Sample records for cross-strand intercalative stacking

  1. Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides

    NASA Astrophysics Data System (ADS)

    Tuite, Eimer Mary; Nordén, Bengt

    2018-01-01

    The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases. With poly(dA)·poly(dT), intercalative binding is unfavourable, although some dye molecules may intercalate at low ionic strength, and groove binding is strongly promoted with increasing concentration of background salt. However, stacking with bases is observed with single-stranded poly(dA) and with triplex poly(dT)*poly(dA)·poly(dT) which suggests that the unusual structure of poly(dA)·poly(dT) precludes intercalation. Thionine behaves similarly to the related dye methylene blue, and small differences may be attributed either to the ability of thionine to form H-bonds that stabilize intercalation or to its improved stacking interactions in the basepair pocket on steric grounds.

  2. Binding of Phenazinium Dye Safranin T to Polyriboadenylic Acid: Spectroscopic and Thermodynamic Study

    PubMed Central

    Roy, Snigdha; Das, Suman

    2014-01-01

    Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na+] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure. PMID:24498422

  3. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study.

    PubMed

    Pradhan, Ankur Bikash; Haque, Lucy; Roy, Snigdha; Das, Suman

    2014-01-01

    Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

  4. Fmoc-RGDS based fibrils: atomistic details of their hierarchical assembly.

    PubMed

    Zanuy, David; Poater, Jordi; Solà, Miquel; Hamley, Ian W; Alemán, Carlos

    2016-01-14

    We describe the 3D supramolecular structure of Fmoc-RGDS fibrils, where Fmoc and RGDS refer to the hydrophobic N-(fluorenyl-9-methoxycarbonyl) group and the hydrophilic Arg-Gly-Asp-Ser peptide sequence, respectively. For this purpose, we performed atomistic all-atom molecular dynamics simulations of a wide variety of packing modes derived from both parallel and antiparallel β-sheet configurations. The proposed model, which closely resembles the cross-β core structure of amyloids, is stabilized by π-π stacking interactions between hydrophobic Fmoc groups. More specifically, in this organization, the Fmoc-groups of β-strands belonging to the same β-sheet form columns of π-stacked aromatic rings arranged in a parallel fashion. Eight of such columns pack laterally forming a compact and dense hydrophobic core, in which two central columns are surrounded by three adjacent columns on each side. In addition to such Fmoc···Fmoc interactions, the hierarchical assembly of the constituent β-strands involves a rich variety of intra- and inter-strand interactions. Accordingly, hydrogen bonding, salt bridges and π-π stacking interactions coexist in the highly ordered packing network proposed for the Fmoc-RGDS amphiphile. Quantum mechanical calculations, which have been performed to quantify the above referred interactions, confirm the decisive role played by the π-π stacking interactions between the rings of the Fmoc groups, even though both inter-strand and intra-strand hydrogen bonds and salt bridges also play a non-negligible role. Overall, these results provide a solid reference to complement the available experimental data, which are not precise enough to determine the fibril structure, and reconcile previous independent observations.

  5. Low-Energy Electron-Induced Strand Breaks in Telomere-Derived DNA Sequences-Influence of DNA Sequence and Topology.

    PubMed

    Rackwitz, Jenny; Bald, Ilko

    2018-03-26

    During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (<20 eV) electrons, which are able to damage DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5'-(TTA GGG) 2 is more sensitive to low-energy electrons than an intermixed sequence 5'-(TGT GTG A) 2 confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5'-(GGG ATT) 2 to 5'-(GGG ATT) 4 ), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K + ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Dual door entry to exciplex emission in a chimeric DNA duplex containing non-nucleoside-nucleoside pair.

    PubMed

    Bag, Subhendu Sekhar; Talukdar, Sangita; Kundu, Rajen; Saito, Isao; Jana, Subhashis

    2014-01-25

    Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate () is paired against a fluorescent nucleosidic base surrogate (). Packing of the nucleobases via intercalative stacking interactions led to an exciplex emission either via FRET from the donor or direct excitation of the FRET acceptor .

  7. Sequence-Dependent Elasticity and Electrostatics of Single-Stranded DNA: Signatures of Base-Stacking

    PubMed Central

    McIntosh, Dustin B.; Duggan, Gina; Gouil, Quentin; Saleh, Omar A.

    2014-01-01

    Base-stacking is a key factor in the energetics that determines nucleic acid structure. We measure the tensile response of single-stranded DNA as a function of sequence and monovalent salt concentration to examine the effects of base-stacking on the mechanical and thermodynamic properties of single-stranded DNA. By comparing the elastic response of highly stacked poly(dA) and that of a polypyrimidine sequence with minimal stacking, we find that base-stacking in poly(dA) significantly enhances the polymer’s rigidity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than mean-field predictions. Further, we provide a model-independent estimate of the free energy difference between stacked poly(dA) and unstacked polypyrimidine, finding it to be ∼−0.25 kBT/base and nearly constant over three orders of magnitude in salt concentration. PMID:24507606

  8. Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

    PubMed

    Sedova, Ada; Banavali, Nilesh K

    2017-03-14

    Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.

  9. Higher-order molecular packing in amyloid-like fibrils constructed with linear arrangements of hydrophobic and hydrogen-bonding side-chains.

    PubMed

    Saiki, Masatoshi; Honda, Shinya; Kawasaki, Kazunori; Zhou, Deshan; Kaito, Akira; Konakahara, Takeo; Morii, Hisayuki

    2005-05-13

    Various mutants of the protein fragment, barnase module-1 (1-24) were investigated in order to reveal the structural principle of amyloid-like fibrils. By means of circular dichroism spectroscopy, X-ray diffraction, electron microscopy, and thioflavin T binding assay, we found that the molecules containing two beta-strands and an intervening turn structure are assembled to form a cross-beta structure. Stabilization by both the hydrophobic interactions and hydrogen bonding between the respective paired side-chains on the coupled beta-strands was essential for fibril formation. These two types of interaction can also arrange the corresponding residues in lines on both sheet surfaces of protofilaments with a cross-beta structure. This leads to the most probable fibril structure constructed with the line-matching interactions between protofilaments. Consideration of the geometrical symmetry resulted in our finding that a limited number of essential models for molecular packing in fibril structure are stable, which would rationally explain the occurrence of two or three morphologies from an identical molecular species. The ribbon-like fibrils exhibited striped texture along the axis, which was assigned to a stacked two-sheet repeat as a structural unit. The comprehensively proposed structural model, that is, the sheet-sheet interaction between left-handed cross-beta structures, results in a slightly right-handed twist of beta-sheet stacking, which reasonably elucidates the intrinsic sizes of the fibril width and its helical period along the fibril axis, as the bias in the orientation of the hydrogen-bonded beta-strand pair at the lateral edge is larger than that at the central protofilament.

  10. Structure and dynamics of proflavine association around DNA.

    PubMed

    Sasikala, Wilbee D; Mukherjee, Arnab

    2016-04-21

    Proflavine is a small molecule that intercalates into DNA and, thereby, acts as an anticancer agent. Intercalation of proflavine is shown to be a two-step process in which the first step is believed to be the formation of a pre-intercalative outside bound state. Experimental studies so far have been unable to capture the nature of the outside bound state. However, the sub-millisecond timescale observed in fluorescence kinetic experiments is often attributed to the binding of proflavine outside of DNA. Here, we have performed molecular dynamics simulations with multiple proflavine molecules to study the structure and dynamics of the formation of the outside bound state of DNA at different ion concentrations. We observed that the timescale of the outside bound state formation is, at least, five orders of magnitude faster (in nanoseconds) than the experimentally reported timescale (sub-milliseconds) attributed to binding outside DNA. Moreover, we also observed the stacked arrangement of proflavine all around DNA, which is different from the experimentally predicted stacking arrangement perpendicular to the helical axis of DNA in the close vicinity of the phosphate groups. This study, therefore, provides insight into the molecular structure and dynamics of the pre-intercalative outside bound state and will help in understanding the overall intercalation mechanism.

  11. Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles.

    PubMed

    Hakker, Lauren; Marchi, Alexandria N; Harris, Kimberly A; LaBean, Thomas H; Agris, Paul F

    2014-01-01

    DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson-Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure's thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2'-deoxyribothymidines, 2'-O-methylribouridines, or abasic 1',2'-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2'-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.

  12. A trait stacking system via intra-genomic homologous recombination.

    PubMed

    Kumar, Sandeep; Worden, Andrew; Novak, Stephen; Lee, Ryan; Petolino, Joseph F

    2016-11-01

    A gene targeting method has been developed, which allows the conversion of 'breeding stacks', containing unlinked transgenes into a 'molecular stack' and thereby circumventing the breeding challenges associated with transgene segregation. A gene targeting method has been developed for converting two unlinked trait loci into a single locus transgene stack. The method utilizes intra-genomic homologous recombination (IGHR) between stably integrated target and donor loci which share sequence homology and nuclease cleavage sites whereby the donor contains a promoterless herbicide resistance transgene. Upon crossing with a zinc finger nuclease (ZFN)-expressing plant, double-strand breaks (DSB) are created in both the stably integrated target and donor loci. DSBs flanking the donor locus result in intra-genomic mobilization of a promoterless selectable marker-containing donor sequence, which can be utilized as a template for homology-directed repair of a concomitant DSB at the target locus resulting in a functional selectable marker via nuclease-mediated cassette exchange (NMCE). The method was successfully demonstrated in maize using a glyphosate tolerance gene as a donor whereby up to 3.3 % of the resulting progeny embryos cultured on selection medium regenerated plants with the donor sequence integrated into the target locus. The process could be extended to multiple cycles of trait stacking by virtue of a unique intron sequence homology for NMCE between the target and the donor loci. This is the first report that describes NMCE via IGHR, thereby enabling trait stacking using conventional crossing.

  13. The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.

    PubMed Central

    Olson, W K

    1975-01-01

    Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed. PMID:1052529

  14. Stereochemical model for proflavin intercalation in A-DNA.

    PubMed Central

    Alden, C J; Arnott, S

    1977-01-01

    Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming trans, with all sugars retaining the characteristics C3'-endo pucker. This extended conformation results in virtually no helical unwinding, suggesting it may be an appropriate model for an intercalative intermediary in mutagenesis by virtue of its similarity to standard helical DNA. PMID:593890

  15. Interaction of phenazinium dyes with double-stranded poly(A): Spectroscopy and isothermal titration calorimetry studies

    NASA Astrophysics Data System (ADS)

    Khan, Asma Yasmeen; Saha, Baishakhi; Kumar, Gopinatha Suresh

    2014-10-01

    A comprehensive study on the binding of phenazinium dyes viz. janus green B, indoine blue, safranine O and phenosafranine with double stranded poly(A) using various spectroscopic and calorimetric techniques is presented. A higher binding of janus green B and indoine blue over safranine O and phenosafranine to poly(A) was observed from all experiments. Intercalative mode of binding of the dyes was inferred from fluorescence polarization anisotropy, iodide quenching and viscosity experiments. Circular dichroism study revealed significant perturbation of the secondary structure of poly(A) on binding of these dyes. Results from isothermal titration calorimetry experiments suggested that the binding was predominantly entropy driven with a minor contribution of enthalpy to the standard molar Gibbs energy. The results presented here may open new opportunities in the application of these dyes as RNA targeted therapeutic agents.

  16. Conformational Ensemble of hIAPP Dimer: Insight into the Molecular Mechanism by which a Green Tea Extract inhibits hIAPP Aggregation

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang; Lei, Jiangtao; Sun, Yunxiang; Zhang, Qingwen; Wei, Guanghong

    2016-09-01

    Small oligomers formed early along human islet amyloid polypeptide (hIAPP) aggregation is responsible for the cell death in Type II diabetes. The epigallocatechin gallate (EGCG), a green tea extract, was found to inhibit hIAPP fibrillation. However, the inhibition mechanism and the conformational distribution of the smallest hIAPP oligomer - dimer are mostly unknown. Herein, we performed extensive replica exchange molecular dynamic simulations on hIAPP dimer with and without EGCG molecules. Extended hIAPP dimer conformations, with a collision cross section value similar to that observed by ion mobility-mass spectrometry, were observed in our simulations. Notably, these dimers adopt a three-stranded antiparallel β-sheet and contain the previously reported β-hairpin amyloidogenic precursor. We find that EGCG binding strongly blocks both the inter-peptide hydrophobic and aromatic-stacking interactions responsible for inter-peptide β-sheet formation and intra-peptide interaction crucial for β-hairpin formation, thus abolishes the three-stranded β-sheet structures and leads to the formation of coil-rich conformations. Hydrophobic, aromatic-stacking, cation-π and hydrogen-bonding interactions jointly contribute to the EGCG-induced conformational shift. This study provides, on atomic level, the conformational ensemble of hIAPP dimer and the molecular mechanism by which EGCG inhibits hIAPP aggregation.

  17. The impact of base stacking on the conformations and electrostatics of single-stranded DNA.

    PubMed

    Plumridge, Alex; Meisburger, Steve P; Andresen, Kurt; Pollack, Lois

    2017-04-20

    Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Technology assessment of future intercity passenger transporation systems. Volume 2: Identification of issues affecting intercity transportation

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Papers on major issues and trends that affect the future of intercity transportation are presented. Specific areas covered include: political, social, technological, institutional, and economic mechanisms, the workings of which determine how future intercity transporation technologies will evolve and be put into service; the major issues of intercity transportation from the point of view of reform, including candidate transporation technologies; and technical analysis of trends affecting the evolution of intercity transportation technologies.

  19. Department of Homeland Security Assistance to States and Localities: A Summary and Issues for the 111th Congress

    DTIC Science & Technology

    2009-12-01

    6 Intercity Passenger Rail Program (Amtrak) .....................................................................7 Intercity Bus Security Grant...20 Additionally Amtrak is eligible to receive funding to continue security enhancements for its intercity rail services between high-risk urban...Research Service 7 Intercity Passenger Rail Program (Amtrak) The Intercity Passenger Rail Program (IPR) is designed to enhance security of the

  20. Structure-spectrophotometric selectivity relationship in interactions of quercetin related flavonoids with double stranded and single stranded RNA

    NASA Astrophysics Data System (ADS)

    Piantanida, Ivo; Mašić, Lozika; Rusak, Gordana

    2009-04-01

    Interactions of five flavonoids with dsRNA and single stranded ssRNA were studied by UV/vis titrations. The results obtained supported the intercalative binding mode as a dominant interaction of studied flavonoids with dsRNA as well as major interaction with ssRNA. Furthermore, changes of the UV/vis spectra of flavonoids induced by addition of poly G or poly C, respectively, are significantly stronger than changes induced by double stranded poly G-poly C, pointing to essential role of the free poly G or poly C sequence (not hydrogen bonded in double helix). Exclusively poly G caused significant batochromic shift of the UV/vis maxima of all studied flavonoids, whereby the intensity of batochromic shift is nicely correlated to the number of OH groups of flavonoid. Unlikely to poly G, addition of poly A and poly U induced measurable changes only in the UV/vis spectra of flavonoids characterised by no OH (galangin) or three OH groups (myricetin) on the phenyl part of the molecule. Consequently, flavonoids with one- or two-OH groups on the phenyl part of the molecule (luteolin, fisetin, kaempferol) specifically differentiate between poly A, poly U (negligible changes in the UV/Vis spectra) and poly G (strong changes in the UV/Vis spectra) as well as poly C (moderate changes in the UV/Vis spectra).

  1. Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

    PubMed Central

    Sheng, Gang; Gogakos, Tasos; Wang, Jiuyu; Zhao, Hongtu; Serganov, Artem; Juranek, Stefan

    2017-01-01

    Abstract We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6’U7’ and 6’A7’ on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. PMID:28911094

  2. Spectroscopic and electrochemical studies of the interaction between oleuropein, the major bio-phenol in olives, and salmon sperm DNA

    NASA Astrophysics Data System (ADS)

    Mohamadi, Maryam; Afzali, Daryoush; Esmaeili-Mahani, Saeed; Mostafavi, Ali; Torkzadeh-Mahani, Masoud

    2015-09-01

    Interaction of oleuropein, the major bio-phenol in olive leaf and fruit, with salmon sperm double-stranded DNA was investigated by employing electronic absorption titrations, fluorescence quenching spectroscopy, competitive fluorescence spectroscopy, thermal denaturation and voltammetric studies. Titration of oleuropein with the DNA caused a hypochromism accompanied with a red shift indicating an intercalative mode of interaction. Binding constant of 1.4 × 104 M-1 was obtained for this interaction. From the curves of fluorescence titration of oleuropein with the DNA, binding constant and binding sites were calculated to be 8.61 × 103 M-1 and 1.05, respectively. Competitive studies with ethidium bromide (a well-known DNA intercalator) showed that the bio-phenol could take the place of ethidium bromide in the DNA intercalation sites. The interaction of oleuropein with DNA was also studied electrochemically. In the presence of the DNA, the anodic and cathodic peak currents of oleuropein decreased accompanied with increases in peak-to-peak potential separation and formal potential, indicating the intercalation of oleuropein into the DNA double helix. Moreover, melting temperature of the DNA was found to increase in the presence of oleuropein, indicating the stabilization of the DNA double helix due to an intercalative interaction.

  3. 75 FR 26839 - Metrics and Standards for Intercity Passenger Rail Service under Section 207 of the Passenger...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-12

    ... performance and service quality of intercity passenger train operations. In compliance with the statute, the FRA and Amtrak jointly drafted performance metrics and standards for intercity passenger rail service... and Standards for Intercity Passenger Rail Service under Section 207 of the Passenger Rail Investment...

  4. Solution structure of a GAAA tetraloop receptor RNA.

    PubMed Central

    Butcher, S E; Dieckmann, T; Feigon, J

    1997-01-01

    The GAAA tetraloop receptor is an 11-nucleotide RNA sequence that participates in the tertiary folding of a variety of large catalytic RNAs by providing a specific binding site for GAAA tetraloops. Here we report the solution structure of the isolated tetraloop receptor as solved by multidimensional, heteronuclear magnetic resonance spectroscopy. The internal loop of the tetraloop receptor has three adenosines stacked in a cross-strand or zipper-like fashion. This arrangement produces a high degree of base stacking within the asymmetric internal loop without extrahelical bases or kinking the helix. Additional interactions within the internal loop include a U. U mismatch pair and a G.U wobble pair. A comparison with the crystal structure of the receptor RNA bound to its tetraloop shows that a conformational change has to occur upon tetraloop binding, which is in good agreement with previous biochemical data. A model for an alternative binding site within the receptor is proposed based on the NMR structure, phylogenetic data and previous crystallographic structures of tetraloop interactions. PMID:9405377

  5. 49 CFR 37.91 - Wheelchair locations and food service on intercity rail trains.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Wheelchair locations and food service on intercity... Entities § 37.91 Wheelchair locations and food service on intercity rail trains. (a) As soon as practicable, but in no event later than July 26, 1995, each person providing intercity rail service shall provide...

  6. 49 CFR 37.89 - Remanufacture of intercity and commuter rail cars and purchase or lease of remanufactured...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 1 2012-10-01 2012-10-01 false Remanufacture of intercity and commuter rail cars and purchase or lease of remanufactured intercity and commuter rail cars. 37.89 Section 37.89... commuter rail cars and purchase or lease of remanufactured intercity and commuter rail cars. (a) This...

  7. 49 CFR 37.89 - Remanufacture of intercity and commuter rail cars and purchase or lease of remanufactured...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 1 2013-10-01 2013-10-01 false Remanufacture of intercity and commuter rail cars and purchase or lease of remanufactured intercity and commuter rail cars. 37.89 Section 37.89... commuter rail cars and purchase or lease of remanufactured intercity and commuter rail cars. (a) This...

  8. 26 CFR 48.6421-2 - Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... gasoline used in intercity, local, or school buses. 48.6421-2 Section 48.6421-2 Internal Revenue INTERNAL... Manufacturers Taxes § 48.6421-2 Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses. (a) In general. If gasoline is used in an intercity or local bus while engaged in...

  9. 26 CFR 48.6421-2 - Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... gasoline used in intercity, local, or school buses. 48.6421-2 Section 48.6421-2 Internal Revenue INTERNAL... Manufacturers Taxes § 48.6421-2 Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses. (a) In general. If gasoline is used in an intercity or local bus while engaged in...

  10. 26 CFR 48.6421-2 - Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... gasoline used in intercity, local, or school buses. 48.6421-2 Section 48.6421-2 Internal Revenue INTERNAL... Manufacturers Taxes § 48.6421-2 Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses. (a) In general. If gasoline is used in an intercity or local bus while engaged in...

  11. 26 CFR 48.6421-2 - Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... gasoline used in intercity, local, or school buses. 48.6421-2 Section 48.6421-2 Internal Revenue INTERNAL... Manufacturers Taxes § 48.6421-2 Credits or payments to ultimate purchasers of gasoline used in intercity, local, or school buses. (a) In general. If gasoline is used in an intercity or local bus while engaged in...

  12. Clinical implementation of stereotaxic brain implant optimization

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

    Rosenow, U.F.; Wojcicka, J.B.

    1991-03-01

    This optimization method for stereotaxic brain implants is based on seed/strand configurations of the basic type developed for the National Cancer Institute (NCI) atlas of regular brain implants. Irregular target volume shapes are determined from delineation in a stack of contrast enhanced computed tomography scans. The neurosurgeon may then select up to ten directions, or entry points, of surgical approach of which the program finds the optimal one under the criterion of smallest target volume diameter. Target volume cross sections are then reconstructed in 5-mm-spaced planes perpendicular to the implantation direction defined by the entry point and the target volumemore » center. This information is used to define a closed line in an implant cross section along which peripheral seed strands are positioned and which has now an irregular shape. Optimization points are defined opposite peripheral seeds on the target volume surface to which the treatment dose rate is prescribed. Three different optimization algorithms are available: linear least-squares programming, quadratic programming with constraints, and a simplex method. The optimization routine is implemented into a commercial treatment planning system. It generates coordinate and source strength information of the optimized seed configurations for further dose rate distribution calculation with the treatment planning system, and also the coordinate settings for the stereotaxic Brown-Roberts-Wells (BRW) implantation device.« less

  13. Sequence and Temperature Dependence of the End-to-End Collision Dynamics of Single-Stranded DNA

    PubMed Central

    Uzawa, Takanori; Isoshima, Takashi; Ito, Yoshihiro; Ishimori, Koichiro; Makarov, Dmitrii E.; Plaxco, Kevin W.

    2013-01-01

    Intramolecular collision dynamics play an essential role in biomolecular folding and function and, increasingly, in the performance of biomimetic technologies. To date, however, the quantitative studies of dynamics of single-stranded nucleic acids have been limited. Thus motivated, here we investigate the sequence composition, chain-length, viscosity, and temperature dependencies of the end-to-end collision dynamics of single-stranded DNAs. We find that both the absolute collision rate and the temperature dependencies of these dynamics are base-composition dependent, suggesting that base stacking interactions are a significant contributor. For example, whereas the end-to-end collision dynamics of poly-thymine exhibit simple, linear Arrhenius behavior, the behavior of longer poly-adenine constructs is more complicated. Specifically, 20- and 25-adenine constructs exhibit biphasic temperature dependencies, with their temperature dependences becoming effectively indistinguishable from that of poly-thymine above 335 K for 20-adenines and 328 K for 25-adenines. The differing Arrhenius behaviors of poly-thymine and poly-adenine and the chain-length dependence of the temperature at which poly-adenine crosses over to behave like poly-thymine can be explained by a barrier friction mechanism in which, at low temperatures, the energy barrier for the local rearrangement of poly-adenine becomes the dominant contributor to its end-to-end collision dynamics. PMID:23746521

  14. Intercity bus service in Virginia.

    DOT National Transportation Integrated Search

    1981-01-01

    The intercity bus industry in Virginia was examined to gain information on the status of the industry and to determine the likely impacts of state policy options relating to assistance and deregulation on the industry. The national intercity bus indu...

  15. Intercity passenger rail : implications for urban, regional, and national mobility.

    DOT National Transportation Integrated Search

    2012-01-01

    Recent policy and regulatory actions by the U.S. government have revived interest in intercity passenger : rail among transportation planners, policymakers, and the general public. As part of a fully integrated : multimodal intercity corridor, passen...

  16. Pennsylvania intercity bus study : final report

    DOT National Transportation Integrated Search

    1984-09-01

    Report presents the findings of a study to inventory the intercity bus industry in Pennsylvania. Objectives were to assemble information about the intercity bus industry in Pennsylvania in a form that can be used for policy formulation and for manage...

  17. Benefit-cost analysis framework for evaluating inter-city transit investment.

    DOT National Transportation Integrated Search

    2008-10-01

    This report describes the development and application of a benefit/cost analysis (BCA) model to support the evaluation of investment decisions for intercity bus services. The model recognizes two principle types of intercity bus benefits: benefits th...

  18. Synthesis Characterization and DNA Interaction Studies of a New Zn(II) Complex Containing Different Dinitrogen Aromatic Ligands

    PubMed Central

    Shahabadi, Nahid; Mohammadi, Somaye

    2012-01-01

    A mononuclear complex of Zn(II), [Zn(DIP)2 (DMP)] (NO3)2 ·2H2O in which DIP is 4,7-diphenyl-1,10-phenanthroline and DMP is 4,4′-dimethyl-2,2′-bipyridine has been prepared and characterized by 1HNMR spectroscopy, FT-IR, UV-Vis and elemental analysis techniques. DNA-binding properties of the complex were studied using UV-vis spectra, circular dichroism (CD) spectra, fluorescence, cyclic voltammetry (CV), and viscosity measurements. The results indicate that this zinc(II) complex can intercalate into the stacked base pairs of DNA and compete with the strong intercalator ethidium bromide for the intercalative binding sites. PMID:22956919

  19. Multistrand superconductor cable

    DOEpatents

    Borden, A.R.

    1984-03-08

    Improved multistrand Rutherford-type superconductor cable is produced by using strands which are preformed, prior to being wound into the cable, so that each strand has a variable cross section, with successive portions having a substantially round cross section, a transitional oval cross section, a rectangular cross section, a transitional oval cross section, a round cross section and so forth, in repetitive cycles along the length of the strand. The cable is wound and flattened so that the portions of rectangular cross section extend across the two flat sides of the cable at the strand angle. The portions of round cross section are bent at the edges of the flattened cable, so as to extend between the two flat sides. The rectangular portions of the strands slide easil

  20. Innovative Funding for Intercity Modes: A Casebook of State, Local, and Private Approaches

    DOT National Transportation Integrated Search

    1987-07-01

    The document reviews non-Federal funding sources for intercity transportation services. The report examines the structure of intercity passenger and freight transportation services, focusing on bus, rail, and short-haul air. It explores public-privat...

  1. Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent.

    PubMed

    Zhang, Yuyuan; de La Harpe, Kimberly; Hariharan, Mahesh; Kohler, Bern

    2018-04-17

    The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

  2. Measuring the benefits of intercity passenger rail : a study of the Heartland Flyer corridor.

    DOT National Transportation Integrated Search

    2010-04-01

    In recent years, the policy and regulatory environment for intercity passenger rail in the United States has : shifted dramatically, sparking a renewed interest in intercity passenger rail among policymakers, : planners, and the general public. As th...

  3. 49 CFR 37.55 - Intercity rail station accessibility.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Intercity rail station accessibility. 37.55 Section 37.55 Transportation Office of the Secretary of Transportation TRANSPORTATION SERVICES FOR INDIVIDUALS WITH DISABILITIES (ADA) Transportation Facilities § 37.55 Intercity rail station accessibility...

  4. System and prospects of China's intercity rail transit technology

    NASA Astrophysics Data System (ADS)

    Gong, Ming

    2018-06-01

    City clusters and metropolitan areas in China are flourishing in the midst of the deepening urbanization in the country, thereby resulting in the emergence of intercity rail transit. Intercity railways connect mainline and urban railways for an integrated regional transportation system that underpins and leads the development of city clusters and metropolitan areas. This study explores the development mode and service characteristics of intercity rail transit, as well as proposes overviews on this system and prospects of its future technology in China.

  5. Multistrand superconductor cable

    DOEpatents

    Borden, Albert R.

    1985-01-01

    Improved multistrand Rutherford-type superconductor cable is produced by using strands which are preformed, prior to being wound into the cable, so that each strand has a variable cross section, with successive portions having a substantially round cross section, a transitional oval cross section, a rectangular cross section, a transitional oval cross section, a round cross section and so forth, in repetitive cycles along the length of the strand. The cable is wound and flattened so that the portions of rectangular cross section extend across the two flat sides of the cable at the strand angle. The portions of round cross section are bent at the edges of the flattened cable, so as to extend between the two flat sides. The rectangular portions of the strands slide easily over one another, so as to facilitate flexing and bending of the cable, while also minimizing the possibility of causing damage to the strands by such flexing or bending. Moreover, the improved cable substantially maintains its compactness and cross-sectional shape when the cable is flexed or bent.

  6. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA

    PubMed Central

    Yang, Zhiyu; Price, Nathan E.; Johnson, Kevin M.

    2017-01-01

    Abstract Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3’ddR5p) at the 3’-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3’ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3’ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems. PMID:28531327

  7. Dye-induced aggregation of single stranded RNA: a mechanistic approach.

    PubMed

    Biver, Tarita; Ciatto, Carlo; Secco, Fernando; Venturini, Marcella

    2006-08-15

    The binding of proflavine (D) to single stranded poly(A) (P) was investigated at pH 7.0 and 25 degrees C using T-jump, stopped-flow and spectrophotometric methods. Equilibrium measurements show that an external complex PD(I) and an internal complex PD(II) form upon reaction between P and D and that their concentrations depend on the polymer/dye concentration ratio (C(P)/C(D)). For C(P)/C(D)<2.5, cooperative formation of stacks external to polymer strands prevails (PD(I)). Equilibria and T-jump experiments, performed at I=0.1M and analyzed according to the Schwarz theory for cooperative binding, provide the values of site size (g=1), equilibrium constant for the nucleation step (K( *)=(1.4+/-0.6)x10(3)M(-1)), equilibrium constant for the growth step (K=(1.2+/-0.6)x10(5)M(-1)), cooperativity parameter (q=85) and rate constants for the growth step (k(r)=1.2x10(7)M(-1)s(-1), k(d)=1.1 x 10(2)s(-1)). Stopped-flow experiments, performed at low ionic strength (I=0.01 M), indicate that aggregation of stacked poly(A) strands do occur provided that C(P)/C(D)<2.5.

  8. 77 FR 69918 - Notice and Request for Comments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-21

    ... Northeast intercity or regional travel experience during the 12 months prior to interview. Estimated Number... information from the public to determine current intercity and regional travel behavior of Northeast residents... experienced a qualifying intercity or regional travel trip to provide more detailed travel information and...

  9. Department of Homeland Security Assistance to States and Localities: A Summary and Issues for the 111th Congress

    DTIC Science & Technology

    2009-02-26

    6 Intercity Passenger Rail Program (Amtrak...6 Intercity Bus Security Grant Program................................................................................. 7...for its intercity rail services between high-risk urban areas. 20 U.S. Department of Homeland Security, Federal Emergency Management Agency

  10. Intercity passenger rail : Amtrak faces challenges in improving its financial condition : statement of Phyllis F. Scheinberg

    DOT National Transportation Integrated Search

    1999-10-28

    The Rail Passenger Service Act of 1970 created Amtrak as the nation's intercity passenger railroad. The act, as amended, gave Amtrak a number of goals, including providing modern, efficient intercity passenger rail service; giving Americans an altern...

  11. Current-voltage characteristics of double stranded versus single stranded DNA molecules

    NASA Astrophysics Data System (ADS)

    Hartzell, B.; Chen, Hong; Heremans, J. J.; McCord, B.; Soghomonian, V.

    2004-03-01

    Investigation of DNA conductivity has focused on the native, duplex structure, with controversial results. Here, we present the influence of the double-helical structure on charge transport through lambda DNA molecules. The current-voltage (I-V) characteristics of both disulfide-labeled double stranded DNA (dsDNA) and disulfide-labeled single stranded DNA (ssDNA) were measured. The ssDNA was formed from the dsDNA using two different methods for comparison purposes: a thermal/chemical denaturation and enzymatic digestion utilizing lambda exonuclease. Resulting I-V characteristics of both the double stranded and single stranded samples were close-to-linear when measured at room temperature. However, the ssDNA samples consistently gave conductivity values about two orders of magnitude smaller in amplitude. Our results suggest an integral relationship between the native structure of DNA with its stacked base pairs and the molecule's ability to support charge transport.(NSF NIRT 0103034)

  12. Intercity passenger rail : decisions on the future of Amtrak and intercity passenger rail are approaching

    DOT National Transportation Integrated Search

    2000-09-26

    Key decisions will soon have to be made regarding the future of Amtrak, the nation's intercity passenger rail operator. If Amtrak does not reach operational self-sufficiency within the next 2 years, federal law requires that the Amtrak Reform Council...

  13. Intercity passenger rail : assessing the benefits of increased federal funding for Amtrak and high-speed passenger rail systems

    DOT National Transportation Integrated Search

    2001-03-21

    The Rail Passenger Service Act of 1970 created Amtrak to provide intercity passenger rail service. Like other major national intercity passenger rail systems in the world, Amtrak has received substantial government support-nearly $24 billion for capi...

  14. Crystal structure of a four-stranded intercalated DNA: d(C4)

    NASA Technical Reports Server (NTRS)

    Chen, L.; Cai, L.; Zhang, X.; Rich, A.

    1994-01-01

    The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

  15. Department of Homeland Security Assistance to States and Localities: A Summary and Issues for the 111th Congress

    DTIC Science & Technology

    2009-06-08

    Security Grant Program ...............................................................................6 Intercity Passenger Rail Program (Amtrak...6 Intercity Bus Security Grant Program...fy2009.pdf. 19 Additionally Amtrak is eligible to receive funding to continue security enhancements for its intercity rail services between high-risk

  16. Department of Homeland Security Assistance to States and Localities: A Summary and Issues for the 111th Congress

    DTIC Science & Technology

    2009-04-21

    6 Intercity Passenger Rail Program (Amtrak) .....................................................................6... Intercity Bus Security Grant Program..............................................................................7 Trucking Security Program...continue security enhancements for its intercity rail services between high-risk urban areas. 20 U.S. Department of Homeland Security, Federal Emergency

  17. Department of Homeland Security Assistance to States and Localities: A Summary and Issues for the 111th Congress

    DTIC Science & Technology

    2009-08-05

    Freight Rail Security Grant Program ...............................................................................6 Intercity Passenger Rail Program...Amtrak) .....................................................................6 Intercity Bus Security Grant Program...overview- fy2009.pdf. 19 Additionally Amtrak is eligible to receive funding to continue security enhancements for its intercity rail services

  18. 75 FR 16564 - High-Speed Intercity Passenger Rail (HSIPR) Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-01

    ... services to avoid shipping delays. Application forms are available at http://www.fra.dot.gov/Pages/2243..., and 501--Intercity Passenger Rail Service Corridor Capital Assistance (codified at 49 U.S.C. chapter... High Speed Rail Corridors and Intercity Passenger Rail Service.'' This document incorporates interim...

  19. The U.S. Rural Population and Scheduled Intercity Transportation in 2010 : A Five-Year Decline in Transportation Access.

    DOT National Transportation Integrated Search

    2011-02-01

    Between 2005 and 2010, 3.5 million rural residents lost access to scheduled intercity transportation, increasing the percent of rural residents without access to intercity transportation from 7 to 11 percent. In 2005, 5.4 million rural residents lack...

  20. Intercity passenger rail : the congress faces critical decisions about the role of and funding for intercity passenger rail systems

    DOT National Transportation Integrated Search

    2001-07-25

    With the growth in the nation's highway and aviation systems in the : previous decades, intercity passenger rail service lost its competitive edge. Highways have enabled cars to be competitive with conventional passenger trains (those operating up to...

  1. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA.

    PubMed

    Yang, Zhiyu; Price, Nathan E; Johnson, Kevin M; Wang, Yinsheng; Gates, Kent S

    2017-06-20

    Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3'ddR5p) at the 3'-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3'ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3'ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Charge separation and charge delocalization identified in long-living states of photoexcited DNA

    PubMed Central

    Bucher, Dominik B.; Pilles, Bert M.; Carell, Thomas; Zinth, Wolfgang

    2014-01-01

    Base stacking in DNA is related to long-living excited states whose molecular nature is still under debate. To elucidate the molecular background we study well-defined oligonucleotides with natural bases, which allow selective UV excitation of one single base in the strand. IR probing in the picosecond regime enables us to dissect the contribution of different single bases to the excited state. All investigated oligonucleotides show long-living states on the 100-ps time scale, which are not observable in a mixture of single bases. The fraction of these states is well correlated with the stacking probabilities and reaches values up to 0.4. The long-living states show characteristic absorbance bands that can be assigned to charge-transfer states by comparing them to marker bands of radical cation and anion spectra. The charge separation is directed by the redox potential of the involved bases and thus controlled by the sequence. The spatial dimension of this charge separation was investigated in longer oligonucleotides, where bridging sequences separate the excited base from a sensor base with a characteristic marker band. After excitation we observe a bleach of all involved bases. The contribution of the sensor base is observable even if the bridge is composed of several bases. This result can be explained by a charge delocalization along a well-stacked domain in the strand. The presence of charged radicals in DNA strands after light absorption may cause reactions—oxidative or reductive damage—currently not considered in DNA photochemistry. PMID:24616517

  3. Woven-grid sealed quasi-bipolar lead-acid battery construction and fabricating method

    NASA Technical Reports Server (NTRS)

    Rippel, Wally E. (Inventor)

    1989-01-01

    A quasi-bipolar lead-acid battery construction includes a plurality of bipolar cells disposed in side-by-side relation to form a stack, and a pair of monoplanar plates at opposite ends of the stack, the cell stack and monopolar plates being contained within a housing of the battery. Each bipolar cell is loaded with an electrolyte and composed of a bipolar electrode plate and a pair of separator plates disposed on opposite sides of the electrode plate and peripherally sealed thereto. Each bipolar electrode plate is composed of a partition sheet and two bipolar electrode elements folded into a hairpin configuration and applied over opposite edges of the partition sheet so as to cover the opposite surfaces of the opposite halves thereof. Each bipolar electrode element is comprised of a woven grid with a hot-melt strip applied to a central longitudinal region of the grid along which the grid is folded into the hairpin configuration, and layers of negative and positive active material pastes applied to opposite halves of the grid on opposite sides of the central hot-melt strip. The grid is made up of strands of conductive and non-conductive yarns composing the respective transverse and longitudinal weaves of the grid. The conductive yarn has a multi-stranded glass core surrounded and covered by a lead sheath, whereas the non-conductive yarn has a multi-stranded glass core surrounded and covered by a thermally activated sizing.

  4. Energetics, Ion and Water Binding of the Unfolding of AA/UU Base Pair Stacks and UAU/UAU Base Triplet Stacks in RNA.

    PubMed

    Carr, Carolyn E; Khutsishvili, Irine; Marky, Luis A

    2018-06-22

    Triplex formation occurs via interaction of a third strand with the major groove of double stranded nucleic acid, through Hoogsteen hydrogen bonding. In this work, we use a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry to determine complete thermodynamic profiles for the unfolding of poly(rA)•poly(rU) (Duplex) and poly(rA)•2poly(rU) (Triplex). Our thermodynamic results are in good agreement with the much earlier work of Krakauer and Sturtevant using only UV melting techniques. The folding of these two helices yielded an uptake of ions, ΔnNa+ = 0.15 mol Na+/mol base-pair (Duplex) and 0.30 mol Na+/mole base-triplet (Triplex), which are consistent with their polymer behavior and the higher charge density parameter of triple helices. The osmotic stress technique yielded a release of structural water, ΔnW = 2 mol H2O/mol base-pair (Duplex unfolding into single strands) and an uptake of structural water, ΔnW = 2 mol H2O/mole base-pair (Triplex unfolding into Duplex and a single strand). However, an overall release of electrostricted waters is obtained for the unfolding of both complexes from pressure perturbation calorimetric experiments. In total, the ΔV values obtained for the unfolding of Triplex into Duplex and a single strand correspond to an immobilization of two structural waters and a release of three electrostricted waters. The ΔV values obtained for the unfolding of Duplex into two single strands correspond to the release of two structural waters and the immobilization of four electrostricted water molecules.

  5. 77 FR 58439 - Environmental Impact Statement for the Northeast Corridor Between Washington, DC, New York, NY...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-20

    ... Regional and Intercity Household Travel Attitudes and Behavior. Type of Request: New information collection... ages of 18 and 74 who have Northeast intercity or regional travel experience during the 12 months prior... just those who experienced a qualifying intercity or regional travel trip to provide more detailed...

  6. State intercity bus plan : a report to the California Legislature in conformity with Chapter 99, item 266-001-041 of the 1981 Budget Act

    DOT National Transportation Integrated Search

    1982-03-01

    The legislative directive for the State Intercity Bus Plan asked that the Department offer alternatives for future State involvement in the intercity bus area, estimates for the projected State capital and operating costs and revenues for each of the...

  7. 75 FR 39325 - Notice of Draft Finding of No Significant Impact for the Washington State Portion of the Pacific...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-08

    ... Washington State is to improve intercity passenger rail service by reducing travel times, achieving greater... intercity travel demand. To achieve these goals WSDOT applied for federal funding through the High Speed Intercity Passenger Rail Program (HSIPR Program) administered by the FRA and funded by the American Recovery...

  8. 77 FR 49854 - Tier 1 Environmental Impact Statement for the Oregon Portion of the Pacific Northwest Rail...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-17

    ... represents other transportation modes such as auto, air travel, intercity bus, and existing rail and the... well as making decisions regarding the level of intercity passenger rail service provided in the... growth of 139% between 2000 and 2008. Current intercity passenger rail service in Oregon includes two...

  9. 49 CFR 37.85 - Purchase or lease of new intercity and commuter rail cars.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... rail cars. 37.85 Section 37.85 Transportation Office of the Secretary of Transportation TRANSPORTATION....85 Purchase or lease of new intercity and commuter rail cars. Amtrak or a commuter authority making a solicitation after August 25, 1990, to purchase or lease a new intercity or commuter rail car for use on the...

  10. 49 CFR 37.85 - Purchase or lease of new intercity and commuter rail cars.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... rail cars. 37.85 Section 37.85 Transportation Office of the Secretary of Transportation TRANSPORTATION....85 Purchase or lease of new intercity and commuter rail cars. Amtrak or a commuter authority making a solicitation after August 25, 1990, to purchase or lease a new intercity or commuter rail car for use on the...

  11. 49 CFR 37.85 - Purchase or lease of new intercity and commuter rail cars.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... rail cars. 37.85 Section 37.85 Transportation Office of the Secretary of Transportation TRANSPORTATION....85 Purchase or lease of new intercity and commuter rail cars. Amtrak or a commuter authority making a solicitation after August 25, 1990, to purchase or lease a new intercity or commuter rail car for use on the...

  12. 49 CFR 37.85 - Purchase or lease of new intercity and commuter rail cars.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... rail cars. 37.85 Section 37.85 Transportation Office of the Secretary of Transportation TRANSPORTATION....85 Purchase or lease of new intercity and commuter rail cars. Amtrak or a commuter authority making a solicitation after August 25, 1990, to purchase or lease a new intercity or commuter rail car for use on the...

  13. 49 CFR 37.91 - Wheelchair locations and food service on intercity rail trains.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... on each train a number of spaces— (1) To park wheelchairs (to accommodate individuals who wish to... providing intercity rail service shall provide on each train a number of spaces— (1) To park wheelchairs (to... providing intercity rail service may not provide more than two spaces to park wheelchairs nor more than two...

  14. Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide

    PubMed Central

    Zhao, Binwu

    2017-01-01

    The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration. Our study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal. The bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. Vertical hydrogen bonds within the β roll structure are considerably weaker than lateral hydrogen bonds, signifying the importance of lateral hydrogen bonds in stabilizing the β roll structure. Finally, an intermediate structure was found containing a β hairpin and an anti-parallel β sheet consisting of strands from the top and bottom molecules, revealing the self-healing ability of the β roll stack. PMID:28329017

  15. Department of Homeland Security Assistance to States and Localities: A Summary and Issues for the 111th Congress

    DTIC Science & Technology

    2010-04-30

    5 Intercity Bus Security Grant Program...eligibility.22 This grant program includes funding for the Freight Rail Security Grant Program (FRSGP), and the Intercity Passenger Rail Program (IPR...eligible to receive funding to continue security enhancements for its intercity rail services between high-risk urban areas. 21 U.S. Department of

  16. Protein stabilization by introduction of cross-strand disulfides.

    PubMed

    Chakraborty, Kausik; Thakurela, Sudhir; Prajapati, Ravindra Singh; Indu, S; Ali, P Shaik Syed; Ramakrishnan, C; Varadarajan, Raghavan

    2005-11-08

    Disulfides cross-link residues in a protein that are separated in primary sequence and stabilize the protein through entropic destabilization of the unfolded state. While the removal of naturally occurring disulfides leads to protein destabilization, introduction of engineered disulfides does not always lead to significant stabilization of a protein. We have analyzed naturally occurring disulfides that span adjacent antiparallel strands of beta sheets (cross-strand disulfides). Cross-strand disulfides have recently been implicated as redox-based conformational switches in proteins such as gp120 and CD4. The propensity of these disulfides to act as conformational switches was postulated on the basis of the hypothesis that this class of disulfide is conformationally strained. In the present analysis, there was no evidence to suggest that cross-strand disulfides are more strained compared to other disulfides as assessed by their torsional energy. It was also observed that these disulfides occur solely at non-hydrogen-bonded (NHB) registered pairs of adjacent antiparallel strands and not at hydrogen-bonded (HB) positions as suggested previously. One of the half-cystines involved in cross-strand disulfide formation often occurs at an edge strand. Experimental confirmation of the stabilizing effects of such disulfides was carried out in Escherichia coli thioredoxin. Four pairs of cross-strand cysteines were introduced, two at HB and two at NHB pairs. Disulfides were formed in all four cases. However, as predicted from our analysis, disulfides at NHB positions resulted in an increase in melting temperature of 7-10 degrees C, while at HB positions there was a corresponding decrease of -7 degrees C. The reduced state of all proteins had similar stability.

  17. A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple.

    PubMed

    Kuryavyi, V; Majumdar, A; Shallop, A; Chernichenko, N; Skripkin, E; Jones, R; Patel, D J

    2001-06-29

    The architecture of G-G-G-G tetrad-aligned DNA quadruplexes in monovalent cation solution is dependent on the directionality of the four strands, which in turn are defined by loop connectivities and the guanine syn/anti distribution along individual strands and within individual G-G-G-G tetrads. The smallest unimolecular G-quadruplex belongs to the d(G2NnG2NnG2NnG2) family, which has the potential to form two stacked G-tetrads linked by Nn loop connectivities. Previous studies have focused on the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), where Nn was T2 for the first and third connecting loops and TGT for the middle connecting loop. This DNA aptamer in K(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(anti)-G(syn)-G(anti) tetrads, adjacent strands which are antiparallel to each other and edge-wise connecting T2, TGT and T2 loops. We now report on the NMR-based solution structure of the d(G2T4G2CAG2GT4G2T) sequence, which differs from the thrombin-binding DNA aptamer sequence in having longer first (T4) and third (GT4) loops and a shorter (CA) middle loop. This d(G2T4G2CAG2GT4G2T) sequence in Na(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads, adjacent strands which have one parallel and one antiparallel neighbors and distinct non-edge-wise loop connectivities. Specifically, the longer first (T4) and third (GT4) loops are of the diagonal type while the shorter middle loop is of the double chain reversal type. In addition, the pair of stacked G-G-G-G tetrads are flanked on one side by a G-(T-T) triad and on the other side by a T-T-T triple. The distinct differences in strand directionalities, loop connectivities and syn/anti distribution within G-G-G-G tetrads between the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2) quadruplex reported previously, and the d(G2T4G2CAG2GT4G2T) quadruplex reported here, reinforces the polymorphic nature of higher-order DNA architectures. Further, these two small unimolecular G-quadruplexes, which are distinct from each other and from parallel-stranded G-quadruplexes, provide novel targets for ligand recognition. Our results demonstrate that the double chain reversal loop connectivity identified previously by our laboratory within the Tetrahymena telomere d(T2G4)4 quadruplex, is a robust folding topology, since it has now also been observed within the d(G2T4G2CAG2GT4G2T) quadruplex. The identification of a G-(T-T) triad and a T-T-T triple, expands on the available recognition alignments for base triads and triples. Copyright 2001 Academic Press.

  18. Bypass of a psoralen DNA interstrand cross-link by DNA polymerases beta, iota, and kappa in vitro

    PubMed Central

    Smith, Leigh A.; Makarova, Alena V.; Samson, Laura; Thiesen, Katherine E.; Dhar, Alok; Bessho, Tadayoshi

    2012-01-01

    Repair of DNA inter-strand cross-links in mammalian cells involves several biochemically distinctive processes, including the release of one of the cross-linked strands and translesion DNA synthesis (TLS). In this report, we investigated in vitro TLS activity of psoralen DNA inter-strand cross-link by three DNA repair polymerases, DNA polymerase beta, kappa and iota. DNA polymerase beta is capable of bypassing a psoralen cross-link with a low efficiency. Cell extracts prepared from DNA polymerase beta knockout mouse embryonic fibroblast showed a reduced bypass activity of the psoralen cross-link and purified DNA polymerase beta restored the bypass activity. In addition, DNA polymerase iota mis-incorporated thymine across the psoralen cross-link and DNA polymerase kappa extended these mis-paired primer ends, suggesting that DNA polymerase iota may serve as an inserter and DNA polymerase kappa may play a role as an extender in the repair of psoralen DNA inter-strand cross-links. The results demonstrated here indicate that multiple DNA polymerases could participate in TLS steps in mammalian DNA inter-strand cross-link repair. PMID:23106263

  19. Theoretical Evidence for the Stronger Ability of Thymine to Disperse SWCNT than Cytosine and Adenine: self-stacking of DNA bases vs their cross-stacking with SWCNT

    PubMed Central

    Wang, Yixuan

    2008-01-01

    Self-stacking of four DNA bases, adenine (A), cytosine (C), guanine (G) and thymine (T), and their cross-stacking with (5,5) as well as (10,0) single walled carbon nanotubes (SWCNTs) were extensively investigated with a novel hybrid DFT method, MPWB1K/cc-pVDZ. The binding energies were further corrected with MP2/6-311++G(d,p) method in both gas phase and aqueous solution, where the solvent effects were included with conductor-like polarized continuum model (CPCM) model and UAHF radii. The strongest self-stacking of G and A takes displaced anti-parallel configuration, but un-displaced or “eclipsed” anti-parallel configuration is the most stable for C and T. In gas phase the self-stacking of nucleobases decreases in the sequence G>A>C>T, while because of quite different solvent effects their self-stacking in aqueous solution exhibits a distinct sequence A>G>T>C. For a given base, cross-stacking is stronger than self-stacking in both gas phase and aqueous solution. Binding energy for cross-stacking in gas phase varies as G>A>T>C for both (10,0) and (5,5) SWCNTs, and the binding of four nucleobases to (10,0) is slightly stronger than to (5,5) SWCNT by a range of 0.1–0.5 kcal/mol. The cross-stacking in aqueous solution varies differently from that gas phase: A>G>T>C for (10,0) SWCNT and G>A>T>C for (5,5) SWCNT. It is suggested that the ability of nucleobases to disperse SWCNT depends on relative strength (ΔΔEbinsol) of self-stacking and cross-stacking with SWCNT in aqueous solution. Of the four investigated nucleobases thymine (T) exhibits the highest (ΔΔEbinsol) which can well explain the experimental finding that T more efficiently functionalizes SWCNT than C and A. PMID:18946514

  20. Technology assessment of future intercity passenger transportation systems. Volume 4: Scenarios

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Four background scenarios that relate to alternative states of society in the next 25 to 50 years are described. The scenarios were developed for use in analyzing and evaluating alternative future intercity transportation technologies. The scenarios are based, in part, on discussions contained in the issue papers and, in part, on separate analysis of social and economic trends considered relevant for the evolution of intercity transportation.

  1. Comparison of direct DNA strand breaks induced by low energy electrons with different inelastic cross sections

    NASA Astrophysics Data System (ADS)

    Li, Jun-Li; Li, Chun-Yan; Qiu, Rui; Yan, Cong-Chong; Xie, Wen-Zhang; Zeng, Zhi; Tung, Chuan-Jong

    2013-09-01

    In order to study the influence of inelastic cross sections on the simulation of direct DNA strand breaks induced by low energy electrons, six different sets of inelastic cross section data were calculated and loaded into the Geant4-DNA code to calculate the DNA strand break yields under the same conditions. The six sets of the inelastic cross sections were calculated by applying the dielectric function method of Emfietzoglou's optical-data treatments, with two different optical datasets and three different dispersion models, using the same Born corrections. Results show that the inelastic cross sections have a notable influence on the direct DNA strand break yields. The yields simulated with the inelastic cross sections based on Hayashi's optical data are greater than those based on Heller's optical data. The discrepancies are about 30-45% for the single strand break yields and 45-80% for the double strand break yields. Among the yields simulated with cross sections of the three different dispersion models, generally the greatest are those of the extended-Drude dispersion model, the second are those of the extended-oscillator-Drude dispersion model, and the last are those of the Ashley's δ-oscillator dispersion model. For the single strand break yields, the differences between the first two are very little and the differences between the last two are about 6-57%. For the double strand break yields, the biggest difference between the first two can be about 90% and the differences between the last two are about 17-70%.

  2. Effects of Strand Lay Direction and Crossing Angle on Tribological Behavior of Winding Hoist Rope.

    PubMed

    Chang, Xiang-Dong; Peng, Yu-Xing; Zhu, Zhen-Cai; Gong, Xian-Sheng; Yu, Zhang-Fa; Mi, Zhen-Tao; Xu, Chun-Ming

    2017-06-09

    Friction and wear behavior exists between hoisting ropes that are wound around the drums of a multi-layer winding hoist. It decreases the service life of ropes and threatens mine safety. In this research, a series of experiments were conducted using a self-made test rig to study the effects of the strand lay direction and crossing angle on the winding rope's tribological behavior. Results show that the friction coefficient in the steady-state period shows a decreasing tendency with an increase of the crossing angle in both cross directions, but the variation range is different under different cross directions. Using thermal imaging, the high temperature regions always distribute along the strand lay direction in the gap between adjacent strands, as the cross direction is the same with the strand lay direction (right cross contact). Additionally, the temperature rise in the steady-state increases with the increase of the crossing angle in both cross directions. The differences of the wear scar morphology are obvious under different cross directions, especially for the large crossing angle tests. In the case of right cross, the variation range of wear mass loss is larger than that in left cross. The damage that forms on the wear surface is mainly ploughing, pits, plastic deformation, and fatigue fracture. The major wear mechanisms are adhesive wear, and abrasive and fatigue wear.

  3. Effects of Strand Lay Direction and Crossing Angle on Tribological Behavior of Winding Hoist Rope

    PubMed Central

    Chang, Xiang-dong; Peng, Yu-xing; Zhu, Zhen-cai; Gong, Xian-sheng; Yu, Zhang-fa; Mi, Zhen-tao; Xu, Chun-ming

    2017-01-01

    Friction and wear behavior exists between hoisting ropes that are wound around the drums of a multi-layer winding hoist. It decreases the service life of ropes and threatens mine safety. In this research, a series of experiments were conducted using a self-made test rig to study the effects of the strand lay direction and crossing angle on the winding rope’s tribological behavior. Results show that the friction coefficient in the steady-state period shows a decreasing tendency with an increase of the crossing angle in both cross directions, but the variation range is different under different cross directions. Using thermal imaging, the high temperature regions always distribute along the strand lay direction in the gap between adjacent strands, as the cross direction is the same with the strand lay direction (right cross contact). Additionally, the temperature rise in the steady-state increases with the increase of the crossing angle in both cross directions. The differences of the wear scar morphology are obvious under different cross directions, especially for the large crossing angle tests. In the case of right cross, the variation range of wear mass loss is larger than that in left cross. The damage that forms on the wear surface is mainly ploughing, pits, plastic deformation, and fatigue fracture. The major wear mechanisms are adhesive wear, and abrasive and fatigue wear. PMID:28772992

  4. Unfolding and Targeting Thermodynamics of a DNA Intramolecular Complex with Joined Triplex-Duplex Domains.

    PubMed

    Johnson, Sarah E; Reiling-Steffensmeier, Calliste; Lee, Hui-Ting; Marky, Luis A

    2018-01-25

    Our laboratory is interested in developing methods that can be used for the control of gene expression. In this work, we are investigating the reaction of an intramolecular complex containing a triplex-duplex junction with partially complementary strands. We used a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectroscopy techniques to determine standard thermodynamic profiles for these targeting reactions. Specifically, we have designed single strands to target one loop (CTTTC) or two loops (CTTTC and GCAA) of this complex. Both reactions yielded exothermic enthalpies of -66.3 and -82.8 kcal/mol by ITC, in excellent agreement with the reaction enthalpies of -72.7 and -88.7 kcal/mol, respectively, obtained from DSC Hess cycles. The favorable heat contributions result from the formation of base-pair stacks involving mainly the unpaired bases of the loops. This shows that each complementary strand is able to invade and disrupt the secondary structure. The simultaneous targeting of two loops yielded a more favorable reaction free energy, by approximately -8 kcal/mol, which corresponds to the formation of roughly four base-pair stacks involving the unpaired bases of the 5'-GCAA loop. The main conclusion is that the targeting of loops with a large number of unpaired bases results in a more favorable reaction free energy.

  5. DNA synthesis arrest sites at the right terminus of rat long interspersed repeated (LINE or L1Rn) DNA family members.

    PubMed Central

    d'Ambrosio, E; Furano, A V

    1987-01-01

    An approximately equal to 150-bp GC-rich (approximately equal to 60%) region is at the right end of rat long interspersed repeated DNA (LINE or L1Rn) family members. We report here that one of the DNA strands from this region contains several non-palindromic sites that strongly arrest DNA synthesis in vitro by the prokaryotic Klenow and T4 DNA polymerases, the eukaryotic alpha polymerase, and AMV reverse transcriptase. The strongest arrest sites are G-rich (approximately equal to 70%) homopurine stretches of 18 or more residues. Shorter homopurine stretches (12 residues or fewer) did not arrest DNA synthesis even if the stretch contains 11/12 G residues. Arrest of the prokaryotic polymerases was not affected by their respective single strand binding proteins or polymerase accessory proteins. The region of duplex DNA which contains DNA synthesis arrest sites reacts with bromoacetaldehyde when present in negatively supercoiled molecules. By contrast, homopurine stretches that do not arrest DNA synthesis do not react with bromoacetaldehyde. The presence of bromoacetaldehyde-reactive bases in a G-rich homopurine-containing duplex under torsional stress is thought to be caused by base stacking in the homopurine strand. Therefore, we suggest that base-stacked regions of the template arrest DNA synthesis. Images PMID:2436148

  6. Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants.

    PubMed

    Liu, Weipeng; Zhu, Minjun; Liu, Hongxing; Wei, Jitao; Zhou, Xiaoming; Xing, Da

    2016-07-15

    Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Stacking interactions in PUF-RNA complexes

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

    Yiling Koh, Yvonne; Wang, Yeming; Qiu, Chen

    2012-07-02

    Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stackingmore » amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to 'target' versus 'off-target' interactions, and thus be an important consideration in the design of proteins with new specificities.« less

  8. Dyes as bifunctional markers of DNA hybridization on surfaces and mutation detection.

    PubMed

    García-Mendiola, Tania; Cerro, María Ramos; López-Moreno, José María; Pariente, Félix; Lorenzo, Encarnación

    2016-10-01

    The interaction of small molecules with DNA has found diagnostic and therapeutic applications. In this work, we propose the use of two different dyes, in particular Azure A and Safranine, as bifunctional markers of on-surface DNA hybridization and potent tools for screening of specific gene mutations directly in real DNA PCR amplicons extracted from blood cells. By combining spectroscopic and electrochemical methods we demonstrate that both dyes can interact with single and double stranded DNA to a different extent, allowing reliable hybridization detection. From these data, we have also elucidated the nature of the interaction. We conclude that the binding mode is fundamentally intercalative with an electrostatic component. The dye fluorescence allows their use as nucleic acid stains for the detection of on-surfaces DNA hybridization. Its redox activity is exploited in the development of selective electrochemical DNA biosensors. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Interstrand cross-linking of DNA by 1,3-bis(2-chloroethyl)-1-nitrosourea and other 1-(2-haloethyl)-1-nitrosoureas.

    PubMed

    Kohn, K W

    1977-05-01

    Bifunctional alkylating agents are known to cross-link DNA by simultaneously alkylating two guanine residues located on opposite strands. Despite this apparent requirement for bifunctionality, 1-(2-chloroethyl)-1-nitrosoureas bearing a single alkylating function were found to cross-link DNA in vitro. Cross-linking was demonstrated by showing inhibition of alkali-induced strand separation. Extensive cross-linking was observed in DNA treated with 1-(2-chloroethyl)-1-nitrosourea, 1,3-bis-(2-chloroethyl)-1-nitrosourea, and 1-(2-chloroethyl(-3-cyclohexyl-1-nitrosourea. The reaction occurs in two steps, an intital binding followed by a second step which can proceed after removal of unbound drug. It is suggested that the first step is chloroethylation of a nucleophilic site on one strand and that the second step involves displacement of Cl- by a nucleophilic site on the opposite strand, resulting in an ethyl bridge between the strands. Consistent with this possibility, 1-(2-fluoroethyl)-3-cyclohexyl-1-nitrosourea produced much less cross-linking, as expected from the known low activity of F-, compared with Cl-, as leaving group. 1-Methyl-1-nitrosourea, which is known to depurinate DNA, produced no detectable cross-linking.

  10. Investigating actinomycin D binding to G-quadruplex, i-motif and double-stranded DNA in 27-nt segment of c-MYC gene promoter.

    PubMed

    Niknezhad, Zhila; Hassani, Leila; Norouzi, Davood

    2016-01-01

    c-MYC DNA is an attractive target for drug design, especially for cancer chemotherapy. Around 90% of c-MYC transcription is controlled by NHE III1, whose 27-nt purine-rich strand has the ability to form G-quadruplex structure. In this investigation, interaction of ActD with 27-nt G-rich strand (G/c-MYC) and its equimolar mixture with the complementary sequence, (GC/c-MYC) as well as related C-rich oligonucleotide (C/c-MYC) was evaluated. Molecular dynamic simulations showed that phenoxazine and lactone rings of ActD come close to the outer G-tetrad nucleotides indicating that ActD binds through end-stacking to the quadruplex DNA. RMSD and RMSF revealed that fluctuation of the quadruplex DNA increases upon interaction with the drug. The results of spectrophotometry and spectrofluorometry indicated that ActD most probably binds to the c-MYC quadruplex and duplex DNA via end-stacking and intercalation, respectively and polarity of ActD environment decreases due to the interaction. It was also found that binding of ActD to the GC-rich DNA is stronger than the two other forms of DNA. Circular dichroism results showed that the type of the three forms of DNA structures doesn't change, but their compactness alters due to their interaction with ActD. Finally, it can be concluded that ActD binds differently to double stranded DNA, quadruplex DNA and i-motif. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. 75 FR 16552 - High-Speed Intercity Passenger Rail (HSIPR) Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-01

    ..., energy savings from traffic diversions from other modes, employment of green building and manufacturing... selections for the High-Speed Intercity Passenger Rail (HSIPR) Program. This notice builds on the program...

  12. Technology assessment of future intercity passenger transportation systems. Volume 5: Workshop proceedings

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Proceedings of a workshop conducted to identify and debate issues and impacts related to future transporation alternatives are presented. Results of the technology assessment of intercity transportation are reviewed.

  13. Intercity Passenger Parametric Analysis: Overview: Maglev Analysis

    DOT National Transportation Integrated Search

    1990-04-02

    This document provides information intended to clarify consideration of some of the technically-based questions which arise in connection with intercity passenger transportation, and to provide insight into the characteristics and potential roles o...

  14. Occupational exposure to whole body vibration-train drivers.

    PubMed

    Birlik, Gülin

    2009-01-01

    Whole body vibration exposure of the train drivers working for State Railway Lines is assessed by referring to ISO standard 2631 -1 and EU directive 2002/44/EC. The vibration measurements were done in the cabins of suburban and intercity train drivers. Suburban train driver performs his job usually in standing posture. Whereas intercity train driver works generally in seated (bending forward) posture and exposed to longer periods of continuous vibration, compared to suburban train drivers. The mean accelerations, a, along lateral, y, and vertical, z, directions measured on the driver seat (on the cabin floor) of the intercity (suburban) train were 1.4a (y) = 0.55 (0.28) m/s(2) and a (z) = 0.65 (0.23) m/s(2). Daily exposure action values suggested in EU directive are exceeded in case of intercity train drivers and their exposure falls within the health caution zone of ISO 2631-1. Intercity train drivers are therefore under the risk of having spinal disorders. A health surveillance plan requiring every five years the reassessment of the state of the spinal system of train drivers is suggested. As an early preventive measure, extended work day or more than one shift in a day is advised to be discouraged.

  15. Intercity Bus Feeder Project Program Analysis

    DOT National Transportation Integrated Search

    1990-09-01

    Following the passage of the Bus Regualtory Reform Act of 1982 (BRRA), intercity : carriers used their increased regulatory flexibility to discontinue many : underutilized rural and small city services. This was understandable, in light : of the comp...

  16. Michigan transportation facts & figures : public transportation

    DOT National Transportation Integrated Search

    2002-08-16

    This on-line document is part of a series, Transportation Facts & Figures, by the Michigan Department of Transportation (MDOT). The Public Transit section of Transportation Facts & Figures cover such topics as intercity bus service, intercity rail se...

  17. Energy intensity of intercity passenger rail.

    DOT National Transportation Integrated Search

    1977-12-01

    This research report deals with the Energy Intensity of Intercity Rail Passenger : Systems. Included in the energy evaluation are the impacts of operating conditions : (speed, load factor) and train consists. The report also documents an : extensive ...

  18. A cross-stacked plasmonic nanowire network for high-contrast femtosecond optical switching.

    PubMed

    Lin, Yuanhai; Zhang, Xinping; Fang, Xiaohui; Liang, Shuyan

    2016-01-21

    We report an ultrafast optical switching device constructed by stacking two layers of gold nanowires into a perpendicularly crossed network, which works at a speed faster than 280 fs with an on/off modulation depth of about 22.4%. The two stacks play different roles in enhancing consistently the optical switching performance due to their different dependence on the polarization of optical electric fields. The cross-plasmon resonance based on the interaction between the perpendicularly stacked gold nanowires and its Fano-coupling with Rayleigh anomaly is the dominant mechanism for such a high-contrast optical switching device.

  19. Technology assessment of future intercity passenger transportation systems. Volume 7: Study recommendations

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Research and analysis tasks to alleviate negative impacts, to augment positive impacts, or to better understand the impacts produced by the potential introduction of the alternate transportation technologies are identified. The project team's recommendations on research and analysis efforts which have resulted from the technology assessment are provided. Many of the recommendations apply to the future supply of intercity passenger transportation services, categorized by mode. Other recommendations pertain to broad issues in intercity transportation--e.g., finance, regulation, traveler values--that will affect all modes.

  20. Performance Analyses of Intercity Ground Passenger Transportation Systems

    DOT National Transportation Integrated Search

    1976-04-01

    This report documents the development of analytical techniques and their use for investigating the performance of intercity ground passenger transportation systems. The purpose of the study is twofold: (1) to provide a capability of evaluating new pa...

  1. 90-94 ITS Intercity Corridor Study - Strategic Deployment Plan

    DOT National Transportation Integrated Search

    1996-12-01

    PUBLIC-PRIVATE PARTNERSHIP, COMMERCIAL VEHICLES OPERATIONS OR CVO : THE IH 90/94 ITS INTERCITY CORRIDOR STRATEGIC DEPLOYMENT PLAN IS AN APPROACH FOR IMPLEMENTING INTELLIGENT TRANSPORTATION SYSTEMS (ITS) IN THE IH 90/94 CORRIDORS THAT TRAVERSE THE ...

  2. Many intercity travelers face longer travel schedules

    DOT National Transportation Integrated Search

    2003-10-01

    Since 1995, scheduled travel times for direct : intercity air, bus, and rail service without an en : route transfer have measurably lengthened in : most major-market city-pairs. : Long-haul rail city-pairs affected by service : changes and short-...

  3. Intercity passenger rail : prospects for Amtrak's financial viability

    DOT National Transportation Integrated Search

    1998-06-01

    Since it began operations in 1971, the National Railroad Passenger Corporation (AmtraK0 has never been profitable and has received about $21 billion in federal subsidies for operating and capital expenses. Amtrak currently provides intercity passenge...

  4. An intercalation-locked parallel-stranded DNA tetraplex

    DOE PAGES

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

  5. Dissociation of single-strand DNA: single-walled carbon nanotube hybrids by Watson-Crick base-pairing.

    PubMed

    Jung, Seungwon; Cha, Misun; Park, Jiyong; Jeong, Namjo; Kim, Gunn; Park, Changwon; Ihm, Jisoon; Lee, Junghoon

    2010-08-18

    It has been known that single-strand DNA wraps around a single-walled carbon nanotube (SWNT) by pi-stacking. In this paper it is demonstrated that such DNA is dissociated from the SWNT by Watson-Crick base-pairing with a complementary sequence. Measurement of field effect transistor characteristics indicates a shift of the electrical properties as a result of this "unwrapping" event. We further confirm the suggested process through Raman spectroscopy and gel electrophoresis. Experimental results are verified in view of atomistic mechanisms with molecular dynamics simulations and binding energy analyses.

  6. Comprehensive Study of Intercity Bus Service in Nebraska

    DOT National Transportation Integrated Search

    1988-03-01

    This study is prompted by the proposed abandonment of regular-route intercity : bus service across northern Nebraska. The current route, which is operated by : Black Hills Stage Lines, provides service from Omaha through Norfolk and Chadron : to Rapi...

  7. Intercity passenger rail : Congress faces critical decisions in developing a national policy

    DOT National Transportation Integrated Search

    2002-04-11

    This document is the statement of JayEtta Z. Hecker, Director, Physical Infrastructure. Testimony before the Subcommittee on Railroads, Committee on Transportation and Infrastructure, House of Representatives on the future of intercity passenger rail...

  8. Montana intercity bus service study.

    DOT National Transportation Integrated Search

    2011-12-01

    Intercity bus service funding from the Federal Transit Administration (FTAs) Section 5311(f) program is a part : of the larger 5311 program known as Formula Grants for Other than Urbanized Areas. The S.5311(f), requires : that 15% of the total 531...

  9. High-speed and intercity passenger rail testing strategy.

    DOT National Transportation Integrated Search

    2013-05-01

    This high-speed and intercity passenger rail (HSIPR) testing strategy addresses the requirements for testing of high-speed train sets and technology before introduction to the North American railroad system. The report documents the results of a surv...

  10. 29 CFR 1982.101 - Definitions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... include school buses, charter, or intercity bus transportation or intercity passenger rail transportation... transportation systems that connect metropolitan areas, without regard to whether those systems use new technologies not associated with traditional railroads, but does not include rapid transit operations in an...

  11. The Human DNA glycosylases NEIL1 and NEIL3 Excise Psoralen-Induced DNA-DNA Cross-Links in a Four-Stranded DNA Structure.

    PubMed

    Martin, Peter R; Couvé, Sophie; Zutterling, Caroline; Albelazi, Mustafa S; Groisman, Regina; Matkarimov, Bakhyt T; Parsons, Jason L; Elder, Rhoderick H; Saparbaev, Murat K

    2017-12-12

    Interstrand cross-links (ICLs) are highly cytotoxic DNA lesions that block DNA replication and transcription by preventing strand separation. Previously, we demonstrated that the bacterial and human DNA glycosylases Nei and NEIL1 excise unhooked psoralen-derived ICLs in three-stranded DNA via hydrolysis of the glycosidic bond between the crosslinked base and deoxyribose sugar. Furthermore, NEIL3 from Xenopus laevis has been shown to cleave psoralen- and abasic site-induced ICLs in Xenopus egg extracts. Here we report that human NEIL3 cleaves psoralen-induced DNA-DNA cross-links in three-stranded and four-stranded DNA substrates to generate unhooked DNA fragments containing either an abasic site or a psoralen-thymine monoadduct. Furthermore, while Nei and NEIL1 also cleave a psoralen-induced four-stranded DNA substrate to generate two unhooked DNA duplexes with a nick, NEIL3 targets both DNA strands in the ICL without generating single-strand breaks. The DNA substrate specificities of these Nei-like enzymes imply the occurrence of long uninterrupted three- and four-stranded crosslinked DNA-DNA structures that may originate in vivo from DNA replication fork bypass of an ICL. In conclusion, the Nei-like DNA glycosylases unhook psoralen-derived ICLs in various DNA structures via a genuine repair mechanism in which complex DNA lesions can be removed without generation of highly toxic double-strand breaks.

  12. Using DNA origami nanostructures to determine absolute cross sections for UV photon-induced DNA strand breakage.

    PubMed

    Vogel, Stefanie; Rackwitz, Jenny; Schürman, Robin; Prinz, Julia; Milosavljević, Aleksandar R; Réfrégiers, Matthieu; Giuliani, Alexandre; Bald, Ilko

    2015-11-19

    We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.

  13. Scheduled intercity transportation : rural service areas in the United States

    DOT National Transportation Integrated Search

    2005-06-01

    To identify how many of the countrys 82.4 million rural residents are within the reasonable coverage radius of at least one intercity transportation facility, in 2003 the Bureau of Transportation Statistics (BTS) undertook a geospatial analysis us...

  14. Commuter-Intercity Rail Improvement Study (Boston-New York)

    DOT National Transportation Integrated Search

    1993-05-01

    This study was carried out under the direction of a departmental task force. The 226 page report identifies and characterizes the costs and benefits of improvements that could be achieved in commuter and intercity rail passenger service on the Boston...

  15. Intercity travel in northeastern rural regions of the U.S.

    DOT National Transportation Integrated Search

    2015-06-01

    Much research exists on intercity travel behavior between large metropolitan centers. : There is an opportunity for more research on travel from less populated areas to large : metropolitan ones. When planning a trip from Northern New England to majo...

  16. Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

    NASA Astrophysics Data System (ADS)

    Nielsen, Lisbeth Munksgaard; Pedersen, Sara Øvad; Kirketerp, Maj-Britt Suhr; Nielsen, Steen Brøndsted

    2012-02-01

    The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (˜3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar to that for the adenine molecule and the dAMP mononucleotide. Desolvation has little effect on the bandwidth, which implies that inhomogenous broadening of the absorption bands in aqueous solution is of minor importance compared to, e.g., conformational disorder. Finally, at high photon energies, internal conversion competes with electron detachment since dissociation of the bare photoexcited ions on the microsecond time scale is measured.

  17. Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity

    DTIC Science & Technology

    2012-10-11

    mismatched base stacks with a conserved phenylalanine in Msh6, and/or (iii) DNA flexibility, since MutSa-bound mismatched DNA is kinked, and a...AB, Watt DL , Watts BE, et al. (2010) Genome instability due to ribonucleotide incorporation into DNA. Nat Chem Biol 6: 774–781. 24. Poloumienko A

  18. Effects of the Ride Environment on Passenger Activities : A Field Study on Intercity Trains

    DOT National Transportation Integrated Search

    1979-01-01

    A three-part field study of passenger activities (e.g. reading, writing, talking, sleeping) was conducted on intercity Amtrak trains in the northeastern United States to determine the relationships between the ride environment, subjective passenger c...

  19. Intercity bus service study 2014.

    DOT National Transportation Integrated Search

    2015-02-01

    Rural transit programs are funded with 5311 funds, named for their description in Section 5311 of United States : Code (49 USC S5311). In Alabama, 15% of 5311 funds are set aside to be spent on improving intercity bus : service through the 5311(f) pr...

  20. The effects of the ride environment on passenger activities : a field study on intercity trains

    DOT National Transportation Integrated Search

    1979-01-01

    A three-part field study of passenger activities (e.g. reading, writing, talking, sleeping) was conducted on intercity Amtrak trains in the northeastern United States to determine the relationships between the ride environment, subjective passenger c...

  1. Productivity Trends in Intercity Trucking

    ERIC Educational Resources Information Center

    Carnes, Richard B.

    1974-01-01

    Productivity trends indicate intercity trucking productivity increased an average 2.7 percent a year, a fairly uniform increased productivity rate but substantially lower as compared to air carrier, railroad, and pipeline transportation. Factors affecting productivity are gradual introduction of technological innovation, larger capacity trucks,…

  2. Public transportation and intercity rail passenger plan for Washington state 1997-2016

    DOT National Transportation Integrated Search

    1996-12-01

    The Public Transportation and Intercity Rail Passenger Plan for Washington : State is a 20-year plan for preserving our current public transportation systems : while improving mobility for a growing population. The plan builds toward a : future in wh...

  3. Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

    PubMed Central

    Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie; Liévin, Jacques; Körzdörfer, Thomas; Rotaru, Alexandru; Gothelf, Kurt V.; Besenbacher, Flemming; Bald, Ilko

    2014-01-01

    The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5′-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10−14 cm2 and 7.06 · 10−14 cm2. The highest cross section was found for 5′-TT(ATA)3TT and 5′-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy. PMID:25487346

  4. Probing the cross-effect of strains in non-linear elasticity of nearly regular polymer networks by pure shear deformation.

    PubMed

    Katashima, Takuya; Urayama, Kenji; Chung, Ung-il; Sakai, Takamasa

    2015-05-07

    The pure shear deformation of the Tetra-polyethylene glycol gels reveals the presence of an explicit cross-effect of strains in the strain energy density function even for the polymer networks with nearly regular structure including no appreciable amount of structural defect such as trapped entanglement. This result is in contrast to the expectation of the classical Gaussian network model (Neo Hookean model), i.e., the vanishing of the cross effect in regular networks with no trapped entanglement. The results show that (1) the cross effect of strains is not dependent on the network-strand length; (2) the cross effect is not affected by the presence of non-network strands; (3) the cross effect is proportional to the network polymer concentration including both elastically effective and ineffective strands; (4) no cross effect is expected exclusively in zero limit of network concentration in real polymer networks. These features indicate that the real polymer networks with regular network structures have an explicit cross-effect of strains, which originates from some interaction between network strands (other than entanglement effect) such as nematic interaction, topological interaction, and excluded volume interaction.

  5. Preliminary concept for statewide intercity bus and rail transit system : priority corridor ranking and analysis.

    DOT National Transportation Integrated Search

    2009-03-01

    This product summarizes the preliminary concept and priority corridors for development of a potential : statewide intercity bus and rail network. The concept is based upon the results of Tasks 1 through 5 of Texas : Department of Transportation Proje...

  6. Intercity passenger rail : Amtrak needs to improve its decision making process for its route and service proposals

    DOT National Transportation Integrated Search

    2002-04-01

    The National Railroad Passenger Corporation (Amtrak) is the nation's intercity passenger rail operator. In recent years, facing the continuing deterioration of its financial condition and its attempt to eliminate its need for federal operating assist...

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

    Otto, C., Thomas, G.A.; Peticolas, W.L.; Rippe, K.

    Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due tomore » changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.« less

  8. Potential development of an intercity passenger transit system in Texas : final project report.

    DOT National Transportation Integrated Search

    2010-05-01

    This report describes the findings of a research study of the potential for development of an intercity rail and : express bus system in the state of Texas. Rather than focus on regional commuter or light rail systems : radiating from urban areas, th...

  9. 47 CFR 74.537 - Temporary authorizations.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Aural Broadcast Auxiliary Stations... STL or intercity relay station operation which cannot be conducted in accordance with § 74.24. Such... intercity relay station must be made in accordance with the procedures of § 1.931(b) of this chapter. (c...

  10. 47 CFR 74.537 - Temporary authorizations.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Aural Broadcast Auxiliary Stations... STL or intercity relay station operation which cannot be conducted in accordance with § 74.24. Such... intercity relay station must be made in accordance with the procedures of § 1.931(b) of this chapter. (c...

  11. 47 CFR 74.537 - Temporary authorizations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Aural Broadcast Auxiliary Stations... STL or intercity relay station operation which cannot be conducted in accordance with § 74.24. Such... intercity relay station must be made in accordance with the procedures of § 1.931(b) of this chapter. (c...

  12. Retrieval of Body-Wave Reflections Using Ambient Noise Interferometry Using a Small-Scale Experiment

    NASA Astrophysics Data System (ADS)

    Dantas, Odmaksuel Anísio Bezerra; do Nascimento, Aderson Farias; Schimmel, Martin

    2018-02-01

    We report the retrieval of body-wave reflections from noise records using a small-scale experiment over a mature oil field. The reflections are obtained by cross-correlation and stacking of the data. We used the stacked correlograms to create virtual source-to-receiver common shot gathers and are able to obtain body-wave reflections. Surface waves that obliterate the body-waves in our noise correlations were attenuated following a standard procedure from active source seismics. Further different strategies were employed to cross-correlate and stack the data: classical geometrical normalized cross-correlation (CCGN), phase cross-correlation (PCC), linear stacking**** and phase weighted stacking (PWS). PCC and PWS are based on the instantaneous phase coherence of analytic signals. The four approaches are independent and reveal the reflections; nevertheless, the combination of PWS and CCGN provided the best results. Our analysis is based on 2145 cross-correlations of 600 s data segments. We also compare the resulted virtual shot gathers with an active 2D seismic line near the passive experiment. It is shown that our ambient noise analysis reproduces reflections which are present in the active seismic data.

  13. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    PubMed

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more accessible for use in microarrays to detect target single strands.

  14. Effect of Variation of Speed Limits on Intercity Bus Fuel Consumption, Coach and Driver Utilization, and Corporate Profitability

    DOT National Transportation Integrated Search

    1975-11-01

    The effect of speed limit and passenger load on fuel consumption was determined using actual intercity buses with simulated passenger loads over different types of terrain. In addition to road tests, laboratory type measurements were made on four int...

  15. Potential development of an intercity passenger transit system in Texas : report on tasks 1-5.

    DOT National Transportation Integrated Search

    2009-11-01

    This report summarizes the results of Tasks 1 through 5 of TxDOT Research Project 0-5930: Potential : Development of an Intercity Passenger Transit System in Texas. Rather than focus on any regional : commuter or light rail systems within or radiatin...

  16. 49 CFR 38.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... mechanical, electrical or other system operates to ensure that cars do not move when the lift is in use. (3... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by...

  17. 49 CFR 38.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... mechanical, electrical or other system operates to ensure that cars do not move when the lift is in use. (3... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by...

  18. 49 CFR 38.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... mechanical, electrical or other system operates to ensure that cars do not move when the lift is in use. (3... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by...

  19. 47 CFR 74.532 - Licensing requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... § 74.532 Licensing requirements. (a) An aural broadcast STL or an aural broadcast intercity relay... booster stations. Aural auxiliary stations licensed to low power FM stations will be assigned on a.... (b) More than one aural broadcast STL or intercity relay station may be licensed to a single licensee...

  20. 47 CFR 74.532 - Licensing requirements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... § 74.532 Licensing requirements. (a) An aural broadcast STL or an aural broadcast intercity relay... booster stations. Aural auxiliary stations licensed to low power FM stations will be assigned on a.... (b) More than one aural broadcast STL or intercity relay station may be licensed to a single licensee...

  1. 47 CFR 74.532 - Licensing requirements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... § 74.532 Licensing requirements. (a) An aural broadcast STL or an aural broadcast intercity relay... booster stations. Aural auxiliary stations licensed to low power FM stations will be assigned on a.... (b) More than one aural broadcast STL or intercity relay station may be licensed to a single licensee...

  2. 47 CFR 74.532 - Licensing requirements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... § 74.532 Licensing requirements. (a) An aural broadcast STL or an aural broadcast intercity relay... booster stations. Aural auxiliary stations licensed to low power FM stations will be assigned on a.... (b) More than one aural broadcast STL or intercity relay station may be licensed to a single licensee...

  3. 47 CFR 74.532 - Licensing requirements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... § 74.532 Licensing requirements. (a) An aural broadcast STL or an aural broadcast intercity relay... booster stations. Aural auxiliary stations licensed to low power FM stations will be assigned on a.... (b) More than one aural broadcast STL or intercity relay station may be licensed to a single licensee...

  4. The Full Cost of Intercity Transportation: A Comparison of High Speed Rail, Air, and Highway Transportation in California

    DOT National Transportation Integrated Search

    1996-06-01

    This study evaluated the full cost of three modes of intercity transportation: air, highway, and high speed rail. The evaluation is done within the context of the California Corridor, connecting the Los Angeles Basin and the San Francisco Bay Area. T...

  5. 49 CFR 38.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by... to be accessible, or mini-high platforms complying with § 38.113(d) are provided, the car is not...

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

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

  7. Antiparallel Triple-strand Architecture for Prefibrillar Aβ42 Oligomers*

    PubMed Central

    Gu, Lei; Liu, Cong; Stroud, James C.; Ngo, Sam; Jiang, Lin; Guo, Zhefeng

    2014-01-01

    Aβ42 oligomers play key roles in the pathogenesis of Alzheimer disease, but their structures remain elusive partly due to their transient nature. Here, we show that Aβ42 in a fusion construct can be trapped in a stable oligomer state, which recapitulates characteristics of prefibrillar Aβ42 oligomers and enables us to establish their detailed structures. Site-directed spin labeling and electron paramagnetic resonance studies provide structural restraints in terms of side chain mobility and intermolecular distances at all 42 residue positions. Using these restraints and other biophysical data, we present a novel atomic-level oligomer model. In our model, each Aβ42 protein forms a single β-sheet with three β-strands in an antiparallel arrangement. Each β-sheet consists of four Aβ42 molecules in a head-to-tail arrangement. Four β-sheets are packed together in a face-to-back fashion. The stacking of identical segments between different β-sheets within an oligomer suggests that prefibrillar oligomers may interconvert with fibrils via strand rotation, wherein β-strands undergo an ∼90° rotation along the strand direction. This work provides insights into rational design of therapeutics targeting the process of interconversion between toxic oligomers and non-toxic fibrils. PMID:25118290

  8. Analyzing Exonuclease-Induced Hyperchromicity by Uv Spectroscopy: An Undergraduate Biochemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Ackerman, Megan M.; Ricciardi, Christopher; Weiss, David; Chant, Alan; Kraemer-Chant, Christina M.

    2016-01-01

    An undergraduate biochemistry laboratory experiment is described that utilizes free online bioinformatics tools along with readily available exonucleases to study the effects of base stacking and hydrogen bonding on the UV absorbance of DNA samples. UV absorbance of double-stranded DNA at the ?[subscript max] is decreased when the DNA bases are…

  9. Effects of urban growth controls on intercity commuting.

    PubMed

    Ogura, Laudo M

    2010-01-01

    This paper presents an empirical study of the effects of urban growth controls on the intercity commuting of workers. Growth controls (land use regulations that attempt to restrict population growth and urban sprawl) have increased housing prices and diverted population growth to uncontrolled cities. It has been suggested that resulting changes in local labour supply might stimulate intercity commuting from uncontrolled to controlled cities. To test this hypothesis, a gravity model of commuting flows between places in California is estimated using alternative econometric methods (OLS, Heckman selection and count-data). The possibility of spatial dependence in commuting flows is also taken into consideration. Results suggest larger commuting flows to destination places that restrict residential growth.

  10. Mechanically stable, high-aspect-ratio, multifilar, wound, ribbon-type conductor and method for manufacturing same

    DOEpatents

    Cottingham, J.G.

    1982-03-15

    A mechanically stable, wound, multifilar, ribbon-type conductor is described having a cross-sectional aspect ratio which may be greater than 12:1, comprising a plurality of conductive strands wound to form a flattened helix containing a plastic strip into which the strands have been pressed so as to form a bond between the strip and the strands. The bond mechanically stabilizes the conductor under tension, preventing it from collapsing into a tubular configuration. In preferred embodiments the plastic strip may be polytetrafluoroethylene, and the conductive strands may be formed from a superconductive material. Conductors in accordance with the present invention may be manufactured by winding a plurality of conductive strands around a hollow mandrel; the cross-section of a hollow mandrel; the cross-section of the mandrel continuously varying from substnatially circular to a high aspect ratio elipse while maintaining a constant circumference. The wound conductive strands are drawn from the mandrel as a multifilar helix while simultaneously a plastic strip is fed through the hollow mandrel so that it is contained within the helix as it is withdrawn from the mandrel. The helical conductor is then compressed into a ribbon-like form and the strands are bonded to the plastic strip by a combination of heat and pressure.

  11. Mechanically stable, high aspect ratio, multifilar, wound, ribbon-type conductor and method for manufacturing same

    DOEpatents

    Cottingham, James G.

    1987-01-01

    A mechanically stable, wound, multifilar, ribbon-type conductor having a cross-sectional aspect ratio which may be greater than 12:1, comprising a plurality of conductive strands wound to form a flattened helix containing a plastic strip into which the strands have been pressed so as to form a bond between the strip and the strands. The bond mechanically stabilizes the conductor under tension, preventing it from collapsing into a tubular configuration. In preferred embodiments the plastic strip may be polytetrafluoroethylene, and the conductive strands may be formed from a superconductive material. Conductors in accordance with the present invention may be manufactured by winding a plurality of conductive strands around a hollow mandrel; the cross-section of a hollow mandrel; the cross-section of the mandrel continuously varying from substantially circular to a high aspect ratio elipse while maintaining a constant circumference. The wound conductive strands are drawn from the mandrel as a multifilar helix while simultaneously a plastic strip is fed through the hollow mandrel so that it is contained within the helix as it is withdrawn from the mandrel. The helical conductor is then compressed into a ribbon-like form and the strands are bonded to the plastic strip by a combination of heat and pressure.

  12. Mechanically stable, high aspect ratio, multifilar, wound, ribbon-type conductor and method for manufacturing same

    DOEpatents

    Cottingham, James G.

    1987-11-03

    A mechanically stable, wound, multifilar, ribbon-type conductor having a cross-sectional aspect ratio which may be greater than 12:1, comprising a plurality of conductive strands wound to form a flattened helix containing a plastic strip into which the strands have been pressed so as to form a bond between the strip and the strands. The bond mechanically stabilizes the conductor under tension, preventing it from collapsing into a tubular configuration. In preferred embodiments the plastic strip may be polytetrafluoroethylene, and the conductive strands may be formed from a superconductive material. Conductors in accordance with the present invention may be manufactured by winding a plurality of conductive strands around a hollow mandrel; the cross-section of a hollow mandrel; the cross-section of the mandrel continuously varying from substantially circular to a high aspect ratio elipse while maintaining a constant circumference. The wound conductive strands are drawn from the mandrel as a multifilar helix while simultaneously a plastic strip is fed through the hollow mandrel so that it is contained within the helix as it is withdrawn from the mandrel. The helical conductor is then compressed into a ribbon-like form and the strands are bonded to the plastic strip by a combination of heat and pressure.

  13. Evaluating Opportunities to Enhance Hoosier State Train Ridership through a Survey of Riders’ Opinions and an Assessment of Access to the Line

    DOT National Transportation Integrated Search

    2017-12-01

    Passenger rail is an integral part of intercity transportation networks, especially in areas where residents do not have access to a car or there are not any other options for intercity travel. The Hoosier State Train (HST) line connects five station...

  14. An evaluation of the effect of level of service and cost on demand for intercity bus travel : final report.

    DOT National Transportation Integrated Search

    1980-01-01

    This report describes an evaluation of the effect on intercity bus ridership of changes in frequency of service and cost. The study was based on a comparison of travel between 19 selected cities in Virginia served by air, bus, or rail. These modes we...

  15. 49 CFR 238.15 - Movement of passenger equipment with power brake defects.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... brakes; (C) Piston travel that is in excess of the Class I brake test limits required in § 238.313 but... where the necessary repairs can be made. (3) Commuter, short-distance intercity, and short-distance Tier... brakes. Commuter, short-distance intercity, and short-distance Tier II passenger trains which develop...

  16. 49 CFR 37.87 - Purchase or lease of used intercity and commuter rail cars.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... rail cars. 37.87 Section 37.87 Transportation Office of the Secretary of Transportation TRANSPORTATION....87 Purchase or lease of used intercity and commuter rail cars. (a) Except as provided elsewhere in... car after August 25, 1990, shall ensure that the car is readily accessible to and usable by...

  17. 49 CFR 37.87 - Purchase or lease of used intercity and commuter rail cars.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... rail cars. 37.87 Section 37.87 Transportation Office of the Secretary of Transportation TRANSPORTATION....87 Purchase or lease of used intercity and commuter rail cars. (a) Except as provided elsewhere in... car after August 25, 1990, shall ensure that the car is readily accessible to and usable by...

  18. 49 CFR 37.87 - Purchase or lease of used intercity and commuter rail cars.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... rail cars. 37.87 Section 37.87 Transportation Office of the Secretary of Transportation TRANSPORTATION....87 Purchase or lease of used intercity and commuter rail cars. (a) Except as provided elsewhere in... car after August 25, 1990, shall ensure that the car is readily accessible to and usable by...

  19. 49 CFR 37.87 - Purchase or lease of used intercity and commuter rail cars.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... rail cars. 37.87 Section 37.87 Transportation Office of the Secretary of Transportation TRANSPORTATION....87 Purchase or lease of used intercity and commuter rail cars. (a) Except as provided elsewhere in... car after August 25, 1990, shall ensure that the car is readily accessible to and usable by...

  20. 49 CFR 37.87 - Purchase or lease of used intercity and commuter rail cars.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... rail cars. 37.87 Section 37.87 Transportation Office of the Secretary of Transportation TRANSPORTATION....87 Purchase or lease of used intercity and commuter rail cars. (a) Except as provided elsewhere in... car after August 25, 1990, shall ensure that the car is readily accessible to and usable by...

  1. 49 CFR 37.49 - Designation of responsible person(s) for intercity and commuter rail stations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Designation of responsible person(s) for intercity and commuter rail stations. 37.49 Section 37.49 Transportation Office of the Secretary of Transportation TRANSPORTATION SERVICES FOR INDIVIDUALS WITH DISABILITIES (ADA) Transportation Facilities § 37.49...

  2. 49 CFR 37.85 - Purchase or lease of new intercity and commuter rail cars.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Purchase or lease of new intercity and commuter rail cars. 37.85 Section 37.85 Transportation Office of the Secretary of Transportation TRANSPORTATION SERVICES FOR INDIVIDUALS WITH DISABILITIES (ADA) Acquisition of Accessible Vehicles By Public Entities § 37...

  3. Economic and demographic impacts of passenger rail systems : the impact of intercity passenger rails on population and employment change in the United States, 2000-2010.

    DOT National Transportation Integrated Search

    2015-12-01

    This research examines the impact of intercity passenger rails on change in population and employment at the county level in the continental United States from 2000 to 2010. This research adopts an integrated spatial regression approach that incorpor...

  4. The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.

    PubMed Central

    Shieh, H S; Berman, H M; Dabrow, M; Neidle, S

    1980-01-01

    A 2:2 complex of proflavine and deoxycytidylyl-3', 5'-guanosine has been crystallized and its structure determined by x-ray crystallography. The two dinucleoside phosphate strands form self complementary duplexes with Watson Crick hydrogen bonds. One proflavin is asymmetrically intercalated between the base pairs and the other is stacked above them. The conformations of the nucleotides are unusual in that one strand has C3',C2'endomixed sugar puckering and the other has C3',C3' endo deoxyribose sugars. These results show that the conformation of the 3'sugar is of secondary importance to the intercalated geometry. PMID:7355129

  5. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    NASA Astrophysics Data System (ADS)

    Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.

    2015-06-01

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  6. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

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

    Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including thosemore » corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.« less

  7. 78 FR 57450 - Notice Rescinding a Notice of Intent To Prepare an Environmental Impact Statement for the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-18

    ... allowed trains to run from one rail line to the other in order to accommodate intercity travel between... Pass and the Tri Valley area capable of supporting intercity and commuter rail passenger services. The... day, reducing travel times, and eliminating freight railroad delays by providing separate passenger...

  8. 76 FR 414 - Tier 1 Environmental Impact Statement for the Los Angeles to San Luis Obispo (LOSSAN North) Rail...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-04

    ... expected growth in population and resulting increases in intercity travel demand between Los Angeles and San Luis Obispo. As a result of this growth in travel demand, their travel delays from the growing... environmental analysis to help make corridor level decisions regarding the level of intercity passenger rail...

  9. 36 CFR § 1192.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ..., electrical or other system operates to ensure that cars do not move when the lift is in use. (3) Emergency... VEHICLES Intercity Rail Cars and Systems § 1192.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by § 1192.111 (a) and (e) of...

  10. 36 CFR 1192.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Intercity Rail Cars and Systems § 1192.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by § 1192.111 (a) and (e) of this subpart...(d) are provided, at stations or stops required to be accessible by 49 CFR part 37, the car is not...

  11. 36 CFR 1192.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Intercity Rail Cars and Systems § 1192.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by § 1192.111 (a) and (e) of this subpart...(d) are provided, at stations or stops required to be accessible by 49 CFR part 37, the car is not...

  12. 36 CFR 1192.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Intercity Rail Cars and Systems § 1192.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by § 1192.111 (a) and (e) of this subpart...(d) are provided, at stations or stops required to be accessible by 49 CFR part 37, the car is not...

  13. 36 CFR 1192.125 - Mobility aid accessibility.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Intercity Rail Cars and Systems § 1192.125 Mobility aid accessibility. (a)(1) General. All intercity rail cars, other than level entry cars, required to be accessible by § 1192.111 (a) and (e) of this subpart...(d) are provided, at stations or stops required to be accessible by 49 CFR part 37, the car is not...

  14. Technology assessment of future intercity passenger transporation systems. Volume 1: Summary report

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Technical, economic, environmental, and sociopolitical issues associated with future intercity transportation system options were assured. Technology assessment was used as a tool to assist in the identification of basic research and technology development tasks that should be undertaken. The emphasis was on domestic passenger transportation, but interfaces with freight and international transportation were considered.

  15. Mode shift strategies in intercity transportation and their effect on energy consumption

    NASA Technical Reports Server (NTRS)

    Sokolsky, S.

    1975-01-01

    Policies are examined which, if implemented, could lead to significant energy savings in intercity travel in the northeast corridor arena, without restricting the traveler's freedom of mode choice. The effects on arena energy consumption of introducing new, more energy-efficient aircraft are investigated; and several strategies unrelated to the implementation of new aircraft are introduced to yield reductions in overall intercity energy use. In both parts of this analysis, resulting changes in patronage (modal share) and energy use are demonstrated, leading to new insights into the effectiveness of different potential policies for achieving energy conservation. Some observations on induced demand trends that could be associated with certain strategies and the resultant potential effect on energy conservation are provided.

  16. Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

    PubMed

    Xu, Weijia; Ozer, Stuart; Gutell, Robin R

    2009-01-01

    With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

  17. Langevin Equation for DNA Dynamics

    NASA Astrophysics Data System (ADS)

    Grych, David; Copperman, Jeremy; Guenza, Marina

    Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

  18. Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

    PubMed Central

    Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

    2010-01-01

    With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

  19. Analysis of Percent On-Cell Reformation of Methane in SOFC Stacks and the Effects on Thermal, Electrical, and Mechanical Performance

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

    Recknagle, Kurtis P.; Koeppel, Brian J.; Sun, Xin

    2007-04-30

    Numerical simulations were performed to determine the effect that varying the percent on-cell steam-methane reformation would have on the thermal, electrical, and mechanical performance of generic, planar solid oxide fuel cell stacks. The study was performed using three-dimensional model geometries for cross-, co-, and counter-flow configuration stacks of 10x10- and 20x20-cm cell sizes. The analysis predicted the stress and temperature difference would be minimized for the 10x10-cm counter- and cross-flow stacks when 40 to 50% of the reformation reaction occurred on the anode. Gross electrical power density was virtually unaffected by the reforming. The co-flow stack benefited most from themore » on-cell reforming and had the lowest anode stresses of the 20x20-cm stacks. The analyses also suggest that airflows associated with 15% air utilization may be required for cooling the larger (20x20-cm) stacks.« less

  20. Sport stacking in auditory and visual attention of grade 3 learners.

    PubMed

    Mortimer, J; Krysztofiak, J; Custard, S; McKune, A J

    2011-08-01

    The effect of sport stacking on auditory and visual attention in 32 Grade 3 children was examined using a randomised, cross-over design. Children were randomly assigned to a sport stacking (n=16) or arts/crafts group (n=16) with these activities performed over 3 wk. (12 30-min. sessions, 4 per week). This was followed by a 3-wk. wash-out period after which there was a cross-over and the 3-wk. intervention repeated, with the sports stacking group performing arts/crafts and the arts/crafts group performing sports stacking. Performance on the Integrated Visual and Auditory Continuous Performance Test, a measure of auditory and visual attention, was assessed before and after each of the 3-wk. interventions for each group. Comparisons indicated that sport stacking resulted in significant improvement in high demand function and fine motor regulation, while it caused a significant reduction in low demand function. Auditory and visual attention adaptations to sport stacking may be specific to the high demand nature of the task.

  1. Stacked-unstacked equilibrium at the nick site of DNA.

    PubMed

    Protozanova, Ekaterina; Yakovchuk, Peter; Frank-Kamenetskii, Maxim D

    2004-09-17

    Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairing between complementary bases. However, their contribution into the duplex stability is yet to be determined. Now we fill this fundamental gap in our knowledge of the DNA double helix. We have prepared a series of 32, 300 bp-long DNA fragments with solitary nicks in the same position differing only in base-pairs flanking the nick. Electrophoretic mobility of these fragments in the gel has been studied. Assuming the equilibrium between stacked and unstacked conformations at the nick site, all 32 stacking free energy parameters have been obtained. Only ten of them are essential and they govern the stacking interactions between adjacent base-pairs in intact DNA double helix. A full set of DNA stacking parameters has been determined for the first time. From these data and from a well-known dependence of DNA melting temperature on G.C content, the contribution of base-pairing into duplex stability has been estimated. The obtained energy parameters of the DNA double helix are of paramount importance for understanding sequence-dependent DNA flexibility and for numerous biotechnology applications.

  2. Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.

    PubMed

    Matsui, Eriko; Abe, Junko; Yokoyama, Hideshi; Matsui, Ikuo

    2004-04-16

    Flap endonuclease-1 (FEN-1) possessing 5'-flap endonuclease and 5'-->3' exonuclease activity plays important roles in DNA replication and repair. In this study, the kinetic parameters of mutants at highly conserved aromatic residues, Tyr33, Phe35, Phe79, and Phe278-Phe279, in the vicinity of the catalytic centers of FEN-1 were examined. The substitution of these aromatic residues with alanine led to a large reduction in kcat values, although these mutants retained Km values similar to that of the wild-type enzyme. Notably, the kcat of Y33A and F79A decreased 333-fold and 71-fold, respectively, compared with that of the wild-type enzyme. The aromatic residues Tyr33 and Phe79, and the aromatic cluster Phe278-Phe279 mainly contributed to the recognition of the substrates without the 3' projection of the upstream strand (the nick, 5'-recess-end, single-flap, and pseudo-Y substrates) for the both exo- and endo-activities, but played minor roles in recognizing the substrates with the 3' projection (the double flap substrate and the nick substrate with the 3' projection). The replacement of Tyr33, Phe79, and Phe278-Phe279, with non-charged aromatic residues, but not with aliphatic hydrophobic residues, recovered the kcat values almost fully for the substrates without the 3' projection of the upstream strand, suggesting that the aromatic groups of Tyr33, Phe79, and Phe278-Phe279 might be involved in the catalytic reaction, probably via multiple stacking interactions with nucleotide bases. The stacking interactions of Tyr33 and Phe79 might play important roles in fixing the template strand and the downstream strand, respectively, in close proximity to the active center to achieve the productive transient state leading to the hydrolysis.

  3. Analysis of the stiffness and load-bearing capacity of glued laminated timber beams reinforced with strands

    NASA Astrophysics Data System (ADS)

    Sardiko, R.; Rocens, K.; Iejavs, J.; Jakovlevs, V.; Ziverts, K.

    2017-10-01

    In this paper a benefit of glulam pinewood beams reinforced strands is discussed. In the first phase, series of pull-out tests were performed on specimens made up of different types of glue (melamine-urea-formaldehyde, epoxy and others) to detect pull-out force and failure mode of a specimens. In the second phase, series of equal cross-section glulam beams with strand and rod reinforcement were theoretically analysed using transformed cross-section method. Additionally, series of experimental testing were made. Benefits of strand reinforcement use as glulam beams’ reinforcement were identified and examined the possibility of one glue type application in all operations of reinforced glulam beams manufacturing.

  4. 75 FR 68021 - Draft Finding of No Significant Impact on the Tier 1 Ohio 3C Quick Start Passenger Rail Tier-1...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-04

    ... purpose of the 3C ``Quick Start'' Passenger Rail Project is to reestablish intercity conventional speed... predictable and consistent travel times. It is intended to provide travel options and develop the passenger... through the High Speed Intercity Passenger Rail Program (HSIPR Program) administered by the FRA and funded...

  5. Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets.

    PubMed

    Indu, S; Kochat, V; Thakurela, S; Ramakrishnan, C; Varadarajan, Raghavan

    2011-01-01

    Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel β-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T(m). All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG⁰ = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. © 2010 Wiley-Liss, Inc.

  6. Dynamic Cooperation of Hydrogen Binding and π Stacking in ssDNA Adsorption on Graphene Oxide.

    PubMed

    Xu, Zhen; Lei, Xiaoling; Tu, Yusong; Tan, Zhi-Jie; Song, Bo; Fang, Haiping

    2017-09-21

    Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on GO surfaces. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and π-π stacking interactions, with preferential binding to the oxidized rather than to the unoxidized region of the GO surface. The adsorption process shows a dynamic cooperation adsorption behavior; the ssDNA segment first captures the oxidized groups of the GO surface by hydrogen bonding interaction, and then the configuration relaxes to maximize the π-π stacking interactions between the aromatic rings of the nucleobases and those of the GO surface. We attributed this behavior to the faster forming hydrogen bonding interaction compared to π-π stacking; the π-π stacking interaction needs more relaxation time to regulate the configuration of the ssDNA segment to fit the aromatic rings on the GO surface. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Recombinant PrPSc shares structural features with brain-derived PrPSc suggesting that they have a similar architecture: Insights from limited proteolysis

    USDA-ARS?s Scientific Manuscript database

    An extensive body of experimental and spectroscopic evidence supports the hypothesis that PrPSc is a multimer of 4-rung ß-solenoids, and that individual PrPSc solenoids stack to form amyloid fibers. We recently used limited proteolysis to map the ß-strands and connecting loops that make up the PrPSc...

  8. Salton Seismic Imaging Project Line 5—the San Andreas Fault and Northern Coachella Valley Structure, Riverside County, California

    NASA Astrophysics Data System (ADS)

    Rymer, M. J.; Fuis, G.; Catchings, R. D.; Goldman, M.; Tarnowski, J. M.; Hole, J. A.; Stock, J. M.; Matti, J. C.

    2012-12-01

    The Salton Seismic Imaging Project (SSIP) is a large-scale, active- and passive-source seismic project designed to image the San Andreas Fault (SAF) and the adjacent basins (Imperial and Coachella Valleys) in southern California. Here, we focus on SSIP Line 5, one of four 2-D NE-SW-oriented seismic profiles that were acquired across the Coachella Valley. The 38-km-long SSIP-Line-5 seismic profile extends from the Santa Rosa Ranges to the Little San Bernardino Mountains and crosses both strands of the SAF, the Mission Creek (MCF) and Banning (BF) strands, near Palm Desert. Data for Line 5 were generated from nine buried explosive sources (most spaced about 2 to 8 km apart) and were recorded on approximately 281 Texan seismographs (average spacing 138 m). First-arrival refractions were used to develop a refraction tomographic velocity image of the upper crust along the seismic profile. The seismic data were also stacked and migrated to develop low-fold reflection images of the crust. From the surface to about 8 km depth, P-wave velocities range from about 2 km/s to more than 7.5 km/s, with the lowest velocities within a well-defined (~2-km-deep, 15-km-wide) basin (< 4 km/s), and the highest velocities below the transition from the Coachella Valley to the Santa Rosa Ranges on the southwest and within the Little San Bernardino Mountains on the northeast. The MCF and BF strands of the SAF bound an approximately 2.5-km-wide horst-type structure on the northeastern side of the Coachella Valley, beneath which the upper crust is characterized by a pronounced low-velocity zone that extends to the bottom of the velocity image. Rocks within the low-velocity zone have significantly lower velocities than those to the northeast and the southwest at the same depths. Conversely, the velocities of rocks on both sides of the Coachella Valley are greater than 7 km/s at depths exceeding about 4 km. The relatively narrow zone of shallow high-velocity rocks between the surface traces of the MCF and BF strands is associated with a zone of uplifted strata. Along SSIP Line 5, we infer that the MCF and BF strands are steeply dipping and merge at about 2 km depth. We base our interpretation on a prominent basement low-velocity zone (fault zone) that is centered southwest of the MCF and BF strands and extends to at least 8 km depth.

  9. Driver Performance Problems of Intercity Bus Public Transportation Safety in Indonesia

    NASA Astrophysics Data System (ADS)

    Suraji, A.; Harnen, S.; Wicaksono, A.; Djakfar, L.

    2017-11-01

    The risk of an inter-city bus public accident can be influenced by various factors such as the driver’s performance. Therefore, knowing the various influential factors related to driver’s performance is very necessary as an effort to realize road traffic safety. This study aims to determine the factors that fall on the accident associated with the driver’s performance and make mathematical modeling factors that affect the accident. Methods of data retrieval were obtained from NTSC secondary data. The data was processed by identifying factors that cause the accident. Furthermore data processing and analysis used the PCA method to obtain mathematical modeling of factors influencing the inter-city bus accidents. The results showed that the main factors that cause accidents are health, discipline, and driver competence.

  10. Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.

    PubMed

    Nonin, S; Phan, A T; Leroy, J L

    1997-09-15

    Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif. NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*. Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize into an i-motif. The change of folding topology resulting from the substitution of a single nucleoside emphasizes the influence of the loop residues on the i-motif structure formed by two folded strands.

  11. Stacked graphene nanofibers for electrochemical oxidation of DNA bases.

    PubMed

    Ambrosi, Adriano; Pumera, Martin

    2010-08-21

    In this article, we show that stacked graphene nanofibers (SGNFs) demonstrate superior electrochemical performance for oxidation of DNA bases over carbon nanotubes (CNTs). This is due to an exceptionally high number of accessible graphene sheet edges on the surface of the nanofibers when compared to carbon nanotubes, as shown by transmission electron microscopy and Raman spectroscopy. The oxidation signals of adenine, guanine, cytosine, and thymine exhibit two to four times higher currents than on CNT-based electrodes. SGNFs also exhibit higher sensitivity than do edge-plane pyrolytic graphite, glassy carbon, or graphite microparticle-based electrodes. We also demonstrate that influenza A(H1N1)-related strands can be sensitively oxidized on SGNF-based electrodes, which could therefore be applied to label-free DNA analysis.

  12. Responses to Fiscal Stress: A Comparative Analysis

    DTIC Science & Technology

    2013-12-01

    of “a significant decline in market share by the middle of the 20th century as travelers and shippers turned increasingly to airlines, trucks, and...1995). Intercity passenger rail: Financial and operating conditions threaten Amtrak’s long-term viability (GAO-95-71). Washington, DC: U.S...I. (1980). Retrenchment and flexibility in public organizations. Fiscal Stress and Public Policy, 159–178. Scheinberg, P. F. (1998). Intercity

  13. Effect of aircraft technology improvements on intercity energy use

    NASA Technical Reports Server (NTRS)

    1976-01-01

    An examination of the growth or decline in energy consumption in short haul, high density intercity transportation is made in relation to changes in aeronautical technology. Improvements or changes in the technology of competitive modes are also included. Certain improvements in air traffic control procedures were included to determine their effectiveness in saving energy along with a fuel efficient turboprop short haul aircraft concept.

  14. RNA synthesis is modulated by G-quadruplex formation in Hepatitis C virus negative RNA strand.

    PubMed

    Chloé, Jaubert; Amina, Bedrat; Laura, Bartolucci; Carmelo, Di Primo; Michel, Ventura; Jean-Louis, Mergny; Samir, Amrane; Marie-Line, Andreola

    2018-05-25

    DNA and RNA guanine-rich oligonucleotides can form non-canonical structures called G-quadruplexes or "G4" that are based on the stacking of G-quartets. The role of DNA and RNA G4 is documented in eukaryotic cells and in pathogens such as viruses. Yet, G4 have been identified only in a few RNA viruses, including the Flaviviridae family. In this study, we analysed the last 157 nucleotides at the 3'end of the HCV (-) strand. This sequence is known to be the minimal sequence required for an efficient RNA replication. Using bioinformatics and biophysics, we identified a highly conserved G4-prone sequence located in the stem-loop IIy' of the negative strand. We also showed that the formation of this G-quadruplex inhibits the in vitro RNA synthesis by the RdRp. Furthermore, Phen-DC3, a specific G-quadruplex binder, is able to inhibit HCV viral replication in cells in conditions where no cytotoxicity was measured. Considering that this domain of the negative RNA strand is well conserved among HCV genotypes, G4 ligands could be of interest for new antiviral therapies.

  15. Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer.

    PubMed

    Li, Ming-Hui; Luo, Quan; Xue, Xiang-Gui; Li, Ze-Sheng

    2011-03-01

    G-rich sequences can fold into a four-stranded structure called a G-quadruplex, and sequences with short loops are able to aggregate to form stable quadruplex multimers. Few studies have characterized the properties of this variety of quadruplex multimers. Using molecular modeling and molecular dynamics simulations, the present study investigated a dimeric G-quadruplex structure formed from a simple sequence of d(GGGTGGGTGGGTGGGT) (G1), and its interactions with a planar ligand of a perylene derivative (Tel03). A series of analytical methods, including free energy calculations and principal components analysis (PCA), was used. The results show that a dimer structure with stacked parallel monomer structures is maintained well during the entire simulation. Tel03 can bind to the dimer efficiently through end stacking, and the binding mode of the ligand stacked with the 3'-terminal thymine base is most favorable. PCA showed that the dominant motions in the free dimer occur on the loop regions, and the presence of the ligand reduces the flexibility of the loops. Our investigation will assist in understanding the geometric structure of stacked G-quadruplex multimers and may be helpful as a platform for rational drug design.

  16. An Intercity Outbreak of Meningococcal Meningitis in Adults

    PubMed Central

    Oill, Phyllis A.; Chow, Anthony W.; Roberto, Ronald R.; Guze, Lucien B.

    1978-01-01

    An intercity outbreak of meningococcal meningitis occurred in five adults, with the acute onset of symptoms developing in two of the patients after they returned to Los Angeles from the San Francisco Bay area. The secondary attack rate was 36.4 percent in this entirely adult household. The authors review reports of secondary cases in civilian epidemics, as well as recommendations for chemoprophylaxis in household contacts. PMID:636407

  17. The Blueprint for a Secure Energy Future: Progress Report

    DTIC Science & Technology

    2012-03-01

    Over the past three years, the Administration has continued to develop and expand America’s high-speed and intercity passenger rail system. In May...2011, DOT announced $2 billion in high-speed rail, bringing our unprecedented investment to $10.1 billion to date. In FY 2011, intercity rail...thousands of jobs, improve and expand travel options, cut energy use and help make our communities more livable. Improving Transportation Choices

  18. 26 CFR 48.6427-2 - Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 16 2011-04-01 2011-04-01 false Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or school buses. 48.6427-2 Section 48.6427-2 Internal... Retailers and Manufacturers Taxes § 48.6427-2 Credits or payments to purchaser of diesel or special motor...

  19. 26 CFR 48.6427-2 - Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 16 2010-04-01 2010-04-01 true Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or school buses. 48.6427-2 Section 48.6427-2 Internal... Retailers and Manufacturers Taxes § 48.6427-2 Credits or payments to purchaser of diesel or special motor...

  20. 26 CFR 48.6427-2 - Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 16 2012-04-01 2012-04-01 false Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or school buses. 48.6427-2 Section 48.6427-2 Internal... Retailers and Manufacturers Taxes § 48.6427-2 Credits or payments to purchaser of diesel or special motor...

  1. 26 CFR 48.6427-2 - Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 16 2013-04-01 2013-04-01 false Credits or payments to purchaser of diesel or special motor fuels used in intercity, local, or school buses. 48.6427-2 Section 48.6427-2 Internal... Retailers and Manufacturers Taxes § 48.6427-2 Credits or payments to purchaser of diesel or special motor...

  2. A new cationic porphyrin derivative (TMPipEOPP) with large side arm substituents: a highly selective G-quadruplex optical probe.

    PubMed

    Zhu, Li-Na; Zhao, Shu-Juan; Wu, Bin; Li, Xiao-Zeng; Kong, De-Ming

    2012-01-01

    The discovery of uncommon DNA structures and speculation about their potential functions in genes has brought attention to specific DNA structure recognition. G-quadruplexes are four-stranded nucleic acid structures formed by G-rich DNA (or RNA) sequences. G-rich sequences with a high potential to form G-quadruplexes have been found in many important genomic regions. Porphyrin derivatives with cationic side arm substituents are important G-quadruplex-binding ligands. For example, 5,10,15,20-Tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin (TMPyP4), interacts strongly with G-quadruplexes, but has poor selectivity for G-quadruplex versus duplex DNA. To increase the G-quadruplex recognition specificity, a new cationic porphyrin derivative, 5,10,15,20-tetra-{4-[2-(1-methyl-1-piperidinyl)ethoxy]phenyl} porphyrin (TMPipEOPP), with large side arm substituents was synthesized, and the interactions between TMPipEOPP and different DNA structures were compared. The results show that G-quadruplexes cause large changes in the UV-Vis absorption and fluorescence spectra of TMPipEOPP, but duplex and single-stranded DNAs do not, indicating that TMPipEOPP can be developed as a highly specific optical probe for discriminating G-quadruplex from duplex and single-stranded DNA. Visual discrimination is also possible. Job plot and Scatchard analysis suggest that a complicated binding interaction occurs between TMPipEOPP and G-quadruplexes. At a low [G-quadruplex]/[TMPipEOPP] ratio, one G-quadruplex binds two TMPipEOPP molecules by end-stacking and outside binding modes. At a high [G-quadruplex]/[TMPipEOPP] ratio, two G-quadruplexes bind to one TMPipEOPP molecule in a sandwich-like end-stacking mode.

  3. Excited state free energy calculations of Cy3 in different environments

    NASA Astrophysics Data System (ADS)

    Sawangsang, Pilailuk; Buranachai, Chittanon; Punwong, Chutintorn

    2015-05-01

    Cy3, a cyanine dye, is one of the most widely used dyes in investigating the structure and dynamics of biomolecules by means of fluorescence methods. However, Cy3 fluorescence emission is strongly competed by trans-cis isomerization, whose efficiency is dictated by the isomerization energy barrier and the environment of Cy3. The fluorescence quantum yield of Cy3 is very low when the dye is free in homogeneous solution but it is considerably enhanced in an environment that rigidifies the structure, e.g. when it is attached to a DNA strand. In this work, the barriers for isomerization on the excited state of free Cy3, and Cy3 attached to single- and double-stranded DNA in methanol, are presented. The free energy and subsequently the isomerization barrier calculations are performed using the umbrella sampling technique with the weighted histogram analysis method. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is employed to provide the potential energy surfaces for the excited state dynamics simulations in umbrella sampling. The semiempirical floating occupation molecular orbital configuration interaction method is used for electronic excited state calculations of the QM region (Cy3). From the free energy calculations, the barrier of Cy3 attached to the single-stranded DNA is highest, in agreement with previously reported experimental results. This is likely due to the stacking interaction between Cy3 and DNA. Such a stacking interaction is likely associated with steric hindrance that prevents the rotation around the conjugated bonds of Cy3. If Cy3 experiences high steric hindrance, it has a higher isomerization barrier and thus the efficiency of fluorescence emission increases.

  4. Role of Sequence and Structural Polymorphism on the Mechanical Properties of Amyloid Fibrils

    PubMed Central

    Kim, Jae In; Na, Sungsoo; Eom, Kilho

    2014-01-01

    Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP) fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD) simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of β strands (peptide chain). Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of β strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture. PMID:24551113

  5. Dissecting the structural determinants for the difference in mechanical stability of silk and amyloid beta-sheet stacks.

    PubMed

    Xiao, Senbo; Xiao, Shijun; Gräter, Frauke

    2013-06-14

    Stacking of β-sheets results in a protein super secondary structure with remarkable mechanical properties. β-Stacks are the determinants of a silk fiber's resilience and are also the building blocks of amyloid fibrils. While both silk and amyloid-type crystals are known to feature a high resistance against rupture, their structural and mechanical similarities and particularities are yet to be fully understood. Here, we systematically compare the rupture force and stiffness of amyloid and spider silk poly-alanine β-stacks of comparable sizes using Molecular Dynamics simulations. We identify the direction of force application as the primary determinant of the rupture strength; β-sheets in silk are orientated along the fiber axis, i.e. the pulling direction, and consequently require high forces in the several nanoNewton range for shearing β-strands apart, while β-sheets in amyloid are oriented vertically to the fiber, allowing a zipper-like rupture at sub-nanoNewton forces. A secondary factor rendering amyloid β-stacks softer and weaker than their spider silk counterparts is the sub-optimal side-chain packing between β-sheets due to the sequence variations of amyloid-forming proteins as opposed to the perfectly packed poly-alanine β-sheets of silk. Taken together, amyloid fibers can reach the stiffness of silk fibers in spite of their softer and weaker β-sheet arrangement as they are missing a softening amorphous matrix.

  6. Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin.

    PubMed

    Kuo, Hsiou-Ting; Liu, Shing-Lung; Chiu, Wen-Chieh; Fang, Chun-Jen; Chang, Hsien-Chen; Wang, Wei-Ren; Yang, Po-An; Li, Jhe-Hao; Huang, Shing-Jong; Huang, Shou-Ling; Cheng, Richard P

    2015-05-01

    β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif.

  7. Dock 'n roll: folding of a silk-inspired polypeptide into an amyloid-like beta solenoid.

    PubMed

    Zhao, Binwu; Cohen Stuart, Martien A; Hall, Carol K

    2016-04-20

    Polypeptides containing the motif ((GA)mGX)n occur in silk and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two hydrophobic shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II' β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state.

  8. 76 FR 79155 - Marine Mammals; Issuance of Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-21

    ... region of significant potential offshore wind farm development. The LOC expires on March 31, 2016. File... stranding network to cross reference stranded animals with photo-identification catalogs. The LOC expires on...

  9. Ocean acoustic interferometry.

    PubMed

    Brooks, Laura A; Gerstoft, Peter

    2007-06-01

    Ocean acoustic interferometry refers to an approach whereby signals recorded from a line of sources are used to infer the Green's function between two receivers. An approximation of the time domain Green's function is obtained by summing, over all source positions (stacking), the cross-correlations between the receivers. Within this paper a stationary phase argument is used to describe the relationship between the stacked cross-correlations from a line of vertical sources, located in the same vertical plane as two receivers, and the Green's function between the receivers. Theory and simulations demonstrate the approach and are in agreement with those of a modal based approach presented by others. Results indicate that the stacked cross-correlations can be directly related to the shaded Green's function, so long as the modal continuum of any sediment layers is negligible.

  10. GIS based analysis of Intercity Fatal Road Traffic Accidents in Iran

    PubMed Central

    Alizadeh, A; Zare, M; Darparesh, M; Mohseni, S; Soleimani-Ahmadi, M

    2015-01-01

    Road traffic accidents including intercity car traffic accidents (ICTAs) are among the most important causes of morbidity and mortality due to the growing number of vehicles, risky behaviors, and changes in lifestyle of the general population. A sound knowledge of the geographical distribution of car traffic accidents can be considered as an approach towards the accident causation and it can be used as an administrative tool in allocating the sources for traffic accidents prevention. This study was conducted to investigate the geographical distribution and the time trend of fatal intercity car traffic accidents in Iran. To conduct this descriptive study, all Iranian intercity road traffic mortality data were obtained from the Police reports in the Statistical Yearbook of the Governor’s Budget and Planning. The obtained data were for 17 complete Iranian calendar years from March 1997 to March 2012. The incidence rate (IR) of fatal ICTAs for each year was calculated as the total number of fatal ICTAs in every 100000 population in specified time intervals. Figures and maps indicating the trends and geographical distribution of fatal ICTAs were prepared while using Microsoft Excel and ArcGis9.2 software. The number of fatal car accidents showed a general increasing trend from 3000 in 1996 to 13500 in 2012. The incidence of fatal intercity car accidents has changed from six in 100000 population in 1996 to 18 in 100000 population in 2012. GIS based data showed that the incidence rate of ICTAs in different provinces of Iran was very divergent. The highest incidence of fatal ICTAs was in Semnan province (IR= 35.2), followed by North Khorasan (IR=22.7), and South Khorasan (IR=22). The least incidence of fatal ICTAs was in Tehran province (IR=2.4) followed by Khozestan (IR=6.5), and Eastern Azarbayejan (IR=6.6). The compensation cost of fatal ICTAs also showed an increasing trend during the studied period. Since an increasing amount of money was being paid yearly for the car accidents, which were in their nature preventable, the key players in road safety including governments, car manufacturers, and road developers were recommended to use GIS based accident data for a more efficient planning and budgeting towards the intercity car accidents reduction. PMID:28255402

  11. GIS based analysis of Intercity Fatal Road Traffic Accidents in Iran.

    PubMed

    Alizadeh, A; Zare, M; Darparesh, M; Mohseni, S; Soleimani-Ahmadi, M

    2015-01-01

    Road traffic accidents including intercity car traffic accidents (ICTAs) are among the most important causes of morbidity and mortality due to the growing number of vehicles, risky behaviors, and changes in lifestyle of the general population. A sound knowledge of the geographical distribution of car traffic accidents can be considered as an approach towards the accident causation and it can be used as an administrative tool in allocating the sources for traffic accidents prevention. This study was conducted to investigate the geographical distribution and the time trend of fatal intercity car traffic accidents in Iran. To conduct this descriptive study, all Iranian intercity road traffic mortality data were obtained from the Police reports in the Statistical Yearbook of the Governor's Budget and Planning. The obtained data were for 17 complete Iranian calendar years from March 1997 to March 2012. The incidence rate (IR) of fatal ICTAs for each year was calculated as the total number of fatal ICTAs in every 100000 population in specified time intervals. Figures and maps indicating the trends and geographical distribution of fatal ICTAs were prepared while using Microsoft Excel and ArcGis9.2 software. The number of fatal car accidents showed a general increasing trend from 3000 in 1996 to 13500 in 2012. The incidence of fatal intercity car accidents has changed from six in 100000 population in 1996 to 18 in 100000 population in 2012. GIS based data showed that the incidence rate of ICTAs in different provinces of Iran was very divergent. The highest incidence of fatal ICTAs was in Semnan province (IR= 35.2), followed by North Khorasan (IR=22.7), and South Khorasan (IR=22). The least incidence of fatal ICTAs was in Tehran province (IR=2.4) followed by Khozestan (IR=6.5), and Eastern Azarbayejan (IR=6.6). The compensation cost of fatal ICTAs also showed an increasing trend during the studied period. Since an increasing amount of money was being paid yearly for the car accidents, which were in their nature preventable, the key players in road safety including governments, car manufacturers, and road developers were recommended to use GIS based accident data for a more efficient planning and budgeting towards the intercity car accidents reduction.

  12. Effects of Complementary DNA and Salt on the Thermoresponsiveness of Poly(N-isopropylacrylamide)-b-DNA.

    PubMed

    Fujita, Masahiro; Hiramine, Hayato; Pan, Pengju; Hikima, Takaaki; Maeda, Mizuo

    2016-02-02

    The thermoresponsive structural transition of poly(N-isopropylacrylamide) (PNIPAAm)-b-DNA copolymers was explored. Molecular assembly of the block copolymers was facilitated by adding salt, and this assembly was not nucleated by the association between DNA strands but by the coil-globule transition of PNIPAAm blocks. Below the lower critical solution temperature (LCST) of PNIPAAm, the copolymer solution remained transparent even at high salt concentrations, regardless of whether DNA was hybridized with its complementary partner to form a double-strand (or single-strand) structure. At the LCST, the hybridized copolymer assembled in spherical nanoparticles, surrounded by double-stranded DNA; subsequently, the non-cross-linking aggregation occurred, while the nanoparticles were dispersed if the salt concentration was low or DNA blocks were unhybridized. When the DNA duplex was denatured to a single-stranded state by heating, the aggregated nanoparticles redispersed owing to the recovery of the steric repulsion of the DNA strands. The changes in the steric and electrostatic effects by hybridization and the addition of salt did not result in any specific attraction between DNA strands but merely decreased the repulsive interactions. The van der Waals attraction between the nanoparticles overcame such repulsive interactions so that the non-cross-linking aggregation of the micellar particles was mediated.

  13. Ethanol-perturbed amyloidogenic self-assembly of insulin: looking for origins of amyloid strains.

    PubMed

    Dzwolak, Wojciech; Grudzielanek, Stefan; Smirnovas, Vytautas; Ravindra, Revanur; Nicolini, Chiara; Jansen, Ralf; Loksztejn, Anna; Porowski, Sylwester; Winter, Roland

    2005-06-28

    A model cosolvent, ethanol, has profound and diversified effects on the amyloidogenic self-assembly of insulin, yielding spectroscopically and morphologically distinguishable forms of beta-aggregates. The alcohol reduces hydrodynamic radii of insulin molecules, decreases enthalpic costs associated with aggregation-prone intermediate states, and accelerates the aggregation itself. Increasing the concentration of the cosolvent promotes curved, amorphous, and finally donut-shaped forms. According to FT-IR data, inter-beta-strand hydrogen bonding is stronger in fibrils formed in the presence of ethanol. Mechanisms underlying the polymorphism of insulin aggregates were investigated by spectroscopic (CD, FT-IR, and fluorescence anisotropy) and calorimetric (DSC and PPC) methods. The nonmonotonic character of the influence of ethanol on insulin aggregation suggests that both preferential exclusion (predominant at the low concentrations) and direct alcohol-protein interactions are involved. The perturbed hydration of aggregation nuclei appears to be a decisive factor in selection of a dominant mode of beta-strand alignment. It may override unfavorable structural consequences of an alternative strand-to-strand stacking, such as strained hydrogen bonding. A hypothetical mechanism of inducing different amyloid "strains" has been put forward. The cooperative character of fibril assembly creates enormous energy barriers for any interstrain transition, which renders the energy landscape comblike-shaped.

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

    Wang, Yanli; Sheng, Gang; Juranek, Stefan

    The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas twomore » critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.« less

  15. Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I.

    PubMed

    Wang, Yanli; Ludwig, Janos; Schuberth, Christine; Goldeck, Marion; Schlee, Martin; Li, Haitao; Juranek, Stefan; Sheng, Gang; Micura, Ronald; Tuschl, Thomas; Hartmann, Gunther; Patel, Dinshaw J

    2010-07-01

    RIG-I is a cytosolic helicase that senses 5'-ppp RNA contained in negative-strand RNA viruses and triggers innate antiviral immune responses. Calorimetric binding studies established that the RIG-I C-terminal regulatory domain (CTD) binds to blunt-end double-stranded 5'-ppp RNA a factor of 17 more tightly than to its single-stranded counterpart. Here we report on the crystal structure of RIG-I CTD bound to both blunt ends of a self-complementary 5'-ppp dsRNA 12-mer, with interactions involving 5'-pp clearly visible in the complex. The structure, supported by mutation studies, defines how a lysine-rich basic cleft within the RIG-I CTD sequesters the observable 5'-pp of the bound RNA, with a stacked phenylalanine capping the terminal base pair. Key intermolecular interactions observed in the crystalline state are retained in the complex of 5'-ppp dsRNA 24-mer and full-length RIG-I under in vivo conditions, as evaluated from the impact of binding pocket RIG-I mutations and 2'-OCH(3) RNA modifications on the interferon response.

  16. Mesoscopic modeling for nucleic acid chain dynamics

    PubMed Central

    Sales-Pardo, M.; Guimerà, R.; Moreira, A. A.; Widom, J.; Amaral, L. A. N.

    2007-01-01

    To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin—a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop—studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands. PMID:16089566

  17. Technology assessment of future intercity passenger transportation systems. Volume 6: Impact assessment

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Consequences that might occur if certain technological developments take place in intercity transportation are described. These consequences are broad ranging, and include economic, environmental, social, institutional, energy-related, and transportation service implications. The possible consequences are traced through direct (primary) impacts to indirect (secondary, tertiary, etc.) impacts. Chains of consequences are traced, reaching as far beyond the original transportation cause as is necessary to identify all impacts felt to be influenced significantly by the technological development considered.

  18. Base Flipping in V(D)J Recombination: Insights into the Mechanism of Hairpin Formation, the 12/23 Rule, and the Coordination of Double-Strand Breaks▿ †

    PubMed Central

    Bischerour, Julien; Lu, Catherine; Roth, David B.; Chalmers, Ronald

    2009-01-01

    Tn5 transposase cleaves the transposon end using a hairpin intermediate on the transposon end. This involves a flipped base that is stacked against a tryptophan residue in the protein. However, many other members of the cut-and-paste transposase family, including the RAG1 protein, produce a hairpin on the flanking DNA. We have investigated the reversed polarity of the reaction for RAG recombination. Although the RAG proteins appear to employ a base-flipping mechanism using aromatic residues, the putatively flipped base is not at the expected location and does not appear to stack against any of the said aromatic residues. We propose an alternative model in which a flipped base is accommodated in a nonspecific pocket or cleft within the recombinase. This is consistent with the location of the flipped base at position −1 in the coding flank, which can be occupied by purine or pyrimidine bases that would be difficult to stabilize using a single, highly specific, interaction. Finally, during this work we noticed that the putative base-flipping events on either side of the 12/23 recombination signal sequence paired complex are coupled to the nicking steps and serve to coordinate the double-strand breaks on either side of the complex. PMID:19720743

  19. RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.

    PubMed

    Martinez, Hugo M; Maizel, Jacob V; Shapiro, Bruce A

    2008-06-01

    Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.

  20. E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats

    PubMed Central

    Pan, Feng; Zhang, Yuan; Man, Viet Hoang; Roland, Christopher

    2018-01-01

    Abstract Atypical DNA secondary structures play an important role in expandable trinucleotide repeat (TR) and hexanucleotide repeat (HR) diseases. The cytosine mismatches in C-rich homoduplexes and hairpin stems are weakly bonded; experiments show that for certain sequences these may flip out of the helix core, forming an unusual structure termed an ‘e-motif’. We have performed molecular dynamics simulations of C-rich TR and HR DNA homoduplexes in order to characterize the conformations, stability and dynamics of formation of the e-motif, where the mismatched cytosines symmetrically flip out in the minor groove, pointing their base moieties towards the 5′-direction in each strand. TRs have two non-equivalent reading frames, (GCC)n and (CCG)n; while HRs have three: (CCCGGC)n, (CGGCCC)n, (CCCCGG)n. We define three types of pseudo basepair steps related to the mismatches and show that the e-motif is only stable in (GCC)n and (CCCGGC)n homoduplexes due to the favorable stacking of pseudo GpC steps (whose nature depends on whether TRs or HRs are involved) and the formation of hydrogen bonds between the mismatched cytosine at position i and the cytosine (TRs) or guanine (HRs) at position i − 2 along the same strand. We also characterize the extended e-motif, where all mismatched cytosines are extruded, their extra-helical stacking additionally stabilizing the homoduplexes. PMID:29190385

  1. Single-Event Transgene Product Levels Predict Levels in Genetically Modified Breeding Stacks.

    PubMed

    Gampala, Satyalinga Srinivas; Fast, Brandon J; Richey, Kimberly A; Gao, Zhifang; Hill, Ryan; Wulfkuhle, Bryant; Shan, Guomin; Bradfisch, Greg A; Herman, Rod A

    2017-09-13

    The concentration of transgene products (proteins and double-stranded RNA) in genetically modified (GM) crop tissues is measured to support food, feed, and environmental risk assessments. Measurement of transgene product concentrations in breeding stacks of previously assessed and approved GM events is required by many regulatory authorities to evaluate unexpected transgene interactions that might affect expression. Research was conducted to determine how well concentrations of transgene products in single GM events predict levels in breeding stacks composed of these events. The concentrations of transgene products were compared between GM maize, soybean, and cotton breeding stacks (MON-87427 × MON-89034 × DAS-Ø15Ø7-1 × MON-87411 × DAS-59122-7 × DAS-40278-9 corn, DAS-81419-2 × DAS-44406-6 soybean, and DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 × MON-88913-8 × DAS-81910-7 cotton) and their component single events (MON-87427, MON-89034, DAS-Ø15Ø7-1, MON-87411, DAS-59122-7, and DAS-40278-9 corn, DAS-81419-2, and DAS-44406-6 soybean, and DAS-21023-5, DAS-24236-5, SYN-IR102-7, MON-88913-8, and DAS-81910-7 cotton). Comparisons were made within a crop and transgene product across plant tissue types and were also made across transgene products in each breeding stack for grain/seed. Scatter plots were generated comparing expression in the stacks to their component events, and the percent of variability accounted for by the line of identity (y = x) was calculated (coefficient of identity, I 2 ). Results support transgene concentrations in single events predicting similar concentrations in breeding stacks containing the single events. Therefore, food, feed, and environmental risk assessments based on concentrations of transgene products in single GM events are generally applicable to breeding stacks composed of these events.

  2. Dynamic properties of unbonded, multi-strand beams subjected to flexural loading

    NASA Astrophysics Data System (ADS)

    Asker, Haval K.; Rongong, Jem A.; Lord, Charles E.

    2018-02-01

    Beam-like structures, constructed from many long strands that are constrained rather than bonded together, can provide appreciable levels of structural damping through friction between individual strands. This paper describes experimental and numerical studies, carried out on square-section metal beams, which are aimed at improving understanding of the relationship between construction and performance. A beam is formed from a pack of square-section strands that is held together at various compression loads with pre-calibrated clamps. Flexural deformation of the assembled beam is simulated using standard finite element analysis employing simple Coulomb friction at the interfaces. The validity of the assumptions used in the models is confirmed by comparison with three point bend tests on a regular nine strand construction at several different clamp loads. Dynamic loss factors for this beam are obtained by conducting forced vibration tests, which show that the damping is insensitive to frequency. Subsequent numerical studies are used to investigate the effects of increasing the number of strands whilst maintaining the overall cross-section geometry of the beam. It is found that the system stiffness drops and loss factor increases when more strands are used for a maintained beam cross-section. Interestingly, the energy dissipated by each beam construction is almost the same. These results provide a vital and necessary insight into the physics for stranded structures and materials that are largely prevalent in mechanical (e.g. cables) and electrical (e.g. wires) elements.

  3. Measurements of Deuteron-Induced Activation Cross Sections for IFMIF Accelerator Structural Materials

    NASA Astrophysics Data System (ADS)

    Nakao, Makoto; Hori, Jun-ichi; Ochiai, Kentaro; Sato, Satoshi; Yamauchi, Michinori; Ishioka, Noriko S.; Nishitani, Takeo

    2005-05-01

    Activation cross sections for deuteron-induced reactions on aluminum, copper, and tungsten were measured by using a stacked-foil method. The stacked foils were irradiated with deuteron beam at the AVF cyclotron in the TIARA facility, JAERI. We obtained the activation cross sections for 27Al(d,2p)27Mg, 27Al(d,x)24Na, natCu(d,x)62,63Zn, 61,64Cu, and natW(d,x)181-184,186Re, 187W in the 22-40 MeV region. These cross sections were compared with other experimental ones and the data in the ACSELAM library calculated by the ALICE-F code.

  4. Unresolved fine-scale structure in solar coronal loop-tops

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

    Scullion, E.; Van der Voort, L. Rouppe; Wedemeyer, S.

    2014-12-10

    New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certainmore » circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.« less

  5. Calculation on spectrum of direct DNA damage induced by low-energy electrons including dissociative electron attachment.

    PubMed

    Liu, Wei; Tan, Zhenyu; Zhang, Liming; Champion, Christophe

    2017-03-01

    In this work, direct DNA damage induced by low-energy electrons (sub-keV) is simulated using a Monte Carlo method. The characteristics of the present simulation are to consider the new mechanism of DNA damage due to dissociative electron attachment (DEA) and to allow determining damage to specific bases (i.e., adenine, thymine, guanine, or cytosine). The electron track structure in liquid water is generated, based on the dielectric response model for describing electron inelastic scattering and on a free-parameter theoretical model and the NIST database for calculating electron elastic scattering. Ionization cross sections of DNA bases are used to generate base radicals, and available DEA cross sections of DNA components are applied for determining DNA-strand breaks and base damage induced by sub-ionization electrons. The electron elastic scattering from DNA components is simulated using cross sections from different theoretical calculations. The resulting yields of various strand breaks and base damage in cellular environment are given. Especially, the contributions of sub-ionization electrons to various strand breaks and base damage are quantitatively presented, and the correlation between complex clustered DNA damage and the corresponding damaged bases is explored. This work shows that the contribution of sub-ionization electrons to strand breaks is substantial, up to about 40-70%, and this contribution is mainly focused on single-strand break. In addition, the base damage induced by sub-ionization electrons contributes to about 20-40% of the total base damage, and there is an evident correlation between single-strand break and damaged base pair A-T.

  6. Frequency domain analysis of errors in cross-correlations of ambient seismic noise

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Ben-Zion, Yehuda; Zigone, Dimitri

    2016-12-01

    We analyse random errors (variances) in cross-correlations of ambient seismic noise in the frequency domain, which differ from previous time domain methods. Extending previous theoretical results on ensemble averaged cross-spectrum, we estimate confidence interval of stacked cross-spectrum of finite amount of data at each frequency using non-overlapping windows with fixed length. The extended theory also connects amplitude and phase variances with the variance of each complex spectrum value. Analysis of synthetic stationary ambient noise is used to estimate the confidence interval of stacked cross-spectrum obtained with different length of noise data corresponding to different number of evenly spaced windows of the same duration. This method allows estimating Signal/Noise Ratio (SNR) of noise cross-correlation in the frequency domain, without specifying filter bandwidth or signal/noise windows that are needed for time domain SNR estimations. Based on synthetic ambient noise data, we also compare the probability distributions, causal part amplitude and SNR of stacked cross-spectrum function using one-bit normalization or pre-whitening with those obtained without these pre-processing steps. Natural continuous noise records contain both ambient noise and small earthquakes that are inseparable from the noise with the existing pre-processing steps. Using probability distributions of random cross-spectrum values based on the theoretical results provides an effective way to exclude such small earthquakes, and additional data segments (outliers) contaminated by signals of different statistics (e.g. rain, cultural noise), from continuous noise waveforms. This technique is applied to constrain values and uncertainties of amplitude and phase velocity of stacked noise cross-spectrum at different frequencies, using data from southern California at both regional scale (˜35 km) and dense linear array (˜20 m) across the plate-boundary faults. A block bootstrap resampling method is used to account for temporal correlation of noise cross-spectrum at low frequencies (0.05-0.2 Hz) near the ocean microseismic peaks.

  7. Three-Point Bending Fracture Behavior of Single Oriented Crossed-Lamellar Structure in Scapharca broughtonii Shell

    PubMed Central

    Ji, Hong-Mei; Zhang, Wen-Qian; Wang, Xu; Li, Xiao-Wu

    2015-01-01

    The three-point bending strength and fracture behavior of single oriented crossed-lamellar structure in Scapharca broughtonii shell were investigated. The samples for bending tests were prepared with two different orientations perpendicular and parallel to the radial ribs of the shell, which corresponds to the tiled and stacked directions of the first-order lamellae, respectively. The bending strength in the tiled direction is approximately 60% higher than that in the stacked direction, primarily because the regularly staggered arrangement of the second-order lamellae in the tiled direction can effectively hinder the crack propagation, whereas the cracks can easily propagate along the interfaces between lamellae in the stacked direction. PMID:28793557

  8. Analysis of strategies to increase external fixator stiffness: is double stacking worth the cost?

    PubMed

    Strebe, Sara; Kim, Hyunchul; Russell, Joseph P; Hsieh, Adam H; Nascone, Jason; O'Toole, Robert V

    2014-07-01

    We compared the mechanical benefits and costs of 3 strategies that are commonly used to increase knee-spanning external fixator stiffness (resistance to deformation): double stacking, cross-linking, and use of an oblique pin. At our academic trauma centre and biomechanical testing laboratory, we used ultra-high-molecular-weight polyethylene bone models and commercially available external fixator components to simulate knee-spanning external fixation. The models were tested in anterior-posterior bending, medial-lateral bending, axial compression, and torsion. We recorded the construct stiffness for each strategy in all loading modes and assessed a secondary outcome of cost per 10% increase in stiffness. Double stacking significantly increased construct stiffness under anterior-posterior bending (109%), medial-lateral bending (22%), axial compression (150%), and torsion (41%) (p<0.05). Use of an oblique pin significantly increased stiffness under torsion (25%) (p<0.006). Cross-linking significantly increased stiffness only under torsion (29%) (p<0.002). Double stacking increased costs by 84%, cross-linking by 28%, and use of an oblique pin by 15% relative to a standard fixator. All 3 strategies increased stiffness under torsion to varying degrees, but only double stacking increased stiffness in all 4 testing modalities (p<0.05). Double stacking is most effective in increasing resistance to bending, particularly under anterior-posterior bending and axial compression, but requires a relatively high cost increase. Clinicians can use these data to help guide the most cost-effective strategy to increase construct stiffness based on the plane in which stiffness is needed. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Cross-species Virus-host Protein-Protein Interactions Inhibiting Innate Immunity

    DTIC Science & Technology

    2016-07-01

    Distribution A: Approved for public release; distribution is unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT The single- stranded negative sense RNA...focused upon members of three negative-sense single- stranded RNA (ssRNA(-)) virus families with know or suspected histories of changes in host-species...however, the N and C-termini are disordered extended strands . In contrast, our covariance analysis mapped hotspots for protein interaction to the

  10. Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

    PubMed

    Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

    2015-07-08

    We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

  11. Dock ’n Roll: Folding of a Silk-Inspired Polypeptide into an Amyloid-like Beta Solenoid

    PubMed Central

    Zhao, Binwu; Cohen Stuart, Martien A.; Hall, Carol K.

    2016-01-01

    Polypeptides containing the motif ((GA)mGX)n occur in silk (we refer to them as ‘silk-like’) and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II’ β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state. PMID:26947809

  12. A study of characteristics of intercity transportation systems. Phase 1: Definition of transportation comparison methodology

    NASA Technical Reports Server (NTRS)

    English, J. M.; Smith, J. L.; Lifson, M. W.

    1978-01-01

    The objectives of this study are: (1) to determine a unified methodological framework for the comparison of intercity passenger and freight transportation systems; (2) to review the attributes of existing and future transportation systems for the purpose of establishing measures of comparison. These objectives were made more specific to include: (1) development of a methodology for comparing long term transportation trends arising from implementation of various R&D programs; (2) definition of value functions and attribute weightings needed for further transportation goals.

  13. DNA-binding studies of a tetraalkyl-substituted porphyrin and the mutually adaptive distortion principle.

    PubMed

    Ghimire, Srijana; Fanwick, Phillip E; McMillin, David R

    2014-10-20

    This investigation explores DNA-binding interactions of various forms of an alkyl-substituted cationic porphyrin, H2TC3 (5,10,15,20-tetra[3-(3'-methylimidazolium-1'-yl)]porphyrin). The motivating idea is that incorporating alkyl rather than aryl substituents in the meso positions will enhance the prospects for intercalative as well as external binding to DNA hosts. The ligands may also be applicable for photodynamic and/or anticancer therapy. Methods employed include absorbance, circular dichroism, and emission spectroscopies, as well as viscometry and X-ray crystallography. By comparison with the classical H2T4 system, H2TC3 exhibits a higher molar extinction coefficient but is more prone to self-association. Findings of note include that the copper(II)-containing form Cu(TC3) is adept at internalizing into single-stranded as well as B-form DNA, regardless of the base composition. Surprisingly, however, external binding of H2TC3 occurs within domains that are rich in adenine-thymine base pairs. The difference in the deformability of H2TC3 versus Cu(TC3) probably accounts for the reactivity difference. Finally, Zn(TC3) binds externally, as the metal center remains five-coordinate.

  14. Role of the third strand in the binding of proflavine and pt-proflavine to poly(rA).2poly(rU): a thermodynamic and kinetic study.

    PubMed

    García, Begoña; Leal, José M; Paiotta, Vittorio; Ruiz, Rebeca; Secco, Fernando; Venturini, Marcella

    2008-06-12

    The interactions of triple strands of poly(rA).2poly(rU) with proflavine (PR) and the proflavine cis-platinum derivative [{PtCl (tmen)} 2{NC 13H 7(NCH 2CH 2) 2}] (+) (PRPt) are examined at pH 7.0, T = 25 degrees C, and 0.2 M ionic strength by spectrophotometry, spectrofluorometry, circular dichroism, viscosimetry, stopped-flow, and T-jump relaxation techniques. The melting experiments demonstrate that both drugs tend to destabilize the triplex structure, although the PRPt effect is more relevant. By contrast, both drugs tend to slightly stabilize the duplex structure. The viscosity and circular dichroism measurements show that, at a low dye-to-polymer ratio ( C D/ C P), the binding is intercalative, whereas at high C D/ C P values, the external binding dominates. The binding kinetics and equilibria have been investigated over the C D/ C P region, where intercalation is operative. Both drugs bind to the RNA triplex according to the excluded site model. With PR, two kinetic effects have been observed, whereas with PRPt, only one has been observed. The results are interpreted according to the reaction schemes D + S right arrow over left arrow DS I, with PRPt, and D + S right arrow over left arrow DS I right arrow over left arrow DS II, with PR. The electrostatic contribution to the formation activation energy for DS I is similar (40%) for both systems. The results suggest that DS I is a partially intercalated species. Absence of the second step with PRPt is put down to groove interaction of the Pt-containing moiety, which prevents the PR residue from further penetration through the base pairs to form the fully intercalated complex, DS II. Comparison with the binding of the same drugs to the duplex reveals that the occupation of the major groove in poly(rA).2poly(rU) by the third strand plays a critical role in the kinetic behavior.

  15. Electrochemical label-free and sensitive nanobiosensing of DNA hybridization by graphene oxide modified pencil graphite electrode.

    PubMed

    Ahour, F; Shamsi, A

    2017-09-01

    Based on the strong interaction between single-stranded DNA (ss-DNA) and graphene material, we have constructed a novel label-free electrochemical biosensor for rapid and facile detection of short sequences ss-DNA molecules related to hepatitis C virus 1a using graphene oxide modified pencil graphite electrode. The sensing mechanism is based on the superior adsorption of single-stranded DNA to GO over double stranded DNA (ds-DNA). The intrinsic guanine oxidation signal measured by differential pulse voltammetry (DPV) has been used for duplex DNA formation detection. The probe ss-DNA adsorbs onto the surface of GO via the π- π* stacking interactions leading to a strong background guanine oxidation signal. In the presence of complementary target, formation of helix which has weak binding ability to GO induced ds-DNA to release from the electrode surface and significant variation in differential pulse voltammetric response of guanine bases. The results indicated that the oxidation peak current was proportional to the concentration of complementary strand in the range of 0.1 nM-0.5 μM with a detection limit of 4.3 × 10 -11  M. The simple fabricated electrochemical biosensor has high sensitivity, good selectivity, and could be applied as a new platform for a range of target molecules in future. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Phosphoric acid electric utility fuel cell technology development

    NASA Astrophysics Data System (ADS)

    Breault, R. D.; Briggs, T. A.; Congdon, J. V.; Gelting, R. L.; Goller, G. J.; Luoma, W. L.; McCloskey, M. W.; Mientek, A. P.; Obrien, J. J.; Randall, S. A.

    1985-07-01

    Improved cross pressure tolerance has been demonstrated for electrodes containing impregnated seals. Electrodes, cooler assemblies, separator plates and reactant manifolds for the third 10-ft(2) short stack were completed. Assembly of the third 10-ft(2) short stack was initiated.

  17. Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated.

    PubMed

    Nielsen, Lisbeth Munksgaard; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

    2013-08-01

    In biology the interplay between multiple light-absorbers gives rise to complex quantum effects such as superposition states that are of extreme importance for life, both for harvesting solar energy and likely protecting nucleic acids from radiation damage. Still the characteristics of these states and their quantum dynamics are a much debated issue. While the electronic properties of single bases are fairly well understood, the situation for strands is complicated by the fact that stacked bases electronically couple when photoexcited. These newly arising states are denoted as exciton states and are simply linear combinations of localised wavefunctions that involve N - 1 ground-state bases and one base in its excited state (cf. the Frenkel exciton model). There is disagreement over the number of bases, N, that coherently couple, i.e., the spatial extent of the exciton, and how electronic deexcitation back to the ground state occurs. The importance of dark charge-transfer states has been inferred both from time-resolved fluorescence and transient absorption experiments. These states were suggested to be responsible for long deexcitation times but it is unclear whether 'long' is tens of picoseconds or nanoseconds. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see the beast in different, correct but incomplete ways.

  18. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

    NASA Astrophysics Data System (ADS)

    Gerling, Thomas; Wagenbauer, Klaus F.; Neuner, Andrea M.; Dietz, Hendrik

    2015-03-01

    We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.

  19. Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing

    PubMed Central

    Lebars, Isabelle; Lamontagne, Bruno; Yoshizawa, Satoko; Abou Elela, Sherif; Fourmy, Dominique

    2001-01-01

    Rnt1p, the yeast orthologue of RNase III, cleaves rRNAs, snRNAs and snoRNAs at a stem capped with conserved AGNN tetraloop. Here we show that 9 bp long stems ending with AGAA or AGUC tetraloops bind to Rnt1p and direct specific but sequence-independent RNA cleavage when provided with stems longer than 13 bp. The solution structures of these two tetraloops reveal a common fold for the terminal loop stabilized by non-canonical A–A or A–C pairs and extensive base stacking. The conserved nucleotides are stacked at the 5′ side of the loop, exposing their Watson–Crick and Hoogsteen faces for recognition by Rnt1p. These results indicate that yeast RNase III recognizes the fold of a conserved single-stranded tetraloop to direct specific dsRNA cleavage. PMID:11743001

  20. Emission inventory estimation of an intercity bus terminal.

    PubMed

    Qiu, Zhaowen; Li, Xiaoxia; Hao, Yanzhao; Deng, Shunxi; Gao, H Oliver

    2016-06-01

    Intercity bus terminals are hotspots of air pollution due to concentrated activities of diesel buses. In order to evaluate the bus terminals' impact on air quality, it is necessary to estimate the associated mobile emission inventories. Since the vehicles' operating condition at the bus terminal varies significantly, conventional calculation of the emissions based on average emission factors suffers the loss of accuracy. In this study, we examined a typical intercity bus terminal-the Southern City Bus Station of Xi'an, China-using a multi-scale emission model-(US EPA's MOVES model)-to quantity the vehicle emission inventory. A representative operating cycle for buses within the station is constructed. The emission inventory was then estimated using detailed inputs including vehicle ages, operating speeds, operating schedules, and operating mode distribution, as well as meteorological data (temperature and humidity). Five functional areas (bus yard, platforms, disembarking area, bus travel routes within the station, and bus entrance/exit routes) at the terminal were identified, and the bus operation cycle was established using the micro-trip cycle construction method. Results of our case study showed that switching to compressed natural gas (CNG) from diesel fuel could reduce PM2.5 and CO emissions by 85.64 and 6.21 %, respectively, in the microenvironment of the bus terminal. When CNG is used, tail pipe exhaust PM2.5 emission is significantly reduced, even less than brake wear PM2.5. The estimated bus operating cycles can also offer researchers and policy makers important information for emission evaluation in the planning and design of any typical intercity bus terminals of a similar scale.

  1. Relationship between occupational stress and cardiovascular diseases risk factors in drivers.

    PubMed

    Biglari, Hamed; Ebrahimi, Mohammad Hossein; Salehi, Maryam; Poursadeghiyan, Mohsen; Ahmadnezhad, Iman; Abbasi, Milad

    2016-11-18

    Of all work stressors, occupational stress is the leading cause of many disorders among workers. Drivers are classified as a high risk group for work related stress. This study set out to determine the relationship between risk factors of cardiovascular diseases and occupational stress among drivers. Two hundred and twenty two Ilam's intercity drivers were selected for the study. For measuring work stress, the Osipow work stress questionnaire was used. After a 10-h fasting period, systolic and diastolic blood pressure was recorded. Intravenous blood samples were taken to determine cholesterol, triglyceride and blood glucose levels. The independent samples t-test and Pearson's correlation test were used to assess the relationship between variables and occupational stress. Seventy-one percent of the intercity drivers suffered from average to acute stress, and 3.1% of them suffered from acute stress. There was no significant relationship between occupational stress and diastolic blood pressure (p = 0.254) among the drivers. Nevertheless, the Pearson's correlation test demonstrated a strong relationship between work stress and blood glucose (p < 0.01), while no strong correlation was found for blood triglycerides and cholesterol levels. Based on the results, high rates of occupational stress were observed in the Ilam's intercity drivers. Occupational stress may have effect on blood glucose levels but the results did not suggest a considerable relationship between risk factors of cardiovascular diseases and occupational stress among intercity drivers. Int J Occup Med Environ Health 2016;29(6):895-901. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

  2. UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases

    PubMed Central

    Takaya, Tomohisa; Su, Charlene; de La Harpe, Kimberly; Crespo-Hernández, Carlos E.; Kohler, Bern

    2008-01-01

    Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)4, and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution. PMID:18647840

  3. UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases.

    PubMed

    Takaya, Tomohisa; Su, Charlene; de La Harpe, Kimberly; Crespo-Hernández, Carlos E; Kohler, Bern

    2008-07-29

    Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)(4), and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.

  4. Pre-Processing and Cross-Correlation Techniques for Time-Distance Helioseismology

    NASA Astrophysics Data System (ADS)

    Wang, N.; de Ridder, S.; Zhao, J.

    2014-12-01

    In chaotic wave fields excited by a random distribution of noise sources a cross-correlation of the recordings made at two stations yield the interstation wave-field response. After early successes in helioseismology, laboratory studies and earth-seismology, this technique found broad application in global and regional seismology. This development came with an increasing understanding of pre-processing and cross-correlation workflows to yield an optimal signal-to-noise ratio (SNR). Helioseismologist rely heavily on stacking to increase the SNR. Until now, they have not studied different spectral-whitening and cross-correlation workflows and relies heavily on stacking to increase the SNR. The recordings vary considerably between sunspots and regular portions of the sun. Within the sunspot the periodic effects of the observation satellite orbit are difficult to remove. We remove a running alpha-mean from the data and apply a soft clip to deal with data glitches. The recordings contain energy of both flow and waves. A frequency domain filter selects the wave energy. Then the data is input to several pre-processing and cross-correlation techniques, common to earth seismology. We anticipate that spectral whitening will flatten the energy spectrum of the cross-correlations. We also expect that the cross-correlations converge faster to their expected value when the data is processed over overlapping windows. The result of this study are expected to aid in decreasing the stacking while maintaining good SNR.

  5. Highly Sensitive DNA Sensor Based on Upconversion Nanoparticles and Graphene Oxide.

    PubMed

    Alonso-Cristobal, P; Vilela, P; El-Sagheer, A; Lopez-Cabarcos, E; Brown, T; Muskens, O L; Rubio-Retama, J; Kanaras, A G

    2015-06-17

    In this work we demonstrate a DNA biosensor based on fluorescence resonance energy transfer (FRET) between NaYF4:Yb,Er nanoparticles and graphene oxide (GO). Monodisperse NaYF4:Yb,Er nanoparticles with a mean diameter of 29.1 ± 2.2 nm were synthesized and coated with a SiO2 shell of 11 nm, which allowed the attachment of single strands of DNA. When these DNA-functionalized NaYF4:Yb,Er@SiO2 nanoparticles were in the proximity of the GO surface, the π-π stacking interaction between the nucleobases of the DNA and the sp(2) carbons of the GO induced a FRET fluorescence quenching due to the overlap of the fluorescence emission of the NaYF4:Yb,Er@SiO2 and the absorption spectrum of GO. By contrast, in the presence of the complementary DNA strands, the hybridization leads to double-stranded DNA that does not interact with the GO surface, and thus the NaYF4:Yb,Er@SiO2 nanoparticles remain unquenched and fluorescent. The high sensitivity and specificity of this sensor introduces a new method for the detection of DNA with a detection limit of 5 pM.

  6. [Study of fusion of bacteriophage f2 double-stranded RNA, poly(A).poly(U), and poly(G).poly(C) in the presence of tetraethylammonium bromide].

    PubMed

    Permogorov, V I; Tiaglov, B V; Minaev, V E

    1980-01-01

    The data on the dependence of the melting curve parameters of double-stranded RNA (replicative form of RNA of f2 bacteriophage) poly(A) times poly(U) and poly(G) times poly(C) on the concentration of (C2H5)4NBr were obtained. The RNA melting range width is shown to pass through the minimum value T =2.1+/-0.1degrees at the point of inversion of relative stability of GC and AU pairs that corresponds to 4.0+/-0.1 M concentration of (C2H5)4NBr. Using the melting temperatures of poly(A) times poly(U) and poly(G) times poly(C) the rependence of Tgc-Tau parameter on (C2H5)4NBr concentration was shown. It was concluded from these data that the effect of the double-stranded RNA stacking heterogeneity was negligible in the 0-3 M range of (C2H5)4NBr concentration. Melting curves of RNA were obtained at various values of Tgc-Tau parameter. It was shown that the profile of fine structure of melting curves depends on the value of Tgc-Tau parameter.

  7. G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme.

    PubMed

    Hirschi, Alexander; Martin, William J; Luka, Zigmund; Loukachevitch, Lioudmila V; Reiter, Nicholas J

    2016-08-01

    Lysine-specific histone demethylase 1 (LSD1) is an essential epigenetic regulator in metazoans and requires the co-repressor element-1 silencing transcription factor (CoREST) to efficiently catalyze the removal of mono- and dimethyl functional groups from histone 3 at lysine positions 4 and 9 (H3K4/9). LSD1 interacts with over 60 regulatory proteins and also associates with lncRNAs (TERRA, HOTAIR), suggesting a regulatory role for RNA in LSD1 function. We report that a stacked, intramolecular G-quadruplex (GQ) forming TERRA RNA (GG[UUAGGG]8UUA) binds tightly to the functional LSD1-CoREST complex (Kd ≈ 96 nM), in contrast to a single GQ RNA unit ([UUAGGG]4U), a GQ DNA ([TTAGGG]4T), or an unstructured single-stranded RNA. Stabilization of a parallel-stranded GQ RNA structure by monovalent potassium ions (K(+)) is required for high affinity binding to the LSD1-CoREST complex. These data indicate that LSD1 can distinguish between RNA and DNA as well as structured versus unstructured nucleotide motifs. Further, cross-linking mass spectrometry identified the primary location of GQ RNA binding within the SWIRM/amine oxidase domain (AOD) of LSD1. An ssRNA binding region adjacent to this GQ binding site was also identified via X-ray crystallography. This RNA binding interface is consistent with kinetic assays, demonstrating that a GQ-forming RNA can serve as a noncompetitive inhibitor of LSD1-catalyzed demethylation. The identification of a GQ RNA binding site coupled with kinetic data suggests that structured RNAs can function as regulatory molecules in LSD1-mediated mechanisms. © 2016 Hirschi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme

    PubMed Central

    Hirschi, Alexander; Martin, William J.; Luka, Zigmund; Loukachevitch, Lioudmila V.; Reiter, Nicholas J.

    2016-01-01

    Lysine-specific histone demethylase 1 (LSD1) is an essential epigenetic regulator in metazoans and requires the co-repressor element-1 silencing transcription factor (CoREST) to efficiently catalyze the removal of mono- and dimethyl functional groups from histone 3 at lysine positions 4 and 9 (H3K4/9). LSD1 interacts with over 60 regulatory proteins and also associates with lncRNAs (TERRA, HOTAIR), suggesting a regulatory role for RNA in LSD1 function. We report that a stacked, intramolecular G-quadruplex (GQ) forming TERRA RNA (GG[UUAGGG]8UUA) binds tightly to the functional LSD1–CoREST complex (Kd ≈ 96 nM), in contrast to a single GQ RNA unit ([UUAGGG]4U), a GQ DNA ([TTAGGG]4T), or an unstructured single-stranded RNA. Stabilization of a parallel-stranded GQ RNA structure by monovalent potassium ions (K+) is required for high affinity binding to the LSD1–CoREST complex. These data indicate that LSD1 can distinguish between RNA and DNA as well as structured versus unstructured nucleotide motifs. Further, cross-linking mass spectrometry identified the primary location of GQ RNA binding within the SWIRM/amine oxidase domain (AOD) of LSD1. An ssRNA binding region adjacent to this GQ binding site was also identified via X-ray crystallography. This RNA binding interface is consistent with kinetic assays, demonstrating that a GQ-forming RNA can serve as a noncompetitive inhibitor of LSD1-catalyzed demethylation. The identification of a GQ RNA binding site coupled with kinetic data suggests that structured RNAs can function as regulatory molecules in LSD1-mediated mechanisms. PMID:27277658

  9. Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5-18 eV) electron interactions with DNA.

    PubMed

    Rezaee, Mohammad; Hunting, Darel J; Sanche, Léon

    2014-07-01

    The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides. Absorbed dose and stopping cross section for the Auger electrons of 5-18 eV emitted by(125)I within DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure-response curves for induction of DNA strand breaks. For a single decay of(125)I within DNA, the Auger electrons of 5-18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm(3) volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break. Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide.

  10. Modelling the protocol stack in NCS with deterministic and stochastic petri net

    NASA Astrophysics Data System (ADS)

    Hui, Chen; Chunjie, Zhou; Weifeng, Zhu

    2011-06-01

    Protocol stack is the basis of the networked control systems (NCS). Full or partial reconfiguration of protocol stack offers both optimised communication service and system performance. Nowadays, field testing is unrealistic to determine the performance of reconfigurable protocol stack; and the Petri net formal description technique offers the best combination of intuitive representation, tool support and analytical capabilities. Traditionally, separation between the different layers of the OSI model has been a common practice. Nevertheless, such a layered modelling analysis framework of protocol stack leads to the lack of global optimisation for protocol reconfiguration. In this article, we proposed a general modelling analysis framework for NCS based on the cross-layer concept, which is to establish an efficiency system scheduling model through abstracting the time constraint, the task interrelation, the processor and the bus sub-models from upper and lower layers (application, data link and physical layer). Cross-layer design can help to overcome the inadequacy of global optimisation based on information sharing between protocol layers. To illustrate the framework, we take controller area network (CAN) as a case study. The simulation results of deterministic and stochastic Petri-net (DSPN) model can help us adjust the message scheduling scheme and obtain better system performance.

  11. CNG as a Feasible Replacement for the U.S. Transportation Sector

    DTIC Science & Technology

    2012-03-01

    not convenient for drivers either to have gigantic fuel tanks on vehicles or to stop several times for refueling even in a short distance travel . In... Intercity 31.4 31.4 School 7.0 69.9 76.9 Medium/heavy trucks 611.5 5,452.7 20.3 6,084.5 237.1 NONHIGHWAY 721.4 0.0...18.4 31.6 Intercity 8.6 5.8 14.4 TOTAL HWY & NONHWY 16,898.5 6,735.0 65.3 2,099.3 839.4 638.7 312.9 27,589.0 Figure 24

  12. Phase 1: Definition of intercity transportation comparison framework. Volume 1: Summary. [operations research of passenger and freight transporatation systems

    NASA Technical Reports Server (NTRS)

    1978-01-01

    A unified framework for comparing intercity passenger and freight transportation systems is presented. Composite measures for cost, service/demand, energy, and environmental impact were determined. A set of 14 basic measures were articulated to form the foundation for computing the composite measures. A parameter dependency diagram, constructed to explicitly interrelate the composite and basic measures is discussed. Ground rules and methodology for developing the values of the basic measures are provided and the use of the framework with existing cost and service data is illustrated for various freight systems.

  13. Protection of 2-(3-Thienyl)ethanol with 3-Thienylacetic Acid and Hard Cross- Linked Conducting Films by Electropolymerization of the Ester

    NASA Technical Reports Server (NTRS)

    Leventis, Nicholas; Dass, Amala; Mulik, Sudir; Sotiriou-Leventis, Chariklia

    2005-01-01

    The ester (compound 1) of 2-(3-thienyl)ethanol (T-etOH) with 3-thienylacetic acid was synthesized as a monomer whose two thiophene groups could be electropolymerized independently, becoming members of different polymer chains in a highly-crosslinked highly-insoluble polymer. Indeed, 1 was electropolymerized successfully alone and together with 3-methylthiophene (3MeT). Films of poly(1) are hard (3H, as opposed to less than 6B for poly(3MeT)), and the close proximity of the polymeric strands creates pi-stacking interactions. The behavior of 1 suggests that by: (a) limiting the potential used for the oxidation of monomeric esters of T-etOH at the foot of their oxidation waves (less than 1.8 V vs. Ag/AgCl); and, (b) compensating for the decrease in the electrogenerated radical concentration by increasing the monomer concentration, practically all esters of T-etOH should be electropolymerizable. This was confirmed by durable film formation from the archetypical ester of T-etOH, the 2-(3-thienyl)ethyl acetate (T-etOAc), whose homo-electropolymerization is reported for the first time.

  14. MULTI-STRAND CORONAL LOOP MODEL AND FILTER-RATIO ANALYSIS

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

    Bourouaine, Sofiane; Marsch, Eckart, E-mail: bourouaine@mps.mpg.d

    2010-01-10

    We model a coronal loop as a bundle of seven separate strands or filaments. Each of the loop strands used in this model can independently be heated (near their left footpoints) by Alfven/ion-cyclotron waves via wave-particle interactions. The Alfven waves are assumed to penetrate the strands from their footpoints, at which we consider different wave energy inputs. As a result, the loop strands can have different heating profiles, and the differential heating can lead to a varying cross-field temperature in the total coronal loop. The simulation of Transition Region and Coronal Explorer (TRACE) observations by means of this loop modelmore » implies two uniform temperatures along the loop length, one inferred from the 171:195 filter ratio and the other from the 171:284 ratio. The reproduced flat temperature profiles are consistent with those inferred from the observed extreme-ultraviolet coronal loops. According to our model, the flat temperature profile is a consequence of the coronal loop consisting of filaments, which have different temperatures but almost similar emission measures in the cross-field direction. Furthermore, when we assume certain errors in the simulated loop emissions (e.g., due to photometric uncertainties in the TRACE filters) and use the triple-filter analysis, our simulated loop conditions become consistent with those of an isothermal plasma. This implies that the use of TRACE or EUV Imaging Telescope triple filters for observation of a warm coronal loop may not help in determining whether the cross-field isothermal assumption is satisfied or not.« less

  15. Method for fabricating multi-strand superconducting cable

    DOEpatents

    Borden, A.R.

    1985-04-01

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet are fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  16. Apparatus and method for fabricating multi-strand superconducting cable

    DOEpatents

    Borden, Albert R.

    1986-01-01

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet is fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  17. Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.

    PubMed

    Nonin, S; Leroy, J L

    1996-08-23

    At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical. The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T.T pair between the sequentially adjacent C2.C2+ pair and the C2*.C2*+ pair of the other duplex. Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s-1 at 0 degree C and the activation energy is 94 kJ/mol. The opening of the T3.T3 pair, the closing of the T3*.T3 pair, and the opening of the C2*.C2*+ pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4.C4+ and C4*.C4*+ pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer. The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.

  18. The Reduction of the Critical Currents in Nb3Sn Cables under Transverse Loads

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

    Van Oort, J.M.; Scanlan, R.M.; Weijers, H.W.

    1992-08-01

    The degradation of the critical current of impregnated Rutherford type Nb{sub 3}Sn cables is investigated as a function of the applied transverse load and magnetic field. The cable is made of TWCA modified jelly-roll type strand material and has a keystone angle of 1.0 degree. The voltage-current characteristics are determined for the magnetic field ranging from 2 to 11 tesla and transverse pressure up to 250 MPa on the cable surface. It is found that the 48-strand cable, made of strands with 6 elements in the matrix, shows a larger critical current degradation than the 26-strand cable with 36 elementsmore » per strand. The global degradation of the 48-strand cable is 63% at 150 MPa, and 40% at 150 MPa for the 26-strand cable. Micro-analysis of the cross-section shows permanent damage to the sharp edge of the cable. The influence of the keystone angle on the critical-current degradation is currently under investigation.« less

  19. [Ru(phen)2DPPZ]2+ is in contact with DNA bases when it forms a luminescent complex with single-stranded oligonucleotides.

    PubMed

    Moon, Seok Joon; Kim, Jong Moon; Choi, Ji Youn; Kim, Seog K; Lee, Je Seung; Jang, Ho G

    2005-05-01

    The luminescence intensity of the Delta- and Lambda-enantiomer of [Ru(phen)2DPPZ]2+ ([Ru(phenanthroline)2 dipyrido[3,2-a:2',3'-c]phenazine]2+) complex enhanced upon binding to double stranded DNA, which has been known as "light switch effect". The enhancement of the luminescence required the intercalation of the large ligand between DNA base pairs. In this study, we report the enhancement in the luminescence intensity when the metal complexes bind to single stranded oligonucleotides, indicating that the "light switch effect" does not require intercalation of the large DPPZ ligand. Oligonucleotides may provide a hydrophobic cavity for the [Ru(phen)2DPPZ]2+ complex to prevent the quenching by the water molecule. In the cavity, the metal complex is in contact with DNA bases as is evidenced by the observation that the excited energy of the DNA bases transfer to the bound metal complex. However, the contact of the metal complex with DNA bases is different from the stacking of DPPZ in the intercalation pocket. In addition to the normal two luminescence lifetimes, a short lifetime in the range of 1-2 ns was found for both the delta- and lambda-enantiomer of [Ru(phen)2DPPZ]2+ when complexed with single stranded oligonucleotides, which may be assigned to the metal complex that is outside of the cavity, interacting with phosphate groups of DNA.

  20. Full Piezoelectric Multilayer-Stacked Hybrid Actuation/Transduction Systems

    NASA Technical Reports Server (NTRS)

    Su, Ji; Jiang, Xiaoning; Zu, Tian-Bing

    2011-01-01

    The Stacked HYBATS (Hybrid Actuation/Transduction system) demonstrates significantly enhanced electromechanical performance by using the cooperative contributions of the electromechanical responses of multilayer, stacked negative strain components and positive strain components. Both experimental and theoretical studies indicate that, for Stacked HYBATS, the displacement is over three times that of a same-sized conventional flextensional actuator/transducer. The coupled resonance mode between positive strain and negative strain components of Stacked HYBATS is much stronger than the resonance of a single element actuation only when the effective lengths of the two kinds of elements match each other. Compared with the previously invented hybrid actuation system (HYBAS), the multilayer Stacked HYBATS can be designed to provide high mechanical load capability, low voltage driving, and a highly effective piezoelectric constant. The negative strain component will contract, and the positive strain component will expand in the length directions when an electric field is applied on the device. The interaction between the two elements makes an enhanced motion along the Z direction for Stacked-HYBATS. In order to dominate the dynamic length of Stacked-HYBATS by the negative strain component, the area of the cross-section for the negative strain component will be much larger than the total cross-section areas of the two positive strain components. The transverse strain is negative and longitudinal strain positive in inorganic materials, such as ceramics/single crystals. Different piezoelectric multilayer stack configurations can make a piezoelectric ceramic/single-crystal multilayer stack exhibit negative strain or positive strain at a certain direction without increasing the applied voltage. The difference of this innovation from the HYBAS is that all the elements can be made from one-of-a-kind materials. Stacked HYBATS can provide an extremely effective piezoelectric constant at both resonance and off resonance frequencies. The effective piezoelectric constant can be alternated by varying the size of each component, the degree of the pre-curvature of the positive strain components, the thickness of each layer in the multilayer stacks, and the piezoelectric constant of the material used. Because all of the elements are piezoelectric components, Stacked HYBATS can serve as projector and receiver for underwater detection. The performance of this innovation can be enhanced by improving the piezoelectric properties.

  1. Three-dimensional cardiac architecture determined by two-photon microtomy

    NASA Astrophysics Data System (ADS)

    Huang, Hayden; MacGillivray, Catherine; Kwon, Hyuk-Sang; Lammerding, Jan; Robbins, Jeffrey; Lee, Richard T.; So, Peter

    2009-07-01

    Cardiac architecture is inherently three-dimensional, yet most characterizations rely on two-dimensional histological slices or dissociated cells, which remove the native geometry of the heart. We previously developed a method for labeling intact heart sections without dissociation and imaging large volumes while preserving their three-dimensional structure. We further refine this method to permit quantitative analysis of imaged sections. After data acquisition, these sections are assembled using image-processing tools, and qualitative and quantitative information is extracted. By examining the reconstructed cardiac blocks, one can observe end-to-end adjacent cardiac myocytes (cardiac strands) changing cross-sectional geometries, merging and separating from other strands. Quantitatively, representative cross-sectional areas typically used for determining hypertrophy omit the three-dimensional component; we show that taking orientation into account can significantly alter the analysis. Using fast-Fourier transform analysis, we analyze the gross organization of cardiac strands in three dimensions. By characterizing cardiac structure in three dimensions, we are able to determine that the α crystallin mutation leads to hypertrophy with cross-sectional area increases, but not necessarily via changes in fiber orientation distribution.

  2. Empirical study of the role of the topology in spreading on communication networks

    NASA Astrophysics Data System (ADS)

    Medvedev, Alexey; Kertesz, Janos

    2017-03-01

    Topological aspects, like community structure, and temporal activity patterns, like burstiness, have been shown to severely influence the speed of spreading in temporal networks. We study the influence of the topology on the susceptible-infected (SI) spreading on time stamped communication networks, as obtained from a dataset of mobile phone records. We consider city level networks with intra- and inter-city connections. The networks using only intra-city links are usually sparse, where the spreading depends mainly on the average degree. The inter-city links serve as bridges in spreading, speeding up considerably the process. We demonstrate the effect also on model simulations.

  3. Measuring Polycentricity of Mega-City Regions in China Based on the Intercity Migration Flows

    NASA Astrophysics Data System (ADS)

    Mu, Xiaoyan; Yeh, Anthony G. O.

    2016-06-01

    This paper uses the intercity migration flows to examine relations between Chinese cities, identify the important mega-city regions and measure each region's polycentricity from an interaction perspective. Data set contains the long-term residential migration trajectories of three million Sina weibo users across 345 cities. Cities with close connectivity deployed around one or several mega cities are identified as mega-city regions. Features of the mega-city regions are characterized by the strength of migration flows, density of connections, and regional migration patterns. The results show that the disparities exist in different mega-city regions; most mega-city regions are lack of polycentricity.

  4. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy.

    PubMed

    Banerjee, T; Banerjee, S; Sett, S; Ghosh, S; Rakshit, T; Mukhopadhyay, R

    2016-01-01

    DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA-the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA-the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.

  5. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy

    PubMed Central

    Sett, S.; Ghosh, S.; Rakshit, T.; Mukhopadhyay, R.

    2016-01-01

    DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time. PMID:27183010

  6. Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5–18 eV) electron interactions with DNA

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

    Rezaee, Mohammad, E-mail: Mohammad.Rezaee@USherbrooke.ca; Hunting, Darel J.; Sanche, Léon

    2014-07-15

    Purpose: The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides. Methods: Absorbed dose and stopping cross section for the Auger electrons of 5–18 eV emitted by{sup 125}I withinmore » DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure–response curves for induction of DNA strand breaks. Results: For a single decay of{sup 125}I within DNA, the Auger electrons of 5–18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm{sup 3} volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break. Conclusions: Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide.« less

  7. Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5–18 eV) electron interactions with DNA

    PubMed Central

    Rezaee, Mohammad; Hunting, Darel J.; Sanche, Léon

    2015-01-01

    Purpose The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides. Methods Absorbed dose and stopping cross section for the Auger electrons of 5–18 eV emitted by 125I within DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure–response curves for induction of DNA strand breaks. Results For a single decay of 125I within DNA, the Auger electrons of 5–18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm3 volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break. Conclusions Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide. PMID:24989405

  8. Investigations of the Binding of [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II) to DNA via Various Cross-Linking Modes

    PubMed Central

    Yue, Hongwei; Yang, Bo; Wang, Yan; Chen, Guangju

    2013-01-01

    We have constructed models for a series of platinum-DNA adducts that represent the binding of two agents, [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II), to DNA via inter- and intra-strand cross-linking, and carried out molecular dynamics simulations and DNA conformational dynamics calculations. The effects of trans- and cis-configurations of the centers of these di-nuclear platinum agents, and of different bridging linkers, have been investigated on the conformational distortions of platinum-DNA adducts formed via inter- and intra-strand cross-links. The results demonstrate that the DNA conformational distortions for the various platinum-DNA adducts with differing cross-linking modes are greatly influenced by the difference between the platinum-platinum distance for the platinum agent and the platinum-bound N7–N7 distance for the DNA molecule, and by the flexibility of the bridging linkers in the platinum agent. However, the effects of trans/cis-configurations of the platinum-centers on the DNA conformational distortions in the platinum-DNA adducts depend on the inter- and intra-strand cross-linking modes. In addition, we discuss the relevance of DNA base motions, including opening, shift and roll, to the changes in the parameters of the DNA major and minor grooves caused by binding of the platinum agent. PMID:24077126

  9. NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded β-sheet peptide.

    PubMed

    Sonti, Rajesh; Rai, Rajkishor; Ragothama, Srinivasarao; Balaram, Padmanabhan

    2012-12-13

    Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel β-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-LFV(D)P(L)PLFV-OMe (peptide 1) favors the β-hairpin conformation nucleated by the type II' β-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded β-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C(α)-C(β)(χ(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

  10. Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target.

    PubMed

    Russo Krauss, Irene; Ramaswamy, Sneha; Neidle, Stephen; Haider, Shozeb; Parkinson, Gary N

    2016-02-03

    We report here on an X-ray crystallographic and molecular modeling investigation into the complex 3' interface formed between putative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric repeat sequence TTAGGG. Our crystallographic approach provides a detailed snapshot of a telomeric 3' quadruplex-duplex junction: a junction that appears to have the potential to form a unique molecular target for small molecule binding and interference with telomere-related functions. This unique target is particularly relevant as current high-affinity compounds that bind putative G-quadruplex forming sequences only rarely have a high degree of selectivity for a particular quadruplex. Here DNA junctions were assembled using different putative quadruplex-forming scaffolds linked at the 3' end to a telomeric duplex sequence and annealed to a complementary strand. We successfully generated a series of G-quadruplex-duplex containing crystals, both alone and in the presence of ligands. The structures demonstrate the formation of a parallel folded G-quadruplex and a B-form duplex DNA stacked coaxially. Most strikingly, structural data reveals the consistent formation of a TAT triad platform between the two motifs. This triad allows for a continuous stack of bases to link the quadruplex motif with the duplex region. For these crystal structures formed in the absence of ligands, the TAT triad interface occludes ligand binding at the 3' quadruplex-duplex interface, in agreement with in silico docking predictions. However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface.

  11. X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A).

    PubMed

    Deng, J; Xiong, Y; Sundaralingam, M

    2001-11-20

    Four-stranded guanine tetraplexes in RNA have been identified to be involved in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)(4) at ultra-high resolution (0.61 A). The space group is P42(1)2, and cell constants are a = b = 36.16 A and c = 74.09 A. The structure was solved by the multiple-wavelength anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative (br)UGGGGU and refined to 0.61-A resolution. Each of the four strands in the asymmetric unit forms a parallel tetraplex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudocontinuous column. All of the 5'-end uridines rotate around the backbone of G2, swing out, and form unique octaplexes with the neighboring G tetraplexes, whereas the 3'-end uridines are stacked-in and form uridine tetrads. All of the bases are anti, and the riboses are in the mixed C2'- and C3'-puckering mode. Strontium ions are observed in every other guanine tetrad plane, sitting on the fourfold axis and associated to the eight O6 atoms of neighboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens are clearly observed in the structure.

  12. The occurrence of double strand DNA breaks is not the sole condition for meiotic crossing over in Drosophila melanogaster.

    PubMed

    Portin, P; Rantanen, M

    2000-01-01

    Analysis of the interchromosomal effects of In(2L + 2R)Cy, In(3L + 3R)LVM and their joint effect on the frequencies of single and double crossovers in the cv-v-f region of the X chromosome as well as interference showed that both inversions, occurring separately, increased the frequency of single as well as double crossovers and the coefficient of coincidence. However, when the inversions occurred together the frequencies of single crossovers no longer increased, but the frequency of double crossovers, as well as the coefficient of coincidence did increase. These results indicate firstly that the interchromosomal effects influence some precondition of exchange, but that this precondition is not an occurrence of double strand DNA breaks. Thus, the occurrence of double strand DNA breaks is not the sole condition for crossing over in Drosophila melanogaster.

  13. Amyloid fibril formation from sequences of a natural beta-structured fibrous protein, the adenovirus fiber.

    PubMed

    Papanikolopoulou, Katerina; Schoehn, Guy; Forge, Vincent; Forsyth, V Trevor; Riekel, Christian; Hernandez, Jean-François; Ruigrok, Rob W H; Mitraki, Anna

    2005-01-28

    Amyloid fibrils are fibrous beta-structures that derive from abnormal folding and assembly of peptides and proteins. Despite a wealth of structural studies on amyloids, the nature of the amyloid structure remains elusive; possible connections to natural, beta-structured fibrous motifs have been suggested. In this work we focus on understanding amyloid structure and formation from sequences of a natural, beta-structured fibrous protein. We show that short peptides (25 to 6 amino acids) corresponding to repetitive sequences from the adenovirus fiber shaft have an intrinsic capacity to form amyloid fibrils as judged by electron microscopy, Congo Red binding, infrared spectroscopy, and x-ray fiber diffraction. In the presence of the globular C-terminal domain of the protein that acts as a trimerization motif, the shaft sequences adopt a triple-stranded, beta-fibrous motif. We discuss the possible structure and arrangement of these sequences within the amyloid fibril, as compared with the one adopted within the native structure. A 6-amino acid peptide, corresponding to the last beta-strand of the shaft, was found to be sufficient to form amyloid fibrils. Structural analysis of these amyloid fibrils suggests that perpendicular stacking of beta-strand repeat units is an underlying common feature of amyloid formation.

  14. Spontaneous translocation of antitumor oxaliplatin, its enantiomeric analogue, and Cisplatin from one strand to another in double-helical DNA.

    PubMed

    Malina, Jaroslav; Natile, Giovanni; Brabec, Viktor

    2013-09-02

    Oxaliplatin and cisplatin belong to the class of platinum-based anticancer agents. Formation of DNA adducts by these complexes and the consequences for its structure and function, is the mechanistic paradigm by which these drugs exert their antitumor activity. We show that employing short oligonucleotide duplexes containing single, site-specific 1,3-intrastrand cross-links of oxaliplatin, its enantiomeric analogue, or cisplatin and by using gel electrophoresis that under physiological conditions the coordination bonds between platinum and the N7 position of guanine residues involved in the cross-links of the Pt(II) complexes can be cleaved. This cleavage may lead to linkage isomerization reactions between these metallodrugs and double-helical DNA. For instance, approximately 25 % 1,3-intrastrand cross-links of the platinum complexes isomerized after 192 h (at 310 K in 200 mM NaClO4). Differential scanning calorimetry of duplexes containing single, site-specific cross-links of oxaliplatin, its enantiomeric analogue, and cisplatin reveals that one of the driving forces that leads to the lability of DNA cross-links of these metallodrugs is a difference between the thermodynamic destabilization induced by the cross-link and by the adduct into which it could isomerize. The rearrangements may proceed in the way that cross-links originally formed in one strand of the DNA can spontaneously translocate from one DNA strand to its complementary counterpart, which may evoke walking of the platinum complex on DNA molecule. In addition, the differences in the kinetics of the rearrangement reactions and the thermodynamic destabilization of DNA observed for adducts of oxaliplatin and its enantiomeric analogue confirm that the chirality at the carrier 1,2-diaminocyclohexane ligand can considerably affect structural and other physical properties of DNA adducts and consequently their biological effects. In aggregate, interesting generalization of the results described in this work might be that the migration of oxaliplatin, its enantiomeric analogue, or cisplatin from one strand to another in double-helical DNA controlled by energetic signatures of these agents might contribute to a better understanding of their cytotoxic and mutagenic potential. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. T.C.G triplet in an antiparallel purine.purine.pyrimidine DNA triplex. Conformational studies by NMR.

    PubMed

    Dittrich, K; Gu, J; Tinder, R; Hogan, M; Gao, X

    1994-04-12

    The antiparallel purine.purine.pyrimidine DNA triplex, RRY6, which contains a T.C.G inverted triplet in the center of the sequence, was examined by proton and phosphorous two-dimensional NMR spectroscopy. The local conformation of the T.C.G triplet (T4.C11.G18) and the effect of this triplet on the global helical structure were analyzed in detail. The formation of the T.C.G triplet is confirmed by a set of cross-strand NOEs, including unusual cross-strand NOEs between the third strand and the pyrimidine strand as opposed to the purine strand of the duplex. NMR data suggest that the T.C.G triplet may be present in an equilibrium between a non-hydrogen-bonded form and a T(O4)-C(NH2) hydrogen-bonded form and that there is a distortion of the in-plane alignment of the three bases. The flanking G.G.C base triplets are well-defined on the 5'-side of T4, but somewhat interrupted on the 3'-side of T4. The effect of the third strand binding on the Watson-Crick duplex was probed by an NMR study of the free duplex RY6. NMR parameters are affected mostly around the T.C.G inversion site. The perturbations extend to at least two adjacent base triplets on either side. The binding of the third purine strand and the accommodation of a central T.C.G inversion in RRY6 does not require a readjustment in sugar pucker, which remains in the range of C2'-endo. 31P resonances of RRY6 distribute over a range of 2.2 ppm. The H-P coupling patterns of the third strand differ from those of the duplex. General spectral patterns defined by the marker protons of the RRY and YRY triplexes are compared.

  16. Charge splitters and charge transport junctions based on guanine quadruplexes

    NASA Astrophysics Data System (ADS)

    Sha, Ruojie; Xiang, Limin; Liu, Chaoren; Balaeff, Alexander; Zhang, Yuqi; Zhang, Peng; Li, Yueqi; Beratan, David N.; Tao, Nongjian; Seeman, Nadrian C.

    2018-04-01

    Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions, and nucleobase stacks can transport charge over long distances. However, nucleobase stacking is often disrupted at junction points, hindering electric charge transport between the two terminals of the junction. Here, we show that a guanine-quadruplex (G4) motif can be used as a connector element for a multi-ended DNA junction. By attaching specific terminal groups to the motif, we demonstrate that charges can enter the structure from one terminal at one end of a three-way G4 motif, and can exit from one of two terminals at the other end with minimal carrier transport attenuation. Moreover, we study four-way G4 junction structures by performing theoretical calculations to assist in the design and optimization of these connectors.

  17. Temperature dependent photoluminescence and micromapping of multiple stacks InAs quantum dots

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

    Xu, Ming, E-mail: ming.xu@lgep.supelec.fr; Jaffré, Alexandre, E-mail: ming.xu@lgep.supelec.fr; Alvarez, José, E-mail: ming.xu@lgep.supelec.fr

    2015-02-27

    We utilized temperature dependent photoluminescence (PL) techniques to investigate 1, 3 and 5 stack InGaAs quantum dots (QDs) grown on cross-hatch patterns. PL mapping can well reproduce the QDs distribution as AFM and position dependency of QD growth. It is possible to observe crystallographic dependent PL. The temperature dependent spectra exhibit the QDs energy distribution which reflects the size and shape. The inter-dot carrier coupling effect is observed and translated as a red shift of 120mV on the [1–10] direction peak is observed at 30K on 1 stack with regards to 3 stacks samples, which is assigned to lateral coupling.

  18. Intercalation of a Zn(II) complex containing ciprofloxacin drug between DNA base pairs.

    PubMed

    Shahabadi, Nahid; Asadian, Ali Ashraf; Mahdavi, Mryam

    2017-11-02

    In this study, an attempt has been made to study the interaction of a Zn(II) complex containing an antibiotic drug, ciprofloxacin, with calf thymus DNA using spectroscopic methods. It was found that Zn(II) complex could bind with DNA via intercalation mode as evidenced by: hyperchromism in UV-Vis spectrum; these spectral characteristics suggest that the Zn(II) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. DNA binding constant (K b = 1.4 × 10 4 M -1 ) from spectrophotometric studies of the interaction of Zn(II) complex with DNA is comparable to those of some DNA intercalative polypyridyl Ru(II) complexes 1.0 -4.8 × 10 4 M -1 . CD study showed stabilization of the right-handed B form of DNA in the presence of Zn(II) complex as observed for the classical intercalator methylene blue. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and Van der Waals play main roles in this binding prose. Competitive fluorimetric studies with methylene blue (MB) dye have shown that Zn(II) complex exhibits the ability of this complex to displace with DNA-MB, indicating that it binds to DNA in strong competition with MB for the intercalation.

  19. Laser pulse stacking method

    DOEpatents

    Moses, Edward I.

    1992-01-01

    A laser pulse stacking method is disclosed. A problem with the prior art has been the generation of a series of laser beam pulses where the outer and inner regions of the beams are generated so as to form radially non-synchronous pulses. Such pulses thus have a non-uniform cross-sectional area with respect to the outer and inner edges of the pulses. The present invention provides a solution by combining the temporally non-uniform pulses in a stacking effect to thus provide a more uniform temporal synchronism over the beam diameter.

  20. Laser pulse stacking method

    DOEpatents

    Moses, E.I.

    1992-12-01

    A laser pulse stacking method is disclosed. A problem with the prior art has been the generation of a series of laser beam pulses where the outer and inner regions of the beams are generated so as to form radially non-synchronous pulses. Such pulses thus have a non-uniform cross-sectional area with respect to the outer and inner edges of the pulses. The present invention provides a solution by combining the temporally non-uniform pulses in a stacking effect to thus provide a more uniform temporal synchronism over the beam diameter. 2 figs.

  1. Aerodynamic improvement of the assembly through which gas conduits are taken into a smoke stack by simulating gas flow on a computer

    NASA Astrophysics Data System (ADS)

    Prokhorov, V. B.; Fomenko, M. V.; Grigor'ev, I. V.

    2012-06-01

    Results from computer simulation of gas flow motion for gas conduits taken on one and two sides into the gas-removal shaft of a smoke stack with a constant cross section carried out using the SolidWorks and FlowVision application software packages are presented.

  2. Spontaneous stacking of purple membranes during immobilization with physical cross-linked poly(vinyl alcohol) hydrogel with retaining native-like functionality of bacteriorhodopsin

    NASA Astrophysics Data System (ADS)

    Yokoyama, Yasunori; Tanaka, Hikaru; Yano, Shunsuke; Takahashi, Hiroshi; Kikukawa, Takashi; Sonoyama, Masashi; Takenaka, Koshi

    2017-05-01

    We previously discovered the correlation between light-induced chromophore color change of a photo-receptor membrane protein bacteriorhodopsin (bR) and its two-dimensional crystalline state in the membrane. To apply this phenomenon to a novel optical memory device, it is necessary that bR molecules are immobilized as maintaining their structure and functional properties. In this work, a poly(vinyl alcohol) (PVA) hydrogel with physical cross-linkages (hydrogen bonds between PVA chains) that resulted from repeated freezing-and-thawing (FT) cycles was used as an immobilization medium. To investigate the effects of physically cross-linked PVA gelation on the structure and function of bR in purple membranes (PMs), spectroscopic techniques were employed against PM/PVA immobilized samples prepared with different FT cycle numbers. Visible circular dichroism spectroscopy strongly suggested PM stacking during gelation. X-ray diffraction data also indicated the PM stacking as well as its native-like crystalline lattice even after gelation. Time-resolved absorption spectroscopy showed that bR photocycle behaviors in PM/PVA immobilized samples were almost identical to that in suspension. These results suggested that a physically cross-linked PVA hydrogel is appropriate for immobilizing membrane proteins in terms of maintaining their structure and functionality.

  3. Virtual Cross-Linking of the Active Nemorubicin Metabolite PNU-159682 to Double-Stranded DNA.

    PubMed

    Scalabrin, Matteo; Quintieri, Luigi; Palumbo, Manlio; Riccardi Sirtori, Federico; Gatto, Barbara

    2017-02-20

    The DNA alkylating mechanism of PNU-159682 (PNU), a highly potent metabolite of the anthracycline nemorubicin, was investigated by gel-electrophoretic, HPLC-UV, and micro-HPLC/mass spectrometry (MS) measurements. PNU quickly reacted with double-stranded oligonucleotides, but not with single-stranded sequences, to form covalent adducts which were detectable by denaturing polyacrylamide gel electrophoresis (DPAGE). Ion-pair reverse-phase HPLC-UV analysis on CG rich duplex sequences having a 5'-CCCGGG-3' central core showed the formation of two types of adducts with PNU, which were stable and could be characterized by micro-HPLC/MS. The first type contained one alkylated species (and possibly one reversibly bound species), and the second contained two alkylated species per duplex DNA. The covalent adducts were found to produce effective bridging of DNA complementary strands through the formation of virtual cross-links reminiscent of those produced by classical anthracyclines in the presence of formaldehyde. Furthermore, the absence of reactivity of PNU with CG-rich sequence containing a TA core (CGTACG), and the minor reactivity between PNU and CGC sequences (TACGCG·CGCGTA) pointed out the importance of guanine sequence context in modulating DNA alkylation.

  4. Plants with stacked genetically modified events: to assess or not to assess?

    PubMed

    Kok, Esther J; Pedersen, Jan; Onori, Roberta; Sowa, Slawomir; Schauzu, Marianna; De Schrijver, Adinda; Teeri, Teemu H

    2014-02-01

    The principles for the safety assessment of genetically modified (GM) organisms (GMOs) are harmonised worldwide to a large extent. There are, however, still differences between the European GMO regulations and the GMO regulations as they have been formulated in other parts of the world. One of these differences relates to the so-called 'stacked GM events', that is, GMOs, plants so far, where new traits are combined by conventional crossing of different GM plants. This paper advocates rethinking the current food/feed safety assessment of stacked GM events in Europe based on an analysis of different aspects that currently form the rationale for the safety assessment of stacked GM events. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Fuel cell system configurations

    DOEpatents

    Kothmann, Richard E.; Cyphers, Joseph A.

    1981-01-01

    Fuel cell stack configurations having elongated polygonal cross-sectional shapes and gaskets at the peripheral faces to which flow manifolds are sealingly affixed. Process channels convey a fuel and an oxidant through longer channels, and a cooling fluid is conveyed through relatively shorter cooling passages. The polygonal structure preferably includes at least two right angles, and the faces of the stack are arranged in opposite parallel pairs.

  6. Force-induced rupture of double-stranded DNA in the absence and presence of covalently bonded anti-tumor drugs: Insights from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Upadhyaya, Anurag; Nath, Shesh; Kumar, Sanjay

    2018-06-01

    DNA intra-strand cross-link (ICL) agents are widely used in the treatment of cancer. ICLs are thought to form a link between the same strand (intra-strand) or complimentary strand (inter-strand) and thereby increase the stability of DNA, which forbids the processes like replication and transcription. As a result, cell death occurs. In this work, we have studied the enhanced stability of a double stranded DNA in the presence of ICLs and compared our findings with the results obtained in the absence of these links. Using atomistic simulations with explicit solvent, a force is applied along and perpendicular to the direction of the helix and we measured the rupture force and the unzipping force of DNA-ICL complexes. Our results show that the rupture and the unzipping forces increase significantly in the presence of these links. The ICLs bind to the minor groove of DNA, which enhance the DNA stabilisation. Such information may be used to design alternative drugs that can stall replication and transcription that are critical to a growing number of anticancer drug discovery efforts.

  7. Direct measurement of interfilament resistance in Nb3Sn strands

    NASA Astrophysics Data System (ADS)

    Corato, V.; Muzzi, L.; Vetrella, U. Besi; della Corte, A.

    2009-05-01

    In modeling the properties of superconducting multifilamentary strands, transverse resistivity plays a crucial role in the definition of the coupling losses in ac regime, as well as of the current transfer length, that affects the transport properties of Nb3Sn wires subject to bending strain. We present the first direct measurement of the interfilament transverse resistance in superconducting strands from room temperature to 4.2 K. Results have been compared to the transverse resistance of a sample on which the outer copper stabilization layer has been removed by chemical etching, obtaining interesting indication on the preferential current paths within the wire cross section. An excellent agreement between experimental data and theoretical models has been found in describing the whole strand, while improvements are required in modeling the filamentary region alone.

  8. Cross sections for the production of fragments with Z greater than or equal to 8 by fragmentation of Z greater than or equal to 9 and less than or equal to 26 nuclei

    NASA Technical Reports Server (NTRS)

    Heinrich, W.; Drechsel, H.; Brechtmann, C.; Beer, J.

    1985-01-01

    Charge changing nuclear collisions in plastic nuclear track detectors were studied using a new experimental technique of automatic track measurement for etched tracks in plastic detectors. Partial cross sections for the production of fragments of charge Z approximately 8 were measured for projectile nuclei of charge 9 approximately Z approximately 26 in the detector material CR39 and in silver. for this purpose three independent experiments were performed using Bevalac beams. The first one was an exposure of a stack of CR39 plastic plates to 1.8 GeV/nucl. Ar-40 nuclei. The second one was an exposure of another CR39 stack of 1.7 GeV/nucl. Fe-56 projectiles. In the third experiment a mixed stack of CR39 plates and silver foils was irradiated with 1.7 GeV/nucl. Fe-56 nuclei. Thus the measurement of nuclear cross sections in a light target (CR39 = C12H18O7) and as well in a heavy target (silver) was possible.

  9. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

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

    Suh, Myungkoo

    1995-12-06

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ~25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases.more » Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G 2 or G 3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N 2-dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N 2-dG.« less

  10. Modeling DNA bubble formation at the atomic scale

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

    Beleva, V; Rasmussen, K. O.; Garcia, A. E.

    We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

  11. Dose-Rate Effects in Breaking DNA Strands by Short Pulses of Extreme Ultraviolet Radiation.

    PubMed

    Vyšín, Luděk; Burian, Tomáš; Ukraintsev, Egor; Davídková, Marie; Grisham, Michael E; Heinbuch, Scott; Rocca, Jorge J; Juha, Libor

    2018-05-01

    In this study, we examined dose-rate effects on strand break formation in plasmid DNA induced by pulsed extreme ultraviolet (XUV) radiation. Dose delivered to the target molecule was controlled by attenuating the incident photon flux using aluminum filters as well as by changing the DNA/buffer-salt ratio in the irradiated sample. Irradiated samples were examined using agarose gel electrophoresis. Yields of single- and double-strand breaks (SSBs and DSBs) were determined as a function of the incident photon fluence. In addition, electrophoresis also revealed DNA cross-linking. Damaged DNA was inspected by means of atomic force microscopy (AFM). Both SSB and DSB yields decreased with dose rate increase. Quantum yields of SSBs at the highest photon fluence were comparable to yields of DSBs found after synchrotron irradiation. The average SSB/DSB ratio decreased only slightly at elevated dose rates. In conclusion, complex and/or clustered damages other than cross-links do not appear to be induced under the radiation conditions applied in this study.

  12. Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.

    PubMed

    Macreadie, I G; Scott, R M; Zinn, A R; Butow, R A

    1985-06-01

    The optional 1143 bp intron in the yeast mitochondrial 21S rRNA gene (omega +) is nearly quantitatively inserted in genetic crosses into 21S rRNA alleles that lack it (omega -). The intron contains an open reading frame that can encode a protein of 235 amino acids, but no function has been ascribed to this sequence. We previously found an in vivo double-strand break in omega - DNA at or close to the intron insertion site only in zygotes of omega + X omega - crosses that appears with the same kinetics as intron insertion. We now show that mutations in the intron open reading frame that would alter the translation product simultaneously inhibit nonreciprocal omega recombination and the in vivo double-strand break in omega - DNA. These results provide evidence that the open reading frame encodes a protein required for intron transposition and support the role of the double-strand break in the process.

  13. Topoisomerase VI senses and exploits both DNA crossings and bends to facilitate strand passage

    PubMed Central

    Wendorff, Timothy J

    2018-01-01

    Type II topoisomerases manage DNA supercoiling and aid chromosome segregation using a complex, ATP-dependent duplex strand passage mechanism. Type IIB topoisomerases and their homologs support both archaeal/plant viability and meiotic recombination. Topo VI, a prototypical type IIB topoisomerase, comprises two Top6A and two Top6B protomers; how these subunits cooperate to engage two DNA segments and link ATP turnover to DNA transport is poorly understood. Using multiple biochemical approaches, we show that Top6B, which harbors the ATPase activity of topo VI, recognizes and exploits the DNA crossings present in supercoiled DNA to stimulate subunit dimerization by ATP. Top6B self-association in turn induces extensive DNA bending, which is needed to support duplex cleavage by Top6A. Our observations explain how topo VI tightly coordinates DNA crossover recognition and ATP binding with strand scission, providing useful insights into the operation of type IIB topoisomerases and related meiotic recombination and GHKL ATPase machineries. PMID:29595473

  14. Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low-Energy Electrons (0.5-9 eV).

    PubMed

    Schürmann, Robin; Tsering, Thupten; Tanzer, Katrin; Denifl, Stephan; Kumar, S V K; Bald, Ilko

    2017-08-28

    Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low-energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross-section for oligonucleotides modified with 8-bromoadenine ( 8Br A). These results were evaluated against DEA measurements with isolated 8Br A in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Temporal changes in shear velocity from ambient noise at New Zealand geothermal fields

    NASA Astrophysics Data System (ADS)

    Civilini, F.; Savage, M. K.; Townend, J.

    2016-12-01

    We use ambient noise to compare shear velocity changes with geothermal production processes at the Ngatamariki and Rotokawa geothermal fields, located in the central North Island of New Zealand. We calculate shear velocity changes through an analysis of cross correlation functions of diffusive seismic wavefields between stations, which are proportional to Green's functions of the station path. Electricity production at Ngatamariki uses an 82 MW binary type power station manufactured by Ormat Technologies, which began operations in mid-2013 and is owned and operated by Mighty River Power. The "Nga Awa Purua" triple flash power plant at the Rotokawa geothermal field was established in 2010 with parnership between Mighty River Power and Tauhara North No. 2 trust and currently operates 174 MW of generation. The seismometers of both networks, deployed primarily to observe microseismicity within the field, were installed prior to well stimulation and the start of production. Although cultural noise dominates the energy spectrum, a strong natural ambient noise signal can be detected when filtering below 1 Hz. Despite similar noise settings, the signal-to-noise ratio of cross correlation stacks at Rotokawa was more than two times greater than at Ngatamariki. We use stacks of cross correlations between stations prior to the onset of production as references, and compare them with cross correlations of moving stacks in time periods of well stimulation and the onset of electricity production.

  16. Repair of O6-methylguanine adducts in human telomeric G-quadruplex DNA by O6-alkylguanine-DNA alkyltransferase

    PubMed Central

    Hellman, Lance M.; Spear, Tyler J.; Koontz, Colton J.; Melikishvili, Manana; Fried, Michael G.

    2014-01-01

    O6-alkylguanine-DNA alkyltransferase (AGT) is a single-cycle DNA repair enzyme that removes pro-mutagenic O6-alkylguanine adducts from DNA. Its functions with short single-stranded and duplex substrates have been characterized, but its ability to act on other DNA structures remains poorly understood. Here, we examine the functions of this enzyme on O6-methylguanine (6mG) adducts in the four-stranded structure of the human telomeric G-quadruplex. On a folded 22-nt G-quadruplex substrate, binding saturated at 2 AGT:DNA, significantly less than the ∼5 AGT:DNA found with linear single-stranded DNAs of similar length, and less than the value found with the telomere sequence under conditions that inhibit quadruplex formation (4 AGT:DNA). Despite these differences, AGT repaired 6mG adducts located within folded G-quadruplexes, at rates that were comparable to those found for a duplex DNA substrate under analogous conditions. Repair was kinetically biphasic with the amplitudes of rapid and slow phases dependent on the position of the adduct within the G-quadruplex: in general, adducts located in the top or bottom tetrads of a quadruplex stack exhibited more rapid-phase repair than did adducts located in the inner tetrad. This distinction may reflect differences in the conformational dynamics of 6mG residues in G-quadruplex DNAs. PMID:25080506

  17. One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting.

    PubMed

    Ensslen, Philipp; Wagenknecht, Hans-Achim

    2015-10-20

    Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.

  18. DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

    PubMed

    Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

    2012-10-11

    Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

  19. Observing Holliday junction branch migration one step at a time

    NASA Astrophysics Data System (ADS)

    Ha, Taekjip

    2004-03-01

    During genetic recombination, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction and the recognition and processing of this species by branch migration and junction resolving enzymes determine the outcome. We have used single molecule fluorescence techniques to study two intrinsic structural dynamics of the Holliday junction, stacking conformer transitions and spontaneous branch migration. Our studies show that the dynamics of branch migration, resolved with one base pair resolution, is determined by the stability of conformers which in turn depends on the local DNA sequences. Therefore, the energy landscape of Holliday junction branch migation is not uniform, but is rugged.

  20. Use of Phenylboronic Acids to Investigate Boron Function in Plants. Possible Role of Boron in Transvacuolar Cytoplasmic Strands and Cell-to-Wall Adhesion

    PubMed Central

    Bassil, Elias; Hu, Hening; Brown, Patrick H.

    2004-01-01

    The only defined physiological role of boron in plants is as a cross-linking molecule involving reversible covalent bonds with cis-diols on either side of borate. Boronic acids, which form the same reversible bonds with cis-diols but cannot cross-link two molecules, were used to selectively disrupt boron function in plants. In cultured tobacco (Nicotiana tabacum cv BY-2) cells, addition of boronic acids caused the disruption of cytoplasmic strands and cell-to-cell wall detachment. The effect of the boronic acids could be relieved by the addition of boron-complexing sugars and was proportional to the boronic acid-binding strength of the sugar. Experiments with germinating petunia (Petunia hybrida) pollen and boronate-affinity chromatography showed that boronic acids and boron compete for the same binding sites. The boronic acids appear to specifically disrupt or prevent borate-dependent cross-links important for the structural integrity of the cell, including the organization of transvacuolar cytoplasmic strands. Boron likely plays a structural role in the plant cytoskeleton. We conclude that boronic acids can be used to rapidly and reversibly induce boron deficiency-like responses and therefore are useful tools for investigating boron function in plants. PMID:15466241

  1. A graphene-based platform for single nucleotide polymorphism (SNP) genotyping.

    PubMed

    Liu, Meng; Zhao, Huimin; Chen, Shuo; Yu, Hongtao; Zhang, Yaobin; Quan, Xie

    2011-06-15

    A facile, rapid, stable and sensitive approach for fluorescent detection of single nucleotide polymorphism (SNP) is designed based on DNA ligase reaction and π-stacking between the graphene and the nucleotide bases. In the presence of perfectly matched DNA, DNA ligase can catalyze the linkage of fluorescein amidite-labeled single-stranded DNA (ssDNA) and a phosphorylated ssDNA, and thus the formation of a stable duplex in high yield. However, the catalytic reaction cannot effectively carry out with one-base mismatched DNA target. In this case, we add graphene to the system in order to produce different quenching signals due to its different adsorption affinity for ssDNA and double-stranded DNA. Taking advantage of the unique surface property of graphene and the high discriminability of DNA ligase, the proposed protocol exhibits good performance in SNP genotyping. The results indicate that it is possible to accurately determine SNP with frequency as low as 2.6% within 40 min. Furthermore, the presented flexible strategy facilitates the development of other biosensing applications in the future. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. A low density microarray method for the identification of human papillomavirus type 18 variants.

    PubMed

    Meza-Menchaca, Thuluz; Williams, John; Rodríguez-Estrada, Rocío B; García-Bravo, Aracely; Ramos-Ligonio, Ángel; López-Monteon, Aracely; Zepeda, Rossana C

    2013-09-26

    We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18's variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings.

  3. A Low Density Microarray Method for the Identification of Human Papillomavirus Type 18 Variants

    PubMed Central

    Meza-Menchaca, Thuluz; Williams, John; Rodríguez-Estrada, Rocío B.; García-Bravo, Aracely; Ramos-Ligonio, Ángel; López-Monteon, Aracely; Zepeda, Rossana C.

    2013-01-01

    We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18's variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings. PMID:24077317

  4. An asymmetric mesoscopic model for single bulges in RNA

    NASA Astrophysics Data System (ADS)

    de Oliveira Martins, Erik; Weber, Gerald

    2017-10-01

    Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.

  5. Multifilament Superconducting Wire Based on NbTi Alloy in a Combined Copper/Copper-Nickel Matrix

    NASA Astrophysics Data System (ADS)

    Vedernikov, G. P.; Shikov, A. K.; Potanina, L. V.; Gubkin, I. N.; Scherbakova, O. V.; Salunin, N. I.; Korpusov, V. U.; Novikov, S. I.; Novikov, M. S.

    2004-06-01

    Model fine filament superconducting 0.65 mm wire based on NbTi alloy, intended for operating in fields having sweep rate from 1 up to 4 T/s, has been developed and manufactured by Bochvar Institute (VNIINM). The wire was fabricated by a single stacking method. Each filament was surrounded by a matrix of commercial MN-5 alloy (Cu-5wt.%Ni). The effects of heat treatment regimes, and twist pitches within the range of 3.5 - 8 mm on Jc of the strand were investigated at fields of 2-8 T. The critical current density is more than 2700 A/mm2 at 5 T, 4.2 K. The magnetization of wire has been measured by a vibrating magnetometer at field amplitude up to ± 3 T. Hysteresis losses and effective diameter were calculated. Total and coupling losses have been determined by Fitz method on strand magnetization at fields, varying in trapezoidal mode. It was shown that the wire of this type is of potential application for the use in the magnets of the GSI-type accelerator to be constructed in Germany.

  6. 49 CFR 38.127 - Sleeping compartments.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.127 Sleeping compartments. (a...., heating and air conditioning controls, lighting controls, call buttons, electrical outlets, etc.) shall be...

  7. 49 CFR 38.127 - Sleeping compartments.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.127 Sleeping compartments. (a...., heating and air conditioning controls, lighting controls, call buttons, electrical outlets, etc.) shall be...

  8. 49 CFR 38.127 - Sleeping compartments.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.127 Sleeping compartments. (a...., heating and air conditioning controls, lighting controls, call buttons, electrical outlets, etc.) shall be...

  9. 49 CFR 38.127 - Sleeping compartments.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.127 Sleeping compartments. (a...., heating and air conditioning controls, lighting controls, call buttons, electrical outlets, etc.) shall be...

  10. 49 CFR 38.127 - Sleeping compartments.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.127 Sleeping compartments. (a...., heating and air conditioning controls, lighting controls, call buttons, electrical outlets, etc.) shall be...

  11. Salton Seismic Imaging Project Line 6: San Andreas Fault and Northern Coachella Valley Structure, Riverside and San Bernardino Counties, California

    NASA Astrophysics Data System (ADS)

    Catchings, R. D.; Fuis, G.; Rymer, M. J.; Goldman, M.; Tarnowski, J. M.; Hole, J. A.; Stock, J. M.; Matti, J. C.

    2012-12-01

    The Salton Seismic Imaging Project (SSIP) is a large-scale, active- and passive-source seismic project designed to image the San Andreas fault (SAF) and adjacent basins (Imperial and Coachella Valleys) in southernmost California. Data and preliminary results from many of the seismic profiles are reported elsewhere (including Fuis et al., Rymer et al., Goldman et al., Langenheim et al., this meeting). Here, we focus on SSIP Line 6, one of four 2-D seismic profiles that were acquired across the Coachella Valley. The 44-km-long, SSIP-Line-6 seismic profile extended from the east flank of Mt. San Jacinto northwest of Palm Springs to the Little San Bernardino Mountains and crossed the SAF (Mission Creek (MCF), Banning (BF), and Garnet Hill (GHF) strands) roughly normal to strike. Data were generated by 10 downhole explosive sources (most spaced about 3 to 5 km apart) and were recorded by approximately 347 Texan seismographs (average spacing 126 m). We used first-arrival refractions to develop a P-wave refraction tomography velocity image of the upper crust along the seismic profile. The seismic data were also stacked and migrated to develop low-fold reflection images of the crust. From the surface to about 7 km depth, P-wave velocities range from about 2.5 km/s to about 7.2 km/s, with the lowest velocities within an ~2-km-deep, ~20-km-wide basin, and the highest velocities below the transition zone from the Coachella Valley to Mt. San Jacinto and within the Little San Bernardino Mountains. The BF and GHF strands bound a shallow sub-basin on the southwestern side of the Coachella Valley, but the underlying shallow-depth (~4 km) basement rocks are P-wave high in velocity (~7.2 km/s). The lack of a low-velocity zone beneath BF and GHF suggests that both faults dip northeastward. In a similar manner, high-velocity basement rocks beneath the Little San Bernardino Mountains suggest that the MCF dips vertically or southwestward. However, there is a pronounced low-velocity zone in basement rocks between about 2 and 7 km depth beneath and southwest of the MCF, suggesting a vertical or slightly southwest-dipping MCF. The apparent northeast dip of the BF and the apparent vertical or southwest dip of the MCF suggests that the two main strands of the SAF (MCF and BF) merge at about 10 km depth. A plot of double-difference earthquake hypocenters (Hauksson, 2000) along the seismic profile shows events that occurred between 1980-2000 (excluding those in 1992, prior to and after the Joshua Tree and Landers earthquakes) are largely confined to the vicinity of the basement low-velocity zone between the MCF and BF. However, a separate alignment of hypocenters occurs southwest of the BF and projects toward the surface beneath Mt. San Jacinto. Collectively, the velocity images and the seismicity data suggest the BF strand of the SAF dips to the northeast at about 50 degrees in the upper 10 km, and the MCF strand is either vertical or dips southwestward about 80 degrees, with both strands merging at about 10 km depth and forming a near-vertical zone of faults to at least 15 km depth. The SSIP Line 6 data are consistent with structures interpreted by Catchings et al. (2009).

  12. SEGR in SiO$${}_2$$ –Si$$_3$$ N$$_4$$ Stacks

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

    Javanainen, Arto; Ferlet-Cavrois, Veronique; Bosser, Alexandre

    2014-04-17

    This work presents experimental SEGR data for MOS-devices, where the gate dielectrics are are made of stacked SiO 2–Si 3N 4 structures. Also a semi-empirical model for predicting the critical gate voltage in these structures under heavy-ion exposure is proposed. Then statistical interrelationship between SEGR cross-section data and simulated energy deposition probabilities in thin dielectric layers is discussed.

  13. Waveguide image-slicers for ultrahigh resolution spectroscopy

    NASA Astrophysics Data System (ADS)

    Beckert, Erik; Strassmeier, Klaus G.; Woche, Manfred; Eberhardt, Ramona; Tünnermann, Andreas; Andersen, Michael

    2008-07-01

    Waveguide image-slicer prototypes with resolutions up to 310.000 for the fiber fed PEPSI echelle spectrograph at the LBT and single waveguide thicknesses of down to 30 μm have been manufactured. The waveguides were macroscopically prepared, stacked up to an order of 7 and thinned back to square stack cross sections. A high filling ratio was achieved by realizing homogenous adhesive gaps of 4.6 μm, using index matching adhesives for TIR within the waveguides. The image-slicer stacks can be used in immersion mode and are miniaturized to be implemented in a set of four, measurements indicate an overall efficiency of above 80% for them.

  14. Measurements of crossed-field demagnetisation rate of trapped field magnets at high frequencies and below 77 K

    NASA Astrophysics Data System (ADS)

    Baskys, A.; Patel, A.; Glowacki, B. A.

    2018-06-01

    Design requirements of the next generation of electric aircraft place stringent requirements on the power density required from electric motors. A future prototype planned in the scope of the European project ‘Advanced Superconducting Motor Experimental Demonstrator’ (ASuMED) considers a permanent magnet synchronous motor, where the conventional ferromagnets are replaced with superconducting trapped field magnets, which promise higher flux densities and thus higher output power without adding weight. Previous work has indicated that stacks of tape show lower cross-field demagnetisation rates to bulk (RE)BCO whilst retaining similar performance for their size, however the crossed-field demagnetisation rate has not been studied in the temperature, the magnetic field and frequency range that are relevant for the operational prototype motor. This work investigates crossed-field demagnetisation in 2G high temperature superconducting stacks at temperatures below 77 K and a frequency range above 10 Hz. This information is crucial in developing designs and determining operational time before re-magnetisation could be required.

  15. Biophysical Characterization of the Strong Stabilization of the RNA Triplex poly(U)•poly(A)*poly(U) by 9-O-(ω-amino) Alkyl Ether Berberine Analogs

    PubMed Central

    Hossain, Maidul; Haq, Lucy; Suresh Kumar, Gopinatha

    2012-01-01

    Background Binding of two 9-O-(ω-amino) alkyl ether berberine analogs BC1 and BC2 to the RNA triplex poly(U)•poly(A)*poly(U) was studied by various biophysical techniques. Methodology/Principal Findings Berberine analogs bind to the RNA triplex non-cooperatively. The affinity of binding was remarkably high by about 5 and 15 times, respectively, for BC1 and BC2 compared to berberine. The site size for the binding was around 4.3 for all. Based on ferrocyanide quenching, fluorescence polarization, quantum yield values and viscosity results a strong intercalative binding of BC1 and BC2 to the RNA triplex has been demonstrated. BC1 and BC2 stabilized the Hoogsteen base paired third strand by about 18.1 and 20.5°C compared to a 17.5°C stabilization by berberine. The binding was entropy driven compared to the enthalpy driven binding of berbeine, most likely due to additional contacts within the grooves of the triplex and disruption of the water structure by the alkyl side chain. Conclusions/Significance Remarkably higher binding affinity and stabilization effect of the RNA triplex by the amino alkyl berberine analogs was achieved compared to berberine. The length of the alkyl side chain influence in the triplex stabilization phenomena. PMID:22666416

  16. 47 CFR 74.655 - Authorization of equipment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... EXPERIMENTAL RADIO, AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Television Broadcast... and regulations. (f) Transmitters designed to be used exclusively for a TV STL station, a TV intercity...

  17. 75 FR 38343 - High-Speed Intercity Passenger Rail (HSIPR) Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-01

    ...This notice details the application requirements and procedures for obtaining funding for high-speed and intercity passenger rail Service Development Programs available under the Transportation, Housing and Urban Development, and Related Agencies Appropriations Act for 2010 (Div. A of the Consolidated Appropriations Act, 2010 (Pub. L. 111-117, Dec. 16, 2009)). The Federal Railroad Administration has issued a separate notice in today's edition of the Federal Register for Fiscal Year 2010 funding made available for Individual Projects. This document incorporates interim guidance required for the HSIPR program pursuant to the Transportation, Housing and Urban Development, and Related Agencies Appropriations Act for 2010 and 49 U.S.C. 24402(a)(2). The funding opportunities described in this notice are available under Catalog of Federal Domestic Assistance (CFDA) number 20.319.

  18. Fast first arrival picking algorithm for noisy microseismic data

    NASA Astrophysics Data System (ADS)

    Kim, Dowan; Byun, Joongmoo; Lee, Minho; Choi, Jihoon; Kim, Myungsun

    2017-01-01

    Most microseismic events occur during hydraulic fracturing. Thus microseismic monitoring, by recording seismic waves from microseismic events, is one of the best methods for locating the positions of hydraulic fractures. However, since microseismic events have very low energy, the data often have a low signal-to-noise ratio (S/N ratio) and it is not easy to pick the first arrival time. In this study, we suggest a new fast picking method optimised for noisy data using cross-correlation and stacking. In this method, a reference trace is selected and the time differences between the first arrivals of the reference trace and those of the other traces are computed by cross-correlation. Then, all traces are aligned with the reference trace by time shifting, and the aligned traces are summed together to produce a stacked reference trace that has a considerably improved S/N ratio. After the first arrival time of the stacked reference trace is picked, the first arrival time of each trace is calculated automatically using the time differences obtained in the cross-correlation process. In experiments with noisy synthetic data and field data, this method produces more reliable results than the traditional method, which picks the first arrival time of each noisy trace separately. In addition, the computation time is dramatically reduced.

  19. Characterization of diode-laser stacks for high-energy-class solid state lasers

    NASA Astrophysics Data System (ADS)

    Pilar, Jan; Sikocinski, Pawel; Pranowicz, Alina; Divoky, Martin; Crump, P.; Staske, R.; Lucianetti, Antonio; Mocek, Tomas

    2014-03-01

    In this work, we present a comparative study of high power diode stacks produced by world's leading manufacturers such as DILAS, Jenoptik, and Quantel. The diode-laser stacks are characterized by central wavelength around 939 nm, duty cycle of 1 %, and maximum repetition rate of 10 Hz. The characterization includes peak power, electrical-to-optical efficiency, central wavelength and full width at half maximum (FWHM) as a function of diode current and cooling temperature. A cross-check of measurements performed at HiLASE-IoP and Ferdinand-Braun-Institut (FBH) shows very good agreement between the results. Our study reveals also the presence of discontinuities in the spectra of two diode stacks. We consider the results presented here a valuable tool to optimize pump sources for ultra-high average power lasers, including laser fusion facilities.

  20. Force-deflection behavior of piezoelectric actuators

    NASA Astrophysics Data System (ADS)

    Singh, Ashok K.; Nagpal, Pawan

    2001-11-01

    In the present endeavour, force - deflection behavior of various piezoelectric actuator configurations has been analyzed for performance comparison. The response of stack actuator has been simulated using MATLAB Simulink, in a stack actuator-pendulum configuration. During simulation, stack actuator has been used in charge control feedback mode, because of the advantage of low hysteresis, and high linearity. The model incorporates three compensation blocks, viz 1) a PID position controller, 2) a PI piezoelectric current controller, and 3) a dynamic force feedback. A typical stack actuator, having 130 layers, 1.20x10-4 m thickness, 3.46x10-5m2 cross sectional area, of PZT-5H type, has been utilized for simulation. The response of the system has been tested by applying a sinusoidal input of frequency 500 Hz, and waveform amplitude of 1x10-3V.

  1. 78 FR 57447 - Environmental Impact Statement for the ACEforward

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-18

    ... intercity passenger rail capital investments and may provide financial assistance for the program, including...) has responsibility for providing Federal funding for intra-city commuter rail capital investments and...

  2. Kansas rail feasibility study

    DOT National Transportation Integrated Search

    2000-03-01

    Intercity passenger transportation in Kansas, as in other Midwest states, is facing enormous : challenges resulting from rapidly changing market forces. These challenges include the : increasing environmental and capital costs of investment in highwa...

  3. Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex

    PubMed Central

    Almaqwashi, Ali A.; Paramanathan, Thayaparan; Lincoln, Per; Rouzina, Ioulia; Westerlund, Fredrik; Williams, Mark C.

    2014-01-01

    DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes. PMID:25245944

  4. Statistical analysis of the Nb3Sn strand production for the ITER toroidal field coils

    NASA Astrophysics Data System (ADS)

    Vostner, A.; Jewell, M.; Pong, I.; Sullivan, N.; Devred, A.; Bessette, D.; Bevillard, G.; Mitchell, N.; Romano, G.; Zhou, C.

    2017-04-01

    The ITER toroidal field (TF) strand procurement initiated the largest Nb3Sn superconducting strand production hitherto. The industrial-scale production started in Japan in 2008 and finished in summer 2015. Six ITER partners (so-called Domestic Agencies, or DAs) are in charge of the procurement and involved eight different strand suppliers all over the world, of which four are using the bronze route (BR) process and four the internal-tin (IT) process. In total more than 500 tons have been produced including excess material covering losses during the conductor manufacturing process, in particular the cabling. The procurement is based on a functional specification where the main strand requirements like critical current, hysteresis losses, Cu ratio and residual resistance ratio are specified but not the strand production process or layout. This paper presents the analysis on the data acquired during the quality control (QC) process that was carried out to ensure the same conductor performance requirements are met by the different strand suppliers regardless of strand design. The strand QC is based on 100% billet testing and on applying statistical process control (SPC) limits. Throughout the production, samples adjacent to the strand pieces tested by the suppliers are cross-checked (‘verified’) by their respective DAs reference labs. The level of verification was lowered from 100% at the beginning of the procurement progressively to approximately 25% during the final phase of production. Based on the complete dataset of the TF strand production, an analysis of the SPC limits of the critical strand parameters is made and the related process capability indices are calculated. In view of the large-scale production and costs, key manufacturing parameters such as billet yield, number of breakages and piece-length distribution are also discussed. The results are compared among all the strand suppliers, focusing on the difference between BR and IT processes. Following the completion of the largest Nb3Sn strand production, our experience gained from monitoring the execution of the QC activities and from auditing the results from the measurements is summarised for future superconducting strand material procurement activities.

  5. How well will stacked transgenic pest/herbicide resistances delay pests from evolving resistance?

    PubMed

    Gressel, Jonathan; Gassmann, Aaron J; Owen, Micheal Dk

    2017-01-01

    Resistance has evolved to single transgenic traits engineered into crops for arthropod and herbicide resistances, and can be expected to evolve to the more recently introduced pathogen resistances. Combining transgenes against the same target pest is being promoted as the solution to the problem. This solution will work if used pre-emptively, but where resistance has evolved to one member of a stack, resistance should easily evolve for the second gene in most cases. We propose and elaborate criteria that could be used to evaluate the value of stacked traits for pest resistance management. Stacked partners must: target the same pest species; be in a tandem construct to preclude segregation; be synchronously expressed in the same tissues; have similar tissue persistence; target pest species that are still susceptible to at least two stacked partners. Additionally, transgene products must not be degraded in the same manner, and there should be a lack of cross-resistance to stacked transgenes or to their products. With stacked herbicide resistance transgenes, both herbicides must be used and have the same persistence. If these criteria are followed, and integrated with other pest management practices, resistance may be considerably delayed. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  6. Prototype Space Fabrication Platform

    DTIC Science & Technology

    1993-12-01

    Wheel Mechanism . . 5-12 5.3.4 Butt Welding of T-Beams ..... .......... 5-14 5.3.5 Application of Cross Members ............ 5-17 5.3.6 Application of...fabrication process and deployed into spece by a drive mechanism on each cap member. The drive mechanism also provided the force necessary to extract...members were stacked closely together and stored in a clip mechanism . The clip had a belt ’ ed mechanism designed to advance the stack, one member at

  7. 77 FR 36586 - Proposed Collection; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-19

    ... (Oct. 17, 2008) (``Rule 204T Adopting Release''). \\2\\ Because failure to comply with the close-out..., trading in municipal securities, and using NSCC's Envelope Settlement Service or Inter-city Envelope...

  8. 2006 public transportation fact book

    DOT National Transportation Integrated Search

    2006-04-01

    This book includes only public transportation data and excludes taxicab, unregulated jitney, school, sightseeing, intercity, charter, : military, and non-public service (e.g., governmental and corporate shuttles), and special application systems (e.g...

  9. 2004 public transportation fact book

    DOT National Transportation Integrated Search

    2004-03-01

    This book includes only public transportation data and excludes taxicab, unregulated jitney, school, sightseeing, intercity, charter, : military, and non-public service (e.g., governmental and corporate shuttles), and special application systems (e.g...

  10. 2005 public transportation fact book

    DOT National Transportation Integrated Search

    2005-04-01

    This book includes only public transportation data and excludes taxicab, unregulated jitney, school, sightseeing, intercity, charter, military, and non-public service (e.g., governmental and corporate shuttles), and special application systems (e.g.,...

  11. 49 CFR 213.3 - Application.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... system railroad for purposes of moving only cars shipped to or from the plant. A plant or installation... no freight, intercity passenger, or commuter passenger railroad operation on the track); or (3) Used...

  12. Study Of The Risks Arising From Natural Disasters And Hazards On Urban And Intercity Motorways By Using Failure Mode Effect Analysis (FMEA) Methods

    NASA Astrophysics Data System (ADS)

    DELİCE, Yavuz

    2015-04-01

    Highways, Located in the city and intercity locations are generally prone to many kind of natural disaster risks. Natural hazards and disasters that may occur firstly from highway project making to construction and operation stages and later during the implementation of highway maintenance and repair stages have to be taken into consideration. And assessment of risks that may occur against adverse situations is very important in terms of project design, construction, operation maintenance and repair costs. Making hazard and natural disaster risk analysis is largely depending on the definition of the likelihood of the probable hazards on the highways. However, assets at risk , and the impacts of the events must be examined and to be rated in their own. With the realization of these activities, intended improvements against natural hazards and disasters will be made with the utilization of Failure Mode Effects Analysis (FMEA) method and their effects will be analyzed with further works. FMEA, is a useful method to identify the failure mode and effects depending on the type of failure rate effects priorities and finding the most optimum economic and effective solution. Although relevant measures being taken for the identified risks by this analysis method , it may also provide some information for some public institutions about the nature of these risks when required. Thus, the necessary measures will have been taken in advance in the city and intercity highways. Many hazards and natural disasters are taken into account in risk assessments. The most important of these dangers can be listed as follows; • Natural disasters 1. Meteorological based natural disasters (floods, severe storms, tropical storms, winter storms, avalanches, etc.). 2. Geological based natural disasters (earthquakes, tsunamis, landslides, subsidence, sinkholes, etc) • Human originated disasters 1. Transport accidents (traffic accidents), originating from the road surface defects (icing, signaling caused malfunctions and risks), fire or explosion etc.- In this study, with FMEA method, risk analysis of the urban and intercity motorways against natural disasters and hazards have been performed and found solutions were brought against these risks. Keywords: Failure Modes Effects Analysis (FMEA), Pareto Analyses (PA), Highways, Risk Management.

  13. Fluorescence Cross-Correlation Spectroscopy Reveals Mechanistic Insights into the Effect of 2′-O-Methyl Modified siRNAs in Living Cells

    PubMed Central

    Ohrt, Thomas; Staroske, Wolfgang; Mütze, Jörg; Crell, Karin; Landthaler, Markus; Schwille, Petra

    2011-01-01

    RNA interference (RNAi) offers a powerful tool to specifically direct the degradation of complementary RNAs, and thus has great therapeutic potential for targeting diseases. Despite the reported preferences of RNAi, there is still a need for new techniques that will allow for a detailed mechanistic characterization of RNA-induced silencing complex (RISC) assembly and activity to further improve the biocompatibility of modified siRNAs. In contrast to previous reports, we investigated the effects of 2′-O-methyl (2′OMe) modifications introduced at specific positions within the siRNA at the early and late stages of RISC assembly, as well as their influence on target recognition and cleavage directly in living cells. We found that six to 10 2′OMe nucleotides on the 3′-end inhibit passenger-strand release as well as target-RNA cleavage without changing the affinity, strand asymmetry, or target recognition. 2′OMe modifications introduced at the 5′-end reduced activated RISC stability, whereas incorporations at the cleavage site showed only minor effects on passenger-strand release when present on the passenger strand. Our new fluorescence cross-correlation spectroscopy assays resolve different steps and stages of RISC assembly and target recognition with heretofore unresolved detail in living cells, which is needed to develop therapeutic siRNAs with optimized in vivo properties. PMID:21689532

  14. Crustal Imaging of the Faroe Islands and North Sea Using Ambient Seismic Noise

    NASA Astrophysics Data System (ADS)

    Sammarco, C.; Rawlinson, N.; Cornwell, D. G.

    2016-12-01

    The recent development of ambient seismic noise imaging offers the potential for obtaining detailed seismic models of the crust. Cross-correlation of long-term recordings from station pairs reveals an empirical "Green's function" which is related to the impulse response of the medium between the two stations. Here, we present new results using two different broadband datasets: one that spans the Faroe Islands and another that spans the North Sea. The smaller scale Faroe Islands study was tackled first, because with only 12 stations, it was well suited for the development and testing of a new data processing and inversion workflow. In the Faroe Islands study cross-correlations with high signal-to-noise ratios were obtained by applying phase weighted stacking, which is shown to be a significant improvement over convectional linear stacking. For example, coherent noise concentrated near the zero time lag of the linearly stacked cross correlations appears to have an influence on the dispersion characteristics beyond 10 s period, but we have managed to minimize these effects with phase weighted stacking. We obtain group velocity maps from 0.5s to 15s period by inverting inter-station travel times using an iterative non-linear inversion scheme. It reveals the presence of significant lateral heterogeneity in the mid-upper crust, including evidence of a low velocity zone in the upper crust, which may mark the base of the basalt layer. This is most clearly revealed by taking the average group velocity dispersion curve for all station pairs and inverting for 1-D shear wave velocity. The computation of a 3-D shear wave speed model both verifies and adds further detail to these results. Application to the North Sea dataset was challenging due to the highly attenuative nature of the crust in this region, which has previously been observed to dramatically reduce the signal-to-noise ratio of short period surface waves. However, with the help of phase-weighted stacking good quality empirical Green's functions can be retrieved for this large dataset. Both group and phase velocity dispersion information are extracted from the cross-correlations, which are then inverted to produce period-dependent velocity maps. The next stage is to invert these maps for 3-D shear wave velocity structure beneath the North Sea region.

  15. Aviation Careers Series: Pilots and Flight Engineers

    DOT National Transportation Integrated Search

    1996-01-31

    Increasing travel in the United States is threatening the mobility the nations surface transportation system provides. Congestion, particularly in urbanized areas and along heavily traveled intercity corridors, is increasing dramatically. The cost...

  16. 49 CFR 374.307 - Baggage service.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... REGULATIONS Adequacy of Intercity Motor Common Carrier Passenger Service § 374.307 Baggage service. (a... travel on the same schedule. Such baggage must then be placed on the next available bus to its...

  17. 2007 public transportation fact book

    DOT National Transportation Integrated Search

    2007-05-01

    This book includes only public transportation data and excludes taxicab, unregulated jitney, school, sightseeing, intercity, charter, : military, and services not available to the general public, or segments of the general public (e.g., governmental ...

  18. Hyperloop Commercial Feasibility Analysis : High Level Overview

    DOT National Transportation Integrated Search

    2016-07-01

    Hyperloop is a concept for very highspeed, fixedguideway, intercity surface transportation, using capsulelike vehicles that operate in sealed partialvacuum tubes. This report provide a highlevel evaluation of hyperloop in terms of its ...

  19. Stacking transgenic event DAS-Ø15Ø7-1 alters maize composition less than traditional breeding.

    PubMed

    Herman, Rod A; Fast, Brandon J; Scherer, Peter N; Brune, Alyssa M; de Cerqueira, Denise T; Schafer, Barry W; Ekmay, Ricardo D; Harrigan, George G; Bradfisch, Greg A

    2017-10-01

    The impact of crossing ('stacking') genetically modified (GM) events on maize-grain biochemical composition was compared with the impact of generating nonGM hybrids. The compositional similarity of seven GM stacks containing event DAS-Ø15Ø7-1, and their matched nonGM near-isogenic hybrids (iso-hybrids) was compared with the compositional similarity of concurrently grown nonGM hybrids and these same iso-hybrids. Scatter plots were used to visualize comparisons among hybrids and a coefficient of identity (per cent of variation explained by line of identity) was calculated to quantify the relationships within analyte profiles. The composition of GM breeding stacks was more similar to the composition of iso-hybrids than was the composition of nonGM hybrids. NonGM breeding more strongly influenced crop composition than did transgenesis or stacking of GM events. These findings call into question the value of uniquely requiring composition studies for GM crops, especially for breeding stacks composed of GM events previously found to be compositionally normal. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  20. Mixed stack charge transfer crystals: Crossing the neutral-ionic borderline by chemical substitution

    NASA Astrophysics Data System (ADS)

    Castagnetti, Nicola; Masino, Matteo; Rizzoli, Corrado; Girlando, Alberto; Rovira, Concepció

    2018-02-01

    We report extensive structural and spectroscopic characterization of four mixed stack charge-transfer (ms-CT) crystals formed by the electron donor 3,3',5 ,5' -tetramethylbenzidine (TMB) with Chloranil (CA), Bromanil (BA), 2,5-difluoro-tetracyanoquinodimethane (TCNQF2), and tetrafluoro-tetracyanoquinodimethane (TCNQF4). Together with the separately studied TMB-TCNQ [Phys. Rev. B 95, 024101 (2017), 10.1103/PhysRevB.95.024101] the TMB-acceptor series spans a wide range of degree of CT, from about 0.14 to 0.91, crossing the neutral-ionic interface, yet retaining similar packing and donor-acceptor CT integrals. First principle calculations of key phenomenological parameters allow us to get insight into the factors determining the degree of CT and other relevant physical properties.

  1. DNA-hosted copper nanoclusters/graphene oxide based fluorescent biosensor for protein kinase activity detection.

    PubMed

    Wang, Mengke; Lin, Zihan; Liu, Qing; Jiang, Shan; Liu, Hua; Su, Xingguang

    2018-07-05

    A novel fluorescent biosensor for protein kinase activity (PKA) detection was designed by applying double-strands DNA-hosted copper nanoclusters (dsDNA-CuNCs) and graphene oxide (GO). One DNA strand of the dsDNA consisted of two domains, one domain can hybridize with another complementary DNA strand to stabilize the fluorescent CuNCs and another domain was adenosine 5'-triphosphate (ATP) aptamer. ATP aptamer of the dsDNA-CuNCs would be spontaneously absorbed onto the GO surface through π-π stacking interactions. Thus GO can efficiently quench the fluorescence (FL) of dsDNA-CuNCs through fluorescence resonance energy transfer (FRET). In the present of ATP, ATP specifically combined with ATP aptamer to form ATP-ATP aptamer binding complexes, which had much less affinity to GO, resulting in the fluorescence recovery of the system. Nevertheless, in the presence of PKA, ATP could be translated into ADP and ADP could not combine with ATP aptamer resulting in the fluorescence quenching of dsDNA-CuNCs again. According to the change of the fluorescence signal, PKA activity could be successfully monitored in the range of 0.1-5.0 U mL -1 with a detection limit (LOD) of 0.039 U mL -1 . Besides, the inhibitory effect of H-89 on PKA activity was studied. The sensor was performed for PKA activity detection in cell lysates with satisfactory results. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. The effects of DNA supercoiling on G-quadruplex formation.

    PubMed

    Sekibo, Doreen A T; Fox, Keith R

    2017-12-01

    Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson-Crick duplex. Quadruplex formation must therefore first require local dissociation (melting) of the duplex strands. Since negative supercoiling is known to facilitate the formation of alternative DNA structures, we have investigated G-quadruplex formation within negatively supercoiled DNA plasmids. Plasmids containing multiple copies of (G3T)n and (G3T4)n repeats, were probed with dimethylsulphate, potassium permanganate and S1 nuclease. While dimethylsulphate footprinting revealed some evidence for G-quadruplex formation in (G3T)n sequences, this was not affected by supercoiling, and permanganate failed to detect exposed thymines in the loop regions. (G3T4)n sequences were not protected from DMS and showed no reaction with permanganate. Similarly, both S1 nuclease and 2D gel electrophoresis of DNA topoisomers did not detect any supercoil-dependent structural transitions. These results suggest that negative supercoiling alone is not sufficient to drive G-quadruplex formation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Differential Targeting of Unpaired Bases within Duplex DNA by the Natural Compound Clerocidin: A Valuable Tool to Dissect DNA Secondary Structure

    PubMed Central

    Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N.

    2012-01-01

    Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures. PMID:23285245

  4. Differential targeting of unpaired bases within duplex DNA by the natural compound clerocidin: a valuable tool to dissect DNA secondary structure.

    PubMed

    Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N

    2012-01-01

    Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures.

  5. Multi-resolution waveguide image slicer for the PEPSI instrument

    NASA Astrophysics Data System (ADS)

    Beckert, Erik; Strassmeier, Klaus G.; Woche, Manfred; Harnisch, Gerd; Hornaff, Marcel; Weber, Michael; Barnes, Stuart

    2016-07-01

    A waveguide image slicer with resolutions up to 270.000 (planned: 300.000) for the fiber fed PEPSI echelle spectrograph at the LBT and single waveguide thicknesses of down to 70 μm has been manufactured and tested. The waveguides were macroscopically prepared, stacked up to an order of seven and thinned back to square stack cross sections. A high filling ratio was achieved by realizing homogenous adhesive gaps of 3.6 μm, using index matching adhesives for TIR within the waveguides. The image slicer stacks are used in immersion mode and are miniaturized to enable implementation in a set of 2x8. The overall efficiency is between 92 % and 96 %.

  6. Fuel cell stack with internal manifolds for reactant gases

    DOEpatents

    Schnacke, Arthur W.

    1985-01-01

    A fuel cell stack includes a plurality of plate-like fuel cells arranged along an axis generally parallel to cell thickness with electrically conductive separator plates between each pair of cells. A plurality of axial manifolds are provided at opposite sides of the stack in outer marginal portions beyond the edges of electrodes and electrolyte tiles. Sealing rings prevent cross-leakage of oxidant fuel gases through use of pairs of outwardly extending lips from opposite tile surfaces bonded to first and second electrode frames respectively. The frames provide transition between electrode edges and manifold perimeters. The pairs of extension lips are sealingly bonded together through an electrically insulative sealing ring with wedge shaped fastening members.

  7. Fuel cell stack with internal manifolds for reactant gases

    DOEpatents

    Schnacke, A.W.

    1983-10-12

    A fuel cell stack includes a plurality of plate-like fuel cells arranged along an axis generally parallel to cell thickness with electrically conductive separator plates between each pair of cells. A plurality of axial manifolds are provided at opposite sides of the stack in outer marginal portions beyond the edges of electrodes and electrolyte tiles. Sealing rings prevent cross-leakage of oxidant fuel gases through use of pairs of outwardly extending lips from opposite tile surfaces bonded to first and second electrode frames respectively. The frames provide transition between electrode edges and manifold perimeters. The pairs of extension lips are sealingly bonded together through an electrically insulative sealing ring with wedge shaped fastening members.

  8. Corrosion of post-tensioning strands in ungrouted ducts - unstressed condition

    NASA Astrophysics Data System (ADS)

    Hutchison, Michael

    Recent failures and severe corrosion distress of post-tensioned (PT) bridges in Florida have revealed corrosion of the 7-wire strands in tendons. Post-tensioned duct assemblies are fitted with multiple 7-wire steel strands and ducts are subsequently filled with grout. During construction, the length of time from the moment in which the strands have been inserted into the ducts, until the ducts are grouted, is referred to as the `ungrouted' period. During this phase, the steel strands are vulnerable to corrosion and consequently the length of this period is restricted (typically to 7 days) by construction guidelines. This investigation focuses on determining the extent of corrosion that may take place during that period, but limited to strands that were in the unstressed condition. Visual inspections and tensile testing were used to identify trends in corrosion development. Corrosion induced cracking mechanisms were also investigated via wire bending and metallographic cross section evaluation. Corrosion damage on unstressed strands during ungrouted periods of durations in the order of those otherwise currently prescribed did not appear to seriously degrade mechanical performance as measured by standardized tests. However the presence of stress in the ungrouted period, as is normally the case, may activate other mechanisms (e.g., EAC) that require further investigation. As expected in the unstressed condition, no evidence of transverse cracking was observed.

  9. Theoretical analysis of stack gas emission velocity measurement by optical scintillation

    NASA Astrophysics Data System (ADS)

    Yang, Yang; Dong, Feng-Zhong; Ni, Zhi-Bo; Pang, Tao; Zeng, Zong-Yong; Wu, Bian; Zhang, Zhi-Rong

    2014-04-01

    Theoretical analysis for an online measurement of the stack gas flow velocity based on the optical scintillation method with a structure of two parallel optical paths is performed. The causes of optical scintillation in a stack are first introduced. Then, the principle of flow velocity measurement and its mathematical expression based on cross correlation of the optical scintillation are presented. The field test results show that the flow velocity measured by the proposed technique in this article is consistent with the value tested by the Pitot tube. It verifies the effectiveness of this method. Finally, by use of the structure function of logarithmic light intensity fluctuations, the theoretical explanation of optical scintillation spectral characteristic in low frequency is given. The analysis of the optical scintillation spectrum provides the basis for the measurement of the stack gas flow velocity and particle concentration simultaneously.

  10. 77 FR 51586 - Submission for OMB Review; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-24

    ... Release''). \\2\\ Because failure to comply with the close-out requirements of Rule 204(a) is a violation of... NSCC's Envelope Settlement Service or Inter-city Envelope Settlement Service. These activities rarely...

  11. Freight Transportation : A Digest of Technical Papers. Volume 1.

    DOT National Transportation Integrated Search

    1976-10-28

    This volume contains a number of technical papers dealing with intercity freight transportation. Collectively, these systems-oriented papers consider a wide range of subject matter including transportation facilitation, commodity flow, regulation, au...

  12. 36 CFR 1192.127 - Sleeping compartments.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Intercity Rail Cars and Systems § 1192.127 Sleeping compartments. (a) Sleeping compartments required to be... controls, call buttons, electrical outlets, etc.) shall be mounted no more than 48 inches, and no less than...

  13. 36 CFR 1192.127 - Sleeping compartments.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Intercity Rail Cars and Systems § 1192.127 Sleeping compartments. (a) Sleeping compartments required to be... controls, call buttons, electrical outlets, etc.) shall be mounted no more than 48 inches, and no less than...

  14. 36 CFR 1192.127 - Sleeping compartments.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Intercity Rail Cars and Systems § 1192.127 Sleeping compartments. (a) Sleeping compartments required to be... controls, call buttons, electrical outlets, etc.) shall be mounted no more than 48 inches, and no less than...

  15. 36 CFR 1192.127 - Sleeping compartments.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Intercity Rail Cars and Systems § 1192.127 Sleeping compartments. (a) Sleeping compartments required to be... controls, call buttons, electrical outlets, etc.) shall be mounted no more than 48 inches, and no less than...

  16. The Effect of Geographical Proximity on Scientific Cooperation among Chinese Cities from 1990 to 2010

    PubMed Central

    Ma, Haitao; Fang, Chuanglin; Pang, Bo; Li, Guangdong

    2014-01-01

    Background The relations between geographical proximity and spatial distance constitute a popular topic of concern. Thus, how geographical proximity affects scientific cooperation, and whether geographically proximate scientific cooperation activities in fact exhibit geographic scale features should be investigated. Methodology Selected statistics from the ISI database on cooperatively authored papers, the authors of which resided in 60 typical cites in China, and which were published in the years 1990, 1995, 2000, 2005, and 2010, were used to establish matrices of geographic distance and cooperation levels between cities. By constructing a distance-cooperation model, the degree of scientific cooperation based on spatial distance was calculated. The relationship between geographical proximity and scientific cooperation, as well as changes in that relationship, was explored using the fitting function. Result (1) Instead of declining, the role of geographical proximity in inter-city scientific cooperation has increased gradually but significantly with the popularization of telecommunication technologies; (2) the relationship between geographical proximity and scientific cooperation has not followed a perfect declining curve, and at certain spatial scales, the distance-decay regularity does not work; (3) the Chinese scientific cooperation network gathers around different regional center cities, showing a trend towards a regional network; within this cooperation network the amount of inter-city cooperation occurring at close range increased greatly. Conclusion The relationship between inter-city geographical distance and scientific cooperation has been enhanced and strengthened over time. PMID:25365449

  17. Bridge cable fracture detection with acoustic emission test (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Qu, Hongya; Li, Tiantian; Chen, Genda

    2017-04-01

    In this study, acoustic emission (AE) tests were conducted to detect and locate wire fracture in strands that are widely used in cable-stayed and suspension bridges. To effectively separate fracture signals from unwanted noises, distinct features of fracture, fracture-induced echo, and artificial tapping signals as well as their dependence on loading levels are characterized with short-time Fourier transform. To associate fracture scenarios with their acoustic features, two 20-foot-long ( 6.1 m) 270 ksi ( 1,862 MPa) steel strands of seven wires were tested with one wire notched off at center and support, respectively, up to 90% of its cross section area by 10% increment. Up to 80% reduction in cross section area of the notched wire, each strand was loaded to 20 kips ( 89 kN) corresponding to 35% of the minimum breaking strength and the acquired AE parameters such as hits, energy, and counts were found to change little. With a reduction of 90% of the section area of one wire, both strands were found to be fractured under approximately 16.5 kips ( 73.4 kN). The hits, energy, and counts of AE signals were all demonstrated to suddenly change with the fracture of the notched wire. However, only the counts of AE signals distributed over the length of the strands allow the localization of fracture point. The frequency band of fracture signals is significantly broader than that of either fracture-induced echo or artificial tapping noise. The time duration of artificial tapping noises is substantially longer than that of either fracture or fracture-induced echo. These distinct characteristics can be used to effectively separate fracture signals from noises for wire fracture detection and localization in practice.

  18. Single Pore Translocation of Folded, Double-Stranded, and Tetra-stranded DNA through Channel of Bacteriophage Phi29 DNA Packaging Motor

    PubMed Central

    Haque, Farzin; Wang, Shaoying; Stites, Chris; Chen, Li; Wang, Chi; Guo, Peixuan

    2015-01-01

    The elegant architecture of the channel of bacteriophage phi29 DNA packaging motor has inspired the development of biomimetics for biophysical and nanobiomedical applications. The reengineered channel inserted into a lipid membrane exhibits robust electrophysiological properties ideal for precise sensing and fingerprinting of dsDNA at the single-molecule level. Herein, we used single channel conduction assays to quantitatively evaluate the translocation dynamics of dsDNA as a function of the length and conformation of dsDNA. We extracted the speed of dsDNA translocation from the dwell time distribution and estimated the various forces involved in the translocation process. A ~35-fold slower speed of translocation per base pair was observed for long dsDNA, a significant contrast to the speed of dsDNA crossing synthetic pores. It was found that the channel could translocate both dsDNA with ~32% of channel current blockage and ~64% for tetra-stranded DNA (two parallel dsDNA). The calculation of both cross-sectional areas of the dsDNA and tetra-stranded DNA suggested that the blockage was purely proportional to the physical space of the channel lumen and the size of the DNA substrate. Folded dsDNA configuration was clearly reflected in their characteristic current signatures. The finding of translocation of tetra-stranded DNA with 64% blockage is in consent with the recently elucidated mechanism of viral DNA packaging via a revolution mode that requires a channel larger than the dsDNA diameter of 2 nm to provide room for viral DNA revolving without rotation. The understanding of the dynamics of dsDNA translocation in the phi29 system will enable us to design more sophisticated single pore DNA translocation devices for future applications in nanotechnology and personal medicine. PMID:25890769

  19. Cross-Linking Interferes With Assessing Sulfur Mustard-Induced DNA Damage in Human Peripheral Blood Lymphocytes Using the Comet Assay

    DTIC Science & Technology

    2004-01-01

    of SM to impede the migration of H,0 2 -damaged mal ian cell lethality with bifunctional alkylating agents . Chemr. Biol. Iriterui. 38:75-86.DNA is an...3100 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010-5400 N-3 position of adenine, and alkylation leads to depurination of Sulfur...mustard (SM) is a blistering agent that produces DNA DNA strands. Subsequent breakage of phosphodiester bonds at strand breaks. To detect SM-induced DNA

  20. Cross-flow electrochemical reactor cells, cross-flow reactors, and use of cross-flow reactors for oxidation reactions

    DOEpatents

    Balachandran, Uthamalingam; Poeppel, Roger B.; Kleefisch, Mark S.; Kobylinski, Thaddeus P.; Udovich, Carl A.

    1994-01-01

    This invention discloses cross-flow electrochemical reactor cells containing oxygen permeable materials which have both electron conductivity and oxygen ion conductivity, cross-flow reactors, and electrochemical processes using cross-flow reactor cells having oxygen permeable monolithic cores to control and facilitate transport of oxygen from an oxygen-containing gas stream to oxidation reactions of organic compounds in another gas stream. These cross-flow electrochemical reactors comprise a hollow ceramic blade positioned across a gas stream flow or a stack of crossed hollow ceramic blades containing a channel or channels for flow of gas streams. Each channel has at least one channel wall disposed between a channel and a portion of an outer surface of the ceramic blade, or a common wall with adjacent blades in a stack comprising a gas-impervious mixed metal oxide material of a perovskite structure having electron conductivity and oxygen ion conductivity. The invention includes reactors comprising first and second zones seprated by gas-impervious mixed metal oxide material material having electron conductivity and oxygen ion conductivity. Prefered gas-impervious materials comprise at least one mixed metal oxide having a perovskite structure or perovskite-like structure. The invention includes, also, oxidation processes controlled by using these electrochemical reactors, and these reactions do not require an external source of electrical potential or any external electric circuit for oxidation to proceed.

  1. Waveguides having patterned, flattened modes

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

    Messerly, Michael J.; Pax, Paul H.; Dawson, Jay W.

    Field-flattening strands may be added to and arbitrarily positioned within a field-flattening shell to create a waveguide that supports a patterned, flattened mode. Patterning does not alter the effective index or flattened nature of the mode, but does alter the characteristics of other modes. Compared to a telecom fiber, a hexagonal pattern of strands allows for a three-fold increase in the flattened mode's area without reducing the separation between its effective index and that of its bend-coupled mode. Hexagonal strand and shell elements prove to be a reasonable approximation, and, thus, to be of practical benefit vis-a-vis fabrication, to thosemore » of circular cross section. Patterned flattened modes offer a new and valuable path to power scaling.« less

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

    Yamada, R.; Ambrosio, G.; Barzi, E.

    The design study of the block type 15-Tesla RHQT Nb{sub 3}Al dipole magnet, and its merits over Nb{sub 3}Sn magnets are presented. The copper stabilized RHQT Nb{sub 3}Al strand is now becoming commercially available for the application to the accelerator magnets. A 1 mm diameter RHQT Nb{sub 3}Al strand with filament size about 50 {mu}, non-copper Jc about 1000 A/mm{sup 2} at 15 Tesla at 4.2K, copper ratio of 50%, can now be produced over several hundred meters. The stress and strain characteristics of the Nb{sub 3}Al strand are superior to the Nb{sub 3}Sn strand. Another advantage is that itmore » can tolerate a longitudinal strain up to 0.55%. The RHQT Nb{sub 3}Al Rutherford cable will have less chance of contamination of the stabilizer, compared to Nb{sub 3}Sn cable. These characteristics of the RHQT Nb{sub 3}Al will be beneficial for designing and producing 15-Tesla dipole magnets. An example 15-Tesla magnet cross section, utilizing the RHQT Nb{sub 3}Sn strand is presented. A systematic investigation on RHQT Nb{sub 3}Al strands, its Rutherford cables, and building a small racetrack magnet for cable testing are proposed.« less

  3. 36 CFR § 1192.127 - Sleeping compartments.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Intercity Rail Cars and Systems § 1192.127 Sleeping compartments. (a) Sleeping compartments required to be... controls, call buttons, electrical outlets, etc.) shall be mounted no more than 48 inches, and no less than...

  4. ADA final rule : rail system accessibility

    DOT National Transportation Integrated Search

    2011-07-31

    This document evaluates the benefits, costs, and other impacts of a DOT rulemaking related to : the accessibility of commuter rail transportation and intercity passenger rail service. In keeping with Executive Order 12866, Executive Order 13563, and ...

  5. Air quality impacts of intercity freight. Volume 2 : appendices

    DOT National Transportation Integrated Search

    1998-07-01

    This document presents best practices and practical advice on how to acquire the software components of Intelligent Transportation Systems (ITS). The executive summary briefly describes the themes and activities developed during the project developme...

  6. Developing a methodology for projecting intercity commuting.

    DOT National Transportation Integrated Search

    2015-12-01

    Texas agencies are investigating passenger rail options in several corridors connecting people : between the states major cities. Popular thinking is that there is commuter travel between a : number of these markets. In specific, Austin to Houston...

  7. Performance Model of Intercity Ground Passenger Transportation Systems

    DOT National Transportation Integrated Search

    1975-08-01

    A preliminary examination of the problems associated with mixed-traffic operations - conventional freight and high speed passenger trains - is presented. Approaches based upon a modest upgrading of existing signal systems are described. Potential cos...

  8. Cross-stacked carbon nanotube film as an additional built-in current collector and adsorption layer for high-performance lithium sulfur batteries.

    PubMed

    Sun, Li; Kong, Weibang; Li, Mengya; Wu, Hengcai; Jiang, Kaili; Li, Qunqing; Zhang, Yihe; Wang, Jiaping; Fan, Shoushan

    2016-02-19

    Cross-stacked carbon nanotube (CNT) film is proposed as an additional built-in current collector and adsorption layer in sulfur cathodes for advanced lithium sulfur (Li-S) batteries. On one hand, the CNT film with high conductivity, microstructural rough surface, high flexibility and mechanical durability retains stable and direct electronic contact with the sulfur cathode materials, therefore decreasing internal resistivity and suppressing polarization of the cathode. On the other hand, the highly porous structure and the high surface area of the CNT film provide abundant adsorption points to support and confine sulfur cathode materials, alleviate their aggregation and promote high sulfur utilization. Moreover, the lightweight and compact structure of the CNT film adds no extra weight or volume to the sulfur cathode, benefitting the improvement of energy densities. Based on these characteristics, the sulfur cathode with a 100-layer cross-stacked CNT film presents excellent rate performances with capacities of 986, 922 and 874 mAh g(-1) at cycling rates of 0.2C, 0.5C and 1C for sulfur loading of 60 wt%, corresponding to an improvement of 52%, 109% and 146% compared to that without a CNT film. Promising cycling performances are also demonstrated, offering great potential for scaled-up production of sulfur cathodes for Li-S batteries.

  9. Chromosome mechanics of fungi under spaceflight conditions--tetrad analysis of two-factor crosses between spore color mutants of Sordaria macrospora.

    PubMed

    Hahn, A; Hock, B

    1999-01-01

    Spore color mutants of the fungus Sordaria macrospora Auersw. were crossed under spaceflight conditions on the space shuttle to MIR mission S/MM 05 (STS-81). The arrangement of spores of different colors in the asci allowed conclusions on the influence of spaceflight conditions on sexual recombination in fungi. Experiments on a 1-g centrifuge in space and in parallel on the ground were used for controls. The samples were analyzed microscopically on their return to earth. Each fruiting body was assessed separately. Statistical analysis of the data showed a significant increase in gene recombination frequencies caused by the heavy ion particle stream in space radiation. The lack of gravity did not influence crossing-over frequencies. Hyphae of the flown samples were assessed for DNA strand breaks. No increase in damage was found compared with the ground samples. It was shown that S. macrospora is able to repair radiation-induced DNA strand breaks within hours.

  10. Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration.

    PubMed

    Estrada-Arriaga, Edson Baltazar; Hernández-Romano, Jesús; García-Sánchez, Liliana; Guillén Garcés, Rosa Angélica; Bahena-Bahena, Erick Obed; Guadarrama-Pérez, Oscar; Moeller Chavez, Gabriela Eleonora

    2018-05-15

    In this study, a continuous flow stack consisting of 40 individual air-cathode MFC units was used to determine the performance of stacked MFC during domestic wastewater treatment operated with unconnected individual MFC and in series and parallel configuration. The voltages obtained from individual MFC units were of 0.08-1.1 V at open circuit voltage, while in series connection, the maximum power and current density were 2500 mW/m 2 and 500 mA/m 2 (4.9 V), respectively. In parallel connection, the maximum power and current density was 5.8 mW/m 2 and 24 mA/m 2 , respectively. When the cells were not connected to each other MFC unit, the main bacterial species found in the anode biofilms were Bacillus and Lysinibacillus. After switching from unconnected to series and parallel connections, the most abundant species in the stacked MFC were Pseudomonas aeruginosa, followed by different Bacilli classes. This study demonstrated that when the stacked MFC was switched from unconnected to series and parallel connections, the pollutants removal, performance electricity and microbial community changed significantly. Voltages drops were observed in the stacked MFC, which was mainly limited by the cathodes. These voltages loss indicated high resistances within the stacked MFC, generating a parasitic cross current. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Examining P-Wave Arrivals of Low-Frequency Earthquakes for Evidence of Attenuation and its Effects on Moment-Duration Scaling

    NASA Astrophysics Data System (ADS)

    Gerzina, J.; Rubin, A. M.

    2017-12-01

    Bostock et. al. (2015) found that low-frequency earthquake (LFE) duration is nearly independent of moment, a result that is surprising enough to warrant investigating whether it might be an artifact of attenuation. Bostock et. al. (2017) found that bulk crustal attenuation could not be the culprit, but suggested that near-source attenuation might cause pronounced depletion of high frequency S-waves. Despite their lower signal-to noise ratio, looking at the P-waves might be enlightening because they aren't expected to attenuate as much as S-waves in the high Vp/Vs region near the tremor source. We have examined P-wave arrivals of LFEs that occurred during episodic tremor in the Cascadia subduction zone with the goal of refining the relationship between LFE magnitude and duration.Bostock et. al's duration measurements were made on stacked templates rather than individual arrivals. Because members of Bostock's LFE families vary in location, and therefore in P-S delay time, aligning the stacks primarily on the S arrival may artificially widen the P pulse. To circumvent this, we used cross-station cross correlations on Bostock's detections to identify and stack events with similar locations and therefore similar P-S delay times, until P arrivals became visible. We then stacked these stacks based on cross-correlating the optimal P component in a small window surrounding the P arrival. Although this procedure narrowed both the P and S pulse widths, it did not dramatically narrow P in relation to S, nor did we observe different P pulse widths for small and large events.We also compared the frequency spectra of small windows around the expected P and S arrivals for each amplitude bin. Although there is more high-frequency content in P-waves than S-waves, we have not yet been able to resolve a difference in P-wave corner frequency for different event sizes. Thus our preliminary results support the notion that LFEs are intrinsically low frequency.

  12. Flexible reusable mandrels

    NASA Technical Reports Server (NTRS)

    Willden, Kurtis S. (Inventor)

    1995-01-01

    A reusable laminate mandrel which is unaffected by extreme temperature changes. The flexible laminate mandrel is comprised of sheets stacked to produce the required configuration, a cover wrap that applies pressure to the mandrel laminate, maintaining the stack cross-section. Then after use, the mandrels can be removed, disassembled, and reused. In the method of extracting the flexible mandrel from one end of a composite stiffener, individual ones of the laminae of the flexible mandrel or all are extracted at the same time, depending on severity of the contour.

  13. A first principles study of commonly observed planar defects in Ti/TiB system

    DOE PAGES

    Nandwana, Peeyush; Gupta, Niraj; Srinivasan, Srivilliputhur G.; ...

    2018-04-20

    Here, TiB exhibits a hexagonal cross-section with growth faults on (1 0 0) planes and contains B27-B f bicrystals. The hexagonal cross-section is presently explained by surface free energy minimization principle. We show that interfacial energy calculations explain the longer (1 0 0) facet compared to (1 0 1) type facets whereas free surface energy arguments do not provide the true picture. No quantitative explanation of stacking faults and B27-B f interfaces in TiB exists. We show that the low formation energy of stacking faults and B27-B f interfaces explain their abundance. The low energy barrier for B f formationmore » is shown to be responsible for their presence in TiB.« less

  14. A first principles study of commonly observed planar defects in Ti/TiB system

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

    Nandwana, Peeyush; Gupta, Niraj; Srinivasan, Srivilliputhur G.

    Here, TiB exhibits a hexagonal cross-section with growth faults on (1 0 0) planes and contains B27-B f bicrystals. The hexagonal cross-section is presently explained by surface free energy minimization principle. We show that interfacial energy calculations explain the longer (1 0 0) facet compared to (1 0 1) type facets whereas free surface energy arguments do not provide the true picture. No quantitative explanation of stacking faults and B27-B f interfaces in TiB exists. We show that the low formation energy of stacking faults and B27-B f interfaces explain their abundance. The low energy barrier for B f formationmore » is shown to be responsible for their presence in TiB.« less

  15. X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

    DOE PAGES

    Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan; ...

    2016-06-02

    We report that observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystallinemore » phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG 3 (TTAG 3) 3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG(4)T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.« less

  16. Binding mode and thermodynamic studies on the interaction of the anticancer drug dacarbazine and dacarbazine-Cu(II) complex with single and double stranded DNA.

    PubMed

    Temerk, Yassien; Ibrahim, Hossieny

    2014-07-01

    The binding mode and thermodynamic characteristics of the anticancer drug dacarbazine (Dac) with double and single stranded DNA were investigated in the absence and presence of Cu(II) using cyclic voltammetry, square wave voltammetry and fluorescence spectroscopy. The interaction of Dac and Dac-Cu(II) complex with dsDNA indicated their intercalation into the base stacking domain of dsDNA double helix and the strength of interaction is independent on the ionic strength. The interaction of Dac with dsDNA in the presence of Cu(II) leads to a much stronger intercalation. The interaction mode of Dac molecules with ssDNA is electrostatic attraction via negative phosphate on the exterior of the ssDNA with Dac. The binding constants, stoichiometric coefficients and thermodynamic parameters of Dac and Dac-Cu(II) complex with dsDNA and ssDNA were evaluated. Comparison of the mode interaction of Dac with dsDNA and ssDNA was discussed. The decrease of peak current of Dac was proportional to DNA concentration, which was applied for determination of dsDNA and ssDNA concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Spontaneous Transport of Single-Stranded DNA through Graphene-MoS2 Heterostructure Nanopores.

    PubMed

    Luan, Binquan; Zhou, Ruhong

    2018-04-24

    The effective transport of a single-stranded DNA (ssDNA) molecule through a solid-state nanopore is essential to the future success of high-throughput and low-cost DNA sequencing. Compatible with current electric sensing technologies, here, we propose and demonstrate by molecular dynamics simulations the ssDNA transport through a quasi-two-dimensional nanopore in a heterostructure stacked together with different 2D materials, such as graphene and molybdenum disulfide (MoS 2 ). Due to different chemical potentials, U, of DNA bases on different 2D materials, it is energetically favorable for a ssDNA molecule to move from the low- U MoS 2 surface to the high- U graphene surface through a nanopore. With the proper attraction between the negatively charged phosphate group in each nucleotide and the positively charged Mo atoms exposed on the pore surface, the ssDNA molecule can be temporarily seized and released thereafter through a thermal activation, that is, a slow and possible nucleotide-by-nucleotide transport. A theoretical formulation is then developed for the free energy of the ssDNA transiting a heterostructure nanopore to properly characterize the non-equilibrium stick-slip-like motion of a ssDNA molecule.

  18. A transmission imaging spectrograph and microfabricated channel system for DNA analysis.

    PubMed

    Simpson, J W; Ruiz-Martinez, M C; Mulhern, G T; Berka, J; Latimer, D R; Ball, J A; Rothberg, J M; Went, G T

    2000-01-01

    In this paper we present the development of a DNA analysis system using a microfabricated channel device and a novel transmission imaging spectrograph which can be efficiently incorporated into a high throughput genomics facility for both sizing and sequencing of DNA fragments. The device contains 48 channels etched on a glass substrate. The channels are sealed with a flat glass plate which also provides a series of apertures for sample loading and contact with buffer reservoirs. Samples can be easily loaded in volumes up to 640 nL without band broadening because of an efficient electrokinetic stacking at the electrophoresis channel entrance. The system uses a dual laser excitation source and a highly sensitive charge-coupled device (CCD) detector allowing for simultaneous detection of many fluorescent dyes. The sieving matrices for the separation of single-stranded DNA fragments are polymerized in situ in denaturing buffer systems. Examples of separation of single-stranded DNA fragments up to 500 bases in length are shown, including accurate sizing of GeneCalling fragments, and sequencing samples prepared with a reduced amount of dye terminators. An increase in sample throughput has been achieved by color multiplexing.

  19. X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

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

    Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan

    We report that observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystallinemore » phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG 3 (TTAG 3) 3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG(4)T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.« less

  20. The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery.

    PubMed

    Kidane, Dawit; Ayora, Silvia; Sweasy, Joann B; Graumann, Peter L; Alonso, Juan C

    2012-01-01

    Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.

  1. The cell pole: The site of cross talk between the DNA uptake and genetic recombination machinery

    PubMed Central

    Kidane, Dawit; Ayora, Silvia; Sweasy, Joann; Graumann, Peter L.; Alonso, Juan C.

    2012-01-01

    Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as “guardians”, protect ssDNA from degradation and limit the RecA recombinase loading. Then, the “mediators” overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by “modulators”, catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or “resolver” cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the “rescuers” will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective. PMID:23046409

  2. The Chicago to Iowa City intercity passenger rail route : business plan.

    DOT National Transportation Integrated Search

    2011-03-21

    Business Plan Highlights : -No Iowa General Fund or RIIF appropriations : -State/local partnership : -Funds operation for the first 10 years : -Local cash commitment to passenger rail : -Conservative and practical financial forecasts : -Three compone...

  3. Intercity passenger rail : financial performance of Amtrak's routes

    DOT National Transportation Integrated Search

    1998-05-14

    Since it began operations in 1971, the National Railroad Passenger Corporation : (Amtrak) has never been profitable and has received about $21 billion in federal : subsidies for operating and capital expenses. In December 1994, at the : direction of ...

  4. Intercity passenger rail : Amtrak's financial viability continues to be threatened

    DOT National Transportation Integrated Search

    1997-03-12

    Amtrak's financial condition is still very precarious and heavily dependent on federal operating and capital funds. We previously reported that Amtrak's financial condition had deteriorated steadily since 1990 and that Amtrak was unlikely to overcome...

  5. 18 CFR 281.202 - Applicability.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    .... Algonquin Gas Transmission Company. Arkansas Louisiana Natural Gas Company. Cities Service Gas Company.... Florida Gas Transmission Company. Great Lakes Gas Transmission Company. Inter-City Minnesota Pipelines... River Transmission Company. Montana Dakota Utilities Company. National Fuel Gas Supply Company. North...

  6. Air quality impacts of intercity freight. Volume 1 : guidebook

    DOT National Transportation Integrated Search

    2000-01-01

    Driver error remains the leading cause of highway crashes. Through the Intelligent Vehicle Initiative (IVI), the Department of Transportation hopes to reduce crashes by helping drivers avoid hazardous mistakes. IVI aims to accelerate the development ...

  7. Demand projections for the northeast corridor : financial analysis

    DOT National Transportation Integrated Search

    1976-06-30

    This report describes the development and results of intercity travel demand projections by city-pair prepared for the Northeast Corridor financial analysis. In addition associated analyses of projected passenger volumes by station and of selected al...

  8. A highly sensitive biosensing platform based on upconversion nanoparticles and graphene quantum dots for the detection of Ag+

    NASA Astrophysics Data System (ADS)

    He, Lu; Yang, Lin; Zhu, Hao; Dong, Wenkui; Ding, Yujie; Zhu, Jun-Jie

    2017-06-01

    A novel luminescence ‘Turn-On’ nanoplatform for the sensitive sensing of Ag+ was fabricated based on luminescence resonance energy transfer technique between sodium citrate functionalized upconversion nanoparticles (Cit-UCNPs, energy donor) and graphene quantum dots (GQDs, energy acceptor). Amino-labeled single-stranded DNA (NH2-ssDNA) containing a number of cytosine (C) was conjugated on the surface of the Cit-UCNPs to capture Ag+ ions. Due to the π-π stacking interaction between NH2-ssDNA and GQDs, the upconversion luminescence can be quenched. However, upon the addition of Ag+, the π-π stacking interaction weakens due to the formation of the hairpin structure of C-Ag+-C on the UCNPs. As a result, GQDs will leave the surface of the UCNPs and the upconversion luminescence can be enhanced (Turn-On). Based on this fact, the sensor was developed for the detection of Ag+ with a linear concentration range from 2 × 10-4 to 1 μM and a detection limit as low as 60 pM. The assay method is fairly simple with high selectivity and sensitivity, which can be used for the determination of Ag+ in environmental water samples.

  9. A study of characteristics of intercity transportation systems. Phase 1: Definition of transportation comparison methodology

    NASA Technical Reports Server (NTRS)

    English, J. M.; Smith, J. L.; Lifson, M. W.

    1978-01-01

    Decision making in early transportation planning must be responsive to complex value systems representing various policies and objectives. The assessment of alternative transportation concepts during the early initial phases of the system life cycle, when supportive research and technology development activities are defined, requires estimates of transportation, environmental, and socio-economic impacts throughout the system life cycle, which is a period of some 40 or 50 years. A unified methodological framework for comparing intercity passenger and freight transportation systems is described and is extended to include the comparison of long term transportation trends arising from implementation of the various R & D programs. The attributes of existing and future transportation systems are reviewed in order to establish measures for comparison, define value functions, and attribute weightings needed for comparing alternative policy actions for furthering transportation goals. Comparison criteria definitions and an illustrative example are included.

  10. Footprinting reveals that nogalamycin and actinomycin shuffle between DNA binding sites.

    PubMed Central

    Fox, K R; Waring, M J

    1986-01-01

    The hypothesis that sequence-selective DNA-binding antibiotics locate their preferred binding sites by a process involving migration from nonspecific sites has been tested by footprinting with DNAase I. Footprinting patterns on the tyrT DNA fragment produced by nogalamycin and actinomycin change with time after mixing the antibiotic with the DNA. Sites of protection as well as enhanced cleavage are seen to develop in a fashion which is both temperature and concentration-dependent. At certain sites cutting is transiently enhanced, then blocked. Limited evidence for slow reaction with echinomycin and mithramycin is presented, but the kinetics of footprinting with daunomycin and distamycin appear instantaneous. The feasibility of adducing direct evidence for shuffling by footprinting seems to be governed by slow dissociation of the antibiotic-DNA complex. It may also be dependent upon the mode of binding, be it intercalative or non-intercalative in character. Images PMID:2421246

  11. On-site detection of stacked genetically modified soybean based on event-specific TM-LAMP and a DNAzyme-lateral flow biosensor.

    PubMed

    Cheng, Nan; Shang, Ying; Xu, Yuancong; Zhang, Li; Luo, Yunbo; Huang, Kunlun; Xu, Wentao

    2017-05-15

    Stacked genetically modified organisms (GMO) are becoming popular for their enhanced production efficiency and improved functional properties, and on-site detection of stacked GMO is an urgent challenge to be solved. In this study, we developed a cascade system combining event-specific tag-labeled multiplex LAMP with a DNAzyme-lateral flow biosensor for reliable detection of stacked events (DP305423× GTS 40-3-2). Three primer sets, both event-specific and soybean species-specific, were newly designed for the tag-labeled multiplex LAMP system. A trident-like lateral flow biosensor displayed amplified products simultaneously without cross contamination, and DNAzyme enhancement improved the sensitivity effectively. After optimization, the limit of detection was approximately 0.1% (w/w) for stacked GM soybean, which is sensitive enough to detect genetically modified content up to a threshold value established by several countries for regulatory compliance. The entire detection process could be shortened to 120min without any large-scale instrumentation. This method may be useful for the in-field detection of DP305423× GTS 40-3-2 soybean on a single kernel basis and on-site screening tests of stacked GM soybean lines and individual parent GM soybean lines in highly processed foods. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations

    NASA Astrophysics Data System (ADS)

    Yoon, Gwonchan; Lee, Myeongsang; Kim, Kyungwoo; In Kim, Jae; Chang, Hyun Joon; Baek, Inchul; Eom, Kilho; Na, Sungsoo

    2015-12-01

    Amyloid fibrils are responsible for pathogenesis of various diseases and exhibit the structural feature of an ordered, hierarchical structure such as multi-stranded helical structure. As the multi-strandedness of amyloid fibrils has recently been found to be highly correlated with their toxicity and infectivity, it is necessary to study how the hierarchical (i.e. multi-stranded) structure of amyloid fibril is formed. Moreover, although it has recently been reported that the nanomechanics of amyloid proteins plays a key role on the amyloid-induced pathogenesis, a critical role that the multi-stranded helical structure of the fibrils plays in their nanomechanical properties has not fully characterized. In this work, we characterize the morphology and mechanical properties of multi-stranded amyloid fibrils by using equilibrium molecular dynamics simulation and elastic network model. It is shown that the helical pitch of multi-stranded amyloid fibril is linearly proportional to the number of filaments comprising the amyloid fibril, and that multi-strandedness gives rise to improving the bending rigidity of the fibril. Moreover, we have also studied the morphology and mechanical properties of a single protofilament (filament) in order to understand the effect of cross-β structure and mutation on the structures and mechanical properties of amyloid fibrils. Our study sheds light on the underlying design principles showing how the multi-stranded amyloid fibril is formed and how the structure of amyloid fibrils governs their nanomechanical properties.

  13. Mechanisms of strand break formation in DNA due to the direct effect of ionizing radiation: the dependency of free base release on the length of alternating CG oligodeoxynucleotides.

    PubMed

    Sharma, Kiran K; Razskazovskiy, Yuriy; Purkayastha, Shubhadeep; Bernhard, William A

    2009-06-11

    The question of how NA base sequence influences the yield of DNA strand breaks produced by the direct effect of ionizing radiation was investigated in a series of oligodeoxynucleotides of the form (d(CG)(n))(2) and (d(GC)(n))(2). The yields of free base release from X-irradiated DNA films containing 2.5 waters/nucleotide were measured by HPLC as a function of oligomer length. For (d(CG)(n))(2), the ratio of the Gua yield to Cyt yield, R, was relatively constant at 2.4-2.5 for n = 2-4 and it decreased to 1.2 as n increased from 5 to 10. When Gua was moved to the 5' end, for example going from d(CG)(5) to d(GC)(5), R dropped from 1.9 +/- 0.1 to 1.1 +/- 0.1. These effects are poorly described if the chemistry at the oligomer ends is assumed to be independent of the remainder of the oligomer. A mathematical model incorporating charge transfer through the base stack was derived to explain these effects. In addition, EPR was used to measure the yield of trapped-deoxyribose radicals at 4 K following X-irradiation at 4 K. The yield of free base release was substantially greater, by 50-100 nmol/J, than the yield of trapped-deoxyribose radicals. Therefore, a large fraction of free base release stems from a nonradical intermediate. For this intermediate, a deoxyribose carbocation formed by two one-electron oxidations is proposed. This reaction pathway requires that the hole (electron loss site) transfers through the base stack and, upon encountering a deoxyribose hole, oxidizes that site to form a deoxyribose carbocation. This reaction mechanism provides a consistent way of explaining both the absence of trapped radical intermediates and the unusual dependence of free base release on oligomer length.

  14. Disulfide-Mediated β-Strand Dimers: Hyperstable β-Sheets Lacking Tertiary Interactions and Turns.

    PubMed

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

    2015-04-29

    Disulfide bonds between cysteine residues are essential to the structure and folding of many proteins. Yet their role in the design of structured peptides and proteins has frequently been limited to use as intrachain covalent staples that reinforce existing structure or induce knot-like conformations. In β-hairpins, their placement at non-H-bonding positions across antiparallel strands has proven useful for achieving fully folded positive controls. Here we report a new class of designed β-sheet peptide dimers with strand-central disulfides as a key element. We have found that the mere presence of a disulfide bond near the middle of a short peptide chain is sufficient to nucleate some antiparallel β-sheet structure; addition of β-capping units and other favorable cross-strand interactions yield hyperstable sheets. Strand-central cystines were found to be superior to the best designed reversing turns in terms of nucleating β-sheet structure formation. We have explored the limitations and possibilities of this technique (the use of disulfides as sheet nucleators), and we provide a set of rules and rationales for the application and further design of disulfide-tethered "turnless" β-sheets.

  15. Visualizing the intercity correlation of PM2.5 time series in the Beijing-Tianjin-Hebei region using ground-based air quality monitoring data.

    PubMed

    Liu, Jianzheng; Li, Weifeng; Wu, Jiansheng; Liu, Yonghong

    2018-01-01

    The Beijing-Tianjin-Hebei area faces a severe fine particulate matter (PM2.5) problem. To date, considerable progress has been made toward understanding the PM2.5 problem, including spatial-temporal characterization, driving factors, and health effects. However, little research has been done on the dynamic interactions and relationships between PM2.5 concentrations in different cities in this area. To address the research gap, this study discovered a phenomenon of time-lagged intercity correlations of PM2.5 time series and proposed a visualization framework based on this phenomenon to visualize the interaction in PM2.5 concentrations between cities. The visualizations produced using the framework show that there are significant time-lagged correlations between the PM2.5 time series in different cities in this area. The visualizations also show that the correlations are more significant in colder months and between cities that are closer, and that there are seasonal changes in the temporal order of the correlated PM2.5 time series. Further analysis suggests that the time-lagged intercity correlations of PM2.5 time series are most likely due to synoptic meteorological variations. We argue that the visualizations demonstrate the interactions of air pollution between cities in the Beijing-Tianjin-Hebei area and the significant effect of synoptic meteorological conditions on PM2.5 pollution. The visualization framework could help determine the pathway of regional transportation of air pollution and may also be useful in delineating the area of interaction of PM2.5 pollution for impact analysis.

  16. Visualizing the intercity correlation of PM2.5 time series in the Beijing-Tianjin-Hebei region using ground-based air quality monitoring data

    PubMed Central

    Li, Weifeng; Wu, Jiansheng; Liu, Yonghong

    2018-01-01

    The Beijing-Tianjin-Hebei area faces a severe fine particulate matter (PM2.5) problem. To date, considerable progress has been made toward understanding the PM2.5 problem, including spatial-temporal characterization, driving factors, and health effects. However, little research has been done on the dynamic interactions and relationships between PM2.5 concentrations in different cities in this area. To address the research gap, this study discovered a phenomenon of time-lagged intercity correlations of PM2.5 time series and proposed a visualization framework based on this phenomenon to visualize the interaction in PM2.5 concentrations between cities. The visualizations produced using the framework show that there are significant time-lagged correlations between the PM2.5 time series in different cities in this area. The visualizations also show that the correlations are more significant in colder months and between cities that are closer, and that there are seasonal changes in the temporal order of the correlated PM2.5 time series. Further analysis suggests that the time-lagged intercity correlations of PM2.5 time series are most likely due to synoptic meteorological variations. We argue that the visualizations demonstrate the interactions of air pollution between cities in the Beijing-Tianjin-Hebei area and the significant effect of synoptic meteorological conditions on PM2.5 pollution. The visualization framework could help determine the pathway of regional transportation of air pollution and may also be useful in delineating the area of interaction of PM2.5 pollution for impact analysis. PMID:29438417

  17. Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

    PubMed

    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.

  18. Deoxyhexanucleotide containing a vinyl chloride induced DNA lesion, 1,N/sup 6/-ethenoadenine: synthesis, physical characterization, and incorporation into a duplex bacteriophage M13 genome as part of an amber codon

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

    Basu, A.K.; Niedernhofer, L.J.; Essigmann, J.M.

    Organic synthesis and recombinant DNA techniques have been used to situate a single 1,N/sup 6/-ethenoadenine (epsilon Ade) DNA adduct at an amber codon in the genome of an M13mp19 phage derivative. The deoxyhexanucleotide d(GCT(epsilon A)GC) was chemically synthesized by the phosphotriester method. Physical studies involving fluorescence, circular dichroism , and /sup 1/H NMR indicated epsilon Ade to be very efficiently stacked in the hexamer, especially with the 5'-thymine. Melting profile and circular dichroism studies provided evidence of the loss of base-pairing capabilities attendant with formation of the etheno ring. The modified hexanucleotide was incorporated into a six-base gap formed inmore » the genome of an M13mp19 insertion mutant. Phage of the insertion mutant, M13mp19-NheI, produced light blue plaques on SupE strains because of the introduced amber codon. Formation of a hybrid between the single-strand DNA (plus strand) of M13mp19-NheI with SmaI-linearized M13mp19 replicative form produced a heteroduplex with a six-base gap in the minus strand. The modified hexamer (5'-/sup 32/P)d-(GCT(epsilon A)GC), after 5'-phosphorylation, was ligated into this gap by using bacteriophage T4 DNA ligase to generate a singly adducted genome with epsilon Ade at minus strand position 6274. Introduction of the radiolabel provided a useful marker for characterization of the singly adducted genome, and indeed the label appeared in the anticipated fragments when digested by several restriction endonucleases. Evidence that ligation occurred on both 5' and 3' sides of the oligonucleotide also was obtained. The M13mp19-NheI genome containing epsilon Ade will be used as a probe for studying mutagenesis and repair of this DNA adduct in Escherichia coli.« less

  19. Identification of G-quadruplex forming sequences in three manatee papillomaviruses

    PubMed Central

    Zahin, Maryam; Dean, William L.; Ghim, Shin-je; Joh, Joongho; Gray, Robert D.; Khanal, Sujita; Bossart, Gregory D.; Mignucci-Giannoni, Antonio A.; Rouchka, Eric C.; Jenson, Alfred B.; Trent, John O.; Chaires, Jonathan B.

    2018-01-01

    The Florida manatee (Trichechus manatus latirotris) is a threatened aquatic mammal in United States coastal waters. Over the past decade, the appearance of papillomavirus-induced lesions and viral papillomatosis in manatees has been a concern for those involved in the management and rehabilitation of this species. To date, three manatee papillomaviruses (TmPVs) have been identified in Florida manatees, one forming cutaneous lesions (TmPV1) and two forming genital lesions (TmPV3 and TmPV4). We identified DNA sequences with the potential to form G-quadruplex structures (G4) across the three genomes. G4 were located on both DNA strands and across coding and non-coding regions on all TmPVs, offering multiple targets for viral control. Although G4 have been identified in several viral genomes, including human PVs, most research has focused on canonical structures comprised of three G-tetrads. In contrast, the vast majority of sequences we identified would allow the formation of non-canonical structures with only two G-tetrads. Our biophysical analysis confirmed the formation of G4 with parallel topology in three such sequences from the E2 region. Two of the structures appear comprised of multiple stacked two G-tetrad structures, perhaps serving to increase structural stability. Computational analysis demonstrated enrichment of G4 sequences on all TmPVs on the reverse strand in the E2/E4 region and on both strands in the L2 region. Several G4 sequences occurred at similar regional locations on all PVs, most notably on the reverse strand in the E2 region. In other cases, G4 were identified at similar regional locations only on PVs forming genital lesions. On all TmPVs, G4 sequences were located in the non-coding region near putative E2 binding sites. Together, these findings suggest that G4 are possible regulatory elements in TmPVs. PMID:29630682

  20. Freight Transportation Information Systems and Their Implications for R&D Policy

    DOT National Transportation Integrated Search

    1974-03-01

    The current use of computerized management information and control systems in intercity freight transportation are examined. Each of the four modes (railroad, motor carrier, maritime and air cargo industries) is investigated. In each case, computer i...

  1. The effects of the ride environment on intercity train passenger activities

    DOT National Transportation Integrated Search

    1979-01-01

    The ability to perform activities such as reading, writing, : talking, and sleeping has frequently been cited in the : ride quality literature as an important factor in passengers' : comfort and satisfaction with transportation systems. A field : stu...

  2. Occupant Volume Integrity Evaluation in Passenger Rail Cars

    DOT National Transportation Integrated Search

    2012-02-01

    This research, which is intended to enable the growth of high-speed and intercity passenger rail transportation, was sponsored by the Federal Railroad Administration (FRA) Office of Research and Development, as part of the train Occupant Protection r...

  3. Occupant volume integrity evaluation in passenger rail cars.

    DOT National Transportation Integrated Search

    2012-02-01

    This research, which is intended to enable the growth of high-speed and intercity passenger rail transportation, was sponsored by the Federal Railroad Administration (FRA) Office of Research and Development, as part of the train Occupant Protection r...

  4. Mechanistic design of concrete crossties and fastening systems - Phase 1.

    DOT National Transportation Integrated Search

    2017-04-28

    The objective of this project is the development and deployment of resilient concrete crossties and fastening systems for heavy haul freight, intercity passenger, and rail transit applications. : For a variety of reasons, concrete crossties are a dom...

  5. The Chicago-Iowa City passenger rail program : fact sheet.

    DOT National Transportation Integrated Search

    2011-02-23

    Project costs : Overall cost: $310 million : Costs allocated between Iowa and Illinois : Iowa and Illinois submitted a joint application for $248 : million (up to 80 percent of the project cost) from the : High-Speed Intercity Passenger R...

  6. Chicago to Iowa City passenger rail : project financial plan.

    DOT National Transportation Integrated Search

    2009-09-01

    The Chicago to Iowa City Intercity Passenger Rail Program (Program) is a joint : undertaking of the Iowa Department of Transportation (Iowa DOT) and the Illinois : Department of Transportation (Illinois DOT). The purpose of the Program is to reestabl...

  7. Locomotive crashworthiness research : volume 5 : cab car crashworthiness report

    DOT National Transportation Integrated Search

    1996-03-01

    Models used to analyze locomotive crashworthiness are modified for application to control cab cars of the types used for intercity and commuter rail passenger service. An existing control cab car is analyzed for crashworthiness based on scenarios dev...

  8. Promoting intermodal connectivity at California's high-speed rail stations.

    DOT National Transportation Integrated Search

    2015-07-01

    High-speed rail (HSR) has emerged as one of the most revolutionary and transformative transportation technologies, having a : profound impact on urban-regional accessibility and inter-city travel across Europe, Japan, and more recently China and othe...

  9. American Airlines Propeller STOL Transport Economic Risk Analysis

    NASA Technical Reports Server (NTRS)

    Ransone, B.

    1972-01-01

    A Monte Carlo risk analysis on the economics of STOL transports in air passenger traffic established the probability of making the expected internal rate of financial return, or better, in a hypothetical regular Washington/New York intercity operation.

  10. Recommended Emergency Preparedness Guidelines for Passenger Trains

    DOT National Transportation Integrated Search

    1993-12-01

    The Federal Railroad Administration (FRA) has recognized the need for intercity and commuter passenger train systems, : regardless of the size of the system and type of service provided, to engage in careful, advance planning in order to : respond ef...

  11. Intercity passenger rail : potential financial issues in the event that Amtrak undergoes liquidation

    DOT National Transportation Integrated Search

    2002-09-01

    If Amtrak had been liquidated on December 31, 2001, secured creditors : and unsecured creditorsincluding the federal government and Amtrak : employeesand stockholders would have had about $44 billion in : potential claims against and ownership ...

  12. Intercity passenger rail : issues associated with a possible Amtrak liquidation

    DOT National Transportation Integrated Search

    1998-03-01

    The National Railroad Passenger Corporation (Amtrak) carries over 20 million : passengers a year through the trains that it operates. It also provides services, : such as dispatching, to state and local commuter rail operators. Since 1971, : Amtrak h...

  13. 75 FR 16562 - High-Speed Intercity Passenger Rail (HSIPR) Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-01

    ...), passenger traffic and services (marketing, ticketing, station, and on- board services), and general... retention, ``green'' environmental outcomes, potential energy savings, and effects on community livability. Program Management Approach--A phased program implementation strategy including a preliminary description...

  14. Passenger train emergency systems : review of egress variables and egress simulation models

    DOT National Transportation Integrated Search

    2013-05-20

    Federal Railroad Administration (FRA) regulations are intended to ensure the safe, timely, and effective evacuation of intercity and commuter rail passengers when necessary during passenger train emergencies. Although it is recognized that during the...

  15. Passenger train emergency systems : review of egress variables and egress simulation models.

    DOT National Transportation Integrated Search

    2013-04-01

    Federal Railroad Administration (FRA) regulations are intended to ensure the safe, timely, and effective evacuation of intercity and commuter rail passengers when necessary during passenger train emergencies. Although it is recognized that during the...

  16. Seattle To Portland Inter-City ITS Corridor Study And Communications Plan, Final Report

    DOT National Transportation Integrated Search

    1996-03-01

    THIS DOCUMENT IS THE FINAL REPORT PRESENTING THE SEATTLE TO PORTLAND INTELLIGENT TRANSPORTATION SYSTEM (ITS) EARLY DEPLOYMENT PLAN. THE FINAL REPORT SYNTHESIZES INFORMATION FROM TECHNICAL MEMORANDUMS 1 THROUGH 5; INCLUDING EXISTING AND FUTURE CONDITI...

  17. The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies

    PubMed Central

    Pant, Kiran; Anderson, Brian; Perdana, Hendrik; Malinowski, Matthew A.; Win, Aye T.; Williams, Mark C.

    2018-01-01

    The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292–296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes. PMID:29634784

  18. Crystal structure of cbbF from Zymomonas mobilis and its functional implication

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

    Hwang, Hyo-Jeong; Park, Suk-Youl; Kim, Jeong-Sun, E-mail: jsunkim@chonnam.ac.kr

    2014-02-28

    Highlights: • The crystal structure of one cbbF from Zymomonas mobilis was revealed. • Scores of residues form two secondary structures with a non-polar protruded residue. • It exists as a dimeric form in solution. - Abstract: A phosphate group at the C1-atom of inositol-monophosphate (IMP) and fructose-1,6-bisphosphate (FBP) is hydrolyzed by a phosphatase IMPase and FBPase in a metal-dependent way, respectively. The two enzymes are almost indiscernible from each other because of their highly similar sequences and structures. Metal ions are bound to residues on the β1- and β2-strands and one mobile loop. However, FBP has another phosphate andmore » FBPases exist as a higher oligomeric state, which may discriminate FBPases from IMPases. There are three genes annotated as FBPases in Zymomonas mobilis, termed also cbbF (ZmcbbF). The revealed crystal structure of one ZmcbbF shows a globular structure formed by five stacked layers. Twenty-five residues in the middle of the sequence form an α-helix and a β-strand, which occupy one side of the catalytic site. A non-polar Leu residue among them is protruded to the active site, pointing out unfavorable access of a bulky charged group to this side. In vitro assays have shown its dimeric form in solution. Interestingly, two β-strands of β1 and β2 are disordered in the ZmcbbF structure. These data indicate that ZmcbbF might structurally belong to IMPase, and imply that its active site would be reorganized in a yet unreported way.« less

  19. Compact piezoelectric tripod manipulator based on a reverse bridge-type amplification mechanism

    NASA Astrophysics Data System (ADS)

    Na, Tae-Won; Choi, Jun-Ho; Jung, Jin-Young; Kim, Hyeong-Geon; Han, Jae-Hung; Park, Kwang-Chun; Oh, Il-Kwon

    2016-09-01

    We report a hierarchical piezoelectric tripod manipulator based on a reverse bridge-type displacement amplifier. The reverse bridge-type amplification mechanism is pre-strained by each piezo-stack actuator up to 60 μm and is cross-stacked in a series arrangement to make a compact and high-stroke manipulator having load-bearing characteristics. The designed manipulator with three degrees of freedom is compact with a height of 56.0 mm, a diameter of 48.6 mm and total weight of 115 g. It achieves a translational stroke of up to 880 μm in heaving motion and a tilting angle of up to 2.0° in rotational motion within the operating voltage and power range of the piezoelectric stack actuator. A key feature of the present design is built-in and pre-strained displacement amplification mechanisms integrated with piezoelectric stacked actuators, resulting in a compact tripod manipulator having exceptionally high stroke and load-bearing capacity.

  20. DNA Photo Lithography with Cinnamate-based Photo-Bio-Nano-Glue

    NASA Astrophysics Data System (ADS)

    Feng, Lang; Li, Minfeng; Romulus, Joy; Sha, Ruojie; Royer, John; Wu, Kun-Ta; Xu, Qin; Seeman, Nadrian; Weck, Marcus; Chaikin, Paul

    2013-03-01

    We present a technique to make patterned functional surfaces, using a cinnamate photo cross-linker and photolithography. We have designed and modified a complementary set of single DNA strands to incorporate a pair of opposing cinnamate molecules. On exposure to 360nm UV, the cinnamate makes a highly specific covalent bond permanently linking only the complementary strands containing the cinnamates. We have studied this specific and efficient crosslinking with cinnamate-containing DNA in solution and on particles. UV addressability allows us to pattern surfaces functionally. The entire surface is coated with a DNA sequence A incorporating cinnamate. DNA strands A'B with one end containing a complementary cinnamated sequence A' attached to another sequence B, are then hybridized to the surface. UV photolithography is used to bind the A'B strand in a specific pattern. The system is heated and the unbound DNA is washed away. The pattern is then observed by thermo-reversibly hybridizing either fluorescently dyed B' strands complementary to B, or colloids coated with B' strands. Our techniques can be used to reversibly and/or permanently bind, via DNA linkers, an assortment of molecules, proteins and nanostructures. Potential applications range from advanced self-assembly, such as templated self-replication schemes recently reported, to designed physical and chemical patterns, to high-resolution multi-functional DNA surfaces for genetic detection or DNA computing.

  1. A hybrid deterministic-probabilistic approach to model the mechanical response of helically arranged hierarchical strands

    NASA Astrophysics Data System (ADS)

    Fraldi, M.; Perrella, G.; Ciervo, M.; Bosia, F.; Pugno, N. M.

    2017-09-01

    Very recently, a Weibull-based probabilistic strategy has been successfully applied to bundles of wires to determine their overall stress-strain behaviour, also capturing previously unpredicted nonlinear and post-elastic features of hierarchical strands. This approach is based on the so-called "Equal Load Sharing (ELS)" hypothesis by virtue of which, when a wire breaks, the load acting on the strand is homogeneously redistributed among the surviving wires. Despite the overall effectiveness of the method, some discrepancies between theoretical predictions and in silico Finite Element-based simulations or experimental findings might arise when more complex structures are analysed, e.g. helically arranged bundles. To overcome these limitations, an enhanced hybrid approach is proposed in which the probability of rupture is combined with a deterministic mechanical model of a strand constituted by helically-arranged and hierarchically-organized wires. The analytical model is validated comparing its predictions with both Finite Element simulations and experimental tests. The results show that generalized stress-strain responses - incorporating tension/torsion coupling - are naturally found and, once one or more elements break, the competition between geometry and mechanics of the strand microstructure, i.e. the different cross sections and helical angles of the wires in the different hierarchical levels of the strand, determines the no longer homogeneous stress redistribution among the surviving wires whose fate is hence governed by a "Hierarchical Load Sharing" criterion.

  2. AIC-based diffraction stacking for local earthquake locations at the Sumatran Fault (Indonesia)

    NASA Astrophysics Data System (ADS)

    Hendriyana, Andri; Bauer, Klaus; Muksin, Umar; Weber, Michael

    2018-05-01

    We present a new workflow for the localization of seismic events which is based on a diffraction stacking approach. In order to address the effects from complex source radiation patterns, we suggest to compute diffraction stacking from a characteristic function (CF) instead of stacking the original waveform data. A new CF, which is called in the following mAIC (modified from Akaike Information Criterion) is proposed. We demonstrate that both P- and S-wave onsets can be detected accurately. To avoid cross-talk between P and S waves due to inaccurate velocity models, we separate the P and S waves from the mAIC function by making use of polarization attributes. Then, the final image function is represented by the largest eigenvalue as a result of the covariance analysis between P- and S-image functions. Results from synthetic experiments show that the proposed diffraction stacking provides reliable results. The workflow of the diffraction stacking method was finally applied to local earthquake data from Sumatra, Indonesia. Recordings from a temporary network of 42 stations deployed for nine months around the Tarutung pull-apart basin were analysed. The seismic event locations resulting from the diffraction stacking method align along a segment of the Sumatran Fault. A more complex distribution of seismicity is imaged within and around the Tarutung basin. Two lineaments striking N-S were found in the centre of the Tarutung basin which support independent results from structural geology.

  3. Study on four polymorphs of bifendate based on X-ray crystallography.

    PubMed

    Nie, Jinju; Yang, Dezhi; Hu, Kun; Lu, Yang

    2016-05-01

    Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C-C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

  4. Walking of antitumor bifunctional trinuclear PtII complex on double-helical DNA

    PubMed Central

    Malina, Jaroslav; Kasparkova, Jana; Farrell, Nicholas P.; Brabec, Viktor

    2011-01-01

    The trinuclear BBR3464 ([{trans-PtCl(NH3)2}2µ-(trans-Pt(NH3)2(H2N(CH2)6NH2)2)]4+) belongs to the polynuclear class of platinum-based anticancer agents. DNA adducts of this complex differ significantly in structure and type from those of clinically used mononuclear platinum complexes, especially, long-range (Pt, Pt) intrastrand and interstrand cross-links are formed in both 5′–5′ and 3′–3′ orientations. We show employing short oligonucleotide duplexes containing single, site-specific cross-links of BBR3464 and gel electrophoresis that in contrast to major DNA adducts of clinically used platinum complexes, under physiological conditions the coordination bonds between platinum and N7 of G residues involved in the cross-links of BBR3464 can be cleaved. This cleavage may lead to the linkage isomerization reactions between this metallodrug and double-helical DNA. Differential scanning calorimetry of duplexes containing single, site-specific cross-links of BBR3464 reveals that one of the driving forces that leads to the lability of DNA cross-links of this metallodrug is a difference between the thermodynamic destabilization induced by the cross-link and by the adduct into which it could isomerize. The rearrangements may proceed in the way that cross-links originally formed in one strand of DNA can spontaneously translocate from one DNA strand to its complementary counterpart, which may evoke walking of the platinum complex on DNA molecule. PMID:20833634

  5. Evaluated activation cross sections of longer-lived radionuclides produced by deuteron-induced reactions on natural copper

    NASA Astrophysics Data System (ADS)

    Takács, S.; Tárkányi, F.; Király, B.; Hermanne, A.; Sonck, M.

    2006-09-01

    Activation cross sections for deuteron-induced reactions on natural copper were measured by using a standard stacked foil technique up to 50 MeV deuteron bombarding energy. Reaction products with half-life longer than half an hour were studied. Experimental elemental cross sections were determined and compared with earlier measured data for 62,63,65Zn, 64Cu, 57,65Ni, 57,58,60Co and 59Fe isotopes.

  6. Reducing the harm in rail crashes : analysis of injury mechanisms and mitigation strategies

    DOT National Transportation Integrated Search

    2016-04-12

    Twenty-three commuter and inter-city passenger train : accidents, which occurred over the past twenty years, have been : analyzed. The analysis has assessed the potential effectiveness : of various injury mitigation strategies. The strategies with th...

  7. Energy and Economic Impacts of Projected Freight Transportation Improvements

    DOT National Transportation Integrated Search

    1977-05-01

    This study examines current and future energy impacts for each major freight mode, by commodity, and, in many cases, by vehicle types. It also discusses potential economic impacts of these anticipated changes. The study is limited to intercity freigh...

  8. Fire Safety of Passenger Trains: A Review of U.S. and Foreign Approaches

    DOT National Transportation Integrated Search

    1993-12-01

    could develop into potentially life-threatening events. Fire safety is an area of particular interest for both : conventional intercity and commuter trains, as well as new alternative high-speed train technologies. These : technologies include steel-...

  9. Iowa rail route alternatives analysis.

    DOT National Transportation Integrated Search

    1998-06-01

    The development of new rail systems in the first part of the 21st century is the result of a wide range : of trends that are making it increasingly difficult to maintain regional mobility using the two : dominant intercity travel modes, auto and air....

  10. Genetic recombination induced by DNA double-strand break in bacteriophage T4: nature of the left/right bias.

    PubMed

    Shcherbakov, Victor P; Shcherbakova, Tamara; Plugina, Lidiya; Sizova, Svetlana; Kudryashova, Elena; Granovsky, Igor

    2008-06-01

    The experimental system combining double-strand breaks (DSBs), produced site-specifically by SegC endonuclease, with the famous advantages of the bacteriophage T4 rII mutant recombination analysis was used here to elucidate the origin of the recombination bias on two sides of the DSB, especially pronounced in gene 39 (topoisomerase II) and gene 59 (41-helicase loader) mutants. Three sources were found to contribute to the bias: (1) the SegC endonuclease may remain bound to the end of the broken DNA and thus protect it from exonuclease degradation; (2) in heteroduplex heterozygotes (HHs), arising as the recombinant products in the left-hand crosses, the transcribed strands are of rII mutant phenotype, so they, in contrast to the right-hand HHs, do not produce plaques on the lawn of the lambda-lysogenic host; and (3) the intrinsic polarity of T4 chromosome, reflected in transcription, may be a cause for discrimination of promoter-proximal and promoter-distal DNA sequences. It is shown that the apparent recombination bias does not imply one-sidedness of the DSB repair but just reflects a different depth of the end processing. It is inferred that the cause, underlying the "intrinsic" bias, might be interference between strand exchange and transcription. Topoisomerase and helicase functions are necessary to turn the process in favor of strand exchange. The idea is substantiated that the double-stranded to single-stranded DNA transition edge (not ss-DNA tip) serves as an actual recombinogenic element.

  11. Characterization of the human SNM1A and SNM1B/Apollo DNA repair exonucleases.

    PubMed

    Sengerová, Blanka; Allerston, Charles K; Abu, Mika; Lee, Sook Y; Hartley, Janet; Kiakos, Konstantinos; Schofield, Christopher J; Hartley, John A; Gileadi, Opher; McHugh, Peter J

    2012-07-27

    Human SNM1A and SNM1B/Apollo have both been implicated in the repair of DNA interstrand cross-links (ICLs) by cellular studies, and SNM1B is also required for telomere protection. Here, we describe studies on the biochemical characterization of the SNM1A and SNM1B proteins. The results reveal some fundamental differences in the mechanisms of the two proteins. Both SNM1A and SNM1B digest double-stranded and single-stranded DNA with a 5'-to-3' directionality in a reaction that is stimulated by divalent cations, and both nucleases are inhibited by the zinc chelator o-phenanthroline. We find that SNM1A has greater affinity for single-stranded DNA over double-stranded DNA that is not observed with SNM1B. Although both proteins demonstrate a low level of processivity on low molecular weight DNA oligonucleotide substrates, when presented with high molecular weight DNA, SNM1A alone is rendered much more active, being capable of digesting kilobase-long stretches of DNA. Both proteins can digest past ICLs induced by the non-distorting minor groove cross-linking agent SJG-136, albeit with SNM1A showing a greater capacity to achieve this. This is consistent with the proposal that SNM1A and SNM1B might exhibit some redundancy in ICL repair. Together, our work establishes differences in the substrate selectivities of SNM1A and SNM1B that are likely to be relevant to their in vivo roles and which might be exploited in the development of selective inhibitors.

  12. Stacked Star Formation Rate Profiles of Bursty Galaxies Exhibit “Coherent” Star Formation

    NASA Astrophysics Data System (ADS)

    Orr, Matthew E.; Hayward, Christopher C.; Nelson, Erica J.; Hopkins, Philip F.; Faucher-Giguère, Claude-André; Kereš, Dušan; Chan, T. K.; Schmitz, Denise M.; Miller, Tim B.

    2017-11-01

    In a recent work based on 3200 stacked Hα maps of galaxies at z˜ 1, Nelson et al. find evidence for “coherent star formation”: the stacked star formation rate (SFR) profiles of galaxies above (below) the “star formation main sequence” (MS) are above (below) that of galaxies on the MS at all radii. One might interpret this result as inconsistent with highly bursty star formation and evidence that galaxies evolve smoothly along the MS rather than crossing it many times. We analyze six simulated galaxies at z˜ 1 from the Feedback in Realistic Environments (FIRE) project in a manner analogous to the observations to test whether the above interpretations are correct. The trends in stacked SFR profiles are qualitatively consistent with those observed. However, SFR profiles of individual galaxies are much more complex than the stacked profiles: the former can be flat or even peak at large radii because of the highly clustered nature of star formation in the simulations. Moreover, the SFR profiles of individual galaxies above (below) the MS are not systematically above (below) those of MS galaxies at all radii. We conclude that the time-averaged coherent star formation evident stacks of observed galaxies is consistent with highly bursty, clumpy star formation of individual galaxies and is not evidence that galaxies evolve smoothly along the MS.

  13. Sub-barrier radioactive ion beam investigations using a new methodology and analysis for the stacked target technique

    NASA Astrophysics Data System (ADS)

    Fisichella, M.; Shotter, A. C.; Di Pietro, A.; Figuera, P.; Lattuada, M.; Marchetta, C.; Privitera, V.; Romano, L.; Ruiz, C.; Zadro, M.

    2015-12-01

    For low energy reaction studies involving radioactive ion beams, the experimental reaction yields are generally small due to the low intensity of the beams. For this reason, the stacked target technique has been often used to measure excitation functions. This technique offers considerable advantages since the reaction cross-section at several energies can be simultaneously measured. In a further effort to increase yields, thick targets are also employed. The main disadvantage of the method is the degradation of the beam quality as it passes through the stack due to the statistical nature of energy loss processes and any nonuniformity of the stacked targets. This degradation can lead to ambiguities of associating effective beam energies to reaction product yields for the targets within the stack and, as a consequence, to an error in the determination of the excitation function for the reaction under study. A thorough investigation of these ambiguities is reported, and a best practice procedure of analyzing data obtained using the stacked target technique with radioactive ion beams is recommended. Using this procedure a re-evaluation is reported of some previously published sub-barrier fusion data in order to demonstrate the possibility of misinterpretations of derived excitation functions. In addition, this best practice procedure has been used to evaluate, from a new data set, the sub-barrier fusion excitation function for the reaction 6Li+120Sn .

  14. Pressurized Testing of Solid Oxide Electrolysis Stacks with Advanced Electrode-Supported Cells

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

    J. E. O'Brien; X. Zhang; G. K. Housley

    2012-06-01

    A new facility has been developed at the Idaho National Laboratory for pressurized testing of solid oxide electrolysis stacks. Pressurized operation is envisioned for large-scale hydrogen production plants, yielding higher overall efficiencies when the hydrogen product is to be delivered at elevated pressure for tank storage or pipelines. Pressurized operation also supports higher mass flow rates of the process gases with smaller components. The test stand can accommodate cell dimensions up to 8.5 cm x 8.5 cm and stacks of up to 25 cells. The pressure boundary for these tests is a water-cooled spool-piece pressure vessel designed for operation upmore » to 5 MPa. The stack is internally manifolded and operates in cross-flow with an inverted-U flow pattern. Feed-throughs for gas inlets/outlets, power, and instrumentation are all located in the bottom flange. The entire spool piece, with the exception of the bottom flange, can be lifted to allow access to the internal furnace and test fixture. Lifting is accomplished with a motorized threaded drive mechanism attached to a rigid structural frame. Stack mechanical compression is accomplished using springs that are located inside of the pressure boundary, but outside of the hot zone. Initial stack heatup and performance characterization occurs at ambient pressure followed by lowering and sealing of the pressure vessel and subsequent pressurization. Pressure equalization between the anode and cathode sides of the cells and the stack surroundings is ensured by combining all of the process gases downstream of the stack. Steady pressure is maintained by means of a backpressure regulator and a digital pressure controller. A full description of the pressurized test apparatus is provided in this paper.« less

  15. 47 CFR 74.582 - Station identification.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Station identification. 74.582 Section 74.582..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Aural Broadcast Auxiliary Stations § 74.582 Station identification. (a) Each aural broadcast STL or intercity relay station, when...

  16. Investigation of material improvements to mitigate the abrasive wear mechanism of concrete crosstie rail seat deterioration (RSD).

    DOT National Transportation Integrated Search

    2014-11-01

    To meet the increasingly stringent design and performance requirements due to increasing cumulative : gross tonnages from heavy-haul freight operations, along with increased high-speed inter-city passenger : rail development, improvements in concrete...

  17. 36 CFR Appendix F to Part 1191 - Modifications Adopted by the Department of Transportation

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... negotiate steps may have to travel compared to the general public. Modification to 406 of Appendix D 406... shall be 8 inches (205 mm) minimum above top of rail. In light rail, commuter rail, and intercity rail...

  18. 49 CFR Appendix A to Part 37 - Modifications to Standards for Accessible Transportation Facilities

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... steps may have to travel compared to the general public. 406.8—Modification to 406 of Appendix D to 36... rail, commuter rail, and intercity rail systems where it is not operationally or structurally feasible...

  19. A structural survey of classes of vehicles for crashworthiness : final report.

    DOT National Transportation Integrated Search

    1978-02-01

    This document reviews three phases of a study conducted to evaluate and improve the crashworthiness of passenger carrying vehicles in intercity service. Phase I surveyed the accident data over a period 1966 to 1973 and identified those areas responsi...

  20. Intercity passenger rail : Amtrak's progress in improving its financial condition has been mixed

    DOT National Transportation Integrated Search

    1999-07-01

    Since its creation in 1971, Amtrak has accumulated massive financial losses, with recent losses averaging more than $800 million per year. To help Amtrak sustain operations and make needed capital investments, the federal government has provided Amtr...

  1. 76 FR 14443 - High-Speed Intercity Passenger Rail (HSIPR) Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-16

    ... Environmental Policy Act (NEPA) documentation, final design (FD), and construction. For the purpose of this... designing, engineering, location surveying, mapping, environmental studies, and acquiring rights-of-way..., final design, and construction activities are eligible to receive funding. For applications for Service...

  2. Chicago to Iowa City intercity passenger rail route : business plan.

    DOT National Transportation Integrated Search

    2011-03-21

    This business plan describes the methods by which the Iowa Department of Transportation (DOT will partner with Iowa counties and cities to fund Iowas share of the operating and maintenance cost for the Chicago-Iowa City passenger-rail service, an ...

  3. Research in Brief.

    ERIC Educational Resources Information Center

    Journalism Quarterly, 1985

    1985-01-01

    Presents summaries of research dealing with (1) news coverage of Africa, (2) diffusion of information about cyanide-laced Tylenol, (3) gender representation in elite newspapers, (4) agreement between reporters and editors in Mississippi, (5) monopoly metropolitan dailies and intercity competition, and (6) the effect of endorsements on the…

  4. Prediction and Control of Noise and Vibration in Rail Transit Systems

    DOT National Transportation Integrated Search

    1978-09-01

    The purpose of this report is to present a balanced introductory view of noise from rail transportation systems and its control, and to provide references to more specialized material. The emphasis is on urban transit systems. However, data on interc...

  5. Biodiesel intercity passenger rail revenue service test.

    DOT National Transportation Integrated Search

    2013-10-01

    Amtrak, with the support of the Federal Railroad Administration, operated a P-32 passenger locomotive in revenue service for a : period of 12 months, on a blend of 20 percent pure biodiesel and 80 percent #2 ultra-low sulfur diesel (ULSD) fuel. The G...

  6. The role of stable isotopes in understanding rainfall interception processes: a review

    EPA Science Inventory

    The isotopic composition of water transmitted by the canopy as throughfall or stemflow reflects important hydrologic processes occurring in the canopy. A synthesis of the literature shows that complex spatiotemporal variations of isotopic composition are created by canopy interce...

  7. Joint Cost, Production Technology and Output Disaggregation in Regulated Motor Carriers

    DOT National Transportation Integrated Search

    1978-11-01

    The study uses a sample of 252 Class I Instruction 27 Motor Carriers (Instruction 27 carriers earned at least 75 percent of their revenues from intercity transportation of general commodities over a three year period) of general freight that existed ...

  8. Impact of Personal Attitudes on Propensity to Use Autonomous Vehicles for Intercity Travel.

    DOT National Transportation Integrated Search

    2016-01-01

    The autonomous vehicles are about to become a reality. The researchers estimate the benefits from each autonomous vehicle to be between $2000 and $4500 per vehicles. The : societal benefits include higher travel time savings, reduced congestion, fuel...

  9. Making connections : intermodal links between scheduled passenger ferries and other public transportation modes

    DOT National Transportation Integrated Search

    2009-02-01

    Just over 40 percent of U.S. passenger ferry terminals : offer connections to other scheduled public transportation : modes. That makes ferries less connected than intercity : rail, where 53 percent of stations have links with other : modes, but more...

  10. Cell wall peptidoglycan architecture in Bacillus subtilis

    PubMed Central

    Hayhurst, Emma J.; Kailas, Lekshmi; Hobbs, Jamie K.; Foster, Simon J.

    2008-01-01

    The bacterial cell wall is essential for viability and shape determination. Cell wall structural dynamics allowing growth and division, while maintaining integrity is a basic problem governing the life of bacteria. The polymer peptidoglycan is the main structural component for most bacteria and is made up of glycan strands that are cross-linked by peptide side chains. Despite study and speculation over many years, peptidoglycan architecture has remained largely elusive. Here, we show that the model rod-shaped bacterium Bacillus subtilis has glycan strands up to 5 μm, longer than the cell itself and 50 times longer than previously proposed. Atomic force microscopy revealed the glycan strands to be part of a peptidoglycan architecture allowing cell growth and division. The inner surface of the cell wall has a regular macrostructure with ≈50 nm-wide peptidoglycan cables [average 53 ± 12 nm (n = 91)] running basically across the short axis of the cell. Cross striations with an average periodicity of 25 ± 9 nm (n = 96) along each cable are also present. The fundamental cabling architecture is also maintained during septal development as part of cell division. We propose a coiled-coil model for peptidoglycan architecture encompassing our data and recent evidence concerning the biosynthetic machinery for this essential polymer. PMID:18784364

  11. Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.

    PubMed

    Gumbart, James C; Beeby, Morgan; Jensen, Grant J; Roux, Benoît

    2014-02-01

    Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.

  12. Mlh1-Mlh3, a Meiotic Crossover and DNA Mismatch Repair Factor, Is a Msh2-Msh3-stimulated Endonuclease*

    PubMed Central

    Rogacheva, Maria V.; Manhart, Carol M.; Chen, Cheng; Guarne, Alba; Surtees, Jennifer; Alani, Eric

    2014-01-01

    Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair. PMID:24403070

  13. Mlh1-Mlh3, a meiotic crossover and DNA mismatch repair factor, is a Msh2-Msh3-stimulated endonuclease.

    PubMed

    Rogacheva, Maria V; Manhart, Carol M; Chen, Cheng; Guarne, Alba; Surtees, Jennifer; Alani, Eric

    2014-02-28

    Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair.

  14. Human Cell Assays for Synthesis-Dependent Strand Annealing and Crossing over During Double-Strand Break Repair.

    PubMed

    Zapotoczny, Grzegorz; Sekelsky, Jeff

    2017-04-03

    DNA double-strand breaks (DSBs) are one of the most deleterious types of lesions to the genome. Synthesis-dependent strand annealing (SDSA) is thought to be a major pathway of DSB repair, but direct tests of this model have only been conducted in budding yeast and Drosophila To better understand this pathway, we developed an SDSA assay for use in human cells. Our results support the hypothesis that SDSA is an important DSB repair mechanism in human cells. We used siRNA knockdown to assess the roles of a number of helicases suggested to promote SDSA. None of the helicase knockdowns reduced SDSA, but knocking down BLM or RTEL1 increased SDSA. Molecular analysis of repair products suggests that these helicases may prevent long-tract repair synthesis. Since the major alternative to SDSA (repair involving a double-Holliday junction intermediate) can lead to crossovers, we also developed a fluorescent assay that detects crossovers generated during DSB repair. Together, these assays will be useful in investigating features and mechanisms of SDSA and crossover pathways in human cells. Copyright © 2017 Zapotoczny and Sekelsky.

  15. Human Cell Assays for Synthesis-Dependent Strand Annealing and Crossing over During Double-Strand Break Repair

    PubMed Central

    Zapotoczny, Grzegorz; Sekelsky, Jeff

    2017-01-01

    DNA double-strand breaks (DSBs) are one of the most deleterious types of lesions to the genome. Synthesis-dependent strand annealing (SDSA) is thought to be a major pathway of DSB repair, but direct tests of this model have only been conducted in budding yeast and Drosophila. To better understand this pathway, we developed an SDSA assay for use in human cells. Our results support the hypothesis that SDSA is an important DSB repair mechanism in human cells. We used siRNA knockdown to assess the roles of a number of helicases suggested to promote SDSA. None of the helicase knockdowns reduced SDSA, but knocking down BLM or RTEL1 increased SDSA. Molecular analysis of repair products suggests that these helicases may prevent long-tract repair synthesis. Since the major alternative to SDSA (repair involving a double-Holliday junction intermediate) can lead to crossovers, we also developed a fluorescent assay that detects crossovers generated during DSB repair. Together, these assays will be useful in investigating features and mechanisms of SDSA and crossover pathways in human cells. PMID:28179392

  16. Lack of close relationship between three strains of human rhinoviruses as determined by their RNA sequences.

    PubMed

    Yin, F H; Lonberg-Holm, K; Chan, S P

    1973-07-01

    The possible genomic homologies between three serotypes of human rhinoviruses (HRV 1A, HRV 2, and HRV 14) were investigated. First we confirmed that these viruses were unrelated by the criterion of the absence of common antigenic determinants on the surfaces of the native virions, as detected by cross-neutralization of complementfixation. RNA-RNA hybridization was then examined with purified, highly radioactive, double-stranded, replicative-form RNA and excess single-stranded virion RNA. Single-stranded RNA showed 100% homology with the minus strand from the replicative-form RNA of the same type of virus. HRV 1A, HRV 2, and HRV 14 showed low intertypic homologies; these were not significantly greater than those found between the rhinoviruses and polivirus, which were used as a negative control. The immunological relationship and the RNA homology between HRV 1A and HRV 1B were also examined by the above techniques. It was confirmed that HRV 1A and HRV 1B share some surface determinants and it was also found that HRV 1B RNA shares 70% homology with HRV 1A RNA.

  17. Evaluating neighborhood structures for modeling intercity diffusion of large-scale dengue epidemics.

    PubMed

    Wen, Tzai-Hung; Hsu, Ching-Shun; Hu, Ming-Che

    2018-05-03

    Dengue fever is a vector-borne infectious disease that is transmitted by contact between vector mosquitoes and susceptible hosts. The literature has addressed the issue on quantifying the effect of individual mobility on dengue transmission. However, there are methodological concerns in the spatial regression model configuration for examining the effect of intercity-scale human mobility on dengue diffusion. The purposes of the study are to investigate the influence of neighborhood structures on intercity epidemic progression from pre-epidemic to epidemic periods and to compare definitions of different neighborhood structures for interpreting the spread of dengue epidemics. We proposed a framework for assessing the effect of model configurations on dengue incidence in 2014 and 2015, which were the most severe outbreaks in 70 years in Taiwan. Compared with the conventional model configuration in spatial regression analysis, our proposed model used a radiation model, which reflects population flow between townships, as a spatial weight to capture the structure of human mobility. The results of our model demonstrate better model fitting performance, indicating that the structure of human mobility has better explanatory power in dengue diffusion than the geometric structure of administration boundaries and geographic distance between centroids of cities. We also identified spatial-temporal hierarchy of dengue diffusion: dengue incidence would be influenced by its immediate neighboring townships during pre-epidemic and epidemic periods, and also with more distant neighbors (based on mobility) in pre-epidemic periods. Our findings suggest that the structure of population mobility could more reasonably capture urban-to-urban interactions, which implies that the hub cities could be a "bridge" for large-scale transmission and make townships that immediately connect to hub cities more vulnerable to dengue epidemics.

  18. Annoyance caused by the sounds of a magnetic levitation train

    NASA Astrophysics Data System (ADS)

    Vos, Joos

    2004-04-01

    In a laboratory study, the annoyance caused by the passby sounds from a magnetic levitation (maglev) train was investigated. The listeners were presented with various sound fragments. The task of the listeners was to respond after each presentation to the question: ``How annoying would you find the sound in the preceding period if you were exposed to it at home on a regular basis?'' The independent variables were (a) the driving speed of the maglev train (varying from 100 to 400 km/h), (b) the outdoor A-weighted sound exposure level (ASEL) of the passbys (varying from 65 to 90 dB), and (c) the simulated outdoor-to-indoor reduction in sound level (windows open or windows closed). As references to the passby sounds from the maglev train (type Transrapid 08), sounds from road traffic (passenger cars and trucks) and more conventional railway (intercity trains) were included for rating also. Four important results were obtained. Provided that the outdoor ASELs were the same, (1) the annoyance was independent of the driving speed of the maglev train, (2) the annoyance caused by the maglev train was considerably higher than that caused by the intercity train, (3) the annoyance caused by the maglev train was hardly different from that caused by road traffic, and (4) the results (1)-(3) held true both for open or closed windows. On the basis of the present results, it might be expected that the sounds are equally annoying if the ASELs of the maglev-train passbys are at least 5 dB lower than those of the intercity train passbys. Consequently, the results of the present experiment do not support application of a railway bonus to the maglev-train sounds.

  19. Annoyance caused by the sounds of a magnetic levitation train.

    PubMed

    Vos, Joos

    2004-04-01

    In a laboratory study, the annoyance caused by the passby sounds from a magnetic levitation (maglev) train was investigated. The listeners were presented with various sound fragments. The task of the listeners was to respond after each presentation to the question: "How annoying would you find the sound in the preceding period if you were exposed to it at home on a regular basis?" The independent variables were (a) the driving speed of the maglev train (varying from 100 to 400 km/h), (b) the outdoor A-weighted sound exposure level (ASEL) of the passbys (varying from 65 to 90 dB), and (c) the simulated outdoor-to-indoor reduction in sound level (windows open or windows closed). As references to the passby sounds from the maglev train (type Transrapid 08), sounds from road traffic (passenger cars and trucks) and more conventional railway (intercity trains) were included for rating also. Four important results were obtained. Provided that the outdoor ASELs were the same, (1) the annoyance was independent of the driving speed of the maglev train, (2) the annoyance caused by the maglev train was considerably higher than that caused by the intercity train, (3) the annoyance caused by the maglev train was hardly different from that caused by road traffic, and (4) the results (1)-(3) held true both for open or closed windows. On the basis of the present results, it might be expected that the sounds are equally annoying if the ASELs of the maglev-train passbys are at least 5 dB lower than those of the intercity train passbys. Consequently, the results of the present experiment do not support application of a railway bonus to the maglev-train sounds.

  20. Winding Pack Height Management During Fabrication of the ITER CS Module

    NASA Astrophysics Data System (ADS)

    Martovetsky, Nicolai N.; Irick, David K.; Reed, Richard P.; Haefelfinger, Rolf; Salazar, Erica

    The Central Solenoid (CS) stack consists of six modules, 2.1 m tall each [1]. In order to verify good impregnation, we performed a vacuum pressure impregnation (VPI) test of a full cross section of the CS module (CSM), 40 conductors tall and 14 conductors wide [2]. It was discovered that after preparation of the full cross section stack until completion of the VPI, the stack shrunk in height by 20-25 mm. Our study of the literature and discussions with the leading experts in VPI did not reveal obvious reasons for this change of height, so we launched a study to address this issue. We assembled two 12x1 (tall by wide) arrays and several 7x1 arrays in order to study characteristics of the dry winding pack under compressive force and effects of different fabrication steps. Then we impregnated these arrays in different conditions under compressive force and studied change of height as a result of compression, impregnation, gelling and curing of the stack of insulated conductors. We showed that by controlling the application of the compressive force, before closing the mold and during impregnation, one can reduce the height uncertainty. Most of the height reduction takes place while the glass is dry under the dead weight and the applied compressive force. Reduction of height during injection of the resin and during gelling, curing and cooling of the coil is noticeable, reproducible and relatively small. The paper presents results of our studies and recommendations for assembly and VPI of tall windings.

  1. Adhesion promoters for large scale fabrication of dielectric elastomer stack transducers (DESTs) made of pre-fabricated dielectric films

    NASA Astrophysics Data System (ADS)

    Grotepaß, T.; Förster-Zügel, F.; Mößinger, H.; Schlaak, H. F.

    2015-04-01

    Multilayer dielectric elastomer stack transducers (DESTs) are a promising new transducer technology with many applications in different industry sectors, like medical devices, human-machine-interaction, etc. Stacked dielectric elastomer transducers show larger thickness contraction driven by lower voltages than transducers made from a single dielectric layer. Traditionally multilayered DESTs are produced by repeatedly cross-linking a liquid elastomeric pre-polymer into the required shape. Our recent research focusses on a novel fabrication method for large scale stack transducers with a surface area over 200 x 300 mm by processing pre-fabricated elastomeric thin films of less than 50 μm thicknesses. The thin films are provided as two- or three-layer composites, where the elastomer is sandwiched between one or two sacrificial liners. Separating the elastomeric film from the residual layers and assembling them into dielectric elastomer stack transducers poses many challenges concerning adhesion, since the dielectric film merely separates from the liner if the adhesive forces between them are overcome. Conversely, during the assembly of a dielectric elastomer stack transducer, adhesive forces have to be established between two elastomeric layers or between the dielectric and the electrode layer. The very low Young's modulus of at least one adhesion partner requires suitable means of increasing the adhesive forces between the different adhesive layers of a dielectric elastomer stack transducer to prevent a delamination of the transducer during its lifetime. This work evaluates different surface activation treatments - corona, low-pressure plasma and UV-light - and their applicability in the production of large scale DESTs made from pre-fabricated elastomeric films.

  2. Evaluation of Land Use Regression Models for Nitrogen Dioxide and Benzene in Four US Cities

    PubMed Central

    Mukerjee, Shaibal; Smith, Luther; Neas, Lucas; Norris, Gary

    2012-01-01

    Spatial analysis studies have included the application of land use regression models (LURs) for health and air quality assessments. Recent LUR studies have collected nitrogen dioxide (NO2) and volatile organic compounds (VOCs) using passive samplers at urban air monitoring networks in El Paso and Dallas, TX, Detroit, MI, and Cleveland, OH to assess spatial variability and source influences. LURs were successfully developed to estimate pollutant concentrations throughout the study areas. Comparisons of development and predictive capabilities of LURs from these four cities are presented to address this issue of uniform application of LURs across study areas. Traffic and other urban variables were important predictors in the LURs although city-specific influences (such as border crossings) were also important. In addition, transferability of variables or LURs from one city to another may be problematic due to intercity differences and data availability or comparability. Thus, developing common predictors in future LURs may be difficult. PMID:23226985

  3. Genetic engineering combined with deep UV resonance Raman spectroscopy for structural characterization of amyloid-like fibrils.

    PubMed

    Sikirzhytski, Vitali; Topilina, Natalya I; Higashiya, Seiichiro; Welch, John T; Lednev, Igor K

    2008-05-07

    Elucidating the structure of the cross-beta core in large amyloid fibrils is a challenging problem in modern structural biology. For the first time, a set of de novo polypeptides was genetically engineered to form amyloid-like fibrils with similar morphology and yet different strand length. Differential ultraviolet Raman spectroscopy allowed for separation of the spectroscopic signatures of the highly ordered beta-sheet strands and turns of the fibril core. The relationship between Raman frequencies and Ramachandran dihedral angles of the polypeptide backbone indicates the nature of the beta-sheet and turn structural elements.

  4. Cell module and fuel conditioner

    NASA Technical Reports Server (NTRS)

    Hoover, D. Q., Jr.

    1980-01-01

    Stack tests indicate that the discrepancies between calculated and measured temperature profiles are due to reactant cross-over and a lower than expected thermal conductivity of cells. Preliminary results indicate that acceptable contact resistance between cooling plane halves can be achieved without the use of paper. The preliminary design of the enclosure, definition of required labor and equipment for manufacturing repeating components, and the assembly procedures for the benchwork design were developed. Fabrication of components for a second 5-cell stack of the MK-2 design and a second 23-cell stack of the MK-1 design was started. The definition of water and fuel for the reforming subsystem was developed along with a preliminary definition of the control system for the subsystem. The construction and shakedown of the differential catalytic reactor was completed and testing of the first catalyst initiated.

  5. 8. VIEW OF VESSEL, SHOWING PORT SIDEPADDLE, SIDE LOCKER (USED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. VIEW OF VESSEL, SHOWING PORT SIDE-PADDLE, SIDE LOCKER (USED FOR TOILET AND STORAGE DURING ATLANTIC CROSSING), MAINMAST, WHEELHOUSE AND STACK - Steam Tug EPPLETON HALL, Hyde Street Pier, San Francisco, San Francisco County, CA

  6. Cross-stacked carbon nanotubes assisted self-separation of free-standing GaN substrates by hydride vapor phase epitaxy

    NASA Astrophysics Data System (ADS)

    Wei, Tongbo; Yang, Jiankun; Wei, Yang; Huo, Ziqiang; Ji, Xiaoli; Zhang, Yun; Wang, Junxi; Li, Jinmin; Fan, Shoushan

    2016-06-01

    We report a novel method to fabricate high quality 2-inch freestanding GaN substrate grown on cross-stacked carbon nanotubes (CSCNTs) coated sapphire by hydride vapor phase epitaxy (HVPE). As nanoscale masks, these CSCNTs can help weaken the interface connection and release the compressive stress by forming voids during fast coalescence and also block the propagation of threading dislocations (TDs). During the cool-down process, thermal stress-induced cracks are initiated at the CSCNTs interface with the help of air voids and propagated all over the films which leads to full self-separation of FS-GaN substrate. Raman and photoluminescence spectra further reveal the stress relief and crystalline improvement of GaN with CSCNTs. It is expected that the efficient, low cost and mass-producible technique may enable new applications for CNTs in nitride optoelectronic fields.

  7. Production of medically useful bromine isotopes via alpha-particle induced nuclear reactions

    NASA Astrophysics Data System (ADS)

    Breunig, Katharina; Scholten, Bernhard; Spahn, Ingo; Hermanne, Alex; Spellerberg, Stefan; Coenen, Heinz H.; Neumaier, Bernd

    2017-09-01

    The cross sections of α-particle induced reactions on arsenic leading to the formation of 76,77,78Br were measured from their respective thresholds up to 37 MeV. Thin sediments of elemental arsenic powder were irradiated together with Al degrader and Cu monitor foils using the established stacked-foil technique. For determination of the effective α-particle energies and of the effective beam current through the stacks the cross-section ratios of the monitor nuclides 67Ga/66Ga were used. This should help resolve discrepancies in existing literature data. Comparison of the data with the available excitation functions shows some slight energy shifts as well as some differences in curve shapes. The calculated thick target yields indicate, that 77Br can be produced in the energy range Eα = 25 → 17 MeV free of isotopic impurities in quantities sufficient for medical application.

  8. Efficient fabrication of carbon nanotube micro tip arrays by tailoring cross-stacked carbon nanotube sheets.

    PubMed

    Wei, Yang; Liu, Peng; Zhu, Feng; Jiang, Kaili; Li, Qunqing; Fan, Shoushan

    2012-04-11

    Carbon nanotube (CNT) micro tip arrays with hairpin structures on patterned silicon wafers were efficiently fabricated by tailoring the cross-stacked CNT sheet with laser. A blade-like structure was formed at the laser-cut edges of the CNT sheet. CNT field emitters, pulled out from the end of the hairpin by an adhesive tape, can provide 150 μA intrinsic emission currents with low beam noise. The nice field emission is ascribed to the Joule-heating-induced desorption of the emitter surface by the hairpin structure, the high temperature annealing effect, and the surface morphology. The CNT emitters with hairpin structures will greatly promote the applications of CNTs in vacuum electronic devices and hold the promises to be used as the hot tips for thermochemical nanolithography. More CNT-based structures and devices can be fabricated on a large scale by this versatile method. © 2012 American Chemical Society

  9. Cross-stacked carbon nanotubes assisted self-separation of free-standing GaN substrates by hydride vapor phase epitaxy.

    PubMed

    Wei, Tongbo; Yang, Jiankun; Wei, Yang; Huo, Ziqiang; Ji, Xiaoli; Zhang, Yun; Wang, Junxi; Li, Jinmin; Fan, Shoushan

    2016-06-24

    We report a novel method to fabricate high quality 2-inch freestanding GaN substrate grown on cross-stacked carbon nanotubes (CSCNTs) coated sapphire by hydride vapor phase epitaxy (HVPE). As nanoscale masks, these CSCNTs can help weaken the interface connection and release the compressive stress by forming voids during fast coalescence and also block the propagation of threading dislocations (TDs). During the cool-down process, thermal stress-induced cracks are initiated at the CSCNTs interface with the help of air voids and propagated all over the films which leads to full self-separation of FS-GaN substrate. Raman and photoluminescence spectra further reveal the stress relief and crystalline improvement of GaN with CSCNTs. It is expected that the efficient, low cost and mass-producible technique may enable new applications for CNTs in nitride optoelectronic fields.

  10. Cross-stacked carbon nanotubes assisted self-separation of free-standing GaN substrates by hydride vapor phase epitaxy

    PubMed Central

    Wei, Tongbo; Yang, Jiankun; Wei, Yang; Huo, Ziqiang; Ji, Xiaoli; Zhang, Yun; Wang, Junxi; Li, Jinmin; Fan, Shoushan

    2016-01-01

    We report a novel method to fabricate high quality 2-inch freestanding GaN substrate grown on cross-stacked carbon nanotubes (CSCNTs) coated sapphire by hydride vapor phase epitaxy (HVPE). As nanoscale masks, these CSCNTs can help weaken the interface connection and release the compressive stress by forming voids during fast coalescence and also block the propagation of threading dislocations (TDs). During the cool-down process, thermal stress-induced cracks are initiated at the CSCNTs interface with the help of air voids and propagated all over the films which leads to full self-separation of FS-GaN substrate. Raman and photoluminescence spectra further reveal the stress relief and crystalline improvement of GaN with CSCNTs. It is expected that the efficient, low cost and mass-producible technique may enable new applications for CNTs in nitride optoelectronic fields. PMID:27340030

  11. Intercity passenger rail : increasing Amtrak's accountability for its Taxpayer Relief Act funds

    DOT National Transportation Integrated Search

    2000-03-15

    Since 1971, the federal government has provided the National Railroad Passenger Corporation (Amtrak) with $23 billion in financial support. This support includes a total of about $2.2 billion in 1998 and 1999 through the Taxpayer Relief Act of 1997 (...

  12. Intercity passenger rail : Amtrak will continue to have difficulty controlling its costs and meeting capital needs

    DOT National Transportation Integrated Search

    2000-05-01

    This report responds to the request to review Amtrak's costs and capital investment needs. In particular, this report discusses changes since 1995 in Amtrak's operating costs, including labor costs, payments to freight railroads to access their track...

  13. 49 CFR 37.21 - Applicability: General.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...: (1) Any public entity that provides designated public transportation or intercity or commuter rail transportation; (2) Any private entity that provides specified public transportation; and (3) Any private entity... 49 Transportation 1 2010-10-01 2010-10-01 false Applicability: General. 37.21 Section 37.21...

  14. 49 CFR 256.13 - Review and approval of applications.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... local public and private investment, by transportation carriers and others, in improved intercity and local public transportation facilities and services; (7) Encourage the preservation of railroad... 49 Transportation 4 2010-10-01 2010-10-01 false Review and approval of applications. 256.13...

  15. Ports of Delaware Bay: Industry And Public Sector Cooperation For Information Sharing

    DTIC Science & Technology

    2010-12-01

    Introduction MIST Fall 2010 high-density tunnels, stations, and bridges. Another $20 million was provided for intercity ...passenger rail to protect infrastructure and the traveling public.12 This commitment of funds at a time of shrinking budgets demonstrates the essential

  16. Development of techniques and data for evaluating ride quality. Volume 2 : ride-quality research

    DOT National Transportation Integrated Search

    1978-03-01

    Ride-quality models for city buses and intercity trains are presented : and discussed in terms of their ability to predict passenger : comfort and ride acceptability. : This, the second of three volumes, contains a technical discussion, : of the ride...

  17. 78 FR 65244 - Rail Vehicles Access Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-31

    ...-0001] RIN 3014-AA42 Rail Vehicles Access Advisory Committee AGENCY: Architectural and Transportation Barriers Compliance Board. ACTION: Notice of advisory committee meeting. SUMMARY: The Rail Vehicles Access... vehicles that operate on fixed guideway systems (e.g., rapid rail, light rail, commuter rail, intercity...

  18. A School-Community Inter-City Project

    ERIC Educational Resources Information Center

    Demaray, Elois

    1976-01-01

    This article briefly outlines the objectives and approaches to be instituted in establishing an environmental studies program for the San Francisco Bay area. The project incorporates community and school resources. The approach will be interdisciplinary combining ecologic concepts with socioeconomic concepts in analyzing the past and present…

  19. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling

    DOE PAGES

    Kilina, Svetlana; Yarotski, Dzmitry A.; Talin, A. Alec; ...

    2011-01-01

    We present a combined approach that relies on computational simulations and scanning tunneling microscopy (STM) measurements to reveal morphological properties and stability criteria of carbon nanotube-DNA (CNT-DNA) constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4 ° and a coiling period of 3.3 nm. Using force field simulations, we determine how the DNA-CNT binding energy depends on the sequence and binding geometry of a single strand DNA. This dependence allows us to quantitatively characterize the stability of a hybrid structure with an optimal π-stacking between DNA nucleotides and themore » tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of a well-defined minimum in the binding energy as a function of an angle between DNA strand and the nanotube chiral vector. This novel approach demonstrates the feasibility of CNT-DNA geometry studies with subnanometer resolution and paves the way towards complete characterization of the structural and electronic properties of drug-delivering systems based on DNA-CNT hybrids as a function of DNA sequence and a nanotube chirality.« less

  20. High-performance superconductors for Fusion Nuclear Science Facility

    DOE PAGES

    Zhai, Yuhu; Kessel, Chuck; Barth, Christian; ...

    2016-11-09

    High-performance superconducting magnets play an important role in the design of the next step large-scale, high-field fusion reactors such as the fusion nuclear science facility (FNSF) and the spherical tokamak (ST) pilot plant beyond ITER. Here, Princeton Plasma Physics Laboratory is currently leading the design studies of the FNSF and the ST pilot plant study. ITER, which is under construction in the south of France, utilizes the state-of-the-art low temperature superconducting magnet technology based on the cable-in-conduit conductor design, where over a thousand multifilament Nb 3Sn superconducting strands are twisted together to form a high-current-carrying cable inserted into a steelmore » jacket for coil windings. We present design options of the high-performance superconductors in the winding pack for the FNSF toroidal field magnet system based on the toroidal field radial build from the system code. For the low temperature superconductor options, the advanced J cNb 3Sn RRP strands (J c > 1000 A/mm 2 at 16 T, 4 K) from Oxford Superconducting Technology are under consideration. For the high-temperature superconductor options, the rectangular-shaped high-current HTS cable made of stacked YBCO tapes will be considered to validate feasibility of TF coil winding pack design for the ST-FNSF magnets.« less

  1. High-performance superconductors for Fusion Nuclear Science Facility

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

    Zhai, Yuhu; Kessel, Chuck; Barth, Christian

    High-performance superconducting magnets play an important role in the design of the next step large-scale, high-field fusion reactors such as the fusion nuclear science facility (FNSF) and the spherical tokamak (ST) pilot plant beyond ITER. Here, Princeton Plasma Physics Laboratory is currently leading the design studies of the FNSF and the ST pilot plant study. ITER, which is under construction in the south of France, utilizes the state-of-the-art low temperature superconducting magnet technology based on the cable-in-conduit conductor design, where over a thousand multifilament Nb 3Sn superconducting strands are twisted together to form a high-current-carrying cable inserted into a steelmore » jacket for coil windings. We present design options of the high-performance superconductors in the winding pack for the FNSF toroidal field magnet system based on the toroidal field radial build from the system code. For the low temperature superconductor options, the advanced J cNb 3Sn RRP strands (J c > 1000 A/mm 2 at 16 T, 4 K) from Oxford Superconducting Technology are under consideration. For the high-temperature superconductor options, the rectangular-shaped high-current HTS cable made of stacked YBCO tapes will be considered to validate feasibility of TF coil winding pack design for the ST-FNSF magnets.« less

  2. The energetics of tightly bent DNA: a composite elastica model including local melting

    NASA Astrophysics Data System (ADS)

    Evans, Arthur; Levine, Alex

    2012-02-01

    Melting transitions are well-known to be affected by the application of mechanical stress. Motivated by the experiments of Zocchi and collaborators (Qu and Zocchi 2011, EPL 94 18003), we explore the effect of the application of mechanical stress on DNA melting in a particular composite of a stiff double stranded piece of DNA (dsDNA), shorter than its own persistence length, whose ends are linked by a flexible single stranded piece of DNA (ssDNA). The flexible ssDNA acts as a Gaussian polymer coil bending the stiff dsDNA through an elastic force that is controllable by the length of the ssDNA chain. In this talk we present theoretical predictions for two experimentally accessible features: the degree of local dsDNA melting and the local elastic energy of the dsDNA/ssDNA construct both as a function of the length of the attached ssDNA. We also address the effect of introducing a nick (broken covalent bond) in the dsDNA backbone on these results and discuss the implications of such data on the relative importance of backbone elasticity versus base stacking and base pairing interactions in determining the elasticity of dsDNA. This work also addresses open questions in the nonlinear elasticity of DNA in tightly bent curves.

  3. A high-sensitivity electrochemical aptasensor of carcinoembryonic antigen based on graphene quantum dots-ionic liquid-nafion nanomatrix and DNAzyme-assisted signal amplification strategy.

    PubMed

    Huang, Jing-Yi; Zhao, Lang; Lei, Wan; Wen, Wei; Wang, Yi-Jia; Bao, Ting; Xiong, Hua-Yu; Zhang, Xiu-Hua; Wang, Sheng-Fu

    2018-01-15

    In this work, we have developed an electrochemical aptasensor for high-sensitivity determination of carcinoembryonic antigen (CEA) based on lead ion (Pb 2+ )-dependent DNAzyme-assisted signal amplification and graphene quantum dot-ionic liquid-nafion (GQDs-IL-NF) composite film. We designed hairpin DNA containing CEA-specific aptamers and DNAzyme chains. In the presence of CEA, hairpin DNA recognized the target and performed a DNAzyme-assisted signal amplification reaction to yield a large number of single-stranded DNA. The GQDs-IL-NF composite film was immobilized on the glassy carbon electrode for the interaction with single-stranded DNA through noncovalent π-π stacking interaction. Therefore, the methylene blue-labeled substrate DNA (MB-substrate) was fixed on the electrode and exhibited an initial electrochemical signal. Under optimal conditions, the response current change was proportional to the concentration of CEA, demonstrating a wide linear range from 0.5fgmL -1 to 0.5ngmL -1 , with a low detection limit of 0.34fgmL -1 . Furthermore, the proposed aptasensor was successfully applied in determining CEA in serum samples, showing its superior prospects in clinical diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Test of 60 kA coated conductor cable prototypes for fusion magnets

    NASA Astrophysics Data System (ADS)

    Uglietti, D.; Bykovsky, N.; Sedlak, K.; Stepanov, B.; Wesche, R.; Bruzzone, P.

    2015-12-01

    Coated conductors could be promising materials for the fabrication of the large magnet systems of future fusion devices. Two prototype conductors (flat cables in steel conduits), each about 2 m long, were manufactured using coated conductor tapes (4 mm wide) from Super Power and SuperOx, with a total tape length of 1.6 km. Each flat cable is assembled from 20 strands, each strand consisting of a stack of 16 tapes surrounded by two half circular copper profiles, twisted and soldered. The tapes were measured at 12 T and 4.2 K and the results of the measurements were used for the assessment of the conductor electromagnetic properties at low temperature and high field. The two conductors were assembled together in a sample that was tested in the European Dipole (EDIPO) facility. The current sharing temperatures of the two conductors were measured at background fields from 8 T up to 12 T and for currents from 30 kA up to 70 kA: the measured values are within a few percent of the values expected from the measurements on tapes (short samples). After electromagnetic cycling, T cs at 12 T and 50 kA decreased from about 12 K to 11 K (about 10%), corresponding to less than 3% of I c.

  5. Imaging Subsurface Structure of Central Zagros Zone/Iran Using Ambient Noise Tomography

    NASA Astrophysics Data System (ADS)

    Vahidravesh, Shaghayegh; Pakzad, Mehrdad, ,, Dr.; Hatami, Mohammad Reza, ,, Dr.

    2017-04-01

    The Central Zagros zone, of west Iran & east Iraq, is surrounded by many active faults (including Main Zagros Reversed Fault, Main Recent Fault, High Zagros Fault, Zagros Fold, & Thrust Belt). Recent studies show that cross-correlation of a long-term ambient seismic noise data recorded in station-pair, includes important information regarding empirical Green's functions (EGFs) between stations. Hence, ambient seismic noise carries valuable information of the wave propagation path (which can be extracted). The 2D model of surface waves (Rayleigh & Love) velocities for the studied area is obtained by seismic ambient noise tomography (ANT) method. Throughout this research, we use continuous records of all three vertical, radial, and tangential components (obtained by rotation) recorded by IRSC (Iranian Seismological Center) and IIEES (International Institute of Earthquake Engineering) networks for this area of interest. The IRSC & IIEES networks are equipped by SS-1 kinematics and Guralp CMG-3T sensors respectively. Data of 20 stations were used for 12 months from 2014/Nov. to 2015/Nov. The performed data processing is similar to the one, put into words in detail by Bensen et al. (2007) including the processed daily base data. Mean, trend, and instrument response were removed and the data were decimated to 5 sps (sample per second) to reduce the amount of storage space and computational time required. We then applied merge to handle data gaps. One-bit time-domain normalization was also applied to suppress the influence of instrument irregularities and earthquake signals followed by spectral (frequency-domain) normalization between 0.05-0.2 Hz (period 5-20 sec). After cross-correlation (processing step), we perform rms stacking (new approach of stacking) to stack many cross-correlation functions based on the highest energy in a time interval which we accordingly anticipate to receive Rayleigh & Love waves fundamental modes. To evaluate quality of the stacking process stability quantitatively, we calculate signal-to-noise ratio (SNR), defined as a ratio of the peak amplitude within a time window to the root-mean-square of noise trailing the signal arrival window (Bensen et al., 2007), for each cross-correlation. The cross-correlated time-series is equivalent to the Green's functions between pairs of receivers. We then apply multiple phase-matched filter method of Herrmann (2005) to measure the correct group velocity dispersion of the interferometric surface waves. Eventually, we apply fast marching surface wave tomography (FMST), the iterative nonlinear inversion package developed by Rawlinson, 2005, to extract the velocity model of shallow structure in Central Zagros zone /Iran.

  6. New Details of the Human Corneal Limbus Revealed With Second Harmonic Generation Imaging.

    PubMed

    Park, Choul Yong; Lee, Jimmy K; Zhang, Cheng; Chuck, Roy S

    2015-09-01

    To report novel findings of the human corneal limbus by using second harmonic generation (SHG) imaging. Corneal limbus was imaged by using an inverted two-photon excitation fluorescence microscope. Laser (Ti:Sapphire) was tuned at 850 nm for two-photon excitation. Backscatter signals of SHG and autofluorescence (AF) were collected through a 425/30-nm emission filter and a 525/45-emission filter, respectively. Multiple, consecutive, and overlapping image stacks (z-stack) were acquired for the corneal limbal area. Two novel collagen structures were revealed by SHG imaging at the limbus: an anterior limbal cribriform layer and presumed anchoring fibers. Anterior limbal cribriform layer is an intertwined reticular collagen architecture just beneath the limbal epithelial niche and is located between the peripheral cornea and Tenon's/scleral tissue. Autofluorescence imaging revealed high vascularity in this structure. Central to the anterior limbal cribriform layer, radial strands of collagen were found to connect the peripheral cornea to the limbus. These presumed anchoring fibers have both collagen and elastin and were found more extensively in the superficial layers than deep layer and were absent in very deep limbus near Schlemm's canal. By using SHG imaging, new details of the collagen architecture of human corneal limbal area were elucidated. High resolution images with volumetric analysis revealed two novel collagen structures.

  7. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model.

    PubMed

    Moreira, Bernardo G; You, Yong; Owczarzy, Richard

    2015-03-01

    Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5' end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2 kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine-purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications. Copyright © 2015. Published by Elsevier B.V.

  8. Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers

    NASA Astrophysics Data System (ADS)

    Himbert, Sebastian; Chapman, Mindy; Deamer, David W.; Rheinstädter, Maikel C.

    2016-08-01

    RNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. However, in the absence of enzymes and metabolism there has been no obvious way for RNA-like molecules to be produced and then encapsulated in cellular compartments. We investigated 5‧-adenosine monophosphate (AMP) and 5‧-uridine monophosphate (UMP) molecules confined in multi-lamellar phospholipid bilayers, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay, previously proposed to promote polymerization. X-ray diffraction was used to determine whether such conditions imposed a degree of order on the nucleotides. Two nucleotide signals were observed in all matrices, one corresponding to a nearest neighbour distance of 4.6 Å attributed to nucleotides that form a disordered, glassy structure. A second, smaller distance of 3.4 Å agrees well with the distance between stacked base pairs in the RNA backbone, and was assigned to the formation of pre-polymers, i.e., the organization of nucleotides into stacks of about 10 monomers. Such ordering can provide conditions that promote the nonenzymatic polymerization of RNA strands under prebiotic conditions. Experiments were modeled by Monte-Carlo simulations, which provide details of the molecular structure of these pre-polymers.

  9. Molecular Beam Epitaxy of Layered Material Superlattices and Heterostructures

    NASA Astrophysics Data System (ADS)

    Vishwanath, Suresh; Liu, Xinyu; Rouvimov, Sergei; Furdyna, Jacek K.; Jena, Debdeep; Xing, Huili Grace

    2014-03-01

    Stacking of various layered materials is being pursued widely to realize various devices and observe novel physics. Mostly, these have been limited to exfoliation and stacking either manually or in solution, where control on rotational alignment or order of stacking is lost. We have demonstrated molecular beam epitaxy (MBE) growth of Bi2Se3/MoSe2 superlatticeand Bi2Se3/MoSe2/SnSe2 heterostructure on sapphire. We have achieved a better control on the order of stacking and number of layers as compared to the solution technique. We have characterized these structures using RHEED, Raman spectroscopy, XPS, AFM, X-ray reflectometry, cross-section (cs) and in-plane (ip) TEM. The rotational alignment is dictated by thermodynamics and is understood using ip-TEM diffraction patterns. Layered growth and long range order is evident from the streaky RHEED pattern. Abrupt change in RHEED pattern, clear demarcation of boundary between layers seen using cs-TEM and observation of Raman peaks corresponding to all the layers suggest van-der-waals epitaxy. In our knowledge this is a first demonstration of as grown superlattices and heterostuctures involving transition metal dichalcogenides and is an important step towards the goal of stacking of 2D crystals like lego blocks.

  10. Reducing respiratory motion artifacts in positron emission tomography through retrospective stacking

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

    Thorndyke, Brian; Schreibmann, Eduard; Koong, Albert

    Respiratory motion artifacts in positron emission tomography (PET) imaging can alter lesion intensity profiles, and result in substantially reduced activity and contrast-to-noise ratios (CNRs). We propose a corrective algorithm, coined 'retrospective stacking' (RS), to restore image quality without requiring additional scan time. Retrospective stacking uses b-spline deformable image registration to combine amplitude-binned PET data along the entire respiratory cycle into a single respiratory end point. We applied the method to a phantom model consisting of a small, hot vial oscillating within a warm background, as well as to {sup 18}FDG-PET images of a pancreatic and a liver patient. Comparisons weremore » made using cross-section visualizations, activity profiles, and CNRs within the region of interest. Retrospective stacking was found to properly restore the lesion location and intensity profile in all cases. In addition, RS provided CNR improvements up to three-fold over gated images, and up to five-fold over ungated data. These phantom and patient studies demonstrate that RS can correct for lesion motion and deformation, while substantially improving tumor visibility and background noise.« less

  11. Alkaline Comet Assay for Assessing DNA Damage in Individual Cells.

    PubMed

    Pu, Xinzhu; Wang, Zemin; Klaunig, James E

    2015-08-06

    Single-cell gel electrophoresis, commonly called a comet assay, is a simple and sensitive method for assessing DNA damage at the single-cell level. It is an important technique in genetic toxicological studies. The comet assay performed under alkaline conditions (pH >13) is considered the optimal version for identifying agents with genotoxic activity. The alkaline comet assay is capable of detecting DNA double-strand breaks, single-strand breaks, alkali-labile sites, DNA-DNA/DNA-protein cross-linking, and incomplete excision repair sites. The inclusion of digestion of lesion-specific DNA repair enzymes in the procedure allows the detection of various DNA base alterations, such as oxidative base damage. This unit describes alkaline comet assay procedures for assessing DNA strand breaks and oxidative base alterations. These methods can be applied in a variety of cells from in vitro and in vivo experiments, as well as human studies. Copyright © 2015 John Wiley & Sons, Inc.

  12. STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

    PubMed Central

    Bryan, Allen W; O’Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

    2012-01-01

    The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively ‘stitches’ strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer’s amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2012. © 2011 Wiley Periodicals, Inc. PMID:22095906

  13. STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

    PubMed

    Bryan, Allen W; O'Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

    2012-02-01

    The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Copyright © 2011 Wiley Periodicals, Inc.

  14. Magnified fluorescence detection of silver(I) ion in aqueous solutions by using nano-graphite-DNA hybrid and DNase I.

    PubMed

    Wei, Yin; Li, Bianmiao; Wang, Xu; Duan, Yixiang

    2014-08-15

    This paper describes a novel approach utilizing nano-graphite-DNA hybrid and DNase I for the amplified detection of silver(I) ion in aqueous solutions for the first time. Nano-graphite can effectively quench the fluorescence of dye-labeled cytosine-rich single-stranded DNA due to its strong π-π stacking interactions; however, in the presence of Ag(+), C-Ag(+)-C coordination induces the probe to fold into a hairpin structure, which does not adsorb on the surface of nano-graphite and thus retains the dye fluorescence. Meanwhile, the hairpin structure can be cleaved by DNase I, and in such case Ag(+) is delivered from the complex. The released Ag(+) then binds other dye-labeled single-stranded DNA on the nano-graphite surface, and touches off another target recycling, resulting in the successive release of dye-labeled single-stranded DNA from the nano-graphite, which leads to significant amplification of the signal. The present magnification sensing system exhibits high sensitivity toward Ag(+) with a limit of detection of 0.3nM (S/N=3), which is much lower than the standard for Ag(+) in drinking water recommended by the Environmental Protection Agency (EPA). The selectivity of the sensor for Ag(+) against other biologically and environmentally related metal ions is outstanding due to the high specificity of C-Ag(+)-C formation. Moreover, the sensing system is used for the determination of Ag(+) in river water samples with satisfying results. The proposed assay is simple, cost-effective, and might open the door for the development of new assays for other metal ions or biomolecules. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Production cross sections of deuteron-induced reactions on natural palladium for Ag isotopes

    NASA Astrophysics Data System (ADS)

    Ukon, Naoyuki; Aikawa, Masayuki; Komori, Yukiko; Haba, Hiromitsu

    2018-07-01

    Activation cross sections for deuteron-induced reactions on natural palladium were measured up to 24 MeV using the stacked-foil method and the high resolution gamma-ray spectroscopy. The production cross sections of 103Ag, the parent of a medical radioactive isotope 103Pd, were obtained. We found that our result is in good agreement with the previous data up to 20.3 MeV, and obtained new data at higher energies. In addition, the production cross sections of 104g+mAg, 105Ag, 106mAg, 110mAg and 111Ag were presented.

  16. Activation cross sections of alpha-induced reactions on natIn for 117mSn production

    NASA Astrophysics Data System (ADS)

    Aikawa, M.; Saito, M.; Ukon, N.; Komori, Y.; Haba, H.

    2018-07-01

    The production of 117mSn by charged-particle induced reactions is an interesting topic for medical application. Production cross sections of α-induced reactions on natIn for 117mSn up to 50 MeV were measured using the stacked foil technique and activation method. The integral yield of 117mSn was estimated using the measured cross sections. The results were compared with experimental data investigated earlier and theoretical calculation. Measured cross sections for 113Sn and 116m,117,118mSb isotopes were also presented.

  17. Wind Tunnel Model Study of the Hot Exhaust Plume from the Compressor Research Facility at Wright-Patterson Air Force Base, Ohio

    DTIC Science & Technology

    1977-10-01

    PLUME FROM THE COMPRESSOR JtESEARCHJAC ILITY AT WRIGHT- /ATTERSON AIR FORCE JBASE, OHIO , r= mrm (.) Gary R./Ludwig 9. PERFORMING ORGANIZATION NAME... ms Mass flux of stack exhaust gas (slugs/sec) nrtfl Mass flux of ambient air and stack exhaust gas mixture st plume cross-section A (slugs/sec...the horizontal momentum flux in the ambient wind be the same in the model as it is in full-scale. /»» Ms M i a. ’ ro P>"S P*» + ’f (3) where 0

  18. Generator stator core vent duct spacer posts

    DOEpatents

    Griffith, John Wesley; Tong, Wei

    2003-06-24

    Generator stator cores are constructed by stacking many layers of magnetic laminations. Ventilation ducts may be inserted between these layers by inserting spacers into the core stack. The ventilation ducts allow for the passage of cooling gas through the core during operation. The spacers or spacer posts are positioned between groups of the magnetic laminations to define the ventilation ducts. The spacer posts are secured with longitudinal axes thereof substantially parallel to the core axis. With this structure, core tightness can be assured while maximizing ventilation duct cross section for gas flow and minimizing magnetic loss in the spacers.

  19. Replication-associated mutational asymmetry in the human genome.

    PubMed

    Chen, Chun-Long; Duquenne, Lauranne; Audit, Benjamin; Guilbaud, Guillaume; Rappailles, Aurélien; Baker, Antoine; Huvet, Maxime; d'Aubenton-Carafa, Yves; Hyrien, Olivier; Arneodo, Alain; Thermes, Claude

    2011-08-01

    During evolution, mutations occur at rates that can differ between the two DNA strands. In the human genome, nucleotide substitutions occur at different rates on the transcribed and non-transcribed strands that may result from transcription-coupled repair. These mutational asymmetries generate transcription-associated compositional skews. To date, the existence of such asymmetries associated with replication has not yet been established. Here, we compute the nucleotide substitution matrices around replication initiation zones identified as sharp peaks in replication timing profiles and associated with abrupt jumps in the compositional skew profile. We show that the substitution matrices computed in these regions fully explain the jumps in the compositional skew profile when crossing initiation zones. In intergenic regions, we observe mutational asymmetries measured as differences between complementary substitution rates; their sign changes when crossing initiation zones. These mutational asymmetries are unlikely to result from cryptic transcription but can be explained by a model based on replication errors and strand-biased repair. In transcribed regions, mutational asymmetries associated with replication superimpose on the previously described mutational asymmetries associated with transcription. We separate the substitution asymmetries associated with both mechanisms, which allows us to determine for the first time in eukaryotes, the mutational asymmetries associated with replication and to reevaluate those associated with transcription. Replication-associated mutational asymmetry may result from unequal rates of complementary base misincorporation by the DNA polymerases coupled with DNA mismatch repair (MMR) acting with different efficiencies on the leading and lagging strands. Replication, acting in germ line cells during long evolutionary times, contributed equally with transcription to produce the present abrupt jumps in the compositional skew. These results demonstrate that DNA replication is one of the major processes that shape human genome composition.

  20. Bloom DNA Helicase Facilitates Homologous Recombination between Diverged Homologous Sequences*

    PubMed Central

    Kikuchi, Koji; Abdel-Aziz, H. Ismail; Taniguchi, Yoshihito; Yamazoe, Mitsuyoshi; Takeda, Shunichi; Hirota, Kouji

    2009-01-01

    Bloom syndrome caused by inactivation of the Bloom DNA helicase (Blm) is characterized by increases in the level of sister chromatid exchange, homologous recombination (HR) associated with cross-over. It is therefore believed that Blm works as an anti-recombinase. Meanwhile, in Drosophila, DmBlm is required specifically to promote the synthesis-dependent strand anneal (SDSA), a type of HR not associating with cross-over. However, conservation of Blm function in SDSA through higher eukaryotes has been a matter of debate. Here, we demonstrate the function of Blm in SDSA type HR in chicken DT40 B lymphocyte line, where Ig gene conversion diversifies the immunoglobulin V gene through intragenic HR between diverged homologous segments. This reaction is initiated by the activation-induced cytidine deaminase enzyme-mediated uracil formation at the V gene, which in turn converts into abasic site, presumably leading to a single strand gap. Ig gene conversion frequency was drastically reduced in BLM−/− cells. In addition, BLM−/− cells used limited donor segments harboring higher identity compared with other segments in Ig gene conversion event, suggesting that Blm can promote HR between diverged sequences. To further understand the role of Blm in HR between diverged homologous sequences, we measured the frequency of gene targeting induced by an I-SceI-endonuclease-mediated double-strand break. BLM−/− cells showed a severer defect in the gene targeting frequency as the number of heterologous sequences increased at the double-strand break site. Conversely, the overexpression of Blm, even an ATPase-defective mutant, strongly stimulated gene targeting. In summary, Blm promotes HR between diverged sequences through a novel ATPase-independent mechanism. PMID:19661064

Some links on this page may take you to non-federal websites. Their policies may differ from this site.
Top