further controlling the buckling phenomena using piezoelectric sensor and actuator along with an ON/OFF controller can effectively and efficiency enhance the performance of the morphing structure during manoeuver.

  4. The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form.

    Science.gov (United States)

    Thomson, J B; Lilley, D M

    1999-01-01

    In the natural form of the hairpin ribozyme the two loop-carrying duplexes that comprise the majority of essential bases for activity form two adjacent helical arms of a four-way RNA junction. In the present work we have manipulated the sequence around the junction in a way known to perturb the global folding properties. We find that replacement of the junction by a different sequence that has the same conformational properties as the natural sequence gives closely similar reaction rate and Arrhenius activation energy for the substrate cleavage reaction. By comparison, rotation of the natural sequence in order to alter the three-dimensional folding of the ribozyme leads to a tenfold reduction in the kinetics of cleavage. Replacement with the U1 four-way junction that is resistant to rotation into the antiparallel structure required to allow interaction between the loops also gives a tenfold reduction in cleavage rate. The results indicate that the conformation of the junction has a major influence on the catalytic activity of the ribozyme. The results are all consistent with a role for the junction in the provision of a framework by which the loops are presented for interaction in order to create the active form of the ribozyme. PMID:10024170

  5. Stable beams

    CERN Multimedia

    2015-01-01

    Stable beams: two simple words that carry so much meaning at CERN. When LHC page one switched from "squeeze" to "stable beams" at 10.40 a.m. on Wednesday, 3 June, it triggered scenes of jubilation in control rooms around the CERN sites, as the LHC experiments started to record physics data for the first time in 27 months. This is what CERN is here for, and it’s great to be back in business after such a long period of preparation for the next stage in the LHC adventure.   I’ve said it before, but I’ll say it again. This was a great achievement, and testimony to the hard and dedicated work of so many people in the global CERN community. I could start to list the teams that have contributed, but that would be a mistake. Instead, I’d simply like to say that an achievement as impressive as running the LHC – a machine of superlatives in every respect – takes the combined effort and enthusiasm of everyone ...

  6. Thermally Stable and Electrically Conductive, Vertically Aligned Carbon Nanotube/Silicon Infiltrated Composite Structures for High-Temperature Electrodes.

    Science.gov (United States)

    Zou, Qi Ming; Deng, Lei Min; Li, Da Wei; Zhou, Yun Shen; Golgir, Hossein Rabiee; Keramatnejad, Kamran; Fan, Li Sha; Jiang, Lan; Silvain, Jean-Francois; Lu, Yong Feng

    2017-10-25

    Traditional ceramic-based, high-temperature electrode materials (e.g., lanthanum chromate) are severely limited due to their conditional electrical conductivity and poor stability under harsh circumstances. Advanced composite structures based on vertically aligned carbon nanotubes (VACNTs) and high-temperature ceramics are expected to address this grand challenge, in which ceramic serves as a shielding layer protecting the VACNTs from the oxidation and erosive environment, while the VACNTs work as a conductor. However, it is still a great challenge to fabricate VACNT/ceramic composite structures due to the limited diffusion of ceramics inside the VACNT arrays. In this work, we report on the controllable fabrication of infiltrated (and noninfiltrated) VACNT/silicon composite structures via thermal chemical vapor deposition (CVD) [and laser-assisted CVD]. In laser-assisted CVD, low-crystalline silicon (Si) was quickly deposited at the VACNT subsurfaces/surfaces followed by the formation of high-crystalline Si layers, thus resulting in noninfiltrated composite structures. Unlike laser-assisted CVD, thermal CVD activated the precursors inside and outside the VACNTs simultaneously, which realized uniform infiltrated VACNT/Si composite structures. The growth mechanisms for infiltrated and noninfiltrated VACNT/ceramic composites, which we attributed to the different temperature distributions and gas diffusion mechanism in VACNTs, were investigated. More importantly, the as-farbicated composite structures exhibited excellent multifunctional properties, such as excellent antioxidative ability (up to 1100 °C), high thermal stability (up to 1400 °C), good high velocity hot gas erosion resistance, and good electrical conductivity (∼8.95 Sm -1 at 823 K). The work presented here brings a simple, new approach to the fabrication of advanced composite structures for hot electrode applications.

  7. 2,6,10-Tris(dialkylamino)trioxatriangulenium ions. Synthesis, structure, and properties of exceptionally stable carbenium ions

    DEFF Research Database (Denmark)

    Laursen, B.W.; Krebs, Frederik C; Nielsen, M.F.

    1998-01-01

    A general synthetic route to a novel type of triamino-substituted planar carbenium ions (5) is reported. The synthetic method is based on a facile and selective nucleophilic aromatic substitution on the 4,6-trimethoxyphenyl)carbenium ion (1) with amines and gives access to a wide variety of more...... complex amino-substituted carbenium ions. X-ray crystallography shows that the cis(N-pyrrolidinyl)-4,8,12-trioxatriangulenium ion (5b) is planar and forms segregated stacks of cations and PF6 anions in the solid phase. The stability of the 2,6, 0-tris(diethylamino)- 4,8,12-trioxatriangulenium ion 5a...... is expressed as the pK(R+) value, which is determined in strongly basic nonaqueous solution on-the basis of a new acidity function C-. The pK(R+) value of 5a is measured to be 19.7, which is 10 orders of magnitude higher than the values found for the most stable carbenium ions previously reported...

  8. More Stable Ties or Better Structure? An Examination of the Impact of Co-author Network on Team Knowledge Creation

    Directory of Open Access Journals (Sweden)

    Mingze Li

    2017-09-01

    Full Text Available This study aims to explore the influence of co-author network on team knowledge creation. Integrating the two traditional perspectives of network relationship and network structure, we examine the direct and interactive effects of tie stability and structural holes on team knowledge creation. Tracking scientific articles published by 111 scholars in the research field of human resource management from the top 8 American universities, we analyze scholars’ scientific co-author networks. The result indicates that tie stability changes the teams’ information processing modes and, when graphed, results in an inverted U-shape relationship between tie stability and team knowledge creation. Moreover, structural holes in co-author network are proved to be harmful to team knowledge sharing and diffusion, thereby impeding team knowledge creation. Also, tie stability and structural hole interactively influence team knowledge creation. When the number of structural hole is low in the co-author network, the graphical representation of the relationship between tie stability and team knowledge creation tends to be a more distinct U-shape.

  9. The use of protein structure/activity relationships in the rational design of stable particulate delivery systems

    Directory of Open Access Journals (Sweden)

    M.H.B. Costa

    2002-06-01

    Full Text Available The recombinant heat shock protein (18 kDa-hsp from Mycobacterium leprae was studied as a T-epitope model for vaccine development. We present a structural analysis of the stability of recombinant 18 kDa-hsp during different processing steps. Circular dichroism and ELISA were used to monitor protein structure after thermal stress, lyophilization and chemical modification. We observed that the 18 kDa-hsp is extremely resistant to a wide range of temperatures (60% of activity is retained at 80ºC for 20 min. N-Acylation increased its ordered structure by 4% and decreased its ß-T1 structure by 2%. ELISA demonstrated that the native conformation of the 18 kDa-hsp was preserved after hydrophobic modification by acylation. The recombinant 18 kDa-hsp resists to a wide range of temperatures and chemical modifications without loss of its main characteristic, which is to be a source of T epitopes. This resistance is probably directly related to its lack of organization at the level of tertiary and secondary structures.

  10. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

    Science.gov (United States)

    Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1995-01-01

    In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

  11. Facile synthesis of stable structured MoS{sub 2}-Mo-CNFs heteroarchitecture with enhanced hydrogen evolution

    Energy Technology Data Exchange (ETDEWEB)

    Mo, Qionghua [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Faculty of Material and Energy, South West University, Chongqing 400700 (China); Yao, Yucen [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Liu, Bitao, E-mail: liubitao007@163.com [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Peng, Lingling; Yan, Hengqing; Hou, Zhupei; Wang, Jun [Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160 (China); Lin, Yue, E-mail: linyue@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Anhui 230026 (China)

    2017-06-01

    3D structured MoS{sub 2} are grown in-situ on Mo particles embedded carbon nanofibers (CNFs) via a hydrothermal method. Due to this special structure, the bonding and effective electron delivery between CNFs and MoS{sub 2} are both enhanced, and which will exhibits a better hydrogen evolution activity. The onset potential of this MoS{sub 2}-Mo-CNFs catalyst will decreased to 60 mV compared to the 90 mV for the MoS{sub 2}-CNFs. And its current density nearly no change with 5000 cycles which is better than the 32.3% decrease of MoS{sub 2}-CNFs at η = 300 mV (V vs RHE). - Highlights: • Newly structured MoS{sub 2}-Mo-CNFs with effectively connection between MoS{sub 2} and CNFs successfully synthesized. • This structure can enhance the charge transfer and significantly increase electrocatalytic efficiency. • Nearly no HER activity loss after 5000 CV cycles.

  12. Microbial food web mapping: linking carbon cycling and community structure in soils through pyrosequencing enabled stable isotope probing

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Daniel H. [Cornell Univ., Ithaca, NY (United States)

    2015-03-15

    Soil represents a massive reservoir of active carbon and climate models vary dramatically in predicting how this carbon will respond to climate change over the coming century. A major cause of uncertainty is that we still have a very limited understand the microorganisms that dominate the soil carbon cycle. The vast majority of soil microbes cannot be cultivated in the laboratory and the diversity of organisms and enzymes that participate in the carbon cycle is staggeringly complex. We have developed a new toolbox for exploring the carbon cycle and the metabolic and ecological characteristics of uncultivated microorganisms. The high-resolution nucleic acid stable isotope probing approach that we have developed makes it possible to characterize microbial carbon cycling dynamics in soil. The approach allows us to track multiple 13C-labeled substrates into thousands of microbial taxa over time. Using this approach we have discovered several major lineages of uncultivated microorganisms that participate in cellulose metabolism and are found widely in soils (including Verrucomicrobia and Chloroflexi, which have not previously been implicated as major players in the soil carbon cycle). Furthermore, isotopic labelling of nucleic acids enables community genomics and permits genome fragment binning for a majority of these cellulolytic microorganisms allowing us to explore the metabolic underpinnings of cellulose degradation. This approach has allowed us to describe unexpected dynamics of carbon metabolism with different microbial taxa exhibiting characteristic patterns of carbon substrate incorporation, indicative of distinct ecological strategies. The data we describe allows us to characterize the activity of novel microorganisms as they occur in the environment and these data provide a basis for understanding how the physiological traits of discrete microorganisms sum to govern the complex responses of the soil carbon cycle.

  13. Modeling food web structure and selenium biomagnification in Lake Macquarie, New South Wales, Australia, using stable carbon and nitrogen isotopes.

    Science.gov (United States)

    Schneider, Larissa; Maher, William A; Potts, Jaimie; Taylor, Anne M; Batley, Graeme E; Krikowa, Frank; Chariton, Anthony A; Gruber, Bernd

    2015-03-01

    As a consequence of coal-fired power station operations, elevated selenium concentrations have been reported in the sediments and biota of Lake Macquarie (New South Wales, Australia). In the present study, an ecosystem-scale model has been applied to determine how selenium in a seagrass food web is processed from sediments and water through diet to predators, using stable isotopes (δ(13) C and δ(15) N) to establish the trophic position of organisms. Trophic position, habitat, and feeding zone were examined as possible factors influencing selenium bioaccumulation. Selenium concentrations ranged from 0.2 μg/g dry weight in macroalgae species to 12.9 μg/g in the carnivorous fish Gerres subfasciatus. A mean magnification factor of 1.39 per trophic level showed that selenium is biomagnifying in the seagrass food web. Habitat and feeding zone influenced selenium concentrations in invertebrates, whereas feeding zone was the only significant factor influencing selenium concentrations in fish. The sediment-water partitioning coefficient (Kd ) of 4180 showed that partitioning of selenium entering the lake to particulate organic material (POM) is occurring, and consequently availability to food webs from POM is high. Trophic transfer factors (invertebrate = 1.9; fish = 1.2) were similar to those reported for other water bodies, showing that input source is not the main determinant of the magnitude of selenium bioaccumulation in a food web, but rather the initial partitioning of selenium into bioavailable POM. Environ Toxicol Chem 2015;34:608-617. © 2014 SETAC. © 2014 SETAC.

  14. Dynamic reorganization of chromatin structure and selective DNA demethylation prior to stable enhancer complex formation during differentiation of primary hematopoietic cells in vitro.

    Science.gov (United States)

    Tagoh, Hiromi; Melnik, Svitlana; Lefevre, Pascal; Chong, Suyinn; Riggs, Arthur D; Bonifer, Constanze

    2004-04-15

    In order to gain insights in the true molecular mechanisms involved in cell fate decisions, it is important to study the molecular details of gene activation where such decisions occur, which is at the level of the chromatin structure of individual genes. In the study presented here we addressed this issue and examined the dynamic development of an active chromatin structure at the chicken lysozyme locus during the differentiation of primary myeloid cells from transgenic mouse bone marrow. Using in vivo footprinting we found that stable enhancer complex assembly and high-level gene expression are late events in cell differentiation. However, even before the onset of gene expression and stable transcription factor binding, specific chromatin alterations are observed. This includes changes in DNA topology and the selective demethylation of CpG dinucleotides located in the cores of critical transcription factor binding sites, but not in flanking DNA. These results firmly support the idea that epigenetic programs guiding blood cell differentiation are engraved into the chromatin of lineage-specific genes and that such chromatin changes are implemented before cell lineage specification.

  15. Eroding dipoles and vorticity growth for Euler flows in {{{R}}}^{3}: the hairpin geometry as a model for finite-time blowup

    Science.gov (United States)

    Childress, Stephen; Gilbert, Andrew D.

    2018-02-01

    A theory of an eroding ‘hairpin’ vortex dipole structure in three-dimensions is developed, extending our previous study of an axisymmetric eroding dipole without swirl. The axisymmetric toroidal dipole was found to lead to maximal growth of vorticity, as {t}4/3. The hairpin is here similarly proposed as a model to produce large ‘self-stretching’ of vorticity, with the possibility of finite-time blow-up. We derive a system of partial differential equations of ‘generalized’ form, involving contour averaging of a locally two-dimensional Euler flow. We do not attempt here to solve the system exactly, but point out that non-existence of physically acceptable solutions would most probably be a result of the axial flow. Because of the axial flow the vorticity distribution within the dipole eddies is no longer of the simple Sadovskii type (vorticity constant over a cross-section) obtained in the axisymmetric problem. Thus the solution of the system depends upon the existence of a larger class of propagating two-dimensional dipoles. The hairpin model is obtained by formal asymptotic analysis. As in the axisymmetric problem a local transformation to ‘shrinking’ coordinates is introduced, but now in a self-similar form appropriate to the study of a possible finite-time singularity. We discuss some properties of the model, including a study of the helicity and a first step in iterating toward a solution from the Sadovskii structure. We also present examples of two-dimensional propagating dipoles not previously studied, which have a vorticity profile consistent with our model. Although no rigorous results can be given, and analysis of the system is only partial, the formal calculations are consistent with the possibility of a finite time blowup of vorticity at a point of vanishing circulation of the dipole eddies, but depending upon the existence of the necessary two-dimensional propagating dipole. Our results also suggest that conservation of kinetic energy as

  16. Fundamental understanding of oxygen reduction and reaction behavior and developing high performance and stable hetero-structured cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xingbo [West Virginia Univ., Morgantown, WV (United States)

    2016-11-14

    New unique hetero-structured cathode has been developed in this project. La2NiO4+δ (LNO) as a surface catalyst with interstitial oxygen defects was introduced onto the state-of-the-art (La0.6Sr0.4)0.95Co0.2Fe0.8O3-δ (LSCF) cathode to enhance the surface-limited ORR kinetics on SOFC cathode. Furthermore, the hetero-structured cathode surface maintains high activity under electrode polarization with much less negative effects from surface cation segregation of Sr, which is known to cause degradation issues for conventional LSCF and LSC cathodes, thus improving the cathode long-term stability. The interface chemistry distribution and oxygen transport properties have been studied to prove the enhancement of power out and stability of LNO-infiltrated LSCF cathode. The further investigation demonstrates that CeO2 & La2-xNiO4+δ (x=0-0.2) co-infiltration is a simple and cost-effective method to improve both performance and stability of LSCF cathode by limiting nano-particles growth/delamination and further improve the surface stability. For the first time, a physical model is proposed to illustrate how unique interstitial species on hetero-structured cathode surface work to regulate the exchange rate of the incorporation reaction. Meanwhile, fundamental investigation of the surface oxygen exchange and bulk oxygen transport properties under over-potential conditions across cathode materials have been carried out in this project, which were discussed and compared to the Nernst equation that is generally applied to treat any oxide electrodes under equilibrium.

  17. Atomic structure of a stable high-index Ge surface: G2(103)-(4x1)

    DEFF Research Database (Denmark)

    Seehofer, L.; Bunk, O.; Falkenberg, G.

    1997-01-01

    Based on scanning tunneling microscopy and surface X-ray diffraction, we propose a complex structural model for the Ge(103)-(4 x 1) reconstruction. Each unit cell contains two (103) double steps, which gives rise to the formation of stripes of Ge atoms oriented in the [] direction....... The stripes and the spaces between them are covered with threefold-coordinated Ge adatoms. Charge is transferred from the bulk-like edge atoms of the double steps to the adatoms. The formation of the reconstruction can be explained in terms of stress relief, charge transfer, and minimization of the dangling...

  18. Stable structures and potential energy surface of the metallic clusters: Ni, Cu, Ag, Au, Pd, and Pt

    Science.gov (United States)

    Wu, Xia; Sun, Yan

    2017-06-01

    Metallic clusters have been widely studied due to their special electrical, optical, and catalytic properties. The many-body Gupta potential is applied to describe the interatomic interaction of Ni, Cu, Ag, Au, Pd, and Pt clusters, and their global minimal structures within 100 atoms are optimized using dynamic lattice searching (DLS) method. The configurational distribution of global minima is analyzed, and the geometrical difference among these clusters is demonstrated. Results show that the dominant motif of Ni and Cu clusters is the icosahedron, and in Ag and Au clusters the number of decahedra is slightly larger than that of the icosahedra. However, more face-centered cubic (fcc), stacking fault fcc, and amorphous structures are formed in Au clusters than in Ag clusters. Furthermore, the main motif of Pd and Pt clusters is the decahedron. In particular, Ni98 adopts a Leary tetrahedral motif, and Pt54 is a central vacant icosahedron. The difference related to the potential parameters of these metallic clusters is further investigated by energy analysis. Moreover, the potential energy surfaces (PES) of 38-atom metallic clusters is characterized in terms of conformational analysis. It was found that the sequence of the number of local minima on the PES from large to low is Ni, Cu, Ag, Pt, Pd, and Au.

  19. Structural and photoluminescence behavior of thermally stable Eu3+activated CaWO4 nanophosphors via Li+ incorporation

    Science.gov (United States)

    Ramakrishna, P. V.; Lakshmana Rao, T.; Singh, Arvind; Benarji, B.; Dash, S.

    2017-12-01

    We have studied the structural and photo physical analogue of Eu3+ activated CaWO4 nanophosphors via Lithium (Li+ = 2, 5 7 and 10 at.%) ion incorporation. As-prepared (APS) samples were annealed at 900 °C to eliminate unwanted organic moieties present in the sample and to improve crystallinity. The samples are characterized employing X-ray diffraction (XRD), Fourier transform IR spectroscopy (FTIR), UV-VIS spectroscopy, photoluminescence studies and lifetime decay studies. FTIR features an absorption band at ∼832 cm-1, which correspond to its antisymmetric vibrations into Osbnd Wsbnd O band in the WO42- tetrahedron. CaWO4 having the scheelite type structure with C4h point group and I41/a space group. The surface morphology of the samples are studied with Scanning Electron Microscopy (SEM). Lithium Co-doped CaWO4:Eu3+ nanoparticles show red luminescence because of strong host contribution and different energy transfer rates from host to Eu3+ ions under 266 nm excitations. Lithium ion enhances the crystallinity and radiative transition rate thus results in higher emissive property. Calculated CIE co-ordinates of these Li+ doped 900 °C annealed samples under 266 nm excitation is x = 0.65 & y = 0.34, which are closer to the standard of NTSC (x = 0.67 & y = 0.33). This material may be potential candidates for white light emitting diodes.

  20. The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

    Directory of Open Access Journals (Sweden)

    Schaefer H Martin

    2011-06-01

    Full Text Available Abstract Background While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes across its wide distributional range in Chile and Argentina. Results Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. Conclusions Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations.

  1. PP3 forms stable tetrameric structures through hydrophobic interactions via the C-terminal amphipathic helix and undergoes reversible thermal dissociation and denaturation.

    Science.gov (United States)

    Pedersen, Lise R L; Nielsen, Søren B; Hansted, Jon G; Petersen, Torben E; Otzen, Daniel E; Sørensen, Esben S

    2012-01-01

    The milk protein proteose peptone component 3 (PP3), also called lactophorin, is a small phosphoglycoprotein that is expressed exclusively in lactating mammary tissue. The C-terminal part of the protein contains an amphipathic helix, which, upon proteolytic liberation, shows antibacterial activity. Previous studies indicate that PP3 forms multimeric structures and inhibits lipolysis in milk. PP3 is the principal component of the proteose peptone fraction of milk. This fraction is obtained by heating and acidifying skimmed milk, and in the dairy industry milk products are also typically exposed to treatments such as pasteurization, which potentially could result in irreversible denaturation and inactivation of bioactive components. We show here, by the use of CD, that PP3 undergoes reversible thermal denaturation and that the α-helical structure of PP3 remains stable even at gastric pH levels. This suggests that the secondary structure survives treatment during the purification and possibly some of the industrial processing of milk. Finally, asymmetric flow field-flow fractionation and multi-angle light scattering reveal that PP3 forms a rather stable tetrameric complex, which dissociates and unfolds in guanidinium chloride. The cooperative unfolding of PP3 was completely removed by the surfactant n-dodecyl-β-d-maltoside and by oleic acid. We interpret this to mean that the PP3 monomers associate through hydrophobic interactions via the hydrophobic surface of the amphipathic helix. These observations suggest that PP3 tetramers act as reservoirs of PP3 molecules, which in the monomeric state may stabilize the milk fat globule. © 2011 The Authors Journal compilation © 2011 FEBS.

  2. Ultra-stable Molecule-Surface Architectures at Metal Oxides: Structure, Bonding, and Electron-transfer Processes

    Energy Technology Data Exchange (ETDEWEB)

    Hamers, Robert John

    2013-12-07

    Research funded by this project focused on the development of improved strategies for functionalization of metal oxides to enhance charge-transfer processes relevant to solar energy conversion. Initial studies included Fe2O3, WO3, TiO2, SnO2, and ZnO as model oxide systems; these systems were chosen due to differences in metal oxidation state and chemical bonding types in these oxides. Later studies focused largely on SnO2 and ZnO, as these materials show particularly promising surface chemistry, have high electron mobility, and can be readily grown in both spherical nanoparticles and as elongated nanorods. New molecules were synthesized that allowed the direct chemical assembly of novel nanoparticle ?dyadic? structures in which two different oxide materials are chemically joined, leading to an interface that enhances the separation of of charge upon illumination. We demonstrated that such junctions enhance photocatalytic efficiency using model organic compounds. A separate effort focused on novel approaches to linking dye molecules to SnO2 and ZnO as a way to enhance solar conversion efficiency. A novel type of surface binding through

  3. Functional Aspects of the Solution Structure and Dynamics of PAF, a Highly Stable Antifungal Protein from Penicillium chrysogenum

    Science.gov (United States)

    Batta, Gyula; Barna, Teréz; Gáspári, Zoltán; Sándor, Szabolcs; Kövér, Katalin E.; Binder, Ulrike; Sarg, Bettina; Kaiserer, Lydia; Chhillar, Anil Kumar; Eigentler, Andrea; Leiter, Éva; Hegedüs, Nikoletta; Pócsi, István; Lindner, Herbert; Marx, Florentine

    2015-01-01

    Summary PAF is a promising antimycotic without toxic effects on mammalian cells and therefore may be a drug candidate against the often lethal Aspergillus infections in human. The pathogenesis of PAF on sensitive fungi involves G-protein coupled signaling followed by apoptosis. Here, the solution structure of this small, cationic, antifungal protein from Penicillium chrysogenum is determined by solution NMR. We proved that PAF belongs to the SCOP fold class of its closest homologue AFP from Aspergillus giganteus. PAF comprises five β—strands forming two orthogonally packed β—sheets sharing a common interface. The ambiguity in the assignment of two disulfide bonds of three was investigated by NMR dynamics combined with restrained molecular dynamics calculations. The clue could not be resolved: two ensembles with different disulfide patterns and the one with no S-S bond exhibit essentially the same fold. 15N relaxation dispersion and interference experiments did not reveal disulfide bond rearrangements via slow exchange. The measured order parameters and the 3.0 ns correlation time is appropriate for a compact monomeric protein of this size. We demonstrated by site-directed mutagenesis that the highly conserved and positively charged lysine-rich domain region on the surface enhances the toxicity of PAF. However, the efficacy of the OB fold is reduced in PAF compared to AFP, due to less solvent exposed aromatic regions explaining the absence of chitobiose binding. The present work lends further support to the understanding of the documented substantial differences between the mode of action of two highly homologous antifungal proteins. PMID:19459942

  4. RNA polymerase II mediated transcription from the polymerase III promoters in short hairpin RNA expression vector

    International Nuclear Information System (INIS)

    Rumi, Mohammad; Ishihara, Shunji; Aziz, Monowar; Kazumori, Hideaki; Ishimura, Norihisa; Yuki, Takafumi; Kadota, Chikara; Kadowaki, Yasunori; Kinoshita, Yoshikazu

    2006-01-01

    RNA polymerase III promoters of human ribonuclease P RNA component H1, human U6, and mouse U6 small nuclear RNA genes are commonly used in short hairpin RNA (shRNA) expression vectors due their precise initiation and termination sites. During transient transfection of shRNA vectors, we observed that H1 or U6 promoters also express longer transcripts enough to express several reporter genes including firefly luciferase, green fluorescent protein EGFP, and red fluorescent protein JRed. Expression of such longer transcripts was augmented by upstream RNA polymerase II enhancers and completely inhibited by downstream polyA signal sequences. Moreover, the transcription of firefly luciferase from human H1 promoter was sensitive to RNA polymerase II inhibitor α-amanitin. Our findings suggest that commonly used polymerase III promoters in shRNA vectors are also prone to RNA polymerase II mediated transcription, which may have negative impacts on their targeted use

  5. Compact Hairpin Bandpass Filter with Wide Stopband and High Attenuation Using Multilayer Broadside-coupled Stripline

    Directory of Open Access Journals (Sweden)

    Xiaowei GU

    2014-11-01

    Full Text Available This paper presents a compact bandpass filter with stopband and high attenuation by using multilayer folded broadside-coupled quarter-wavelength stripline resonators in a low- temperature co-fired ceramic (LTCC substrate. The proposed bandpass filter centered at 1.1 GHz with a fractional bandwith of 4.5 % shows the first spurious frequency at 3.8 times the center frequency. In comparison to the conventional half-wavelength hairpin bandpass filter with the same passband performance, the proposed bandpass filter shows not only a 50 % size reduction but also a wider stopband from 1.3 GHz -3.8 GHz with a high rejection level up to 60 dB.

  6. Decay of the electron number density in the nitrogen afterglow using a hairpin resonator probe

    International Nuclear Information System (INIS)

    Siefert, Nicholas S.; Ganguly, Biswa N.; Sands, Brian L.; Hebner, Greg A.

    2006-01-01

    A hairpin resonator was used to measure the electron number density in the afterglow of a nitrogen glow discharge (p=0.25-0.75 Torr). Electron number densities were measured using a time-dependent approach similar to the approach used by Spencer et al. [J. Phys. D 20, 923 (1987)]. The decay time of the electron number density was used to determine the electron temperature in the afterglow, assuming a loss of electrons via ambipolar diffusion to the walls. The electron temperature in the near afterglow remained between 0.4 and 0.6 eV, depending on pressure. This confirms the work by Guerra et al. [IEEE Trans. Plasma. Sci. 31, 542 (2003)], who demonstrated experimentally and numerically that the electron temperature stays significantly above room temperature via superelastic collisions with highly vibrationally excited ground state molecules and metastables, such as A 3 Σ u +

  7. One-step isothermal detection of multiple KRAS mutations by forming SNP specific hairpins on a gold nanoshell.

    Science.gov (United States)

    Chung, Chan Ho; Kim, Joong Hyun

    2018-04-24

    We developed a one-step isothermal method for typing multiple KRAS mutations using a designed set of primers to form a hairpin on a gold nanoshell upon being ligated by a SNP specific DNA ligase after binding of targets. As a result, we could detect as low as 20 attomoles of KRAS mutations within 1 h.

  8. Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations.

    NARCIS (Netherlands)

    Smith, A.W.; Lessing, J.; Ganim, Z.; Peng, C.S.; Tokmakoff, A.; Roy, S.; Jansen, T.L.Th.A.; Knoester, J.

    2010-01-01

    Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn

  9. Melting of a beta-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations

    NARCIS (Netherlands)

    Smith, Adam W.; Lessing, Joshua; Ganim, Ziad; Peng, Chunte Sam; Tokmakoff, Andrei; Roy, Santanu; Jansen, Thomas L. C.; Knoester, Jasper

    2010-01-01

    Isotope-edited two-dimensional infrared spectroscopy has been used! to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (17.2) across its thermal unfolding transition Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn

  10. A New Computational Approach for Mechanical Folding Kinetics of RNA Hairpins

    Science.gov (United States)

    Cao, Song; Chen, Shi-Jie

    2009-01-01

    Based on an ensemble of kinetically accessible conformations, we propose a new analytical model for RNA folding kinetics. The model gives populational kinetics, kinetic rates, transition states, and pathways from the rate matrix. Applications of the new kinetic model to mechanical folding of RNA hairpins such as trans-activation-responsive RNA reveal distinct kinetic behaviors in different force regimes, from zero force to forces much stronger than the critical force for the folding-unfolding transition. In the absence of force or a low force, folding can be initiated (nucleated) at any position by forming the first base stack and there exist many pathways for the folding process. In contrast, for a higher force, the folding/unfolding would predominantly proceed along a single zipping/unzipping pathway. Studies for different hairpin-forming sequences indicate that depending on the nucleotide sequence, a kinetic intermediate can emerge in the low force regime but disappear in high force regime, and a new kinetic intermediate, which is absent in the low and high force regimes, can emerge in the medium force range. Variations of the force lead to changes in folding cooperativity and rate-limiting steps. The predicted network of pathways for trans-activation-responsive RNA suggests two parallel dominant pathways. The rate-limiting folding steps (at f = 8 pN) are the formation of specific basepairs that are 2–4 basepairs away from the loop. At a higher force (f = 11 pN), the folding rate is controlled by the formation of the bulge loop. The predicted rates and transition states are in good agreement with the experimental data for a broad force regime. PMID:19450474

  11. Effects of osmolytes and macromolecular crowders on stable GAAA tetraloops and their preference for a CG closing base pair

    Directory of Open Access Journals (Sweden)

    Kaethe N. Leonard

    2018-02-01

    Full Text Available Osmolytes and macromolecular crowders have the potential to influence the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in vivo. To further understand the cellular function of RNA we observed the effects of a model osmolyte, polyethylene glycol (PEG 200, and a model macromolecular crowding agent, PEG 8000, on the GAAA tetraloop motif. GAAA tetraloops are conserved, stable tetraloops, and are critical participants in RNA tertiary structure. They also have a thermodynamic preference for a CG closing base pair. The thermal denaturation of model hairpins containing GAAA loops was monitored using UV-Vis spectroscopy in the presence and absence of PEG 200 or PEG 8000. Both of the cosolutes tested influenced the thermodynamic preference for a CG base pair by destabilizing the loop with a CG closing base pair relative to the loop with a GC closing base pair. This result also extended to a related DNA triloop, which provides further evidence that the interactions between the loop and closing base pair are identical for the d(GCA triloop and the GAAA tetraloop. Our results suggest that in the presence of model PEG molecules, loops with a GC closing base pair may retain some preferential interactions with the cosolutes that are lost in the presence of the CG closing base pair. These results reveal that relatively small structural changes could influence how neutral cosolutes tune the stability and function of secondary structure motifs in vivo.

  12. Application of nitrogen and carbon stable isotopes (δ(15N and δ(13C to quantify food chain length and trophic structure.

    Directory of Open Access Journals (Sweden)

    Matthew J Perkins

    Full Text Available Increasingly, stable isotope ratios of nitrogen (δ(15N and carbon (δ(13C are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR using δ(15N, and carbon range (CR using δ(13C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ(15N or δ(13C from source to consumer between trophic levels and among food chains. δ(15N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰, and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ(13C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ(13C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority

  13. Application of Nitrogen and Carbon Stable Isotopes (δ15N and δ13C) to Quantify Food Chain Length and Trophic Structure

    Science.gov (United States)

    Perkins, Matthew J.; McDonald, Robbie A.; van Veen, F. J. Frank; Kelly, Simon D.; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ15N, and carbon range (CR) using δ13C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ15N or δ13C from source to consumer) between trophic levels and among food chains. δ15N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ13C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ13C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of ecological systems

  14. Application of nitrogen and carbon stable isotopes (δ(15)N and δ(13)C) to quantify food chain length and trophic structure.

    Science.gov (United States)

    Perkins, Matthew J; McDonald, Robbie A; van Veen, F J Frank; Kelly, Simon D; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ(15)N) and carbon (δ(13)C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ(15)N, and carbon range (CR) using δ(13)C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ(15)N or δ(13)C from source to consumer) between trophic levels and among food chains. δ(15)N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ(13)C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ(13)C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of

  15. Towards tricking a pathogen's protease into fighting infection: the 3D structure of a stable circularly permuted onconase variant cleavedby HIV-1 protease.

    Directory of Open Access Journals (Sweden)

    Mariona Callís

    Full Text Available Onconase® is a highly cytotoxic amphibian homolog of Ribonuclease A. Here, we describe the construction of circularly permuted Onconase® variants by connecting the N- and C-termini of this enzyme with amino acid residues that are recognized and cleaved by the human immunodeficiency virus protease. Uncleaved circularly permuted Onconase® variants are unusually stable, non-cytotoxic and can internalize in human T-lymphocyte Jurkat cells. The structure, stability and dynamics of an intact and a cleaved circularly permuted Onconase® variant were determined by Nuclear Magnetic Resonance spectroscopy and provide valuable insight into the changes in catalytic efficiency caused by the cleavage. The understanding of the structural environment and the dynamics of the activation process represents a first step toward the development of more effective drugs for the treatment of diseases related to pathogens expressing a specific protease. By taking advantage of the protease's activity to initiate a cytotoxic cascade, this approach is thought to be less susceptible to known resistance mechanisms.

  16. Post-transcriptional modulation of protein phosphatase PPP2CA and tumor suppressor PTEN by endogenous siRNA cleaved from hairpin within PTEN mRNA 3'UTR in human liver cells.

    Science.gov (United States)

    Gao, Yu-En; Wang, Yuan; Chen, Fu-Quan; Feng, Jin-Yan; Yang, Guang; Feng, Guo-Xing; Yang, Zhe; Ye, Li-Hong; Zhang, Xiao-Dong

    2016-07-01

    Increasing evidence shows that mRNAs exert regulatory function along with coding proteins. Recently we report that a hairpin within YAP mRNA 3'UTR can modulate the Hippo signaling pathway. PTEN is a tumor suppressor, and is mutated in human cancers. In this study we examined whether PTEN mRNA 3'UTR contained a hairpin structure that could regulate gene regulation at the post-transcriptional level. The secondary structure of PTEN mRNA 3'UTR was analyzed using RNAdraw and RNAstructure. Function of hairpin structure derived from the PTEN mRNA 3'UTR was examined using luciferase reporter assay, RT-PCR and Western blotting. RNA-immunoprecipitation (RIP) assay was used to analyze the interaction between PTEN mRNA and microprocessor Drosha and DGCR8. Endogenous siRNA (esiRNA) derived from PTEN mRNA 3'UTR was identified by RT-PCR and rt-PCR, and its target genes were predicted using RNAhybrid. A bioinformatics analysis revealed that PTEN mRNA contained a hairpin structure (termed PTEN-sh) within 3'UTR, which markedly increased the reporter activities of AP-1 and NF-κB in 293T cells. Moreover, treatment with PTEN-sh (1 and 2 μg) dose-dependently inhibited the expression of PTEN in human liver L-O2 cells. RIP assay demonstrated that the microprocessor Drosha and DGCR8 was bound to PTEN-sh in L-O2 cells, leading to the cleavage of PTEN-sh from PTEN mRNA 3'UTR. In addition, microprocessor Dicer was involved in the processing of PTEN-sh. Interestingly, esiRNA (termed PTEN-sh-3p21) cleaved from PTEN-sh was identified in 293T cells and human liver tissues, which was found to target the mRNA 3'UTRs of protein phosphatase PPP2CA and PTEN in L-O2 cells. Treatment of L-O2 or Chang liver cells with PTEN-sh-3p21 (50, 100 nmol/L) promoted the cell proliferation in dose- and time-dependent manners. The endogenous siRNA (PTEN-sh-3p21) cleaved from PTEN-sh within PTEN mRNA 3'UTR modulates PPP2CA and PTEN at the post-transcriptional level in liver cells.

  17. Post-transcriptional modulation of protein phosphatase PPP2CA and tumor suppressor PTEN by endogenous siRNA cleaved from hairpin within PTEN mRNA 3′UTR in human liver cells

    Science.gov (United States)

    Gao, Yu-en; Wang, Yuan; Chen, Fu-quan; Feng, Jin-yan; Yang, Guang; Feng, Guo-xing; Yang, Zhe; Ye, Li-hong; Zhang, Xiao-dong

    2016-01-01

    Aim: Increasing evidence shows that mRNAs exert regulatory function along with coding proteins. Recently we report that a hairpin within YAP mRNA 3′UTR can modulate the Hippo signaling pathway. PTEN is a tumor suppressor, and is mutated in human cancers. In this study we examined whether PTEN mRNA 3′UTR contained a hairpin structure that could regulate gene regulation at the post-transcriptional level. Methods: The secondary structure of PTEN mRNA 3′UTR was analyzed using RNAdraw and RNAstructure. Function of hairpin structure derived from the PTEN mRNA 3′UTR was examined using luciferase reporter assay, RT-PCR and Western blotting. RNA-immunoprecipitation (RIP) assay was used to analyze the interaction between PTEN mRNA and microprocessor Drosha and DGCR8. Endogenous siRNA (esiRNA) derived from PTEN mRNA 3′UTR was identified by RT-PCR and rt-PCR, and its target genes were predicted using RNAhybrid. Results: A bioinformatics analysis revealed that PTEN mRNA contained a hairpin structure (termed PTEN-sh) within 3′UTR, which markedly increased the reporter activities of AP-1 and NF-κB in 293T cells. Moreover, treatment with PTEN-sh (1 and 2 μg) dose-dependently inhibited the expression of PTEN in human liver L-O2 cells. RIP assay demonstrated that the microprocessor Drosha and DGCR8 was bound to PTEN-sh in L-O2 cells, leading to the cleavage of PTEN-sh from PTEN mRNA 3′UTR. In addition, microprocessor Dicer was involved in the processing of PTEN-sh. Interestingly, esiRNA (termed PTEN-sh-3p21) cleaved from PTEN-sh was identified in 293T cells and human liver tissues, which was found to target the mRNA 3′UTRs of protein phosphatase PPP2CA and PTEN in L-O2 cells. Treatment of L-O2 or Chang liver cells with PTEN-sh-3p21 (50, 100 nmol/L) promoted the cell proliferation in dose- and time-dependent manners. Conclusion: The endogenous siRNA (PTEN-sh-3p21) cleaved from PTEN-sh within PTEN mRNA 3′UTR modulates PPP2CA and PTEN at the post

  18. In vitro inhibition of transmissible gastroenteritis coronavirus replication in swine testicular cells by short hairpin RNAs targeting the ORF 7 gene.

    Science.gov (United States)

    He, Lei; Zhang, Yan-ming; Dong, Ling-juan; Cheng, Min; Wang, Jing; Tang, Qing-hai; Wang, Gang

    2012-08-28

    Transmissible gastroenteritis (TGE) is a highly contagious viral disease of swine, characterized by severe vomiting, diarrhea, and high mortality. Currently, the vaccines for it are only partially effective and no specific drug is available for treatment of TGE virus (TGEV) infection. RNA interference has been confirmed as a new approach for controlling viral infections. In this study, the inhibitory effect of short hairpin RNAs (shRNAs) targeting the ORF 7 gene of TGEV on virus replication was examined. Four theoretically effective sequences of TGEV ORF 7 gene were designed and selected for construction of shRNA expression plasmids. In the reporter assays, three of four shRNA expression plasmids were able to inhibit significantly the expression of ORF 7 gene and replication of TGEV, as shown by real-time quantitative RT-PCR analysis of viral ORF 7 and N genes and detection of virus titers (TCID50/ml). Stable swine testicular (ST) cells expressing the shRNAs were established. Observation of the cytopathic effect and apoptosis, as well as a cell proliferation assay demonstrated that the three shRNAs were capable of protecting ST cells against TGEV destruction, with high specificity and efficiency. Our results indicated that plasmid-transcribed shRNAs targeting the ORF 7 gene in the TGEV genome effectively inhibited expression of the viral target gene and viral replication in vitro. These findings provide evidence that the shRNAs have potential therapeutic application for treatment of TGE.

  19. In vitro inhibition of transmissible gastroenteritis coronavirus replication in swine testicular cells by short hairpin RNAs targeting the ORF 7 gene

    Directory of Open Access Journals (Sweden)

    He Lei

    2012-08-01

    Full Text Available Abstract Background Transmissible gastroenteritis (TGE is a highly contagious viral disease of swine, characterized by severe vomiting, diarrhea, and high mortality. Currently, the vaccines for it are only partially effective and no specific drug is available for treatment of TGE virus (TGEV infection. RNA interference has been confirmed as a new approach for controlling viral infections. In this study, the inhibitory effect of short hairpin RNAs (shRNAs targeting the ORF 7 gene of TGEV on virus replication was examined. Results Four theoretically effective sequences of TGEV ORF 7 gene were designed and selected for construction of shRNA expression plasmids. In the reporter assays, three of four shRNA expression plasmids were able to inhibit significantly the expression of ORF 7 gene and replication of TGEV, as shown by real-time quantitative RT-PCR analysis of viral ORF 7 and N genes and detection of virus titers (TCID50/ml. Stable swine testicular (ST cells expressing the shRNAs were established. Observation of the cytopathic effect and apoptosis, as well as a cell proliferation assay demonstrated that the three shRNAs were capable of protecting ST cells against TGEV destruction, with high specificity and efficiency. Conclusions Our results indicated that plasmid-transcribed shRNAs targeting the ORF 7 gene in the TGEV genome effectively inhibited expression of the viral target gene and viral replication in vitro. These findings provide evidence that the shRNAs have potential therapeutic application for treatment of TGE.

  20. Preliminary examination of food web structure of Nicola Lake (Taim Hydrological System, south Brazil using dual C and N stable isotope analyses

    Directory of Open Access Journals (Sweden)

    Alexandre M. Garcia

    Full Text Available Taim Ecological Reserve is located within the Taim Hydrological System and was created to protect a heterogeneous and productive landscape harboring exceptional biological diversity in southern Brazil. Using stable isotope ratio analyses of carbon (delta13C and nitrogen (delta15N, we provide a preliminary description of the food web structure, including estimates of production sources supporting fish populations and vertical trophic structure, within a representative lake of this system. A total of 21 organisms (5 macrophytes, 3 mollusks and 13 adult fishes representing 16 species were collected for isotope analysis. Fishes had delta13C values ranging from -24.30º/oo to -28.31º/oo , showing concordance with the range of values observed for macrophytes (-25.49 to -27.10º/oo, and suggesting that these plants could be a major carbon source supporting these fishes. delta13C signatures of Corbicula (-30.81º/oo and Pomacea (-24.26º/oo indirectly suggest that phytoplankton and benthic algae could be alternative carbon sources for some consumers. Nitrogen isotope ratios indicated approximately three consumer trophic levels. The pearl cichlid Geophagus brasiliensis was a primary consumer. Two catfishes (Trachelyopterus lucenai and Loricariichthys anus were secondary consumers. Two congeneric pike cichclids (Crenicichla lepidota and C. punctata, a catfish (Pimelodus maculatus and the characids Astyanax fasciatus and Oligosarcus robustus were tertiary consumers. Further studies including additional primary producers and consumers and greater sample numbers should be conducted to provide a more complete and detailed description of food web structure and dynamics within the reserve.

  1. Novel guanidinylated bioresponsive poly(amidoamines designed for short hairpin RNA delivery

    Directory of Open Access Journals (Sweden)

    Yu J

    2016-12-01

    Full Text Available Jiankun Yu,1 Jinmin Zhang,1 Haonan Xing,1 Yanping Sun,1 Zhen Yang,1 Tianzhi Yang,2 Cuifang Cai,1 Xiaoyun Zhao,3 Li Yang,1 Pingtian Ding1 1School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China; 2Department of Basic Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME, USA; 3Department of Microbiology and Cell Biology, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China Abstract: Two different disulfide (SS-containing poly(amidoamine (PAA polymers were constructed using guanidino (Gua-containing monomers (ie, arginine [Arg] and agmatine [Agm] and N,N'-cystamine bisacrylamide (CBA by Michael-addition polymerization. In order to characterize these two Gua-SS-PAA polymers and investigate their potentials as short hairpin RNA (shRNA-delivery carriers, pSilencer 4.1-CMV FANCF shRNA was chosen as a model plasmid DNA to form complexes with these two polymers. The Gua-SS-PAAs and plasmid DNA complexes were determined with particle sizes less than 90 nm and positive ζ-potentials under 20 mV at nucleic acid:polymer weight ratios lower than 1:24. Bioresponsive release of plasmid DNA was observed from both newly constructed complexes. Significantly lower cytotoxicity was observed for both polymer complexes compared with polyethylenimine and Lipofectamine 2000, two widely used transfection reagents as reference carriers. Arg-CBA showed higher transfection efficiency and gene-silencing efficiency in MCF7 cells than Agm-CBA and the reference carriers. In addition, the cellular uptake of Arg-CBA in MCF7 cells was found to be higher and faster than Agm-CBA and the reference carriers. Similarly, plasmid DNA transport into the nucleus mediated by Arg-CBA was more than that by Agm-CBA and the reference carriers. The study suggested that guanidine and carboxyl introduced into Gua-SS-PAAs polymers resulted in a better nuclear localization effect, which played a key role in the

  2. Efficient and stable, structurally inverted poly(3-hexylthiopen): [6,6]-phenyl-C61-butyric acid methyl ester heterojunction solar cells with fibrous like poly(3-hexylthiopen)

    International Nuclear Information System (INIS)

    Bandara, Jayasundera; Shankar, Karthik; Grimes, Craig A.; Thelakkat, Mukundan

    2011-01-01

    We investigated an inverted organic photovoltaic device structure in which a densely packed ∼ 100 nm thin TiO 2 layer on fluorine doped conducting glass serves as anode and poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate)/Au layer on top of the active layer serves as cathode. The active layer is comprised of a blend of poly(3-hexylthiopene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). The rectification behavior of such a device is improved significantly and injection losses are minimized compared to devices without any compact TiO 2 layer. Moreover, nanostructured P3HT active layer was achieved in-situ by spin coating concentrated pure P3HT and P3HT:PCBM blend and solar cell performances on thickness of the active layer were also investigated. For the inverted solar cells constructed with different concentrations of P3HT and PCBM keeping the P3HT:PCBM ratio 1:0.8 (wt.%), the highest short circuit current and efficiency was observed when the P3HT and PCBM concentration was equal to 1.5 (wt.%) and 1.2 (wt.%) respectively. This leads to highly stable and reproducible power conversion efficiency above 3.7% at 100 mW/cm 2 light intensity under AM 1.5 conditions.

  3. Synthesis and X-ray Crystal Structure of a Stable cis-1,2-bis(diphenylphosphinoethene Monodentate Thiolate Platinum Complex and TGA Studies of its Precursors

    Directory of Open Access Journals (Sweden)

    Vaz Rodrigo H.

    2002-01-01

    Full Text Available The stable Pt(II complex [Pt(SPh2(dppen (4, (dppen, Ph2PCH=CHPPh2 was obtained from [PtCl(SPh2(SnPh3cod] (1 (cod = 1,5-cyclooctadiene by reductive elimination reaction of SnClPh3 and substitution of the cod ligand by the diphosphine, albeit in low yields. Yields of 80% were obtained when [Pt(SPh2cod] (3 was used as the starting material instead. The viability of these reactions was suggested by a TG study, performed on the starting materials. Complex 4 was characterized by multinuclear NMR (195Pt, 31P, ¹H and 13C and IR spectroscopies and elemental analysis. The molecular structure, solved by an X-ray diffraction study, exhibted a slightly distorted square-planar geometry and short C=C and Pt-P bond distances which were interpreted in terms of a p interaction between the double bond and the metal-ligand bond, as observed for other diphosphine compounds described previously.

  4. Synergetic effects of solution-processable fluorinated graphene and PEDOT as a hole-transporting layer for highly efficient and stable normal-structure perovskite solar cells.

    Science.gov (United States)

    Yu, Jae-Hun; Lee, Cheol-Ho; Joh, Han-Ik; Yeo, Jun-Seok; Na, Seok-In

    2017-11-16

    We demonstrate that a bi-interlayer consisting of water-free poly(3,4-ethylenedioxythiophene) (PEDOT) and fluorinated reduced graphene oxide (FrGO) noticeably enhances the efficiency and the stability of the normal-structure perovskite solar cells (PeSCs). With simple and low temperature solution-processing, the PeSC employing the PEDOT + FrGO interlayer exhibits a significantly improved power conversion efficiency (PCE) of 14.9%. Comprehensive investigations indicate that the enhanced PCE is mostly attributed to the retarded recombination in the devices. The minimized recombination phenomena are related to the interfacial dipoles at the PEDOT/FrGO interface, which facilitates the electron-blocking and the higher built-in potential in the devices. Furthermore, the PEDOT + FrGO device shows a better stability by maintaining 70% of the initial PCE over the 30 days exposure to ambient conditions. This is because the more hydrophobic graphitic sheets of the FrGO on the PEDOT further protect the perovskite films from oxygen/water penetration. Consequently, the introduction of composite interfacial layers including graphene derivatives can be an effective and versatile strategy for high-performing, stable, and cost-effective PeSCs.

  5. Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish

    KAUST Repository

    Priest, Mark

    2012-11-19

    We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing pressure. Our primary hypothesis was to test whether the individuals resident in the southern Mariana Island chain were genetically distinct and hence should be managed as discrete stocks. In addition to spatial sampling of adults, newly-settled individuals were sampled on Guam over four recruitment events to assess the temporal stability of the observed spatial patterns, and evidence of self-recruitment. We found significant genetic structure in S. spinus across the western Pacific, with Bayesian analyses revealing three genetically distinct clusters: the southernMariana Islands, east Micronesia, and the west Pacific; with the southern Mariana Islands beingmore strongly differentiated fromthe rest of the region. Analyses of temporal samples from Guam indicated the southern Mariana cluster was stable over time, with no genetic differentiation between adults versus recruits, or between samples collected across four separate recruitment events spanning 11 months. Subsequent assignment tests indicated seven recruits had self-recruited from within the Southern Mariana Islands population. Our results confirm the relative isolation of the southern Mariana Islands population and highlight how local processes can act to isolate populations that, by virtue of their broad-scale distribution, have been subject to traditionally high gene flows. Our results add to a growing consensus that self-recruitment is a highly significant influence on the population dynamics of tropical reef fish. 2012 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.

  6. Stable Isotope Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tissue samples (skin, bone, blood, muscle) are analyzed for stable carbon, stable nitrogen, and stable sulfur analysis. Many samples are used in their entirety for...

  7. Comparison of Cytotoxic Activity in Leukemic Lineages Reveals Important Features of β-Hairpin Antimicrobial Peptides.

    Science.gov (United States)

    Buri, Marcus V; Torquato, Heron F Vieira; Barros, Carlos Castilho; Ide, Jaime S; Miranda, Antonio; Paredes-Gamero, Edgar J

    2017-07-01

    Several reports described different modes of cell death triggered by antimicrobial peptides (AMPs) due to direct effects on membrane disruption, and more recently by apoptosis and necrosis-like patterns. Cytotoxic curves of four β-hairpin AMPs (gomesin, protegrin, tachyplesin, and polyphemusin) were obtained from several human leukemic lineages and normal monocytes and Two cell lines were then selected based on their cytotoxic sensitivity. One was sensitive to AMPs (K562) and the other resistant (KG-1) and their effect compared between these lineages. Thus, these lineages were chosen to further investigate biological features related with their cytotoxicities to AMPs. Stimulation with AMPs produced cell death, with activation of caspase-3, in K562 lineage. Increase on the fluidity of plasmatic membrane by reducing cholesterol potentiated cytotoxicity of AMPs in both lineages. Quantification of internal and external gomesin binding to the cellular membrane of both K562 and KG-1 cells showed that more peptide is accumulated inside of K562 cells. Additionally, evaluation of multi-drug resistant pumps activity showed that KG-1 has more activity than K562 lineage. A comparison of intrinsic gene patterns showed great differences between K562 and KG-1, but stimulation with gomesin promoted few changes in gene expression patterns. Differences in internalization process through the plasma membrane, multidrug resistance pumps activity, and gene expression pattern are important features to AMPs regulated cell death. J. Cell. Biochem. 118: 1764-1773, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  8. Construction of equalized short hairpin RNA library from human brain cDNA.

    Science.gov (United States)

    Xu, Lei; Li, Jingqi; Liu, Li; Lu, Lixia; Gao, Jingxia; Li, Xueli

    2007-02-20

    Short hairpin RNA (shRNA) library is a powerful new tool for high-throughput loss-of-function genetic screens in mammalian cells. An shRNA library can be constructed from synthetic oligonucleotides or enzymatically cleaved natural cDNA. Here, we describe a new method for constructing equalized shRNA libraries from cDNA. First, enzymatically digested cDNA fragments are equalized by a suppression PCR-based method modified from suppression subtractive hybridization. The efficiency of equalization was confirmed by quantitative real-time PCR. The fragments are then converted into an shRNA library by a series of enzymatic treatments. With this new technology, we constructed a library from human brain cDNA. Sequence analysis showed that most of the randomly selected clones had inverted repeat sequences converted from different cDNA. After transfecting HEK 293T cells and detecting gene expression, three out of eight clones were demonstrated to significantly inhibit their target genes.

  9. The Inverse Autotransporter Intimin Exports Its Passenger Domain via a Hairpin Intermediate*

    Science.gov (United States)

    Oberhettinger, Philipp; Leo, Jack C.; Linke, Dirk; Autenrieth, Ingo B.; Schütz, Monika S.

    2015-01-01

    Autotransporter proteins comprise a large family of virulence factors that consist of a β-barrel translocation unit and an extracellular effector or passenger domain. The β-barrel anchors the protein to the outer membrane of Gram-negative bacteria and facilitates the transport of the passenger domain onto the cell surface. By inserting an epitope tag into the N terminus of the passenger domain of the inverse autotransporter intimin, we generated a mutant defective in autotransport. Using this stalled mutant, we could show that (i) at the time point of stalling, the β-barrel appears folded; (ii) the stalled autotransporter is associated with BamA and SurA; (iii) the stalled intimin is decorated with large amounts of SurA; (iv) the stalled autotransporter is not degraded by periplasmic proteases; and (v) inverse autotransporter passenger domains are translocated by a hairpin mechanism. Our results suggest a function for the BAM complex not only in insertion and folding of the β-barrel but also for passenger translocation. PMID:25488660

  10. The inverse autotransporter intimin exports its passenger domain via a hairpin intermediate.

    Science.gov (United States)

    Oberhettinger, Philipp; Leo, Jack C; Linke, Dirk; Autenrieth, Ingo B; Schütz, Monika S

    2015-01-16

    Autotransporter proteins comprise a large family of virulence factors that consist of a β-barrel translocation unit and an extracellular effector or passenger domain. The β-barrel anchors the protein to the outer membrane of Gram-negative bacteria and facilitates the transport of the passenger domain onto the cell surface. By inserting an epitope tag into the N terminus of the passenger domain of the inverse autotransporter intimin, we generated a mutant defective in autotransport. Using this stalled mutant, we could show that (i) at the time point of stalling, the β-barrel appears folded; (ii) the stalled autotransporter is associated with BamA and SurA; (iii) the stalled intimin is decorated with large amounts of SurA; (iv) the stalled autotransporter is not degraded by periplasmic proteases; and (v) inverse autotransporter passenger domains are translocated by a hairpin mechanism. Our results suggest a function for the BAM complex not only in insertion and folding of the β-barrel but also for passenger translocation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Co-expression of Argonaute2 enhances short hairpin RNA-induced RNA interference in Xenopus CNS neurons in vivo

    Directory of Open Access Journals (Sweden)

    Chih-ming Chen

    2009-07-01

    Full Text Available RNA interference (RNAi is an evolutionarily conserved mechanism for sequence-specific gene silencing. Recent advances in our understanding of RNAi machinery make it possible to reduce protein expression by introducing short hairpin RNA (shRNA into cells of many systems, however, the efficacy of RNAi-mediated protein knockdown can be quite variable, especially in intact animals, and this limits its application. We built adaptable molecular tools, pSilencer (pSi and pReporter (pRe constructs, to evaluate the impact of different promoters, shRNA structures and overexpression of Ago2, the key enzyme in the RNA-induced silencing complex (RISC, on the efficiency of RNAi. The magnitude of RNAi knockdown was evaluated in cultured cells and intact animals by comparing fluorescence intensity levels of GFP, the RNAi target, relative to mCherry, which was not targeted. Co-expression of human Ago2 with shRNA significantly enhanced efficiency of GFP knockdown in cell lines and in neurons of intact Xenopus tadpoles. Human H1- and U6-promotors alone or the U6-promotor with an enhancer element were equally effective at driving GFP knockdown. shRNA derived from the microRNA-30 design (shRNAmir30 enhanced the efficiency of GFP knockdown. Expressing pSi containing Ago2 with shRNA increased knockdown efficiency of an endogenous neuronal protein, the GluR2 subunit of the AMPA receptor, functionally accessed by recording AMPA receptor-mediated spontaneous synaptic currents in Xenopus CNS neurons. Our data suggest that co-expression of Ago2 and shRNA is a simple method to enhance RNAi in intact animals. While morpholino antisense knockdown is effective in Xenopus and Zebrafish, a principle advantage of the RNAi method is the possibility of spatial and temporal control of protein knockdown by use of cell type specific and regulatable pol II promoters to drive shRNA and Ago2. This should extend the application of RNAi to study gene function of intact brain circuits.

  12. Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms.

    Science.gov (United States)

    Huang, Xuhui; Yao, Yuan; Bowman, Gregory R; Sun, Jian; Guibas, Leonidas J; Carlsson, Gunnar; Pande, Vijay S

    2010-01-01

    Simulating biologically relevant timescales at atomic resolution is a challenging task since typical atomistic simulations are at least two orders of magnitude shorter. Markov State Models (MSMs) provide one means of overcoming this gap without sacrificing atomic resolution by extracting long time dynamics from short simulations. MSMs coarse grain space by dividing conformational space into long-lived, or metastable, states. This is equivalent to coarse graining time by integrating out fast motions within metastable states. By varying the degree of coarse graining one can vary the resolution of an MSM; therefore, MSMs are inherently multi-resolution. Here we introduce a new algorithm Super-level-set Hierarchical Clustering (SHC), to our knowledge, the first algorithm focused on constructing MSMs at multiple resolutions. The key insight of this algorithm is to generate a set of super levels covering different density regions of phase space, then cluster each super level separately, and finally recombine this information into a single MSM. SHC is able to produce MSMs at different resolutions using different super density level sets. To demonstrate the power of this algorithm we apply it to a small RNA hairpin, generating MSMs at four different resolutions. We validate these MSMs by showing that they are able to reproduce the original simulation data. Furthermore, long time folding dynamics are extracted from these models. The results show that there are no metastable on-pathway intermediate states. Instead, the folded state serves as a hub directly connected to multiple unfolded/misfolded states which are separated from each other by large free energy barriers.

  13. Stable convergence and stable limit theorems

    CERN Document Server

    Häusler, Erich

    2015-01-01

    The authors present a concise but complete exposition of the mathematical theory of stable convergence and give various applications in different areas of probability theory and mathematical statistics to illustrate the usefulness of this concept. Stable convergence holds in many limit theorems of probability theory and statistics – such as the classical central limit theorem – which are usually formulated in terms of convergence in distribution. Originated by Alfred Rényi, the notion of stable convergence is stronger than the classical weak convergence of probability measures. A variety of methods is described which can be used to establish this stronger stable convergence in many limit theorems which were originally formulated only in terms of weak convergence. Naturally, these stronger limit theorems have new and stronger consequences which should not be missed by neglecting the notion of stable convergence. The presentation will be accessible to researchers and advanced students at the master's level...

  14. Interaction of Zn(II)bleomycin-A2 and Zn(II)peplomycin with a DNA hairpin containing the 5'-GT-3' binding site in comparison with the 5'-GC-3' binding site studied by NMR spectroscopy.

    Science.gov (United States)

    Follett, Shelby E; Ingersoll, Azure D; Murray, Sally A; Reilly, Teresa M; Lehmann, Teresa E

    2017-10-01

    Bleomycins are a group of glycopeptide antibiotics synthesized by Streptomyces verticillus that are widely used for the treatment of various neoplastic diseases. These antibiotics have the ability to chelate a metal center, mainly Fe(II), and cause site-specific DNA cleavage. Bleomycins are differentiated by their C-terminal regions. Although this antibiotic family is a successful course of treatment for some types of cancers, it is known to cause pulmonary fibrosis. Previous studies have identified that bleomycin-related pulmonary toxicity is linked to the C-terminal region of these drugs. This region has been shown to closely interact with DNA. We examined the binding of Zn(II)peplomycin and Zn(II)bleomycin-A 2 to a DNA hairpin of sequence 5'-CCAGTATTTTTACTGG-3', containing the binding site 5'-GT-3', and compared the results with those obtained from our studies of the same MBLMs bound to a DNA hairpin containing the binding site 5'-GC-3'. We provide evidence that the DNA base sequence has a strong impact in the final structure of the drug-target complex.

  15. SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA.

    Science.gov (United States)

    Sakuragi, Sayuri; Yokoyama, Masaru; Shioda, Tatsuo; Sato, Hironori; Sakuragi, Jun-Ichi

    2016-11-11

    The dimer initiation site/dimer linkage sequence (DIS/DLS) region of HIV is located on the 5' end of the viral genome and suggested to form complex secondary/tertiary structures. Within this structure, stem-loop 1 (SL1) is believed to be most important and an essential key to dimerization, since the sequence and predicted secondary structure of SL1 are highly stable and conserved among various virus subtypes. In particular, a six-base palindromic sequence is always present at the hairpin loop of SL1 and the formation of kissing-loop structure at this position between the two strands of genomic RNA is suggested to trigger dimerization. Although the higher-order structure model of SL1 is well accepted and perhaps even undoubted lately, there could be stillroom for consideration to depict the functional SL1 structure while in vivo (in virion or cell). In this study, we performed several analyses to identify the nucleotides and/or basepairing within SL1 which are necessary for HIV-1 genome dimerization, encapsidation, recombination and infectivity. We unexpectedly found that some nucleotides that are believed to contribute the formation of the stem do not impact dimerization or infectivity. On the other hand, we found that one G-C basepair involved in stem formation may serve as an alternative dimer interactive site. We also report on our further investigation of the roles of the palindromic sequences on viral replication. Collectively, we aim to assemble a more-comprehensive functional map of SL1 on the HIV-1 viral life cycle. We discovered several possibilities for a novel structure of SL1 in HIV-1 DLS. The newly proposed structure model suggested that the hairpin loop of SL1 appeared larger, and genome dimerization process might consist of more complicated mechanism than previously understood. Further investigations would be still required to fully understand the genome packaging and dimerization of HIV.

  16. Herbivory of Omnivorous Fish Shapes the Food Web Structure of a Chinese Tropical Eutrophic Lake: Evidence from Stable Isotope and Fish Gut Content Analyses

    Directory of Open Access Journals (Sweden)

    Jian Gao

    2017-01-01

    Full Text Available Studies suggest that, unlike the situation in temperate lakes, high biomasses of omnivorous fish are maintained in subtropical and tropical lakes when they shift from a turbid phytoplankton-dominated state to a clear water macrophyte-dominated state, and the predation pressure on large-bodied zooplankton therefore remains high. Whether this reflects a higher degree of herbivory in warm lakes than in temperate lakes is debatable. We combined food web studies using stable isotopes with gut content analyses of the most dominant fish species to elucidate similarities and differences in food web structure between a clear water macrophyte-dominated basin (MDB and a turbid phytoplankton-dominated basin (PDB of Huizhou West Lake, a shallow tropical Chinese lake. The δ13C–δ15N biplot of fish and invertebrates revealed community-wide differences in isotope-based metrics of the food webs between MDB and PDB. The range of consumer δ15N (NR was lower in MDB than in PDB, indicating shorter food web length in MDB. The mean nearest neighbor distance (MNND and standard deviation around MNND (SDNND were higher in MDB than in PDB, showing a markedly low fish trophic overlap and a more uneven packing of species in niches in MDB than in PDB. The range of fish δ13C (CR of consumers was more extensive in MDB than in PDB, indicating a wider feeding range for fish in MDB. Mixing model results showed that macrophytes and associated periphyton constituted a large fraction of basal production sources for the fish in MDB, while particulate organic matter (POM contributed a large fraction in PDB. In MDB, the diet of the dominant fish species, crucian carp (Carassius carassius, consisted mainly of vegetal matter (macrophytes and periphyton and zooplankton, while detritus was the most important food item in PDB. Our results suggest that carbon from macrophytes with associated periphyton may constitute an important food resource for omnivorous fish, and this may strongly

  17. A novel bidirectional expression system for simultaneous expression of both the protein-coding genes and short hairpin RNAs in mammalian cells

    International Nuclear Information System (INIS)

    Hung, C.-F.; Cheng, T.-L.; Wu, R.-H.; Teng, C.-F.; Chang, W.-T.

    2006-01-01

    RNA interference (RNAi) is an extremely powerful and widely used gene silencing approach for reverse functional genomics and molecular therapeutics. In mammals, the conserved poly(ADP-ribose) polymerase 2 (PARP-2)/RNase P bidirectional control promoter simultaneously expresses both the PARP-2 protein and RNase P RNA by RNA polymerase II- and III-dependent mechanisms, respectively. To explore this unique bidirectional control system in RNAi-mediated gene silencing strategy, we have constructed two novel bidirectional expression vectors, pbiHsH1 and pbiMmH1, which contained the PARP-2/RNase P bidirectional control promoters from human and mouse, for simultaneous expression of both the protein-coding genes and short hairpin RNAs. Analyses of the dual transcriptional activities indicated that these two bidirectional expression vectors could not only express enhanced green fluorescent protein as a functional reporter but also simultaneously transcribe shLuc for inhibiting the firefly luciferase expression. In addition, to extend its utility for the establishment of inherited stable clones, we have also reconstructed this bidirectional expression system with the blasticidin S deaminase gene, an effective dominant drug resistance selectable marker, and examined both the selection and inhibition efficiencies in drug resistance and gene expression. Moreover, we have further demonstrated that this bidirectional expression system could efficiently co-regulate the functionally important genes, such as overexpression of tumor suppressor protein p53 and inhibition of anti-apoptotic protein Bcl-2 at the same time. In summary, the bidirectional expression vectors, pbiHsH1 and pbiMmH1, should provide a simple, convenient, and efficient novel tool for manipulating the gene function in mammalian cells

  18. Tuning the Structure and Ionic Interactions in a Thermochemically Stable Hybrid Layered Titanate-Based Nanocomposite for High Temperature Solid Lubrication

    NARCIS (Netherlands)

    Gonzalez Rodriguez, P.; Lubbers, Roy; Veldhuis, Sjoerd; Narygina, Olga; Lette, Walter; Schipper, Dirk J.; ten Elshof, Johan E.

    2017-01-01

    Solid inorganic lubricants are thermally stable but they are often limited by their lack of deformability, while organic lubricants have limitations in terms of thermal stability. In this study, a novel solid organic–inorganic nanocomposite lubricant that synergistically combines the

  19. Eutectic Gallium-Indium (EGaIn) : A Liquid Metal Alloy for the Formation of Stable Structures in Microchannels at Room Temperature

    NARCIS (Netherlands)

    Dickey, Michael D.; Chiechi, Ryan C.; Larsen, Ryan J.; Weiss, Emily A.; Weitz, David A.; Whitesides, George M.

    2008-01-01

    This paper describes the rheological behavior of the liquid metal eutectic gallium-indium (EGaIn) as it is injected into microfluidic channels to form stable microstructures of liquid metal. EGaIn is well-suited for this application because of its rheological properties at room temperature: it

  20. An efficient method to enhance gene silencing by using precursor microRNA designed small hairpin RNAs.

    Science.gov (United States)

    Shan, Zhixin; Lin, Qiuxiong; Deng, Chunyu; Li, Xiaohong; Huang, Wei; Tan, Honghong; Fu, Yongheng; Yang, Min; Yu, Xi-Yong

    2009-07-01

    Gene silencing can be mediated by small interfering RNA (siRNA) and microRNA (miRNA). To investigate the potential application of using a precursor microRNA (pre-miRNA) backbone for gene silencing, we studied the inhibition efficiency of exogenous GFP and endogenous GAPDH by conventional shRNA- and pre-miRNA-designed hairpins, respectively. In this study, the conventional shRNA-, pre-miRNA-30-, and pre-miRNA-155-designed hairpins targeting either GFP or GAPDH were transfected into the HEK293 cells that were mediated by the pSilencer-4.1-neo vector, which carries a modified RNA polymerase II-type CMV promoter. Comparisons with conventional GFP shRNA showed that GFP levels were reduced markedly by pre-miRNA-30- and pre-miRNA-155-designed GFP shRNAs by fluorescence microscopy. The consistent results from semi-quantitative RT-PCR and Western blot analysis revealed that pre-miRNA-30- and pre-miRNA-155-designed GFP shRNAs could suppress GFP expression significantly. As for endogenous GAPDH, the results from semi-quantitative RT-PCR and Western blot analysis showed that pre-miRNA-30- and pre-miRNA-155-designed GAPDH shRNAs could suppress GAPDH expression even more efficiently than conventional GAPDH shRNA. Together, this study confirmed the efficiency of gene silencing mediated by pre-miRNA-30- and pre-miRNA-155-designed shRNAs, demonstrating that pre-miRNA-designed hairpins are a good strategy for gene silencing.

  1. Short Hairpin RNA Suppression of Thymidylate Synthase Produces DNA Mismatches and Results in Excellent Radiosensitization

    International Nuclear Information System (INIS)

    Flanagan, Sheryl A.; Cooper, Kristin S.; Mannava, Sudha; Nikiforov, Mikhail A.; Shewach, Donna S.

    2012-01-01

    Purpose: To determine the effect of short hairpin ribonucleic acid (shRNA)-mediated suppression of thymidylate synthase (TS) on cytotoxicity and radiosensitization and the mechanism by which these events occur. Methods and Materials: shRNA suppression of TS was compared with 5-fluoro-2′-deoxyuridine (FdUrd) inactivation of TS with or without ionizing radiation in HCT116 and HT29 colon cancer cells. Cytotoxicity and radiosensitization were measured by clonogenic assay. Cell cycle effects were measured by flow cytometry. The effects of FdUrd or shRNA suppression of TS on dNTP deoxynucleotide triphosphate imbalances and consequent nucleotide misincorporations into deoxyribonucleic acid (DNA) were analyzed by high-pressure liquid chromatography and as pSP189 plasmid mutations, respectively. Results: TS shRNA produced profound (≥90%) and prolonged (≥8 days) suppression of TS in HCT116 and HT29 cells, whereas FdUrd increased TS expression. TS shRNA also produced more specific and prolonged effects on dNTPs deoxynucleotide triphosphates compared with FdUrd. TS shRNA suppression allowed accumulation of cells in S-phase, although its effects were not as long-lasting as those of FdUrd. Both treatments resulted in phosphorylation of Chk1. TS shRNA alone was less cytotoxic than FdUrd but was equally effective as FdUrd in eliciting radiosensitization (radiation enhancement ratio: TS shRNA, 1.5-1.7; FdUrd, 1.4-1.6). TS shRNA and FdUrd produced a similar increase in the number and type of pSP189 mutations. Conclusions: TS shRNA produced less cytotoxicity than FdUrd but was equally effective at radiosensitizing tumor cells. Thus, the inhibitory effect of FdUrd on TS alone is sufficient to elicit radiosensitization with FdUrd, but it only partially explains FdUrd-mediated cytotoxicity and cell cycle inhibition. The increase in DNA mismatches after TS shRNA or FdUrd supports a causal and sufficient role for the depletion of dTTP thymidine triphosphate and consequent DNA

  2. Short Hairpin RNA Suppression of Thymidylate Synthase Produces DNA Mismatches and Results in Excellent Radiosensitization

    Energy Technology Data Exchange (ETDEWEB)

    Flanagan, Sheryl A., E-mail: sflan@umich.edu [Department of Pharmacology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Cooper, Kristin S. [Department of Pharmacology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Mannava, Sudha; Nikiforov, Mikhail A. [Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York (United States); Shewach, Donna S. [Department of Pharmacology, University of Michigan Medical Center, Ann Arbor, Michigan (United States)

    2012-12-01

    Purpose: To determine the effect of short hairpin ribonucleic acid (shRNA)-mediated suppression of thymidylate synthase (TS) on cytotoxicity and radiosensitization and the mechanism by which these events occur. Methods and Materials: shRNA suppression of TS was compared with 5-fluoro-2 Prime -deoxyuridine (FdUrd) inactivation of TS with or without ionizing radiation in HCT116 and HT29 colon cancer cells. Cytotoxicity and radiosensitization were measured by clonogenic assay. Cell cycle effects were measured by flow cytometry. The effects of FdUrd or shRNA suppression of TS on dNTP deoxynucleotide triphosphate imbalances and consequent nucleotide misincorporations into deoxyribonucleic acid (DNA) were analyzed by high-pressure liquid chromatography and as pSP189 plasmid mutations, respectively. Results: TS shRNA produced profound ({>=}90%) and prolonged ({>=}8 days) suppression of TS in HCT116 and HT29 cells, whereas FdUrd increased TS expression. TS shRNA also produced more specific and prolonged effects on dNTPs deoxynucleotide triphosphates compared with FdUrd. TS shRNA suppression allowed accumulation of cells in S-phase, although its effects were not as long-lasting as those of FdUrd. Both treatments resulted in phosphorylation of Chk1. TS shRNA alone was less cytotoxic than FdUrd but was equally effective as FdUrd in eliciting radiosensitization (radiation enhancement ratio: TS shRNA, 1.5-1.7; FdUrd, 1.4-1.6). TS shRNA and FdUrd produced a similar increase in the number and type of pSP189 mutations. Conclusions: TS shRNA produced less cytotoxicity than FdUrd but was equally effective at radiosensitizing tumor cells. Thus, the inhibitory effect of FdUrd on TS alone is sufficient to elicit radiosensitization with FdUrd, but it only partially explains FdUrd-mediated cytotoxicity and cell cycle inhibition. The increase in DNA mismatches after TS shRNA or FdUrd supports a causal and sufficient role for the depletion of dTTP thymidine triphosphate and consequent DNA

  3. stableGP

    Data.gov (United States)

    National Aeronautics and Space Administration — The code in the stableGP package implements Gaussian process calculations using efficient and numerically stable algorithms. Description of the algorithms is in the...

  4. Stabilization of the beta-hairpin in Mason-Pfizer monkey virus capsid protein- a critical step for infectivity

    Czech Academy of Sciences Publication Activity Database

    Obr, M.; Hadravová, Romana; Doležal, Michal; Křížová, Ivana; Papoušková, V.; Žídek, L.; Hrabal, R.; Ruml, T.; Rumlová, Michaela

    2014-01-01

    Roč. 11, Oct 30 (2014), 94/1-94/14 ISSN 1742-4690 R&D Projects: GA ČR(CZ) GA14-15326S; GA MŠk LO1302 Grant - others:GA MŠk(CZ) ED1.1.00/02.0068; Seventh Framework Programme of the European Union(XE) FP7-261863 Program:ED Institutional support: RVO:61388963 Keywords : retrovirus * assembly * M-PMV * capsid protein * maturation * beta-hairpin Subject RIV: EE - Microbiology, Virology Impact factor: 4.185, year: 2014 http://www.retrovirology.com/content/11/1/94

  5. Engineering HIV-1-resistant T-cells from short-hairpin RNA-expressing hematopoietic stem/progenitor cells in humanized BLT mice.

    Directory of Open Access Journals (Sweden)

    Gene-Errol E Ringpis

    Full Text Available Down-regulation of the HIV-1 coreceptor CCR5 holds significant potential for long-term protection against HIV-1 in patients. Using the humanized bone marrow/liver/thymus (hu-BLT mouse model which allows investigation of human hematopoietic stem/progenitor cell (HSPC transplant and immune system reconstitution as well as HIV-1 infection, we previously demonstrated stable inhibition of CCR5 expression in systemic lymphoid tissues via transplantation of HSPCs genetically modified by lentiviral vector transduction to express short hairpin RNA (shRNA. However, CCR5 down-regulation will not be effective against existing CXCR4-tropic HIV-1 and emergence of resistant viral strains. As such, combination approaches targeting additional steps in the virus lifecycle are required. We screened a panel of previously published shRNAs targeting highly conserved regions and identified a potent shRNA targeting the R-region of the HIV-1 long terminal repeat (LTR. Here, we report that human CD4(+ T-cells derived from transplanted HSPC engineered to co-express shRNAs targeting CCR5 and HIV-1 LTR are resistant to CCR5- and CXCR4- tropic HIV-1-mediated depletion in vivo. Transduction with the combination vector suppressed CXCR4- and CCR5- tropic viral replication in cell lines and peripheral blood mononuclear cells in vitro. No obvious cytotoxicity or interferon response was observed. Transplantation of combination vector-transduced HSPC into hu-BLT mice resulted in efficient engraftment and subsequent stable gene marking and CCR5 down-regulation in human CD4(+ T-cells within peripheral blood and systemic lymphoid tissues, including gut-associated lymphoid tissue, a major site of robust viral replication, for over twelve weeks. CXCR4- and CCR5- tropic HIV-1 infection was effectively inhibited in hu-BLT mouse spleen-derived human CD4(+ T-cells ex vivo. Furthermore, levels of gene-marked CD4(+ T-cells in peripheral blood increased despite systemic infection with either

  6. HTS dual-band bandpass filters using stub-loaded hair-pin resonators for mobile communication systems

    Energy Technology Data Exchange (ETDEWEB)

    Sekiya, N., E-mail: nsekiya@yamanashi.ac.jp; Sugiyama, S.

    2014-09-15

    Highlights: • We have developed a HTS five-pole dual-band bandpass filter using stub-loaded hair-pin resonators. • The proposed dual-band BPF can independently control of the center frequency. • Flexibly adjustment of the bandwidth can be achieved by the H-shaped waveguide. • The proposed BPF is evaluated by simulation and measurement with good agreement. - Abstract: A HTS dual-band bandpass filter is developed to obtain sharp-cut off characteristics for mobile communication systems. The filter is composed of five stub-loaded hair-pin resonators with H-shaped waveguides between them. The main advantage of the proposed filter is to allow independent control of the center frequency of the first and second bands. The bandwidths can be flexibly adjusted using the H-shaped waveguide. An electromagnetic simulator was used to design and analyze the filter, which have a 3.5-GHz center frequency and a 70-MHz (2%) bandwidth for the first band and a 5.0-GHz center frequency and a 100-MHz (2%) bandwidth for the second band. The filter was fabricated using YBa{sub 2}Cu{sub 3}O{sub y} thin film on an Al{sub 2}O{sub 3} substrate. Ground plane was fabricated using Au thin film. The measured frequency responses of the filter tally well with the simulated ones.

  7. Selective inhibition of HIV-1 reverse transcriptase (HIV-1 RT) RNase H by small RNA hairpins and dumbbells.

    Science.gov (United States)

    Hannoush, Rami N; Carriero, Sandra; Min, Kyung-Lyum; Damha, Masad J

    2004-04-02

    We present here the design of a novel class of RNA inhibitors of the RNase H domain of HIV-1 RT, a ribonuclease activity that is essential for viral replication in vivo. Specifically, we show that small RNA hairpins and dumbbells can selectively inhibit the RNase H activity of HIV-1 RT without affecting other cellular RNases H (e.g., E. coli and human RNase H). These results suggest that the inhibitors do not interact with the nucleic acid binding site of RT RNase H, as this region should be well conserved among the various enzymes. The most potent inhibitors displayed IC50 values in the 3-8 microM range. Remarkably, the DNA polymerase activity, an intrinsic property of HIV RT, was not inhibited by the hairpin and dumbbell aptamers, a property not previously observed for any nucleic acid aptamer directed against RT RNase H. The results described here suggest a noncompetitive binding mechanism, as outlined in the differential inhibitory characteristics of each of the nucleic acid aptamers against the bacterial, human, and viral RNase H homologues.

  8. DNA triplex structures in neurodegenerative disorder, Friedreich's ...

    Indian Academy of Sciences (India)

    The unusual DNA structures like DNA-hairpin, cruciform, Z-DNA, triplex and tetraplex are represented as hotspots of chromosomal breaks, homologous recombination and gross chromosomal rearrangements since they are prone to the structural alterations. Friedreich's ataxia (FRDA), the autosomal recessive degenerative ...

  9. Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme.

    Science.gov (United States)

    Wilson, T J; Zhao, Z Y; Maxwell, K; Kontogiannis, L; Lilley, D M

    2001-02-20

    The hairpin ribozyme in its natural context consists of two loops in RNA duplexes that are connected as arms of a four-way helical junction. Magnesium ions induce folding into the active conformation in which the two loops are in proximity. In this study, we have investigated nucleotides that are important to this folding process. We have analyzed the folding in terms of the cooperativity and apparent affinity for magnesium ions as a function of changes in base sequence and functional groups, using fluorescence resonance energy transfer. Our results suggest that the interaction between the loops is the sum of a number of component interactions. Some sequence variants such as A10U, G+1A, and C25U exhibit loss of cooperativity and reduced affinity of apparent magnesium ion binding. These variants are also very impaired in ribozyme cleavage activity. Nucleotides A10, G+1, and C25 thus appear to be essential in creating the conformational environment necessary for ion binding. The double variant G+1A/C25U exhibits a marked recovery of both folding and catalytic activity compared to either individual variant, consistent with the proposal of a triple-base interaction among A9, G+1, and C25 [Pinard, R., Lambert, D., Walter, N. G., Heckman, J. E., Major, F., and Burke, J. M. (1999) Biochemistry 38, 16035-16039]. However, substitution of A9 leads to relatively small changes in folding properties and cleavage activity, and the double variant G+1DAP/C25U (DAP is 2,6-diaminopurine), which could form an isosteric triple-base interaction, exhibits folding and cleavage activities that are both very impaired compared to those of the natural sequence. Our results indicate an important role for a Watson--Crick base pair between G+1 and C25; this may be buttressed by an interaction with A9, but the loss of this has less significant consequences for folding. 2'-Deoxyribose substitution leads to folding with reduced magnesium ion affinity in the following order: unmodified RNA > dA9

  10. Duplex structural differences and not 2′-hydroxyls explain the more stable binding of HIV-reverse transcriptase to RNA-DNA versus DNA-DNA

    OpenAIRE

    Olimpo, Jeffrey T.; DeStefano, Jeffrey J.

    2010-01-01

    Human immunodeficiency virus reverse transcriptase (HIV-RT) binds more stably in binary complexes with RNA–DNA versus DNA–DNA. Current results indicate that only the -2 and -4 RNA nucleotides (-1 hybridized to the 3′ recessed DNA base) are required for stable binding to RNA–DNA, and even a single RNA nucleotide conferred significantly greater stability than DNA–DNA. Replacing 2′- hydroxyls on pivotal RNA bases with 2′-O-methyls did not affect stability, indicating that interactions between hy...

  11. Increased electrocatalyzed performance through hairpin oligonucleotide aptamer-functionalized gold nanorods labels and graphene-streptavidin nanomatrix: Highly selective and sensitive electrochemical biosensor of carcinoembryonic antigen.

    Science.gov (United States)

    Wen, Wei; Huang, Jing-Yi; Bao, Ting; Zhou, Jun; Xia, Hong-Xing; Zhang, Xiu-Hua; Wang, Sheng-Fu; Zhao, Yuan-Di

    2016-09-15

    We report a triplex signal amplification strategy for sensitive biosensing of cancer biomarker by taking advantage of hairpin-shaped oligonucleotide-functionalized gold nanorods (HO-GNRs), graphene and the avidin-biotin reation. The strategy expands electrochemical detection of carcinoembryonic antigen (CEA) by using an aptamer as biosensor's recognition element and HO-GNRs as signal enhancer. To construct this biosensor, the GNR was used as a carrier of horseradish peroxidase (HRP) and HO aptamer with a biotin at the 3'-end and a thiol at the 5'-end, which amplified the electrochemical response because of a large molar ratio of HRP to HO. In the presence of target CEA, the binding reactions of CEA with the loop portions of the HOs caused HOs' loop-stem structure opened and exposed the biotins, and then HRP-GNRs-HO conjugates were captured on graphene and streptavidin modified electrodes via the reaction between the exposed biotins and preimmobilized streptavidins. The accumulation of HRP effectively catalyzed the hydrogen peroxide-mediated oxidation of o-phenylenediamine to generate an electrochemical reduction current for CEA detection. Under optimal conditions, the electrochemical biosensor exhibited a wide dynamic range of 5pgmL(-1) and 50ngmL(-1) toward CEA standards with a low detection limit of 1.5pgmL(-1) (signal-to-noise ratio of 3). The proposed biosensor accurately detected CEA concentration in 8 human serum samples from patients with lung diseases, showing excellent correlations with standard chemiluminescence immunoassay. Furthermore, these results of target DNA detection made it abundantly clear that the proposed strategy can also be extended for detection of other relative biomarkers using different functional DNA structures, which shows great prospects in single-nucleotide polymorphisms analysis, biomedical sensing and application for accurate clinical diseases diagnostic. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. A Cell-Permeable Hairpin Peptide Inhibits Hepatitis C Viral Nonstructural Protein 5A Mediated Translation and Virus Production

    Science.gov (United States)

    Khachatoorian, Ronik; Arumugaswami, Vaithilingaraja; Ruchala, Piotr; Raychaudhuri, Santanu; Maloney, Eden M.; Miao, Edna; Dasgupta, Asim; French, Samuel W.

    2012-01-01

    NS5A is a key regulator of hepatitis C virus (HCV) life cycle including RNA replication, assembly, and translation. We and others have shown NS5A to augment HCV IRES-mediated translation. Further, Quercetin treatment and heat shock protein (HSP) 70 knockdown inhibit NS5A-driven augmentation of IRES-mediated translation and infectious virus production. We have also co-immunoprecipitated HSP70 with NS5A and demonstrated cellular colocalization leading to the hypothesis that the NS5A/HSP70 complex formation is important for IRES-mediated translation. Here, we have identified the NS5A region responsible for complex formation through in vitro deletion analyses. Deletion of NS5A domains II and III failed to reduce HSP70 binding, whereas domain I deletion eliminated complex formation. NS5A domain I alone also bound HSP70. Deletion mapping of domain I identified the C-terminal 34 amino acids (C34) to be the interaction site. Further, addition of C34 to domains II and III restored complex formation. C34 expression significantly reduced intracellular viral protein levels, in contrast to same size control peptides from other NS5A domains. C34 also competitively inhibited NS5A-augmented IRES-mediated translation, while controls did not. Triple-alanine scan mutagenesis identified an exposed beta-sheet hairpin in C34 to be primarily responsible for NS5A-augmented IRES-mediated translation. Moreover, treatment with a 10 amino acid peptide derivative of C34 suppressed NS5A-augmented IRES-mediated translation and significantly inhibited intracellular viral protein synthesis, with no associated cytotoxicity. Conclusion: These results support the hypothesis that the NS5A/HSP70 complex augments viral IRES-mediated translation, identify a sequence-specific hairpin element in NS5A responsible for complex formation, and demonstrate the functional significance of C34 hairpin-mediated NS5A/HSP70 interaction. Identification of this element may allow for further interrogation of NS5A

  13. Stable isotopes labelled compounds

    International Nuclear Information System (INIS)

    1982-09-01

    The catalogue on stable isotopes labelled compounds offers deuterium, nitrogen-15, and multiply labelled compounds. It includes: (1) conditions of sale and delivery, (2) the application of stable isotopes, (3) technical information, (4) product specifications, and (5) the complete delivery programme

  14. Stable Boundary Layer Issues

    NARCIS (Netherlands)

    Steeneveld, G.J.

    2012-01-01

    Understanding and prediction of the stable atmospheric boundary layer is a challenging task. Many physical processes are relevant in the stable boundary layer, i.e. turbulence, radiation, land surface coupling, orographic turbulent and gravity wave drag, and land surface heterogeneity. The

  15. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    IAS Admin

    After Maynard-Smith and Price [1] mathematically derived why a given behaviour or strategy was adopted by a certain proportion of the population at a given time, it was shown that a strategy which is currently stable in a population need not be stable in evolutionary time (across generations). Additionally it was sug-.

  16. Synthesis and characterization of highly efficient and stable Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt ternary hybrid structure

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Jiatao; Liu, Lin; Niu, Tongjun; Sun, Xiaosong, E-mail: sunxs@scu.edu.cn

    2017-05-01

    Highlights: • Visible-light-driven Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt photocatalysts were prepared. • Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt showed highly efficient and stable photocatalystic activity. • The photocatalytic mechanism of Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt composite was given. - Abstract: Ag{sub 3}PO{sub 4} is an excellent photocatalyst with high efficiency and quantum yield, but suffers from the fast recombination of photogenerated electron-hole pairs and photo-corrosion. Hereby, the highly efficient and stable visible-light-driven Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt photocatalyst were prepared via a three-step wet chemical approach. The as-prepared Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt composite was characterized by X-ray diffraction, US-vis diffuse reflectance spectroscopy, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, photoluminescence spectra and transient photocurrent as well. Comparing with single Pr{sub 6}O{sub 11} or Ag{sub 3}PO{sub 4}, the prepared Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt composite exhibited much higher photocatalytic activity and stability for the degradation of Rhodamine B under visible light irradiation (>420 nm). The enhanced photocatalytic performance of Pr{sub 6}O{sub 11}/Ag{sub 3}PO{sub 4}/Pt composite has been attributed to the efficient separation of photo-generated electron-hole pairs through a scheme system composed of Pr{sub 6}O{sub 11,} Ag{sub 3}PO{sub 4} and Pt.

  17. Two stable steady states in the Hodgkin-Huxley axons

    OpenAIRE

    Aihara, K.; Matsumoto, G.

    1983-01-01

    Two stable steady states were found in the numerical solution of the Hodgkin-Huxley equations for the intact squid axon bathed in potassium-rich sea water with an externally applied inward current. Under the conditions the two stable steady-states exist, the Hodgkin-Huxley equations have a complex bifurcation structure including, in addition to the two stable steady-states, a stable limit cycle, two unstable equilibrium points, and one asymptotically stable equilibrium point. It was also conc...

  18. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

    Science.gov (United States)

    Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

    2014-07-01

    Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

  19. Differential RNAi responses of Nicotiana benthamiana individuals transformed with a hairpin-inducing construct during Plum pox virus challenge.

    Science.gov (United States)

    Montes, Christian; Castro, Álvaro; Barba, Paola; Rubio, Julia; Sánchez, Evelyn; Carvajal, Denisse; Aguirre, Carlos; Tapia, Eduardo; DelÍ Orto, Paola; Decroocq, Veronique; Prieto, Humberto

    2014-10-01

    Gene silencing and large-scale small RNA analysis can be used to develop RNA interference (RNAi)-based resistance strategies for Plum pox virus (PPV), a high impact disease of Prunus spp. In this study, a pPPViRNA hairpin-inducing vector harboring two silencing motif-rich regions of the PPV coat protein (CP) gene was evaluated in transgenic Nicotiana benthamiana (NB) plants. Wild-type NB plants infected with a chimeric PPV virus (PPV::GFP) exhibited affected leaves with mosaic chlorosis congruent to GFP fluorescence at 21 day post-inoculation; transgenic lines depicted a range of phenotypes from fully resistant to susceptible. ELISA values and GFP fluorescence intensities were used to select transgenic-resistant (TG-R) and transgenic-susceptible (TG-S) lines for further characterization of small interfering RNAs (siRNAs) by large-scale small RNA sequencing. In infected TG-S and untransformed (WT) plants, the observed siRNAs were nearly exclusively 21- and 22-nt siRNAs that targeted the whole PPV::GFP genome; 24-nt siRNAs were absent in these individuals. Challenged TG-R plants accumulated a full set of 21- to 24-nt siRNAs that were primarily associated with the selected motif-rich regions, indicating that a trans-acting siRNAs process prevented viral multiplication. BLAST analysis identified 13 common siRNA clusters targeting the CP gene. 21-nt siRNA sequences were associated with the 22-nt siRNAs and the scarce 23- and 24-nt molecules in TG-S plants and with most of the observed 22-, 23-, and 24-nt siRNAs in TG-R individuals. These results validate the use of a multi-hot spot silencing vector against PPV and elucidate the molecules by which hairpin-inducing vectors initiate RNAi in vivo.

  20. Normal modified stable processes

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole Eiler; Shephard, N.

    2002-01-01

    This paper discusses two classes of distributions, and stochastic processes derived from them: modified stable (MS) laws and normal modified stable (NMS) laws. This extends corresponding results for the generalised inverse Gaussian (GIG) and generalised hyperbolic (GH) or normal generalised inverse...... Gaussian (NGIG) laws. The wider framework thus established provides, in particular, for added flexibility in the modelling of the dynamics of financial time series, of importance especially as regards OU based stochastic volatility models for equities. In the special case of the tempered stable OU process...

  1. Applications of stable isotopes

    International Nuclear Information System (INIS)

    Letolle, R.; Mariotti, A.; Bariac, T.

    1991-06-01

    This report reviews the historical background and the properties of stable isotopes, the methods used for their measurement (mass spectrometry and others), the present technics for isotope enrichment and separation, and at last the various present and foreseeable application (in nuclear energy, physical and chemical research, materials industry and research; tracing in industrial, medical and agronomical tests; the use of natural isotope variations for environmental studies, agronomy, natural resources appraising: water, minerals, energy). Some new possibilities in the use of stable isotope are offered. A last chapter gives the present state and forecast development of stable isotope uses in France and Europe

  2. Trophic structure in a pilot system for the integrated multi-trophic aquaculture off the east coast of Korean peninsula as determined by stable isotopes

    International Nuclear Information System (INIS)

    Park, Hyun Je; Han, Eunah; Lee, Won Chan; Kwak, Jung Hyun; Kim, Hyung Chul; Park, Mi Seon; Kang, Chang-Keun

    2015-01-01

    Highlights: • A pilot system for the integrated multi-trophic aquaculture was installed. • The black rockfish, sea cucumber, oyster, and macroalgae were co-cultured. • Co-cultured sea cucumber at the IMTA site assimilated aquaculture wastes. • Fish cage-waste contribution to food web in/around the IMTA system was minor. • The sea cucumber was identified as an extractive species of fish cage wastes. - Abstract: To assess the potential for nutritional exploitation of caged-fish-derived waste through the use of extractive co-cultured species in a pilot system for an integrated multi-trophic aquaculture (IMTA), we compared their C and N stable isotope ratios with those of uncultured macroinvertebrates in and around the system. Black rockfish were co-cultured with sea cucumber, oyster, and two macroalgae as extractive species. Isotope signatures of the co-cultured sea cucumber at the IMTA site differed from those at the control site, indicating their assimilation of aquaculture wastes. In contrast, δ 13 C and δ 15 N of individual taxa of the cultured oyster and uncultured invertebrates were consistent between sites, suggesting a minor contribution of the aquaculture waste to benthic and pelagic food chains in and around the IMTA system. These results provide evidence of the suitability of using sea cucumber as an extractive species to reduce the impact of a monoculture system on the ambient environment

  3. Trophic structure in a pilot system for the integrated multi-trophic aquaculture off the east coast of Korean peninsula as determined by stable isotopes.

    Science.gov (United States)

    Park, Hyun Je; Han, Eunah; Lee, Won Chan; Kwak, Jung Hyun; Kim, Hyung Chul; Park, Mi Seon; Kang, Chang-Keun

    2015-06-15

    To assess the potential for nutritional exploitation of caged-fish-derived waste through the use of extractive co-cultured species in a pilot system for an integrated multi-trophic aquaculture (IMTA), we compared their C and N stable isotope ratios with those of uncultured macroinvertebrates in and around the system. Black rockfish were co-cultured with sea cucumber, oyster, and two macroalgae as extractive species. Isotope signatures of the co-cultured sea cucumber at the IMTA site differed from those at the control site, indicating their assimilation of aquaculture wastes. In contrast, δ(13)C and δ(15)N of individual taxa of the cultured oyster and uncultured invertebrates were consistent between sites, suggesting a minor contribution of the aquaculture waste to benthic and pelagic food chains in and around the IMTA system. These results provide evidence of the suitability of using sea cucumber as an extractive species to reduce the impact of a monoculture system on the ambient environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Hierarchical MoS2 tubular structures internally wired by carbon nanotubes as a highly stable anode material for lithium-ion batteries.

    Science.gov (United States)

    Chen, Yu Ming; Yu, Xin Yao; Li, Zhen; Paik, Ungyu; Lou, Xiong Wen David

    2016-07-01

    Molybdenum disulfide (MoS2), a typical two-dimensional material, is a promising anode material for lithium-ion batteries because it has three times the theoretical capacity of graphite. The main challenges associated with MoS2 anodes are the structural degradation and the low rate capability caused by the low intrinsic electric conductivity and large strain upon cycling. Here, we design hierarchical MoS2 tubular structures internally wired by carbon nanotubes (CNTs) to tackle these problems. These porous MoS2 tubular structures are constructed from building blocks of ultrathin nanosheets, which are believed to benefit the electrochemical reactions. Benefiting from the unique structural and compositional characteristics, these CNT-wired MoS2 tubular structures deliver a very high specific capacity of ~1320 mAh g(-1) at a current density of 0.1 A g(-1), exceptional rate capability, and an ultralong cycle life of up to 1000 cycles. This work may inspire new ideas for constructing high-performance electrodes for electrochemical energy storage.

  5. Structure and replication of hepatitis delta virus

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-29

    Dec 29, 2008 ... important feature of the virus genomic and antigenomic. RNA molecules is the 85 nucleotide ribozyme ... overall secondary structure consisting of base-paired elements, joining sequences and hairpin .... accumulation of specific HDV components in discrete foci in the nucleus is not probably relevant for ...

  6. Analysing Stable Time Series

    National Research Council Canada - National Science Library

    Adler, Robert

    1997-01-01

    We describe how to take a stable, ARMA, time series through the various stages of model identification, parameter estimation, and diagnostic checking, and accompany the discussion with a goodly number...

  7. Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs

    Directory of Open Access Journals (Sweden)

    Ricardo eFlores

    2012-06-01

    Full Text Available As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunvioidae adopt multibranched conformations occasionally stabilized by kissing loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunvioidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures ⎯either global or local ⎯ determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

  8. Variability in the combustion-derived fraction of urban humidity in Salt Lake City winter estimated from stable water vapor isotopes and its relationship to atmospheric stability and inversion structure

    Science.gov (United States)

    Fiorella, R.; Bares, R.; Lin, J. C.; Strong, C.; Bowen, G. J.

    2017-12-01

    Water released from the combustion of fossil fuels, while a negligible part of the global hydrological cycle, may be a significant contributor to urban humidity as fossil fuel emissions are strongly concentrated in space and time. The fraction of urban humidity comprised of combustion-derived vapor (CDV) cannot be observed through humidity measurements alone. However, the distinct stable isotopic composition of CDV, which arises from the reaction of 18O-enriched atmospheric O2 with 2H-depleted organic molecules, represents a promising method to apportion observed humidity between CDV and advected vapor. We apply stable water vapor isotopes to investigate variability in CDV amount and its relationship to atmospheric conditions in Salt Lake City, Utah. The Salt Lake Valley experiences several periods of atmospheric stratification during winter known as cold air pools, during which concentrations of CDV and pollutants can be markedly elevated due to reduced atmospheric mixing. Therefore, the SLV during winter is an ideal place to investigate variability in CDV fraction across a spectrum of boundary layer conditions, ranging from well-mixed to very stable. We present water vapor isotope data from four winters (2013-2017) from the top of a 30 m building on the University of Utah (U of U) Campus. Additionally, we present water vapor isotope data from the summit of Hidden Peak from the 2016-2017 winter, 25 km SE and 2000 m above the U of U site. The Hidden Peak site is consistently above the cold air pool emplaced in the SLV during stable events. We find the expression of the CDV signal in the valley is related to the atmospheric structure of the cold air pools in the SLV, and that the fraction of CDV inferred in the valley is likely related to the mixing height within the cold air pool. Furthermore, we find that patterns between the Hidden Peak and U of U sites during inversion events may record the large-scale atmospheric dynamics promoting emplacement of the cold air

  9. Structural basis for the function of DEAH helicases

    DEFF Research Database (Denmark)

    He, Yangzi; Andersen, Gregers Rom; Nielsen, Klaus Hvid

    2010-01-01

    DEAH helicases participate in pre‐messenger RNA splicing and ribosome biogenesis. The structure of yeast Prp43p‐ADP reveals the homology of DEAH helicases to DNA helicases and the presence of an oligonucleotide‐binding motif. A β‐hairpin from the second RecA domain is wedged between two carboxy......‐terminal domains and blocks access to the occluded RNA binding site formed by the RecA domains and a C‐terminal domain. ATP binding and hydrolysis are likely to induce conformational changes in the hairpin that are important for RNA unwinding or ribonucleoprotein remodelling. The structure of Prp43p provides...

  10. The influence of nitrogen inputs on biomass and trophic structure of ocean plankton: a study using biomass and stable isotope size-spectra

    KAUST Repository

    Mompeán, Carmen

    2016-08-18

    Large scale patterns in planktonic food web structure were studied by applying continuous size-scaled models of biomass and δ15N to plankton samples, collected at 145 stations during the Malaspina-2010 Expedition across three ocean basins and including major biomes. Carbon biomass and δ15N were determined in size-fractionated samples (40 to 5000 μm) collected by vertical hauls (0–200 m). Biomass-normalized size-spectra were constructed to summarize food web structure and spatial patterns in spectral parameters were analyzed using geographically-weighted regression analysis. Except in the northwestern Atlantic, size-spectra showed low variability, reflecting a homogeneity in nitrogen sources and food web structure for the central oceans. Estimated predator-to-prey mass ratios <104 and mean trophic transfer efficiency values between 16% (coastal biome) and >20% (Trades and Westerlies biomes) suggested that oceanic plankton food webs may support a larger number of trophic levels than current estimates based on high efficiency values. The largest changes in spectral parameters and nitrogen sources were related to inputs of atmospheric nitrogen, either from diazotrophic organisms or dust deposition. These results suggest geographic homogeneity in the net transfer of nitrogen up the food web.

  11. Stable hydrogen and oxygen isotopes of tap water reveal structure of the San Francisco Bay Area's water system and adjustments during a major drought.

    Science.gov (United States)

    Tipple, Brett J; Jameel, Yusuf; Chau, Thuan H; Mancuso, Christy J; Bowen, Gabriel J; Dufour, Alexis; Chesson, Lesley A; Ehleringer, James R

    2017-08-01

    Water availability and sustainability in the Western United States is a major flashpoint among expanding communities, growing industries, and productive agricultural lands. This issue came to a head in 2015 in the State of California, when the State mandated a 25% reduction in urban water use following a multi-year drought that significantly depleted water resources. Water demands and challenges in supplying water are only expected to intensify as climate perturbations, such as the 2012-2015 California Drought, become more common. As a consequence, there is an increased need to understand linkages between urban centers, water transport and usage, and the impacts of climate change on water resources. To assess if stable hydrogen and oxygen isotope ratios could increase the understanding of these relationships within a megalopolis in the Western United States, we collected and analyzed 723 tap waters across the San Francisco Bay Area during seven collection campaigns spanning 21 months during 2013-2015. The San Francisco Bay Area was selected as it has well-characterized water management strategies and the 2012-2105 California Drought dramatically affected its water resources. Consistent with known water management strategies and previously collected isotope data, we found large spatiotemporal variations in the δ 2 H and δ 18 O values of tap waters within the Bay Area. This is indicative of complex water transport systems and varying municipality-scale management decisions. We observed δ 2 H and δ 18 O values of tap water consistent with waters originating from snowmelt from the Sierra Nevada Mountains, local precipitation, ground water, and partially evaporated reservoir sources. A cluster analysis of the isotope data collected in this study grouped waters from 43 static sampling sites that were associated with specific water utility providers within the San Francisco Bay Area and known management practices. Various management responses to the drought, such as

  12. Structure-property relationship of bifunctional MnO2 nanostructures: highly efficient, ultra-stable electrochemical water oxidation and oxygen reduction reaction catalysts identified in alkaline media.

    Science.gov (United States)

    Meng, Yongtao; Song, Wenqiao; Huang, Hui; Ren, Zheng; Chen, Sheng-Yu; Suib, Steven L

    2014-08-13

    Manganese oxides of various structures (α-, β-, and δ-MnO2 and amorphous) were synthesized by facile methods. The electrocatalytic properties of these materials were systematically investigated for catalyzing both oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) in alkaline media. Extensive characterization was correlated with the activity study by investigating the crystal structures (XRD, HRTEM), morphologies (SEM), porosities (BET), surfaces (XPS, O2-TPD/MS), and electrochemical properties (Tafel analysis, Koutechy-Levich plots, and constant-current electrolysis). These combined results show that the electrocatalytic activities are strongly dependent on the crystallographic structures, and follow an order of α-MnO2 > AMO > β-MnO2 > δ-MnO2. Both OER studies and ORR studies reveal similar structure-determined activity trends in alkaline media. In the OER studies, α-MnO2 displays an overpotential of 490 mV compared to 380 mV shown by an Ir/C catalyst in reaching 10 mA cm(-2). Meanwhile, α-MnO2 also exhibits stability for 3 h when supplying a constant current density of 5 mA cm(-2). This was further improved by adding Ni(2+) dopants (ca. 8 h). The superior OER activity was attributed to several factors, including abundant di-μ-oxo bridges existing in α-MnO2 as the protonation sites, analogous to the OEC in PS-II of the natural water oxidation system; the mixed valencies (AOS = 3.7); and the lowest charge transfer resistances (91.8 Ω, η = 430 mV) as revealed from in situ electrochemical impedance spectroscopy (EIS). In the ORR studies, when reaching 3 mA cm(-2), α-MnO2 shows 760 mV close to 860 mV for the best ORR catalyst (20% Pt/C). The outstanding ORR activity was due to the strongest O2 adsorption capability of α-MnO2 suggested by temperature-programmed desorption. As a result, this discovery of the structure-related electrocatalytic activities could provide guidance in the further development of easily prepared, scalable, and low

  13. Stabilization of a β-hairpin in monomeric Alzheimer's amyloid-β peptide inhibits amyloid formation

    OpenAIRE

    Hoyer, Wolfgang; Grönwall, Caroline; Jonsson, Andreas; Ståhl, Stefan; Härd, Torleif

    2008-01-01

    According to the amyloid hypothesis, the pathogenesis of Alzheimer's disease is triggered by the oligomerization and aggregation of the amyloid-β (Aβ) peptide into protein plaques. Formation of the potentially toxic oligomeric and fibrillar Aβ assemblies is accompanied by a conformational change toward a high content of β-structure. Here, we report the solution structure of Aβ(1–40) in complex with the phage-display selected affibody protein ZAβ3, a binding protein of nanomolar affinity. Boun...

  14. Syntheses, structures and photoelectrochemical properties of three water-stable, visible light absorbing mental-organic frameworks based on tetrakis(4-carboxyphenyl)silane and 1,4-bis(pyridyl)benzene mixed ligands

    Science.gov (United States)

    Guo, Tiantian; Yang, Xiaowei; Li, Ruyan; Liu, Xiaoyu; Gao, Yanling; Dai, Zhihui; Fang, Min; Liu, Hong-Ke; Wu, Yong

    2017-09-01

    Photovoltaics (PV), which directly convert solar energy into electricity generally using semiconductors, offer a practical and sustainable solution to the current energy shortage and environmental pollution crisis. Photovoltaic applications of metal-organic frameworks (MOFs) belong to a relatively new area of research. Given that UV light accounts for only 4% while visible light contributes 43% of solar energy, it is rather imperative to develop semiconductors with narrow band gaps so that they could absorb visible light. In this work, three water-stable, narrow band semiconducting MOFs of [Cu(H2TCS)(H2O)] (1), [Co(H2TCS)(BPB)] (2) and [Ni(H2TCS)(BPB)] (3) were synthesized using tetrakis(4-carboxyphenyl)silane (H4TCS) and 1,4-bis (pyridyl)benzene (BPB) in water, and structurally characterized by single-crystal X-ray diffractions. MOF 1 has a 2D structure. MOF 2 and 3 are isostructrual and have 3D frameworks formed by interwoven 2D layers. All three MOFs are stable in acidic water solutions and can be stable in water for 7 days. MOFs 1-3 absorb UV and visible light and have band gaps of 0.50, 1.77 and 1.49 eV, respectively. Rapid and stable photocurrent responses of MOFs 1-3 under UV and visible light illuminations are observed. This work demonstrates that using electron rich Cu2+, Co2+, or Ni2+ as metal nodes can effectively decrease the band gaps of MOFs to make them absorbing visible light. To increase the conjugation in the linker is generally considered to be the method to decrease the band gap of MOFs. The conjugation in H4TCS is not significant and this ligand basically only absorbs UV light. However, by using electron rich Cu2+ ions as metal nodes, the prepared [Cu(H2TCS)(H2O)]·H2O (1) absorbs broadly in the visible light region. Thus, this work suggests that by using electron rich Cu2+, many narrow-band semiconductor MOFs can be prepared even by using ligands which only absorbs UV light.

  15. Synthesis and X-Ray Crystal Structure of the First Pure and Air-Stable Salt of Peroxymonosulphuric Acid: (Ph4PHSO5

    Directory of Open Access Journals (Sweden)

    Marco Crisma

    2000-06-01

    Full Text Available In this paper we describe the synthesis of tetraphenylphosphonium peroxymonosulphate, its crystal structure and packing mode. The asymmetric unit accomodates two independent molecules of the monopersulphate anion, which are held together by hydrogen bonds. In the packing mode, rows of such dimers are surrounded by four rows of tetraphenyl cations. The consequence is that the highly water sensitive HSO5¯ anions are segregated inside hydrophobic channels composed by the lipophilic cations. This circumstance presumably accounts for the exceptional stability of the title compound.

  16. Comparative trophic structures of macrobenthic food web in two macrotidal wetlands with and without a dike on the temperate coast of Korea as revealed by stable isotopes.

    Science.gov (United States)

    Park, Hyun Je; Kang, Hee Yoon; Park, Tae Hee; Kang, Chang-Keun

    2017-10-01

    This study characterized trophic structures of the macrobenthic food webs in two contrasting estuarine wetlands, with and without a dike, on the southern coast of Korea, based on the δ 13 C and δ 15 N values of dominant macrobenthic consumers. The pelagic algal biomasses were similar in the upper Phragmites australis-covered and lower bare intertidal habitats partitioned by the dike, but the microphytobenthos (MPB) biomasses were extremely low in the Phragmites bed. The consumer δ 13 C values were more negative and their isotopic niche width was much narrower in the upper than in the lower habitat at the diked site. These dissimilar spatial patterns between sites suggest a simplified food-web structure, which reflects the reduced availability of MPB in the upper habitat in the dike-impacted site. Overall, our findings suggest that restriction of the tides by dike construction induces local changes in basal resource availability and faunal composition, leading to macrobenthic community trophic reorganization. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Structure of long human telomeric RNA (TERRA): G-quadruplexes formed by four and eight UUAGGG repeats are stable building blocks.

    Science.gov (United States)

    Martadinata, Herry; Heddi, Brahim; Lim, Kah Wai; Phan, Anh Tuân

    2011-07-26

    The discovery of long RNA transcripts of telomeric repeats (TERRA) and their potential to form G-quadruplexes stimulated studies on the possible arrangements of G-quadruplexes along TERRA. Here we performed ribonuclease protection assay to investigate the structures formed by long human TERRA. We found that G-quadruplexes comprising four and eight UUAGGG repeats were most resistant to RNase T1 digestion, presumably with the former adopting an all-parallel-stranded propeller-type conformation and the latter forming a structure with two tandemly stacked G-quadruplex subunits each containing three G-tetrad layers. Molecular dynamics simulations of eight-repeat human TERRA sequences consisting of different stacking interfaces between the two G-quadruplex subunits, i.e., 5'-5', 3'-3', 3'-5', and 5'-3', demonstrated stacking feasibility for all but the 5'-3' arrangement. A continuous stacking of the loop bases from one G-quadruplex subunit to the next was observed for the 5'-5' stacking conformation. We also put forward other possible stacking arrangements that involve more than one linker connecting the two G-quadruplex subunits. On the basis of these results, we propose a "beads-on-a-string"-like arrangement along human TERRA, whereby each bead is made up of either four or eight UUAGGG repeats in a one- or two-block G-quadruplex arrangement, respectively. © 2011 American Chemical Society

  18. Thermally induced solid-state transformation of cimetidine. A multi-spectroscopic/chemometrics determination of the kinetics of the process and structural elucidation of one of the products as a stable N{sub 3}-enamino tautomer

    Energy Technology Data Exchange (ETDEWEB)

    Calvo, Natalia L.; Simonetti, Sebastian O.; Maggio, Rubén M.; Kaufman, Teodoro S., E-mail: kaufman@iquir-conicet.gov.ar

    2015-05-22

    Highlights: • Thermally stressed cimetidine above its melting point affords a stable N{sub 3} tautomer. • Multi-spectroscopic/chemometric approach developed to monitor tautomerization. • First combined use of NMR, UV and IR spectroscopies with chemometrics. • Solid cimetidine suffers first order degradation upon submission to dry heat. • Theoretical chemistry analysis confirmed the relative stability of cimetidine tautomer. - Abstract: Exposure of cimetidine (CIM) to dry heat (160–180 °C) afforded, upon cooling, a glassy solid containing new and hitherto unknown products. The kinetics of this process was studied by a second order chemometrics-assisted multi-spectroscopic approach. Proton and carbon-13 nuclear magnetic resonance (NMR), as well as ultraviolet and infrared spectroscopic data were jointly used, whereas multivariate curve resolution with alternating least squares (MCR-ALS) was employed as the chemometrics method to extract process information. It was established that drug degradation follows a first order kinetics. One of the products was structurally characterized by mono- and bi-dimensional NMR experiments. It was found to be the N{sub 3}-enamino tautomer (TAU) of CIM, resulting from the thermal isomerization of the double bond of the cyanoguanidine moiety of the drug, from the imine form to its N{sub 3}-enamine state. The thus generated tautomer demonstrated to be stable for months in the glassy solid and in methanolic solutions. A theoretical study of CIM and TAU revealed that the latter is less stable; however, the energy barrier for tautomer interconversion is high enough, precluding the process to proceed rapidly at room temperature.

  19. Calcium stable isotope geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Gausonne, Nikolaus [Muenster Univ. (Germany). Inst. fuer Mineralogie; Schmitt, Anne-Desiree [Strasbourg Univ. (France). LHyGeS/EOST; Heuser, Alexander [Bonn Univ. (Germany). Steinmann-Inst. fuer Geologie, Mineralogie und Palaeontologie; Wombacher, Frank [Koeln Univ. (Germany). Inst. fuer Geologie und Mineralogie; Dietzel, Martin [Technische Univ. Graz (Austria). Inst. fuer Angewandte Geowissenschaften; Tipper, Edward [Cambridge Univ. (United Kingdom). Dept. of Earth Sciences; Schiller, Martin [Copenhagen Univ. (Denmark). Natural History Museum of Denmark

    2016-08-01

    This book provides an overview of the fundamentals and reference values for Ca stable isotope research, as well as current analytical methodologies including detailed instructions for sample preparation and isotope analysis. As such, it introduces readers to the different fields of application, including low-temperature mineral precipitation and biomineralisation, Earth surface processes and global cycling, high-temperature processes and cosmochemistry, and lastly human studies and biomedical applications. The current state of the art in these major areas is discussed, and open questions and possible future directions are identified. In terms of its depth and coverage, the current work extends and complements the previous reviews of Ca stable isotope geochemistry, addressing the needs of graduate students and advanced researchers who want to familiarize themselves with Ca stable isotope research.

  20. Purification, biochemical characterization and structural modelling of alkali-stable β-1,4-xylan xylanohydrolase from Aspergillus fumigatus R1 isolated from soil.

    Science.gov (United States)

    Deshmukh, Rehan Ahmed; Jagtap, Sharmili; Mandal, Madan Kumar; Mandal, Suraj Kumar

    2016-02-04

    Aspergillus fumigatus R1 produced xylanase under submerged fermentation which degrades the complex hemicelluloses contained in agricultural substrates. Xylanases have gained considerable attention because of their tremendous applications in industries. The purpose of our study was to purify xylanase and study its biochemical properties. We have predicted the secondary structure of purified xylanase and evaluated its active site residues and substrate binding sites based on the global and local structural similarity. Various microorganisms were isolated from Puducherry soil and screened by Congo-red test. The best isolate was identified to be Aspergillus fumigatus R1. The production kinetics showed the highest xylanase production (208 IU/ml) by this organism in 96 h using 1 % rice bran as the only carbon source. The purification of extracellular xylanase was carried out by fractional ammonium sulphate precipitation (30-55 %), followed by extensive dialysis and Bio-Gel P-60 Gel-filtration chromatography. The enzyme was purified 58.10 folds with a specific activity of 38196.22 IU/mg. The biochemical characterization of the pure enzyme was carried out for its optimum pH and temperature (5.0 and 50(0)C), pH and temperature stability, molecular mass (Mr) (24.5 kDa) and pI (6.29). The complete sequence of protein was obtained by mass spectrometry analysis. Apparent Km and Vmax values of the xylanase for birchwood xylan were 11.66 mg/ml and 87.6 μmol min(-1) mg(-1) respectively. Purified xylanase was analyzed by mass-spectrometry which revealed 2 unique peptides. Xylanase under current study showed significant production using agricultural residues and a broad range of pH stability in the alkaline region. Xylanase produced by Aspergillus fumigatus R1 could serve as the enzyme of choice in industries.

  1. Stable Hemiaminals: 2-Aminopyrimidine Derivatives

    Directory of Open Access Journals (Sweden)

    Anna Kwiecień

    2015-08-01

    Full Text Available Stable hemiaminals can be obtained in the one-pot reaction between 2-aminopyrimidine and nitrobenzaldehyde derivatives. Ten new hemiaminals have been obtained, six of them in crystal state. The molecular stability of these intermediates results from the presence of both electron-withdrawing nitro groups as substituents on the phenyl ring and pyrimidine ring, so no further stabilisation by intramolecular interaction is required. Hemiaminal molecules possess a tetrahedral carbon atom constituting a stereogenic centre. As the result of crystallisation in centrosymmetric space groups both enantiomers are present in the crystal structure.

  2. Design of a new hairpin DNAzyme: The activity controlled by TMPyP4

    African Journals Online (AJOL)

    Jane

    2011-08-01

    . The formation and stability of the G-quadruplex structure as the DNAzyme stem in the absence or the presence of TMPyP4 ..... presence of 100 nM 32P-labeled RNA substrate as indicated, the reaction product was visualized ...

  3. Facile construction of novel CoMoO4 microplates@CoMoO4 microprisms structures for well-stable supercapacitors

    Directory of Open Access Journals (Sweden)

    Xuewen Geng

    2016-06-01

    Full Text Available A simple and controllable strategy has been developed to fabricate CoMoO4 microplates/CoMoO4 microprisms (CMCMs structures on Ni foam via a facile, cost-effective, two-step hydrothermal route. The as-grown 3D architecture exhibited excellent areal capacitance of 4.33 F cm−2 at a galvanostatic charge-discharge current density of 50 mA cm−2 (6 A g−1 and outstanding cycle performance with only 2.8% degradation over 6500 cycles in the 3 M KOH solution. The asymmetric all-solid-state supercapacitors based on activated carbon (AC and CMCMs exhibited much better electrochemical performance than the symmetric counterpart, showing an areal capacitance of 95.22 mF cm−2 at the current density of 12 mA cm−2 and excellent cycling stability with 92.27% of the initial capacitance after 5000 cycles. These results may provide useful guidelines for materials selection and configuration designs for the novel energy storage devices based on CoMoO4 components and substrates.

  4. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General ... Using some examples of classical games, we show how evolutionary game theory can help understand behavioural decisions of animals.

  5. The Stable Concordance Genus

    OpenAIRE

    Kearney, M. Kate

    2013-01-01

    The concordance genus of a knot is the least genus of any knot in its concordance class. Although difficult to compute, it is a useful invariant that highlights the distinction between the three-genus and four-genus. In this paper we define and discuss the stable concordance genus of a knot, which describes the behavior of the concordance genus under connected sum.

  6. Manifolds admitting stable forms

    Czech Academy of Sciences Publication Activity Database

    Le, Hong-Van; Panák, Martin; Vanžura, Jiří

    2008-01-01

    Roč. 49, č. 1 (2008), s. 101-11 ISSN 0010-2628 R&D Projects: GA ČR(CZ) GP201/05/P088 Institutional research plan: CEZ:AV0Z10190503 Keywords : stable forms * automorphism groups Subject RIV: BA - General Mathematics

  7. Interactive Stable Ray Tracing

    DEFF Research Database (Denmark)

    Dal Corso, Alessandro; Salvi, Marco; Kolb, Craig

    2017-01-01

    Interactive ray tracing applications running on commodity hardware can suffer from objectionable temporal artifacts due to a low sample count. We introduce stable ray tracing, a technique that improves temporal stability without the over-blurring and ghosting artifacts typical of temporal post-pr...

  8. The stable subgroup graph

    Directory of Open Access Journals (Sweden)

    Behnaz Tolue

    2018-07-01

    Full Text Available In this paper we introduce stable subgroup graph associated to the group $G$. It is a graph with vertex set all subgroups of $G$ and two distinct subgroups $H_1$ and $H_2$ are adjacent if $St_{G}(H_1\\cap H_2\

  9. Recognition of a 10 base pair sequence of DNA and stereochemical control of the binding affinity of chiral hairpin polyamide-Hoechst 33258 conjugates.

    Science.gov (United States)

    Reddy, Putta Mallikarjuna; Toporowski, Joseph W; Kahane, Alexandra L; Bruice, Thomas C

    2005-12-15

    Chiral hairpin polyamides linked to a Hoechst 33258 analogue at the alpha-position of the hairpin turn amino acid (1,2) were synthesized on solid phase by adopting Fmoc and ivDde techniques. The DNA-binding properties of enantiomeric conjugates 1 and 2, and N-terminal linked conjugate 3 for 8-14bp sequences were determined by spectrofluorometric and thermal melting studies. Conjugates 1 and 2 recognize a 10bp sequence, while conjugate 3 recognizes a 9bp sequence. Interestingly, R-enantiomer 1 exhibited 10- to 30-fold higher binding affinities than S-enantiomer 2 for the DNA sequences studied. These binding differences were accounted for by molecular modeling studies, which revealed that the amide proton nearest to the chiral center in R-conjugate 1 is better positioned to form hydrogen bonds to the DNA bases, while S-conjugate 2 does not.

  10. Active Site Sharing and Subterminal Hairpin Recognition in a New Class of DNA Transposases

    Energy Technology Data Exchange (ETDEWEB)

    Ronning, Donald R.; Guynet, Catherine; Ton-Hoang, Bao; Perez, Zhanita N.; Ghirlando, Rodolfo; Chandler, Michael; Dyda, Fred (Centre Nat); (NIH)

    2010-07-20

    Many bacteria harbor simple transposable elements termed insertion sequences (IS). In Helicobacter pylori, the chimeric IS605 family elements are particularly interesting due to their proximity to genes encoding gastric epithelial invasion factors. Protein sequences of IS605 transposases do not bear the hallmarks of other well-characterized transposases. We have solved the crystal structure of full-length transposase (TnpA) of a representative member, ISHp608. Structurally, TnpA does not resemble any characterized transposase; rather, it is related to rolling circle replication (RCR) proteins. Consistent with RCR, Mg{sup 2+} and a conserved tyrosine, Tyr127, are essential for DNA nicking and the formation of a covalent intermediate between TnpA and DNA. TnpA is dimeric, contains two shared active sites, and binds two DNA stem loops representing the conserved inverted repeats near each end of ISHp608. The cocrystal structure with stem-loop DNA illustrates how this family of transposases specifically recognizes and pairs ends, necessary steps during transposition.

  11. Core-shell structural nanodiamond@TiN supported Pt nanoparticles as a highly efficient and stable electrocatalyst for direct methanol fuel cells

    International Nuclear Information System (INIS)

    Zhao, Yuling; Wang, Yanhui; Dong, Liang; Zhang, Yan; Huang, Junjie; Zang, Jianbing; Lu, Jing; Xu, Xipeng

    2014-01-01

    Highlights: • Core-shell structural nanodiamond@TiN was used as a novel support for Pt catalysts. • The ND@TiN support possessed a high electrochemical stability than carbon black. • The Pt/ND@TiN showed a higher catalytic activity for MOR and ORR than the Pt/C. • The Pt/ND@TiN demonstrated a much better durability compared with the Pt/C. - Abstract: A novel core-shell support material was designed with nanodiamond (ND) as core possessed excellent stability and TiN as shell improved the conductivity of support. The nano-TiN shell was decorated on the surface of ND by annealing TiO 2 in nitrogen atmosphere, and the obtained ND@TiN was employed to support Pt nanoparticles (NPs). The ND@TiN support and Pt/ND@TiN electrocatalyst were characterized by X-ray diffraction and transmission electron microscopy. ND particles were coated uniformly by the TiN layer and Pt NPs with a mean size of 4.2 nm were highly dispersed on the surface of ND@TiN. The electrochemical results confirmed that the ND@TiN support possessed a much more stability than the carbon black and exhibited a bigger background current density than the ND. The Pt/ND@TiN catalyst showed higher catalytic activity and better stability in methanol oxidation and oxygen reduction reactions compared with the Pt/C and Pt/ND

  12. Seasonal and inter-annual dynamics of growth, non-structural carbohydrates and C stable isotopes in a Mediterranean beech forest.

    Science.gov (United States)

    Scartazza, Andrea; Moscatello, Stefano; Matteucci, Giorgio; Battistelli, Alberto; Brugnoli, Enrico

    2013-07-01

    Seasonal and inter-annual dynamics of growth, non-structural carbohydrates (NSC) and carbon isotope composition (δ(13)C) of NSC were studied in a beech forest of Central Italy over a 2-year period characterized by different environmental conditions. The net C assimilated by forest trees was mainly used to sustain growth early in the season and to accumulate storage carbohydrates in trunk and root wood in the later part of the season, before leaf shedding. Growth and NSC concentration dynamics were only slightly affected by the reduced soil water content (SWC) during the drier year. Conversely, the carbon isotope analysis on NSC revealed seasonal and inter-annual variations of photosynthetic and post-carboxylation fractionation processes, with a significant increase in δ(13)C of wood and leaf soluble sugars in the drier summer year than in the wetter one. The highly significant correlation between δ(13)C of leaf soluble sugars and SWC suggests a decrease of the canopy C isotope discrimination and, hence, an increased water-use efficiency with decreasing soil water availability. This may be a relevant trait for maintaining an acceptable plant water status and a relatively high C sink capacity during dry seasonal periods. Our results suggest a short- to medium-term homeostatic response of the Collelongo beech stand to variations in water availability and solar radiation, indicating that this Mediterranean forest was able to adjust carbon-water balance in order to prevent C depletion and to sustain plant growth and reserve accumulation during relatively dry seasons.

  13. Design of hybrid β-hairpin peptides with enhanced cell specificity and potent anti-inflammatory activity.

    Science.gov (United States)

    Liu, YiFan; Xia, Xi; Xu, Liang; Wang, YiZhen

    2013-01-01

    Antimicrobial peptides (AMPs) have attracted considerable attention for their broad-spectrum antimicrobial activity and reduced tendency to cause bacterial resistance. Emerging concerns over the host cytotoxicity of AMPs, however, may ultimately compromise their development as pharmaceuticals. In order to optimize AMPs with potent cell specificity and anti-inflammatory activity, we designed β-hairpin hybrid peptides based upon progetrin-1, bovine lactoferricin and cecropin A. The synthetic hybrid peptides LB-PG and CA-PG demonstrated high selectivity over a wide range of microbes from Gram-positive and Gram-negative bacteria in porcine red blood cells. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) show that these peptides kill microbial cells by penetrating the cell membrane and damaging the membrane envelope. Gel retardation demonstrates that the peptides have a high affinity for DNA, indicating an additional possible intracellular bactericidal mechanism. Moreover, the hybrid peptides inhibit the expression of LPS-induced proinflammatory cytokines and chemokines, such as tumor necrosis factor-α (TNF-α), inducible nitric oxide synthase (iNOS), macrophage inflammatory protein-1α (MIP-1α) and monocyte chemoattractant protein 1(MCP-1), following LPS stimulation in RAW264.7 cells. Our results indicate that these hybrid peptides have considerable potential for future development as antimicrobial and anti-inflammatory agents. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene.

    Science.gov (United States)

    Wang, Li; Dai, Xianjin; Song, Han; Yuan, Peng; Yang, Zhou; Dong, Wei; Song, Zhenhui

    2017-04-01

    The membrane (M) protein is the most abundant component of the porcine transmissible gastroenteritis virus (TGEV) particle. To exploit the possibility of using RNA interference (RNAi) as a strategy against TGEV infection, three plasmids (pRNAT-1, pRNAT-2, and pRNAT-3) expressing short hairpin RNAs were designed to target three different coding regions of the M gene of TGEV. The plasmids were constructed and transiently transfected into a porcine kidney cells, PK-15, to determine whether these constructs inhibited TGEV production. The analysis of cytopathic effects demonstrated that pRNAT-2 and pRNAT-3 could protect PK-15 cells against pathological changes specifically and efficiently. Additionally, indirect immunofluorescence and 50% tissue culture infectious dose (TCID 50 ) assays showed that pRNAT-2 and pRNAT-3 inhibited the multiplication of the virus at the protein level effectively. Quantitative real-time PCR further confirmed that the amounts of viral RNAs in cell cultures pre-transfected with the three plasmids were reduced by 13, 68, and 70%, respectively. This is the first report showing that RNAi targeting of the M gene. Our results could promote studies of the specific function of viral genes associated with TGEV infection and might provide a theoretical basis for potential therapeutic applications.

  15. Comparison of approaches for efficient gene silencing induced by microRNA-based short hairpin RNA and indicator gene expression.

    Science.gov (United States)

    Shan, Z X; Lin, Q X; Deng, C Y; Zhou, Z L; Tan, H H; Fu, Y H; Li, X H; Zhu, J N; Mai, L P; Kuang, S J; Lin, S G; Yu, X Y

    2010-04-01

    MicroRNA-based short hairpin RNAs (shRNAs) are natural inducers of RNA interference and have been increasingly used in shRNA expression strategies. In the present study, we compared the efficiencies of exogenous green fluorescence protein (GFP) and endogenous glyceraldehyde-3-phosphate dehydrogenase (GAPDH) knockdown and red fluorescent protein (RFP) indicator expression mediated by three differently designed plasmids. RFP was introduced either at the 5' end, at the 3' end of the human mir155-based target gene (TG) (e.g., GFP or GAPDH) shRNA expression cassette (EC), or at the 3' end of the chimeric intron-containing TG shRNA EC. Comparisons with the control vector showed an obvious reduction of GFP or GAPDH expression with the various shRNA expression plasmids (P < 0.05). When RFP was located at the 5' end or at the 3' end of the TG shRNA EC, RFP expression was low; whereas when RFP was connected with the chimeric intron-containing TG shRNA EC, RFP expression was high. Taken together, this study demonstrated an efficient plasmid design for both TG silencing induced by microRNA-based shRNA and indicator gene expression in vitro.

  16. An optimized lentiviral vector system for conditional RNAi and efficient cloning of microRNA embedded short hairpin RNA libraries.

    Science.gov (United States)

    Adams, Felix F; Heckl, Dirk; Hoffmann, Thomas; Talbot, Steven R; Kloos, Arnold; Thol, Felicitas; Heuser, Michael; Zuber, Johannes; Schambach, Axel; Schwarzer, Adrian

    2017-09-01

    RNA interference (RNAi) and CRISPR-Cas9-based screening systems have emerged as powerful and complementary tools to unravel genetic dependencies through systematic gain- and loss-of-function studies. In recent years, a series of technical advances helped to enhance the performance of virally delivered RNAi. For instance, the incorporation of short hairpin RNAs (shRNAs) into endogenous microRNA contexts (shRNAmiRs) allows the use of Tet-regulated promoters for synchronous onset of gene knockdown and precise interrogation of gene dosage effects. However, remaining challenges include lack of efficient cloning strategies, inconsistent knockdown potencies and leaky expression. Here, we present a simple, one-step cloning approach for rapid and efficient cloning of miR-30 shRNAmiR libraries. We combined a human miR-30 backbone retaining native flanking sequences with an optimized all-in-one lentiviral vector system for conditional RNAi to generate a versatile toolbox characterized by higher doxycycline sensitivity, reduced leakiness and enhanced titer. Furthermore, refinement of existing shRNA design rules resulted in substantially improved prediction of powerful shRNAs. Our approach was validated by accurate quantification of the knockdown potency of over 250 single shRNAmiRs. To facilitate access and use by the scientific community, an online tool was developed for the automated design of refined shRNA-coding oligonucleotides ready for cloning into our system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Enzyme-free amplification for sensitive electrochemical detection of DNA via target-catalyzed hairpin assembly assisted current change.

    Science.gov (United States)

    Qian, Yong; Wang, Chunyan; Gao, Fenglei

    2014-12-01

    An isothermal, enzyme-free and sensitive method for electrochemical detection of DNA is proposed based on target catalyzed hairpin assembly and for signal amplification. Molecular beacon 1 (MB1) contains a ferrocene (Fc) tag, which was immobilized on the gold electrode as recognition probe to hybridize with target DNA. Then, molecular beacon 2 hybridized with the opened MB1, allowing the target to be displaced. The displaced target again triggered the next round of strand exchange reaction resulting in many Fc far away from the GE to achieve signal amplification for sensitive DNA detection. The current signal amplification strategy is relatively simple and inexpensive owing to avoid the use of any kind of enzyme or sophisticated equipment. It can achieve a sensitivity of 42 fM with a wide linear dynamic range from 10(-13) to 10(-9)M and discriminate mismatched DNA from perfect matched target DNA with a high selectivity. The proposed method showed excellent specificity, high sensitivity and low detection limit, and could be applied in analysis of real samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. SHARP-2 gene silencing by lentiviral-based short hairpin RNA interference prolonged rat kidney transplant recipients' survival time.

    Science.gov (United States)

    Shou, Z; Xiao, H; Xu, Y; Wang, Y; Yang, Y; Jiang, H; Chen, J; Yamada, K; Miyamoto, K

    2009-01-01

    Split- and hairy-related protein-2 (SHARP-2) controls the expression of interleukin-2 (IL-2) and interferon-gamma (IFN-gamma), which both play a key role in transplant rejection. This study was designed to investigate whether SHARP-2 short hairpin RNA interference (shRNAi) could prolong the survival of rat kidney transplant recipients. A lentiviral-based shRNAi construct, LV-SHARP-2iC, showed a SHARP-2 gene silencing efficiency of 84% in normal rat kidney cells. In activated T-cells, SHARP-2 gene silencing with the LV-SHARP-2iC construct resulted in 61% and 69% down-regulation of IL-2 and IFN-gamma, respectively, compared with a scramble control construct. When donor kidney was perfused with 5 x 10(7) transforming units of the LV-SHARP-2iC construct, the median survival time of the transplant recipients was prolonged by 4 - 5 days compared with control groups. In conclusion, recombinant lentiviral LV-SHARP-2iC construct effectively silenced SHARP-2 gene expression, which reduced IL-2 and IFN-gamma mRNA expression and prolonged rat kidney transplant recipients' survival.

  19. Fast and quantitative differentiation of single-base mismatched DNA by initial reaction rate of catalytic hairpin assembly.

    Science.gov (United States)

    Li, Chenxi; Li, Yixin; Xu, Xiao; Wang, Xinyi; Chen, Yang; Yang, Xiaoda; Liu, Feng; Li, Na

    2014-10-15

    The widely used catalytic hairpin assembly (CHA) amplification strategy generally needs several hours to accomplish one measurement based on the prevailingly used maximum intensity detection mode, making it less practical for assays where high throughput or speed is desired. To make the best use of the kinetic specificity of toehold domain for circuit reaction initiation, we developed a mathematical model and proposed an initial reaction rate detection mode to quantitatively differentiate the single-base mismatch. Using the kinetic mode, assay time can be reduced substantially to 10 min for one measurement with the comparable sensitivity and single-base mismatch differentiating ability as were obtained by the maximum intensity detection mode. This initial reaction rate based approach not only provided a fast and quantitative differentiation of single-base mismatch, but also helped in-depth understanding of the CHA system, which will be beneficial to the design of highly sensitive and specific toehold-mediated hybridization reactions. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Significant inhibition of Tembusu virus envelope and NS5 gene using an adenovirus-mediated short hairpin RNA delivery system.

    Science.gov (United States)

    Wang, Hongzhi; Feng, Qiang; Wei, Lei; Zhuo, Liling; Chen, Hao; Diao, Youxiang; Tang, Yi

    2017-10-01

    Tembusu virus (TMUV) is a mosquito-borne flavivirus, which was first isolated in the tropics during the 1970s. Recently, a disease characterized by ovarian haemorrhage and neurological symptoms was observed in ducks in China, which threatens poultry production. However, there is no suitable vaccination strategy or effective antiviral drugs to combat TMUV infections. Consequently, there is an urgent need to develop a new anti-TMUV therapy. In this study, we report an efficient short hairpin RNA (shRNA) delivery strategy for the inhibition of TMUV production using an adenovirus vector system. Using specifically designed shRNAs based on the E and NS5 protein genes of TMUV, the vector-expressed viral genes, TMUV RNA replication and infectious virus production were downregulated at different levels in Vero cells, where the shRNA (NS52) was highly effective in inhibiting TMUV. Using the human adenovirus type 5 shRNA delivery system, the recombinant adenovirus (rAd-NS52) inhibited TMUV multiplication with high efficiency. Furthermore, the significant dose-dependent inhibition of viral RNA copies induced by rAd-NS52 was found in TMUV-infected cells, which could last for at least 96h post infection. Our results indicated that the adenovirus-mediated delivery of shRNAs could play an active role in future TMUV antiviral therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Is TNF-a-targeted short hairpin RNA (shRNA) a novel potential therapeutic tool in psoriasis treatment?

    DEFF Research Database (Denmark)

    Stenderup, Karin; Jakobsen, Maria; Rosada, Cecilia

    2008-01-01

      TNF-α is a well known target in psoriasis treatment and biological treatments targeting TNF-a are already clinically used against psoriasis and psoriasis arthritis. Attention is however given to a novel therapeutic tool: RNA interference that controls gene silencing. This study investigates...... the efficiency of targeting TNF-a with specific short hairpin RNA (shRNA) and explores its potential in treating psoriasis. ShRNAs targeting human TNF-α mRNA were generated. Their efficiency in down-regulating TNF-a protein expression was evaluated using a Renilla luciferase screening-assay and a transient co...... TNF-a shRNA was used to transduce HEK293 cells and verify vector-derived TNF-a knockdown in vitro. In vivo, psoriasis skin was exposed to lentiviral TNF-a shRNAs by a single intra-dermal injection. Psoriasis skin for the in vivo study was obtained from psoriatic plaque skin biopsies that were...

  2. The carbonaceous phyllite rock-hosted Pedra Verde copper mine, Borborema Province, Brazil: Stable isotope constraints, structural controls and metallogenic evolution

    Science.gov (United States)

    da Silva Nogueira de Matos, José Henrique; Saraiva dos Santos, Ticiano José; Virgínia Soares Monteiro, Lena

    2017-12-01

    The Pedra Verde Copper Mine is located in the Viçosa do Ceará municipality, State of Ceará, NE Brazil. The copper mineralization is hosted by the Pedra Verde Phyllite, which is a carbonaceous chlorite-calcite phyllite with subordinate biotite. It belongs to the Neoproterozoic Martinópole Group of the Médio Coreaú Domain, Borborema Province. The Pedra Verde deposit is stratabound and its ore zoning is conspicuous, according to the following sequence, from bottom to top: marcasite/pyrite, native silver, chalcopyrite, bornite, chalcocite, native copper and hematite. Barite and carbonaceous material are reported in ore zones. Zoning reflects the ore formation within a redox boundary developed due to the interaction between oxidized copper- and sulfate-bearing fluids and the reduced phyllite. Structural control on mineralization is evidenced by the association of the ore minerals with veins, hinge folds, shadow pressures, and mylonitic foliation. It was mainly exercised by a dextral transcurrent shear zone developed during the third deformational stage identified in the Médio Coreaú Domain between 590 Ma and 570 Ma. This points to the importance of epigenetic, post-metamorphic deformational events for ore formation. Oxygen isotopic composition (δ18OH2O = 8.94 to 11.28‰, at 250 to 300 °C) estimated for the hydrothermal fluids in equilibrium with calcite indicates metamorphic or evolved meteoric isotopic signatures. The δ13CPDB values (-2.60 to -9.25‰) obtained for hydrothermal calcite indicate mixing of carbon sources derived from marine carbonate rocks and carbonaceous material. The δ34SCDT values (14.88 to 36.91‰) of sulfides suggest evaporites as sulfate sources or a closed system in relation to SO42- availability to form H2S. Carbonaceous matter had a key role in thermochemical sulfate processes and sulfide precipitation. The Pedra Verde Copper Mine is considered the first stratabound meta-sedimentary rock-hosted copper deposit described in Brazil

  3. A systematic analysis of the effect of target RNA structure on RNA interference

    NARCIS (Netherlands)

    Westerhout, Ellen M.; Berkhout, Ben

    2007-01-01

    RNAi efficiency is influenced by local RNA structure of the target sequence. We studied this structure-based resistance in detail by targeting a perfect RNA hairpin and subsequently destabilized its tight structure by mutation, thereby gradually exposing the target sequence. Although the tightest

  4. Stable isotope analysis

    International Nuclear Information System (INIS)

    Tibari, Elghali; Taous, Fouad; Marah, Hamid

    2014-01-01

    This report presents results related to stable isotopes analysis carried out at the CNESTEN DASTE in Rabat (Morocco), on behalf of Senegal. These analyzes cover 127 samples. These results demonstrate that Oxygen-18 and Deuterium in water analysis were performed by infrared Laser spectroscopy using a LGR / DLT-100 with Autosampler. Also, the results are expressed in δ values (‰) relative to V-SMOW to ± 0.3 ‰ for oxygen-18 and ± 1 ‰ for deuterium.

  5. Forensic Stable Isotope Biogeochemistry

    Science.gov (United States)

    Cerling, Thure E.; Barnette, Janet E.; Bowen, Gabriel J.; Chesson, Lesley A.; Ehleringer, James R.; Remien, Christopher H.; Shea, Patrick; Tipple, Brett J.; West, Jason B.

    2016-06-01

    Stable isotopes are being used for forensic science studies, with applications to both natural and manufactured products. In this review we discuss how scientific evidence can be used in the legal context and where the scientific progress of hypothesis revisions can be in tension with the legal expectations of widely used methods for measurements. Although this review is written in the context of US law, many of the considerations of scientific reproducibility and acceptance of relevant scientific data span other legal systems that might apply different legal principles and therefore reach different conclusions. Stable isotopes are used in legal situations for comparing samples for authenticity or evidentiary considerations, in understanding trade patterns of illegal materials, and in understanding the origins of unknown decedents. Isotope evidence is particularly useful when considered in the broad framework of physiochemical processes and in recognizing regional to global patterns found in many materials, including foods and food products, drugs, and humans. Stable isotopes considered in the larger spatial context add an important dimension to forensic science.

  6. HIV-1 splicing at the major splice donor site is restricted by RNA structure.

    Science.gov (United States)

    Mueller, Nancy; van Bel, Nikki; Berkhout, Ben; Das, Atze T

    2014-11-01

    The 5' leader region of the HIV-1 RNA contains the major 5' splice site (ss) that is used in the production of all spliced viral RNAs. This splice-donor (SD) region can fold a stem-loop structure. We demonstrate that whereas stabilization of this SD hairpin reduces splicing efficiency, destabilization increases splicing. Both stabilization and destabilization reduce viral fitness. These results demonstrate that the stability of the SD hairpin can modulate the level of splicing, most likely by controlling the accessibility of the 5'ss for the splicing machinery. The natural stability of the SD hairpin restricts splicing and this stability seems to be fine-tuned to reach the optimal balance between unspliced and spliced RNAs for efficient virus replication. The 5'ss region of different HIV-1 isolates and the related SIVmac239 can fold a similar structure. This evolutionary conservation supports the importance of this structure in viral replication. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Dimensionally Stable Structural Space Cable, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Jet Propulsion Laboratory (JPL) is involved in an ongoing effort to design and demonstrate a full-scale (30-32m diameter) Starshade engineering demonstrator that...

  8. Dimensionally Stable Structural Space Cable, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — In response to the need for an affordable exoplanet-analysis science mission, NASA has recently embarked on the ROSES Technology Development for Exoplanet Missions...

  9. Multi-Stable Morphing Cellular Structures

    Science.gov (United States)

    2015-05-14

    varying thickness and height were waterjet cut from a 0.02-m-thick sheet of DuPont Delrin II 150SA NC010 (see Figure 9). The waterjet cut through the...from strips cut from a NiTiNOL sheet on the waterjet machine. Based on the availability, the superelastic, 56.1% nickel NDC SE 508 alloy was chosen...conforming to American Society for Testing Materials (ASTM) standard D638-10 was cut from the same sheet. The superelastic NiTiNOL arches originated

  10. Short Hairpin RNA Silencing of PHD-2 Improves Neovascularization and Functional Outcomes in Diabetic Wounds and Ischemic Limbs.

    Directory of Open Access Journals (Sweden)

    Kevin J Paik

    Full Text Available The transcription factor hypoxia-inducible factor 1-alpha (HIF-1α is responsible for the downstream expression of over 60 genes that regulate cell survival and metabolism in hypoxic conditions as well as those that enhance angiogenesis to alleviate hypoxia. However, under normoxic conditions, HIF-1α is hydroxylated by prolyl hydroxylase 2, and subsequently degraded, with a biological half-life of less than five minutes. Here we investigated the therapeutic potential of inhibiting HIF-1α degradation through short hairpin RNA silencing of PHD-2 in the setting of diabetic wounds and limb ischemia. Treatment of diabetic mouse fibroblasts with shPHD-2 in vitro resulted in decreased levels of PHD-2 transcript demonstrated by qRT-PCR, higher levels of HIF-1α as measured by western blot, and higher expression of the downstream angiogenic genes SDF-1 and VEGFα, as measured by qRT-PCR. In vivo, shPHD-2 accelerated healing of full thickness excisional wounds in diabetic mice compared to shScr control, (14.33 ± 0.45 days vs. 19 ± 0.33 days and was associated with an increased vascular density. Delivery of shPHD-2 also resulted in improved perfusion of ischemic hind limbs compared to shScr, prevention of distal digit tip necrosis, and increased survival of muscle tissue. Knockdown of PHD-2 through shRNA treatment has the potential to stimulate angiogenesis through overexpression of HIF-1α and upregulation of pro-angiogenic genes downstream of HIF-1α, and may represent a viable, non-viral approach to gene therapy for ischemia related applications.

  11. Triplet repeat DNA structures and human genetic disease: dynamic ...

    Indian Academy of Sciences (India)

    Unknown

    alternative to double-stranded DNA (table 2). These include single-stranded hairpins, triplex and quadruplex. DNA, and slipped-strand DNA. Studies have also con- firmed that the formation of alternative structures occurs in trinucleotide repeat sequences. Linear DNA molecules containing triplet repeats have unusual ...

  12. Structure and sequence motifs in the HIV-1 RNA genome

    NARCIS (Netherlands)

    van Bel, N.

    2015-01-01

    The untranslated leader of the HIV-1 RNA genome contains some 350 nucleotides and is highly conserved among virus isolates. Several characteristic hairpin structures that regulate important virus replication steps, such as dimerization and packaging in virion particles, are clustered in this leader.

  13. Defining fish community structure in Lake Winnipeg using stable isotopes (δ{sup 13}C, δ{sup 15}N, δ{sup 34}S): Implications for monitoring ecological responses and trophodynamics of mercury and other trace elements

    Energy Technology Data Exchange (ETDEWEB)

    Ofukany, Amy F.A. [Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, Saskatchewan S7N 5B3 (Canada); Wassenaar, Leonard I. [Environment Canada, 11 Innovation Boulevard, Saskatoon, Saskatchewan S7N 3H5 (Canada); Bond, Alexander L., E-mail: alex.bond@rspb.org.uk [Environment Canada, 11 Innovation Boulevard, Saskatoon, Saskatchewan S7N 3H5 (Canada); Hobson, Keith A. [Environment Canada, 11 Innovation Boulevard, Saskatoon, Saskatchewan S7N 3H5 (Canada)

    2014-11-01

    The ecological integrity of freshwater lakes is influenced by atmospheric and riverine deposition of contaminants, shoreline development, eutrophication, and the introduction of non-native species. Changes to the trophic structure of Lake Winnipeg, Canada, and consequently, the concentrations of contaminants and trace elements measured in tissues of native fishes, are likely attributed to agricultural runoff from the 977,800 km{sup 2} watershed and the arrival of non-native zooplankters and fishes. We measured δ{sup 13}C, δ{sup 15}N, and δ{sup 34}S along with concentrations of 15 trace elements in 17 native fishes from the north and south basins of Lake Winnipeg in 2009 and 2010. After adjusting for differences in isotopic baseline values between the two basins, fishes in the south basin had consistently higher δ{sup 13}C and δ{sup 34}S, and lower δ{sup 15}N. We found little evidence of biomagnification of trace elements at the community level, but walleye (Sander vitreus) and freshwater drum (Aplodinotus grunniens) had higher mercury and selenium concentrations with increased trophic position, coincident with increased piscivory. There was evidence of growth dilution of cobalt, copper, manganese, molybdenum, thallium, and vanadium, and bioaccumulation of mercury, which could be explained by increases in algal (and consequently, lake and fish) productivity. We conclude that the north and south basins of Lake Winnipeg represent very different communities with different trophic structures and trace element concentrations. - Highlights: • Anthropogenic eutrophication and non-native species affect Lake Winnipeg’s ecosystem. • We measured stable isotopes and trace elements in 15 native fish species. • There was more evidence for growth dilution than biomagnification for most elements. • The trophic structures of the north and south basins were different. • These results will help determine the effects of recent arrival of zebra mussels.

  14. Defining fish community structure in Lake Winnipeg using stable isotopes (δ13C, δ15N, δ34S): Implications for monitoring ecological responses and trophodynamics of mercury and other trace elements

    International Nuclear Information System (INIS)

    Ofukany, Amy F.A.; Wassenaar, Leonard I.; Bond, Alexander L.; Hobson, Keith A.

    2014-01-01

    The ecological integrity of freshwater lakes is influenced by atmospheric and riverine deposition of contaminants, shoreline development, eutrophication, and the introduction of non-native species. Changes to the trophic structure of Lake Winnipeg, Canada, and consequently, the concentrations of contaminants and trace elements measured in tissues of native fishes, are likely attributed to agricultural runoff from the 977,800 km 2 watershed and the arrival of non-native zooplankters and fishes. We measured δ 13 C, δ 15 N, and δ 34 S along with concentrations of 15 trace elements in 17 native fishes from the north and south basins of Lake Winnipeg in 2009 and 2010. After adjusting for differences in isotopic baseline values between the two basins, fishes in the south basin had consistently higher δ 13 C and δ 34 S, and lower δ 15 N. We found little evidence of biomagnification of trace elements at the community level, but walleye (Sander vitreus) and freshwater drum (Aplodinotus grunniens) had higher mercury and selenium concentrations with increased trophic position, coincident with increased piscivory. There was evidence of growth dilution of cobalt, copper, manganese, molybdenum, thallium, and vanadium, and bioaccumulation of mercury, which could be explained by increases in algal (and consequently, lake and fish) productivity. We conclude that the north and south basins of Lake Winnipeg represent very different communities with different trophic structures and trace element concentrations. - Highlights: • Anthropogenic eutrophication and non-native species affect Lake Winnipeg’s ecosystem. • We measured stable isotopes and trace elements in 15 native fish species. • There was more evidence for growth dilution than biomagnification for most elements. • The trophic structures of the north and south basins were different. • These results will help determine the effects of recent arrival of zebra mussels

  15. Periodicity of the stable isotopes

    CERN Document Server

    Boeyens, J C A

    2003-01-01

    It is demonstrated that all stable (non-radioactive) isotopes are formally interrelated as the products of systematically adding alpha particles to four elementary units. The region of stability against radioactive decay is shown to obey a general trend based on number theory and contains the periodic law of the elements as a special case. This general law restricts the number of what may be considered as natural elements to 100 and is based on a proton:neutron ratio that matches the golden ratio, characteristic of biological and crystal growth structures. Different forms of the periodic table inferred at other proton:neutron ratios indicate that the electronic configuration of atoms is variable and may be a function of environmental pressure. Cosmic consequences of this postulate are examined. (author)

  16. Stable States of Biological Organisms

    Science.gov (United States)

    Yukalov, V. I.; Sornette, D.; Yukalova, E. P.; Henry, J.-Y.; Cobb, J. P.

    2009-04-01

    A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole. The organism is modeled by a five-dimensional dynamical system. The organism homeostasis is described by the evolution equations for five interacting components: healthy cells, ill cells, innate immune cells, specific immune cells, and pathogens. The stability analysis demonstrates that, in a wide domain of the parameter space, the system exhibits robust structural stability. There always exist four stable stationary solutions characterizing four qualitatively differing states of the organism: alive state, boundary state, critical state, and dead state.

  17. Stable magnetic remanence in antiferromagnetic goethite.

    Science.gov (United States)

    Strangway, D W; McMahon, B E; Honea, R M

    1967-11-10

    Goethite, known to be antiferromagnetic, acquires thermoremanent magnetization at its Neel temperature of 120 degrees C. This remanence, extremely stable, is due to the presence of unbalanced spins in the antiferromagnetic structure; the spins may result from grain size, imperfections, or impurities.

  18. Marginally Stable Nuclear Burning

    Science.gov (United States)

    Strohmayer, Tod E.; Altamirano, D.

    2012-01-01

    Thermonuclear X-ray bursts result from unstable nuclear burning of the material accreted on neutron stars in some low mass X-ray binaries (LMXBs). Theory predicts that close to the boundary of stability oscillatory burning can occur. This marginally stable regime has so far been identified in only a small number of sources. We present Rossi X-ray Timing Explorer (RXTE) observations of the bursting, high- inclination LMXB 4U 1323-619 that reveal for the first time in this source the signature of marginally stable burning. The source was observed during two successive RXTE orbits for approximately 5 ksec beginning at 10:14:01 UTC on March 28, 2011. Significant mHz quasi- periodic oscillations (QPO) at a frequency of 8.1 mHz are detected for approximately 1600 s from the beginning of the observation until the occurrence of a thermonuclear X-ray burst at 10:42:22 UTC. The mHz oscillations are not detected following the X-ray burst. The average fractional rms amplitude of the mHz QPOs is 6.4% (3 - 20 keV), and the amplitude increases to about 8% below 10 keV.This phenomenology is strikingly similar to that seen in the LMXB 4U 1636-53. Indeed, the frequency of the mHz QPOs in 4U 1323-619 prior to the X-ray burst is very similar to the transition frequency between mHz QPO and bursts found in 4U 1636-53 by Altamirano et al. (2008). These results strongly suggest that the observed QPOs in 4U 1323-619 are, like those in 4U 1636-53, due to marginally stable nuclear burning. We also explore the dependence of the energy spectrum on the oscillation phase, and we place the present observations within the context of the spectral evolution of the accretion-powered flux from the source.

  19. Studying of cellular interaction of hairpin-like peptide EcAMP1 from barnyard grass (Echinochloa crusgalli L.) seeds with plant pathogenic fungus Fusarium solani using microscopy techniques.

    Science.gov (United States)

    Vasilchenko, Alexey S; Yuryev, Mikhail; Ryazantsev, Dmitry Yu; Zavriev, Sergey K; Feofanov, Alexey V; Grishin, Eugene V; Rogozhin, Eugene A

    2016-11-01

    An interaction of recombinant hairpin-like cationic peptide EcAMP1 with conidia of plant pathogenic fungus Fusarium solani at the cellular level was studied by a combination of microscopic methods. EcAMP1 is from barnyard grass (Echinochloa crusgalli L.), and obtained by heterologous expression in Escherichia coli system. As a result, a direct relationship between hyphal growth inhibition and increasing active peptide concentration, time of incubation and fungal physiological condition has been determined. Dynamics of accumulation and redistribution of the peptide studied on fungal cellular cover and inside the conidia cells has been shown. The dynamics are dependent on time of coupling, as well as, a dissimilarity of EcAMP1 binding with cover of fungal conidia and its stepwise accumulation and diffuse localization in the cytoplasm. Correlation between structural disruption of fungal conidia and the presence of morphological changes has also been found. The correlation was found under the influence of peptide high concentrations at concentrations above 32 μM. The results indicate the presence of a binding of EcAMP1 with the surface of fungal conidia, thus, demonstrating a main specificity for its antifungal action at the cellular level. These results, however, cannot exclude the existence of attendant EcAMP1 action based on its intracellular localization on some specific targets. SCANNING 38:591-598, 2016. © 2016 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

  20. Dual Core-Shell Structured Si@SiOx@C Nanocomposite Synthesized via a One-Step Pyrolysis Method as a Highly Stable Anode Material for Lithium-Ion Batteries.

    Science.gov (United States)

    Jiang, Bolun; Zeng, Shi; Wang, Hui; Liu, Daotan; Qian, Jiangfeng; Cao, Yuliang; Yang, Hanxi; Ai, Xinping

    2016-11-23

    Silicon (Si) has been regarded as a promising high-capacity anode material for developing advanced lithium-ion batteries (LIBs), but the practical application of Si anodes is still unsuccessful mainly due to the insufficient cyclability. To deal with this issue, we propose a new route to construct a dual core-shell structured Si@SiO x @C nanocomposite by direct pyrolysis of poly(methyl methacrylate) (PMMA) polymer on the surface of Si nanoparticles. Since the PMMA polymers can be chemically bonded on the nano-Si surface through the interaction between ester group and Si surface group, and thermally decomposed in the subsequent pyrolysis process with their alkyl chains converted to carbon and the residue oxygen recombining with Si to form SiO x , the dual core-shell structure can be conveniently formed in a one-step procedure. Benefiting from the strong buffering effect of the SiO x interlayer and the efficient blocking action of dense outer carbon layer in preventing electrolyte permeation, the obtained nanocomposite demonstrates a high capacity of 1972 mA h g -1 , a stable cycling performance with a capacity retention of >1030 mA h g -1 over 500 cycles, and particularly a superiorly high Coulombic efficiency of >99.5% upon extended cycling, exhibiting a great promise for practical uses. More importantly, the synthetic method proposed in this work is facile and low cost, making it more suitable for large-scale production of high capacity anode for advanced LIBs.

  1. Tukey max-stable processes for spatial extremes

    KAUST Repository

    Xu, Ganggang

    2016-09-21

    We propose a new type of max-stable process that we call the Tukey max-stable process for spatial extremes. It brings additional flexibility to modeling dependence structures among spatial extremes. The statistical properties of the Tukey max-stable process are demonstrated theoretically and numerically. Simulation studies and an application to Swiss rainfall data indicate the effectiveness of the proposed process. © 2016 Elsevier B.V.

  2. [Structure and stability of nucleic acids]. Progress report, July 1, 1988--June 30, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Tinoco, I. Jr.

    1991-12-01

    We study the conformations of DNA and RNA oligonucleotides in order to understand their biological roles. We have determined the structure of the most common type of hairpin loop found in ribosomal RNA--the extra-stable tetraloop. It is actually a biloop with the other two bases in the loop forming a non-Watson-Crick base pair. This is the highest resolution structure reported for an RNA molecule in solution so far. We have obtained structures of pseudoknots and we have deduced general rules for their formation. We are presently studying a pseudoknot which is necessary for the replication of a retrovirus. The research done in the laboratory has been reported in 24 publications, plus 7 manuscripts in press or submitted. The research was done by 14 graduate students and 7 postdoctoral fellows. Five graduate students have received their Ph.D.s and 4 postdoctorals have finished their stay here. There are presently 9 graduate students and 3 postdoctorals working on the project; 2 new postdoctorals are expected this summer. One undergraduate student usually participates in the research during the year; this summer two undergraduates are working on the project. 31 refs., 4 figs.

  3. Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

    Science.gov (United States)

    Kékedy-Nagy, László; Shipovskov, Stepan; Ferapontova, Elena E

    2016-08-16

    Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the "on-off" signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami , E. ; Clima , L. ; Gothelf , K. ; Ferapontova , E. E. Anal. Chem. 2011 , 83 , 1594 ) providing the robust "off-on" nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.

  4. Short hairpin RNA targeting insulin-like growth factor binding protein-3 restores the bioavailability of insulin-like growth factor-1 in diabetic rats

    Directory of Open Access Journals (Sweden)

    Zhang-Yan Zhou

    2016-02-01

    Full Text Available ABSTRACT Purpose To investigate whether intracavernosal injection of short hairpin RNA for IGFBP-3 could improve erectile function in streptozotocin-induced diabetic rats. Materials and methods After 12 weeks of IGFBP-3 short hairpin RNA injection treatment, intracavernous pressure responses to electrical stimulation of cavernous nerves were evaluated. The expression of IGFBP-3 and IGF-1 at mRNA and protein levels were detected by quantitative real-time PCR analysis and Western blot, respectively. The concentration of cavernous cyclic guanosine monophosphate was detected by enzyme-linked immunosorbent assay. Results At 12 weeks after intracavernous administration of IGFBP-3 shRNA, the cavernosal pressure was significantly increased in response to the cavernous nerves stimulation compared to the diabetic group (P<0.05. Cavernous IGFBP-3 expression at both mRNA and protein levels was significantly inhibited. At the same time, cavernous IGF-1 expression was significantly increased in the IGFBP-3 shRNA treatment group compared to the diabetic group (P<0.01. Cavernous cyclic guanosine monophosphate concentration was significantly increased in the IGFBP-3 shRNA treatment group compared to the diabetic group (P<0.01. Conclusions Gene transfer of IGFBP-3 shRNA could improve erectile function via the restoration of cavernous IGF-1 bioavailability and an increase of cavernous cGMP concentration in the pathogenesis of erectile dysfunction in streptozotocin-induced diabetic rats.

  5. Dynamical attraction to stable processes

    OpenAIRE

    Fisher, Albert M.; Talet, Marina

    2012-01-01

    We apply dynamical ideas within probability theory, proving an almost-sure invariance principle in log density for stable processes. The familiar scaling property (self-similarity) of the stable process has a stronger expression, that the scaling flow on Skorokhod path space is a Bernoulli flow. We prove that typical paths of a random walk with i.i.d. increments in the domain of attraction of a stable law can be paired with paths of a stable process so that, after applying a non-random regula...

  6. Stable propagation of interacting crack systems and modeling of damage

    International Nuclear Information System (INIS)

    Bazant, Z.P.; Tabbara, M.R.

    1989-01-01

    This paper presents general thermodynamic criteria for the stable states and stable path of structures with an interacting system of cracks. In combination with numerical finite element results for various cracked structure geometries, these criteria indicate that the crack response path of structures may exhibit bifurcations, after which the symmetry of the crack system is broken and some cracks grow preferentially. The problem is of interest for the prediction of ultimate loads, ductility and energy absorption capability of nuclear concrete structures as well as structures made of composites and ceramics

  7. Proximity hybridization-regulated catalytic DNA hairpin assembly for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Fuyi [School of Chemistry and Chemical Engineering, Jiangsu Normal University, Xuzhou 221116 (China); Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Yao, Yao; Luo, Jianjun; Zhang, Xing; Zhang, Yu; Yin, Dengyang [Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Gao, Fenglei, E-mail: jsxzgfl@sina.com [Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Wang, Po, E-mail: wangpo@jsnu.edu.cn [School of Chemistry and Chemical Engineering, Jiangsu Normal University, Xuzhou 221116 (China)

    2017-05-29

    Novel hybridization proximity-regulated catalytic DNA hairpin assembly strategy has been proposed for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles as signal label. The DNA template-synthesized Pd nanoparticles were characterized with atomic force microscopic and X-ray photoelectron spectroscopy. The highly efficient electrocatalysis by DNA template synthesized Pd nanoparticles for NaBH{sub 4} oxidation produced an intense detection signal. The label-free electrochemical method achieved the detection of carcinoembryonic antigen (CEA) with a linear range from 10{sup −15} to 10{sup −11} g mL{sup −1} and a detection limit of 0.43 × 10{sup −15} g mL{sup −1}. Through introducing a supersandwich reaction to increase the DNA length, the electrochemical signal was further amplified, leading to a detection limit of 0.52 × 10{sup −16} g mL{sup −1}. And it rendered satisfactory analytical performance for the determination of CEA in serum samples. Furthermore, it exhibited good reproducibility and stability; meanwhile, it also showed excellent specificity due to the specific recognition of antigen by antibody. Therefore, the DNA template synthesized Pd nanoparticles based signal amplification approach has great potential in clinical applications and is also suitable for quantification of biomarkers at ultralow level. - Graphical abstract: A novel label-free and enzyme-free electrochemical immunoassay based on proximity hybridization-regulated catalytic DNA hairpin assemblies for recycling of the CEA. - Highlights: • A novel enzyme-free electrochemical immunosensor was developed for detection of CEA. • The signal amplification was based on catalytic DNA hairpin assembly and DNA-template-synthesized Pd nanoparticles. • The biosensor could detect CEA down to 0.52 × 10{sup −16} g mL{sup −1} level with a dynamic range spanning 5 orders of magnitude.

  8. Structural profiles of human miRNA families from pairwise clustering

    DEFF Research Database (Denmark)

    Kaczkowski, Bogumil; Þórarinsson, Elfar; Reiche, Kristin

    2009-01-01

    MicroRNAs (miRNAs) are a group of small, approximately 21 nt long, riboregulators inhibiting gene expression at a post-transcriptional level. Their most distinctive structural feature is the foldback hairpin of their precursor pre-miRNAs. Even though each pre-miRNA deposited in miRBase has its se...

  9. Stable isotopes in Lithuanian bioarcheological material

    Science.gov (United States)

    Skipityte, Raminta; Jankauskas, Rimantas; Remeikis, Vidmantas

    2015-04-01

    Investigation of bioarcheological material of ancient human populations allows us to understand the subsistence behavior associated with various adaptations to the environment. Feeding habits are essential to the survival and growth of ancient populations. Stable isotope analysis is accepted tool in paleodiet (Schutkowski et al, 1999) and paleoenvironmental (Zernitskaya et al, 2014) studies. However, stable isotopes can be useful not only in investigating human feeding habits but also in describing social and cultural structure of the past populations (Le Huray and Schutkowski, 2005). Only few stable isotope investigations have been performed before in Lithuanian region suggesting a quite uniform diet between males and females and protein intake from freshwater fish and animal protein. Previously, stable isotope analysis has only been used to study a Stone Age population however, more recently studies have been conducted on Iron Age and Late medieval samples (Jacobs et al, 2009). Anyway, there was a need for more precise examination. Stable isotope analysis were performed on human bone collagen and apatite samples in this study. Data represented various ages (from 5-7th cent. to 18th cent.). Stable carbon and nitrogen isotope analysis on medieval populations indicated that individuals in studied sites in Lithuania were almost exclusively consuming C3 plants, C3 fed terrestrial animals, and some freshwater resources. Current investigation demonstrated social differences between elites and country people and is promising in paleodietary and daily life reconstruction. Acknowledgement I thank prof. dr. G. Grupe, Director of the Anthropological and Palaeoanatomical State Collection in Munich for providing the opportunity to work in her laboratory. The part of this work was funded by DAAD. Antanaitis-Jacobs, Indre, et al. "Diet in early Lithuanian prehistory and the new stable isotope evidence." Archaeologia Baltica 12 (2009): 12-30. Le Huray, Jonathan D., and Holger

  10. A Dual-Band Band-Pass Filter with Overlap Step-Impedance and Capacitively Loaded Hairpin Resonators for Wireless LAN Systems

    Directory of Open Access Journals (Sweden)

    P. Chomtong

    2011-01-01

    Full Text Available This paper presents a dual-band band-pass filter using modified cross-coupled step-impedance and capacitively loaded hairpin resonators for WLAN systems. The proposed filter has been designed to operate at a fundamental frequency of 2.4 GHz and the first harmonics frequency of 5.2 GHz. The techniques of step impedance and load capacitor are combined in the design of the proposed filter. In particular, the techniques of modified cross-coupling and overlap resonators are applied to improve the response of insertion losses 21 at the first harmonic frequency of 5.2 GHz. The simulated and experimental results of insertion losses and return losses are better than 3 dB and 20 dB, respectively, at the operating frequencies.

  11. Adeno-Associated Viral Vector-Mediated mTOR Inhibition by Short Hairpin RNA Suppresses Laser-Induced Choroidal Neovascularization

    Directory of Open Access Journals (Sweden)

    Tae Kwann Park

    2017-09-01

    Full Text Available Choroidal neovascularization (CNV is the defining characteristic feature of the wet subtype of age-related macular degeneration (AMD and may result in irreversible blindness. Based on anti-vascular endothelial growth factor (anti-VEGF, the current therapeutic approaches to CNV are fraught with difficulties, and mammalian target of rapamycin (mTOR has recently been proposed as a possible therapeutic target, although few studies have been conducted. Here, we show that a recombinant adeno-associated virus-delivered mTOR-inhibiting short hairpin RNA (rAAV-mTOR shRNA, which blocks the activity of both mTOR complex 1 and 2, represents a promising therapeutic approach for the treatment of CNV. Eight-week-old male C57/B6 mice were treated with the short hairpin RNA (shRNA after generating CNV lesions in the eyes via laser photocoagulation. The recombinant adeno-associated virus (rAAV delivery vehicle was able to effectively transduce cells in the inner retina, and significantly fewer inflammatory cells and less extensive CNV were observed in the animals treated with rAAV-mTOR shRNA when compared with control- and rAAV-scrambled shRNA-treated groups. Presumably related to the reduction of CNV, increased autophagy was detected in CNV lesions treated with rAAV-mTOR shRNA, whereas significantly fewer apoptotic cells detected in the outer nuclear layer around the CNV indicate that mTOR inhibition may also have neuroprotective effects. Taken together, these results demonstrate the therapeutic potential of mTOR inhibition, resulting from rAAV-mTOR shRNA activity, in the treatment of AMD-related CNV. Keywords: retinal neovascularization, choroidal neovascularization, adeno-associated virus, mTOR, RNA interference, mTOR shRNA, autophagy

  12. Shelf-Stable Food Safety

    Science.gov (United States)

    ... is an MRE? Is an MRE shelf stable? What foods are packaged in retort packages? What is aseptic ... type of package is used for aseptic processing? What foods are packaged in aseptic packages? Can I microwave ...

  13. Pharmaceuticals labelled with stable isotopes

    International Nuclear Information System (INIS)

    Krumbiegel, P.

    1986-11-01

    The relatively new field of pharmaceuticals labelled with stable isotopes is reviewed. Scientific, juridical, and ethical questions are discussed concerning the application of these pharmaceuticals in human medicine. 13 C, 15 N, and 2 H are the stable isotopes mainly utilized in metabolic function tests. Methodical contributions are given to the application of 2 H, 13 C, and 15 N pharmaceuticals showing new aspects and different states of development in the field under discussion. (author)

  14. Stable isotope research pool inventory

    International Nuclear Information System (INIS)

    1984-03-01

    This report contains a listing of electromagnetically separated stable isotopes which are available at the Oak Ridge National Laboratory for distribution for nondestructive research use on a loan basis. This inventory includes all samples of stable isotopes in the Research Materials Collection and does not designate whether a sample is out on loan or is in reprocessing. For some of the high abundance naturally occurring isotopes, larger amounts can be made available; for example, Ca-40 and Fe-56

  15. Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

    NARCIS (Netherlands)

    Singh, S.; Folkers, G.E.; Bonvin, A.M.J.J.; Boelens, R.; Wechselberger, R.W.; Niztayev, A.; Kaptein, R.

    2002-01-01

    The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix±hairpin±helix (HhH) motifs

  16. Stable Boundary Layer Education (STABLE) Final Campaign Summary

    Energy Technology Data Exchange (ETDEWEB)

    Turner, David D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-03-01

    The properties of, and the processes that occur in, the nocturnal stable boundary layer are not well understood, making it difficult to represent adequately in numerical models. The nocturnal boundary layer often is characterized by a temperature inversion and, in the Southern Great Plains region, a low-level jet. To advance our understanding of the nocturnal stable boundary layer, high temporal and vertical resolution data on the temperature and wind properties are needed, along with both large-eddy simulation and cloud-resolving modeling.

  17. Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

    Directory of Open Access Journals (Sweden)

    Hervé Seligmann

    2018-02-01

    Full Text Available We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (tRNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5′ UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing.

  18. Detonation of Meta-stable Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Kuhl, Allen; Kuhl, Allen L.; Fried, Laurence E.; Howard, W. Michael; Seizew, Michael R.; Bell, John B.; Beckner, Vincent; Grcar, Joseph F.

    2008-05-31

    We consider the energy accumulation in meta-stable clusters. This energy can be much larger than the typical chemical bond energy (~;;1 ev/atom). For example, polymeric nitrogen can accumulate 4 ev/atom in the N8 (fcc) structure, while helium can accumulate 9 ev/atom in the excited triplet state He2* . They release their energy by cluster fission: N8 -> 4N2 and He2* -> 2He. We study the locus of states in thermodynamic state space for the detonation of such meta-stable clusters. In particular, the equilibrium isentrope, starting at the Chapman-Jouguet state, and expanding down to 1 atmosphere was calculated with the Cheetah code. Large detonation pressures (3 and 16 Mbar), temperatures (12 and 34 kilo-K) and velocities (20 and 43 km/s) are a consequence of the large heats of detonation (6.6 and 50 kilo-cal/g) for nitrogen and helium clusters respectively. If such meta-stable clusters could be synthesized, they offer the potential for large increases in the energy density of materials.

  19. A Study on the Condensation Reaction of 4-Amino-3,5-dimethyl-1,2,4-triazole with Benzaldehydes: Structure and Spectroscopic Properties of Some New Stable Hemiaminals

    Directory of Open Access Journals (Sweden)

    Katarzyna Wajda-Hermanowicz

    2015-09-01

    Full Text Available Studies on the stable hemiaminals and Schiff bases formation in the reaction of substituted benzaldehydes with primary 3,5-dimethyl-1,2,4-triazole 4-amine were carried out under neutral conditions. These products were investigated by IR, Raman, MS, 1H- and 13C-NMR spectra as well as by X-ray crystallography. The effect of reaction conditions: temperature, polarity of the solvents utilized, substrate concentration and the ortho and para benzaldehyde substituents on the yield of products was also examined.

  20. Expression of self-complementary hairpin RNA under the control of the rolC promoter confers systemic disease resistance to plum pox virus without preventing local infection.

    Science.gov (United States)

    Pandolfini, Tiziana; Molesini, Barbara; Avesani, Linda; Spena, Angelo; Polverari, Annalisa

    2003-06-25

    Homology-dependent selective degradation of RNA, or post-transcriptional gene silencing (PTGS), is involved in several biological phenomena, including adaptative defense mechanisms against plant viruses. Small interfering RNAs mediate the selective degradation of target RNA by guiding a multicomponent RNAse. Expression of self-complementary hairpin RNAs within two complementary regions separated by an intron elicits PTGS with high efficiency. Plum pox virus (PPV) is the etiological agent of sharka disease in Drupaceae, although it can also be transmitted to herbaceous species (e.g. Nicotiana benthamiana). Once inside the plant, PPV is transmitted via plasmodesmata from cell to cell, and at longer distances, via phloem. The rolC promoter drives expression in phloem cells. RolC expression is absent in both epidermal and mesophyll cells. The aim of the present study was to confer systemic disease resistance without preventing local viral infection. In the ihprolC-PP197 gene (intron hair pin rolC PPV 197), a 197 bp sequence homologous to the PPV RNA genome (from base 134 to 330) was placed as two inverted repeats separated by the DNA sequence of the rolA intron. This hairpin construct is under the control of the rolC promoter.N. benthamiana plants transgenic for the ihprolC-PP197 gene contain siRNAs homologous to the 197 bp sequence. The transgenic progeny of ihprolC-PP197 plants are resistant to PPV systemic infection. Local infection is unaffected. Most (80%) transgenic plants are virus free and symptomless. Some plants (20%) contain virus in uninoculated apical leaves; however they show only mild symptoms of leaf mottling. PPV systemic resistance cosegregates with the ihprolC-PP197 transgene and was observed in progeny plants of all independent transgenic lines analyzed. SiRNAs of 23-25 nt homologous to the PPV sequence used in the ihprolC-PP197 construct were detected in transgenic plants before and after inoculation. Transitivity of siRNAs was observed in

  1. Expression of self-complementary hairpin RNA under the control of the rolC promoter confers systemic disease resistance to plum pox virus without preventing local infection

    Directory of Open Access Journals (Sweden)

    Spena Angelo

    2003-06-01

    Full Text Available Abstract Background Homology-dependent selective degradation of RNA, or post-transcriptional gene silencing (PTGS, is involved in several biological phenomena, including adaptative defense mechanisms against plant viruses. Small interfering RNAs mediate the selective degradation of target RNA by guiding a multicomponent RNAse. Expression of self-complementary hairpin RNAs within two complementary regions separated by an intron elicits PTGS with high efficiency. Plum pox virus (PPV is the etiological agent of sharka disease in Drupaceae, although it can also be transmitted to herbaceous species (e.g. Nicotiana benthamiana. Once inside the plant, PPV is transmitted via plasmodesmata from cell to cell, and at longer distances, via phloem. The rolC promoter drives expression in phloem cells. RolC expression is absent in both epidermal and mesophyll cells. The aim of the present study was to confer systemic disease resistance without preventing local viral infection. Results In the ihprolC-PP197 gene (intron hair pin rolC PPV 197, a 197 bp sequence homologous to the PPV RNA genome (from base 134 to 330 was placed as two inverted repeats separated by the DNA sequence of the rolA intron. This hairpin construct is under the control of the rolC promoter.N. benthamiana plants transgenic for the ihprolC-PP197 gene contain siRNAs homologous to the 197 bp sequence. The transgenic progeny of ihprolC-PP197 plants are resistant to PPV systemic infection. Local infection is unaffected. Most (80% transgenic plants are virus free and symptomless. Some plants (20% contain virus in uninoculated apical leaves; however they show only mild symptoms of leaf mottling. PPV systemic resistance cosegregates with the ihprolC-PP197 transgene and was observed in progeny plants of all independent transgenic lines analyzed. SiRNAs of 23–25 nt homologous to the PPV sequence used in the ihprolC-PP197 construct were detected in transgenic plants before and after inoculation

  2. Radiation-stable polyolefin compositions

    International Nuclear Information System (INIS)

    Rekers, J.W.

    1986-01-01

    This invention relates to compositions of olefinic polymers suitable for high energy radiation treatment. In particular, the invention relates to olefinic polymer compositions that are stable to sterilizing dosages of high energy radiation such as a gamma radiation. Stabilizers are described that include benzhydrol and benzhydrol derivatives; these stabilizers may be used alone or in combination with secondary antioxidants or synergists

  3. Monitoring of stable glaucoma patients

    NARCIS (Netherlands)

    K.M. Holtzer-Goor (Kim); N.S. Klazinga (Niek); M.A. Koopmanschap (Marc); H.G. Lemij (Hans); T. Plochg; E. van Sprundel (Esther)

    2010-01-01

    textabstractA high workload for ophthalmologists and long waiting lists for patients challenge the organization of ophthalmic care. Tasks that require less specialized skills, like the monitoring of stable (well controlled) glaucoma patients could be substituted from ophthalmologists to other

  4. The N-terminal 45-kDa Domain of Dna2 Endonuclease/Helicase Targets the Enzyme to Secondary Structure DNA*

    Science.gov (United States)

    Lee, Chul-Hwan; Lee, Miju; Kang, Hyo-Jin; Kim, Do-Hyung; Kang, Young-Hoon; Bae, Sung-Ho; Seo, Yeon-Soo

    2013-01-01

    The removal of initiating primers from the 5′-ends of each Okazaki fragment, required for the generation of contiguous daughter strands, can be catalyzed by the combined action of DNA polymerase δ and Fen1. When the flaps generated by displacement of DNA synthesis activity of polymerase δ become long enough to bind replication protein A or form hairpin structures, the helicase/endonuclease enzyme, Dna2, becomes critical because of its ability to remove replication protein A-coated or secondary structure flaps. In this study, we show that the N-terminal 45-kDa domain of Dna2 binds hairpin structures, allowing the enzyme to target secondary structure flap DNA. We found that this activity was essential for the efficient removal of hairpin flaps by the endonuclease activity of Dna2 with the aid of its helicase activity. Thus, the efficient removal of hairpin structure flaps requires the coordinated action of all three functional domains of Dna2. We also found that deletion of the N-terminal 45-kDa domain of Dna2 led to a partial loss of the intra-S-phase checkpoint function and an increased rate of homologous recombination in yeast. We discuss the potential roles of the N-terminal domain of Dna2 in the maintenance of genomic stability. PMID:23344960

  5. High-throughput sequencing as an effective approach in profiling small RNAs derived from a hairpin RNA expression vector in woody plants.

    Science.gov (United States)

    Zhao, Dongyan; Song, Guo-Qing

    2014-11-01

    Hairpin RNA (hpRNA)-mediated gene silencing has proved to be an efficient approach to develop virus-resistant transgenic plants. To characterize small RNA molecules (sRNAs) derived from an hpRNA expression vector in transgenic cherry rootstock plants, we conducted small RNA sequencing of (1) a transgenic rootstock containing an inverted repeat of the partial coat protein of Prunus necrotic ring spot virus (PNRSV-hpRNA); (2) a nontransgenic rootstock; and (3) a PNRSV-infected sweet cherry plant. Analysis of the PNRSV sRNA pools indicated that 24-nt (nucleotide) small interfering RNAs (siRNAs) were the most prevalent sRNAs in the transgenic rootstock whereas the most abundant sRNAs in the PNRSV-infected nontransgenic rootstock were 21-nt siRNAs. In addition, the 24-nt siRNAs of the PNRSV-hpRNA were more abundant on the sense strand than those on the antisense strand in the transgenic rootstock. In contrast, preference in generating PNRSV sRNAs, ranging from 19-nt to 30-nt for sense and antisense strands, was not distinct in the PNRSV-infected nontransgenic sweet cherry. Taken together, this is the first report on profiling hpRNA-derived sRNAs in woody plants using high-throughput sequencing technology, which is an efficient way to verify the presence/absence, the abundance, and the sequence features of certain sRNAs. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  6. Preclinical safety and efficacy of an anti–HIV-1 lentiviral vector containing a short hairpin RNA to CCR5 and the C46 fusion inhibitor

    Directory of Open Access Journals (Sweden)

    Orit Wolstein

    2014-01-01

    Full Text Available Gene transfer has therapeutic potential for treating HIV-1 infection by generating cells that are resistant to the virus. We have engineered a novel self-inactivating lentiviral vector, LVsh5/C46, using two viral-entry inhibitors to block early steps of HIV-1 cycle. The LVsh5/C46 vector encodes a short hairpin RNA (shRNA for downregulation of CCR5, in combination with the HIV-1 fusion inhibitor, C46. We demonstrate here the effective delivery of LVsh5/C46 to human T cell lines, peripheral blood mononuclear cells, primary CD4+ T lymphocytes, and CD34+ hematopoietic stem/progenitor cells (HSPC. CCR5-targeted shRNA (sh5 and C46 peptide were stably expressed in the target cells and were able to effectively protect gene-modified cells against infection with CCR5- and CXCR4-tropic strains of HIV-1. LVsh5/C46 treatment was nontoxic as assessed by cell growth and viability, was noninflammatory, and had no adverse effect on HSPC differentiation. LVsh5/C46 could be produced at a scale sufficient for clinical development and resulted in active viral particles with very low mutagenic potential and the absence of replication-competent lentivirus. Based on these in vitro results, plus additional in vivo safety and efficacy data, LVsh5/C46 is now being tested in a phase 1/2 clinical trial for the treatment of HIV-1 disease.

  7. Blocking the Wnt/β-Catenin Pathway by Lentivirus-Mediated Short Hairpin RNA Targeting β-Catenin Gene Suppresses Silica-Induced Lung Fibrosis in Mice

    Science.gov (United States)

    Wang, Xin; Dai, Wujing; Wang, Yanrang; Gu, Qing; Yang, Deyi; Zhang, Ming

    2015-01-01

    Silicosis is a form of occupational lung disease caused by inhalation of crystalline silica dust. While the pathogenesis of silicosis is not clearly understood, the Wnt/β-catenin signaling pathway is thought to play a major role in lung fibrosis. To explore the role of Wnt/β-catenin pathway in silicosis, we blocked Wnt/β-catenin pathway both in silica-treated MLE-12 cells (a mouse pulmonary epithelial cell line) and in a mouse silicosis model by using a lentiviral vector expressing a short hairpin RNA silencing β-catenin (Lv-shβ-catenin). In vitro, Lv-shβ-catenin significantly decreased the expression of β-catenin, MMP2 and MMP9, and secretion of TGF-β1. In vivo, intratracheal treatment with Lv-shβ-catenin significantly reduced expression of β-catenin in the lung and levels of TGF-β1 in bronchoalveolar lavage fluid, and notably attenuated pulmonary fibrosis as evidenced by hydroxyproline content and collagen I\\III synthesis in silica-administered mice. These results indicate that blockade of the Wnt/β-catenin pathway can prevent the development of silica-induced lung fibrosis. Thus Wnt/β-catenin pathway may be a target in prevention and treatment of silicosis. PMID:26340635

  8. Short hairpin RNA targeting 2B gene of coxsackievirus B3 exhibits potential antiviral effects both in vitro and in vivo

    Directory of Open Access Journals (Sweden)

    Yao Hailan

    2012-08-01

    Full Text Available Abstract Background Coxsackievirus B3 is an important infectious agent of viral myocarditis, pancreatitis and aseptic meningitis, but there are no specific antiviral therapeutic reagents in clinical use. RNA interference-based technology has been developed to prevent the viral infection. Methods To evaluate the impact of RNA interference on viral replication, cytopathogenicity and animal survival, short hairpin RNAs targeting the viral 2B region (shRNA-2B expressed by a recombinant vector (pGCL-2B or a recombinant lentivirus (Lenti-2B were tansfected in HeLa cells or transduced in mice infected with CVB3. Results ShRNA-2B exhibited a significant effect on inhibition of viral production in HeLa cells. Furthermore, shRNA-2B improved mouse survival rate, reduced the viral tissues titers and attenuated tissue damage compared with those of the shRNA-NC treated control group. Lenti-2B displayed more effective role in inhibition of viral replication than pGCL-2B in vivo. Conclusions Coxsackievirus B3 2B is an effective target of gene silencing against coxsackievirus B3 infection, suggesting that shRNA-2B is a potential agent for further development into a treatment for enterviral diseases.

  9. Toward Practical Secure Stable Matching

    Directory of Open Access Journals (Sweden)

    Riazi M. Sadegh

    2017-01-01

    Full Text Available The Stable Matching (SM algorithm has been deployed in many real-world scenarios including the National Residency Matching Program (NRMP and financial applications such as matching of suppliers and consumers in capital markets. Since these applications typically involve highly sensitive information such as the underlying preference lists, their current implementations rely on trusted third parties. This paper introduces the first provably secure and scalable implementation of SM based on Yao’s garbled circuit protocol and Oblivious RAM (ORAM. Our scheme can securely compute a stable match for 8k pairs four orders of magnitude faster than the previously best known method. We achieve this by introducing a compact and efficient sub-linear size circuit. We even further decrease the computation cost by three orders of magnitude by proposing a novel technique to avoid unnecessary iterations in the SM algorithm. We evaluate our implementation for several problem sizes and plan to publish it as open-source.

  10. Towards stable acceleration in LINACS

    CERN Document Server

    Dubrovskiy, A D

    2014-01-01

    Ultra-stable and -reproducible high-energy particle beams with short bunches are needed in novel linear accelerators and, in particular, in the Compact Linear Collider CLIC. A passive beam phase stabilization system based on a bunch compression with a negative transfer matrix element R56 and acceleration at a positive off-crest phase is proposed. The motivation and expected advantages of the proposed scheme are outlined.

  11. Medieval horse stable; the results of multi proxy interdisciplinary research.

    Science.gov (United States)

    Dejmal, Miroslav; Lisá, Lenka; Fišáková Nývltová, Miriam; Bajer, Aleš; Petr, Libor; Kočár, Petr; Kočárová, Romana; Nejman, Ladislav; Rybníček, Michal; Sůvová, Zdenka; Culp, Randy; Vavrčík, Hanuš

    2014-01-01

    A multi proxy approach was applied in the reconstruction of the architecture of Medieval horse stable architecture, the maintenance practices associated with that structure as well as horse alimentation at the beginning of 13th century in Central Europe. Finally, an interpretation of the local vegetation structure along Morava River, Czech Republic is presented. The investigated stable experienced two construction phases. The infill was well preserved and its composition reflects maintenance practices. The uppermost part of the infill was composed of fresh stabling, which accumulated within a few months at the end of summer. Horses from different backgrounds were kept in the stable and this is reflected in the results of isotope analyses. Horses were fed meadow grasses as well as woody vegetation, millet, oat, and less commonly hemp, wheat and rye. Three possible explanations of stable usage are suggested. The stable was probably used on a temporary basis for horses of workers employed at the castle, courier horses and horses used in battle.

  12. Medieval Horse Stable; The Results of Multi Proxy Interdisciplinary Research

    Science.gov (United States)

    Dejmal, Miroslav; Lisá, Lenka; Fišáková Nývltová, Miriam; Bajer, Aleš; Petr, Libor; Kočár, Petr; Kočárová, Romana; Nejman, Ladislav; Rybníček, Michal; Sůvová, Zdenka; Culp, Randy; Vavrčík, Hanuš

    2014-01-01

    A multi proxy approach was applied in the reconstruction of the architecture of Medieval horse stable architecture, the maintenance practices associated with that structure as well as horse alimentation at the beginning of 13th century in Central Europe. Finally, an interpretation of the local vegetation structure along Morava River, Czech Republic is presented. The investigated stable experienced two construction phases. The infill was well preserved and its composition reflects maintenance practices. The uppermost part of the infill was composed of fresh stabling, which accumulated within a few months at the end of summer. Horses from different backgrounds were kept in the stable and this is reflected in the results of isotope analyses. Horses were fed meadow grasses as well as woody vegetation, millet, oat, and less commonly hemp, wheat and rye. Three possible explanations of stable usage are suggested. The stable was probably used on a temporary basis for horses of workers employed at the castle, courier horses and horses used in battle. PMID:24670874

  13. Medieval horse stable; the results of multi proxy interdisciplinary research.

    Directory of Open Access Journals (Sweden)

    Miroslav Dejmal

    Full Text Available A multi proxy approach was applied in the reconstruction of the architecture of Medieval horse stable architecture, the maintenance practices associated with that structure as well as horse alimentation at the beginning of 13th century in Central Europe. Finally, an interpretation of the local vegetation structure along Morava River, Czech Republic is presented. The investigated stable experienced two construction phases. The infill was well preserved and its composition reflects maintenance practices. The uppermost part of the infill was composed of fresh stabling, which accumulated within a few months at the end of summer. Horses from different backgrounds were kept in the stable and this is reflected in the results of isotope analyses. Horses were fed meadow grasses as well as woody vegetation, millet, oat, and less commonly hemp, wheat and rye. Three possible explanations of stable usage are suggested. The stable was probably used on a temporary basis for horses of workers employed at the castle, courier horses and horses used in battle.

  14. Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-Spin Coupling Constants: An Experimental and Quantum Chemical Investigation

    Czech Academy of Sciences Publication Activity Database

    Sychrovský, Vladimír; Vacek, Jaroslav; Hobza, Pavel; Žídek, L.; Sklenář, V.; Cremer, D.

    2002-01-01

    Roč. 106, - (2002), s. 10242-10250 ISSN 1089-5639 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : DNA * help of NMR spin-spin coupling constants * quantum chemical investigation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.765, year: 2002

  15. Crystal structure of ATVORF273, a new fold for a thermo- and acido-stable protein from the Acidianus two-tailed virus

    DEFF Research Database (Denmark)

    Felisberto-Rodrigues, Catarina; Blangy, Stéphanie; Goulet, Adeline

    2012-01-01

    in the viral world. To understand this intriguing phenomenon, we have undertaken structural studies of ATV virion proteins and here we present the crystal structure of one of these proteins, ATV[Formula: see text]. ATV[Formula: see text] forms tetramers in solution and a molecular envelope is provided...... for the tetramer, computed from small-angle X-ray scattering (SAXS) data. The crystal structure has properties typical of hyperthermostable proteins, including a relatively high number of salt bridges. However, the protein also exhibits flexible loops and surface pockets. Remarkably, ATV[Formula: see text......] displays a new [Formula: see text] protein fold, consistent with the absence of homologues of this protein in public sequence databases....

  16. Application of stable isotope to breath test

    International Nuclear Information System (INIS)

    Sasaki, Yasuto

    1988-01-01

    Needles to say, radioisotopes have good characteristics as a tracer for examining biological functions. In fact, scyntigraphy is widely used over Japan. It is true, however, that there are some difficulties in applying radioisotopes to humans. Thus, greater attention began to be attracted to stable isotopes in the late 1960s, because these substances can be used for infants and pregnant women. They can be stored for a long period of time since they do not suffer damping as in the case of radioisotopes. In addition to serving as a tracer, stable isotopes can provide structural-chemical information including the position of isotope labels, and the mass and atomic composition of fragment ions. Such techniques as NMR spectroscopy is employed for this purpose. The method is currently used to perform examinations of congenital metabolic disorders. The carbon isotopes of 13 C and 14 C are used for breath test. Compounds labeled with these isotopes are administered and their ratio to the total CO 2 in breath is measured to diagnose diseases. In the early 1970s, 13 C has come into use for breath test. Similar breath test is applied to diagnosis of the bacterial overgrowth syndrome and ileal dysfunction syndrome. (Nogami, K.)

  17. Stable states in a strong IR field

    Science.gov (United States)

    Zhong, Changchun; Robicheaux, Francis

    2015-05-01

    It is found that 10% of atoms stay in the quasi-stable states after being exposed to intense laser or microwave (MW) pulses, even though the pulses' intensity is much stronger than that needed for static fields ionization. The reason why atoms survive those strong pulses has attracted growing attentions. A. Arakelyan et al. have observed the optical spectra of the surviving Lithium atoms after interaction with intense 38-GHz MW fields for more than 1000 cycles, and the spectra exhibit a periodic train of peaks 38 GHz apart. It suggests that those weakly bound Rydberg electrons seldom go back to the ionic core, where the cycle average energy exchange happens. In this study, we are interested in the electron behavior in the presence of intense infrared fields with a much shorter wavelength (1000 nm). By solving the full 3D time dependent Schrodinger equation, we calculate the spectra of the surviving atoms under intense IR fields. Our numerical calculations show atoms survive the intense field in quasi-stable states for a long time, and the optical spectra are obviously modulated by the IR frequency. Through tuning the ponderomotive energy, we see how field parameters affect the behavior of electrons. Different atoms, such as Hydrogen, Helium, Lithium, and Sodium, are tested to see how atom's energy structures influence the results.

  18. Organic synthesis with stable isotopes

    International Nuclear Information System (INIS)

    Daub, G.H.; Kerr, V.N.; Williams, D.L.; Whaley, T.W.

    1978-01-01

    Some general considerations concerning organic synthesis with stable isotopes are presented. Illustrative examples are described and discussed. The examples include DL-2-amino-3-methyl- 13 C-butanoic-3,4- 13 C 2 acid (DL-valine- 13 C 3 ); methyl oleate-1- 13 C; thymine-2,6- 13 C 2 ; 2-aminoethanesulfonic- 13 C acid (taurine- 13 C); D-glucose-6- 13 C; DL-2-amino-3-methylpentanoic-3,4- 13 C 2 acid (DL-isoleucine- 13 C 2 ); benzidine- 15 N 2 ; and 4-ethylsulfonyl-1-naphthalene-sulfonamide- 15 N

  19. Stable agents for imaging investigations

    International Nuclear Information System (INIS)

    Tofe, A.J.

    1976-01-01

    This invention concerns highly stable compounds useful in preparing technetium 99m based scintiscanning exploration agents. The compounds of this invention include a pertechnetate reducing agent or a solution of oxidized pertechnetate and an efficient proportion, sufficient to stabilize the compounds in the presence of oxygen and of radiolysis products, of ascorbic acid or a pharmaceutically acceptable salt or ester of this acid. The invention also concerns a perfected process for preparing a technetium based exploration agent, consisting in codissolving the ascorbic acid or a pharmaceutically acceptable salt or ester of such an acid and a pertechnetate reducing agent in a solution of oxidized pertechnetate [fr

  20. Expression Analysis of Hairpin RNA Carrying Sugarcane mosaic virus (SCMV Derived Sequences and Transgenic Resistance Development in a Model Rice Plant

    Directory of Open Access Journals (Sweden)

    Sehrish Akbar

    2017-01-01

    Full Text Available Developing transgenic resistance in monocotyledonous crops against pathogens remains a challenging area of research. Sugarcane mosaic virus (SCMV is a serious pathogen of many monocotyledonous crops including sugarcane. The objective of present study was to analyze transgenic expression of hairpin RNA (hpRNA, targeting simultaneously CP (Coat Protein and Hc-Pro (helper component-proteinase genes of SCMV, in a model rice plant. Conserved nucleotide sequences, exclusive for DAG (Aspartic acid-Alanine-Glycine and KITC (Lycine-Isoleucine-Threonine-Cysteine motifs, derived from SCMV CP and Hc-Pro genes, respectively, were fused together and assembled into the hpRNA cassette under maize ubiquitin promoter to form Ubi-hpCP:Hc-Pro construct. The same CP:Hc-Pro sequence was fused with the β-glucuronidase gene (GUS at the 3′ end under CaMV 35S promoter to develop 35S-GUS:CP:Hc-Pro served as a target reporter gene construct. When delivered into rice callus tissues by particle bombardment, the Ubi-hpCP:Hc-Pro construct induced strong silencing of 35S-GUS:CP:Hc-Pro. Transgenic rice plants, containing Ubi-hpCP:Hc-Pro construct, expressed high level of 21–24 nt small interfering RNAs, which induced specific suppression against GUS:CP:Hc-Pro delivered by particle bombardment and conferred strong resistance to mechanically inoculated SCMV. It is concluded that fusion hpRNA approach is an affordable method for developing resistance against SCMV in model rice plant and it could confer SCMV resistance when transformed into sugarcane.

  1. Effective relief of neuropathic pain by adeno-associated virus-mediated expression of a small hairpin RNA against GTP cyclohydrolase 1

    Directory of Open Access Journals (Sweden)

    Chang Jin

    2009-11-01

    Full Text Available Abstract Background Recent studies show that transcriptional activation of GTP cyclohydrolase I (GCH1 in dorsal root ganglia (DRG is significantly involved in the development and persistency of pain symptoms. We thus hypothesize that neuropathic pain may be attenuated by down-regulation of GCH1 expression, and propose a gene silencing system for this purpose. Results To interrupt GCH1 synthesis, we designed a bidirectional recombinant adeno-associated virus encoding both a small hairpin RNA against GCH1 and a GFP reporter gene (rAAV-shGCH1. After rAAV-shGCH1 was introduced into the sciatic nerve prior to or following pain-inducing surgery, therapeutic efficacy and the underlying mechanisms were subsequently validated in animal models. The GFP expression data indicates that rAAV effectively delivered transgenes to DRG. Subsequently reduced GCH1 expression was evident from immunohistochemistry and western-blotting analysis. Along with the down-regulation of GCH1, the von Frey test correspondingly indicated a sharp decline in pain symptoms upon both pre- and post-treatment with rAAV-shGCH1. Interestingly, GCH1 down-regulation additionally led to decreased microglial activation in the dorsal horn, implying an association between pain attenuation and reduced inflammation. Conclusion Therefore, the data suggests that GCH1 levels can be reduced by introducing rAAV-shGCH1, leading to pain relief. Based on the results, we propose that GCH1 modulation may be developed as a clinically applicable gene therapy strategy to treat neuropathic pain.

  2. Stable cosmology in chameleon bigravity

    Science.gov (United States)

    De Felice, Antonio; Mukohyama, Shinji; Oliosi, Michele; Watanabe, Yota

    2018-02-01

    The recently proposed chameleonic extension of bigravity theory, by including a scalar field dependence in the graviton potential, avoids several fine-tunings found to be necessary in usual massive bigravity. In particular it ensures that the Higuchi bound is satisfied at all scales, that no Vainshtein mechanism is needed to satisfy Solar System experiments, and that the strong coupling scale is always above the scale of cosmological interest all the way up to the early Universe. This paper extends the previous work by presenting a stable example of cosmology in the chameleon bigravity model. We find a set of initial conditions and parameters such that the derived stability conditions on general flat Friedmann background are satisfied at all times. The evolution goes through radiation-dominated, matter-dominated, and de Sitter eras. We argue that the parameter space allowing for such a stable evolution may be large enough to encompass an observationally viable evolution. We also argue that our model satisfies all known constraints due to gravitational wave observations so far and thus can be considered as a unique testing ground of gravitational wave phenomenologies in bimetric theories of gravity.

  3. The secondary structure of the 5′ end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem–loop

    Science.gov (United States)

    Kenyon, Julia C.; Ghazawi, Akela; Cheung, Winsome K.S.; Phillip, Pretty S.; Rizvi, Tahir A.; Lever, Andrew M.L.

    2008-01-01

    Feline immunodeficiency virus (FIV) is a lentivirus that infects cats and is related to human immunodeficiency virus (HIV). Although it is a common worldwide infection, and has potential uses as a human gene therapy vector and as a nonprimate model for HIV infection, little detail is known of the viral life cycle. Previous experiments have shown that its packaging signal includes two or more regions within the first 511 nucleotides of the genomic RNA. We have undertaken a secondary structural analysis of this RNA by minimal free-energy structural prediction, biochemical mapping, and phylogenetic analysis, and show that it contains five conserved stem–loops and a conserved long-range interaction between heptanucleotide sequences 5′-CCCUGUC-3′ in R/U5 and 5′-GACAGGG-3′ in gag. This long-range interaction is similar to that seen in primate lentiviruses where it is thought to be functionally important. Along with strains that infect domestic cats, this heptanucleotide interaction can also occur in species-specific FIV strains that infect pumas, lions, and Pallas' cats where the heptanucleotide sequences involved vary. We have analyzed spliced and genomic FIV RNAs and see little structural change or sequence conservation within single-stranded regions of the 5′ UTR that are important for viral packaging, suggesting that FIV may employ a cotranslational packaging mechanism. PMID:18974279

  4. Efficient and facile synthesis of novel stable monodeuterium labeled ractopamine.

    Science.gov (United States)

    Su, Feifei; Wu, Fulong; Tang, He; Wang, Zhonghua; Wu, Fanhong

    2015-01-01

    A novel synthetic route to stable deuterium labeled ractopamine was disclosed with 6.49% total yield and 97.7% isotopic abundance. Its structure and the isotope-abundance were confirmed according to (1)H-NMR and high-resolution mass spectrometry. Copyright © 2015 John Wiley & Sons, Ltd.

  5. Stable isotope mass spectrometry in petroleum exploration

    International Nuclear Information System (INIS)

    Mathur, Manju

    1997-01-01

    The stable isotope mass spectrometry plays an important role to evaluate the stable isotopic composition of hydrocarbons. The isotopic ratios of certain elements in petroleum samples reflect certain characteristics which are useful for petroleum exploration

  6. Stable rotating dipole solitons in nonlocal media

    DEFF Research Database (Denmark)

    Lopez-Aguayo, Servando; Skupin, Stefan; Desyatnikov, Anton S.

    2006-01-01

    We present the first example of stable rotating two-soliton bound states in nonlinear optical media with nonlocal response. We show that, in contrast to media with local response, nonlocality opens possibilities to generate stable azimuthons.......We present the first example of stable rotating two-soliton bound states in nonlinear optical media with nonlocal response. We show that, in contrast to media with local response, nonlocality opens possibilities to generate stable azimuthons....

  7. Stable double helical iodine chains inside single-walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Zhen [College of Science, Liaoning University of Technology, Jinzhou, Liaoning, 121001 (China); Liu, Chun-Jian [College of Mathematics and Physics, Bohai University, Jinzhou, Liaoning, 121000 (China); Lv, Hang [Institute of New Energy, Bohai University, Jinzhou, Liaoning, 121000 (China); Liu, Bing-Bing, E-mail: liubb@jlu.edu.cn [State Key Laboratory of Superhard Materials, Jilin University, Changchun, 130012 (China)

    2016-08-12

    The helicity of stable double helical iodine chains inside single-walled carbon nanotubes (SWCNTs) is studied by calculating the systematic interaction energy. Our results present clear images of stable double helical structures inside SWCNTs. The optimum helical radius and helical angle increase and decrease with increasing diameter, respectively. The tube's diameter plays a leading role in the helicity of encapsulated structures, while the tube's chirality may induce different metastable structures. This study indicates that the observed double helical iodine chains in experiments are not necessarily the optimum structures, but may also be metastable structures. - Highlights: • The stable double helical iodine chain inside single-walled carbon nanotubes is proposed. • The influence of tube's diameter and chirality on the stability of encapsulated iodine chains is studied. • The metastable double helical structures may be co-existence with the stable structure but not in the same tubes.

  8. Phosphorus K4 Crystal: A New Stable Allotrope

    OpenAIRE

    Jie Liu; Shunhong Zhang; Yaguang Guo; Qian Wang

    2016-01-01

    The intriguing properties of phosphorene motivate scientists to further explore the structures and properties of phosphorus materials. Here, we report a new allotrope named K 4 phosphorus composed of three-coordinated phosphorus atoms in non-layered structure which is not only dynamically and mechanically stable, but also possesses thermal stability comparable to that of the orthorhombic black phosphorus (A17). Due to its unique configuration, K 4 phosphorus exhibits exceptional properties: i...

  9. Uses of stable isotopes in fish ecology

    Science.gov (United States)

    Analyses of fish tissues (other than otoliths) for stable isotope ratios can provide substantial information on fish ecology, including physiological ecology. Stable isotopes of nitrogen and carbon frequently are used to determine the mix of diet sources for consumers. Stable i...

  10. Preventing structural degradation from Na3V2(PO4)3 to V2(PO4)3: F-doped Na3V2(PO4)3/C cathode composite with stable lifetime for sodium ion batteries

    Science.gov (United States)

    Chen, Yanjun; Xu, Youlong; Sun, Xiaofei; Zhang, Baofeng; He, Shengnan; Li, Long; Wang, Chao

    2018-02-01

    A prospective NASICON-type F-doped Na3V2(PO4)2.93F0.07/C (F-0.07-NVP/C) composite is synthesized by a solid-state reaction method. F-doping can restrain the structural degradation from Na3V2(PO4)3 to V2(PO4)3 and enhance the structural stability. Meanwhile, it can decrease the particle size to diminish the pathway of Na+ diffusion, which can increase ionic conductivity efficiently. The kinetic behavior is significantly improved and it is beneficial to reinforcing the electrochemical performance of F-doping composites. Compared with Undoped-NVP/C sample, F-0.07-NVP/C composite delivers a 113 mAh g-1 discharge capacity at 10 mA g-1, which is very close to the theoretical capacity (117 mAh g-1). As for cycle performance, a reversible capacity of 97.8 mAh g-1 can be obtained and it retains 86% capacity after 1000 cycles at 200 mA g-1. F-0.07-NVP/C composite presents the highest DNa+ (2.62 × 10-15 cm2s-1), two orders of magnitude higher than the undoped sample (4.8 × 10-17 cm2s-1). This outstanding electrochemical performance is ascribed to the synergetic effect from improved kinetic behavior and enhanced structural stability due to F-doping. Hence, the F-doped composite would be a promising cathode material in SIB for energy storage and conversion.

  11. Theory of stable allocations II

    Directory of Open Access Journals (Sweden)

    Pantelić Svetlana

    2015-01-01

    Full Text Available The Swedish Royal Academy awarded the 2012 Nobel Prize in Economics to Lloyd Shapley and Alvin Roth, for the theory of stable allocations and the practice of market design. These two American researchers worked independently from each other, combining basic theory and empirical investigations. Through their experiments and practical design they generated a flourishing field of research and improved the performance of many markets. Shapley provided the fundamental theoretical contribution to this field of research, whereas Roth, a professor at the Harvard University in Boston, developed and upgraded these theoretical investigations by applying them to the American market of medical doctors. Namely, their research helps explain the market processes at work, for instance, when doctors are assigned to hospitals, students to schools and human organs for transplant to recipients.

  12. Stable massive particles at colliders

    Energy Technology Data Exchange (ETDEWEB)

    Fairbairn, M.; /Stockholm U.; Kraan, A.C.; /Pennsylvania U.; Milstead, D.A.; /Stockholm U.; Sjostrand, T.; /Lund U.; Skands, P.; /Fermilab; Sloan, T.; /Lancaster U.

    2006-11-01

    We review the theoretical motivations and experimental status of searches for stable massive particles (SMPs) which could be sufficiently long-lived as to be directly detected at collider experiments. The discovery of such particles would address a number of important questions in modern physics including the origin and composition of dark matter in the universe and the unification of the fundamental forces. This review describes the techniques used in SMP-searches at collider experiments and the limits so far obtained on the production of SMPs which possess various colour, electric and magnetic charge quantum numbers. We also describe theoretical scenarios which predict SMPs, the phenomenology needed to model their production at colliders and interactions with matter. In addition, the interplay between collider searches and open questions in cosmology such as dark matter composition are addressed.

  13. Defining fish community structure in Lake Winnipeg using stable isotopes (δ(13)C, δ(15)N, δ(34)S): implications for monitoring ecological responses and trophodynamics of mercury & other trace elements.

    Science.gov (United States)

    Ofukany, Amy F A; Wassenaar, Leonard I; Bond, Alexander L; Hobson, Keith A

    2014-11-01

    The ecological integrity of freshwater lakes is influenced by atmospheric and riverine deposition of contaminants, shoreline development, eutrophication, and the introduction of non-native species. Changes to the trophic structure of Lake Winnipeg, Canada, and consequently, the concentrations of contaminants and trace elements measured in tissues of native fishes, are likely attributed to agricultural runoff from the 977,800 km(2) watershed and the arrival of non-native zooplankters and fishes. We measured δ(13)C, δ(15)N, and δ(34)S along with concentrations of 15 trace elements in 17 native fishes from the north and south basins of Lake Winnipeg in 2009 and 2010. After adjusting for differences in isotopic baseline values between the two basins, fishes in the south basin had consistently higher δ(13)C and δ(34)S, and lower δ(15)N. We found little evidence of biomagnification of trace elements at the community level, but walleye (Sander vitreus) and freshwater drum (Aplodinotus grunniens) had higher mercury and selenium concentrations with increased trophic position, coincident with increased piscivory. There was evidence of growth dilution of cobalt, copper, manganese, molybdenum, thallium, and vanadium, and bioaccumulation of mercury, which could be explained by increases in algal (and consequently, lake and fish) productivity. We conclude that the north and south basins of Lake Winnipeg represent very different communities with different trophic structures and trace element concentrations. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage.

    Directory of Open Access Journals (Sweden)

    Hisae Tateishi-Karimata

    Full Text Available The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG. Transcriptional arrest was induced when the stability of the G-quadruplex structure (-ΔG°37 in the presence of 20 wt% PEG was more than 8.2 kcal mol(-1. Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs.

  15. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  16. Stable three-dimensional metallic carbon with interlocking hexagons.

    Science.gov (United States)

    Zhang, Shunhong; Wang, Qian; Chen, Xiaoshuang; Jena, Puru

    2013-11-19

    Design and synthesis of 3D metallic carbon that is stable under ambient conditions has been a long-standing dream. We predict the existence of such phases, T6- and T14-carbon, consisting of interlocking hexagons. Their dynamic, mechanical, and thermal stabilities are confirmed by carrying out a variety of state-of-the-art theoretical calculations. Unlike the previously studied K4 and the simple cubic high pressure metallic phases, the structures predicted in this work are stable under ambient conditions. Equally important, they may be synthesized chemically by using benzene or polyacenes molecules.

  17. Applications of C and N stable isotopes to ecological and environmental studies in seagrass ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Lepoint, Gilles [Centre MARE, Laboratoire d' Oceanologie, Institut de Chimie, B6, Universite de Liege, B-4000 Liege (Belgium)]. E-mail: g.lepoint@ulg.ac.be; Dauby, Patrick [Centre MARE, Laboratoire d' Oceanologie, Institut de Chimie, B6, Universite de Liege, B-4000 Liege (Belgium); Institut Royal des Sciences Naturelles de Belgique, rue Vautier, B1000 Brussels (Belgium); Gobert, Sylvie [Centre MARE, Laboratoire d' Oceanologie, Institut de Chimie, B6, Universite de Liege, B-4000 Liege (Belgium)

    2004-12-01

    Stable isotopes of carbon and nitrogen are increasingly used in marine ecosystems, for ecological and environmental studies. Here, we examine some applications of stable isotopes as ecological integrators or tracers in seagrass ecosystem studies. We focus on both the use of natural isotope abundance as food web integrators or environmental tracers and on the use of stable isotopes as experimental tools. As ecosystem integrators, stable isotopes have helped to elucidate the general structure of trophic webs in temperate, Mediterranean and tropical seagrass ecosystems. As environmental tracers, stable isotopes have proven their utility in sewage impact measuring and mapping. However, to make such environmental studies more comprehensible, future works on understanding of basic reasons for variations of N and C stable isotopes in seagrasses should be encouraged. At least, as experimental tracers, stable isotopes allow the study of many aspects of N and C cycles at the scale of a plant or at the scale of the seagrass ecosystem.

  18. STABLE ISOTOPE GEOCHEMISTRY OF MASSIVE ICE

    Directory of Open Access Journals (Sweden)

    Yurij K. Vasil’chuk

    2016-01-01

    Full Text Available The paper summarises stable-isotope research on massive ice in the Russian and North American Arctic, and includes the latest understanding of massive-ice formation. A new classification of massive-ice complexes is proposed, encompassing the range and variabilityof massive ice. It distinguishes two new categories of massive-ice complexes: homogeneousmassive-ice complexes have a similar structure, properties and genesis throughout, whereasheterogeneous massive-ice complexes vary spatially (in their structure and properties andgenetically within a locality and consist of two or more homogeneous massive-ice bodies.Analysis of pollen and spores in massive ice from Subarctic regions and from ice and snow cover of Arctic ice caps assists with interpretation of the origin of massive ice. Radiocarbon ages of massive ice and host sediments are considered together with isotope values of heavy oxygen and deuterium from massive ice plotted at a uniform scale in order to assist interpretation and correlation of the ice.

  19. Ranking stability and super-stable nodes in complex networks.

    Science.gov (United States)

    Ghoshal, Gourab; Barabási, Albert-László

    2011-07-19

    Pagerank, a network-based diffusion algorithm, has emerged as the leading method to rank web content, ecological species and even scientists. Despite its wide use, it remains unknown how the structure of the network on which it operates affects its performance. Here we show that for random networks the ranking provided by pagerank is sensitive to perturbations in the network topology, making it unreliable for incomplete or noisy systems. In contrast, in scale-free networks we predict analytically the emergence of super-stable nodes whose ranking is exceptionally stable to perturbations. We calculate the dependence of the number of super-stable nodes on network characteristics and demonstrate their presence in real networks, in agreement with the analytical predictions. These results not only deepen our understanding of the interplay between network topology and dynamical processes but also have implications in all areas where ranking has a role, from science to marketing.

  20. Stable Treemaps via Local Moves.

    Science.gov (United States)

    Sondag, Max; Speckmann, Bettina; Verbeek, Kevin

    2018-01-01

    Treemaps are a popular tool to visualize hierarchical data: items are represented by nested rectangles and the area of each rectangle corresponds to the data being visualized for this item. The visual quality of a treemap is commonly measured via the aspect ratio of the rectangles. If the data changes, then a second important quality criterion is the stability of the treemap: how much does the treemap change as the data changes. We present a novel stable treemapping algorithm that has very high visual quality. Whereas existing treemapping algorithms generally recompute the treemap every time the input changes, our algorithm changes the layout of the treemap using only local modifications. This approach not only gives us direct control over stability, but it also allows us to use a larger set of possible layouts, thus provably resulting in treemaps of higher visual quality compared to existing algorithms. We further prove that we can reach all possible treemap layouts using only our local modifications. Furthermore, we introduce a new measure for stability that better captures the relative positions of rectangles. We finally show via experiments on real-world data that our algorithm outperforms existing treemapping algorithms also in practice on either visual quality and/or stability. Our algorithm scores high on stability regardless of whether we use an existing stability measure or our new measure.

  1. A crawling robot driven by multi-stable origami

    Science.gov (United States)

    Pagano, Alexander; Yan, Tongxi; Chien, Brian; Wissa, A.; Tawfick, S.

    2017-09-01

    Using origami folding to construct and actuate mechanisms and machines offers attractive opportunities from small, scalable, and cheap robots to deployable adaptive structures. This paper presents the design of a bio-inspired origami crawling robot constructed by folding sheets of paper. The origami building block structure is based on the Kresling crease pattern (CP), a chiral tower with a polygonal base, which expands and contracts through coupled longitudinal and rotational motion similar to a screw. We design the origami to have multi-stable structural equilibria which can be tuned by changing the folding CP. Kinematic analysis of these structures based on rigid-plates and hinges at fold lines precludes the shape transformation associated with the bistability of the physical models. To capture the kinematics of the bi-stable origami, the panels’ deformation behavior is modeled utilizing principles of virtual folds. Virtual folds approximate material bending by hinged, rigid panels, which facilitates the development of a kinematic solution via rigid-plate rotation analysis. As such, the kinetics and stability of folded structures are investigated by assigning suitable torsional spring constants to the fold lines. The results presented demonstrate the effect of fold-pattern geometries on the snapping behavior of the bi-stable origami structure based on the Kresling pattern. The crawling robot is presented as a case study for the use of this origami structure to mimic crawling locomotion. The robot is comprised of two origami towers nested inside a paper bellow, and connected by 3D printed end plates. DC motors are used to actuate the expansion and contraction of the internal origami structures to achieve forward locomotion and steering. Beyond locomotion, this simple design can find applications in manipulators, booms, and active structures.

  2. Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel β sheet fusion peptide structure in the final six-helix bundle state.

    Science.gov (United States)

    Sackett, Kelly; Nethercott, Matthew J; Zheng, Zhaoxiong; Weliky, David P

    2014-03-06

    The HIV gp41 protein catalyzes fusion between viral and target cell membranes. Although the ~20-residue N-terminal fusion peptide (FP) region is critical for fusion, the structure of this region is not well characterized in large gp41 constructs that model the gp41 state at different times during fusion. This paper describes solid-state NMR (SSNMR) studies of FP structure in a membrane-associated construct (FP-Hairpin), which likely models the final fusion state thought to be thermostable trimers with six-helix bundle structure in the region C-terminal of the FP. The SSNMR data show that there are populations of FP-Hairpin with either α helical or β sheet FP conformation. For the β sheet population, measurements of intermolecular (13)C-(13)C proximities in the FP are consistent with a significant fraction of intermolecular antiparallel β sheet FP structure with adjacent strand crossing near L7 and F8. There appears to be negligible in-register parallel structure. These findings support assembly of membrane-associated gp41 trimers through interleaving of N-terminal FPs from different trimers. Similar SSNMR data are obtained for FP-Hairpin and a construct containing the 70 N-terminal residues of gp41 (N70), which is a model for part of the putative pre-hairpin intermediate state of gp41. FP assembly may therefore occur at an early fusion stage. On a more fundamental level, similar SSNMR data are obtained for FP-Hairpin and a construct containing the 34 N-terminal gp41 residues (FP34) and support the hypothesis that the FP is an autonomous folding domain. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Advanced thermally stable jet fuels

    Energy Technology Data Exchange (ETDEWEB)

    Schobert, H.H.

    1999-01-31

    The Pennsylvania State University program in advanced thermally stable coal-based jet fuels has five broad objectives: (1) Development of mechanisms of degradation and solids formation; (2) Quantitative measurement of growth of sub-micrometer and micrometer-sized particles suspended in fuels during thermal stressing; (3) Characterization of carbonaceous deposits by various instrumental and microscopic methods; (4) Elucidation of the role of additives in retarding the formation of carbonaceous solids; (5) Assessment of the potential of production of high yields of cycloalkanes by direct liquefaction of coal. Future high-Mach aircraft will place severe thermal demands on jet fuels, requiring the development of novel, hybrid fuel mixtures capable of withstanding temperatures in the range of 400--500 C. In the new aircraft, jet fuel will serve as both an energy source and a heat sink for cooling the airframe, engine, and system components. The ultimate development of such advanced fuels requires a thorough understanding of the thermal decomposition behavior of jet fuels under supercritical conditions. Considering that jet fuels consist of hundreds of compounds, this task must begin with a study of the thermal degradation behavior of select model compounds under supercritical conditions. The research performed by The Pennsylvania State University was focused on five major tasks that reflect the objectives stated above: Task 1: Investigation of the Quantitative Degradation of Fuels; Task 2: Investigation of Incipient Deposition; Task 3: Characterization of Solid Gums, Sediments, and Carbonaceous Deposits; Task 4: Coal-Based Fuel Stabilization Studies; and Task 5: Exploratory Studies on the Direct Conversion of Coal to High Quality Jet Fuels. The major findings of each of these tasks are presented in this executive summary. A description of the sub-tasks performed under each of these tasks and the findings of those studies are provided in the remainder of this volume

  4. Population Games, Stable Games, and Passivity

    Directory of Open Access Journals (Sweden)

    Michael J. Fox

    2013-10-01

    Full Text Available The class of “stable games”, introduced by Hofbauer and Sandholm in 2009, has the attractive property of admitting global convergence to equilibria under many evolutionary dynamics. We show that stable games can be identified as a special case of the feedback-system-theoretic notion of a “passive” dynamical system. Motivated by this observation, we develop a notion of passivity for evolutionary dynamics that complements the definition of the class of stable games. Since interconnections of passive dynamical systems exhibit stable behavior, we can make conclusions about passive evolutionary dynamics coupled with stable games. We show how established evolutionary dynamics qualify as passive dynamical systems. Moreover, we exploit the flexibility of the definition of passive dynamical systems to analyze generalizations of stable games and evolutionary dynamics that include forecasting heuristics as well as certain games with memory.

  5. Miniature Microwave Bandpass Filter Based on EBG Structures

    DEFF Research Database (Denmark)

    Zhurbenko, Vitaliy; Krozer, Viktor; Meincke, Peter

    2006-01-01

    as compared to stepped-impedance hairpin (SIH) resonators with similar response. The new bandpass filter has a reduced footprint and can be fabricated in standard thick-film manufacturing technology. Measured and simulated results exhibit good agreement. The measured results show improvement in the filter......A new design of a planar microwave filter, based on rejection band properties of an electrically small electromagnetic bandgap (EBG) structure, is proposed. The proposed EBG structure demonstrates effective impedance manipulation, exhibits a simple analysis, and is about three times smaller...... characteristics in comparison to existing SIH filter design....

  6. Canonical, stable, general mapping using context schemes.

    Science.gov (United States)

    Novak, Adam M; Rosen, Yohei; Haussler, David; Paten, Benedict

    2015-11-15

    Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. We introduce context schemes: a method that allows the unambiguous recognition of a reference base in a query sequence by testing the query for substrings from an algorithmically defined set. Context schemes only map when there is a unique best mapping, and define this criterion uniformly for all reference bases. Mappings under context schemes can also be made stable, so that extension of the query string (e.g. by increasing read length) will not alter the mapping of previously mapped positions. Context schemes are general in several senses. They natively support the detection of arbitrary complex, novel rearrangements relative to the reference. They can scale over orders of magnitude in query sequence length. Finally, they are trivially extensible to more complex reference structures, such as graphs, that incorporate additional variation. We demonstrate empirically the existence of high-performance context schemes, and present efficient context scheme mapping algorithms. The software test framework created for this study is available from https://registry.hub.docker.com/u/adamnovak/sequence-graphs/. anovak@soe.ucsc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Chemically Stable Lipids for Membrane Protein Crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Ishchenko, Andrii; Peng, Lingling; Zinovev, Egor; Vlasov, Alexey; Lee, Sung Chang; Kuklin, Alexander; Mishin, Alexey; Borshchevskiy, Valentin; Zhang, Qinghai; Cherezov, Vadim (MIPT); (USC); (Scripps)

    2017-05-01

    The lipidic cubic phase (LCP) has been widely recognized as a promising membrane-mimicking matrix for biophysical studies of membrane proteins and their crystallization in a lipidic environment. Application of this material to a wide variety of membrane proteins, however, is hindered due to a limited number of available host lipids, mostly monoacylglycerols (MAGs). Here, we designed, synthesized, and characterized a series of chemically stable lipids resistant to hydrolysis, with properties complementary to the widely used MAGs. In order to assess their potential to serve as host lipids for crystallization, we characterized the phase properties and lattice parameters of mesophases made of two most promising lipids at a variety of different conditions by polarized light microscopy and small-angle X-ray scattering. Both lipids showed remarkable chemical stability and an extended LCP region in the phase diagram covering a wide range of temperatures down to 4 °C. One of these lipids has been used for crystallization and structure determination of a prototypical membrane protein bacteriorhodopsin at 4 and 20 °C.

  8. Stable configurations of graphene on silicon

    Energy Technology Data Exchange (ETDEWEB)

    Javvaji, Brahmanandam; Shenoy, Bhamy Maithry [Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012 (India); Mahapatra, D. Roy, E-mail: droymahapatra@aero.iisc.ernet.in [Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012 (India); Ravikumar, Abhilash [Department of Metallurgical and Materials Engineering, National Institute of Technology Karnataka, Surathkal 575025 (India); Hegde, G.M. [Center for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012 (India); Rizwan, M.R. [Department of Metallurgical and Materials Engineering, National Institute of Technology Karnataka, Surathkal 575025 (India)

    2017-08-31

    Highlights: • Simulations of epitaxial growth process for silicon–graphene system is performed. • Identified the most favourable orientation of graphene sheet on silicon substrate. • Atomic local strain due to the silicon–carbon bond formation is analyzed. - Abstract: Integration of graphene on silicon-based nanostructures is crucial in advancing graphene based nanoelectronic device technologies. The present paper provides a new insight on the combined effect of graphene structure and silicon (001) substrate on their two-dimensional anisotropic interface. Molecular dynamics simulations involving the sub-nanoscale interface reveal a most favourable set of temperature independent orientations of the monolayer graphene sheet with an angle of ∽15° between its armchair direction and [010] axis of the silicon substrate. While computing the favorable stable orientations, both the translation and the rotational vibrations of graphene are included. The possible interactions between the graphene atoms and the silicon atoms are identified from their coordination. Graphene sheet shows maximum bonding density with bond length 0.195 nm and minimum bond energy when interfaced with silicon substrate at 15° orientation. Local deformation analysis reveals probability distribution with maximum strain levels of 0.134, 0.047 and 0.029 for 900 K, 300 K and 100 K, respectively in silicon surface for 15° oriented graphene whereas the maximum probable strain in graphene is about 0.041 irrespective of temperature. Silicon–silicon dimer formation is changed due to silicon–carbon bonding. These results may help further in band structure engineering of silicon–graphene lattice.

  9. Quasi-stable injection channels in a wakefield accelerator

    OpenAIRE

    Wiltshire-Turkay, Mara; Farmer, John P.; Pukhov, Alexander

    2016-01-01

    The influence of initial position on the acceleration of externally-injected electrons in a plasma wakefield is investigated. Test-particle simulations show previously unobserved complex structure in the parameter space, with quasi-stable injection channels forming for particles injected in narrow regions away from the wake centre. Particles injected into these channels remain in the wake for a considerable time after dephasing, and as a result achieve significantly higher energy than their n...

  10. Gas phase thermal diffusion of stable isotopes

    International Nuclear Information System (INIS)

    Eck, C.F.

    1979-01-01

    The separation of stable isotopes at Mound Facility is reviewed from a historical perspective. The historical development of thermal diffusion from a laboratory process to a separation facility that handles all the noble gases is described. In addition, elementary thermal diffusion theory and elementary cascade theory are presented along with a brief review of the uses of stable isotopes

  11. physico-chemical and stable isotopes

    African Journals Online (AJOL)

    This paper details the mineralogical, chemical and stable isotope abundances of calcrete in the Letlhakeng fossil valley. The stable isotope abundances (O and C) of calcretes yielded some values which were tested against the nature of the calcretes – pedogenic or groundwater type. The Kgalagadi (Kalahari) is a vast ...

  12. Modelling stable atmospheric boundary layers over snow

    NARCIS (Netherlands)

    Sterk, H.A.M.

    2015-01-01

    Thesis entitled:

    Modelling Stable Atmospheric Boundary Layers over Snow

    H.A.M. Sterk

    Wageningen, 29th of April, 2015

    Summary

    The emphasis of this thesis is on the understanding and forecasting of the Stable Boundary Layer (SBL) over snow-covered surfaces. SBLs

  13. Modelling stable atmospheric boundary layers over snow

    NARCIS (Netherlands)

    Sterk, H.A.M.

    2015-01-01

    Thesis entitled: Modelling Stable Atmospheric Boundary Layers over Snow H.A.M. Sterk Wageningen, 29th of April, 2015 Summary The emphasis of this thesis is on the understanding and forecasting of the Stable Boundary Layer (SBL) over snow-covered surfaces. SBLs typically form at night and in polar

  14. Stable isotopes and biomarkers in microbial ecology

    NARCIS (Netherlands)

    Boschker, H.T.S.; Middelburg, J.J.

    2002-01-01

    The use of biomarkers in combination with stable isotope analysis is a new approach in microbial ecology and a number of papers on a variety of subjects have appeared. We will first discuss the techniques for analysing stable isotopes in biomarkers, primarily gas chromatography-combustion-isotope

  15. Stable Agrobacterium -mediated transformation of the halophytic ...

    African Journals Online (AJOL)

    Stable Agrobacterium-mediated transformation of the halophytic Leymus chinensis (Trin.) Yan-Lin Sun, Soon-Kwan Hong. Abstract. In this study, an efficient procedure for stable Agrobacterium-mediated transformation of Leymus chinensis (Trin.) was established. Agrobacterium tumefaciens strain EHA105, harboring a ...

  16. Stable Fly, (L., Dispersal and Governing Factors

    Directory of Open Access Journals (Sweden)

    Allan T. Showler

    2015-01-01

    Full Text Available Although the movement of stable fly, Stomoxys calcitrans (L., has been studied, its extent and significance has been uncertain. On a local scale (13 km is mainly wind-driven by weather fronts that carry stable flies from inland farm areas for up to 225 km to beaches of northwestern Florida and Lake Superior. Stable flies can reproduce for a short time each year in washed-up sea grass, but the beaches are not conducive to establishment. Such movement is passive and does not appear to be advantageous to stable fly's survival. On a regional scale, stable flies exhibit little genetic differentiation, and on the global scale, while there might be more than one “lineage”, the species is nevertheless considered to be panmictic. Population expansion across much of the globe likely occurred from the late Pleistocene to the early Holocene in association with the spread of domesticated nomad livestock and particularly with more sedentary, penned livestock.

  17. [Biomechanics and imaging evaluation on stable structure of pelvis].

    Science.gov (United States)

    Ma, Zhi-Jian; Bai, Li-Ping; Zeng, Xiang-Sen; Ya, Jun; Wang, Qiu-Gen

    2016-12-25

    The treatment of difficulty and prognosis of pelvic fracture are directly related to the pelvic girdle stability. Diagnosis of pelvic fracture is mainly imaging manifestations based on biomechanics of pelvic anatomy. With the progress of biomechanics experiment technology, previousopinion has changed, such as separation of symphysis pubis 2.5 cm could not be seen as distinguishing feature of type I and II for anterior-posterior compression;displacement of sacroilliac joints less than 1 cm could cause loss of vertical stability;lateral extrusion could also cause vertical instability;part description of Young-Burgess classification is not suitable for experiment results;ligament plays an important role in restricting displacement and having proprioceptors;SPECT-CT could improve sensitivity of diagnosis, but could not evaluate stability of pelvic fractures precisely. Copyright© 2016 by the China Journal of Orthopaedics and Traumatology Press.

  18. Structural studies of thermally stable, combustion-resistant polymer composites

    OpenAIRE

    Smith, G.N.; Hallett, J.E.; Joseph, P.; Tretsiakova-McNally, S.; Zhang, T.; Blum, F.D.; Eastoe, J.

    2017-01-01

    Composites of the industrially important polymer, poly(methyl methacrylate) (PMMA), were prepared by free-radical polymerization of MMA with varying amounts (1–30 wt. %) of sodium dioctylsulfosuccinate (Aerosol OT or AOT) surfactant added to the reaction mixture. The composites with AOT incorporated show enhanced resistance to thermal degradation compared to pure PMMA homopolymer, and micro-cone combustion calorimetry measurements also show that the composites are combustion-resistant. The ph...

  19. Study of coherent structures of turbulence with large wall-normal gradients in thermophysical properties using direct numerical simulation

    Science.gov (United States)

    Reinink, Shawn K.; Yaras, Metin I.

    2015-06-01

    Forced-convection heat transfer in a heated working fluid at a thermodynamic state near its pseudocritical point is poorly predicted by correlations calibrated with data at subcritical temperatures and pressures. This is suggested to be primarily due to the influence of large wall-normal thermophysical property gradients that develop in proximity of the pseudocritical point on the concentration of coherent turbulence structures near the wall. The physical mechanisms dominating this influence remain poorly understood. In the present study, direct numerical simulation is used to study the development of coherent vortical structures within a turbulent spot under the influence of large wall-normal property gradients. A turbulent spot rather than a fully turbulent boundary layer is used for the study, for the coherent structures of turbulence in a spot tend to be in a more organized state which may allow for more effective identification of cause-and-effect relationships. Large wall-normal gradients in thermophysical properties are created by heating the working fluid which is near the pseudocritical thermodynamic state. It is found that during improved heat transfer, wall-normal gradients in density accelerate the growth of the Kelvin-Helmholtz instability mechanism in the shear layer enveloping low-speed streaks, causing it to roll up into hairpin vortices at a faster rate. It is suggested that this occurs by the baroclinic vorticity generation mechanism which accelerates the streamwise grouping of vorticity during shear layer roll-up. The increased roll-up frequency leads to reduced streamwise spacing between hairpin vortices in wave packets. The density gradients also promote the sinuous instability mode in low-speed streaks. The resulting oscillations in the streaks in the streamwise-spanwise plane lead to locally reduced spanwise spacing between hairpin vortices forming over adjacent low-speed streaks. The reduction in streamwise and spanwise spacing between

  20. Study of coherent structures of turbulence with large wall-normal gradients in thermophysical properties using direct numerical simulation

    Energy Technology Data Exchange (ETDEWEB)

    Reinink, Shawn K.; Yaras, Metin I., E-mail: Metin.Yaras@carleton.ca [Department of Mechanical and Aerospace Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6 (Canada)

    2015-06-15

    Forced-convection heat transfer in a heated working fluid at a thermodynamic state near its pseudocritical point is poorly predicted by correlations calibrated with data at subcritical temperatures and pressures. This is suggested to be primarily due to the influence of large wall-normal thermophysical property gradients that develop in proximity of the pseudocritical point on the concentration of coherent turbulence structures near the wall. The physical mechanisms dominating this influence remain poorly understood. In the present study, direct numerical simulation is used to study the development of coherent vortical structures within a turbulent spot under the influence of large wall-normal property gradients. A turbulent spot rather than a fully turbulent boundary layer is used for the study, for the coherent structures of turbulence in a spot tend to be in a more organized state which may allow for more effective identification of cause-and-effect relationships. Large wall-normal gradients in thermophysical properties are created by heating the working fluid which is near the pseudocritical thermodynamic state. It is found that during improved heat transfer, wall-normal gradients in density accelerate the growth of the Kelvin-Helmholtz instability mechanism in the shear layer enveloping low-speed streaks, causing it to roll up into hairpin vortices at a faster rate. It is suggested that this occurs by the baroclinic vorticity generation mechanism which accelerates the streamwise grouping of vorticity during shear layer roll-up. The increased roll-up frequency leads to reduced streamwise spacing between hairpin vortices in wave packets. The density gradients also promote the sinuous instability mode in low-speed streaks. The resulting oscillations in the streaks in the streamwise-spanwise plane lead to locally reduced spanwise spacing between hairpin vortices forming over adjacent low-speed streaks. The reduction in streamwise and spanwise spacing between

  1. Hermitian-Einstein metrics on parabolic stable bundles

    International Nuclear Information System (INIS)

    Li Jiayu; Narasimhan, M.S.

    1995-12-01

    Let M-bar be a compact complex manifold of complex dimension two with a smooth Kaehler metric and D a smooth divisor on M-bar. If E is a rank 2 holomorphic vector bundle on M-bar with a stable parabolic structure along D, we prove the existence of a metric on E' = E module MbarD (compatible with the parabolic structure) which is Hermitian-Einstein with respect to the restriction of Kaehler metric of M-barD. A converse is also proved. (author). 24 refs

  2. Stable Organic Neutral Diradical via Reversible Coordination.

    Science.gov (United States)

    Lu, Zhenpin; Quanz, Henrik; Burghaus, Olaf; Hofmann, Jonas; Logemann, Christian; Beeck, Sebastian; Schreiner, Peter R; Wegner, Hermann A

    2017-12-27

    We report the formation of a stable neutral diboron diradical simply by coordination of an aromatic dinitrogen compound to an ortho-phenyldiborane. This process is reversible upon addition of pyridine. The diradical species is stable above 200 °C. Computations are consistent with an open-shell triplet diradical with a very small open-shell singlet-triplet energy gap that is indicative of the electronic disjointness of the two radical sites. This opens a new way of generating stable radicals with fascinating electronic properties useful for a large variety of applications.

  3. Stable Isotope Group 1983 progress report

    International Nuclear Information System (INIS)

    Stewart, M.K.

    1984-06-01

    The work of the Stable Isotope Group of the Institute of Nuclear Sciences in the fields of isotope geology, isotope hydrology, geochronology, isotope biology and related fields, and mass spectrometer instrumentation, during 1983, is described

  4. Stable Isotope Group 1982 progress report

    International Nuclear Information System (INIS)

    Stewart, M.K.

    1983-06-01

    The work of the Stable Isotope Group of the Institute of Nuclear Sciences during 1982, in the fields of isotope geology, isotope hydrology, geochronology, isotope biology and mass spectrometer instrumentation, is described

  5. Bartolome Island, Galapagos Stable Oxygen Calibration Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Galapagos Coral Stable Oxygen Calibration Data. Sites: Bartolome Island: 0 deg, 17'S, 90 deg 33' W. Champion Island: 1 deg, 15'S, 90 deg, 05' W. Urvina Bay (Isabela...

  6. Allan Hills Stable Water Isotopes, Version 1

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set includes stable water isotope values at 10 m resolution along an approximately 5 km transect through the main icefield of the Allan Hills Blue Ice...

  7. Applications of stable isotopes in clinical pharmacology

    Science.gov (United States)

    Schellekens, Reinout C A; Stellaard, Frans; Woerdenbag, Herman J; Frijlink, Henderik W; Kosterink, Jos G W

    2011-01-01

    This review aims to present an overview of the application of stable isotope technology in clinical pharmacology. Three main categories of stable isotope technology can be distinguished in clinical pharmacology. Firstly, it is applied in the assessment of drug pharmacology to determine the pharmacokinetic profile or mode of action of a drug substance. Secondly, stable isotopes may be used for the assessment of drug products or drug delivery systems by determination of parameters such as the bioavailability or the release profile. Thirdly, patients may be assessed in relation to patient-specific drug treatment; this concept is often called personalized medicine. In this article, the application of stable isotope technology in the aforementioned three areas is reviewed, with emphasis on developments over the past 25 years. The applications are illustrated with examples from clinical studies in humans. PMID:21801197

  8. Tannaka duality and stable infinity-categories

    OpenAIRE

    Iwanari, Isamu

    2014-01-01

    We introduce the notion of fine tannakian infinity-categories and prove Tannaka duality results for symmetric monoidal stable infinity-categories over a field of characteristic zero. We also discuss several examples.

  9. On Stable Marriages and Greedy Matchings

    Energy Technology Data Exchange (ETDEWEB)

    Manne, Fredrik; Naim, Md; Lerring, Hakon; Halappanavar, Mahantesh

    2016-12-11

    Research on stable marriage problems has a long and mathematically rigorous history, while that of exploiting greedy matchings in combinatorial scientific computing is a younger and less developed research field. In this paper we consider the relationships between these two areas. In particular we show that several problems related to computing greedy matchings can be formulated as stable marriage problems and as a consequence several recently proposed algorithms for computing greedy matchings are in fact special cases of well known algorithms for the stable marriage problem. However, in terms of implementations and practical scalable solutions on modern hardware, the greedy matching community has made considerable progress. We show that due to the strong relationship between these two fields many of these results are also applicable for solving stable marriage problems.

  10. The Reactivity of Stable Metallacyclobutenes and Vinylcarbenes

    OpenAIRE

    Holland, Ryan Lynn

    2016-01-01

    Chapter 1. Historical Development of Stable Metallacyclobutenes Fred Tebbe and co-workers synthesized the first stable metallacyclobutene complexes in the late 1970’s by treatment of an intermediate titanium methylene species – later popularized as the “Tebbe reagent” – with acetylenes. Robert Grubbs at Caltech further studied this system, using it to detail a degenerate metathesis reaction and to isolate a metallacyclobutane complex – which was implicated in the emerging field of alkene meta...

  11. Stable atomic hydrogen: Polarized atomic beam source

    International Nuclear Information System (INIS)

    Niinikoski, T.O.; Penttilae, S.; Rieubland, J.M.; Rijllart, A.

    1984-01-01

    We have carried out experiments with stable atomic hydrogen with a view to possible applications in polarized targets or polarized atomic beam sources. Recent results from the stabilization apparatus are described. The first stable atomic hydrogen beam source based on the microwave extraction method (which is being tested ) is presented. The effect of the stabilized hydrogen gas density on the properties of the source is discussed. (orig.)

  12. Stereoselective synthesis of stable-isotope-labeled amino acids

    International Nuclear Information System (INIS)

    Unkefer, C.J.; Martinez, R.A.; Silks, L.A. III; Lodwig, S.N.

    1994-01-01

    For magnetic resonance and vibrational spectroscopies to reach their full potential, they must be used in combination with sophisticated site-specific stable isotope labeling of biological macromolecules. Labeled amino acids are required for the study of the structure and function of enzymes and proteins. Because there are 20 common amino acids, each with its own distinguishing chemistry, they remain a synthetic challenge. The Oppolzer chiral auxiliary provides a general tool with which to approach the synthesis of labeled amino acids. By using the Oppolzer auxiliary, amino acids can be constructed from several small molecules, which is ideal for stable isotope labeling. In addition to directing the stereochemistry at the α-carbon, the camphorsultam can be used for stereo-specific isotope labeling at prochiral centers in amino acids. By using the camphorsultam auxiliary we have the potential to synthesize virtually any isotopomer of all of the common amino acids

  13. On the stable Mg-Zn-Y quasicrystals

    Science.gov (United States)

    Luo, Z. P.; Sui, H. X.; Zhang, S. Q.

    1996-07-01

    By the conventional air-cooled casting method, bulk ingots with a large fraction of stable Mg-Zn-Y icosahedral quasicrystals, both simple and face-centered, were obtained. The quasicrystal structures were directly confirmed by high-resolution electron microscopy (HREM) observations. The electron diffraction patterns from the quasicrystals were studied by computer simulations. A coexisting crys-talline phase of the quasicrystals was identified as the Mg7Zn3 phase, which was proved to be the (1/1) approximant of the quasicrystals. The quasicrystals were stable during a continuous heating process. However, at high temperature, oxidation occurred, and thus, Y2O3 and MgO products were formed. Oxidation at high temperatures is characteristic for the Mg-Zn-Y alloys and differs from Al-base alloys.

  14. Highly scalable multichannel mesh electronics for stable chronic brain electrophysiology.

    Science.gov (United States)

    Fu, Tian-Ming; Hong, Guosong; Viveros, Robert D; Zhou, Tao; Lieber, Charles M

    2017-11-21

    Implantable electrical probes have led to advances in neuroscience, brain-machine interfaces, and treatment of neurological diseases, yet they remain limited in several key aspects. Ideally, an electrical probe should be capable of recording from large numbers of neurons across multiple local circuits and, importantly, allow stable tracking of the evolution of these neurons over the entire course of study. Silicon probes based on microfabrication can yield large-scale, high-density recording but face challenges of chronic gliosis and instability due to mechanical and structural mismatch with the brain. Ultraflexible mesh electronics, on the other hand, have demonstrated negligible chronic immune response and stable long-term brain monitoring at single-neuron level, although, to date, it has been limited to 16 channels. Here, we present a scalable scheme for highly multiplexed mesh electronics probes to bridge the gap between scalability and flexibility, where 32 to 128 channels per probe were implemented while the crucial brain-like structure and mechanics were maintained. Combining this mesh design with multisite injection, we demonstrate stable 128-channel local field potential and single-unit recordings from multiple brain regions in awake restrained mice over 4 mo. In addition, the newly integrated mesh is used to validate stable chronic recordings in freely behaving mice. This scalable scheme for mesh electronics together with demonstrated long-term stability represent important progress toward the realization of ideal implantable electrical probes allowing for mapping and tracking single-neuron level circuit changes associated with learning, aging, and neurodegenerative diseases. Copyright © 2017 the Author(s). Published by PNAS.

  15. Local Search Approaches in Stable Matching Problems

    Directory of Open Access Journals (Sweden)

    Toby Walsh

    2013-10-01

    Full Text Available The stable marriage (SM problem has a wide variety of practical applications, ranging from matching resident doctors to hospitals, to matching students to schools or, more generally, to any two-sided market. In the classical formulation, n men and n women express their preferences (via a strict total order over the members of the other sex. Solving an SM problem means finding a stable marriage where stability is an envy-free notion: no man and woman who are not married to each other would both prefer each other to their partners or to being single. We consider both the classical stable marriage problem and one of its useful variations (denoted SMTI (Stable Marriage with Ties and Incomplete lists where the men and women express their preferences in the form of an incomplete preference list with ties over a subset of the members of the other sex. Matchings are permitted only with people who appear in these preference lists, and we try to find a stable matching that marries as many people as possible. Whilst the SM problem is polynomial to solve, the SMTI problem is NP-hard. We propose to tackle both problems via a local search approach, which exploits properties of the problems to reduce the size of the neighborhood and to make local moves efficiently. We empirically evaluate our algorithm for SM problems by measuring its runtime behavior and its ability to sample the lattice of all possible stable marriages. We evaluate our algorithm for SMTI problems in terms of both its runtime behavior and its ability to find a maximum cardinality stable marriage. Experimental results suggest that for SM problems, the number of steps of our algorithm grows only as O(n log(n, and that it samples very well the set of all stable marriages. It is thus a fair and efficient approach to generate stable marriages. Furthermore, our approach for SMTI problems is able to solve large problems, quickly returning stable matchings of large and often optimal size, despite the

  16. Stable nocturnal spectral characteristics over a vineyard (Conference Presentation)

    Science.gov (United States)

    Prueger, John H.; Alfieri, joesph G.; Hipps, Lawrence E.; Kustas, William P.; Neale, Christopher M.

    2016-10-01

    Vineyards are agricultural surfaces that present a unique structural perturbation to the mean wind flow. As part of the Grape Remote Sensing Atmospheric Profiling and Evapotranspiration Experiment (GRAPEX) a 10-m profile tower of three sonic anemometers at 2, 3.75 and 8 m above ground level in in a mature vineyard having was deployed to measure high frequency diurnal variations of 3-dimensional velocity components (u, v, w) and temperature (T) throughout the growing season. Previous work has been published involving eddy covariance measurements in vineyards but these mostly represented convective daytime unstable conditions. Significantly less has been published about turbulence in vineyards during stable nocturnal periods. Hence, in this study we focused on the nocturnal stable periods under clear skies and relatively light winds typical of the northern portion of California's Central Valley. Our objective was to characterize and evaluate turbulent exchange processes in the layer near the top of a vine canopy during nocturnal periods which are often characterized by weak and intermittent turbulence. Spectra, cospectra and coherence plots were evaluated for nocturnal periods. The spectra suggest there are periods of intermittent turbulence with features indicative of local and regional scale processes. Additionally the impact of the vine structure and spacing on slow meandering flows enhance the decomposition of organized turbulent eddies resulting in intricate mechanical turbulence generated by intermittent eddies that are rapidly decomposed as eddies interact with the vine structure and spacing. Preliminary results will be discussed that provide insight into turbulence characteristics at several heights above a canopy vineyard as affected by vine structure and spacing, wind speed, direction and stable conditions.

  17. Stable chaos in fluctuation driven neural circuits

    International Nuclear Information System (INIS)

    Angulo-Garcia, David; Torcini, Alessandro

    2014-01-01

    Highlights: • Nonlinear instabilities in fluctuation driven (balanced) neural circuits are studied. • Balanced networks display chaos and stable phases at different post-synaptic widths. • Linear instabilities coexists with nonlinear ones in the chaotic regime. • Erratic motion appears also in linearly stable phase due to stable chaos. - Abstract: We study the dynamical stability of pulse coupled networks of leaky integrate-and-fire neurons against infinitesimal and finite perturbations. In particular, we compare mean versus fluctuations driven networks, the former (latter) is realized by considering purely excitatory (inhibitory) sparse neural circuits. In the excitatory case the instabilities of the system can be completely captured by an usual linear stability (Lyapunov) analysis, whereas the inhibitory networks can display the coexistence of linear and nonlinear instabilities. The nonlinear effects are associated to finite amplitude instabilities, which have been characterized in terms of suitable indicators. For inhibitory coupling one observes a transition from chaotic to non chaotic dynamics by decreasing the pulse-width. For sufficiently fast synapses the system, despite showing an erratic evolution, is linearly stable, thus representing a prototypical example of stable chaos

  18. Metabolic studies in man using stable isotopes

    International Nuclear Information System (INIS)

    Faust, H.; Jung, K.; Krumbiegel, P.

    1993-01-01

    In this project, stable isotope compounds and stable isotope pharmaceuticals were used (with emphasis on the application of 15 N) to study several aspects of nitrogen metabolism in man. Of the many methods available, the 15 N stable isotope tracer technique holds a special position because the methodology for application and nitrogen isotope analysis is proven and reliable. Valid routine methods using 15 N analysis by emission spectrometry have been demonstrated. Several methods for the preparation of biological material were developed during our participation in the Coordinated Research Programme. In these studies, direct procedures (i.e. use of diluted urine as a samples without chemical preparation) or rapid isolation methods were favoured. Within the scope of the Analytical Quality Control Service (AQCS) enriched stable isotope reference materials for medical and biological studies were prepared and are now available through the International Atomic Energy Agency. The materials are of special importance as the increasing application of stable isotopes as tracers in medical, biological and agricultural studies has focused interest on reliable measurements of biological material of different origin. 24 refs

  19. MicroRNA prediction using a fixed-order Markov model based on the secondary structure pattern.

    Directory of Open Access Journals (Sweden)

    Wei Shen

    Full Text Available Predicting miRNAs is an arduous task, due to the diversity of the precursors and complexity of enzyme processes. Although several prediction approaches have reached impressive performances, few of them could achieve a full-function recognition of mature miRNA directly from the candidate hairpins across species. Therefore, researchers continue to seek a more powerful model close to biological recognition to miRNA structure. In this report, we describe a novel miRNA prediction algorithm, known as FOMmiR, using a fixed-order Markov model based on the secondary structural pattern. For a training dataset containing 809 human pre-miRNAs and 6441 human pseudo-miRNA hairpins, the model's parameters were defined and evaluated. The results showed that FOMmiR reached 91% accuracy on the human dataset through 5-fold cross-validation. Moreover, for the independent test datasets, the FOMmiR presented an outstanding prediction in human and other species including vertebrates, Drosophila, worms and viruses, even plants, in contrast to the well-known algorithms and models. Especially, the FOMmiR was not only able to distinguish the miRNA precursors from the hairpins, but also locate the position and strand of the mature miRNA. Therefore, this study provides a new generation of miRNA prediction algorithm, which successfully realizes a full-function recognition of the mature miRNAs directly from the hairpin sequences. And it presents a new understanding of the biological recognition based on the strongest signal's location detected by FOMmiR, which might be closely associated with the enzyme cleavage mechanism during the miRNA maturation.

  20. Temperature and Humidity Control in Livestock Stables

    DEFF Research Database (Denmark)

    Hansen, Michael; Andersen, Palle; Nielsen, Kirsten M.

    2010-01-01

    The paper describes temperature and humidity control of a livestock stable. It is important to have a correct air flow pattern in the livestock stable in order to achieve proper temperature and humidity control as well as to avoid draught. In the investigated livestock stable the air flow...... is controlled using wall mounted ventilation flaps. In the paper an algorithm for air flow control is presented meeting the needs for temperature and humidity while taking the air flow pattern in consideration. To obtain simple and realisable controllers a model based control design method is applied....... In the design dynamic models for temperature and humidity are very important elements and effort is put into deriving and testing the models. It turns out that non-linearities are dominating in both models making feedback linearization the natural design method. The air controller as well as the temperature...

  1. On some topological properties of stable measures

    DEFF Research Database (Denmark)

    Nielsen, Carsten Krabbe

    1996-01-01

    Summary The paper shows that the set of stable probability measures and the set of Rational Beliefs relative to a given stationary measure are closed in the strong topology, but not closed in the topology of weak convergence. However, subsets of the set of stable probability measures which...... are characterized by uniformity of convergence of the empirical distribution are closed in the topology of weak convergence. It is demonstrated that such subsets exist. In particular, there is an increasing sequence of sets of SIDS measures who's union is the set of all SIDS measures generated by a particular...... system and such that each subset consists of stable measures. The uniformity requirement has a natural interpretation in terms of plausibility of Rational Beliefs...

  2. Concentration of stable elements in food products

    Energy Technology Data Exchange (ETDEWEB)

    Montford, M.A.; Shank, K.E.; Hendricks, C.; Oakes, T.W.

    1980-01-01

    Food samples were taken from commercial markets and analyzed for stable element content. The concentrations of most stable elements (Ag, Al, As, Au, Ba, Br, Ca, Ce, Cl, Co, Cr, Cs, Cu, Fe, Hf, I, K, La, Mg, Mn, Mo, Na, Rb, Sb, Sc, Se, Sr, Ta, Th, Ti, V, Zn, Zr) were determined using multiple-element neutron activation analysis, while the concentrations of other elements (Cd, Hg, Ni, Pb) were determined using atomic absorption. The relevance of the concentrations found are noted in relation to other literature values. An earlier study was extended to include the determination of the concentration of stable elements in home-grown products in the vicinity of the Oak Ridge National Laboratory. Comparisons between the commercial and local food-stuff values are discussed.

  3. Visualization and manipulation of meta-stable polarization variants in multiferroic materials

    Directory of Open Access Journals (Sweden)

    Moonkyu Park

    2013-04-01

    Full Text Available Here we demonstrate the role of meta-stable polarization variants in out-of-plane polarization switching behavior in epitaxially grown BiFeO3 thin films using angle-resolved piezoresponse force microscopy (AR-PFM. The out-of-plane polarization switching mainly occurred at the boundary between meta-stable and stable polarization domains, and was accompanied by a significant change in in-plane domain configuration from complicated structure with 12 polarization variants to simple stripe structure with 4 polarization variants. These results imply that the biased tip rearranges the delicately balanced domain configuration, which is determined by the competition between electrostatic and strain energies, into simple interweaving one that is more thermodynamically stable.

  4. On the joint statistics of stable random processes

    International Nuclear Information System (INIS)

    Hopcraft, K I; Jakeman, E

    2011-01-01

    A utilitarian continuous bi-variate random process whose first-order probability density function is a stable random variable is constructed. Results paralleling some of those familiar from the theory of Gaussian noise are derived. In addition to the joint-probability density for the process, these include fractional moments and structure functions. Although the correlation functions for stable processes other than Gaussian do not exist, we show that there is coherence between values adopted by the process at different times, which identifies a characteristic evolution with time. The distribution of the derivative of the process, and the joint-density function of the value of the process and its derivative measured at the same time are evaluated. These enable properties to be calculated analytically such as level crossing statistics and those related to the random telegraph wave. When the stable process is fractal, the proportion of time it spends at zero is finite and some properties of this quantity are evaluated, an optical interpretation for which is provided. (paper)

  5. The stable nonequilibrium state of bicarbonate aqueous systems

    Science.gov (United States)

    Voeikov, V. L.; Vilenskaya, N. D.; Ha, Do Minh; Malyshenko, S. I.; Buravleva, E. V.; Yablonskaya, O. I.; Timofeev, K. N.

    2012-09-01

    Data obtained by electron paramagnetic resonance (EPR) and chemiluminescence analysis indicate that in aqueous solutions of bicarbonates, superoxide radical and other reactive oxygen species (ROS) are constantly produced. The stationary level of the superoxide radical is found to increase when a solution is illuminated. Reactions involving ROS are shown to be accompanied by the generation of electron excitation energy, keeping bicarbonate solutions in a stable nonequilibrium state. The system can emit part of this energy. Variations in emitting activity are found to correlate with variations in the cosmophysical factors. The emitting activity of solutions is found to vary in the presence of low and ultralow concentrations of hydrated fullerenes. It is noted that the phenomenon of spontaneous charge separation in aqueous systems (G. H. Pollack) could play a role in maintaining a stable nonequilibrium state in bicarbonate systems where the reactions with ROS participation are catalyzed by forms of carbonate. It is concluded that the abovementioned properties of bicarbonate aqueous systems most likely keep living matter whose structural basis is formed by these systems in a stable excited state, thereby making it highly sensitive to the action of external factors with low and ultralow intensities.

  6. Studies of Stable Octupole Deformations in the Radium Region

    CERN Multimedia

    2002-01-01

    The purpose of the present project is to locate and identify states in the atomic nuclei possessing stable pearshaped octupole deformation. Such states, formally related to the structures known in molecular physics, manifest themselves as families of parity doublets in odd nuclei.\\\\ \\\\ The best possibilities for observing stable octupole deformations are offered in the Ra-region. Both theoretical calculations and experimental indications support such expectations. Such indications are the non-observation of two-phonon octupole vibrational states in the ISOLDE studies of the even-even radium nuclei, and the reversed sign of the decoupling factor of the ground state band in |2|2|5Ra observed in the single-neutron transfer reactions. In order to establish the predicted strong E1 and E3-transitions between the parity doublets in odd nuclei with stable octupole deformations it is proposed to study conversion electrons in odd-mass francium radium and radon isotopes following the @b-decay of francium and astatine. \\...

  7. Faster and Simpler Approximation of Stable Matchings

    Directory of Open Access Journals (Sweden)

    Katarzyna Paluch

    2014-04-01

    Full Text Available We give a 3 2 -approximation algorithm for finding stable matchings that runs in O(m time. The previous most well-known algorithm, by McDermid, has the same approximation ratio but runs in O(n3/2m time, where n denotes the number of people andm is the total length of the preference lists in a given instance. In addition, the algorithm and the analysis are much simpler. We also give the extension of the algorithm for computing stable many-to-many matchings.

  8. Bordism, stable homotopy and adams spectral sequences

    CERN Document Server

    Kochman, Stanley O

    1996-01-01

    This book is a compilation of lecture notes that were prepared for the graduate course "Adams Spectral Sequences and Stable Homotopy Theory" given at The Fields Institute during the fall of 1995. The aim of this volume is to prepare students with a knowledge of elementary algebraic topology to study recent developments in stable homotopy theory, such as the nilpotence and periodicity theorems. Suitable as a text for an intermediate course in algebraic topology, this book provides a direct exposition of the basic concepts of bordism, characteristic classes, Adams spectral sequences, Brown-Peter

  9. Modelling stable water isotopes: Status and perspectives

    Directory of Open Access Journals (Sweden)

    Werner M.

    2010-12-01

    Full Text Available Modelling of stable water isotopes H2 18O and HDO within various parts of the Earth’s hydrological cycle has clearly improved our understanding of the interplay between climatic variations and related isotope fractionation processes. In this article key principles and major research results of stable water isotope modelling studies are described. Emphasis is put on research work using explicit isotope diagnostics within general circulation models as this highly complex model setup bears many resemblances with studies using simpler isotope modelling approaches.

  10. Trimethyl Lock: A Stable Chromogenic Substrate for Esterases

    Directory of Open Access Journals (Sweden)

    Ronald T. Raines

    2008-01-01

    Full Text Available p-Nitrophenyl acetate is the most commonly used substrate for detecting thecatalytic activity of esterases, including those that activate prodrugs in human cells. Thissubstrate is unstable in aqueous solution, limiting its utility. Here, a stable chromogenicsubstrate for esterases is produced by the structural isolation of an acetyl ester andp-nitroaniline group using a trimethyl lock moiety. Upon ester hydrolysis, unfavorablesteric interactions between the three methyl groups of this o-hydroxycinnamic acidderivative encourage rapid lactonization to form a hydrocoumarin and releasep-nitroaniline. This “prochromophore” could find use in a variety of assays.

  11. Ferroelectric nanostructure having switchable multi-stable vortex states

    Science.gov (United States)

    Naumov, Ivan I [Fayetteville, AR; Bellaiche, Laurent M [Fayetteville, AR; Prosandeev, Sergey A [Fayetteville, AR; Ponomareva, Inna V [Fayetteville, AR; Kornev, Igor A [Fayetteville, AR

    2009-09-22

    A ferroelectric nanostructure formed as a low dimensional nano-scale ferroelectric material having at least one vortex ring of polarization generating an ordered toroid moment switchable between multi-stable states. A stress-free ferroelectric nanodot under open-circuit-like electrical boundary conditions maintains such a vortex structure for their local dipoles when subject to a transverse inhomogeneous static electric field controlling the direction of the macroscopic toroidal moment. Stress is also capable of controlling the vortex's chirality, because of the electromechanical coupling that exists in ferroelectric nanodots.

  12. Highly Photoluminescent and Stable Aqueous ZnS Quantum Dots

    OpenAIRE

    Li, Hui; Shih, Wan Y.; Shih, Wei-Heng

    2010-01-01

    We report an all-aqueous synthesis of highly photoluminescent and stable ZnS quantum dots (QDs) with water as the medium, i.e. first synthesizing ZnS QDs with 3-mercaptopropionic acid (MPA) as the capping molecule, followed by replacing some of MPA with (3-mercaptopropyl) trimethoxysilane (MPS). The resultant MPS-replaced ZnS QDs were about 5 nm in size with a cubic zinc blende crystalline structure, and had both MPA and MPS on the surface as confirmed by the Fourier Transform Infrared (FTIR)...

  13. Nonlinear density waves in a marginally stable gravitating disk

    International Nuclear Information System (INIS)

    Korchagin, V.I.

    1986-01-01

    The evolution of short nonlinear density waves in a disk at the stability limit is studied for arbitrary values of the radial wave number k/sub r/. For waves with wave numbers that do not lie at the minimum of the dispersion curve, the behavior of the amplitude is described by a nonlinear parabolic equation; however, stationary soliton solutions cannot exist in such a system since there is no dispersion spreading of a packet. For wave numbers lying at the minimum of the dispersion curve, soliton structures with determined amplitude are possible. In stable gravitating disks and in a disk at the stability limit, two physically different types of soliton can exist

  14. A novel thermooxidatively stable poly(ester-imide-benzoxazole)

    Energy Technology Data Exchange (ETDEWEB)

    Sundar, R.A.; Mathias, L.J. [Univ. of Sothern Mississippi, Hattiesburg, MS (United States)

    1993-12-31

    A poly(ester-amide-imide) was synthesized by the low temperature solution polycondensation of 4-amino-5-hydroxy-N,4{prime}-hydroxyphenyl phthalimide with isophthaloyl chloride. Subsequent thermal cyclodehydration of the poly(ester-amide-imide) at 320{degrees}C in vacuum afforded the poly(ester-imide-benzoxazole). This polymer was only soluble in sulfuric acid. FTIR and NMR spectra confirmed structure. The poly(ester-imide-benzoxazole) had no detectable thermal transitions up to 500{degrees}C in nitrogen, and was reasonably stable in air and nitrogen, with weight retentions of 95% at 500{degrees}C.

  15. Stable locality sensitive discriminant analysis for image recognition.

    Science.gov (United States)

    Gao, Quanxue; Liu, Jingjing; Cui, Kai; Zhang, Hailin; Wang, Xiaogang

    2014-06-01

    Locality Sensitive Discriminant Analysis (LSDA) is one of the prevalent discriminant approaches based on manifold learning for dimensionality reduction. However, LSDA ignores the intra-class variation that characterizes the diversity of data, resulting in unstableness of the intra-class geometrical structure representation and not good enough performance of the algorithm. In this paper, a novel approach is proposed, namely stable locality sensitive discriminant analysis (SLSDA), for dimensionality reduction. SLSDA constructs an adjacency graph to model the diversity of data and then integrates it in the objective function of LSDA. Experimental results in five databases show the effectiveness of the proposed approach. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Quasi-stable injection channels in a wakefield accelerator

    CERN Document Server

    Wiltshire-Turkay, Mara; Pukhov, Alexander

    2016-01-01

    Particle-driven plasma-wakefield acceleration is a promising alternative to conventional electron acceleration techniques, potentially allowing electron acceleration to energies orders of magnitude higher than can currently be achieved. In this work we investigate the dependence of the energy gain on the position at which electrons are injected into the wake. Test particle simulations show previously unobserved complex structure in the parameter space, with quasi-stable injection channels forming for particles injected in narrow regions away from the centre of the wake. The result is relevant to the planning and tuning of experiments making use of external injection.

  17. Stable isotope analysis of dynamic lipidomics.

    Science.gov (United States)

    Brandsma, Joost; Bailey, Andrew P; Koster, Grielof; Gould, Alex P; Postle, Anthony D

    2017-08-01

    Metabolic pathway flux is a fundamental element of biological activity, which can be quantified using a variety of mass spectrometric techniques to monitor incorporation of stable isotope-labelled substrates into metabolic products. This article contrasts developments in electrospray ionisation mass spectrometry (ESI-MS) for the measurement of lipid metabolism with more established gas chromatography mass spectrometry and isotope ratio mass spectrometry methodologies. ESI-MS combined with diagnostic tandem MS/MS scans permits the sensitive and specific analysis of stable isotope-labelled substrates into intact lipid molecular species without the requirement for lipid hydrolysis and derivatisation. Such dynamic lipidomic methodologies using non-toxic stable isotopes can be readily applied to quantify lipid metabolic fluxes in clinical and metabolic studies in vivo. However, a significant current limitation is the absence of appropriate software to generate kinetic models of substrate incorporation into multiple products in the time domain. Finally, we discuss the future potential of stable isotope-mass spectrometry imaging to quantify the location as well as the extent of lipid synthesis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Petrography, compositional characteristics and stable isotope ...

    African Journals Online (AJOL)

    Petrography, compositional characteristics and stable isotope geochemistry of the Ewekoro formation from Ibese Corehole, eastern Dahomey basin, southwestern Nigeria. ME Nton, MO ... Preserved pore types such as; intercrystaline, moldic and vuggy pores were observed as predominant conduits for fluids. The major ...

  19. petrography, compositional characteristics and stable isotope ...

    African Journals Online (AJOL)

    PROF EKWUEME

    Subsurface samples of the predominantly carbonate Ewekoro Formation, obtained from Ibese core hole within the Dahomey basin were used in this study. Investigations entail petrographic, elemental composition as well as stable isotopes (carbon and oxygen) geochemistry in order to deduce the different microfacies and ...

  20. Substitution of stable isotopes in Chlorella

    Science.gov (United States)

    Flaumenhaft, E.; Katz, J. J.; Uphaus, R. A.

    1969-01-01

    Replacement of biologically important isotopes in the alga Chlorella by corresponding heavier stable isotopes produces increasingly greater deviations from the normal cell size and changes the quality and distribution of certain cellular components. The usefulness of isotopically altered organisms increases interest in the study of such permuted organisms.

  1. Champion Island, Galapagos Stable Oxygen Calibration Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Galapagos Coral Stable Oxygen Calibration Data. Sites: Bartolome Island: 0 deg, 17 min S, 90 deg 33 min W. Champion Island: 1 deg, 15 min S, 90 deg, 05 min W. Urvina...

  2. Stable propagation of 'selfish'genetic elements

    Indian Academy of Sciences (India)

    Unknown

    viruses such as the Epstein-Barr virus (Harris et al 1985;. Kanda et al 2001) and bovine papilloma virus (Lehman and Botchan 1998; Ilves et al 1999), which exist pre- dominantly as extrachromosomal episomes, have been shown to utilize chromosome tethering as a means for stable segregation. The tethering mechanism ...

  3. Unconditionally stable perfectly matched layer boundary conditions

    NARCIS (Netherlands)

    De Raedt, H.; Michielsen, K.

    2007-01-01

    A brief review is given of a systematic, product-formula based approach to construct unconditionally stable algorithms for solving the time-dependent Maxwell equations. The fundamental difficulties that arise when we want to incorporate uniaxial perfectly matched layer boundary conditions into this

  4. Facies, dissolution seams and stable isotope compositions

    Indian Academy of Sciences (India)

    Stable isotope analysis of the limestone shows that 13C and 18O values are compatible with the early Mesoproterozoic open seawater composition. The ribbon limestone facies in the Rohtas Limestone is characterized by micritic beds, each decoupled in a lower band enriched and an upper band depleted in dissolution ...

  5. Connected domination stable graphs upon edge addition ...

    African Journals Online (AJOL)

    A set S of vertices in a graph G is a connected dominating set of G if S dominates G and the subgraph induced by S is connected. We study the graphs for which adding any edge does not change the connected domination number. Keywords: Connected domination, connected domination stable, edge addition ...

  6. Strontium stable isotope behaviour accompanying basalt weathering

    Science.gov (United States)

    Burton, K. W.; Parkinson, I. J.; Gíslason, S. G. R.

    2016-12-01

    The strontium (Sr) stable isotope composition of rivers is strongly controlled by the balance of carbonate to silicate weathering (Krabbenhöft et al. 2010; Pearce et al. 2015). However, rivers draining silicate catchments possess distinctly heavier Sr stable isotope values than their bedrock compositions, pointing to significant fractionation during weathering. Some have argued for preferential release of heavy Sr from primary phases during chemical weathering, others for the formation of secondary weathering minerals that incorporate light isotopes. This study presents high-precision double-spike Sr stable isotope data for soils, rivers, ground waters and estuarine waters from Iceland, reflecting both natural weathering and societal impacts on those environments. The bedrock in Iceland is dominantly basaltic, d88/86Sr ≈ +0.27, extending to lighter values for rhyolites. Geothermal waters range from basaltic Sr stable compositions to those akin to seawater. Soil pore waters reflect a balance of input from primary mineral weathering, precipitation and litter recycling and removal into secondary phases and vegetation. Rivers and ground waters possess a wide range of d88/86Sr compositions from +0.101 to +0.858. Elemental and isotope data indicate that this fractionation primarily results from the formation or dissolution of secondary zeolite (d88/86Sr ≈ +0.10), but also carbonate (d88/86Sr ≈ +0.22) and sometimes anhydrite (d88/86Sr ≈ -0.73), driving the residual waters to heavier or lighter values, respectively. Estuarine waters largely reflect mixing with seawater, but are also be affected by adsorption onto particulates, again driving water to heavy values. Overall, these data indicate that the stability and nature of secondary weathering phases, exerts a strong control on the Sr stable isotope composition of silicate rivers. [1] Krabbenhöft et al. (2010) Geochim. Cosmochim. Acta 74, 4097-4109. [2] Pearce et al. (2015) Geochim. Cosmochim. Acta 157, 125-146.

  7. Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.

    Science.gov (United States)

    Kato, Yuki; Sato, Kengo; Asai, Kiyoshi; Akutsu, Tatsuya

    2012-07-01

    We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins. Both servers can run much faster than existing services with the same purpose on large data sets as well as being at least comparable in prediction accuracy. The Rtips web server along with the stand-alone programs is freely accessible at http://rna.naist.jp/.

  8. Development of a Safety Management Web Tool for Horse Stables.

    Science.gov (United States)

    Leppälä, Jarkko; Kolstrup, Christina Lunner; Pinzke, Stefan; Rautiainen, Risto; Saastamoinen, Markku; Särkijärvi, Susanna

    2015-11-12

    Managing a horse stable involves risks, which can have serious consequences for the stable, employees, clients, visitors and horses. Existing industrial or farm production risk management tools are not directly applicable to horse stables and they need to be adapted for use by managers of different types of stables. As a part of the InnoEquine project, an innovative web tool, InnoHorse, was developed to support horse stable managers in business, safety, pasture and manure management. A literature review, empirical horse stable case studies, expert panel workshops and stakeholder interviews were carried out to support the design. The InnoHorse web tool includes a safety section containing a horse stable safety map, stable safety checklists, and examples of good practices in stable safety, horse handling and rescue planning. This new horse stable safety management tool can also help in organizing work processes in horse stables in general.

  9. A catalytic and dual recycling amplification ATP sensor based on target-driven allosteric structure switching of aptamer beacons.

    Science.gov (United States)

    Peng, Ying; Li, Daxiu; Yuan, Ruo; Xiang, Yun

    2018-05-15

    Abnormal concentrations of ATP are associated with many diseases and cancers, and quantitative detection of ATP is thus of great importance for disease diagnosis and prognosis. In the present work, we report a new dual recycling amplification sensor integrated with catalytic hairpin assembly (CHA) to achieve high sensitivity for fluorescent detection of ATP. The association of the target ATP with the aptamer beacons causes the allosteric structure switching of the aptamer beacons to expose the toehold regions, which hybridize with and unfold the fluorescently quenched hairpin signal probes (HP1) to recycle the target ATP and to trigger CHA between HP1 and the secondary hairpin probes (HP2) to form HP1/HP2 duplexes. Due to the recycling amplification, the presence of ATP leads to the formation of many HP1/HP2 duplexes, generating dramatically amplified fluorescent signals for sensitive detection of ATP. Under optimal experimental conditions, our sensor linearly responds to ATP in the range from 25 to 600nM with a calculated detection limit of 8.2nM. Furthermore, the sensor shows a high selectivity and can also be used to detect ATP in human serums to realize its application for real samples. With the distinct advantage of significant signal amplification without the involvement of any nanomaterial and enzyme, the developed sensor thus holds great potential for simple and sensitive detection of different small molecules and proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. A timeline of stable isotopes and mass spectrometry in the life sciences.

    Science.gov (United States)

    Lehmann, Wolf D

    2017-01-01

    This review retraces the role of stable isotopes and mass spectrometry in the life sciences. The timeline is divided into four segments covering the years 1920-1950, 1950-1980, 1980-2000, and 2000 until today. For each period methodic progress and typical applications are discussed. Application of stable isotopes is driven by improvements of mass spectrometry, chromatography, and related fields in sensitivity, mass accuracy, structural specificity, complex sample handling ability, data output, and data evaluation. We currently experience the vision of omics-type analyses, that is, the comprehensive identification and quantification of a complete compound class within one or a few analytical runs. This development is driven by stable isotopes without competition by radioisotopes. In metabolic studies as classic field of isotopic tracer experiments, stable isotopes and radioisotopes were competing solutions, with stable isotopes as the long-term junior partner. Since the 1990s the number of metabolic studies with radioisotopes decreases, whereas stable isotope studies retain their slow but stable upward tendency. Unique fields of stable isotopes are metabolic tests in newborns, metabolic experiments in healthy controls, newborn screening for inborn errors, quantification of drugs and drug metabolites in doping control, natural isotope fractionation in geology, ecology, food authentication, or doping control, and more recently the field of quantitative omics-type analyses. There, cells or whole organisms are systematically labeled with stable isotopes to study proteomic differences or specific responses to stimuli or genetic manipulation. The duo of stable isotopes and mass spectrometry will probably continue to grow in the life sciences, since it delivers reference-quality quantitative data with molecular specificity, often combined with informative isotope effects. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:58-85, 2017. © 2016 Wiley Periodicals, Inc.

  11. AFM Imaging of Hybridization Chain Reaction-Mediated Signal Transmission Between two DNA Origami Structures

    DEFF Research Database (Denmark)

    Helmig, Sarah Wendelbo; Gothelf, Kurt Vesterager

    2017-01-01

    transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins - of which one is immobilized in specific points along tracks on DNA origami structures - are polymerized to form a continuous DNA duplex, which is visible using atomic force...... microscopy (AFM). Upon addition of a designed initiator, the initiation signal is efficiently transferred >200 nm from a specific location on one origami structure to an end point on another origami structure. The system shows no significant loss of signal when crossing from one nanostructure to another...

  12. Evidence of a stable binary CdCa quasicrystalline phase

    DEFF Research Database (Denmark)

    Jiang, Jianzhong; Jensen, C.H.; Rasmussen, A.R.

    2001-01-01

    Quasicrystals with a primitive icosahedral structure and a quasilattice constant of 5.1215 Angstrom have been synthesized in a binary Cd-Ca system. The thermal stability of the quasicrystal has been investigated by in situ high-temperature x-ray powder diffraction using synchrotron radiation. It ....... It is demonstrated that the binary CdCa quasicrystal is thermodynamic stable up to its melting temperature. The linear thermal expansion coefficient of the quasicrystal is 2.765x10(-5) K-1. (C) 2001 American Institute of Physics.......Quasicrystals with a primitive icosahedral structure and a quasilattice constant of 5.1215 Angstrom have been synthesized in a binary Cd-Ca system. The thermal stability of the quasicrystal has been investigated by in situ high-temperature x-ray powder diffraction using synchrotron radiation...

  13. On The Roman Domination Stable Graphs

    Directory of Open Access Journals (Sweden)

    Hajian Majid

    2017-11-01

    Full Text Available A Roman dominating function (or just RDF on a graph G = (V,E is a function f : V → {0, 1, 2} satisfying the condition that every vertex u for which f(u = 0 is adjacent to at least one vertex v for which f(v = 2. The weight of an RDF f is the value f(V (G = Pu2V (G f(u. The Roman domination number of a graph G, denoted by R(G, is the minimum weight of a Roman dominating function on G. A graph G is Roman domination stable if the Roman domination number of G remains unchanged under removal of any vertex. In this paper we present upper bounds for the Roman domination number in the class of Roman domination stable graphs, improving bounds posed in [V. Samodivkin, Roman domination in graphs: the class RUV R, Discrete Math. Algorithms Appl. 8 (2016 1650049].

  14. Design of optically stable image reflector system.

    Science.gov (United States)

    Tsai, Chung-Yu

    2013-08-01

    The design of a partially optically stable (POS) reflector system, in which the exit ray direction and image pose are unchanged as the reflector system rotates about a specific directional vector, was presented in an earlier study by the current group [Appl. Phys. B100, 883-890 (2010)]. The present study further proposes an optically stable image (OSI) reflector system, in which not only is the optical stability property of the POS system retained, but the image position and total ray path length are also fixed. An analytical method is proposed for the design of OSI reflector systems comprising multiple reflectors. The validity of the proposed approach is demonstrated by means of two illustrative examples.

  15. Stable microfluidic flow focusing using hydrostatics.

    Science.gov (United States)

    Gnyawali, Vaskar; Saremi, Mohammadali; Kolios, Michael C; Tsai, Scott S H

    2017-05-01

    We present a simple technique to generate stable hydrodynamically focused flows by driving the flow with hydrostatic pressure from liquid columns connected to the inlets of a microfluidic device. Importantly, we compare the focused flows generated by hydrostatic pressure and classical syringe pump driven flows and find that the stability of the hydrostatic pressure driven technique is significantly better than the stability achieved via syringe pumps, providing fluctuation-free focused flows that are suitable for sensitive microfluidic flow cytometry applications. We show that the degree of flow focusing with the hydrostatic method can be accurately controlled by the simple tuning of the liquid column heights. We anticipate that this approach to stable flow focusing will find many applications in microfluidic cytometry technologies.

  16. Utilization of stable isotopes in medicine

    International Nuclear Information System (INIS)

    1980-11-01

    The ten lectures given at this round table are presented together with a discussion. Five lectures, relating to studies in which deuterium oxide was employed as a tracer of body water, dealt with pulmonary water measurements in man and animals, the total water pool in adipose subjects, and liquid compartments in children undergoing hemodyalisis. The heavy water is analysed by infrared spectrometry and a new double spectrodoser is described. Two studies using 13 C as tracer, described the diagnosis of liver troubles and diabetes respectively. A general review of the perspectives of the application of stable isotopes in clinical medicine is followed by a comparison of the use of stable and radioactive isotopes in France [fr

  17. Thermally Stable, Latent Olefin Metathesis Catalysts

    OpenAIRE

    Thomas, Renee M.; Fedorov, Alexey; Keitz, Benjamin K.; Grubbs, Robert H.

    2011-01-01

    Highly thermally stable N-aryl,N-alkyl N-heterocyclic carbene (NHC) ruthenium catalysts were designed and synthesized for latent olefin metathesis. These catalysts showed excellent latent behavior toward metathesis reactions, whereby the complexes were inactive at ambient temperature and initiated at elevated temperatures, a challenging property to achieve with second generation catalysts. A sterically hindered N-tert-butyl substituent on the NHC ligand of the ruthenium complex was found to i...

  18. The nature of stable insomnia phenotypes.

    Science.gov (United States)

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L

    2015-01-01

    We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Longitudinal. Urban, community-based. Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). None. At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the 'neither criterion' phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With the exception of daytime sleepiness, few clinical differences are apparent across stable phenotypes.

  19. A belief-based evolutionarily stable strategy

    OpenAIRE

    Deng, Xinyang; Wang, Zhen; Liu, Qi; Deng, Yong; Mahadevan, Sankaran

    2014-01-01

    As an equilibrium refinement of the Nash equilibrium, evolutionarily stable strategy (ESS) is a key concept in evolutionary game theory and has attracted growing interest. An ESS can be either a pure strategy or a mixed strategy. Even though the randomness is allowed in mixed strategy, the selection probability of pure strategy in a mixed strategy may fluctuate due to the impact of many factors. The fluctuation can lead to more uncertainty. In this paper, such uncertainty involved in mixed st...

  20. Stable iodine prophylaxis. Recommendations of the 2nd UK Working Group on Stable Iodine Prophylaxis

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    The Working Group reviewed the revised Who guidance and the information published since 1991 on the risks of thyroid cancer in children from radioiodine and the risks of side effects from stable iodine. In particular, it reviewed data compiled on the incidence of thyroid cancers in children following the accident at the Chernobyl nuclear power plant in 1986. It considered whether the NRPB Earls were still appropriate, in the light of the new data. It also reviewed a range of other recommendations given by the 1st Working Group, concerning the chemical form of stable iodine tablets and practical issues concerning implementation of stable iodine prophylaxis. Finally, it reviewed the Patient Information Leaflet that is required, by law, to be included in each box of tablets and provided suggestions for information to be included in a separate information leaflet to be handed out to the public when stable iodine tablets are distributed.