Effect of laser shock processing on fatigue life of 2205 duplex stainless steel notched specimens

NASA Astrophysics Data System (ADS)

Vázquez Jiménez, César A.; Gómez Rosas, Gilberto; Rubio González, Carlos; Granados Alejo, Vignaud; Hereñú, Silvina

2017-12-01

The effect laser shock processing (LSP) on high cycle fatigue behavior of 2205 duplex stainless steel (DSS) notched samples was investigated. The swept direction parallel (LSP 1) and perpendicular (LSP 2) to rolling were used in order to examine the sensitivity of LSP to manufacturing process since this steel present significantly anisotropy. The Nd:YAG pulsed laser operating at 10 Hz frequency and 1064 nm wavelength was utilized. The LSP configuration was the water jet mode without protective coating. Notched specimens 4 mm thick were treated on both sides, and then fatigue loading was applied with R = 0.1. The results showed that the LSP 2 condition induces higher compressive residual stresses as well as a higher fatigue life than the LSP 1 condition. By applying LSP 2 condition, an enhancement of fatigue life up to 402% is reported. In addition, the microhardness profiles showed different depths of hardening layer for each direction, according to the anisotropy observed.

Terminal Duplex Stability and Nucleotide Identity Differentially Control siRNA Loading and Activity in RNA Interference

PubMed Central

Angart, Phillip A.; Carlson, Rebecca J.; Adu-Berchie, Kwasi

2016-01-01

Efficient short interfering RNA (siRNA)-mediated gene silencing requires selection of a sequence that is complementary to the intended target and possesses sequence and structural features that encourage favorable functional interactions with the RNA interference (RNAi) pathway proteins. In this study, we investigated how terminal sequence and structural characteristics of siRNAs contribute to siRNA strand loading and silencing activity and how these characteristics ultimately result in a functionally asymmetric duplex in cultured HeLa cells. Our results reiterate that the most important characteristic in determining siRNA activity is the 5′ terminal nucleotide identity. Our findings further suggest that siRNA loading is controlled principally by the hybridization stability of the 5′ terminus (Nucleotides: 1–2) of each siRNA strand, independent of the opposing terminus. Postloading, RNA-induced silencing complex (RISC)–specific activity was found to be improved by lower hybridization stability in the 5′ terminus (Nucleotides: 3–4) of the loaded siRNA strand and greater hybridization stability toward the 3′ terminus (Nucleotides: 17–18). Concomitantly, specific recognition of the 5′ terminal nucleotide sequence by human Argonaute 2 (Ago2) improves RISC half-life. These findings indicate that careful selection of siRNA sequences can maximize both the loading and the specific activity of the intended guide strand. PMID:27399870

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

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

Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) 2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP2 1lattice of hexagonal metric. The various twinning criteria give somewhatmore » conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.« less

Development of a panel of seven duplex real-time PCR assays for detecting 13 streptococcal superantigens.

PubMed

Yang, Peng; Peng, Xiaomin; Cui, Shujuan; Shao, Junbin; Zhu, Xuping; Zhang, Daitao; Liang, Huijie; Wang, Quanyi

2013-07-30

Streptococcal superantigens (SAgs) are the major virulence factors of infection in humans for group A Streptococcus (GAS) bacteria. A panel consisting of seven duplex real-time PCR assays was developed to simultaneously detect 13 streptococcal SAgs and one internal control which may be important in the control of GAS-mediated diseases. Primer and probe sequences were selected based on the highly conserved region from an alignment of nucleotide sequences of the 13 streptococcal SAgs. The reaction conditions of the duplex real-time PCR were optimized and the specificity of the duplex assays was evaluated using SAg positive strains. The limit of detection of the duplex assays was determined by using 10-fold serial dilutions of the DNA of 13 streptococcal SAgs and compared to a conventional polymerase chain reaction (PCR) method for evaluating the duplex assays sensitivity. Using the duplex assays, we were able to differentiate between 13 SAgs from Streptococcus strains and other non-Streptococcus bacteria without cross-reaction. On the other hand, the limit of detection of the duplex assays was at least one or two log dilutions lower than that of the conventional PCR. The panel was highly specific (100%) and the limit of detection of these duplex groups was at least ten times lower than that obtained by using a conventional PCR method.

Cyclic stress effect on stress corrosion cracking of duplex stainless steel in chloride and caustic solutions

NASA Astrophysics Data System (ADS)

Yang, Di

Duplex stainless steel (DSS) is a dual-phase material with approximately equal volume amount of austenite and ferrite. It has both great mechanical properties (good ductility and high tensile/fatigue strength) and excellent corrosion resistance due to the mixture of the two phases. Cyclic loadings with high stress level and low frequency are experienced by many structures. However, the existing study on corrosion fatigue (CF) study of various metallic materials has mainly concentrated on relatively high frequency range. No systematic study has been done to understand the ultra-low frequency (˜10-5 Hz) cyclic loading effect on stress corrosion cracking (SCC) of DSSs. In this study, the ultra-low frequency cyclic loading effect on SCC of DSS 2205 was studied in acidified sodium chloride and caustic white liquor (WL) solutions. The research work focused on the environmental effect on SCC of DSS 2205, the cyclic stress effect on strain accumulation behavior of DSS 2205, and the combined environmental and cyclic stress effect on the stress corrosion crack initiation of DSS 2205 in the above environments. Potentiodynamic polarization tests were performed to investigate the electrochemical behavior of DSS 2205 in acidic NaCl solution. Series of slow strain rate tests (SSRTs) at different applied potential values were conducted to reveal the optimum applied potential value for SCC to happen. Room temperature static and cyclic creep tests were performed in air to illustrate the strain accumulation effect of cyclic stresses. Test results showed that cyclic loading could enhance strain accumulation in DSS 2205 compared to static loading. Moreover, the strain accumulation behavior of DSS 2205 was found to be controlled by the two phases of DSS 2205 with different crystal structures. The B.C.C. ferrite phase enhanced strain accumulation due to extensive cross-slips of the dislocations, whereas the F.C.C. austenite phase resisted strain accumulation due to cyclic strain hardening. Cyclic SSRTs were performed under the conditions that SCC occurs in sodium chloride and WL solutions. Test results show that cyclic stress facilitated crack initiations in DSS 2205. Stress corrosion cracks initiated from the intermetallic precipitates in acidic chloride environment, and the cracks initiated from austenite phase in WL environment. Cold-working has been found to retard the crack initiations induced by cyclic stresses.

TAF11 Assembles the RISC Loading Complex to Enhance RNAi Efficiency.

PubMed

Liang, Chunyang; Wang, Yibing; Murota, Yukiko; Liu, Xiang; Smith, Dean; Siomi, Mikiko C; Liu, Qinghua

2015-09-03

Assembly of the RNA-induced silencing complex (RISC) requires formation of the RISC loading complex (RLC), which contains the Dicer-2 (Dcr-2)-R2D2 complex and recruits duplex siRNA to Ago2 in Drosophila melanogaster. However, the precise composition and action mechanism of Drosophila RLC remain unclear. Here we identified the missing factor of RLC as TATA-binding protein-associated factor 11 (TAF11) by genetic screen. Although it is an annotated nuclear transcription factor, we found that TAF11 also associated with Dcr-2/R2D2 and localized to cytoplasmic D2 bodies. Consistent with defective RLC assembly in taf11(-/-) ovary extract, we reconstituted the RLC in vitro using the recombinant Dcr-2-R2D2 complex, TAF11, and duplex siRNA. Furthermore, we showed that TAF11 tetramer facilitates Dcr-2-R2D2 tetramerization to enhance siRNA binding and RISC loading activities. Together, our genetic and biochemical studies define the molecular nature of the Drosophila RLC and elucidate a cytoplasmic function of TAF11 in organizing RLC assembly to enhance RNAi efficiency. Copyright © 2015 Elsevier Inc. All rights reserved.

Tackling optimization challenges in industrial load control and full-duplex radios

NASA Astrophysics Data System (ADS)

Gholian, Armen

In price-based demand response programs in smart grid, utilities set the price in accordance with the grid operating conditions and consumers respond to price signals by conducting optimal load control to minimize their energy expenditure while satisfying their energy needs. Industrial sector consumes a large portion of world electricity and addressing optimal load control of energy-intensive industrial complexes, such as steel industry and oil-refinery, is of practical importance. Formulating a general industrial complex and addressing issues in optimal industrial load control in smart grid is the focus of the second part of this dissertation. Several industrial load details are considered in the proposed formulation, including those that do not appear in residential or commercial load control problems. Operation under different smart pricing scenarios, namely, day-ahead pricing, time-of-use pricing, peak pricing, inclining block rates, and critical peak pricing are considered. The use of behind-the-meter renewable generation and energy storage is also considered. The formulated optimization problem is originally nonlinear and nonconvex and thus hard to solve. However, it is then reformulated into a tractable linear mixed-integer program. The performance of the design is assessed through various simulations for an oil refinery and a steel mini-mill. In the third part of this dissertation, a novel all-analog RF interference canceler is proposed. Radio self-interference cancellation (SIC) is the fundamental enabler for full-duplex radios. While SIC methods based on baseband digital signal processing and/or beamforming are inadequate, an all-analog method is useful to drastically reduce the self-interference as the first stage of SIC. It is shown that a uniform architecture with uniformly distributed RF attenuators has a performance highly dependent on the carrier frequency. It is also shown that a new architecture with the attenuators distributed in a clustered fashion has important advantages over the uniform architecture. These advantages are shown numerically through random multipath interference channels, number of control bits in step attenuators, attenuation-dependent phases, single and multi-level structures, etc.

Tribological Properties of Surface-Textured and Plasma-Nitrided Pure Titanium Under Oil Lubrication Condition

NASA Astrophysics Data System (ADS)

Zhang, Baosen; Dong, Qiangsheng; Ba, Zhixin; Wang, Zhangzhong; Shi, Hancheng; Xue, Yanting

2018-01-01

Plasma nitriding was conducted as post-treatment for surface texture on pure titanium to obtain a continuous nitriding layer. Supersonic fine particles bombarding (SFPB) was carried out to prepare surface texture. The surface morphologies and chemical composition were analyzed using scanning electron microscope and energy disperse spectroscopy. The microstructures of modified layers were characterized by transmission electron microscope. The tribological properties of surface-textured and duplex-treated pure titanium under oil lubrication condition were systematically investigated in the ball-on-plate reciprocating mode. The effects of applied load and sliding velocity on the tribological behavior were analyzed. The results show that after duplex treatments, the grains size in modified layer becomes slightly larger, and hardness is obviously improved. Wear resistance of duplex-treated pure titanium is significantly improved referenced to untreated and surface-textured pure titanium, which is 3.22 times as much as untreated pure titanium and 2.15 times of that for surface-textured pure titanium, respectively.

Analysis of singular interface stresses in dissimilar material joints for plasma facing components

NASA Astrophysics Data System (ADS)

You, J. H.; Bolt, H.

2001-10-01

Duplex joint structures are typical material combinations for the actively cooled plasma facing components of fusion devices. The structural integrity under the incident heat loads from the plasma is one of the most crucial issues in the technology of these components. The most critical domain in a duplex joint component is the free surface edge of the bond interface between heterogeneous materials. This is due to the fact that the thermal stress usually shows a singular intensification in this region. If the plasma facing armour tile consists of a brittle material, the existence of the stress singularity can be a direct cause of failure. The present work introduces a comprehensive analytical tool to estimate the impact of the stress singularity for duplex PFC design and quantifies the relative stress intensification in various materials joints by use of a model formulated by Munz and Yang. Several candidate material combinations of plasma facing armour and metallic heat sink are analysed and the results are compared with each other.

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

Ye, Xuecheng; Huang, Nian; Liu, Ying

Assembly of the RNA-induced silencing complex (RISC) consists of loading duplex (guide-passenger) siRNA onto Argonaute (Ago2) and removing the passenger strand. Ago2 contributes critically to RISC activation by nicking the passenger strand. Here we reconstituted duplex siRNA-initiated RISC activity using recombinant human Ago2 (hAgo2) and C3PO, indicating that C3PO has a critical role in hAgo2-RISC activation. Consistently, genetic depletion of C3PO compromised RNA silencing in mammalian cells. We determined the crystal structure of hC3PO, which reveals an asymmetric octamer barrel consisting of six translin and two TRAX subunits. This asymmetric assembly is critical for the function of C3PO as anmore » endonuclease that cleaves RNA at the interior surface. The current work supports a Dicer-independent mechanism for human RISC activation, in which Ago2 directly binds duplex siRNA and nicks the passenger strand, and then C3PO activates RISC by degrading the Ago2-nicked passenger strand.« less

Structure of C3PO and Mechanism of Human RISC Activation

PubMed Central

Ye, Xuecheng; Huang, Nian; Liu, Ying; Paroo, Zain; Huerta, Carlos; Li, Peng; Chen, She; Liu, Qinghua; Zhang, Hong

2011-01-01

Assembly of the RNA-induced silencing complex (RISC) consists of loading duplex (guide/passenger) siRNA onto and removing the passenger strand from Argonaute (Ago2). Ago2 contributes critically to RISC activation by nicking the passenger strand. Here, we reconstituted duplex siRNA-initiated RISC activity using recombinant human (h)Ago2 and C3PO, indicating a critical role for C3PO in hAgo2-RISC activation. Consistently, genetic depletion of C3PO compromised RNA silencing in mammalian cells. We determined the crystal structure of hC3PO, which reveals an asymmetric octamer barrel consisting of six Translin and two TRAX subunits. This asymmetric assembly is critical for the function of C3PO as a novel endonuclease that cleaves RNA at the interior surface. The current work supports a Dicer-independent mechanism for human RISC activation: 1) Ago2 directly binds duplex siRNA and nicks the passenger strand; 2) C3PO activates RISC by degrading Ago2-nicked passenger strand. PMID:21552258

Low cost high temperature, duplex coating for superalloys

NASA Technical Reports Server (NTRS)

Young, S. G.; Deadmore, D. L.

1981-01-01

Duplex silicon-slurry/aluminide coating substantially improves high temperature resistance to oxidation and corrosion of nickel base alloys. Coating used in critical sections of power systems like turbojet engines extends their operating capabilities.

Microarray Detection of Duplex and Triplex DNA Binders with DNA-Modified Gold Nanoparticles

PubMed Central

Lytton-Jean, Abigail K. R.; Han, Min Su; Mirkin, Chad A.

2008-01-01

We have designed a chip-based assay, using microarray technology, for determining the relative binding affinities of duplex and triplex DNA binders. This assay combines the high discrimination capabilities afforded by DNA-modified Au nanoparticles with the high-throughput capabilities of DNA microarrays. The detection and screening of duplex DNA binders are important because these molecules, in many cases, are potential anticancer agents as well as toxins. Triplex DNA binders are also promising drug candidates. These molecules, in conjunction with triplex forming oligonucleotides, could potentially be used to achieve control of gene expression by interfering with transcription factors that bind to DNA. Therefore, the ability to screen for these molecules in a high-throughput fashion could dramatically improve the drug screening process. The assay reported here provides excellent discrimination between strong, intermediate, and weak duplex and triplex DNA binders in a high-throughput fashion. PMID:17614366

Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

PubMed Central

König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

2013-01-01

G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

H-Bond Self-Assembly: Folding versus Duplex Formation.

PubMed

Núñez-Villanueva, Diego; Iadevaia, Giulia; Stross, Alexander E; Jinks, Michael A; Swain, Jonathan A; Hunter, Christopher A

2017-05-17

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

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.

Anatomy of RISC: how do small RNAs and chaperones activate Argonaute proteins?

PubMed Central

2016-01-01

RNA silencing is a eukaryote‐specific phenomenon in which microRNAs and small interfering RNAs degrade messenger RNAs containing a complementary sequence. To this end, these small RNAs need to be loaded onto an Argonaute protein (AGO protein) to form the effector complex referred to as RNA‐induced silencing complex (RISC). RISC assembly undergoes multiple and sequential steps with the aid of Hsc70/Hsp90 chaperone machinery. The molecular mechanisms for this assembly process remain unclear, despite their significance for the development of gene silencing techniques and RNA interference‐based therapeutics. This review dissects the currently available structures of AGO proteins and proposes models and hypotheses for RISC assembly, covering the conformation of unloaded AGO proteins, the chaperone‐assisted duplex loading, and the slicer‐dependent and slicer‐independent duplex separation. The differences in the properties of RISC between prokaryotes and eukaryotes will also be clarified. WIREs RNA 2016, 7:637–660. doi: 10.1002/wrna.1356 For further resources related to this article, please visit the WIREs website. PMID:27184117

Anatomy of RISC: how do small RNAs and chaperones activate Argonaute proteins?

PubMed

Nakanishi, Kotaro

2016-09-01

RNA silencing is a eukaryote-specific phenomenon in which microRNAs and small interfering RNAs degrade messenger RNAs containing a complementary sequence. To this end, these small RNAs need to be loaded onto an Argonaute protein (AGO protein) to form the effector complex referred to as RNA-induced silencing complex (RISC). RISC assembly undergoes multiple and sequential steps with the aid of Hsc70/Hsp90 chaperone machinery. The molecular mechanisms for this assembly process remain unclear, despite their significance for the development of gene silencing techniques and RNA interference-based therapeutics. This review dissects the currently available structures of AGO proteins and proposes models and hypotheses for RISC assembly, covering the conformation of unloaded AGO proteins, the chaperone-assisted duplex loading, and the slicer-dependent and slicer-independent duplex separation. The differences in the properties of RISC between prokaryotes and eukaryotes will also be clarified. WIREs RNA 2016, 7:637-660. doi: 10.1002/wrna.1356 For further resources related to this article, please visit the WIREs website. © 2016 The Authors. WIREs RNA published by Wiley Periodicals, Inc.

Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent.

PubMed

Mulholland, Kelly; Siddiquei, Farzana; Wu, Chun

2017-07-19

RHPS4, a potent binder to human telomeric DNA G-quadruplex, shows high efficacy in tumor cell growth inhibition. However, it's preferential binding to DNA G-quadruplex over DNA duplex (about 10 fold) remains to be improved toward its clinical application. A high resolution structure of the single-stranded telomeric DNA G-quadruplexes, or B-DNA duplex, in complex with RHPS4 is not available yet, and the binding nature of this ligand to these DNA forms remains to be elusive. In this study, we carried out 40 μs molecular dynamics binding simulations with a free ligand to decipher the binding pathway of RHPS4 to a DNA duplex and three G-quadruplex folders (parallel, antiparallel and hybrid) of the human telomeric DNA sequence. The most stable binding mode identified for the duplex, parallel, antiparallel and hybrid G-quadruplexes is an intercalation, bottom stacking, top intercalation and bottom intercalation mode, respectively. The intercalation mode with similar binding strength to both the duplex and the G-quadruplexes, explains the lack of binding selectivity of RHPS4 to the G-quadruplex form. Therefore, a ligand modification that destabilizes the duplex intercalation mode but stabilizes the G-quadruplex intercalation mode will improve the binding selectivity toward G-quadruplex. The intercalation mode of RHPS4 to both the duplex and the antiparallel and the hybrid G-quadruplex follows a base flipping-insertion mechanism rather than an open-insertion mechanism. The groove binding, the side binding and the intercalation with flipping out of base were observed to be intermediate states before the full intercalation state with paired bases.

Creep deformation in near-γ TiAl: Part 1. the influence of microstructure on creep deformation in Ti-49Al-1V

NASA Astrophysics Data System (ADS)

Worth, Brian D.; Jones, J. Wayne; Allison, John E.

1995-11-01

The influence of microstructure on creep deformation was examined in the near-y TiAl alloy Ti-49A1-1V. Specifically, microstructures with varying volume fractions of lamellar constituent were produced through thermomechanical processing. Creep studies were conducted on these various microstructures under constant load in air at temperatures between 760 °C and 870 °C and at stresses ranging from 50 to 200 MPa. Microstructure significantly influences the creep behavior of this alloy, with a fully lamellar microstructure yielding the highest creep resistance of the microstructures examined. Creep resistance is dependent on the volume fraction of lamellar constituent, with the lowest creep resistance observed at intermediate lamellar volume fractions. Examination of the creep deformation structure revealed planar slip of dislocations in the equiaxed y microstructure, while subboundary formation was observed in the duplex microstructure. The decrease in creep resistance of the duplex microstructure, compared with the equiaxed y microstructure, is attributed to an increase in dislocation mobility within the equiaxed y constituent, that results from partitioning of oxygen from the γ phase to the α2 phase. Dislocation motion in the fully lamellar microstructure was confined to the individual lamellae, with no evidence of shearing of γ/γ or γ/α2 interfaces. This suggests that the high creep resistance of the fully lamellar microstructure is a result of the fine spacing of the lamellar structure, which results in a decreased effective slip length for dislocation motion over that found in the duplex and equiaxed y microstructures.

A novel duplex real time quantitative reverse transcription polymerase chain reaction for rubella virus with armored RNA as a noncompetitive internal positive control.

PubMed

Zhao, Lihong; Li, Ruiying; Liu, Aihua; Zhao, Shuping

2015-07-01

The objective of this study was to build and apply a duplex real time quantitative reverse transcription-polymerase chain reaction (RT-PCR) for rubella virus. Firstly, a 60-bp-long armored RV RNA was constructed in the laboratory. Secondly, a duplex real time RT-PCR assay was established. Thirdly, the 60-bp-long armored RV RNA was used as an internal positive control (IPC) for the duplex real time RT-PCR. And finally the duplex real time RT-PCR assay was applied to detect RV RNA in clinical specimens. The in-house assay has a high amplification efficiency (0.99), a high analytical sensitivity (200 copies/mL), and a good reproducibility. The diagnostic specificity and sensitivity of the in-house assay were both 100%, due to the monitoring of the armored RV RNA IPC. Therefore, the in-house duplex real time quantitative RT-PCR assay is a specific, sensitive, reproducible and accurate assay for quantitation of RV RNA in clinical specimens. And noncompetitive armored RV RNA IPC can monitor RT-PCR inhibition and prevent false-negative and inaccurate results in the real time detection system. Copyright © 2015 Elsevier B.V. All rights reserved.

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

PubMed Central

Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

1998-01-01

The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions. PMID:9443977

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

PubMed

Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

1998-02-01

The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.

Duplex Healing of Selectively Thiolated Guanosine Mismatches through a Cd2+ Chemical Stimulus.

PubMed

Lunn, Samantha M L; Hribesh, Samira; Whitfield, Colette J; Hall, Michael J; Houlton, Andrew; Bronowska, Agnieszka K; Tuite, Eimer M; Pike, Andrew R

2018-03-25

The on-column selective conversion of guanosine to thioguanosine (tG) yields modified oligomers that exhibit destabilisation over the fully complementary duplex. Restoration to a stabilised duplex is induced through thio-directed Cd 2+ coordination; a route for healing DNA damage. Short oligomers are G-specifically thiolated through a modified on-column protocol without the need for costly thioguanosine phosphoramidites. Addition of Cd 2+ ions to a duplex containing a highly disrupted tG central mismatch sequence, 3'-A 6 tG 4 T 6 -5', suggests a (tG) 8 Cd 2 central coordination regime, resulting in increased base stacking and duplex stability. Equilibrium molecular dynamic calculations support the hypothesis of metal-induced healing of the thiolated duplex. The 2 nm displacement of the central tG mismatched region is dramatically reduced after the addition of a chemical stimuli, Cd 2+ ions, returning to a minimized fluctuational state comparable to the unmodified fully complementary oligomer. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Base opening in RNA and DNA duplexes: implication for RNA stability.

PubMed

Chen, Y Z; Mohan, V; Griffey, R H

2000-05-01

The energetics of a low-energy single base opening in several RNA duplex crystal structures has been calculated and compared to DNA duplexes. Base opening in RNA appears to have an overall preference towards the major groove, similar to results previously reported for B-DNA. Movement of each of the adenine, uracil, and cytosine bases into the minor groove is blocked by a high-energy barrier due to severe close contact with neighboring bases. Guanine bases are able to open towards both grooves because of the unique orientation of the base that avoids steric clash along the opening pathway. RNA bases are found to have a substantially smaller major groove opening extent than that of their B-DNA counterparts. A comparison with base opening behavior of A-DNA duplexes suggests that this difference results from helix constraint associated with A-form backbone conformation. The reduced opening extent correlates with the RNA duplex stability and is consistent with observed slower imino proton exchange rates in RNA duplexes.

Modified naphthalene diimide as a suitable tetraplex DNA ligand: application to cancer diagnosis and anti-cancer drug

NASA Astrophysics Data System (ADS)

Takenaka, Shigeori

2017-07-01

It is known that naphthalene diimide carrying two substituents binds to DNA duplex with threading intercalation. Naphthalene diimide carrying ferrocene moieties, ferrocenylnaphthalene diimide (FND), formed a stable complex with DNA duplex and an electrochemical gene detection was achieved with current signal generated from FND bound to the DNA duplex between target DNA and DNA probe immobilized electrode. FND couldn't bind to the mismatched and its surrounding region of DNA duplex and thus FND was applied to the precision detection of single nucleotide polymorphisms (SNPs) using the improved discrimination ability between fully matched and mismatched DNA hybrids and multi-electrode chip. Some of FND derivatives bound to telomere DNA tetraplex stronger than to DNA duplex and was applied to cancer diagnosis as a measure of the elongated telomere DNA with telomerase as a suitable maker of cancer. Furthermore, cyclic naphthalene diimides realized the extremely high preference for DNA tetraplex over DNA duplex. Such molecules will open an effective anti-cancer drug based on telomerase specific inhibitor.

Development of duplex real-time PCR for the detection of WSSV and PstDV1 in cultivated shrimp.

PubMed

Leal, Carlos A G; Carvalho, Alex F; Leite, Rômulo C; Figueiredo, Henrique C P

2014-07-05

The White spot syndrome virus (WSSV) and Penaeus stylirostris penstyldensovirus 1 (previously named Infectious hypodermal and hematopoietic necrosis virus-IHHNV) are two of the most important viral pathogens of penaeid shrimp. Different methods have been applied for diagnosis of these viruses, including Real-time PCR (qPCR) assays. A duplex qPCR method allows the simultaneous detection of two viruses in the same sample, which is more cost-effective than assaying for each virus separately. Currently, an assay for the simultaneous detection of the WSSV and the PstDV1 in shrimp is unavailable. The aim of this study was to develop and standardize a duplex qPCR assay for the simultaneous detection of the WSSV and the PstDV1 in clinical samples of diseased L. vannamei. In addition, to evaluate the performance of two qPCR master mixes with regard to the clinical sensitivity of the qPCR assay, as well as, different methods for qPCR results evaluation. The duplex qPCR assay for detecting WSSV and PstDV1 in clinical samples was successfully standardized. No difference in the amplification of the standard curves was observed between the duplex and singleplex assays. Specificities and sensitivities similar to those of the singleplex assays were obtained using the optimized duplex qPCR. The analytical sensitivities of duplex qPCR were two copies of WSSV control plasmid and 20 copies of PstDV1 control plasmid. The standardized duplex qPCR confirmed the presence of viral DNA in 28 from 43 samples tested. There was no difference for WSSV detection using the two kits and the distinct methods for qPCR results evaluation. High clinical sensitivity for PstDV1 was obtained with TaqMan Universal Master Mix associated with relative threshold evaluation. Three cases of simultaneous infection by the WSSV and the PstDV1 were identified with duplex qPCR. The standardized duplex qPCR was shown to be a robust, highly sensitive, and feasible diagnostic tool for the simultaneous detection of the WSSV and the PstDV1 in whiteleg shrimp. The use of the TaqMan Universal Master Mix and the relative threshold method of data analysis in our duplex qPCR method provided optimal levels of sensitivity and specificity.

A ready-to-use duplex qPCR to detect Leishmania infantum DNA in naturally infected dogs.

PubMed

Rampazzo, Rita de Cássia Pontello; Solcà, Manuela da Silva; Santos, Liliane Celestino Sales; Pereira, Lais de Novaes; Guedes, José Carlos Oliveira; Veras, Patrícia Sampaio Tavares; Fraga, Deborah Bittencourt Mothé; Krieger, Marco Aurélio; Costa, Alexandre Dias Tavares

2017-11-15

Canine visceral leishmaniasis (CVL) is a systemic disease caused by Leishmania infantum. A precise CVL diagnosis would allow for a faster and more specific treatment. Quantitative PCR (qPCR) is a sensitive and specific technique that can diagnose CVL and also monitor parasite load in the animal during the course of the infection or treatment. The aim of this study was to develop a ready-to-use (gelified and freezer-free) duplex qPCR for the identification of infected animals. We combined a new qPCR protocol that detects the canine 18S rRNA gene with an existing protocol for L. infantum kDNA detection, creating a duplex qPCR. This duplex method was then developed into a ready-to-use format. The performance of the duplex and singleplex reactions were compared in the traditional format (liquid and freezer-stored). Furthermore, the duplex qPCR performance was compared between the ready-to-use and traditional formats. The singleplex and new duplex qPCR exhibited the same detection limit in the traditional format (0.1 parasites/reaction). The ready-to-use format showed a detection limit of 1 parasite/reaction without affecting the reaction efficiency. The performance of the new qPCR protocol in the two formats was assessed using canine tissue samples from 82 dogs in an endemic CVL area that were previously characterized by standard serological and parasitological protocols. Splenic aspirates provided a higher rate of positivity (92.9%) followed by skin (50%) and blood (35.7%). The reported detection limits were observed for all tissues studied. Our results show that the amplification of L. infantum kDNA and canine DNA in a single tube, using either the traditional or ready-to-use format, exhibited the same diagnostic performance as amplification of the parasite kDNA alone. The detection of the host gene strengthens the qPCR results by confirming the presence and quality of DNA in the samples and the absence of polymerase inhibitors. The ready-to-use duplex qPCR format has many advantages. By joining two qPCR protocols into one, more results can be obtained in the same amount of time with reduced costs and embedded quality control. Reagents are preloaded and stored on the plate, reducing the operator's hands-on time to set up a reaction, as well as decreasing manipulation steps, which reduces the risk of mistakes or contamination. Thus, the ready-to-use duplex format turns qPCR into a robust, easy-to-use tool, which could help increase the availability of qPCR for CVL diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection and differentiation of wild-type and vaccine strains of canine distemper virus by a duplex reverse transcription polymerase chain reaction

PubMed Central

Dong, X. Y.; Li, W. H.; Zhu, J. L.; Liu, W. J.; Zhao, M. Q.; Luo, Y. W.; Chen, J. D.

2015-01-01

Canine distemper virus (CDV) is the cause of canine distemper (CD) which is a severe and highly contagious disease in dogs. In the present study, a duplex reverse transcription polymerase chain reaction (RT-PCR) method was developed for the detection and differentiation of wild-type and vaccine strains of CDV. Four primers were designed to detect and discriminate the two viruses by generating 638- and 781-bp cDNA products, respectively. Furthermore, the duplex RT-PCR method was used to detect 67 field samples suspected of CD from Guangdong province in China. Results showed that, 33 samples were to be wild-type-like. The duplex RT-PCR method exhibited high specificity and sensitivity which could be used to effectively detect and differentiate wild-type and vaccine CDV, indicating its use for clinical detection and epidemiological surveillance. PMID:27175171

Development of duplex real-time RT-PCR based on Taqman technology for detecting simultaneously the genome of pan-enterovirus and enterovirus 71.

PubMed

Hwang, Seoyeon; Kang, Byunghak; Hong, Jiyoung; Kim, Ahyoun; Kim, Hyejin; Kim, Kisang; Cheon, Doo-Sung

2013-07-01

Human enterovirus (EV) 71 is the main etiological agent of hand, foot, and mouth disease (HFMD). It is associated with neurological complications, and caused fatalities during recent outbreaks in the Asia-Pacific region. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. In this study, a duplex real-time RT-PCR assay was developed in order to simultaneously detect pan-EV and EV71. EV71-specific primers and probes were designed based on the highly conserved VP1 region of EV71. Five EV71 strains were detected as positive, and no positive fluorescence signal was observed in the duplex real-time RT-PCR for other viral RNA, which showed 100% specificity for the selected panel, and no cross-reactions were observed in this duplex real-time RT-PCR. The EV71-specific duplex real-time RT-PCR was more sensitive than conventional RT-PCR, and detected viral titers that were 10-fold lower than those measured by the latter. Of the 381 HFMD clinical specimens, 196 (51.4%) cases were pan-EV-positive, of which 170 (86.7%) were EV71-positive when tested by pan-EV and EV71-specific duplex real-time RT-PCR. EV71-specific duplex real-time RT-PCR offers a rapid and sensitive method to detect EV71 from clinical specimens, and will allow quarantine measures to be taken more effectively during outbreaks. Copyright © 2013 Wiley Periodicals, Inc.

l-Proline and RNA Duplex m-Value Temperature Dependence.

PubMed

Schwinefus, Jeffrey J; Baka, Nadia L; Modi, Kalpit; Billmeyer, Kaylyn N; Lu, Shutian; Haase, Lucas R; Menssen, Ryan J

2017-08-03

The temperature dependence of l-proline interactions with the RNA dodecamer duplex surface exposed after unfolding was quantified using thermal and isothermal titration denaturation monitored by uv-absorbance. The m-value quantifying proline interactions with the RNA duplex surface area exposed after unfolding was measured using RNA duplexes with GC content ranging between 17 and 83%. The m-values from thermal denaturation decreased with increasing GC content signifying increasingly favorable proline interactions with the exposed RNA surface area. However, m-values from isothermal titration denaturation at 25.0 °C were independent of GC content and less negative than those from thermal denaturation. The m-value from isothermal titration denaturation for a 50% GC RNA duplex decreased (became more negative) as the temperature increased and was in nearly exact agreement with the m-value from thermal denaturation. Since RNA duplex transition temperatures increased with GC content, the more favorable proline interactions with the high GC content duplex surface area observed from thermal denaturation resulted from the temperature dependence of proline interactions rather than the RNA surface chemical composition. The enthalpy contribution to the m-value was positive and small (indicating a slight increase in duplex unfolding enthalpy with proline) while the entropic contribution to the m-value was positive and increased with temperature. Our results will facilitate proline's use as a probe of solvent accessible surface area changes during biochemical reactions at different reaction temperatures.

Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay

PubMed Central

Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen

2015-01-01

Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility. PMID:26544710

Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay.

PubMed

Huang, Yong; Xing, Na; Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen

2015-01-01

Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility.

Influence of ageing time on hardness, microstructure and wear behaviour of AISI2507 super duplex stainless steel

NASA Astrophysics Data System (ADS)

Davanageri, Mahesh; Narendranath, S.; Kadoli, Ravikiran

2017-08-01

The effect of ageing time on hardness, microstructure and wear behaviour of super duplex stainless AISI 2507 is examined. The material was solution treated at 1050 °C and water quenched, further the ageing has been carried out at 850 °C for 30 min, 60 min and 90 min. The chromium (Cr) and molybdenum (Mo) enriched intermetallic sigma phase (σ) were found to precipitate at the ferrite/austenite interface and within the ferrite region. The concentration of intermetallic sigma phase (σ), which was quantified by a combination of scanning electron microscopy and image analysis, increases with increasing ageing time, leading to significant increase in the hardness. The x-ray diffraction (XRD) and energy dispersive x-ray (EDX) was employed to investigate the element distribution and phase identification. Wear characterstics of the aged super duplex stainless steel were measured by varying normal loads, sliding speeds, sliding distance and compared with solution treated (as-cast) specimens. Scanning electron microscopy was used to assist in analysis of worn out surfaces. The outcomes suggested that the increase in percentage of sigma phase increases hardness and wear resistance in heat-treated specimens compared to solution treated specimens (as-cast).

Gas-fired duplex free-piston Stirling refrigerator

NASA Astrophysics Data System (ADS)

Urieli, L.

1984-03-01

The duplex free-piston Stirling refrigerator is a potentially high efficiency, high reliability device which is ideally suited to the home appliance field, in particular as a gas-fired refrigerator. It has significant advantages over other equivalent devices including freedom from halogenated hydrocarbons, extremely low temperatures available at a high efficiency, integrated water heating, and simple burner system control. The design and development of a portable working demonstration gas-fired duplex Stirling refrigeration unit is described. A unique combination of computer aided development and experimental development was used, enabling a continued interaction between the theoretical analysis and practical testing and evaluation. A universal test rig was developed in order to separately test and evaluate major subunits, enabling a smooth system integration phase.

Dextranomer/hyaluronic acid endoscopic injection is effective in the treatment of intermediate and high grade vesicoureteral reflux in patients with complete duplex systems.

PubMed

Hunziker, Manuela; Mohanan, Nochiparambil; Puri, Prem

2013-05-01

Endoscopic subureteral injection of dextranomer/hyaluronic acid has become an established alternative to long-term antibiotic prophylaxis or surgical treatment for vesicoureteral reflux. We evaluated the effectiveness of endoscopic injection of dextranomer/hyaluronic acid in intermediate and high grade vesicoureteral reflux in patients with complete duplex collecting systems. A total of 123 children underwent endoscopic correction of intermediate or high grade vesicoureteral reflux using injection of dextranomer/hyaluronic acid into complete duplex systems between 2001 and 2010. Vesicoureteral reflux was diagnosed by voiding cystourethrogram, and dimercapto-succinic acid scan was performed to evaluate the presence of renal scarring. Followup ultrasound and voiding cystourethrogram were performed 3 months after the outpatient procedure and renal ultrasound thereafter every 2 years. Mean followup was 6.7 years. Complete duplex systems were unilateral in 110 patients and bilateral in 13. Reflux severity in the 136 refluxing units was grade II in 1 (0.7%), III in 52 (38.2%), IV in 61 (44.9%) and V in 22 (16.2%). Dimercapto-succinic acid scan revealed renal functional abnormalities in 63 children (51.2%). Vesicoureteral reflux resolved after the first endoscopic injection of dextranomer/hyaluronic acid in 93 ureters (68.4%), after a second injection in 35 (25.7%) and after a third injection in 8 (5.9%). Febrile urinary tract infection developed in 5 patients (4.1%) during followup. No patient required ureteral reimplantation or experienced significant complications. Our results confirm the safety and efficacy of endoscopic injection of dextranomer/hyaluronic acid in eradicating intermediate and high grade vesicoureteral reflux in patients with complete duplex systems. We recommend this minimally invasive, 15-minute outpatient procedure as a viable option for treating intermediate and high grade vesicoureteral reflux in patients with complete duplex collecting systems. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

A Prospective, Randomized Trial of Routine Duplex Ultrasound Surveillance on Arteriovenous Fistula Maturation.

PubMed

Han, Ahram; Min, Seung-Kee; Kim, Mi-Sook; Joo, Kwon Wook; Kim, Jungsun; Ha, Jongwon; Lee, Joongyub; Min, Sang-Il

2016-10-07

Use of arteriovenous fistulas, the most preferred type of access for hemodialysis, is limited by their high maturation failure rate. The aim of this study was to assess whether aggressive surveillance with routine duplex ultrasound and intervention can decrease the maturation failure rate of arteriovenous fistulas. We conducted a single-center, parallel-group, randomized, controlled trial of patients undergoing autogenous arteriovenous fistula. Patients were randomly assigned (1:1) to either the routine duplex or selective duplex group. In the routine duplex group, duplex ultrasound and physical examination were performed 2, 4, and 8 weeks postoperatively. In the selective duplex group, duplex examination was performed only when physical examination detected an abnormality. The primary end point was the maturation failure rate 8 weeks after fistula creation. Maturation failure was defined as the inability to achieve clinical maturation ( i.e. , a successful first use) and failure to achieve sonographic maturation (fistula flow >500 ml/min and diameter >6 mm) within 8 weeks. Between June 14, 2012, and June 25, 2014, 150 patients were enrolled (75 patients in each group), and 118 of those were included in the final analysis. The maturation failure rate was lower in the routine duplex group (8 of 59; 13.6%) than in the selective duplex group (15 of 59; 25.4%), but the difference was not statistically significant (odds ratio, 0.46; 95% confidence interval, 0.18 to 1.19; P =0.10). Factors associated with maturation failure were women (odds ratio, 3.84; 95% confidence interval, 1.05 to 14.06; P =0.04), coronary artery disease (odds ratio, 6.36; 95% confidence interval, 1.62 to 24.95; P <0.01), diabetes (odds ratio, 6.10; 95% confidence interval, 1.76 to 21.19; P <0.01), and the preoperative cephalic vein diameter (odds ratio, 0.30; 95% confidence interval, 0.13 to 0.71; P <0.01). Postoperative routine duplex surveillance failed to prove superiority compared with selective duplex after physical examination for reducing arteriovenous fistula maturation failure. However, the wide 95% confidence interval for the effect of intervention precludes a firm conclusion that routine duplex surveillance was not beneficial. Copyright © 2016 by the American Society of Nephrology.

A failure of preoperative duplex imaging to diagnose a lower extremity venous aneurysm in a patient with severe chronic venous insufficiency.

PubMed

Jones, Roy Wesley; Parkerson, Godfrey Ross; Ottinger, Mary; Rodriguez, Eduardo; Park, Brian

2017-01-01

We present a case of recurrent bilateral lower extremity venous stasis ulcers in association with a superficial venous aneurysm at the right saphenofemoral junction that was misdiagnosed on preoperative duplex scanning. A 53-year-old female presented to our clinic with 6-year history of bilateral lower extremity venous stasis ulcers. Her past medical history was significant for refractory venous stasis ulcers of the bilateral lower extremities present for 6 years and morbid obesity. Preoperative venous duplex demonstrated severe venous insufficiency of the superficial and deep systems, but a venous aneurysm was not appreciated. During the high ligation of the right saphenofemoral junction, a 3 × 4 × 5 cm aneurysm was encountered. Repair consisted of aneurysm resection, high ligation of the greater saphenous vein, dissociation of the great saphenous and anterior saphenous veins, and stab phlebectomy of large varicose veins of the thigh and lower leg. The patient recovered uneventfully and experienced complete healing of the venous stasis ulcer in several weeks. Superficial venous aneurysms of the lower extremity are rare and can be often missed on preoperative duplex ultrasound imaging. Large diameter measurements of the proximal greater saphenous vein and obesity increase the risk of misdiagnosing venous aneurysms with duplex imaging; therefore, clinical suspicion must remain high. These aneurysms can be associated with significant symptoms for which repair is indicated.

Duplex-assisted carotid artery stenting without administration of contrast medium for patients with chronic kidney disease or allergic reaction.

PubMed

Mizowaki, Takashi; Fujita, Atsushi; Imahori, Taichiro; Uyama, Atsushi; Inoue, Satoshi; Kohta, Masaaki; Hamaguchi, Hirotoshi; Sasayama, Takashi; Hosoda, Kohkichi; Kohmura, Eiji

2016-07-01

We aimed to investigate the safety and feasibility of duplex-assisted carotid artery stenting (CAS) without administration of contrast medium for the prevention of adverse reactions. Fifteen patients (9 % of all CASs) with severe carotid stenosis (≥70 %) associated with chronic kidney disease (CKD) (stage ≥3) or allergy to contrast medium underwent duplex-assisted CAS without administration of contrast medium over 4 years. The procedural success rate and perioperative complication rates were compared between the duplex-assisted CAS (n = 15) and conventional CAS (n = 153) groups. The technical success rate was 100 % in both groups. Combined stroke or death rates during the post-procedural period did not differ significantly between the duplex-assisted CAS group (0/15, 0 %) and conventional CAS group (4/153, 2.6 %). None of the 14 patients with CKD in the duplex-assisted CAS group experienced further deterioration of renal function. The mean surface radiation dose of participants in the duplex-assisted CAS group (n = 13, 312 ± 131 mGy) was significantly lower than that of the conventional CAS group (n = 31, 1036 ± 571 mGy) (p < 0.001). The mean duration of CAS procedure was not significantly different between the duplex-assisted CAS group (156 ± 39.7 min) and the conventional CAS group (156 ± 37.4 min). Duplex-assisted CAS without administration of contrast medium could be an alternative option in selected patients deemed to be at high risk for renal failure from nephrotoxic contrast medium or who have an allergy to contrast medium.

Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy.

PubMed

Dutta, Samrat; Armitage, Bruce A; Lyubchenko, Yuri L

2016-03-15

Peptide nucleic acids (PNA) are synthetic polymers, the neutral peptide backbone of which provides elevated stability to PNA-PNA and PNA-DNA hybrid duplexes. It was demonstrated that incorporation of diethylene glycol (miniPEG) at the γ position of the peptide backbone increased the thermal stability of the hybrid duplexes (Sahu, B. et al. J. Org. Chem. 2011, 76, 5614-5627). Here, we applied atomic force microscopy (AFM) based single molecule force spectroscopy and dynamic force spectroscopy (DFS) to test the strength and stability of the hybrid 10 bp duplex. This hybrid duplex consisted of miniPEGγ-PNA and DNA of the same length (γ(MP)PNA-DNA), which we compared to a DNA duplex with a homologous sequence. AFM force spectroscopy data obtained at the same conditions showed that the γ(MP)PNA-DNA hybrid is more stable than the DNA counterpart, 65 ± 15 pN vs 47 ± 15 pN, respectively. The DFS measurements performed in a range of pulling speeds analyzed in the framework of the Bell-Evans approach yielded a dissociation constant, koff ≈ 0.030 ± 0.01 s⁻¹ for γ(MP)PNA-DNA hybrid duplex vs 0.375 ± 0.18 s⁻¹ for the DNA-DNA duplex suggesting that the hybrid duplex is much more stable. Correlating the high affinity of γ(MP)PNA-DNA to slow dissociation kinetics is consistent with prior bulk characterization by surface plasmon resonance. Given the growing interest in γ(MP)PNA as well as other synthetic DNA analogues, the use of single molecule experiments along with computational analysis of force spectroscopy data will provide direct characterization of various modifications as well as higher order structures such as triplexes and quadruplexes.

The Crystal Structure of Non-Modified and Bipyridine-Modified PNA Duplexes

PubMed Central

Yeh, Joanne I.; Pohl, Ehmke; Truan, Daphne; He, Wei; Sheldrick, George M.; Du, Shoucheng; Achim, Catalina

2011-01-01

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)2 (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes. PMID:20859960

Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

PubMed Central

Toh, Desiree-Faye Kaixin; Devi, Gitali; Patil, Kiran M.; Qu, Qiuyu; Maraswami, Manikantha; Xiao, Yunyun; Loh, Teck Peng; Zhao, Yanli; Chen, Gang

2016-01-01

RNA duplex regions are often involved in tertiary interactions and protein binding and thus there is great potential in developing ligands that sequence-specifically bind to RNA duplexes. We have developed a convenient synthesis method for a modified peptide nucleic acid (PNA) monomer with a guanidine-modified 5-methyl cytosine base. We demonstrated by gel electrophoresis, fluorescence and thermal melting experiments that short PNAs incorporating the modified residue show high binding affinity and sequence specificity in the recognition of an RNA duplex containing an internal inverted Watson-Crick C-G base pair. Remarkably, the relatively short PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. The attached guanidine group stabilizes the base triple through hydrogen bonding with the G base in a C-G pair. Selective binding towards an RNA duplex over a single-stranded RNA can be rationalized by the fact that alkylation of the amine of a 5-methyl C base blocks the Watson–Crick edge. PNAs incorporating multiple guanidine-modified cytosine residues are able to enter HeLa cells without any transfection agent. PMID:27596599

Duplex-guided percutaneous transluminal angioplasty in iliac arterial occlusive disease.

PubMed

Krasznai, A G; Sigterman, T A; Welten, R J; Heijboer, R; Sikkink, C J J M; van de Akker, L H J M; Bouwman, L H

2013-11-01

Chronic renal insufficiency (CRI) is a growing global problem. PTA can be performed without nephrotoxic contrast, utilizing Doppler-ultrasound (Duplex) guidance. Duplex-guided infra-inguinal interventions and access-related interventions have been reported. Duplex-guided iliac interventions have not been performed to any extent because of the anatomic location. In our study we evaluated the safety and efficacy of Duplex-guided percutaneous transluminal angioplasty (DuPTA) in iliac arteries. From June 2012 until February 2013, 31 patients (35 iliac lesions), underwent DuPTA. Indications ranged from Rutherford 3 to 5. Preoperative evaluation included Ankle Brachial Index (ABI), Duplex and MRA. Procedural success was defined as crossing the lesion with a guidewire and dilating or stenting the lesion. Clinical success was defined as 50% reduction in peak systolic velocity (PSV) or clinical improvement. PSV was evaluated after PTA, then at 2 weeks. Clinical results were assessed 2 weeks after the procedure. Procedural success was achieved in 94% of patients (33/35), all of whom also had clinical success. Post-procedural PSV reduction showed an average improvement of 63% (431 cm/s to 153 cm/s). Mean preoperative ABI was 0.72 and improved to 0.88 postoperatively. PTA using Duplex-guidance in significant iliac stenosis is a safe method with major advantages in patients at high risk for developing contrast-induced nephropathy. Copyright © 2013 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

The microstructure and formation of duplex and black plessite in iron meteorites

NASA Technical Reports Server (NTRS)

Zhang, J.; Williams, D. B.; Goldstein, J. I.

1993-01-01

Two of the most common plessite structures, duplex and black plessite, in the taenite region of the Windmanstatten pattern of two iron meteorites (Grant and Carlton) are characterized using high-resolution electron microscopy and microanalysis techniques. Two types of gamma precipitates, found in the duplex plessite and black plessite regions, respectively, are identified, and their morphologies are described. The formation of the plessite structure is discussed using the information obtained in this study and results of a parallel investigation of decomposed martensitic Fe-Ni laboratory alloys.

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

NASA Astrophysics Data System (ADS)

Hari, Yvonne; Dugovič, Branislav; Istrate, Alena; Fignolé, Annabel; Leumann, Christian J.; Schürch, Stefan

2016-07-01

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

Duplex/quadruplex oligonucleotides: Role of the duplex domain in the stabilization of a new generation of highly effective anti-thrombin aptamers.

PubMed

Russo Krauss, Irene; Napolitano, Valeria; Petraccone, Luigi; Troisi, Romualdo; Spiridonova, Vera; Mattia, Carlo Andrea; Sica, Filomena

2018-02-01

Recently, mixed duplex/quadruplex oligonucleotides have attracted great interest for use as biomedical aptamers. In the case of anti-thrombin aptamers, the addition of duplex-forming sequences to a G-quadruplex module identical or very similar to the best-known G-quadruplex of the Thrombin Binding Aptamer (HD1) results in new or improved biological properties, such as higher activity or different recognition properties with respect to HD1. Remarkably, this bimodular fold was hypothesized, based on its sequence, for the only anti-thrombin aptamer in advanced clinical trial, NU172. Whereas cation modulation of G-quadruplex conformation and stability is well characterized, only few data from similar analysis on duplex/quadruplex oligonucleotides exist. Here we have performed a characterization of structure and stability of four different duplex/quadruplex anti-thrombin aptamers, including NU172, in the presence of different cations and in physiological-mimicking conditions in comparison to HD1, by means of spectroscopic techniques (UV and circular dichroism) and differential scanning calorimetry. Our data show a strong reciprocal influence of each domain on the stability of the other and in particular suggest a stabilizing effect of the duplex region in the presence of solutions mimicking the physiological conditions, strengthening the idea that bimodular aptamers present better therapeutic potentialities than those containing a single G-quadruplex domain. Copyright © 2017 Elsevier B.V. All rights reserved.

The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”

PubMed Central

Lee, Joon-Hwa; Bae, Sung-Hun; Choi, Byong-Seok

2000-01-01

In contrast to the highly mutagenic pyrimidine(6–4)pyrimidone photoproduct, its Dewar valence isomer (Dewar product) has low mutagenic potential and produces a broad range of mutations [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991) Proc. Natl. Acad. Sci. USA 88, 9685–9689]. To determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar-lesion DNA decamer duplex. This DNA decamer duplex (DW/GA duplex) contains a mismatched base pair between the 3′ T residue of the Dewar lesion (T6) and an opposed G residue (G15). The 3′ T (T6) of the Dewar lesion formed stable hydrogen bonds with the opposing G15 residue. However, the helical bending and unwinding angles of the DW/GA duplex were much larger than those of a second duplex that contains the Dewar lesion and opposing A15 and A16 residues (DW/AA duplex). The DW/GA duplex showed poorer stacking interactions at the two bases of the Dewar product and at the adjacent A7⋅T14 base pair than did the DW/AA duplex. These structural features imply that no thermal stability or conformational benefit is obtained by incorporating a G instead of an A opposite the 3′ T of the Dewar lesion. These properties may thus facilitate the preferential incorporation of an A in accordance with the A rule during translesion replication and lead to the low frequency of 3′ T→C mutations observed at this site. PMID:10758155

Genotyping by alkaline dehybridization using graphically encoded particles.

PubMed

Zhang, Huaibin; DeConinck, Adam J; Slimmer, Scott C; Doyle, Patrick S; Lewis, Jennifer A; Nuzzo, Ralph G

2011-03-01

This work describes a nonenzymatic, isothermal genotyping method based on the kinetic differences exhibited in the dehybridization of perfectly matched (PM) and single-base mismatched (MM) DNA duplexes in an alkaline solution. Multifunctional encoded hydrogel particles incorporating allele-specific oligonucleotide (ASO) probes in two distinct regions were fabricated by using microfluidic-based stop-flow lithography. Each particle contained two distinct ASO probe sequences differing at a single base position, and thus each particle was capable of simultaneously probing two distinct target alleles. Fluorescently labeled target alleles were annealed to both probe regions of a particle, and the rate of duplex dehybridization was monitored by using fluorescence microscopy. Duplex dehybridization was achieved through an alkaline stimulus using either a pH step function or a temporal pH gradient. When a single target probe sequence was used, the rate of mismatch duplex dehybridization could be discriminated from the rate of perfect match duplex dehybridization. In a more demanding application in which two distinct probe sequences were used, we found that the rate profiles provided a means to discriminate probe dehybridizations from both of the two mismatched duplexes as well as to distinguish at high certainty the dehybridization of the two perfectly matched duplexes. These results demonstrate an ability of alkaline dehybridization to correctly discriminate the rank hierarchy of thermodynamic stability among four sets of perfect match and single-base mismatch duplexes. We further demonstrate that these rate profiles are strongly temperature dependent and illustrate how the sensitivity can be compensated beneficially by the use of an actuating gradient pH field. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular detection of infectious bronchitis and Newcastle disease viruses in broiler chickens with respiratory signs using Duplex RT-PCR.

PubMed

Saba Shirvan, Aylar; Mardani, Karim

2014-01-01

Infectious bronchitis (IB) and Newcastle disease (ND) are highly contagious and the most economically important diseases of the poultry affecting respiratory tract and causing economic losses in poultry industry throughout the world. In the present study, the simultaneous detection and differentiation of causative agents of these diseases were investigated using duplex-RT-PCR. RNA was extracted from vaccinal and reference strains of infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) and then cDNA was synthesized. Using two universal primer sets for detection of IBV and NDV, the duplex-RT-PCR was developed. In order to assess the efficiency of the developed duplex RT-PCR, a number of 12 broiler farms with the symptoms of respiratory tract infection was sampled (trachea, lung and kidney were sampled from affected birds suspicious for IBV and NDV infections). After RNA extraction from tissues and cDNA synthesis, the presence of IBV and NDV genome were investigated using duplex-PCR. The results showed that three of twelve examined broiler farms were positive for IBV and two farms were positive for NDV and IBV. The results revealed that the duplex-RT-PCR is a quick and sensitive procedure for simultaneously detecting IBV and NDV in birds with respiratory infections.

Reversed-phase ion-pair liquid chromatography method for purification of duplex DNA with single base pair resolution

PubMed Central

Wysoczynski, Christina L.; Roemer, Sarah C.; Dostal, Vishantie; Barkley, Robert M.; Churchill, Mair E. A.; Malarkey, Christopher S.

2013-01-01

Obtaining quantities of highly pure duplex DNA is a bottleneck in the biophysical analysis of protein–DNA complexes. In traditional DNA purification methods, the individual cognate DNA strands are purified separately before annealing to form DNA duplexes. This approach works well for palindromic sequences, in which top and bottom strands are identical and duplex formation is typically complete. However, in cases where the DNA is non-palindromic, excess of single-stranded DNA must be removed through additional purification steps to prevent it from interfering in further experiments. Here we describe and apply a novel reversed-phase ion-pair liquid chromatography purification method for double-stranded DNA ranging in lengths from 17 to 51 bp. Both palindromic and non-palindromic DNA can be readily purified. This method has the unique ability to separate blunt double-stranded DNA from pre-attenuated (n-1, n-2, etc) synthesis products, and from DNA duplexes with single base pair overhangs. Additionally, palindromic DNA sequences with only minor differences in the central spacer sequence of the DNA can be separated, and the purified DNA is suitable for co-crystallization of protein–DNA complexes. Thus, double-stranded ion-pair liquid chromatography is a useful approach for duplex DNA purification for many applications. PMID:24013567

Duplex Design Project: Science Pilot Test.

ERIC Educational Resources Information Center

Center for Research on Evaluation, Standards, and Student Testing, Los Angeles, CA.

Work is reported towards the completion of a prototype duplex-design assessment instrument for grade-12 science. The student course-background questionnaire and the pretest section of the two-stage instrument that was developed were administered to all 134 12th-grade students at St. Clairsville High School (Ohio). Based on the information obtained…

46. (Credit LSU) High service pumping room, c1904. The # ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

46. (Credit LSU) High service pumping room, c1904. The # 1 Worthington horizontal, triple expansion, high service engine is in the background. The pump whose steam end is in the foreground is a Blake compound, duplex horizontal engine, installed c1904. The engine in the center of the illustration is one of the original 1887 Blake high service engines (compound, duplex). It was shortly after removed. (From: Shreveport Progressive League, Shreveport of To-Day, September 1904, p. 47) - McNeil Street Pumping Station, McNeil Street & Cross Bayou, Shreveport, Caddo Parish, LA

Venous filling time using air-plethysmography correlates highly with great saphenous vein reflux time using duplex.

PubMed

Lattimer, C R; Azzam, M; Kalodiki, E; Geroulakos, G

2014-03-01

Venous filling time (VFT90) is the time taken to reach 90% of the venous volume in the calf. It is recorded by air-plethysmography (APG(®)) and is assumed to measure global venous reflux duration. However, this has never been confirmed by duplex. The aim of the study was to compare VFT on APG to venous reflux time/duration (RT) measured simultaneously with duplex on the same patients. Twenty-six consecutive patients, M:F = 16:10, age (25-78), C1 = 1, C2 = 4, C3 = 8, C4a = 6, C4b = 4, C5 = 2, C6 = 1, underwent simultaneous APG with duplex. The venous filling index (VFI, mL/second), VFT90 (seconds), great saphenous vein (GSV) RT on duplex, averaged thigh GSV diameter and thigh length (length) between the APG sensor air-cuff and duplex transducer were recorded. The VFT100 was calculated by VFT90/0.9. The additional time taken to fill the thigh was achieved using the VFI, length and deep vein diameter (d), to determine the corrected reflux duration: CRD = VFT100 + (length × πd(2)/4 (1/VFI)). Twenty-five patients are presented. One patient with very mild reflux (VFT90 = 55.9 seconds) had an indeterminate endpoint on duplex and was excluded. The median (range) VFI and GSV diameter was 4.9(1.3-15.5) mL/second and 7(4-17) mm, respectively. The VFT90 and VFT100 both correlated with RT on duplex (Spearman, P < 0.0005) at: r = 0.933, r(2) linear = 0.72 and r = 0.933, r(2) linear = 0.68, respectively. The median (interquartile range) filling time with VFT90 was less than the duplex RT at 24 (16.9) versus 28 (20) seconds respectively, P < 0.0005 (Wilcoxon). The median percentage underestimation improved from 24% to 16% and then 4% using the VFT90, VFT100 and CRD, respectively. This is the first study to compare APG parameters with duplex by performing simultaneous measurements. There was an excellent correlation between the VFT90 versus duplex RT, thereby comparing reverse flow in a single superficial vein against the legs overall venous haemodynamic status. These tests can both be used in the quantification of reflux.

On the Formation and Properties of Interstrand DNA-DNA Cross-links Forged by Reaction of an Abasic Site With the Opposing Guanine Residue of 5′-CAp Sequences in Duplex DNA

PubMed Central

Johnson, Kevin M.; Price, Nathan E.; Wang, Jin; Fekry, Mostafa I.; Dutta, Sanjay; Seiner, Derrick R.; Wang, Yinsheng; Gates, Kent S.

2014-01-01

We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5′-CAp sequence under conditions of reductive amination (NaCNBH3, pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions and, once formed, the cross-link was stable to a variety of work-up conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LCMS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N2-amino group of the opposing guanine residue in 5′-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH3/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N2-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH3. PMID:23215239

United States Air Force Research Initiation Program for 1988. Volume 3

DTIC Science & Technology

1990-04-01

Assignment for Dr. Kenneth M. Sobel Flight Control Design 210-9MG-035 90 Comparative Burning Rates and Duplex Dr. Forrest Thomas (1987) Loads of Solid...Patterson Air Force Base. The test configuration has been designed for injecting fuel droplets in a well controlled laminar on well-characterized turbulent...its counter response may be significant, our system has thus achieved some measure of control over when non -critical processing is actually performed

Low-Load Space Conditioning Needs Assessment

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

Puttagunta, Srikanth

Heating, ventilating, and air-conditioning (HVAC) equipment must be right-sized to ensure energy performance and comfort. With limited low-load options in the HVAC market, many new-construction housing units are being fitted with oversized equipment that creates system efficiency, comfort, and cost penalties. To bridge the gap between currently available HVAC equipment that is oversized or inefficient and the rising demand for low-load HVAC equipment in the marketplace, HVAC equipment manufacturers need to be fully aware of the needs of the multifamily building and attached single-family (duplex and townhouse) home market. Over the past decade, Steven Winter Associates, Inc. (SWA) has providedmore » certification and consulting services for hundreds of housing projects and has accrued a large pool of data that describe multifamily and attached single-family home characteristics. The U.S. Department of Energy’s Building America research team Consortium for Advanced Residential Buildings (CARB) compiled and analyzed these data to outline the characteristics of low-load dwellings such as the heating and cooling design loads.« less

CMOS serial link for fully duplexed data communication

NASA Astrophysics Data System (ADS)

Lee, Kyeongho; Kim, Sungjoon; Ahn, Gijung; Jeong, Deog-Kyoon

1995-04-01

This paper describes a CMOS serial link allowing fully duplexed 500 Mbaud serial data communication. The CMOS serial link is a robust and low-cost solution to high data rate requirements. A central charge pump PLL for generating multiphase clocks for oversampling is shared by several serial link channels. Fully duplexed serial data communication is realized in the bidirectional bridge by separating incoming data from the mixed signal on the cable end. The digital PLL accomplishes process-independent data recovery by using a low-ratio oversampling, a majority voting, and a parallel data recovery scheme. Mostly, digital approach could extend its bandwidth further with scaled CMOS technology. A single channel serial link and a charge pump PLL are integrated in a test chip using 1.2 micron CMOS process technology. The test chip confirms upto 500 Mbaud unidirectional mode operation and 320 Mbaud fully duplexed mode operation with pseudo random data patterns.

Gadolinium-enhanced versus time-of-flight magnetic resonance angiography: what is the benefit of contrast enhancement in evaluating carotid stenosis?

PubMed

Muhs, Bart E; Gagne, Paul; Wagener, Jael; Baker, Jessica; Ortega, Marta Ramirez; Adelman, Mark A; Cayne, Neal S; Rockman, Caron B; Maldonado, Thomas

2005-11-01

Accurate patient selection based on preoperative imaging is imperative to good risk reduction in patients undergoing carotid endarterectomy (CEA). The goal of this study was to assess the accuracy of gadolinium-enhanced magnetic resonance angiography (GE MRA) versus time-of-flight (TOF) MRA in the work-up of patients undergoing CEA. Patients undergoing CEA between 1999 and 2001 were identified from a prospectively maintained institutional database. GE or TOF MRA was obtained on extracranial carotid arteries (n = 319) in patients undergoing CEA. Stenosis on MRA images was graded as moderate (n = 76) or severe (n = 243) by an attending radiologist who was blind to duplex results. Duplex imaging was performed in an Intersocietal Commission for the Accreditation of Vascular Labs (ICAVL) accredited lab, and stenosis was stratified as moderate (50-79%, n = 76) or high (80-99%, n = 243) grade using University of Washington criteria. For each patient, the degree of stenosis as determined by MRA (GE versus TOF) was compared to percent stenosis on duplex. For moderate-grade lesions, GE MRA concurred with duplex in 11.1% (4/36), underestimated in 2.8% (1/36), and overestimated in 86.1% (31/36) of carotid arteries imaged. TOF MRA concurred with duplex in 35% (14/40), underestimated in 0% (0/40), and overestimated in 65% (26/40) of carotid arteries. High-grade lesions demonstrated improved concordance between MRA and duplex. For these lesions, GE MRA concurred with duplex in 95.6% (130/136) of carotid arteries imaged, never overestimated stenosis (0/136), and underestimated in 4.4% (6/136). TOF MRA concurred with duplex 96.3% (103/107), overestimated stenosis as an occlusion in 0.9% (1/107), and underestimated in 2.8% (3/107). In addition to neck visualization, the GE technique allowed simultaneous aortic arch imaging. This was accomplished in 79.1% (136/172) of all GE MRAs. Simultaneous aortic arch imaging was not technically feasible with TOF MRA. For moderate-grade lesions, both MR techniques are inaccurate predictors of degree of carotid stenosis and result in a significant overestimation of stenosis. Each technique demonstrates improved concordance with duplex ultrasound in the setting of severe carotid artery stenoses. The ability of GE MRA to simultaneously image the aortic arch and the neck may allow for detection of occult tandem lesions and other anatomic variations, which may be particularly important in preoperative planning for carotid artery stenting.

Comparison of duplex ultrasound with digital subtraction angiography in the assessment of infra-inguinal autologous vein bypass grafts.

PubMed

Griffin, Nick M R; Wright, Isabel A; Buckenham, Tim M

2006-11-01

Postoperative surveillance of infra-inguinal vein grafts has arisen because of the high incidence of vein graft stenoses, which frequently progress to vein graft occlusion. The use of duplex ultrasound as the primary imaging method for graft surveillance is well established. This study aims to compare the accuracy of duplex ultrasound with the reference standard of digital subtraction angiography in the assessment of infra-inguinal vein grafts. Sixty patients underwent routine postoperative duplex ultrasound as part of the local graft surveillance programme. Angiography was subsequently carried out on 18 grafts. Each lower limb arterial tree was divided into three segments (native arteries proximal to the graft, the graft itself and native arteries distal to the graft) resulting in a total of 42 comparisons. Degree of diameter stenosis on ultrasound was compared with angiography findings to determine concordance. Agreement was also expressed as a kappa value. Overall accuracy of duplex ultrasound was 88% (37/42). A kappa value of 0.80 indicates good agreement. In three of the five discordant cases, ultrasound correctly identified a stenosis, but overestimated the degree of stenosis compared with angiography. In each of the remaining two discordant cases, ultrasound identified a focal stenosis that was not apparent on angiography. In both cases, the area of duplex described abnormality responded to balloon angioplasty. Duplex ultrasound as part of the local vein graft surveillance programme is a reliable and accurate method in the detection of failing grafts and in some instances may be more sensitive.

[Can TOF MRA replace duplex and Doppler sonography in preoperative assessment of the carotid arteries? A prospective comparison and review of the literature].

PubMed

Krappel, F A; Bauer, E; Harland, U

2002-01-01

To examine the quality and usefulness of time-of-flight MR-angiography and duplex-doppler sonography, respectively, in assessment of the extracranial arteries before cervical spine operations. Patients scheduled for operations of the cervical spine had an MRI plus TOF as well as a duplex and Doppler scan. At the time of the examination the radiologist and the neurologist in charge were blinded for the study. Endpoints were not only the accuracy of the procedures but more so which method improved the preoperative process most. Twenty patients were examined so far. Only in one case did the result differ when a complete occlusion diagnosed sonographically was judged as a severe stenosis on MRA. One patient did not tolerate the MRA for the extra 5 minutes necessary, therefore a contrast-enhanced MRA was performed. MRA eased the preoperative process as imaging of the pathology and the carotids were realised in one step. The costs were slightly higher for MRA than for duplex-doppler sonography. TOF-MRA can replace the duplex-doppler examination in the preoperative assessment of the carotids and has the potential to streamline the preoperative time schedule. Similar to duplex and doppler, in order to be accurate enough the method requires a high degree of expertise from the radiologist.

Microstructure and Antiwear Property of Laser Cladding Ni-Co Duplex Coating on Copper.

PubMed

Wang, Yiyong; Liang, Zhipeng; Zhang, Junwei; Ning, Zhe; Jin, Hui

2016-07-28

Ni-Co duplex coatings were cladded onto Cu to improve the antiwear properties of Cu products. Prior to laser cladding, n-Al₂O₃/Ni layers were introduced as interlayers between laser cladding coatings and Cu substrates to improve the laser absorptivity of these substrates and ensure defect-free laser cladding coatings. The structure and morphology of the coatings were characterized by scanning electron microscopy and optical microscopy, and the phases of the coatings were analyzed by X-ray diffraction. Their hardness was measured using a microhardness tester. Experimental results showed that defect-free composite coatings were obtained and that the coatings were metallurgically bonded to the substrates. The surface of the Ni-Co duplex coatings comprised a Co-based solid solution, Cr₇C₃, (Fe,Ni) 23 C₆, and other strengthening phases. The microhardness and wear resistance of the duplex coatings were significantly improved compared with the Cu substrates. The average microhardness of the cladded coatings was 845.6 HV, which was approximately 8.2 times greater than that of the Cu substrates (102.6 HV). The volume loss of the Cu substrates was approximately 7.5 times greater than that of the Ni-Co duplex coatings after 60 min of sliding wear testing. The high hardness of and lack of defects in the Ni-Co duplex coatings reduced the plastic deformation and adhesive wear of the Cu substrates, resulting in improved wear properties.

Electromagnetic Interaction between the Component Coils of Multi-Plex Magnets

DOE PAGES

Nguyen, Quyen V. M.; Torrez, Lynette; Nguyen, Doan Ngoc

2017-12-04

Ultra-high field pulsed magnets are usually designed as a group of nested, concentric coils driven by separated power sources to reduce the required driving voltages and to distribute the mechanical load and to reduce the driving voltages. Since the magnet operates in a fast transient mode, there will be strong and complicated electromagnetic couplings between the component coils. The high eddy currents generated in the reinforcement shells of the component coils during the pulses also strongly affect these couplings. Therefore, understanding the electromagnetic interaction between the component coils will allow safer, more optimized design and operation of our magnets. Asmore » a result, this paper will focus on our finite element modeling and experimental results for the electromagnetic interactions between the component coils of the 100-T nondestructive magnet and 80-T duplex magnet at our facility.« less

Electromagnetic Interaction between the Component Coils of Multi-Plex Magnets

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

Nguyen, Quyen V. M.; Torrez, Lynette; Nguyen, Doan Ngoc

Ultra-high field pulsed magnets are usually designed as a group of nested, concentric coils driven by separated power sources to reduce the required driving voltages and to distribute the mechanical load and to reduce the driving voltages. Since the magnet operates in a fast transient mode, there will be strong and complicated electromagnetic couplings between the component coils. The high eddy currents generated in the reinforcement shells of the component coils during the pulses also strongly affect these couplings. Therefore, understanding the electromagnetic interaction between the component coils will allow safer, more optimized design and operation of our magnets. Asmore » a result, this paper will focus on our finite element modeling and experimental results for the electromagnetic interactions between the component coils of the 100-T nondestructive magnet and 80-T duplex magnet at our facility.« less

Properties of Native High-Density Lipoproteins Inspire Synthesis of Actively Targeted In Vivo siRNA Delivery Vehicles.

PubMed

McMahon, Kaylin M; Plebanek, Michael P; Thaxton, C Shad

2016-11-15

Efficient systemic administration of therapeutic short interfering RNA (siRNA) is challenging. High-density lipoproteins (HDL) are natural in vivo RNA delivery vehicles. Specifically, native HDLs: 1) Load single-stranded RNA; 2) Are anionic, which requires charge reconciliation between the RNA and HDL, and 3) Actively target scavenger receptor type B-1 (SR-B1) to deliver RNA. Emphasizing these particular parameters, we employed templated lipoprotein particles (TLP), mimics of spherical HDLs, and self-assembled them with single-stranded complements of, presumably, any highly unmodified siRNA duplex pair after formulation with a cationic lipid. Resulting siRNA templated lipoprotein particles (siRNA-TLP) are anionic and tunable with regard to RNA assembly and function. Data demonstrate that the siRNA-TLPs actively target SR-B1 to potently reduce androgen receptor (AR) and enhancer of zeste homolog 2 (EZH2) proteins in multiple cancer cell lines. Systemic administration of siRNA-TLPs demonstrated no off-target toxicity and significantly reduced the growth of prostate cancer xenografts. Thus, native HDLs inspired the synthesis of a hybrid siRNA delivery vehicle that can modularly load single-stranded RNA complements after charge reconciliation with a cationic lipid, and that function due to active targeting of SR-B1.

Toward a 3D dynamic model of a faulty duplex ball bearing

NASA Astrophysics Data System (ADS)

Kogan, Gideon; Klein, Renata; Kushnirsky, Alex; Bortman, Jacob

2015-03-01

Bearings are vital components for safe and proper operation of machinery. Increasing efficiency of bearing diagnostics usually requires training of health and usage monitoring systems via expensive and time-consuming ground calibration tests. The main goal of this research, therefore, is to improve bearing dynamics modeling tools in order to reduce the time and budget needed to implement the health and usage monitoring approach. The proposed three-dimensional ball bearing dynamic model is based on the classic dynamic and kinematic equations. Interactions between the bodies are simulated using non-linear springs combined with dampers described by Hertz-type contact relation. The force friction is simulated using the hyperbolic-tangent function. The model allows simulation of a wide range of mechanical faults. It is validated by comparison to known bearing behavior and to experimental results. The model results are verified by demonstrating numerical convergence. The model results for the two cases of single and duplex angular ball bearings with axial deformation in the outer ring are presented. The qualitative investigation provides insight into bearing dynamics, the sensitivity study generalizes the qualitative findings for similar cases, and the comparison to the test results validates model reliability. The article demonstrates the variety of the cases that the 3D bearing model can simulate and the findings to which it may lead. The research allowed the identification of new patterns generated by single and duplex bearings with axially deformed outer race. It also enlightened the difference between single and duplex bearing manifestation. In the current research the dynamic model enabled better understanding of the physical behavior of the faulted bearings. Therefore, it is expected that the modeling approach has the potential to simplify and improve the development process of diagnostic algorithms. • A deformed outer race of a single axially loaded bearing is simulated. • The model results are subjected to a sensitivity study. • Duplex bearing with deformed outer race is simulated as well as tested. • The simulation results are in a good agreement with the experimental results.

An unusual mode of DNA duplex association: Watson-Crick interaction of all-purine deoxyribonucleic acids.

PubMed

Battersby, Thomas R; Albalos, Maria; Friesenhahn, Michel J

2007-05-01

Nucleic acid duplexes associating through purine-purine base pairing have been constructed and characterized in a remarkable demonstration of nucleic acids with mixed sequence and a natural backbone in an alternative duplex structure. The antiparallel deoxyribose all-purine duplexes associate specifically through Watson-Crick pairing, violating the nucleobase size-complementarity pairing convention found in Nature. Sequence-specific recognition displayed by these structures makes the duplexes suitable, in principle, for information storage and replication fundamental to molecular evolution in all living organisms. All-purine duplexes can be formed through association of purines found in natural ribonucleosides. Key to the formation of these duplexes is the N(3)-H tautomer of isoguanine, preferred in the duplex, but not in aqueous solution. The duplexes have relevance to evolution of the modern genetic code and can be used for molecular recognition of natural nucleic acids.

Assessment of Stress Corrosion Cracking Resistance of Activated Tungsten Inert Gas-Welded Duplex Stainless Steel Joints

NASA Astrophysics Data System (ADS)

Alwin, B.; Lakshminarayanan, A. K.; Vasudevan, M.; Vasantharaja, P.

2017-12-01

The stress corrosion cracking behavior of duplex stainless steel (DSS) weld joint largely depends on the ferrite-austenite phase microstructure balance. This phase balance is decided by the welding process used, heat input, welding conditions and the weld metal chemistry. In this investigation, the influence of activated tungsten inert gas (ATIG) and tungsten inert gas (TIG) welding processes on the stress corrosion cracking (SCC) resistance of DSS joints was evaluated and compared. Boiling magnesium chloride (45 wt.%) environment maintained at 155 °C was used. The microstructure and ferrite content of different weld zones are correlated with the outcome of sustained load, SCC test. Irrespective of the welding processes used, SCC resistance of weld joints was inferior to that of the base metal. However, ATIG weld joint exhibited superior resistance to SCC than the TIG weld joint. The crack initiation and final failure were in the weld metal for the ATIG weld joint; they were in the heat-affected zone for the TIG weld joint.

Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks

NASA Astrophysics Data System (ADS)

Singleton, Martin R.; Dillingham, Mark S.; Gaudier, Martin; Kowalczykowski, Stephen C.; Wigley, Dale B.

2004-11-01

RecBCD is a multi-functional enzyme complex that processes DNA ends resulting from a double-strand break. RecBCD is a bipolar helicase that splits the duplex into its component strands and digests them until encountering a recombinational hotspot (Chi site). The nuclease activity is then attenuated and RecBCD loads RecA onto the 3' tail of the DNA. Here we present the crystal structure of RecBCD bound to a DNA substrate. In this initiation complex, the DNA duplex has been split across the RecC subunit to create a fork with the separated strands each heading towards different helicase motor subunits. The strands pass along tunnels within the complex, both emerging adjacent to the nuclease domain of RecB. Passage of the 3' tail through one of these tunnels provides a mechanism for the recognition of a Chi sequence by RecC within the context of double-stranded DNA. Gating of this tunnel suggests how nuclease activity might be regulated.

Renal pelvis urothelial carcinoma of the upper moiety in complete right renal duplex: a case report.

PubMed

Zhang, Yiran; Yu, Quanfeng; Zhang, Zhihong; Liu, Ranlu; Xu, Yong

2015-01-01

Urothelial carcinoma (UC) originated from renal pelvis is the common tumor of the urinary system, however, neoplasia of the renal pelvis in duplex kidneys is extremely rare, especially in the complete renal and ureteral duplex cases. We present the first case of renal pelvis UC of the upper moiety in a complete right renal duplex. This male patient has bilateral complete renal and ureteral duplex. To the best of our knowledge, this is the first reported case of renal pelvis UC in a complete renal duplex system. After this experience we feel that the diagnosis of renal pelvis UC in duplex kidneys is not so easy, and once the diagnosis is determined, the whole renal duplex units and bladder cuff or ectopic orifice should be excised radically.

Microstructure and Antiwear Property of Laser Cladding Ni–Co Duplex Coating on Copper

PubMed Central

Wang, Yiyong; Liang, Zhipeng; Zhang, Junwei; Ning, Zhe; Jin, Hui

2016-01-01

Ni–Co duplex coatings were cladded onto Cu to improve the antiwear properties of Cu products. Prior to laser cladding, n-Al2O3/Ni layers were introduced as interlayers between laser cladding coatings and Cu substrates to improve the laser absorptivity of these substrates and ensure defect-free laser cladding coatings. The structure and morphology of the coatings were characterized by scanning electron microscopy and optical microscopy, and the phases of the coatings were analyzed by X-ray diffraction. Their hardness was measured using a microhardness tester. Experimental results showed that defect-free composite coatings were obtained and that the coatings were metallurgically bonded to the substrates. The surface of the Ni–Co duplex coatings comprised a Co-based solid solution, Cr7C3, (Fe,Ni)23C6, and other strengthening phases. The microhardness and wear resistance of the duplex coatings were significantly improved compared with the Cu substrates. The average microhardness of the cladded coatings was 845.6 HV, which was approximately 8.2 times greater than that of the Cu substrates (102.6 HV). The volume loss of the Cu substrates was approximately 7.5 times greater than that of the Ni–Co duplex coatings after 60 min of sliding wear testing. The high hardness of and lack of defects in the Ni–Co duplex coatings reduced the plastic deformation and adhesive wear of the Cu substrates, resulting in improved wear properties. PMID:28773755

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

PubMed Central

2017-01-01

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M–1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor–acceptor sequences are avoided. PMID:28857551

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.

PubMed

Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

2016-03-22

Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

NASA Astrophysics Data System (ADS)

Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

2016-03-01

Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

Structure and stability of the consecutive stereoregulated chiral phosphorothioate DNA duplex.

PubMed

Kanaori, K; Tamura, Y; Wada, T; Nishi, M; Kanehara, H; Morii, T; Tajima, K; Makino, K

1999-12-07

The duplex structures of the stereoregulated phosphorothioate DNAs, [R(p),R(p)]- and [S(p),S(p)]-[d(GC(ps)T(ps)ACG)] (ps, phosphorothioate; PS-DNA), with their complementary RNA have been investigated by combined use of (1)H NMR and restrained molecular dynamics calculation. Compared to those obtained for the unmodified duplex structures (PO-DNA.RNA), the NOE cross-peak intensities are virtually identical for the PS-DNA.RNA hybrid duplexes. The structural analysis on the basis of the NOE restraints reveals that all of the three DNA.RNA duplexes take a A-form conformation and that there is no significant difference in the base stacking for the DNA.RNA hybrid duplexes. On the other hand, the NOE cross-peak intensities of the protons around the central T(ps)A step of the PS-DNA.DNA duplexes are apparently different from those of PO-DNA. DNA. The chemical shifts of H8/6 and H1' at the T(ps)A step are also largely different among PS-DNA.DNAs and PO-DNA.DNA, suggesting that the DNA.DNA structure is readily changed by the introduction of the phosphorothioate groups to the central T(p)A step. The structure calculations indicate that all of these DNA.DNA duplexes are B-form although there exist some small differences in helical parameters between the [R(p),R(p)]- and [S(p),S(p)]PS-DNA.DNA duplexes. The melting temperatures (T(m)) were determined for all of the duplexes by plotting the chemical shift change of isolated peaks as a function of temperature. For the PS-DNA.RNA hybrid duplexes, the [S(p),S(p)] isomer is less stable than the [R(p),R(p)] isomer while this trend is reversed for the PS-DNA.DNA duplexes. Consequently, although the PS-DNA.RNA duplexes take the similar A-form structure, the duplex stability is different between PS-DNA.RNA duplexes. The stability of the DNA.RNA duplexes may not be governed by the A-form structure itself but by some other factors such as the hydration around the phosphorothioate backbone, although the T(m) difference of the DNA.DNA duplexes could be explained by the structural factor.

Architecture Studies Done for High-Rate Duplex Direct Data Distribution (D4) Services

NASA Technical Reports Server (NTRS)

2002-01-01

A study was sponsored to investigate a set of end-to-end system concepts for implementing a high-rate duplex direct data distribution (D4) space-to-ground communications link. The NASA Glenn Research Center is investigating these systems (both commercial and Government) as a possible method of providing a D4 communications service between NASA spacecraft in low Earth orbit and the respective principal investigators using or monitoring instruments aboard these spacecraft. Candidate commercial services were assessed regarding their near-term potential to provide a D4 type of service. The candidates included K-band and V-band geostationary orbit and nongeostationary orbit satellite relay services and direct downlink (D3) services. Internet protocol (IP) networking technologies were evaluated to enable the user-directed distribution and delivery of science data. Four realistic, near-future concepts were analyzed: 1) A duplex direct link (uplink plus downlink communication paths) between a low-Earth-orbit spacecraft and a principal-investigator-based autonomous Earth station; 2) A space-based relay using a future K-band nongeosynchronous-orbit system to handle both the uplink and downlink communication paths; 3) A hybrid link using both direct and relay services to achieve full duplex capability; 4) A dual-mode concept consisting of both a duplex direct link and a space relay duplex link operating independently. The concepts were analyzed in terms of contact time between the NASA spacecraft and the communications service and the achievable data throughput. Throughput estimates for the D4 systems were based on the infusion of advanced communications technology products (single and multibeam K-band phased-arrays and digital modems) being developed by Glenn. Cost estimates were also performed using extrapolated information from both terrestrial and current satellite communications providers. The throughput and cost estimates were used to compare the concepts.

Detection of Anaplasma marginale and A. phagocytophilum in Bovine Peripheral Blood Samples by Duplex Real-Time Reverse Transcriptase PCR Assay ▿

PubMed Central

Reinbold, James B.; Coetzee, Johann F.; Sirigireddy, Kamesh R.; Ganta, Roman R.

2010-01-01

Insufficient diagnostic sensitivity and specificity coupled with the potential for cross-reactivity among closely related Anaplasma species has made the accurate determination of infection status problematic. A method for the development of simplex and duplex real-time quantitative reverse transcriptase PCR (qRT-PCR) assays for the detection of A. marginale and A. phagocytophilum 16S rRNA in plasma-free bovine peripheral blood samples is described. The duplex assay was able to detect as few as 100 copies of 16S rRNA of both A. marginale and A. phagocytophilum in the same reaction. The ratio of 16S rRNA to 16S DNA copies for A. marginale was determined to be 117.9:1 (95% confidence interval [95% CI], 100.7:1, 135.2:1). Therefore, the detection limit is the minimum infective unit of one A. marginale bacterium. The duplex assay detected nonequivalent molar ratios as high as 100-fold. Additionally, the duplex assay and a competitive enzyme-linked immunosorbent assay (cELISA) were used to screen 237 samples collected from herds in which anaplasmosis was endemic. When the cELISA was evaluated by the results of the qRT-PCR, its sensitivity and specificity for the detection of A. marginale infection were found to be 65.2% (95% CI, 55.3%, 75.1%) and 97.3% (95% CI, 94.7%, 99.9%), respectively. A. phagocytophilum infection was not detected in the samples analyzed. One- and two-way receiver operator characteristic curves were constructed in order to recommend the optimum negative cutoff value for the cELISA. Percentages of inhibition of 20 and 15.3% were recommended for the one- and two-way curves, respectively. In conclusion, the duplex real-time qRT-PCR assay is a highly sensitive and specific diagnostic tool for the accurate and precise detection of A. marginale and A. phagocytophilum infections in cattle. PMID:20463162

Efficacy and safety of Duplex-guided polidocanol foam sclerotherapy for venous malformations.

PubMed

Ali, Haitham; Saleh, Mahmoud; Mohammed, Walid

2017-06-01

The aim of our study was to report our experience regarding the safety, efficacy of duplex-guided polidocanol (POL) foam sclerotherapy on the overall status of signs and symptoms in patients with venous malformations (VMs). Thirty seven patients with symptomatic extratruncular VMs were treated with duplex-guided POL foam sclerotherapy using Tessari's method. Twenty five patients had limited VMs, while twelve had infiltrating VMs. Postsclerotherapy surveillance was done 6 months after the last sclerotherapy session and comprised both clinical and duplex evaluation. Clinical evaluation entailed a patient self-assessment questionnaire using a four-point scale to rate the degree of symptoms improvement as follows: disappeared, decreased, worsened, or recurred. Findings obtained by duplex scanning were divided into four groups: 1) disappeared group; 2) partially recanalized group; 3) totally recanalized group; and 4) worsened group. There were 20 males and 17 females with mean age of 22.8±5.5 years. There was a significant reduction in the total amount of POL (P=0.0037), the number of sclerotherapy sessions was significantly lesser (P=0.0019), and treatment success was significantly higher (P=0.0495) in patients with limited VMs in comparison to those with infiltrating VMs. No major complications related to sclerotherapy were encountered in both groups. Polidocanol foam sclerotherapy is effective, and safe for treatment of VMs, with high success rate and low risk of major complications. Although associated with relatively high recurrence rate compared with ethanol sclerotherapy, this can be overcome by additional treatment sessions, given the relative simplicity, speed, and safety.

Multi-shell model of ion-induced nucleic acid condensation

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

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois

2016-04-21

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes in- duced by tri-valent cobalt hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. The duplex aggregation free energy is de- composed into attraction and repulsion components represented by simple analytic expressions. The source of the short-range attraction between NA duplexes in the aggregated phase is the in- teraction of CoHex ions in the overlapping regions of the “external” shells with the oppositely chargedmore » duplexes. The attraction depends on CoHex binding affinity to the “external” shell of nearly neutralized duplex and the number of ions in the shell overlapping volume. For a given NA duplex sequence and structure, these parameters are estimated from molecular dynamics simula- tion. The attraction is opposed by the residual repulsion of nearly neutralized duplexes as well as duplex configurational entropy loss upon aggregation. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA conden- sation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. The model also predicts that longer NA fragments will condense easier than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation, lends support to proposed NA condensation picture based on the multivalent “ion binding shells”.« less

Duplex Ultrasonography Has Limited Utility in Detection of Postoperative DVT After Primary Total Joint Arthroplasty.

PubMed

Vira, Shaleen; Ramme, Austin J; Alaia, Michael J; Steiger, David; Vigdorchik, Jonathan M; Jaffe, Frederick

2016-07-01

Duplex ultrasound is routinely used to evaluate suspected deep venous thrombosis after total joint arthroplasty. When there is a clinical suspicion for a pulmonary embolism, a chest angiogram (chest CTA) is concomitantly obtained. Two questions were addressed: First, for the population of patients who receive duplex ultrasound after total joint arthroplasty, what is the rate of positive results? Second, for these patients, how many of these also undergo chest CTA for clinical suspicion of pulmonary embolus and how many of these tests are positive? Furthermore, what is the correlation between duplex ultrasound results and chest CTA results? A retrospective chart review was conducted of total joint replacement patients in 2011 at a single institution. Inclusion criteria were adult patients who underwent a postoperative duplex ultrasonography for clinical suspicion of deep venous thrombosis (DVT). Demographic data, result of duplex scan, clinical indications for obtaining the duplex scan, and DVT prophylaxis used were recorded. Additionally, if a chest CTA was obtained for clinical suspicion for pulmonary embolus, results and clinical indication for obtaining the test were recorded. The rate of positive results for duplex ultrasonography and chest CTA was computed and correlated based on clinical indications. Two hundred ninety-five patients underwent duplex ultrasonography of which only 0.7% were positive for a DVT. One hundred three patients underwent a chest CTA for clinical suspicion of a pulmonary embolism (PE) of which 26 revealed a pulmonary embolus, none of which had a positive duplex ultrasound. Postoperative duplex scans have a low rate of positive results. A substantial number of patients with negative duplex results subsequently underwent chest CTA for clinical suspicion for which a pulmonary embolus was found, presumably resulting from a DVT despite negative duplex ultrasound result. A negative duplex ultrasonography should not rule out the presence of a DVT which can embolize to the lungs and thus should not preclude further workup when clinical suspicion exists for a pulmonary embolus.

Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach

NASA Technical Reports Server (NTRS)

Liu, W. T.; Mirzabekov, A. D.; Stahl, D. A.

2001-01-01

The utility of a high-density oligonucleotide microarray (microchip) for identifying strains of five closely related bacilli (Bacillus anthracis, Bacillus cereus, Bacillus mycoides, Bacillus medusa and Bacillus subtilis) was demonstrated using an approach that compares the non-equilibrium dissociation rates ('melting curves') of all probe-target duplexes simultaneously. For this study, a hierarchical set of 30 oligonucleotide probes targeting the 16S ribosomal RNA of these bacilli at multiple levels of specificity (approximate taxonomic ranks of domain, kingdom, order, genus and species) was designed and immobilized in a high-density matrix of gel pads on a glass slide. Reproducible melting curves for probes with different levels of specificity were obtained using an optimized salt concentration. Clear discrimination between perfect match (PM) and mismatch (MM) duplexes was achieved. By normalizing the signals to an internal standard (a universal probe), a more than twofold discrimination (> 2.4x) was achieved between PM and 1-MM duplexes at the dissociation temperature at which 50% of the probe-target duplexes remained intact. This provided excellent differentiation among representatives of different Bacillus species, both individually and in mixtures of two or three. The overall pattern of hybridization derived from this hierarchical probe set also provided a clear 'chip fingerprint' for each of these closely related Bacillus species.

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors.

PubMed

Mosayebi, Majid; Louis, Ard A; Doye, Jonathan P K; Ouldridge, Thomas E

2015-12-22

The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.

Unique Dynamic Properties of DNA Duplexes Containing Interstrand Crosslinks†

PubMed Central

Friedman, Joshua I.; Jiang, Yu Lin; Miller, Paul S.; Stivers, James T.

2010-01-01

Bifunctional DNA alkylating agents form a diverse assortment of covalent DNA interstrand crosslinked (ICL) structures that are potent cytotoxins. Since it is implausible that cells could possess distinct DNA repair systems for each individual ICL, it is believed that common structural and dynamic features of ICL damage are recognized, rather than specific structural characteristics of each cross-linking agent. Investigation of the structural and dynamic properties of ICLs that might be important for recognition has been complicated by heterogeneous incorporation of these lesions into DNA. To address this problem we have synthesized and characterized several homogenous ICL-DNAs containing site–specific staggered N4-cytosine-ethyl-N4-cytosine crosslinks. Staggered crosslinks were introduced in two ways: in a manner that preserves the overall structure of B-form duplex DNA, and in a manner that highly distorts the DNA structure, with the goal of understanding how structural and dynamic properties of diverse ICL duplexes might flag these sites for repair. Measurements of base pair opening dynamics in the B-form ICL duplex by 1H NMR linewidth or imino proton solvent exchange showed that the guanine base opposite to the crosslinked cytosine opened at least an order of magnitude more slowly than when in a control matched normal duplex. To a lesser degree, the B-form ICL also induced a decrease in base pair opening dynamics that extended from the site of the crosslink to adjacent base pairs. In contrast, the non-B-form ICL showed extensive conformational dynamics at the site of the cross link, which extended over the entire DNA sequence. Since DNA duplexes containing the B-form and non-B-form ICL crosslinks have both been shown to be incised when incubated in mammalian whole cell extracts, while a matched normal duplex is not, we conclude that intrinsic DNA dynamics is not a requirement for specific damage incision of these ICLs. Instead, we propose a general model where destabilized ICL-duplexes serve to energetically facilitate binding of DNA repair factors that must induce bubbles or other distortions in the duplex. However, the essential requirement for incision is an immobile Y-junction where the repair factors are stably bound at the site of the ICL, and the two DNA strands are unpaired. PMID:21174443

Zoster duplex: a clinical report and etiologic analysis.

PubMed

Zhang, Feng; Zhou, Jin

2015-01-01

Herpes zoster (HZ) duplex is a rare disease presentation. The mechanisms of varicella zoster virus (VZV) reactivation in multiple dermal regions are unknown. To present a HZ duplex case occurring in an immunocompetent woman and to analyze the possible underlying causes of HZ duplex. We present a HZ duplex case in an immunocompetent woman and analyzed the possible contributing factors in 36 HZ duplex cases. Continuously distributed variables were categorized by numbers and percentages. In our study, 24 cases (66.7%) were from Asia, 16 cases (44.4%) were in individuals ≥ 50 years of age, and 17 cases (47.2%) occurred in immunocompromised patients. Of the 36 cases, 23 involved women (63.9%) and 13 involved men. Eighteen patients suffering from HZ duplex, 13 of which were women (72.2%), did not suffer from any chronic systemic disease or have a long history of taking drugs. HZ duplex is a rare event that can occur in both immunocompetent and immunosuppressed individuals. HZ duplex might be associated with the Asia region, advanced age, immunosuppression, and being female.

Magnetic bead/capture DNA/glucose-loaded nanoliposomes for amplifying the glucometer signal in the rapid screening of hepatitis C virus RNA.

PubMed

Tu, Haijian; Lin, Kun; Lun, Yongzhi; Yu, Liuming

2018-06-01

A digital detection strategy based on a portable personal glucometer (PGM) was developed for the simple, rapid, and sensitive detection of hepatitis C virus (HCV) RNA, involving the release of glucose-loaded nanoliposomes due to coupling-site-specific cleavage by the endonuclease BamHI. The glucose-loaded nanoliposomes were synthesized using a reversed-phase evaporation method and provided an amplified signal at the PGM in the presence of HCV RNA. Initially, a 21-mer oligonucleotide complementary to HCV RNA was covalently conjugated to a magnetic bead through the amino group at the 5' end of the oligonucleotide, and then bound to a glucose-loaded liposome by typical carbodiimide coupling at its 3' end. In the presence of the target HCV RNA, the target hybridized with the oligonucleotide to form double-stranded DNA. The symmetrical duplex sequence 5'-GGATCC-3' between guanines was then catalytically cleaved by BamHI, which detached the glucose-loaded liposome from the magnetic bead. Following magnetic separation of the bead, the detached glucose-loaded liposome was lysed using Triton X-100 to release the glucose molecules within it, which were then detected as an amplified signal at the digital PGM. Under optimal conditions, the PGM signal increased with increasing HCV RNA, and displayed a strongly linear dependence on the level of HCV RNA for concentrations ranging from 10 pM to 1.0 μM. The detection limit (LOD) of the system was 1.9 pM. Good reproducibility and favorable specificity were achieved in the analysis of the target HCV RNA. Human serum samples containing HCV RNA were analyzed using this strategy, and the developed sensing platform was observed to yield satisfactory results based on a comparison with the corresponding results from a Cobas ® Amplicor HCV Test Analyzer. Graphical abstract A digital detection strategy utilizing a personal glucometer was developed for the detection of hepatitis C virus RNA. The strategy involved the use of the endonuclease BamHI along with a 21-mer oligonucleotide conjugated to both a magnetic bead and a glucose-loaded nanoliposome. Hybridization of the nucleotide with the target RNA triggered the coupling-site-specific cleavage of the duplex by BamHI, leading to the release of the glucose-loaded nanoliposome. Following separation of the magnetic bead, the free nanoliposome was dissolved, liberating the glucose molecules within it, which in turn were detected as an amplified signal by the glucometer.

Modeling of rolling element bearing mechanics. Theoretical manual

NASA Technical Reports Server (NTRS)

Merchant, David H.; Greenhill, Lyn M.

1994-01-01

This report documents the theoretical basis for the Rolling Element Bearing Analysis System (REBANS) analysis code which determines the quasistatic response to external loads or displacement of three types of high-speed rolling element bearings: angular contact ball bearings; duplex angular contact ball bearings; and cylindrical roller bearings. The model includes the effects of bearing ring and support structure flexibility. It is comprised of two main programs: the Preprocessor for Bearing Analysis (PREBAN) which creates the input files for the main analysis program; and Flexibility Enhanced Rolling Element Bearing Analysis (FEREBA), the main analysis program. A companion report addresses the input instructions for and features of the computer codes. REBANS extends the capabilities of the SHABERTH (Shaft and Bearing Thermal Analysis) code to include race and housing flexibility, including such effects as dead band and preload springs.

Structural polymorphism exhibited by a quasipalindrome present in the locus control region (LCR) of the human beta-globin gene cluster.

PubMed

Kaushik, Mahima; Kukreti, Shrikant

2006-01-01

Structural polymorphism of DNA is a widely accepted property. A simple addition to this perception has been our recent finding, where a single nucleotide polymorphism (SNP) site present in a quasipalindromic sequence of beta-globin LCR exhibited a hairpin-duplex equilibrium. Our current studies explore that secondary structures adopted by individual complementary strands compete with formation of a perfect duplex. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation, circular dichroism (CD) techniques, we have demonstrated the structural transitions within a perfect duplex containing 11 bp quasipalindromic stretch (TGGGG(G/C)CCCCA), to hairpins and bulge duplex forms. The extended version of the 11 bp duplex, flanked by 5 bp on both sides also demonstrated conformational equilibrium between duplex and hairpin species. Gel-electrophoresis confirms that the duplex coexists with hairpin and bulge duplex/cruciform species. Further, in CD spectra of duplexes, presence of two overlapping positive peaks at 265 and 285 nm suggest the features of A- as well as B-type DNA conformation and show oligomer concentration dependence, manifested in A --> B transition. This indicates the possibility of an architectural switching at quasipalindromic region between linear duplex to a cruciform structure. Such DNA structural variations are likely to be found in the mechanics of molecular recognition and manipulation by proteins.

Molecular architecture: construction of self-assembled organophosphonate duplexes and their electrochemical characterization.

PubMed

Cattani-Scholz, Anna; Liao, Kung-Ching; Bora, Achyut; Pathak, Anshuma; Hundschell, Christian; Nickel, Bert; Schwartz, Jeffrey; Abstreiter, Gerhard; Tornow, Marc

2012-05-22

Self-assembled monolayers of phosphonates (SAMPs) of 11-hydroxyundecylphosphonic acid, 2,6-diphosphonoanthracene, 9,10-diphenyl-2,6-diphosphonoanthracene, and 10,10'-diphosphono-9,9'-bianthracene and a novel self-assembled organophosphonate duplex ensemble were synthesized on nanometer-thick SiO(2)-coated, highly doped silicon electrodes. The duplex ensemble was synthesized by first treating the SAMP prepared from an aromatic diphosphonic acid to form a titanium complex-terminated one; this was followed by addition of a second equivalent of the aromatic diphosphonic acid. SAMP homogeneity, roughness, and thickness were evaluated by AFM; SAMP film thickness and the structural contributions of each unit in the duplex were measured by X-ray reflection (XRR). The duplex was compared with the aliphatic and aromatic monolayer SAMPs to determine the effect of stacking on electrochemical properties; these were measured by impedance spectroscopy using aqueous electrolytes in the frequency range 20 Hz to 100 kHz, and data were analyzed using resistance-capacitance network based equivalent circuits. For the 11-hydroxyundecylphosphonate SAMP, C(SAMP) = 2.6 ± 0.2 μF/cm(2), consistent with its measured layer thickness (ca. 1.1 nm). For the anthracene-based SAMPs, C(SAMP) = 6-10 μF/cm(2), which is attributed primarily to a higher effective dielectric constant for the aromatic moieties (ε = 5-10) compared to the aliphatic one; impedance spectroscopy measured the additional capacitance of the second aromatic monolayer in the duplex (2ndSAMP) to be C(Ti/2ndSAMP) = 6.8 ± 0.7 μF/cm(2), in series with the first.

Multi-shell model of ion-induced nucleic acid condensation

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois; Baker, Nathan A.; Onufriev, Alexey V.

2016-04-01

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into "external" and "internal" ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the "external" shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the "internal" shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent "ion binding shells."

The simulation of the alternate turbopump development high pressure oxygen and fuel turbopumps for the space shuttle main engine using the Shaberth computer program

NASA Technical Reports Server (NTRS)

Mcdonald, Gary H.

1988-01-01

The Space Shuttle Main Engine (SSME) is basically comprised of a combustion chamber and nozzle, high and low pressure oxygen turbopumps and high and low pressure fuel turbopumps. In the current configuration, the high pressure fuel (HPTFP) and high pressure oxygen turbopumps (HPOTP) have experienced a history of ball bearing wear. The wear problem can be attributed to numerous factors including the hydrodynamic axial and radial loads caused by the flow of liquid oxygen and liquid hydrogen through the turbopump impellers and turbine. Also, friction effects between the rolling elements, races, and cage can create thermally induced bearing geometry changes. To alleviate some of the current configuration problems, an alternate turbopump development (ATD) was proposed. However, the ATD HPOTP and HPTFP are constrained to operate interchangeably with the current turbopumps, thus, the operation conditions must be similar. The ATD configuration features a major change in bearings used to support the integrated shaft, impeller, and turbine system. A single ball and single roller will replace the pump-end and turbine and duplex ball bearings. The Shaft-Bearing-Thermal (SHABERTH) computer code was used to model the ATD HPOTP and ATD HPFTP configurations. A two bearing model was used to simulate the HPOTP and HPFTP bearings and shaft geometry. From SHABERTH, a comparison of bearing reaction loads, frictional heat generation rates, and Hertz contact stresses will be attempted with analysis at the 109 percent and 65 percent power levels.

Influence of drug binding on DNA hydration: acoustic and densimetric characterizations of netropsin binding to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes and the poly(dT).poly(dA).poly(dT) triplex at 25 degrees C.

PubMed

Chalikian, T V; Plum, G E; Sarvazyan, A P; Breslauer, K J

1994-07-26

We use high-precision acoustic and densimetric techniques to determine, at 25 degrees C, the changes in volume, delta V, and adiabatic compressibility, delta Ks, that accompany the binding of netropsin to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes, as well as to the poly(dT).poly(dA).poly(dT) triplex. We find that netropsin binding to the heteropolymeric poly(dAdT).poly(dAdT) duplex is accompanied by negative changes in volume, delta V, and small positive changes in compressibility, delta Ks. By contrast, netropsin binding to the homopolymeric poly(dA).poly(dT) duplex is accompanied by large positive changes in both volume, delta V, and compressibility, delta Ks. Furthermore, netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes changes in both volume and compressibility that are nearly twice as large as those observed when netropsin binds to the poly(dA).poly(dT) duplex. We interpret these macroscopic data in terms of binding-induced microscopic changes in the hydration of the DNA structures and the drug. Specifically, we find that netropsin binding induces the release of approximately 22 waters from the hydration shell of the poly(dAdT).poly(dAdT) heteropolymeric duplex, approximately 40 waters from the hydration shell of the poly(dA).poly(dT) homopolymeric duplex, and about 53 waters from the hydration shell of the poly(dA).poly(dT), induces the release of 18 more water molecules than netropsin binding to the heteropolymeric duplex, poly(dAdT).poly(dAdT). On the basis of apparent molar volume, phi V, and apparent molar adiabatic compressibility, phi Ks, values for the initial drug-free and final drug-bound states of the two all-AT duplexes, we propose that the larger dehydration of the poly(dA).poly(dT) duplex reflects, in part, the formation of a less hydrated poly(dA).poly(dT)-netropsin complex compared with the corresponding poly(dAdT).poly(dAdT)-netropsin complex. In conjunction with our previously published entropy data [Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363], we calculate that each water of hydration released to the bulk solvent by ligand binding contributes 1.6 cal K-1 mol-1 to the entropy of binding. This value corresponds to the average difference between the partial molar entropy of water in the bulk state and water in the hydration shells of the two all-AT duplexes. When netropsin binds to the poly(dT).poly(dA).poly(dT) triplex, the changes in both volume and compressibility suggest that the binding event induces more dehydration of the triplex than of the duplex state. Specifically, we calculate that netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes the release of 13 more waters than netropsin binding to the poly(dA).poly(dT) duplex.(ABSTRACT TRUNCATED AT 400 WORDS)

The application of a duplex reverse transcription real-time PCR for the surveillance of porcine reproductive and respiratory syndrome virus and porcine circovirus type 2.

PubMed

Chang, Chia-Yi; Deng, Ming-Chung; Wang, Fun-In; Tsai, Hsiang-Jung; Yang, Chia-Huei; Chang, Chieh; Huang, Yu-Liang

2014-06-01

The porcine respiratory disease complex (PRDC) is the most common disease in commercial pork production worldwide. Porcine circovirus type 2 (PCV2) and porcine reproductive and respiratory syndrome virus (PRRSV), the most important agents of PRDC, usually co-infect in the same pigs. In order to survey the prevalence of PCV2 and PRRSV in pigs of various ages, a duplex reverse transcription real-time PCR (DRT-rPCR) was developed and applied in the present study. The DRT-rPCR did not cross-react with 10 swine viruses other than PCV2 and PRRSV, with detection limits of 1 TCID50/ml for PCV2 and 6.3 TCID50/ml for PRRSV. Surveillance using DRT-rPCR together with serology revealed that in the five farms studied, pigs were most susceptible to PRRSV at 6-14 weeks of age, whereas susceptibility to PCV2 varied by the management system but was mostly at 10-14 weeks of age. Cross analysis of viral loads versus antibody titers revealed that PCV2 load was affected negatively by anti-PCV2 ORF2 antibody, which constituted the most important non-infectious factor affecting the development of PMWS. These results indicated that DRT-rPCR was developed and applied successfully to the surveillance of PCV2 and PRRSV in the field. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular requirements for RNA-induced silencing complex assembly in the Drosophila RNA interference pathway.

PubMed

Pham, John W; Sontheimer, Erik J

2005-11-25

Complexes in the Drosophila RNA-induced silencing complex (RISC) assembly pathway can be resolved using native gel electrophoresis, revealing an initiator called R1, an intermediate called R2, and an effector called R3 (now referred to as holo-RISC). Here we show that R1 forms when the Dicer-2/R2D2 heterodimer binds short interfering RNA (siRNA) duplexes. The heterodimer alone can initiate RISC assembly, indicating that other factors are dispensable for initiation. During assembly, R2 requires Argonaute 2 to convert into holo-RISC. This requirement is reminiscent of the RISC-loading complex, which also requires Argonaute 2 for assembly into RISC. We have compared R2 to the RISC-loading complex and show that the two complexes are similar in their sensitivities to ATP and to chemical modifications on siRNA duplexes, indicating that they are likely to be identical. We have examined the requirements for RISC formation and show that the siRNA 5'-termini are repeatedly monitored during RISC assembly, first by the Dcr-2/R2D2 heterodimer and again after R2 formation, before siRNA unwinding. The 2'-position of the 5'-terminal nucleotide also affects RISC assembly, because an siRNA strand bearing a 2'-deoxyribose at this position can inhibit the cognate strand from entering holo-RISC; in contrast, the 2'-deoxyribose-modified strand has enhanced activity in the RNA interference pathway.

Investigation of hot cracking resistance of 2205 duplex steel

NASA Astrophysics Data System (ADS)

Adamiec, J.; Ścibisz, B.

2010-02-01

Austenitic duplex steel of the brand 2205 according to Avesta Sheffield is used for welded constructions (pipelines, tanks) in the petrol industry, chemical industry and food industry. It is important to know the range of high-temperature brittleness in designing welding technology for constructions made of this steel type. There is no data in literature concerning this issue. High-temperature brittleness tests using the simulator of heat flow device Gleeble 3800 were performed. The tests results allowed the evaluation of the characteristic temperatures in the brittleness temperature range during the joining of duplex steels, specifically the nil-strength temperature (NST) and nil-ductility temperatures (NDT) during heating, the strength and ductility recovery temperatures (DRT) during cooling, the Rfparameter (Rf = (Tliquidus - NDT)/NDT) describing the duplex steel inclination for hot cracking, and the brittleness temperature range (BTR). It has been stated that, for the examined steel, this range is wide and amounts to ca. 90 °C. The joining of duplex steels with the help of welding techniques creates a significant risk of hot cracks. After analysis of the DTA curves a liquidus temperature of TL = 1465 °C and a solidus temperature of TS = 1454 °C were observed. For NST a mean value was assumed, in which the cracks appeared for six samples; the temperature was 1381 °C. As the value of the NDT temperature 1367 °C was applied while for DRT the assumed temperature was 1375 °C. The microstructure of the fractures was observed using a Hitachi S-3400N scanning electron microscope (SEM). The analyses of the chemical composition were performed using an energy-dispersive X-ray spectrometer (EDS), Noran System Six of Thermo Fisher Scientific. Essential differences of fracture morphology type over the brittle temperature range were observed and described.

Methods And Devices For Characterizing Duplex Nucleic Acid Molecules

DOEpatents

Akeson, Mark; Vercoutere, Wenonah; Haussler, David; Winters-Hilt, Stephen

2005-08-30

Methods and devices are provided for characterizing a duplex nucleic acid, e.g., a duplex DNA molecule. In the subject methods, a fluid conducting medium that includes a duplex nucleic acid molecule is contacted with a nanopore under the influence of an applied electric field and the resulting changes in current through the nanopore caused by the duplex nucleic acid molecule are monitored. The observed changes in current through the nanopore are then employed as a set of data values to characterize the duplex nucleic acid, where the set of data values may be employed in raw form or manipulated, e.g., into a current blockade profile. Also provided are nanopore devices for practicing the subject methods, where the subject nanopore devices are characterized by the presence of an algorithm which directs a processing means to employ monitored changes in current through a nanopore to characterize a duplex nucleic acid molecule responsible for the current changes. The subject methods and devices find use in a variety of applications, including, among other applications, the identification of an analyte duplex DNA molecule in a sample, the specific base sequence at a single nulceotide polymorphism (SNP), and the sequencing of duplex DNA molecules.

Study of Sigma Phase in Duplex SAF 2507

NASA Astrophysics Data System (ADS)

Fellicia, D. M.; Sutarsis; Kurniawan, B. A.; Wulanari, D.; Purniawan, A.; Wibisono, A. T.

2017-05-01

Super duplex stainless steel is one of the stainless steel which has a combination between high strength properties and excellent corrosion resistance. However, the resistance can decrease by precipitation of sigma phase which is formed at high temperature, for example after welding processes. A series of experiments has been performed to study the effect of solution annealing to existence of sigma phase on super duplex SAF 2507. Variations of solution-annealing temperatures were 1000 °C, 1065 °C and 1125 °C with holding time of 15 and 30 minutes for each temperature. Effect of solution annealing process was characterized by using XRD, SEM, and Optical Microscopy. The result showed precipitation of sigma phase completely dissolved at 1065 °C and 1125 °C because it reformed to austenite. After it was heated at 1065 °C, chromium carbide appeared in ferrite site and grain boundary. The amount of chromium carbide increased with the increasing of solution annealing temperature.

Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

PubMed

Cafferty, Brian J; Musetti, Caterina; Kim, Keunsoo; Horowitz, Eric D; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

2016-04-07

Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

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

Winter-Warnars, Hillegonda A.O.; Graaf, Yolanda van der; Mali, Willem P.T.M.

Purpose: Comparison of the relative values of the ankle-arm index (AAI) at rest and after exercise, angiography, and duplex ultrasonography for the follow-up of percutaneous transluminal angioplasty (PTA) in patients with peripheral vascular disease. Methods: Thirty-two patients were prospectively followed after technically and clinically successful PTA of a femoropopliteal occlusion. The patency of the femoropopliteal artery was assessed for 1 year using AAI measurements at rest and after exercise; duplex ultrasonography at 4, 12, 24, 36, and 52 weeks; and angiography at 3 and 12 months after PTA. Results: Patency was highly dependent on the measurement technique. The cumulative patencymore » after 1 year determined with the AAI at rest and during exercise, by angiography, and by duplex ultrasonography was 74%, 19%, 31%, and 32%, respectively. Seventy-five percent of the restenoses occurred at the site of the treated occlusion. Conclusion: Duplex ultrasonography is most suitable for this assessment, as it causes no patient discomfort and the specificity is better than AAI after exercise because vascular disease in other, proximal segments does not interfere with the results.« less

Contributions of 3'-overhang to the dissociation of small interfering RNAs from the PAZ domain: molecular dynamics simulation study.

PubMed

Lee, Hui Sun; Lee, Soo Nam; Joo, Chul Hyun; Lee, Heuiran; Lee, Han Saem; Yoon, Seung Yong; Kim, Yoo Kyum; Choe, Han

2007-03-01

RNA interference (RNAi) is a 'knock-down' reaction to reduce expression of a specific gene through highly regulated, enzyme-mediated processes. Small interfering RNAs (siRNAs) are RNA molecules that play an effector role in RNAi and can bind the PAZ domains present in Dicer and RISC. We investigated the interaction between the PAZ domain and the siRNA-like duplexes through dissociation molecular dynamics (DMD) simulations. Specifically, we focused on the response of the PAZ domain to various 3'-overhang structures of the siRNA-like duplexes. We found that the siRNA-like duplex with the 3' UU-overhang made relatively more stable complex with the PAZ domain compared to those with 3' CC-, AA-, and GG-overhangs. The siRNA-like duplex with UU-overhang was easily dissociated from the PAZ domain once the structural stability of the complex is impaired. Interestingly, the 3' UU-overhang spent the least time at the periphery region of the binding pocket during the dissociation process, which can be mainly attributable to UU-overhang's smallest number of hydrogen bonds.

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus.

PubMed

Kang, Xiao-ping; Jiang, Tao; Li, Yong-qiang; Lin, Fang; Liu, Hong; Chang, Guo-hui; Zhu, Qing-yu; Qin, E-de; Qin, Cheng-feng; Yang, Yin-hui

2010-06-02

A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID50 (50% tissue culture infective dose) for H5N1 and 0.2 TCID50 for the pandemic H1N1, which was the same as that of each single-target RT-PCR for pandemic H1N1 and even more sensitive for H5N1 with the same primers and probes. No cross reactivity of detecting other subtype influenza viruses or respiratory tract viruses was observed. Two hundred and thirty-six clinical specimens were tested by comparing with single real-time RT-PCR and result from the duplex assay was 100% consistent with the results of single real-time RT-PCR and sequence analysis.

Fabrication and life testing of thermionic converters

NASA Technical Reports Server (NTRS)

Yang, L.; Bruce, R.

1973-01-01

An unfueled converter containing a chloride-fluoride duplex tungsten emitter of 4.78 eV vacuum work function was tested for 46,647 hours at an emitter temperature of 1973 K and an electrode power output of about 8 watts/sq cm. The test demonstrated the superior and stable performance of the (110) oriented tungsten emitter at high temperatures. Three 90 UC-10 ZrC(C/U = 1.04, tungsten additive = 4 wt %) fueled converters were fabricated and tested at an emitter temperature of 1873 K. Converter containing chloride-arc-cast duplex tungsten cladding showed temperature thermionic performance and slower rate of performance drop than converter containing chloride-fluoride duplex tungsten cladding. This is believed to be due to the superior fuel component diffusion resistance of the arc-cast tungsten substrate used in the fuel cladding. It was shown that a converter containing a carbide fueled chloride-arc-cast duplex tungsten emitter with an initial electrode power output of 6.80 watts/sq cm could still deliver an electrode power output of 6.16 watts/sq cm after 18,632 hours of operation at an emitter temperature of 1873 K.

Clinical utility of carotid duplex ultrasound prior to cardiac surgery.

PubMed

Lin, Judith C; Kabbani, Loay S; Peterson, Edward L; Masabni, Khalil; Morgan, Jeffrey A; Brooks, Sara; Wertella, Kathleen P; Paone, Gaetano

2016-03-01

Clinical utility and cost-effectiveness of carotid duplex examination prior to cardiac surgery have been questioned by the multidisciplinary committee creating the 2012 Appropriate Use Criteria for Peripheral Vascular Laboratory Testing. We report the clinical outcomes and postoperative neurologic symptoms in patients who underwent carotid duplex ultrasound prior to open heart surgery at a tertiary institution. Using the combined databases from our clinical vascular laboratory and the Society of Thoracic Surgery, a retrospective analysis of all patients who underwent carotid duplex ultrasound within 13 months prior to open heart surgery from March 2005 to March 2013 was performed. The outcomes between those who underwent carotid duplex scanning (group A) and those who did not (group B) were compared. Among 3233 patients in the cohort who underwent cardiac surgery, 515 (15.9%) patients underwent a carotid duplex ultrasound preoperatively, and 2718 patients did not (84.1%). Among the patients who underwent carotid screening vs no screening, there was no statistically significant difference in the risk factors of cerebrovascular disease (10.9% vs 12.7%; P = .26), prior stroke (8.2% vs 7.2%; P = .41), and prior transient ischemic attack (2.9% vs 3.3%; P = .24). For those undergoing isolated coronary artery bypass grafting (CABG), 306 (17.8%) of 1723 patients underwent preoperative carotid duplex ultrasound. Among patients who had carotid screening prior to CABG, the incidence of carotid disease was low: 249 (81.4%) had minimal or mild stenosis (<50%); 25 (8.2%) had unilateral moderate stenosis (50%-69%); 10 (3.3%) had bilateral moderate stenosis; 9 (2.9%) had unilateral severe stenosis (70%-99%); 5 (1.6%) had contralateral moderate stenosis; 2 (0.7%) had bilateral severe stenosis; 4 (1.3%) had unilateral occluded with contralateral less than 50% stenosis, 1 (0.3%) had unilateral occluded with contralateral (70%-99%) stenosis; and 1 had bilateral occluded carotid arteries. Primary outcomes of patients who underwent isolated CABG showed no difference in the perioperative mortality (2.9% vs 4.3%; P = .27) and stroke (2.9% vs 2.6%; P = .70) between patients undergoing preoperative duplex scanning and those who did not. Primary outcomes of patients who underwent open heart surgery also showed no difference in the perioperative mortality (5.1% vs 6.9%; P = .14) and stroke (2.6% vs 2.4%; P = .85) between patients undergoing preoperative duplex scanning and those who did not. Operative intervention of severe carotid stenosis prior to isolated CABG occurred in 2 of the 17 patients (11.8%) identified who underwent carotid endarterectomy with CABG. In this study, the correlation between preoperative duplex-documented high-grade carotid stenosis and postoperative stroke was low. Prudent use of preoperative carotid duplex ultrasound should be based on the presence of cerebrovascular symptoms and the type of open heart surgery. Copyright © 2016 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Non-invasive assessment of peripheral arterial disease: Automated ankle brachial index measurement and pulse volume analysis compared to duplex scan.

PubMed

Lewis, Jane Ea; Williams, Paul; Davies, Jane H

2016-01-01

This cross-sectional study aimed to individually and cumulatively compare sensitivity and specificity of the (1) ankle brachial index and (2) pulse volume waveform analysis recorded by the same automated device, with the presence or absence of peripheral arterial disease being verified by ultrasound duplex scan. Patients (n=205) referred for lower limb arterial assessment underwent ankle brachial index measurement and pulse volume waveform recording using volume plethysmography, followed by ultrasound duplex scan. The presence of peripheral arterial disease was recorded if ankle brachial index <0.9; pulse volume waveform was graded as 2, 3 or 4; or if haemodynamically significant stenosis >50% was evident with ultrasound duplex scan. Outcome measure was agreement between the measured ankle brachial index and interpretation of pulse volume waveform for peripheral arterial disease diagnosis, using ultrasound duplex scan as the reference standard. Sensitivity of ankle brachial index was 79%, specificity 91% and overall accuracy 88%. Pulse volume waveform sensitivity was 97%, specificity 81% and overall accuracy 85%. The combined sensitivity of ankle brachial index and pulse volume waveform was 100%, specificity 76% and overall accuracy 85%. Combining these two diagnostic modalities within one device provided a highly accurate method of ruling out peripheral arterial disease, which could be utilised in primary care to safely reduce unnecessary secondary care referrals.

Base pairing and structural insights into the 5-formylcytosine in RNA duplex

PubMed Central

Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

2016-01-01

Abstract 5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

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

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox.

PubMed

Weidmann, Chase A; Mustoe, Anthony M; Weeks, Kevin M

2016-09-01

While a variety of powerful tools exists for analyzing RNA structure, identifying long-range and intermolecular base-pairing interactions has remained challenging. Recently, three groups introduced a high-throughput strategy that uses psoralen-mediated crosslinking to directly identify RNA-RNA duplexes in cells. Initial application of these methods highlights the preponderance of long-range structures within and between RNA molecules and their widespread structural dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

A novel universal real-time PCR system using the attached universal duplex probes for quantitative analysis of nucleic acids.

PubMed

Yang, Litao; Liang, Wanqi; Jiang, Lingxi; Li, Wenquan; Cao, Wei; Wilson, Zoe A; Zhang, Dabing

2008-06-04

Real-time PCR techniques are being widely used for nucleic acids analysis, but one limitation of current frequently employed real-time PCR is the high cost of the labeled probe for each target molecule. We describe a real-time PCR technique employing attached universal duplex probes (AUDP), which has the advantage of generating fluorescence by probe hydrolysis and strand displacement over current real-time PCR methods. AUDP involves one set of universal duplex probes in which the 5' end of the fluorescent probe (FP) and a complementary quenching probe (QP) lie in close proximity so that fluorescence can be quenched. The PCR primer pair with attached universal template (UT) and the FP are identical to the UT sequence. We have shown that the AUDP technique can be used for detecting multiple target DNA sequences in both simplex and duplex real-time PCR assays for gene expression analysis, genotype identification, and genetically modified organism (GMO) quantification with comparable sensitivity, reproducibility, and repeatability with other real-time PCR methods. The results from GMO quantification, gene expression analysis, genotype identification, and GMO quantification using AUDP real-time PCR assays indicate that the AUDP real-time PCR technique has been successfully applied in nucleic acids analysis, and the developed AUDP real-time PCR technique will offer an alternative way for nucleic acid analysis with high efficiency, reliability, and flexibility at low cost.

Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition.

PubMed

Teng, Ye; Pramanik, Smritimoy; Tateishi-Karimata, Hisae; Ohyama, Tatsuya; Sugimoto, Naoki

2018-02-05

The trinucleotide repeat d(CXG) (X = A, C, G or T) is the most common sequence causing repeat expansion disorders. The formation of non-canonical structures, such as hairpin structures with X-X mismatches, has been proposed to affect gene expression and regulation, which are important in pathological studies of these devastating neurological diseases. However, little information is available regarding the thermodynamics of the repeat sequence under crowded cellular conditions where many non-canonical structures such as G-quadruplexes are highly stabilized, while duplexes are destabilised. In this study, we investigated the different stabilities of X-X mismatches in the context of internal d(CXG) self-complementary sequences in an environment with a high concentration of cosolutes to mimic the crowding conditions in cells. The stabilities of full-matched duplexes and duplexes with A-A, G-G, and T-T mismatched base pairs under molecular crowding conditions were notably decreased compared to under dilute conditions. However, the stability of the DNA duplex with a C-C mismatch base pair was only slightly destabilised. Investigating different stabilities of X-X mismatches in d(CXG) sequences is important for improving our understanding of the formation and transition of multiple non-canonical structures in trinucleotide repeat diseases, and may provide insights for pathological studies and drug development. Copyright © 2018 Elsevier Inc. All rights reserved.

Simultaneous detection of bovine and porcine DNA in pharmaceutical gelatin capsules by duplex PCR assay for Halal authentication.

PubMed

Nikzad, Jafar; Shahhosseini, Soraya; Tabarzad, Maryam; Nafissi-Varcheh, Nastaran; Torshabi, Maryam

2017-02-14

In the pharmaceutical industry, hard- and soft-shelled capsules are typically made from gelatin, commonly derived from bovine and porcine sources. To ensure that pharmaceutical products comply with halal regulations in Muslim countries (no porcine products allowed), development of a valid, reliable, quick, and most importantly, cost-effective tests are of utmost importance. We developed a species-specific duplex polymerase chain reaction (PCR) assay targeting 149 bp porcine and 271 bp bovine mitochondrial DNA (mtDNA) to simultaneously detect both porcine and bovine DNA (in one reaction at the same time) in gelatin. Some additional simplex PCR tests (targeting 126 bp bovine and 212 bp porcine mtDNA) and real-time PCR using a commercially available kit (for identification of porcine DNA) were used to verify the selectivity and sensitivity of our duplex PCR. After optimization of DNA extraction and PCR methods, hard/soft pharmaceutical gelatin capsules (containing drug) were tested for the presence of porcine and/or bovine DNA. Duplex PCR detected the presence of as little as 0.1% porcine DNA, which was more accurate than the commercially available kit. Of all gelatin capsules tested (n = 24), 50% contained porcine DNA (pure porcine gelatin alone or in combination with bovine gelatin). Duplex PCR presents an easy-to-follow, quick, low-cost and reliable method to simultaneously detect porcine and bovine DNAs (>100 bp) in minute amounts in highly processed gelatin-containing pharmaceutical products (with a 0.1% sensitivity for porcine DNA) which may be used for halal authentication. Simultaneous detection of porcine and bovine DNA in gelatin capsules by duplex PCR.

Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex.

PubMed

Xie, Ping

2015-10-09

Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by "hungry" codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel.

Thermal stability of DNA quadruplex-duplex hybrids.

PubMed

Lim, Kah Wai; Khong, Zi Jian; Phan, Anh Tuân

2014-01-14

DNA has the capacity to adopt several distinct structural forms, such as duplex and quadruplex helices, which have been implicated in cellular processes and shown to exhibit important functional properties. Quadruplex-duplex hybrids, generated from the juxtaposition of these two structural elements, could find applications in therapeutics and nanotechnology. Here we used NMR and CD spectroscopy to investigate the thermal stability of two classes of quadruplex-duplex hybrids comprising fundamentally distinct modes of duplex and quadruplex connectivity: Construct I involves the coaxial orientation of the duplex and quadruplex helices with continual base stacking across the two components; Construct II involves the orthogonal orientation of the duplex and quadruplex helices with no base stacking between the two components. We have found that for both constructs, the stability of the quadruplex generally increases with the length of the stem-loop incorporated, with respect to quadruplexes comprising nonstructured loops of the same length, which showed a continuous drop in stability with increasing loop length. The stability of these complexes, particularly Construct I, can be substantially influenced by the base-pair steps proximal to the quadruplex-duplex junction. Bulges at the junction are largely detrimental to the adoption of the desired G-quadruplex topology for Construct I but not for Construct II. These findings should facilitate future design and prediction of quadruplex-duplex hybrids.

Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex

PubMed Central

Xie, Ping

2015-01-01

Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by “hungry” codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel. PMID:26473825

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

PubMed

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Water-evaporation reduction by duplex films: application to the human tear film.

PubMed

Cerretani, Colin F; Ho, Nghia H; Radke, C J

2013-09-01

Water-evaporation reduction by duplex-oil films is especially important to understand the physiology of the human tear film. Secreted lipids, called meibum, form a duplex film that coats the aqueous tear film and purportedly reduces tear evaporation. Lipid-layer deficiency is correlated with the occurrence of dry-eye disease; however, in-vitro experiments fail to show water-evaporation reduction by tear-lipid duplex films. We review the available literature on water-evaporation reduction by duplex-oil films and outline the theoretical underpinnings of spreading and evaporation kinetics that govern behavior of these systems. A dissolution-diffusion model unifies the data reported in the literature and identifies dewetting of duplex films into lenses as a key challenge to obtaining significant evaporation reduction. We develop an improved apparatus for measuring evaporation reduction by duplex-oil films including simultaneous assessment of film coverage, stability, and temperature, all under controlled external mass transfer. New data reported in this study fit into the larger body of work conducted on water-evaporation reduction by duplex-oil films. Duplex-oil films of oxidized mineral oil/mucin (MOx/BSM), human meibum (HM), and bovine meibum (BM) reduce water evaporation by a dissolution-diffusion mechanism, as confirmed by agreement between measurement and theory. The water permeability of oxidized-mineral-oil duplex films agrees with those reported in the literature, after correction for the presence of mucin. We find that duplex-oil films of bovine and human meibum at physiologic temperature reduce water evaporation only 6-8% for a 100-nm film thickness pertinent to the human tear film. Comparison to in-vivo human tear-evaporation measurements is inconclusive because evaporation from a clean-water surface is not measured and because the mass-transfer resistance is not characterized. Copyright © 2013 Elsevier B.V. All rights reserved.

Multi-shell model of ion-induced nucleic acid condensation

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

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(III) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derivedmore » from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion binding shells.”.« less

Multi-shell model of ion-induced nucleic acid condensation

PubMed Central

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois; Onufriev, Alexey V.

2016-01-01

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion binding shells.” PMID:27389241

Duplex gall bladder: bystander or culprit.

PubMed

Kumar, Jogender; Yadav, Arushi

2017-08-30

Gall bladder (GB) duplication is a rare anatomical malformation, which can be detected by preoperative imaging study. We present a case of duplex gall bladder in a 14-year-old boy who presented with abdominal pain. On ultrasound, he had right nephrolithiasis and duplex gall bladder. Duplex gall bladder was confirmed on MR cholangiopancreatography. There was a dilemma for surgical management of duplex gall bladder; however, he became asymptomatic after conservative treatment. Prophylactic surgery is not recommended for asymptomatic incidentally detected duplex gall bladder. Radiologists and paediatric surgeons should be sensitised about the exact anatomy of this entity. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Enhancing the corrosion resistance of the 2205 duplex stainless steel bipolar plates in PEMFCs environment by surface enriched molybdenum

NASA Astrophysics Data System (ADS)

Jinlong, Lv; Zhuqing, Wang; Tongxiang, Liang; Ken, Suzuki; Hideo, Miura

Surface molybdenum enrichment on 2205 duplex stainless steel was obtained by the ball milling technique. The electrochemical results showed molybdenum enrichment on the surface of 2205 duplex stainless steel improved its corrosion resistance in a typical proton exchange membrane fuel cell environment. This was mainly attributed to higher molybdenum content in the passive film formed on 2205 duplex stainless steel after ball milling. The decreased donor and acceptor concentrations improved significantly the corrosion resistance of surface molybdenum-enriched 2205 duplex stainless steel bipolar plates in the simulated cathodic proton exchange membrane fuel cells environment. In addition, the interfacial contact resistance of the 2205 duplex stainless steel bipolar plates slightly decreased due to surface molybdenum enrichment.

Competition between siRNA duplexes: impact of RNA-induced silencing complex loading efficiency and comparison between conventional-21 bp and Dicer-substrate siRNAs.

PubMed

Tanudji, Marcel; Machalek, Dorothy; Arndt, Greg M; Rivory, Laurent

2010-02-01

Cotransfection of a mixture of siRNAs species is typically used when simultaneous targeting of more than one mRNA is required. However, competition between siRNAs could occur and reduce the activity of some siRNAs within the mixture. To further study the factors affecting the degree of competition between siRNAs, we cotransfected luciferase targeting siRNAs with various irrelevant (ie, nonluciferase targeting) siRNAs into cells and examined differences in their competition profiles by assessing the effect on luciferase expression. We show that the degree of competition varies between irrelevant siRNAs and occurs at the point of RISC loading. Although the competition profile appears to be related to the calculated RNA-induced silencing complex (RISC) loading potential, empirical testing is required to confirm the competitive effects. We also observed reduced competition with siRNAs in the Dicer-substrate format, presumably due to more efficient RISC loading as a consequence of the physical transfer of the processed siRNA from Dicer.

Modeling of rolling element bearing mechanics. Computer program user's manual

NASA Technical Reports Server (NTRS)

Greenhill, Lyn M.; Merchant, David H.

1994-01-01

This report provides the user's manual for the Rolling Element Bearing Analysis System (REBANS) analysis code which determines the quasistatic response to external loads or displacement of three types of high-speed rolling element bearings: angular contact ball bearings, duplex angular contact ball bearings, and cylindrical roller bearings. The model includes the defects of bearing ring and support structure flexibility. It is comprised of two main programs: the Preprocessor for Bearing Analysis (PREBAN) which creates the input files for the main analysis program, and Flexibility Enhanced Rolling Element Bearing Analysis (FEREBA), the main analysis program. This report addresses input instructions for and features of the computer codes. A companion report addresses the theoretical basis for the computer codes. REBANS extends the capabilities of the SHABERTH (Shaft and Bearing Thermal Analysis) code to include race and housing flexibility, including such effects as dead band and preload springs.

Magnetic resonance angiography in the follow-up of distal lower-extremity bypass surgery: comparison with duplex ultrasound and digital subtraction angiography.

PubMed

Meissner, Oliver A; Verrel, Frauke; Tató, Federico; Siebert, Uwe; Ramirez, Heldin; Ruppert, Volker; Schoenberg, Stefan O; Reiser, Maximilian

2004-11-01

The danger of limb loss as a consequence of acute occlusion of infrapopliteal bypasses underscores the requirement for careful patient follow-up. The objective of this study was to determine the agreement and accuracy of contrast material-enhanced moving-table magnetic resonance (MR) angiography and duplex ultrasonography (US) in the assessment of failing bypass grafts. In cases of discrepancy, digital subtraction angiography (DSA) served as the reference standard. MR angiography was performed in 24 consecutive patients with 26 femorotibial or femoropedal bypass grafts. Each revascularized limb was divided into five segments--(i) native arteries proximal to the graft; (ii) proximal anastomosis; (iii) graft course; (iv) distal anastomosis; and (v) native arteries distal to the graft-resulting in 130 vascular segments. Three readers evaluated all MR angiograms for image quality and the presence of failing grafts. The degree of stenosis was compared to the findings of duplex US, and in case of discrepancy, to DSA findings. Two separate analyses were performed with use of DSA only and a combined diagnostic endpoint as the reference standard. Image quality was rated excellent or intermediate in 119 of 130 vascular segments (92%). Venous overlay was encountered in 26 of 130 segments (20%). In only two segments was evaluation of the outflow region not feasible. One hundred seventeen of 130 vascular segments were available for quantitative analysis. In 109 of 117 segments (93%), MR angiography and duplex US showed concordant findings. In the eight discordant segments in seven patients, duplex US overlooked four high-grade stenoses that were correctly identified by MR angiography and confirmed by DSA. Percutaneous transluminal angioplasty was performed in these cases. In no case did MR angiography miss an area of stenosis of sufficient severity to require treatment. Total accuracy for duplex US ranged from 0.90 to 0.97 depending on the reference standard used, whereas MR angiography was completely accurate (1.00) regardless of the standard definition. Our data strongly suggest that the accuracy of MR angiography for identifying failing grafts in the infrapopliteal circulation is equal to that of duplex US and superior to that of duplex US in cases of complex revascularization. MR angiography should be included in routine follow-up of patients undergoing infrapopliteal bypass surgery.

Influence of the Martensitic Transformation on the Microscale Plastic Strain Heterogeneities in a Duplex Stainless Steel

NASA Astrophysics Data System (ADS)

Lechartier, Audrey; Martin, Guilhem; Comby, Solène; Roussel-Dherbey, Francine; Deschamps, Alexis; Mantel, Marc; Meyer, Nicolas; Verdier, Marc; Veron, Muriel

2017-01-01

The influence of the martensitic transformation on microscale plastic strain heterogeneity of a duplex stainless steel has been investigated. Microscale strain heterogeneities were measured by digital image correlation during an in situ tensile test within the SEM. The martensitic transformation was monitored in situ during tensile testing by high-energy synchrotron X-ray diffraction. A clear correlation is shown between the plasticity-induced transformation of austenite to martensite and the development of plastic strain heterogeneities at the phase level.

Development of new duplex treatments on 100Cr6steel combining Thermochemical Treatments, Laser Shock Peening and Physical Vapour Deposition

NASA Astrophysics Data System (ADS)

Osés, J.; Fuentes, G. G.; Santo Domingo, S.; Miguel, I.; Gimeno, S.; Carreras, L.; Peyre, P.; Gorny, C.

2017-05-01

100Cr6 steel (AISI 52100) is one of the most used steel grades in the manufacturing of through hardening bearings mainly due to its properties: controlled impurities during steel making process, high hardenability and well known mechanical properties such as wear and fatigue resistance on clean environments. These characteristics play an important role on the performance of a bearing together with the bearing design, loads and environment. However, there is an increasing set of demanding applications where the above mentioned steel does not fulfil the required needs and thus, bearing manufacturers continuously work on the development of technologies to improve the bearing performance. Nowadays thermochemical treatments (TCT), such as carbonitriding are being applied to this steel in order to enhance the performance of such pieces in contaminated environment, where particles can produce defects on the raceway, increasing the onset of defects that eventually lead to premature fail. These treatments induce the formation of carbides and nitrides which are directly related to the enhancement of the wear resistance and also to increasing the amount of Retained Austenite (RA) in the surface which may have a beneficial effect as it delays the crack propagation on subsurface regions, then increasing bearing fatigue life. In this work, different TCTs have been applied to 100Cr6 steel flat samples. Using a tribometer (ball-on-disc configuration) and a grinding machine, surface and in-depth wear resistance measurements have been carried out, obtaining wear resistance profiles that have been correlated with the microstructure, microhardness profiles and RA content. The most promising TCT has been combined either with Laser Shock Peening (LSP) treatments or carbonaceous Physical Vapour Deposition (PVD) coatings with the aim of improving not only the wear resistance but also the CoF of the duplex treated sample. The results obtained on flat samples are promising; the combination of treatments produces long-lasting low CoF and a reduction of 60% in the wear rate. However, the treatments should be applied on real pieces and tested in a test bench in order to obtain more appropriate data about the lifespan of duplex treated bearings.

Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study.

PubMed

Suresh, Gorle; Priyakumar, U Deva

2015-09-01

Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes. Copyright © 2015 Elsevier Inc. All rights reserved.

Validation of a novel duplex ultrasound objective structured assessment of technical skills (DUOSATS) for arterial stenosis detection.

PubMed

Jaffer, U; Singh, P; Pandey, V A; Aslam, M; Standfield, N J

2014-01-01

Duplex ultrasound facilitates bedside diagnosis and hence timely patient care. Its uptake has been hampered by training and accreditation issues. We have developed an assessment tool for Duplex arterial stenosis measurement for both simulator and patient based training. A novel assessment tool: duplex ultrasound assessment of technical skills was developed. A modified duplex ultrasound assessment of technical skills was used for simulator training. Novice, intermediate experience and expert users of duplex ultrasound were invited to participate. Participants viewed an instructional video and were allowed ample time to familiarize with the equipment. Participants' attempts were recorded and independently assessed by four experts using the modified duplex ultrasound assessment of technical skills. 'Global' assessment was also done on a four point Likert scale. Content, construct and concurrent validity as well as reliability were evaluated. Content and construct validity as well as reliability were demonstrated. The simulator had good satisfaction rating from participants: median 4; range 3-5. Receiver operator characteristic analysis has established a cut point of 22/ 34 and 25/ 40 were most appropriate for simulator and patient based assessment respectively. We have validated a novel assessment tool for duplex arterial stenosis detection. Further work is underway to establish transference validity of simulator training to improved skill in scanning patients. We have developed and validated duplex ultrasound assessment of technical skills for simulator training.

Quantitative Detection of Small Molecule/DNA Complexes Employing a Force-Based and Label-Free DNA-Microarray

PubMed Central

Ho, Dominik; Dose, Christian; Albrecht, Christian H.; Severin, Philip; Falter, Katja; Dervan, Peter B.; Gaub, Hermann E.

2009-01-01

Force-based ligand detection is a promising method to characterize molecular complexes label-free at physiological conditions. Because conventional implementations of this technique, e.g., based on atomic force microscopy or optical traps, are low-throughput and require extremely sensitive and sophisticated equipment, this approach has to date found only limited application. We present a low-cost, chip-based assay, which combines high-throughput force-based detection of dsDNA·ligand interactions with the ease of fluorescence detection. Within the comparative unbinding force assay, many duplicates of a target DNA duplex are probed against a defined reference DNA duplex each. The fractions of broken target and reference DNA duplexes are determined via fluorescence. With this assay, we investigated the DNA binding behavior of artificial pyrrole-imidazole polyamides. These small compounds can be programmed to target specific dsDNA sequences and distinguish between D- and L-DNA. We found that titration with polyamides specific for a binding motif, which is present in the target DNA duplex and not in the reference DNA duplex, reliably resulted in a shift toward larger fractions of broken reference bonds. From the concentration dependence nanomolar to picomolar dissociation constants of dsDNA·ligand complexes were determined, agreeing well with prior quantitative DNAase footprinting experiments. This finding corroborates that the forced unbinding of dsDNA in presence of a ligand is a nonequilibrium process that produces a snapshot of the equilibrium distribution between dsDNA and dsDNA·ligand complexes. PMID:19486688

Exploring the Interactions of the Dietary Plant Flavonoids Fisetin and Naringenin with G-Quadruplex and Duplex DNA, Showing Contrasting Binding Behavior: Spectroscopic and Molecular Modeling Approaches.

PubMed

Bhattacharjee, Snehasish; Chakraborty, Sandipan; Sengupta, Pradeep K; Bhowmik, Sudipta

2016-09-01

Guanine-rich sequences have the propensity to fold into a four-stranded DNA structure known as a G-quadruplex (G4). G4 forming sequences are abundant in the promoter region of several oncogenes and become a key target for anticancer drug binding. Here we have studied the interactions of two structurally similar dietary plant flavonoids fisetin and naringenin with G4 as well as double stranded (duplex) DNA by using different spectroscopic and modeling techniques. Our study demonstrates the differential binding ability of the two flavonoids with G4 and duplex DNA. Fisetin more strongly interacts with parallel G4 structure than duplex DNA, whereas naringenin shows stronger binding affinity to duplex rather than G4 DNA. Molecular docking results also corroborate our spectroscopic results, and it was found that both of the ligands are stacked externally in the G4 DNA structure. C-ring planarity of the flavonoid structure appears to be a crucial factor for preferential G4 DNA recognition of flavonoids. The goal of this study is to explore the critical effects of small differences in the structure of closely similar chemical classes of such small molecules (flavonoids) which lead to the contrasting binding properties with the two different forms of DNA. The resulting insights may be expected to facilitate the designing of the highly selective G4 DNA binders based on flavonoid scaffolds.

N(4)C-ethyl-N(4)C cross-linked DNA: synthesis and characterization of duplexes with interstrand cross-links of different orientations.

PubMed

Noronha, Anne M; Noll, David M; Wilds, Christopher J; Miller, Paul S

2002-01-22

The preparation and physical properties of short DNA duplexes that contain a N(4)C-ethyl-N(4)C interstrand cross-link are described. Duplexes that contain an interstrand cross-link between mismatched C-C residues and duplexes in which the C residues of a -CG- or -GC- step are linked to give "staggered" interstrand cross-links were prepared using a novel N(4)C-ethyl-N(4)C phosphoramidite reagent. Duplexes with the C-C mismatch cross-link have UV thermal transition temperatures that are 25 degrees C higher than the melting temperatures of control duplexes in which the cross-link is replaced with a G-C base pair. It appears that this cross-link stabilizes adjacent base pairs and does not perturb the structure of the helix, a conclusion that is supported by the CD spectrum of this duplex and by molecular models. An even higher level of stabilization, 49 degrees C, is seen with the duplex that contains a -CG- staggered cross-link. Molecular models suggest that this cross-link may induce propeller twisting in the cross-linked base pairs, and the CD spectrum of this duplex exhibits an unusual negative band at 298 nm, although the remainder of the spectrum is similar to that of B-form DNA. Mismatched C-C or -CG- staggered cross-linked duplexes that have complementary overhanging ends can undergo self-ligation catalyzed by T4 DNA ligase. Analysis of the ligated oligomers by nondenaturing polyacrylamide gel electrophoresis shows that the resulting oligomers migrate in a manner similar to that of a mixture of non-cross-linked control oligomers and suggests that these cross-links do not result in significant bending of the helix. However, the orientation of the staggered cross-link can have a significant effect on the structure and stability of the cross-linked duplex. Thus, the thermal stability of the duplex that contains a -GC- staggered cross-link is 10 degrees C lower than the melting temperature of the control, non-cross-linked duplex. Unlike the -CG- staggered cross-link, in which the cross-linked base pairs can still maintain hydrogen bond contacts, molecular models suggest that formation of the -GC- staggered cross-link disrupts hydrogen bonding and may also perturb adjacent base pairs leading to an overall reduction in helix stability. Duplexes with specifically positioned and oriented cross-links can be used as substrates to study DNA repair mechanisms.

Fabrication and investigation of electrochromatographic columns with a simplex configuration.

PubMed

Liu, Qing; Yang, Lijun; Wang, Qiuquan; Zhang, Bo

2014-07-04

Duplex capillary columns with a packed and an open section are widely used in electrochromatography (CEC). The duplex column configuration leads to non-uniform voltage drop, electrical field distribution and separation performance. It also adds to the complexity in understanding and optimizing electrochromatographic process. In this study, we introduced a simplex column configuration based on single particle fritting technology. The new column configuration has an essentially uniform packed bed through the entire column length, with only 1mm length left unpacked serving as the optical detection window. The study shows that a simplex column has higher separation efficiency than a duplex column, especially at the high voltage range, due to the consistent distribution of electrical field over the column length. In comparison to the duplex column, the simplex column presented a lower flow rate at the same applied voltage, suggesting that an open section may support a higher speed than a packed section. In practice, the long and short ends of the simplex column could be used as independent CEC columns respectively. This "two-in-one" bi-functional column configuration provided extra flexibilities in selecting and optimizing electrochromatographic conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of pork contamination in meatball using genetic marker mitochondrial DNA cytochrome b gene by duplex-PCR

NASA Astrophysics Data System (ADS)

Novianty, E.; Kartikasari, L. R.; Lee, J. H.; Cahyadi, M.

2017-04-01

Meat based food products have a big opportunity to mix and adulterated with other meats. Muslim communities are prohibited to consume pork-containing product or other pig derivatives in food. Therefore, the high sensitivity, fast, cheap and accurate approach is needed to detect pig contamination in raw meat and meat-processed product such as meatball. The aim of this study was to identify pork contamination in meatball using genetic marker of mitochondrial DNA cytochrome b gene by duplex-PCR. Samples were prepared and designed by following the proportions 0, 1, 5, 10, 25% of pork in meatballs, respectively. The DNA genome was extracted from meatballs and polymerase chain reaction (PCR) was performed using species specific primer to isolate mt-DNA cytochrome b gene. The results showed that the DNA genome was successfully isolated from pork, beef, and contaminated meatballs. Furthermore, 2% agarose gels was able to visualize of duplex-PCR to identify pork contamination in meatballs up to very small proportion (1%). It can be concluded that duplex-PCR of mt-DNA cytochrome b gene was very sensitive to identify pork contamination in meatball with the presence of specific 398 bp DNA band.

Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts

PubMed Central

Kusano, Shuhei; Ishiyama, Shogo; Lam, Sik Lok; Mashima, Tsukasa; Katahira, Masato; Miyamoto, Kengo; Aida, Misako; Nagatsugi, Fumi

2015-01-01

DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to react selectively with guanine. The AOVP CFO exhibited selective crosslinking reactivity with guanine and thymine in DNA, and with guanine in RNA. These crosslinking reactions with guanine were accelerated in the presence of CoCl2, NiCl2, ZnCl2 and MnCl2. In addition, we demonstrated that the AOVP CFO was reactive toward 8-oxoguanine opposite AOVP in the duplex DNA. The structural analysis of each guanine and 8-oxoguanine adduct in the duplex DNA was investigated by high-resolution NMR. The results suggested that AOVP reacts at the N2 amine in guanine and at the N1 or N2 amines in 8-oxoguanine in the duplex DNA. This study demonstrated the first direct determination of the adduct structure in duplex DNA without enzyme digestion. PMID:26245348

PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader

PubMed Central

Jarrige, Anne-Charlotte; Mathy, Nathalie; Portier, Claude

2001-01-01

Polynucleotide phosphorylase synthesis is autocontrolled at a post-transcriptional level in an RNase III-dependent mechanism. RNase III cleaves a long stem–loop in the pnp leader, which triggers pnp mRNA instability, resulting in a decrease in the synthesis of polynucleotide phosphorylase. The staggered cleavage by RNase III removes the upper part of the stem–loop structure, creating a duplex with a short 3′ extension. Mutations or high temperatures, which destabilize the cleaved stem–loop, decrease expression of pnp, while mutations that stabilize the stem increase expression. We propose that the dangling 3′ end of the duplex created by RNase III constitutes a target for polynucleotide phosphorylase, which binds to and degrades the upstream half of this duplex, hence inducing pnp mRNA instability. Consistent with this interpretation, a pnp mRNA starting at the downstream RNase III processing site exhibits a very low level of expression, regardless of the presence of polynucleotide phosphorylase. Moreover, using an in vitro synthesized pnp leader transcript, it is shown that polynucleotide phosphorylase is able to digest the duplex formed after RNase III cleavage. PMID:11726520

Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA

PubMed Central

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

2002-01-01

The introduction of cationic 5-(ω-aminoalkyl)-2′-deoxypyrimidines into duplex DNA has been shown to induce DNA bending. In order to understand the energetic and hydration contributions for the incorporation of a cationic side chain in DNA a combination of spectroscopy, calorimetry and density techniques were used. Specifically, the temperature unfolding and isothermal formation was studied for a pair of duplexes with sequence d(CGTAGUCG TGC)/d(GCACGACTACG), where U represents 2′-deoxyuridine (‘control’) or 5-(3-aminopropyl)-2′-deoxyuridine (‘modified’). Continuous variation experiments confirmed 1:1 stoichiometries for each duplex and the circular dichroism spectra show that both duplexes adopted the B conformation. UV and differential scanning calorimetry melting experiments reveal that each duplex unfolds in two-state transitions. In low salt buffer, the ‘modified’ duplex is more stable and unfolds with a lower endothermic heat and lower release of counterion and water. This electrostatic stabilization is entropy driven and disappears at higher salt concentrations. Complete thermodynamic profiles at 15°C show that the favorable formation of each duplex results from the compensation of a favorable exothermic heat with an unfavorable entropy contribution. However, the isothermal profiles yielded a differential enthalpy of 8.8 kcal/mol, which is 4.3 kcal/mol higher than the differential enthalpy observed in the unfolding profiles. This indicates that the presence of the aminopropyl chain induces an increase in base stacking interactions in the modified single strand and a decrease in base stacking interactions in the modified duplex. Furthermore, the formation of the ‘control’ duplex releases water while the ‘modified’ duplex takes up water. Relative to the control duplex, formation of the modified duplex at 15°C yielded a marginal differential ΔG° term, positive ΔΔHITC–Δ(TΔS) compensation, negative ΔΔV and a net release of counterions. The opposite signs of the differential enthalpy–entropy compensation and differential volume change terms show a net uptake of structural water around polar and non-polar groups. This indicates that incorporation of the aminopropyl chain induces a higher exposure of aromatic bases to the solvent, which may be consistent with a small and local bend in the ‘modified’ duplex. PMID:12136099

The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer.

PubMed

Zhuang, Zhihao; Yoder, Bonita L; Burgers, Peter M J; Benkovic, Stephen J

2006-02-21

Numerous proteins that function in DNA metabolic pathways are known to interact with the proliferating cell nuclear antigen (PCNA). The important function of PCNA in stimulating various cellular activities requires its topological linkage with DNA. Loading of the circular PCNA onto duplex DNA requires the activity of a clamp-loader [replication factor C (RFC)] complex and the energy derived from ATP hydrolysis. The mechanistic and structural details regarding PCNA loading by the RFC complex are still developing. In particular, the positive identification of a long-hypothesized structure of an open clamp-RFC complex as an intermediate in loading has remained elusive. In this study, we capture an open yeast PCNA clamp in a complex with RFC through fluorescence energy transfer experiments. We also follow the topological transitions of PCNA in the various steps of the clamp-loading pathway through both steady-state and stopped-flow fluorescence studies. We find that ATP effectively drives the clamp-loading process to completion with the formation of the closed PCNA bound to DNA, whereas ATPgammaS cannot. The information derived from this work complements that obtained from previous structural and mechanistic studies and provides a more complete picture of a eukaryotic clamp-loading pathway using yeast as a paradigm.

Benefits of Automatic Duplexing Fact Sheet

EPA Pesticide Factsheets

This resource provides a how-to duplex guide, informs the reader on the benefits and cost savings from automatic duplexing, and several off the shelf print management software options for your facility.

Electron Beam Welding of Duplex Steels with using Heat Treatment

NASA Astrophysics Data System (ADS)

Schwarz, Ladislav; Vrtochová, Tatiana; Ulrich, Koloman

2010-01-01

This contribution presents characteristics, metallurgy and weldability of duplex steels with using concentrated energy source. The first part of the article describes metallurgy of duplex steels and the influence of nitrogen on their solidification. The second part focuses on weldability of duplex steels with using electron beam aimed on acceptable structure and corrosion resistance performed by multiple runs of defocused beam over the penetration weld.

Duplex development and abandonment during evolution of the Lewis thrust system, southern Glacier National Park, Montana

NASA Astrophysics Data System (ADS)

Yin, An; Kelty, Thomas K.; Davis, Gregory A.

1989-09-01

Geologic mapping in southern Glacier National Park, Montana, reveals the presence of two duplexes sharing the same floor thrust fault, the Lewis thrust. The westernmost duplex (Brave Dog Mountain) includes the low-angle Brave Dog roof fault and Elk Mountain imbricate system, and the easternmost (Rising Wolf Mountain) duplex includes the low-angle Rockwell roof fault and Mt. Henry imbricate system. The geometry of these duplexes suggests that they differ from previously described geometric-kinematic models for duplex development. Their low-angle roof faults were preexisting structures that were locally utilized as roof faults during the formation of the imbricate systems. Crosscutting of the Brave Dog fault by the Mt. Henry imbricate system indicates that the two duplexes formed at different times. The younger Rockwell-Mt. Henry duplex developed 20 km east of the older Brave Dog-Elk Mountain duplex; the roof fault of the former is at a higher structural level. Field relations confirm that the low-angle Rockwell fault existed across the southern Glacier Park area prior to localized formation of the Mt. Henry imbricate thrusts beneath it. These thrusts kinematically link the Rockwell and Lewis faults and may be analogous to P shears that form between two synchronously active faults bounding a simple shear system. The abandonment of one duplex and its replacement by another with a new and higher roof fault may have been caused by (1) warping of the older and lower Brave Dog roof fault during the formation of the imbricate system (Elk Mountain) beneath it, (2) an upward shifting of the highest level of a simple shear system in the Lewis plate to a new decollement level in subhorizontal belt strata (= the Rockwell fault) that lay above inclined strata within the first duplex, and (3) a reinitiation of P-shear development (= Mt. Henry imbricate faults) between the Lewis thrust and the subparallel, synkinematic Rockwell fault.

Effect of Prestrain on Precipitation Behaviors of Ti-2.5Cu Alloy

NASA Astrophysics Data System (ADS)

Lincai, Zhang; Xiaoming, Ding; Wei, Ye; Man, Zhang; Zhenya, Song

2018-04-01

As a special hardenable α titanium alloy, Ti-2.5 Cu alloy was a candidate material for high temperature components requiring high strength and plasticity. The effect of prestrain on the precipitation behaviors was investigated in the present study. Tensile tests show that elongation up to 22 % can be obtained after solid solution (SS) treatment. Thereafter, prestrain in tension with 5 %, 10 %, 15 % and 20 % was carried out for the SS samples and then duplex aging was applied. Transmitting electron microscopy (TEM) investigations show that larger Ti2Cu particles were observed in the prestrained condition than free aging one, as prestrain significantly speeds up the precipitation kinetics. The strength firstly increases and then decreases for the prestrained samples after duplex aging, where the competition between precipitation hardening and recovery softening should be responsible. With the consideration of SS, precipitation and recovery, a strength model for duplex aging combined with prestrain was established, which is in well agreement with experiments. Present study may provide a promising way to obtain the strength of deformed hcp materials in industry application.

Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

PubMed Central

Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

2014-01-01

The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

A novel universal real-time PCR system using the attached universal duplex probes for quantitative analysis of nucleic acids

PubMed Central

Yang, Litao; Liang, Wanqi; Jiang, Lingxi; Li, Wenquan; Cao, Wei; Wilson, Zoe A; Zhang, Dabing

2008-01-01

Background Real-time PCR techniques are being widely used for nucleic acids analysis, but one limitation of current frequently employed real-time PCR is the high cost of the labeled probe for each target molecule. Results We describe a real-time PCR technique employing attached universal duplex probes (AUDP), which has the advantage of generating fluorescence by probe hydrolysis and strand displacement over current real-time PCR methods. AUDP involves one set of universal duplex probes in which the 5' end of the fluorescent probe (FP) and a complementary quenching probe (QP) lie in close proximity so that fluorescence can be quenched. The PCR primer pair with attached universal template (UT) and the FP are identical to the UT sequence. We have shown that the AUDP technique can be used for detecting multiple target DNA sequences in both simplex and duplex real-time PCR assays for gene expression analysis, genotype identification, and genetically modified organism (GMO) quantification with comparable sensitivity, reproducibility, and repeatability with other real-time PCR methods. Conclusion The results from GMO quantification, gene expression analysis, genotype identification, and GMO quantification using AUDP real-time PCR assays indicate that the AUDP real-time PCR technique has been successfully applied in nucleic acids analysis, and the developed AUDP real-time PCR technique will offer an alternative way for nucleic acid analysis with high efficiency, reliability, and flexibility at low cost. PMID:18522756

Microstructure and yield strength effects on hydrogen and tritium induced cracking in HERF (high-energy-rate-forged) stainless steel

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

Morgan, M J; Tosten, M H

1989-01-01

Rising-load J-integral measurements and falling-load threshold stress intensity measurements were used to characterize hydrogen and tritium induced cracking in high-energy-rate-forged (HERF) 21-6-9 stainless steel. Samples having yield strengths in the range 517--930 MPa were thermally charged with either hydrogen or tritium and tested at room temperature in either air or high-pressure hydrogen gas. In general, the hydrogen isotopes reduced the fracture toughness by affecting the fracture process. Static recrystallization in the HERF microstructures affected the material's fracture toughness and its relative susceptibility to hydrogen and tritium induced fracture. In hydrogen-exposed samples, the reduction in fracture toughness was primarily dependent onmore » the susceptibility of the microstructure to intergranular fracture and only secondarily affected by strength in the range of 660 to 930 MPa. Transmission-electron microscopy observations revealed that the microstructures least susceptible to hydrogen-induced intergranular cracking contained patches of fully recrystallized grains. These grains are surrounded by highly deformed regions containing a high number density of dislocations. The microstructure can best be characterized as duplex'', with soft recrystallized grains embedded in a hard, deformed matrix. The microstructures most susceptible to hydrogen-induced intergranular fracture showed no well-developed recrystallized grains. The patches of recrystallized grains seemed to act as crack barriers to hydrogen-induced intergranular fracture. In tritium-exposed-and-aged samples, the amount of static recrystallization also affected the fracture toughness properties but to a lesser degree. 7 refs., 25 figs.« less

Hole Transport in A-form DNA/RNA Hybrid Duplexes

NASA Astrophysics Data System (ADS)

Wong, Jiun Ru; Shao, Fangwei

2017-01-01

DNA/RNA hybrid duplexes are prevalent in many cellular functions and are an attractive target form for electrochemical biosensing and electric nanodevice. However the electronic conductivities of DNA/RNA hybrid duplex remain relatively unexplored and limited further technological applications. Here cyclopropyl-modified deoxyribose- and ribose-adenosines were developed to explore hole transport (HT) in both DNA duplex and DNA/RNA hybrids by probing the transient hole occupancies on adenine tracts. HT yields through both B-form and A-form double helixes displayed similar shallow distance dependence, although the HT yields of DNA/RNA hybrid duplexes were lower than those of DNA duplexes. The lack of oscillatory periods and direction dependence in HT through both helixes implied efficient hole propagation can be achieved via the hole delocalization and coherent HT over adenine tracts, regardless of the structural variations.

Hole Transport in A-form DNA/RNA Hybrid Duplexes

PubMed Central

Wong, Jiun Ru; Shao, Fangwei

2017-01-01

DNA/RNA hybrid duplexes are prevalent in many cellular functions and are an attractive target form for electrochemical biosensing and electric nanodevice. However the electronic conductivities of DNA/RNA hybrid duplex remain relatively unexplored and limited further technological applications. Here cyclopropyl-modified deoxyribose- and ribose-adenosines were developed to explore hole transport (HT) in both DNA duplex and DNA/RNA hybrids by probing the transient hole occupancies on adenine tracts. HT yields through both B-form and A-form double helixes displayed similar shallow distance dependence, although the HT yields of DNA/RNA hybrid duplexes were lower than those of DNA duplexes. The lack of oscillatory periods and direction dependence in HT through both helixes implied efficient hole propagation can be achieved via the hole delocalization and coherent HT over adenine tracts, regardless of the structural variations. PMID:28084308

Development of duplex RT-PCR-ELISA for the simultaneous detection of hepatitis A virus and hepatitis E virus.

PubMed

Tahk, Hongmin; Lee, Min Hwa; Lee, Kang Bum; Cheon, Doo-Sung; Choi, Changsun

2011-07-01

This study aimed to develop a specific and sensitive duplex reverse transcription polymerase chain reaction enzyme-linked immunosorbent assay (duplex RT-PCR-ELISA) for hepatitis A virus (HAV) and hepatitis E virus (HEV). Duplex RT-PCR-ELISA could detect and differentiate HAV and HEV with specific probes. When ELISA technique was used to detect probe-bound RT-PCR products, duplex RT-PCR-ELISA could detect as little as 0.1 ng/μL HAV and HEV from clinical samples. Human norovirus, enterovirus, poliovirus, murine norovirus and feline calicivirus were used for the specificity test; all were negative. Therefore duplex RT-PCR-ELISA can be used for the simultaneous detection of HAV and HEV in contaminated fecal samples. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

Nick-free formation of reciprocal heteroduplexes: a simple solution to the topological problem.

PubMed Central

Wilson, J H

1979-01-01

Because the individual strands of DNA are intertwined, formation of heteroduplex structures between duplexes--as in presumed recombination intermediates--presents a topological puzzle, known as the winding problem. Previous approaches to this problem have assumed that single-strand breaks are required to permit formation of fully coiled heteroduplexes. This paper describes a simple, nick-free solution to the winding problem that satisfies all topological constraints. Homologous duplexes associated by their minor-groove surfaces can switch strand pairing to form reciprocal heteroduplexes that coil together into a compact, four-stranded helix throughout the region of pairing. Model building shows that this fused heteroduplex structure is plausible, being composed entirely of right-handed primary helices with Watson-Crick base pairing throughout. Its simplicity of formation, structural symmetry, and high degree of specificity are suggestive of a natural mechanism for alignment by base pairing between intact homologous duplexes. Implications for genetic recombination are discussed. Images PMID:291028

Progress Towards the Development of a Long-Lived Venus Lander Duplex System

NASA Technical Reports Server (NTRS)

Dyson, Roger W.; Bruder, Geoffrey A.

2010-01-01

NASA has begun the development of a combined Stirling cycle power and cooling system (duplex) to enable the long-lived surface exploration of Venus and other harsh environments in the solar system. The duplex system will operate from the heat provided by decaying radioisotope plutonium-238 or its substitute. Since the surface of Venus has a thick, hot, and corrosive atmosphere, it is a challenging proposition to maintain sensitive lander electronics under survivable conditions. This development effort requires the integration of: a radioisotope or fission heat source; heat pipes; high-temperature, corrosion-resistant material; multistage cooling; a novel free-displacer Stirling convertor for the lander; and a minimal vibration thermoacoustic Stirling convertor for the seismometer. The first year effort includes conceptual system design and control studies, materials development, and prototype hardware testing. A summary of these findings and test results is presented in this report.

The Effect of Surface Preparation on the Precipitation of Sigma During High Temperature Exposure of S32205 Duplex Stainless Steel

NASA Astrophysics Data System (ADS)

Jepson, Mark A. E.; Rowlett, Matthew; Higginson, Rebecca L.

2017-03-01

Although the formation of sigma phase in duplex stainless steels is reasonably well documented, the effect of surface finish on its formation rate in surface regions has not been previously noted. The growth of the sigma phase precipitated in the subsurface region (to a maximum depth of 120 μm) has been quantified after heat treatment of S32205 duplex stainless steel at 1073 K (800 °C) and 1173 K (900 °C) after preparation to two surface finishes. Here, results are presented that show that there is a change in the rate of sigma phase formation in the surface region of the material, with a coarser surface finish leading to a greater depth of precipitation at a given time and temperature of heat treatment. The growth rate and morphology of the precipitated sigma has been examined and explored in conjunction with thermodynamic equilibrium phase calculations.

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.

PubMed

Jasiński, Maciej; Feig, Michael; Trylska, Joanna

2018-06-06

Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.

Progress Towards the Development of a Long-Lived Venus Lander Duplex System

NASA Technical Reports Server (NTRS)

Dyson, Rodger, W.; Bruder, Geoffrey A.

2011-01-01

NASA has begun the development of a combined Stirling cycle power and cooling system (duplex) to enable the long-lived surface exploration of Venus and other harsh environments in the solar system. The duplex system will operate from the heat provided by decaying radioisotope plutonium-238 or its substitute. Since the surface of Venus has a thick, hot, and corrosive atmosphere, it is a challenging proposition to maintain sensitive lander electronics under survivable conditions. This development effort requires the integration of: a radioisotope or fission heat source; heat pipes; high-temperature, corrosion-resistant material; multistage cooling; a novel free-displacer Stirling convertor for the lander; and a minimal vibration thermoacoustic Stirling convertor for the seismometer. The first year effort includes conceptual system design and control studies, materials development, and prototype hardware testing. A summary of these findings and test results is presented in this report.

Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA.

PubMed

Zeng, Tao; Fleming, Aaron M; Ding, Yun; Ren, Hang; White, Henry S; Burrows, Cynthia J

2018-04-06

In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.

Reducing the background fluorescence in mice receiving fluorophore/inhibitor DNA duplexes.

PubMed

Liang, Minmin; Liu, Xinrong; Liu, Guozheng; Dou, Shuping; Cheng, Dengfeng; Liu, Yuxia; Rusckowski, Mary; Hnatowich, Donald J

2011-02-07

In principle, a DNA duplex consisting of an antisense fluorophore-conjugated major strand hybridized to a shorter complementary inhibitor-conjugated minor strand should provide fluorescence only in the tumor after intravenous administration if designed to remain intact except in the presence in tumor of its mRNA target. While we have obtained impressive tumor images in mice using this approach, there remains some background fluorescence. In this study, tissue homogenates of selected mouse organs were incubated with a test duplex and the kinetics of duplex dissociation in normal tissues were measured. In this manner we were able to identify the liver as the likely major source responsible for the duplex dissociation providing this fluorescence background. Thereafter liver homogenates were used to screen a series of duplex candidates with variable-length minor strands, and dissociation was measured by gel electrophoresis. The selected fluorophore/inhibitor duplex with improved stability displayed an insignificant (P > 0.05) background fluorescence after administration to SKH-1 normal mice and apparently without affecting target mRNA binding in vitro in cell culture or in vivo in tumor bearing mice.

Synthesis of 5-(1,2,3-triazol-4-yl)-2'-deoxyuridines by a click chemistry approach: stacking of triazoles in the major groove gives increased nucleic acid duplex stability.

PubMed

Kocalka, Petr; Andersen, Nicolai K; Jensen, Frank; Nielsen, Poul

2007-11-23

A general protocol for converting alkyl and aryl halides into azides and for converting these in situ into 1,4-disubstituted triazoles was applied with 5-ethynyl-2'-deoxyuridine. This afforded three modified 2'-deoxyuridine analogues with either unsubstituted or 1-phenyl-/1-benzyl-substituted triazoles in their 5-positions. Modelling demonstrates coplanarity of the two heteroaromatic rings, and UV spectroscopy showed the uracil pK(a) values to be almost unchanged. The three nucleosides were introduced into nonamer oligonucleotides by phosphoramidite chemistry. The heteroaromatic triazoles became positioned in the major grooves of the short dsDNA and DNA-RNA duplexes. While single modifications led to decreased duplex stability, the stacking of four consecutive modifications led to enhanced duplex stability, especially for DNA-RNA duplexes. The duplex structures were studied by CD spectroscopy and molecular dynamics simulations, which supported the conjecture that the duplex stabilizing effect is due to efficient stacking of the heteroaromatic triazoles.

A Raman spectroscopic analysis of the sequence-dependent structures of oligo-DNA duplexes: d(CGCG) 2, d(GCGC) 2, d(GGCC) 2, and d(CCGG) 2 in aqueous solution

NASA Astrophysics Data System (ADS)

Torigoe, Chikako; Nishimura, Yoshifumi; Tsuboi, Masamichi; Matsuzaki, Jun-ichi; Hotoda, Hitoshi; Sekine, Mitsuo; Hata, Tsujiaki

Raman spectra of four self-complementary tetradeoxyribonucleoside triphosphates containing only guanosine and cytidine residues have been examined in aqueous solutions of different ionic strengths and at different temperatures. Both in low salt (0.15 M NaCl) and in high salt (4 M NaCl) solutions (at -2°C) all of the four duplexes have different conformations, distinguishable by Raman spectroscopy from one another. Thus, the duplex conformation is sequence-dependent. On the basis of several rules proposed recently for structure—spectrum correlations, new information was provided on the local conformations of the duplexes of these oligo-DNAs. In the low-salt solution, d(CCGG) 2 is B-DNA like in its overall conformation, but in detail the backbone conformation of the CpC portion is considered to be different from that in the GpG portion. In either one of these two portions, the torsion angle (β) around the O5'C5' bond must be somewhat higher than the usual values for B-DNA (150-170°), so that it causes a 815 cm -1 Raman line instead of the usual B marker 830 cm -1 line. This may be related to the peculiar circular dichroism spectrum of d(CCGG) 2. On going to the high-salt solution, about 5% of the d(CCGG) 2 molecules are converted into the A form. In the high-salt form (Z form) of d(CGCG) 2, the terminal guanosine was concluded to be in a C2' endo-syn conformation, whereas the internal one is in C3' endo-syn.

Synthesis of native-like crosslinked duplex RNA and study of its properties.

PubMed

Onizuka, Kazumitsu; Hazemi, Madoka E; Thomas, Justin M; Monteleone, Leanna R; Yamada, Ken; Imoto, Shuhei; Beal, Peter A; Nagatsugi, Fumi

2017-04-01

A variety of enzymes have been found to interact with double-stranded RNA (dsRNA) in order to carry out its functions. We have endeavored to prepare the covalently crosslinked native-like duplex RNA, which could be useful for biochemical studies and RNA nanotechnology. In this study, the interstrand covalently linked duplex RNA was formed by a crosslinking reaction between vinylpurine (VP) and the target cytosine or uracil in RNA. We measured melting temperatures and CD spectra to identify the properties of the VP crosslinked duplex RNA. The crosslinking formation increased the thermodynamic stability without disturbing the natural conformation of dsRNA. In addition, a competitive binding experiment with the duplex RNA binding enzyme, ADAR2, showed the crosslinked dsRNA bound the protein with nearly the same binding affinity as the natural dsRNA, confirming that it has finely preserved the natural traits of duplex RNA. Copyright © 2017. Published by Elsevier Ltd.

'Passive-roof' duplex geometry in the frontal structures of the Kirthar and Sulaiman mountain belts, Pakistan

NASA Astrophysics Data System (ADS)

Banks, C. J.; Warburton, J.

Exploration for hydrocarbons over the past few years has greatly improved our understanding of the geometry of frontal mountain belt structures. In this study we introduce and discuss the concept of the 'Passive-roof duplex', using as the main example the Kirthar and Sulaiman Ranges in the Baluchistan Province of Pakistan. Structures similar to those described here have been recognized previously in other mountain belts, and they appear to exist as a common feature in many more frontal regions of mountain belts. Our example of a Passive-roof duplex which we describe from Pakistan is compared briefly with similar structures reported by others. The Passive-roof duplex is here defined as a duplex whose roof thrust has backthrust sense ( Passive-roof thrust) and whose roof sequence (those rocks lying above the roof thrust) remains relatively 'stationary' during foreland directed piggy-back style propagation of horses within the duplex.

Enzymatic Reaction with Unnatural Substrates: DNA Photolyase (Escherichia coli) Recognizes and Reverses Thymine [2+2] Dimers in the DNA Strand of a DNA/PNA Hybrid Duplex

NASA Astrophysics Data System (ADS)

Ramaiah, Danaboyina; Kan, Yongzhi; Koch, Troels; Orum, Henrik; Schuster, Gary B.

1998-10-01

Peptide nucleic acids (PNA) are mimics with normal bases connected to a pseudopeptide chain that obey Watson--Crick rules to form stable duplexes with itself and natural nucleic acids. This has focused attention on PNA as therapeutic or diagnostic reagents. Duplexes formed with PNA mirror some but not all properties of DNA. One fascinating aspect of PNA biochemistry is their reaction with enzymes. Here we show an enzyme reaction that operates effectively on a PNA/DNA hybrid duplex. A DNA oligonucleotide containing a cis, syn-thymine [2+2] dimer forms a stable duplex with PNA. The hybrid duplex is recognized by photolyase, and irradiation of the complex leads to the repair of the thymine dimer. This finding provides insight into the enzyme mechanism and provides a means for the selective repair of thymine photodimers.

Final Report on Developing Microstructure-Property Correlation in Reactor Materials using in situ High-Energy X-rays

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

Li, Meimei; Almer, Jonathan D.; Yang, Yong

2016-01-01

This report provides a summary of research activities on understanding microstructure – property correlation in reactor materials using in situ high-energy X-rays. The report is a Level 2 deliverable in FY16 (M2CA-13-IL-AN_-0403-0111), under the Work Package CA-13-IL-AN_- 0403-01, “Microstructure-Property Correlation in Reactor Materials using in situ High Energy Xrays”, as part of the DOE-NE NEET Program. The objective of this project is to demonstrate the application of in situ high energy X-ray measurements of nuclear reactor materials under thermal-mechanical loading, to understand their microstructure-property relationships. The gained knowledge is expected to enable accurate predictions of mechanical performance of these materialsmore » subjected to extreme environments, and to further facilitate development of advanced reactor materials. The report provides detailed description of the in situ X-ray Radiated Materials (iRadMat) apparatus designed to interface with a servo-hydraulic load frame at beamline 1-ID at the Advanced Photon Source. This new capability allows in situ studies of radioactive specimens subject to thermal-mechanical loading using a suite of high-energy X-ray scattering and imaging techniques. We conducted several case studies using the iRadMat to obtain a better understanding of deformation and fracture mechanisms of irradiated materials. In situ X-ray measurements on neutron-irradiated pure metal and model alloy and several representative reactor materials, e.g. pure Fe, Fe-9Cr model alloy, 316 SS, HT-UPS, and duplex cast austenitic stainless steels (CASS) CF-8 were performed under tensile loading at temperatures of 20-400°C in vacuum. A combination of wide-angle X-ray scattering (WAXS), small-angle X-ray scattering (SAXS), and imaging techniques were utilized to interrogate microstructure at different length scales in real time while the specimen was subject to thermal-mechanical loading. In addition, in situ X-ray studies were complemented and benchmarked by ex situ characterization using advanced electron microscopy, atom probe tomography (APT) and micro/nano-indentation. The report presented in situ tensile test results on neutron-irradiated pure Fe, Fe-9Cr model alloy, 316 SS and CASS CF-8. These in situ experiments demonstrate the broad applications of the new capability in understanding several outstanding issues related to irradiated materials.« less

The Scientific Work We Love: A Duplex Theory of Scientific Impact and Its Application to the Top-Cited Articles in the First 30 Years of APS Journals.

PubMed

Sternberg, Robert J

2018-03-01

This article proposes a duplex theory for understanding the scientific impact of contributions to psychological science. I argue that articles that we "love" can be understood in terms of (a) triangular elements of intimacy, passion, and commitment and (b) types of stories that characterize high-impact articles. Certain kinds of stories (e.g., review articles) are more likely to have lasting impact, on average, than other kinds of stories (e.g., data-driven empirical articles).

Impact of Duplex arterial mapping on decision making in non-acute ischemic limb patients.

PubMed

Elbadawy, A; Aly, H; Ibrahim, M; Bakr, H

2015-12-01

The aim of this study was to demonstrate the impact of Duplex arterial mapping on decision making in non-acute ischemic limb patient group reporting pain onset between 15 days and 3 months. We prospectively evaluated patients presented with critical limb ischemia who reported pain onset of duration between 15 days and 3 months in one-year period. Our series included thirty cases (mean age=61.3 years old), as Duplex arterial mapping was the sole preoperative imaging tool performed in all of them. All patients, in whom duplex indicated thrombosis in long occluded segments, were candidates for fluoroscopically guided thrombectomy. When Duplex defined chronic arterial occlusions, patients underwent endovascular or bypass revascularisation procedures. Impact of Duplex wall interrogation on decision-making between the two groups (subacute and chronic) was measured. Duplex arterial mapping categorized correctly all 30 patients into either subacute ischemia with removable clot (N.=14) or chronic ischemia (N.=16). Fluoroscopic guided thrombectomy was performed in 14 cases when Duplex advised long occluded arterial segments as indicted by intact intima with echogenic thrombus inside. Bypass surgery was performed in 8 patients. Percutaneous transluminal angioplasty (PTA) was done in 7 cases and thrombendartrectomy of common femoral artery in a single case. One-year patency rate in our series was 86.6%. It was 71.4% in thrombosis group. Limb salvage rate was 93.3%. Duplex arterial mapping could be used to differentiate the subacute ischemia with removable thrombus and chronic arterial occlusions guiding for the best revascularization procedure accordingly.

Development and properties of duplex MgF2/PCL coatings on biodegradable magnesium alloy for biomedical applications.

PubMed

Makkar, Preeti; Kang, Hoe Jin; Padalhin, Andrew R; Park, Ihho; Moon, Byoung-Gi; Lee, Byong Taek

2018-01-01

The present work addresses the performance of polycaprolactone (PCL) coating on fluoride treated (MgF2) biodegradable ZK60 magnesium alloy (Mg) for biomedical application. MgF2 conversion layer was first produced by immersing Mg alloy substrate in hydrofluoric acid solution. The outer PCL coating was then prepared using dip coating technique. Morphology, elements profile, phase structure, roughness, mechanical properties, invitro corrosion, and biocompatibility of duplex MgF2/PCL coating were then characterized and compared to those of fluoride coated and uncoated Mg samples. The invivo degradation behavior and biocompatibility of duplex MgF2/PCL coating with respect to ZK60 Mg alloy were also studied using rabbit model for 2 weeks. SEM and TEM analysis showed that the duplex coating was uniform and comprised of porous PCL film (~3.3 μm) as upper layer with compact MgF2 (~2.2 μm) as inner layer. No significant change in microhardness was found on duplex coating compared with uncoated ZK60 Mg alloy. The duplex coating showed improved invitro corrosion resistance than single layered MgF2 or uncoated alloy samples. The duplex coating also resulted in better cell viability, cell adhesion, and cell proliferation compared to fluoride coated or uncoated alloy. Preliminary invivo studies indicated that duplex MgF2/PCL coating reduced the degradation rate of ZK60 Mg alloy and exhibited good biocompatibility. These results suggested that duplex MgF2/PCL coating on magnesium alloy might have great potential for orthopedic applications.

Development and properties of duplex MgF2/PCL coatings on biodegradable magnesium alloy for biomedical applications

PubMed Central

Makkar, Preeti; Kang, Hoe Jin; Padalhin, Andrew R.; Park, Ihho; Moon, Byoung-Gi

2018-01-01

The present work addresses the performance of polycaprolactone (PCL) coating on fluoride treated (MgF2) biodegradable ZK60 magnesium alloy (Mg) for biomedical application. MgF2 conversion layer was first produced by immersing Mg alloy substrate in hydrofluoric acid solution. The outer PCL coating was then prepared using dip coating technique. Morphology, elements profile, phase structure, roughness, mechanical properties, invitro corrosion, and biocompatibility of duplex MgF2/PCL coating were then characterized and compared to those of fluoride coated and uncoated Mg samples. The invivo degradation behavior and biocompatibility of duplex MgF2/PCL coating with respect to ZK60 Mg alloy were also studied using rabbit model for 2 weeks. SEM and TEM analysis showed that the duplex coating was uniform and comprised of porous PCL film (~3.3 μm) as upper layer with compact MgF2 (~2.2 μm) as inner layer. No significant change in microhardness was found on duplex coating compared with uncoated ZK60 Mg alloy. The duplex coating showed improved invitro corrosion resistance than single layered MgF2 or uncoated alloy samples. The duplex coating also resulted in better cell viability, cell adhesion, and cell proliferation compared to fluoride coated or uncoated alloy. Preliminary invivo studies indicated that duplex MgF2/PCL coating reduced the degradation rate of ZK60 Mg alloy and exhibited good biocompatibility. These results suggested that duplex MgF2/PCL coating on magnesium alloy might have great potential for orthopedic applications. PMID:29608572

Discussion Starter: The Case for Duplexing without Channel Flow During the Development and Emplacement of the Himalayan Middle Crust

NASA Astrophysics Data System (ADS)

Webb, A. G.; He, D.; Yu, H.

2015-12-01

This presentation and another presentation led by Dawn Kellett will preface a ten-minute open discussion on how the Himalayan middle crust was developed and emplaced. Current hypotheses are transitioning from a set including wedge extrusion, channel flow with focused denudation, and tectonic wedging to a revised dichotomy: models with intense upper plate out-of-sequence activity (i.e., tunneling of channel flow, and critical taper wedge behavior) versus models in which the upper plate mainly records basal accretion of horses (i.e., duplexing). Critical taper and duplexing offer a simple contrast that can be illustrated via food analogies. If a wedge is critical, it churns internally like a pile of CheeriosTM cereal pushed up an inclined plane. Stacking of a duplex acts like a deli meat-slicing machine: slice after slice is cut from the intact block to a stack of slices, but neither the block (~down-going plate) nor the stack (~upper plate) features much internal deformation. Thus critical taper and channel tunneling models predict much processing via out-of-sequence deformation, whereas duplexing predicts in-sequence thrusting. The two concepts may be considered end-members. Recent work shows that the Himalayan middle crust has been assembled along a series of mainly southwards-younging thrust faults. The thrust faults separate 1-5 km thick panels that experienced similar metamorphic cycles during different time periods. Out-of-sequence deformation is rare, with its apparent significance enhanced because of the high throw-to-heave ratio of out-of-sequence thrusting. Flattening fabrics developed prior to thrusting have been interpreted to record either (1) southwards channel tunneling across the upper plate, or (2) fabric development during metamorphism of the down-going plate. We will argue that the thrust faults dominantly represent in-sequence duplexing, and therefore conclude that the Himalaya and analogous hot orogens behave like other accretionary orogens.

Compact, precision duplex bearing mount for high vibration environments

NASA Technical Reports Server (NTRS)

Bouzakis, George Elias (Inventor); Bowman, James Edward (Inventor); Devine, Edward J. (Inventor); Joffe, Benjamin (Inventor); Segal, Kenneth Neal (Inventor); Webb, Merritt J. (Inventor)

2002-01-01

A duplex bearing mount including at least one duplex bearing having an inner race and an outer race, the inner race disposed within the outer race and being rotatable relative to the outer race about an axis, the inner race having substantially no relative movement relative to the outer race in at least one direction along the axis, the inner and outer races each having first and second axial faces which are respectively located at the same axial end of the duplex bearing. The duplex bearing is radially supported by a housing, and a shaft extends through the inner race, the shaft radially and axially supported by the inner race. A first retainer is connected to the housing and engages the first axial surface of a bearing race, the movement of which race in a first direction along the axis being constrained by the first retainer. A second, resilient retainer is connected to the housing or the shaft and is deflected through engagement with the second axial face of a bearing race, the movement of which race in a second direction along the axis, opposite to the first direction, being constrained by the deflected second retainer. The bearing is preloaded by its being clamped between the first and second retainers, and the second retainer forms at least a portion of a spring having the characteristic of a substantially constant force value correlating to a range of various deflection values, whereby the preload of the bearing is substantially unaffected by variations in the deflection of the second retainer.

Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes

DTIC Science & Technology

2007-10-01

reverse-complement unless otherwise stated. For strand x, let Nx denote its complement. A (perfect) Watson - Crick duplex is the joining of complement...is possible for complementary sequences to form a non-perfectly aligned duplex, we will call any x W Nx duplex a Watson - Crick (WC) duplex. Two...DATES COVERED (From - To) 4. TITLE AND SUBTITLE FREE ENERGY GAP AND STATISTICAL THERMODYNAMIC FIDELITY OF DNA CODES 5a. CONTRACT NUMBER FA8750-07

Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes (Postprint)

DTIC Science & Technology

2007-01-01

reverse-complement unless otherwise stated. For strand x, let Nx denote its complement. A (perfect) Watson - Crick duplex is the joining of complement...is possible for complementary sequences to form a non-perfectly aligned duplex, we will call any x W Nx duplex a Watson - Crick (WC) duplex. Two...DATES COVERED (From - To) 4. TITLE AND SUBTITLE FREE ENERGY GAP AND STATISTICAL THERMODYNAMIC FIDELITY OF DNA CODES 5a. CONTRACT NUMBER FA8750-07

Prolonged CT urography in duplex kidney.

PubMed

Gong, Honghan; Gao, Lei; Dai, Xi-Jian; Zhou, Fuqing; Zhang, Ning; Zeng, Xianjun; Jiang, Jian; He, Laichang

2016-05-13

Duplex kidney is a common anomaly that is frequently associated with multiple complications. Typical computed tomography urography (CTU) includes four phases (unenhanced, arterial, parenchymal and excretory) and has been suggested to considerably aid in the duplex kidney diagnosi. Unfortunately, regarding duplex kidney with prolonged dilatation, the affected parenchyma and tortuous ureters demonstrate a lack of or delayed excretory opacification. We used prolonged-delay CTU, which consists of another prolonged-delay phase (1- to 72-h delay; mean delay: 24 h) to opacify the duplicated ureters and affected parenchyma. Seventeen patients (9 males and 8 females; age range: 2.5-56 y; mean age: 40.4 y) with duplex kidney were included in this study. Unenhanced scans did not find typical characteristics of duplex kidney, except for irregular perirenal morphology. Duplex kidney could not be confirmed on typical four-phase CTU, whereas it could be easily diagnosed in axial and CT-3D reconstruction using prolonged CTU (prolonged-delay phase). Between January 2005 and October 2010, in this review board-approved study (with waived informed consent), 17 patients (9 males and 8 females; age range: 2.5 ~ 56 y; mean age: 40.4 y) with suspicious duplex kidney underwent prolonged CTU to opacify the duplicated ureters and confirm the diagnosis. Our results suggest the validity of prolonged CTU to aid in the evaluation of the function of the affected parenchyma and in the demonstration of urinary tract malformations.

[A Duplex PCR Method for Detection of Babesia caballi and Theileria equi].

PubMed

Zhang, Yang; Zhang, Yu-ting; Wang, Zhen-bao; Bolati; Li, Hai; Bayinchahan

2015-04-01

To develop a duplex PCR assay for detection of Babesia caballi and Theileria equi. Two pairs of primers were designed according to the BC48 gene of B. caballi and 18 s rRNA gene of T. equi, and a duplex PCR assay was developed by the optimization of reaction conditions. The specificity, sensitivity and reliability of the method were tested. The horse blood samples of suspected cases were collected from Yili region, and detected by the duplex PCR, microspopy, conventional PCR, and fluorescence quantitative PCR, and the results were compared. Using the duplex PCR assay, the specific fragments of 155 bp and 280 bp were amplified from DNA samples of B. caballi and T. equi, respectively. No specific fragment was amplified from DNA samples of B. bigemina, Theilerdia annulata, Theilerdia sergenti, Toxoplasma gondii, Neospora caninum, and Trypanosoma evansi. The limit of detection was 4.85 x 10(5) copies/L for B. caballi DNA and 4.85 x 10(4) copies/µl for T. equi DNA, respectively. Among the 24 blood samples, 11 were found B. caballi-positive by the duplex PCR assay, and 18 were T. equi-positive. The coincidence rate of microscopy, conventional PCR, and fluorescence quantitative PCR with duplex PCR was 91.7% (22/24), 95.8% (23/24), and 95.8% (23/24), respectively. A duplex PCR assay for simultaneous detection of B. caballi and T. equi is established.

Translational Entropy and DNA Duplex Stability.

PubMed

Privalov, Peter L; Crane-Robinson, Colyn

2018-01-09

Investigation of folding/unfolding DNA duplexes of various size and composition by superprecise calorimetry has revised several long-held beliefs concerning the forces responsible for the formation of the double helix. It was established that: 1) the enthalpy and the entropy of duplex unfolding are temperature dependent, increasing with temperature rise and having the same heat capacity increment for CG and AT pairs; 2) the enthalpy of AT melting is greater than that of the CG pair, so the stabilizing effect of the CG pair in comparison with AT results not from its larger enthalpic contribution (as expected from its extra hydrogen bond), but from the larger entropic contribution of the AT pair that results from its ability to fix ordered water in the minor groove and release it upon duplex unfolding; 3) the translation entropy, resulting from the appearance of a new kinetic unit on duplex dissociation, determines the dependence of duplex stability on its length and its concentration (it is an order-of-magnitude smaller than predicted from the statistical mechanics of gases and is fully expressed by the stoichiometric correction term); 4) changes in duplex stability on reshuffling the sequence (the "nearest-neighbor effect") result from the immobilized water molecules fixed by AT pairs in the minor groove; and 5) the evaluated thermodynamic components permit a quantitative expression of DNA duplex stability. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch

PubMed Central

Pack, Seung Pil; Morimoto, Hirohisa; Makino, Keisuke; Tajima, Kunihiko; Kanaori, Kenji

2012-01-01

Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of 1H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO6CACTG)/d(CAGTGX17GTCAC), X = C or T]. 1H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation. Exchangeable resonances of C17 4-amino proton of the O:C duplex and of T17 imino proton of O:T duplex showed unusual chemical shifts, and disappeared with temperature increasing up to 30°C, although the melting temperatures were >50°C. The O:C mismatch takes a wobble geometry with positive shear parameter where the Oxa ring shifted toward the major groove and the paired C17 toward the minor groove, while, in the O:T mismatch pair with the negative shear, the Oxa ring slightly shifted toward the minor groove and the paired T17 toward the major groove. The Oxa mismatch pairs can be wobbled largely because of no hydrogen bond to the O1 position of the Oxa base, and may occupy positions in the strands that optimize the stacking with adjacent bases. PMID:22039100

Analysis of Structural Flexibility of Damaged DNA Using Thiol-Tethered Oligonucleotide Duplexes

PubMed Central

Fujita, Masashi; Watanabe, Shun; Yoshizawa, Mariko; Yamamoto, Junpei; Iwai, Shigenori

2015-01-01

Bent structures are formed in DNA by the binding of small molecules or proteins. We developed a chemical method to detect bent DNA structures. Oligonucleotide duplexes in which two mercaptoalkyl groups were attached to the positions facing each other across the major groove were prepared. When the duplex contained the cisplatin adduct, which was proved to induce static helix bending, interstrand disulfide bond formation under an oxygen atmosphere was detected by HPLC analyses, but not in the non-adducted duplex, when the two thiol-tethered nucleosides were separated by six base pairs. When the insert was five and seven base pairs, the disulfide bond was formed and was not formed, respectively, regardless of the cisplatin adduct formation. The same reaction was observed in the duplexes containing an abasic site analog and the (6–4) photoproduct. Compared with the cisplatin case, the disulfide bond formation was slower in these duplexes, but the reaction rate was nearly independent of the linker length. These results indicate that dynamic structural changes of the abasic site- and (6–4) photoproduct-containing duplexes could be detected by our method. It is strongly suggested that the UV-damaged DNA-binding protein, which specifically binds these duplexes and functions at the first step of global-genome nucleotide excision repair, recognizes the easily bendable nature of damaged DNA. PMID:25679955

Development of nano-structured duplex and ferritic stainless steels by pulverisette planetary milling followed by pressureless sintering

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

R, Shashanka, E-mail: shashankaic@gmail.com; Chaira, D., E-mail: chaira.debasis@gmail.com

Nano-structured duplex and ferritic stainless steel powders are prepared by planetary milling of elemental Fe, Cr and Ni powder for 40 h and then consolidated by conventional pressureless sintering. The progress of milling and the continuous refinement of stainless steel powders have been confirmed by means of X-ray diffraction and scanning electron microscopy. Activation energy for the formation of duplex and ferritic stainless steels is calculated by Kissinger method using differential scanning calorimetry and is found to be 159.24 and 90.17 KJ/mol respectively. Both duplex and ferritic stainless steel powders are consolidated at 1000, 1200 and 1400 °C in argonmore » atmosphere to study microstructure, density and hardness. Maximum sintered density of 90% and Vickers microhardness of 550 HV are achieved for duplex stainless steel sintered at 1400 °C for 1 h. Similarly, 92% sintered density and 263 HV microhardness are achieved for ferritic stainless steel sintered at 1400 °C. - Highlights: • Synthesized duplex and ferritic stainless steels by pulverisette planetary milling • Calculated activation energy for the formation of duplex and ferritic stainless steels • Studied the effect of sintering temperature on density, hardness and microstructure • Duplex stainless steel exhibits 90% sintered density and microhardness of 550 HV. • Ferritic stainless steel shows 92% sintered density and 263 HV microhardness.« less

A duplex DNA-gold nanoparticle probe composed as a colorimetric biosensor for sequence-specific DNA-binding proteins.

PubMed

Ahn, Junho; Choi, Yeonweon; Lee, Ae-Ree; Lee, Joon-Hwa; Jung, Jong Hwa

2016-03-21

Using duplex DNA-AuNP aggregates, a sequence-specific DNA-binding protein, SQUAMOSA Promoter-binding-Like protein 12 (SPL-12), was directly determined by SPL-12-duplex DNA interaction-based colorimetric actions of DNA-Au assemblies. In order to prepare duplex DNA-Au aggregates, thiol-modified DNA 1 and DNA 2 were attached onto the surface of AuNPs, respectively, by the salt-aging method and then the DNA-attached AuNPs were mixed. Duplex-DNA-Au aggregates having the average size of 160 nm diameter and the maximum absorption at 529 nm were able to recognize SPL-12 and reached the equivalent state by the addition of ∼30 equivalents of SPL-12 accompanying a color change from red to blue with a red shift of the maximum absorption at 570 nm. As a result, the aggregation size grew to about 247 nm. Also, at higher temperatures of the mixture of duplex-DNA-Au aggregate solution and SPL-12, the equivalent state was reached rapidly. On the contrary, in the control experiment using Bovine Serum Albumin (BSA), no absorption band shift of duplex-DNA-Au aggregates was observed.

Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides

PubMed Central

Pasternak, Anna; Wengel, Jesper

2010-01-01

Thermodynamics provides insights into the influence of modified nucleotide residues on stability of nucleic acids and is crucial for designing duplexes with given properties. In this article, we introduce detailed thermodynamic analysis of RNA duplexes modified with unlocked nucleic acid (UNA) nucleotide residues. We investigate UNA single substitutions as well as model mismatch and dangling end effects. UNA residues placed in a central position makes RNA duplex structure less favourable by 4.0–6.6 kcal/mol. Slight destabilization, by ∼0.5–1.5 kcal/mol, is observed for 5′- or 3′-terminal UNA residues. Furthermore, thermodynamic effects caused by UNA residues are extremely additive with ΔG°37 conformity up to 98%. Direct mismatches involving UNA residues decrease the thermodynamic stability less than unmodified mismatches in RNA duplexes. Additionally, the presence of UNA residues adjacent to unpaired RNA residues reduces mismatch discrimination. Thermodynamic analysis of UNA 5′- and 3′-dangling ends revealed that stacking interactions of UNA residues are always less favourable than that of RNA residues. Finally, circular dichroism spectra imply no changes in overall A-form structure of UNA–RNA/RNA duplexes relative to the unmodified RNA duplexes. PMID:20562222

Estimation of brachial artery volume flow by duplex ultrasound imaging predicts dialysis access maturation.

PubMed

Ko, Sae Hee; Bandyk, Dennis F; Hodgkiss-Harlow, Kelley D; Barleben, Andrew; Lane, John

2015-06-01

This study validated duplex ultrasound measurement of brachial artery volume flow (VF) as predictor of dialysis access flow maturation and successful hemodialysis. Duplex ultrasound was used to image upper extremity dialysis access anatomy and estimate access VF within 1 to 2 weeks of the procedure. Correlation of brachial artery VF with dialysis access conduit VF was performed using a standardized duplex testing protocol in 75 patients. The hemodynamic data were used to develop brachial artery flow velocity criteria (peak systolic velocity and end-diastolic velocity) predictive of three VF categories: low (<600 mL/min), acceptable (600-800 mL/min), or high (>800 mL/min). Brachial artery VF was then measured in 148 patients after a primary (n = 86) or revised (n = 62) upper extremity dialysis access procedure, and the VF category correlated with access maturation or need for revision before hemodialysis usage. Access maturation was conferred when brachial artery VF was >600 mL/min and conduit imaging indicated successful cannulation based on anatomic criteria of conduit diameter >5 mm and skin depth <6 mm. Measurements of VF from the brachial artery and access conduit demonstrated a high degree of correlation (R(2) = 0.805) for autogenous vein (n = 45; R(2) = 0.87) and bridge graft (n = 30; R(2) = 0.78) dialysis accesses. Access VF of >800 mL/min was predicted when the brachial artery lumen diameter was >4.5 mm, peak systolic velocity was >150 cm/s, and the diastolic-to-systolic velocity ratio was >0.4. Brachial artery velocity spectra indicating VF <800 mL/min was associated (P < .0001) with failure of access maturation. Revision was required in 15 of 21 (71%) accesses with a VF of <600 mL/min, 4 of 40 accesses (10%) with aVF of 600 to 800 mL/min, and 2 of 87 accesses (2.3%) with an initial VF of >800 mL/min. Duplex testing to estimate brachial artery VF and assess the conduit for ease of cannulation can be performed in 5 minutes during the initial postoperative vascular clinic evaluation. Estimation of brachial artery VF using the duplex ultrasound, termed the "Fast, 5-min Dialysis Duplex Scan," facilitates patient evaluation after new or revised upper extremity dialysis access procedures. Brachial artery VF correlates with access VF measurements and has the advantage of being easier to perform and applicable for forearm and also arm dialysis access. When brachial artery velocity spectra criteria confirm a VF >800 mL/min, flow maturation and successful hemodialysis are predicted if anatomic criteria for conduit cannulation are also present. Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

A novel magneto-DNA duplex probe for bacterial DNA detection based on exonuclease III-aided cycling amplification.

PubMed

Zeng, Yan; Wan, Yi; Zhang, Dun; Qi, Peng

2015-01-01

A novel magneto-DNA duplex probe for bacterial DNA detection based on exonuclease III (Exo-III) aided cycling amplification has been developed. This magneto-DNA duplex probe contains a partly hybrid fluorophore-modified capture probe and a fluorophore-modified signal probe with magnetic microparticle as carrier. In the presence of a perfectly matched target bacterial DNA, blunt 3'-terminus of the capture probe is formed, activating the Exo-III aided cycling amplification. Thus, Exo-III catalyzes the stepwise removal of mononucleotides from this terminus, releasing both fluorophore-modified signal probe, fluorescent dyes of the capture probe and target DNA. The released target DNA then starts a new cycle, while released fluorescent fragments are recovered with magnetic separation for fluorescence signal collection. This system exhibited sensitive detection of bacterial DNA, with a detection limit of 14 pM because of the unique cleavage function of Exo-III, high fluorescence intensity, and separating function of magneto-DNA duplex probes. Besides this sensitivity, this strategy exhibited excellent selectivity with mismatched bacterial DNA targets and other bacterial species targets and good applicability in real seawater samples, hence, this strategy could be potentially used for qualitative and quantitative analysis of bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

PubMed Central

Nakano, Shu-ichi; Kitagawa, Yuichi; Miyoshi, Daisuke; Sugimoto, Naoki

2014-01-01

Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol), small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds. PMID:25161873

Conformational control and DNA-binding mechanism of the metazoan origin recognition complex.

PubMed

Bleichert, Franziska; Leitner, Alexander; Aebersold, Ruedi; Botchan, Michael R; Berger, James M

2018-06-26

In eukaryotes, the heterohexameric origin recognition complex (ORC) coordinates replication onset by facilitating the recruitment and loading of the minichromosome maintenance 2-7 (Mcm2-7) replicative helicase onto DNA to license origins. Drosophila ORC can adopt an autoinhibited configuration that is predicted to prevent Mcm2-7 loading; how the complex is activated and whether other ORC homologs can assume this state are not known. Using chemical cross-linking and mass spectrometry, biochemical assays, and electron microscopy (EM), we show that the autoinhibited state of Drosophila ORC is populated in solution, and that human ORC can also adopt this form. ATP binding to ORC supports a transition from the autoinhibited state to an active configuration, enabling the nucleotide-dependent association of ORC with both DNA and Cdc6. An unstructured N-terminal region adjacent to the conserved ATPase domain of Orc1 is shown to be required for high-affinity ORC-DNA interactions, but not for activation. ORC optimally binds DNA duplexes longer than the predicted footprint of the ORC ATPases associated with a variety of cellular activities (AAA + ) and winged-helix (WH) folds; cryo-EM analysis of Drosophila ORC bound to DNA and Cdc6 indicates that ORC contacts DNA outside of its central core region, bending the DNA away from its central DNA-binding channel. Our findings indicate that ORC autoinhibition may be common to metazoans and that ORC-Cdc6 remodels origin DNA before Mcm2-7 recruitment and loading.

Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications

PubMed Central

Nam, Seungyoon; Ryu, Hyojung; Son, Won-joon; Kim, Yon Hui; Kim, Kyung Tae; Balch, Curt; Nephew, Kenneth P.; Lee, Jinhyuk

2014-01-01

RNA interference (RNAi), mediated by small non-coding RNAs (e.g., miRNAs, siRNAs), influences diverse cellular functions. Highly complementary miRNA-target RNA (or siRNA-target RNA) duplexes are recognized by an Argonaute family protein (Ago2), and recent observations indicate that the concentration of Mg2+ ions influences miRNA targeting of specific mRNAs, thereby modulating miRNA-mRNA networks. In the present report, we studied the thermodynamic effects of differential [Mg2+] on slicing (RNA silencing cycle) through molecular dynamics simulation analysis, and its subsequent statistical analysis. Those analyses revealed different structural conformations of the RNA duplex in Ago2, depending on Mg2+ concentration. We also demonstrate that cation effects on Ago2 structural flexibility are critical to its catalytic/functional activity, with low [Mg2+] favoring greater Ago2 flexibility (e.g., greater entropy) and less miRNA/mRNA duplex stability, thus favoring slicing. The latter finding was supported by a negative correlation between expression of an Mg2+ influx channel, TRPM7, and one miRNA’s (miR-378) ability to downregulate its mRNA target, TMEM245. These results imply that thermodynamics could be applied to siRNA-based therapeutic strategies, using highly complementary binding targets, because Ago2 is also involved in RNAi slicing by exogenous siRNAs. However, the efficacy of a siRNA-based approach will differ, to some extent, based on the Mg2+ concentration even within the same disease type; therefore, different siRNA-based approaches might be considered for patient-to-patient needs. PMID:25330448

MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology

PubMed Central

Karathanasis, Nestoras; Tsamardinos, Ioannis; Poirazi, Panayiota

2015-01-01

We address the problem of predicting the position of a miRNA duplex on a microRNA hairpin via the development and application of a novel SVM-based methodology. Our method combines a unique problem representation and an unbiased optimization protocol to learn from mirBase19.0 an accurate predictive model, termed MiRduplexSVM. This is the first model that provides precise information about all four ends of the miRNA duplex. We show that (a) our method outperforms four state-of-the-art tools, namely MaturePred, MiRPara, MatureBayes, MiRdup as well as a Simple Geometric Locator when applied on the same training datasets employed for each tool and evaluated on a common blind test set. (b) In all comparisons, MiRduplexSVM shows superior performance, achieving up to a 60% increase in prediction accuracy for mammalian hairpins and can generalize very well on plant hairpins, without any special optimization. (c) The tool has a number of important applications such as the ability to accurately predict the miRNA or the miRNA*, given the opposite strand of a duplex. Its performance on this task is superior to the 2nts overhang rule commonly used in computational studies and similar to that of a comparative genomic approach, without the need for prior knowledge or the complexity of performing multiple alignments. Finally, it is able to evaluate novel, potential miRNAs found either computationally or experimentally. In relation with recent confidence evaluation methods used in miRBase, MiRduplexSVM was successful in identifying high confidence potential miRNAs. PMID:25961860

Photophysical Characterization of Enhanced 6-Methylisoxanthopterin Fluorescence in Duplex DNA.

PubMed

Moreno, Andrew; Knee, J L; Mukerji, Ishita

2016-12-08

The structure and dynamic motions of bases in DNA duplexes and other constructs are important for understanding mechanisms of selectivity and recognition of DNA-binding proteins. The fluorescent guanine analogue, 6-methylisoxanthopterin 6-MI, is well suited to this purpose as it exhibits an unexpected 3- to 4-fold increase in relative quantum yield upon duplex formation when incorporated into the following sequences: ATFAA, AAFTA, or ATFTA (where F represents 6-MI). To better understand some of the factors leading to the 6-MI fluorescence increase upon duplex formation, we characterized the effect of local sequence and structural perturbations on 6-MI photophysics through temperature melts, quantum yield measurements, fluorescence quenching assays, and fluorescence lifetime measurements. By examining 21 sequences we have determined that the duplex-enhanced fluorescence (DEF) depends on the composition of bases adjacent to 6-MI and the presence of adenines at locations n ± 2 from the probe. Investigation of duplex stability and local solvent accessibility measurements support a model in which the DEF arises from a constrained geometry of 6-MI in the duplex, which remains H-bonded to cytosine, stacked with adjacent bases and inaccessible to quenchers. Perturbation of DNA structure through the introduction of an unpaired base 3' to 6-MI or a mismatched basepair increases 6-MI dynamic motion leading to fluorescence quenching and a reduction in quantum yield. Molecular dynamics simulations suggest the enhanced fluorescence results from a greater degree of twist at the X-F step relative to the quenched duplexes examined. These results point to a model where adenine residues located at n ± 2 from 6-MI induce a structural geometry with greater twist in the duplex that hinders local motion reducing dynamic quenching and producing an increase in 6-MI fluorescence.

Transcranial Duplex Sonography Predicts Outcome following an Intracerebral Hemorrhage.

PubMed

Camps-Renom, P; Méndez, J; Granell, E; Casoni, F; Prats-Sánchez, L; Martínez-Domeño, A; Guisado-Alonso, D; Martí-Fàbregas, J; Delgado-Mederos, R

2017-08-01

Several radiologic features such as hematoma volume are related to poor outcome following an intracerebral hemorrhage and can be measured with transcranial duplex sonography. We sought to determine the prognostic value of transcranial duplex sonography in patients with intracerebral hemorrhage. We conducted a prospective study of patients diagnosed with spontaneous intracerebral hemorrhage. Transcranial duplex sonography examinations were performed within 2 hours of baseline CT, and we recorded the following variables: hematoma volume, midline shift, third ventricle and lateral ventricle diameters, and the pulsatility index in both MCAs. We correlated these data with the CT scans and assessed the prognostic value of the transcranial duplex sonography measurements. We assessed early neurologic deterioration during hospitalization and mortality at 1-month follow-up. We included 35 patients with a mean age of 72.2 ± 12.8 years. Median baseline hematoma volume was 9.85 mL (interquartile range, 2.74-68.29 mL). We found good agreement and excellent correlation between transcranial duplex sonography and CT when measuring hematoma volume ( r = 0.791; P < .001) and midline shift ( r = 0.827; P < .001). The logistic regression analysis with transcranial duplex sonography measurements showed that hematoma volume was an independent predictor of early neurologic deterioration (OR, 1.078; 95% CI, 1.023-1.135) and mortality (OR, 1.089; 95% CI, 1.020-1.160). A second regression analysis with CT variables also demonstrated that hematoma volume was associated with early neurologic deterioration and mortality. When we compared the rating operation curves of both models, their predictive power was similar. Transcranial duplex sonography showed an excellent correlation with CT in assessing hematoma volume and midline shift in patients with intracerebral hemorrhage. Hematoma volume measured with transcranial duplex sonography was an independent predictor of poor outcome. © 2017 by American Journal of Neuroradiology.

Effect of ultrafine grain on tensile behaviour and corrosion resistance of the duplex stainless steel.

PubMed

Jinlong, Lv; Tongxiang, Liang; Chen, Wang; Limin, Dong

2016-05-01

The ultrafine grained 2205 duplex stainless steel was obtained by cold rolling and annealing. The tensile properties were investigated at room temperature. Comparing with coarse grained stainless steel, ultrafine grained sample showed higher strength and plasticity. In addition, grain size changed deformation orientation. The strain induced α'-martensite was observed in coarse grained 2205 duplex stainless steel with large strain. However, the grain refinement inhibited the transformation of α'-martensite;nevertheless, more deformation twins improved the strength and plasticity of ultrafine grained 2205 duplex stainless steel. In addition, the grain refinement improved corrosion resistance of the 2205 duplex stainless steel in sodium chloride solution. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of Microstructure and Mechanical Properties in Dissimilar Austenitic/Super Duplex Stainless Steel Joint

NASA Astrophysics Data System (ADS)

Rahmani, Mehdi; Eghlimi, Abbas; Shamanian, Morteza

2014-10-01

To study the effect of chemical composition on microstructural features and mechanical properties of dissimilar joints between super duplex and austenitic stainless steels, welding was attempted by gas tungsten arc welding process with a super duplex (ER2594) and an austenitic (ER309LMo) stainless steel filler metal. While the austenitic weld metal had vermicular delta ferrite within austenitic matrix, super duplex stainless steel was mainly comprised of allotriomorphic grain boundary and Widmanstätten side plate austenite morphologies in the ferrite matrix. Also the heat-affected zone of austenitic base metal comprised of large austenite grains with little amounts of ferrite, whereas a coarse-grained ferritic region was observed in the heat-affected zone of super duplex base metal. Although both welded joints showed acceptable mechanical properties, the hardness and impact strength of the weld metal produced using super duplex filler metal were found to be better than that obtained by austenitic filler metal.

Effect of Cavity Size of Mesoporous Silica on Short DNA Duplex Stability.

PubMed

Masuda, Tsubasa; Shibuya, Yuuta; Arai, Shota; Kobayashi, Sayaka; Suzuki, Sotaro; Kijima, Jun; Itoh, Tetsuji; Sato, Yusuke; Nishizawa, Seiichi; Yamaguchi, Akira

2018-05-15

We studied the stabilities of short (4- and 3-bp) DNA duplexes within silica mesopores modified with a positively charged trimethyl aminopropyl (TMAP) monolayer (BJH pore diameter 1.6-7.4 nm). The DNA fragments with fluorescent dye were introduced into the pores, and their fluorescence resonance energy transfer (FRET) response was measured to estimate the structuring energies of the short DNA duplexes under cryogenic conditions (temperature 233-323 K). The results confirmed the enthalpic stability gain of the duplex within size-matched pores (1.6 and 2.3 nm). The hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for large pores (≥3.5 nm), and this size-matching effect for the enhanced duplex stability was explained by a tight electrostatic interaction between the duplex and the surface TMAP groups. These results indicate the requirement of the precise regulation of mesopore size to ensure the stabilization of hydrogen-bonded supramolecular assemblies.

Transformation and Precipitation Reactions by Metal Active Gas Pulsed Welded Joints from X2CrNiMoN22-5-3 Duplex Stainless Steels

PubMed Central

Utu, Ion-Dragos; Mitelea, Ion; Urlan, Sorin Dumitru; Crăciunescu, Corneliu Marius

2016-01-01

The high alloying degree of Duplex stainless steels makes them susceptible to the formation of intermetallic phases during their exposure to high temperatures. Precipitation of these phases can lead to a decreasing of the corrosion resistance and sometimes of the toughness. Starting from the advantages of the synergic Metal Active Gas (MAG) pulsed welding process, this paper analyses the structure formation particularities of homogeneous welded joints from Duplex stainless steel. The effect of linear welding energy on the structure morphology of the welded joints was revealed by macro- and micrographic examinations, X-ray energy dispersion analyses, measurements of ferrite proportion and X-ray diffraction analysis. The results obtained showed that the transformation of ferrite into austenite is associated with the chromium, nickel, molybdenum and nitrogen distribution between these two phases and their redistribution degree is closely linked to the overall heat cycle of the welding process. The adequate control of the energy inserted in the welded components provides an optimal balance between the two microstructural constituents (Austenite and Ferrite) and avoids the formation of undesirable intermetallic phases. PMID:28773727

Transformation and Precipitation Reactions by Metal Active Gas Pulsed Welded Joints from X2CrNiMoN22-5-3 Duplex Stainless Steels.

PubMed

Utu, Ion-Dragos; Mitelea, Ion; Urlan, Sorin Dumitru; Crăciunescu, Corneliu Marius

2016-07-21

The high alloying degree of Duplex stainless steels makes them susceptible to the formation of intermetallic phases during their exposure to high temperatures. Precipitation of these phases can lead to a decreasing of the corrosion resistance and sometimes of the toughness. Starting from the advantages of the synergic Metal Active Gas (MAG) pulsed welding process, this paper analyses the structure formation particularities of homogeneous welded joints from Duplex stainless steel. The effect of linear welding energy on the structure morphology of the welded joints was revealed by macro- and micrographic examinations, X-ray energy dispersion analyses, measurements of ferrite proportion and X-ray diffraction analysis. The results obtained showed that the transformation of ferrite into austenite is associated with the chromium, nickel, molybdenum and nitrogen distribution between these two phases and their redistribution degree is closely linked to the overall heat cycle of the welding process. The adequate control of the energy inserted in the welded components provides an optimal balance between the two microstructural constituents (Austenite and Ferrite) and avoids the formation of undesirable intermetallic phases.

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

PubMed

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A superstructure-based electrochemical assay for signal-amplified detection of DNA methyltransferase activity.

PubMed

Zhang, Hui; Yang, Yin; Dong, Huilei; Cai, Chenxin

2016-12-15

DNA methyltransferase (MTase) activity is highly correlated with the occurrence and development of cancer. This work reports a superstructure-based electrochemical assay for signal-amplified detection of DNA MTase activity using M.SssI as an example. First, low-density coverage of DNA duplexes on the surface of the gold electrode was achieved by immobilized mercaptohexanol, followed by immobilization of DNA duplexes. The duplex can be cleaved by BstUI endonuclease in the absence of DNA superstructures. However, the cleavage is blocked after the DNA is methylated by M.SssI. The DNA superstructures are formed with the addition of helper DNA. By using an electroactive complex, RuHex, which can bind to DNA double strands, the activity of M.SssI can be quantitatively detected by differential pulse voltammetry. Due to the high site-specific cleavage by BstUI and signal amplification by the DNA superstructure, the biosensor can achieve ultrasensitive detection of DNA MTase activity down to 0.025U/mL. The method can be used for evaluation and screening of the inhibitors of MTase, and thus has potential in the discovery of methylation-related anticancer drugs. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessing the effect of different operation techniques on postoperative duplex ultrasound quality after carotid endarterectomy.

PubMed

Grambow, E; Heller, T; Wieneke, P; Weiß, C; Klar, E; Weinrich, M

2018-01-01

Duplex ultrasound is the first choice in diagnostics and surveillance of stenoses of the internal carotid arteries before and even after surgery. Therefore, the quality of duplex ultrasound is crucial to investigate these vascular pathologies. Aim of this study was the evaluation whether different surgical techniques affect the postoperative quality of duplex ultrasound. In a time period from January to May 2015 duplex ultrasound of the cervical vessels was performed in 75 patients after unilateral endarterectomy of the internal carotid artery at our department between 2006 and 2012. Thereby, the non-operated contralateral side served as a control. Study groups were defined by the surgical techniques of eversion- or thrombendarterectomy with patch plasty using different patch materials and/or a haemostatic sealant. Duplex ultrasound analysis included acoustic impedance, extinction of ultrasound, thickness of skin and individual anatomic aspects of the patients. Carotid endarterectomy itself reduced intravascular grey levels, skin thickness and increased extinction of duplex ultrasound when compared to the non-operated side of the neck. In contrast, neither the kind of chosen operative technique nor the use of different patch materials or the application of a haemostatic sealant showed an effect in this regards. Whereas carotid endarterectomy per se worsens the quality of postoperative duplex ultrasound, the different analysed surgical techniques as well as used patches and the application of a haemostatic sealant can be assumed to be equal regarding the quality of postoperative ultrasound.

The effect of S-substitution at the O6-guanine site on the structure and dynamics of a DNA oligomer containing a G:T mismatch

PubMed Central

2017-01-01

The effect of S-substitution on the O6 guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with S-substitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (GS:T) as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening. PMID:28910418

Evidence of a sewer vapor transport pathway at the USEPA ...

EPA Pesticide Factsheets

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into the duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. These test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope. Highlights • The sewer line is an important pathway for VOC transport at the USEPA duplex. • The importance of this pathway was not identified during prior study of the duplex. • Sewer lines should be routinely evaluated

Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex.

PubMed

Ueda, Yu-Mi; Zouzumi, Yu-Ki; Maruyama, Atsushi; Nakano, Shu-Ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2016-01-01

We systematically investigated effects of molecular crowding with trimethylamine N -oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex. These results are useful not only to predict DNA structures and their thermodynamics under physiological environments in living cells, but also design of polymers and materials to regulate structure and stability of DNA sequences.

Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex

PubMed Central

Ueda, Yu-mi; Zouzumi, Yu-ki; Maruyama, Atsushi; Nakano, Shu-ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2016-01-01

Abstract We systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex. These results are useful not only to predict DNA structures and their thermodynamics under physiological environments in living cells, but also design of polymers and materials to regulate structure and stability of DNA sequences. PMID:27933115

Tribocorrosion Failure Mechanism of TiN/SiOx Duplex Coating Deposited on AISI304 Stainless Steel.

PubMed

Chen, Qiang; Xie, Zhiwen; Chen, Tian; Gong, Feng

2016-11-26

TiN/SiO x duplex coatings were synthesized on AISI304 stainless steel by plasma immersion ion implantation and deposition (PIIID) followed by radio frequency magnetron sputtering (RFMS). The microstructure and tribocorrosion failure behaviors of the duplex coatings were investigated by X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, atomic force microscopy, reciprocating-sliding tribometer, and electrochemical tests. The as-deposited duplex coating had a two-layered columnar growth structure consisting of face-centered cubic TiN and amorphous SiO x . Sliding tests showed that the TiN interlayer had good adhesion with the substrate, but the SiO x layer suffered from severe delamination failure. Friction force induced a number of micro-cracks in the coating, which provided channels for the diffusion of NaCl solution. The tribocorrosion test showed that the duplex coating exhibited a lower wear-performance in NaCl solution than in ambient atmosphere. Multi-scale chloride ion corrosion occurred simultaneously and substantially degraded the bonding strength of the columnar crystals or neighboring layers. Force-corrosion synergy damage eventually led to multi-degradation failure of the duplex coating. The presented results provide a comprehensive understanding of the tribocorrosion failure mechanism in coatings with duplex architecture.

Tertiary structure-based analysis of microRNA–target interactions

PubMed Central

Gan, Hin Hark; Gunsalus, Kristin C.

2013-01-01

Current computational analysis of microRNA interactions is based largely on primary and secondary structure analysis. Computationally efficient tertiary structure-based methods are needed to enable more realistic modeling of the molecular interactions underlying miRNA-mediated translational repression. We incorporate algorithms for predicting duplex RNA structures, ionic strength effects, duplex entropy and free energy, and docking of duplex–Argonaute protein complexes into a pipeline to model and predict miRNA–target duplex binding energies. To ensure modeling accuracy and computational efficiency, we use an all-atom description of RNA and a continuum description of ionic interactions using the Poisson–Boltzmann equation. Our method predicts the conformations of two constructs of Caenorhabditis elegans let-7 miRNA–target duplexes to an accuracy of ∼3.8 Å root mean square distance of their NMR structures. We also show that the computed duplex formation enthalpies, entropies, and free energies for eight miRNA–target duplexes agree with titration calorimetry data. Analysis of duplex–Argonaute docking shows that structural distortions arising from single-base-pair mismatches in the seed region influence the activity of the complex by destabilizing both duplex hybridization and its association with Argonaute. Collectively, these results demonstrate that tertiary structure-based modeling of miRNA interactions can reveal structural mechanisms not accessible with current secondary structure-based methods. PMID:23417009

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex.

PubMed

McHugh, Thomas; Beckley, Lila; Sullivan, Terry; Lutes, Chris; Truesdale, Robert; Uppencamp, Rob; Cosky, Brian; Zimmerman, John; Schumacher, Brian

2017-11-15

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into the duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. These test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope. Copyright © 2017 Elsevier B.V. All rights reserved.

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

DOE PAGES

McHugh, Thomas; Beckley, Lila; Sullivan, Terry; ...

2017-04-26

We report the role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into themore » duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. Finally, these test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope.« less

Synergistic effects between analogs of DNA and RNA improve the potency of siRNA-mediated gene silencing

PubMed Central

Deleavey, Glen F.; Watts, Jonathan K.; Alain, Tommy; Robert, Francis; Kalota, Anna; Aishwarya, Veenu; Pelletier, Jerry; Gewirtz, Alan M.; Sonenberg, Nahum; Damha, Masad J.

2010-01-01

We report that combining a DNA analog (2′F-ANA) with rigid RNA analogs [2′F-RNA and/or locked nucleic acid (LNA)] in siRNA duplexes can produce gene silencing agents with enhanced potency. The favored conformations of these two analogs are different, and combining them in a 1–1 pattern led to reduced affinity, whereas alternating short continuous regions of individual modifications increased affinity relative to an RNA:RNA duplex. Thus, the binding affinity at key regions of the siRNA duplex could be tuned by changing the pattern of incorporation of DNA-like and RNA-like nucleotides. These heavily or fully modified duplexes are active against a range of mRNA targets. Effective patterns of modification were chosen based on screens using two sequences targeting firefly luciferase. We then applied the most effective duplex designs to the knockdown of the eIF4E binding proteins 4E-BP1 and 4E-BP2. We identified modified duplexes with potency comparable to native siRNA. Modified duplexes showed dramatically enhanced stability to serum nucleases, and were characterized by circular dichroism and thermal denaturation studies. Chemical modification significantly reduced the immunostimulatory properties of these siRNAs in human peripheral blood mononuclear cells. PMID:20413581

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

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

McHugh, Thomas; Beckley, Lila; Sullivan, Terry

We report the role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into themore » duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. Finally, these test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope.« less

Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

NASA Technical Reports Server (NTRS)

Urakawa, Hidetoshi; Noble, Peter A.; El Fantroussi, Said; Kelly, John J.; Stahl, David A.

2002-01-01

The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

PubMed Central

Qi, Zhi; Pugh, Robert A; Spies, Maria; Chemla, Yann R

2013-01-01

Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be understood. This necessitates monitoring helicase activity directly, at high spatio-temporal resolution. Using optical tweezers with single base pair (bp) resolution, we analyzed DNA unwinding by XPD helicase, a Superfamily 2 (SF2) DNA helicase involved in DNA repair and transcription initiation. We show that monomeric XPD unwinds duplex DNA in 1-bp steps, yet exhibits frequent backsteps and undergoes conformational transitions manifested in 5-bp backward and forward steps. Quantifying the sequence dependence of XPD stepping dynamics with near base pair resolution, we provide the strongest and most direct evidence thus far that forward, single-base pair stepping of a helicase utilizes the spontaneous opening of the duplex. The proposed unwinding mechanism may be a universal feature of DNA helicases that move along DNA phosphodiester backbones. DOI: http://dx.doi.org/10.7554/eLife.00334.001 PMID:23741615

The Mentawai forearc sliver off Sumatra: A model for a strike-slip duplex at a regional scale

NASA Astrophysics Data System (ADS)

Berglar, Kai; Gaedicke, Christoph; Ladage, Stefan; Thöle, Hauke

2017-07-01

At the Sumatran oblique convergent margin the Mentawai Fault and Sumatran Fault zones accommodate most of the trench parallel component of strain. These faults bound the Mentawai forearc sliver that extends from the Sunda Strait to the Nicobar Islands. Based on multi-channel reflection seismic data, swath bathymetry and high resolution sub-bottom profiling we identified a set of wrench faults obliquely connecting the two major fault zones. These wrench faults separate at least four horses of a regional strike-slip duplex forming the forearc sliver. Each horse comprises an individual basin of the forearc with differing subsidence and sedimentary history. Duplex formation started in Mid/Late Miocene southwest of the Sunda Strait. Initiation of new horses propagated northwards along the Sumatran margin over 2000 km until Early Pliocene. These results directly link strike-slip tectonics to forearc evolution and may serve as a model for basin evolution in other oblique subduction settings.

5'-(E)-Vinylphosphonate: A Stable Phosphate Mimic Can Improve the RNAi Activity of siRNA-GalNAc Conjugates.

PubMed

Parmar, Rubina; Willoughby, Jennifer L S; Liu, Jingxuan; Foster, Donald J; Brigham, Benjamin; Theile, Christopher S; Charisse, Klaus; Akinc, Akin; Guidry, Erin; Pei, Yi; Strapps, Walter; Cancilla, Mark; Stanton, Matthew G; Rajeev, Kallanthottathil G; Sepp-Lorenzino, Laura; Manoharan, Muthiah; Meyers, Rachel; Maier, Martin A; Jadhav, Vasant

2016-06-02

Small interfering RNA (siRNA)-mediated silencing requires siRNA loading into the RNA-induced silencing complex (RISC). Presence of 5'-phosphate (5'-P) is reported to be critical for efficient RISC loading of the antisense strand (AS) by anchoring it to the mid-domain of the Argonaute2 (Ago2) protein. Phosphorylation of exogenous duplex siRNAs is thought to be accomplished by cytosolic Clp1 kinase. However, although extensive chemical modifications are essential for siRNA-GalNAc conjugate activity, they can significantly impair Clp1 kinase activity. Here, we further elucidated the effect of 5'-P on the activity of siRNA-GalNAc conjugates. Our results demonstrate that a subset of sequences benefit from the presence of exogenous 5'-P. For those that do, incorporation of 5'-(E)-vinylphosphonate (5'-VP), a metabolically stable phosphate mimic, results in up to 20-fold improved in vitro potency and up to a threefold benefit in in vivo activity by promoting Ago2 loading and enhancing metabolic stability. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficacy of duplex ultrasound surveillance after infrainguinal vein bypass may be enhanced by identification of characteristics predictive of graft stenosis development.

PubMed

Tinder, Chelsey N; Chavanpun, Joe P; Bandyk, Dennis F; Armstrong, Paul A; Back, Martin R; Johnson, Brad L; Shames, Murray L

2008-09-01

Controversy regarding the efficacy of duplex ultrasound surveillance after infrainguinal vein bypass led to an analysis of patient and bypass graft characteristics predictive for development of graft stenosis and a decision of secondary intervention. Retrospective analysis of a contemporary, consecutive series of 353 clinically successful infrainguinal vein bypasses performed in 329 patients for critical (n = 284; 80%) or noncritical (n = 69; 20%) limb ischemia enrolled in a surveillance program to identify and repair duplex-detected graft stenosis. Variables correlated with graft stenosis and bypass repair included: procedure indication, conduit type (saphenous vs nonsaphenous vein; reversed vs nonreversed orientation), prior bypass graft failure, postoperative ankle-brachial index (ABI) < 0.85, and interpretation of the first duplex surveillance study as "normal" or "abnormal" based on peak systolic velocity (PSV) and velocity ratio (Vr) criteria. Overall, 126 (36%) of the 353 infrainguinal bypasses had 174 secondary interventions (endovascular, 100; surgery, 74) based on duplex surveillance; resulting in 3-year Kaplan-Meier primary (46%), assisted-primary (80%), and secondary (81%) patency rates. Characteristics predictive of duplex-detected stenosis leading to intervention (PSV: 443 +/- 94 cm/s; Vr: 8.6 +/- 9) were: "abnormal" initial duplex testing indicating moderate (PSV: 180-300 cm/s, Vr: 2-3.5) stenosis (P < .0001), non-single segment saphenous vein conduit (P < .01), warfarin drug therapy (P < .01), and redo bypass grafting (P < .001). Procedure indication, postoperative ABI level, statin drug therapy, and vein conduit orientation were not predictive of graft revision. The natural history of 141 (40%) bypasses with an abnormal first duplex scan differed from "normal" grafts by more frequent (51% vs 24%, P < .001) and earlier (7 months vs 11 months) graft revision for severe stenosis and a lower 3-year assisted primary patency (68% vs 87%; P < .001). In 52 (15%) limbs, the bypass graft failed and 20 (6%) limbs required amputation. The efficacy of duplex surveillance after infrainguinal vein bypass may be enhanced by modifying testing protocols, eg, rigorous surveillance for "higher risk" bypasses, based on the initial duplex scan results and other characteristics (warfarin therapy, non- single segment saphenous vein conduit, redo bypass) predictive for stenosis development.

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.

Hydrogen-Induced Delayed Cracking in TRIP-Aided Lean-Alloyed Ferritic-Austenitic Stainless Steels.

PubMed

Papula, Suvi; Sarikka, Teemu; Anttila, Severi; Talonen, Juho; Virkkunen, Iikka; Hänninen, Hannu

2017-06-03

Susceptibility of three lean-alloyed ferritic-austenitic stainless steels to hydrogen-induced delayed cracking was examined, concentrating on internal hydrogen contained in the materials after production operations. The aim was to study the role of strain-induced austenite to martensite transformation in the delayed cracking susceptibility. According to the conducted deep drawing tests and constant load tensile testing, the studied materials seem not to be particularly susceptible to delayed cracking. Delayed cracks were only occasionally initiated in two of the materials at high local stress levels. However, if a delayed crack initiated in a highly stressed location, strain-induced martensite transformation decreased the crack arrest tendency of the austenite phase in a duplex microstructure. According to electron microscopy examination and electron backscattering diffraction analysis, the fracture mode was predominantly cleavage, and cracks propagated along the body-centered cubic (BCC) phases ferrite and α'-martensite. The BCC crystal structure enables fast diffusion of hydrogen to the crack tip area. No delayed cracking was observed in the stainless steel that had high austenite stability. Thus, it can be concluded that the presence of α'-martensite increases the hydrogen-induced cracking susceptibility.

Hydrogen-Induced Delayed Cracking in TRIP-Aided Lean-Alloyed Ferritic-Austenitic Stainless Steels

PubMed Central

Papula, Suvi; Sarikka, Teemu; Anttila, Severi; Talonen, Juho; Virkkunen, Iikka; Hänninen, Hannu

2017-01-01

Susceptibility of three lean-alloyed ferritic-austenitic stainless steels to hydrogen-induced delayed cracking was examined, concentrating on internal hydrogen contained in the materials after production operations. The aim was to study the role of strain-induced austenite to martensite transformation in the delayed cracking susceptibility. According to the conducted deep drawing tests and constant load tensile testing, the studied materials seem not to be particularly susceptible to delayed cracking. Delayed cracks were only occasionally initiated in two of the materials at high local stress levels. However, if a delayed crack initiated in a highly stressed location, strain-induced martensite transformation decreased the crack arrest tendency of the austenite phase in a duplex microstructure. According to electron microscopy examination and electron backscattering diffraction analysis, the fracture mode was predominantly cleavage, and cracks propagated along the body-centered cubic (BCC) phases ferrite and α’-martensite. The BCC crystal structure enables fast diffusion of hydrogen to the crack tip area. No delayed cracking was observed in the stainless steel that had high austenite stability. Thus, it can be concluded that the presence of α’-martensite increases the hydrogen-induced cracking susceptibility. PMID:28772975

Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA

PubMed Central

Copp, William; Denisov, Alexey Y.; Xie, Jingwei; Noronha, Anne M.; Liczner, Christopher; Safaee, Nozhat

2017-01-01

Abstract Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2′-deoxyribose, 2′-O-methyl-ribose, 2′-deoxy-2′-fluoro-ribose, arabinose and 2′-deoxy-2′-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2’ modifications gave a variety of effects. Arabinose and 2′-deoxy-2′-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2′-O-methyl and 2′-deoxy-2′-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. PMID:28973475

Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

PubMed

Copp, William; Denisov, Alexey Y; Xie, Jingwei; Noronha, Anne M; Liczner, Christopher; Safaee, Nozhat; Wilds, Christopher J; Gehring, Kalle

2017-09-29

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Duplex kidney: not just a drooping lily.

PubMed

Doery, Ashlea J; Ang, Eileen; Ditchfield, Michael R

2015-04-01

Duplex kidneys are common, mostly asymptomatic and of no clinical significance. However, they can be associated with significant pathology, often with long-term morbidity. There is minimal literature on the review of the duplex kidney, its associated anomalies and complications. The purpose of this paper is to review our experience of imaging the spectrum of abnormalities associated with duplex kidneys in the paediatric population and correlate this with contemporary literature. A retrospective review of the radiology database in a tertiary paediatric centre was performed. A word search of the Radiology Information System for 'duplex' of patients under the age of 16 was undertaken and limited to studies performed between 2006 and 2013. Two hundred seventy-four patients were identified (age range 0-16, median 3 years, gender 59.9% female) who had 836 studies: ultrasound 598/836 (71.6%), nuclear medicine 180/836 (21.5%), micturating cystourethrogram 52/836 (6.2%), MRI 5/836 (<1%) and CT scan 1/836 (<1%). Patients were categorised as duplex and no complication (151/274 = 55.1%), upper moiety obstruction, lower moiety reflux/scarring, multicystic dysplastic kidney, abnormal ureteric insertion and other pathology. Duplex kidneys are common and often not clinically significant. However, this study demonstrates almost 50% of paediatric patients investigated for duplex kidneys had complications requiring treatment. The most common complications were upper moiety obstruction associated with a ureterocele and lower moiety vesicoureteric reflux. Ultrasound was the most common modality for early detection of these complications. © 2015 The Royal Australian and New Zealand College of Radiologists.

52. Photocopy of copy of original Officers' Duplex Quarters drawing ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

52. Photocopy of copy of original Officers' Duplex Quarters drawing by Copeland, 7 April 1932 (Original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Heating - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

53. Photocopy of copy of original Officers' Duplex Quarters drawing ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

53. Photocopy of copy of original Officers' Duplex Quarters drawing by A.G.D., 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Electrical - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

51. Photocopy of copy of original Officers' Duplex Quarters drawing ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

51. Photocopy of copy of original Officers' Duplex Quarters drawing by B.S. Elliott, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Plumbing - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

Criteria for the Segmentation of Vowels on Duplex Oscillograms.

ERIC Educational Resources Information Center

Naeser, Margaret A.

This paper develops criteria for the segmentation of vowels on duplex oscillograms. Previous vowel duration studies have primarily used sound spectrograms. The use of duplex oscillograms, rather than sound spectrograms, permits faster production (real time) at less expense (adding machine paper may be used). The speech signal can be more spread…

Duplex ultrasound surveillance after carotid artery endarterectomy.

PubMed

Al Shakarchi, Julien; Lowry, Danielle; Nath, Jay; Khawaja, Aurangzaib Z; Inston, Nicholas; Tiwari, Alok

2016-06-01

After carotid endarterectomy (CEA), patients have been regularly followed up by duplex ultrasound imaging. However, the evidence for long-term follow-up is not clear, especially if the results from an early duplex scan are normal. This study assessed and systematically reviewed the evidence base for long-term surveillance after CEA and a normal early scan. Electronic databases were searched for studies assessing duplex surveillance after CEA in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The primary outcome for this study was the incidence of restenosis after a normal early scan. The secondary outcome was the number of reinterventions after a normal early scan. The review included seven studies that reported 2317 procedures. Of those patients with a normal early scan, 2.8% (95% confidence interval, 0.7%-6%) developed a restenosis, and 0.4% (95% confidence interval, 0%-0.9%) underwent a reintervention for their restenosis during the follow-up period. This review confirms that routine postoperative duplex ultrasound surveillance after CEA is not necessary if the early duplex scan is normal. Copyright © 2016 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Comparative NMR analysis of the decadeoxynucleotide d-(GCATTAATGC)2 and an analogue containing 2-aminoadenine.

PubMed Central

Chazin, W J; Rance, M; Chollet, A; Leupin, W

1991-01-01

The dodecadeoxynucleotide duplex d-(GCATTAATGC)2 has been prepared with all adenine bases replaced by 2-NH2-adenine. This modified duplex has been characterized by nuclear magnetic resonance (NMR) spectroscopy. Complete sequence-specific 1H resonance assignments have been obtained by using a variety of 2D NMR methods. Multiple quantum-filtered and multiple quantum experiments have been used to completely assign all sugar ring protons, including 5'H and 5'H resonances. The assignments form the basis for a detailed comparative analysis of the 1H NMR parameters of the modified and parent duplex. The structural features of both decamer duplexes in solution are characteristic of the B-DNA family. The spin-spin coupling constants in the sugar rings and the relative spatial proximities of protons in the bases and sugars (as determined from the comparison of corresponding nuclear Overhauser effects) are virtually identical in the parent and modified duplexes. Thus, substitution by this adenine analogue in oligonucleotides appears not to disturb the global or local conformation of the DNA duplex. PMID:1945828

Circularly polarized luminescence of helically assembled pyrene π-stacks on RNA and DNA duplexes.

PubMed

Nakamura, Mitsunobu; Ota, Fuyuki; Takada, Tadao; Akagi, Kazuo; Yamana, Kazushige

2018-05-01

In this report, we describe the circularly polarized luminescence (CPL) of the RNA duplexes having one to four 2'-O-pyrene modified uridines (Upy) and the DNA duplexes having two, four, and six pyrene modified non-nucleosidic linkers (Py). Both the pyrene π-stack arrays formed on the RNA and DNA double helical structures exhibited pyrene excimer fluorescence. In the pyrene-modified RNA systems, the RNA duplex having four Upys gives CPL emission with g lum value of <0.01 at 480 nm. The structure of pyrene stacks on the RNA duplex may be rigidly regulated with increase in the Upy domains, which resulted in the CPL emission. In the DNA systems, the pyrene-modified duplexes containing two and four Pys exhibited CPL emission with g lum values of <0.001 at 505 nm. The pyrene π-stack arrays presented here show CPL emission. However, the g lum values are relatively small when compared with our previous system consisting of the pyrene-zipper arrays on RNA. © 2018 Wiley Periodicals, Inc.

Rapid method to detect duplex formation in sequencing by hybridization methods

DOEpatents

Mirzabekov, A.D.; Timofeev, E.N.; Florentiev, V.L.; Kirillov, E.V.

1999-01-19

A method for determining the existence of duplexes of oligonucleotide complementary molecules is provided. A plurality of immobilized oligonucleotide molecules, each of a specific length and each having a specific base sequence, is contacted with complementary, single stranded oligonucleotide molecules to form a duplex. Each duplex facilitates intercalation of a fluorescent dye between the base planes of the duplex. The invention also provides for a method for constructing oligonucleotide matrices comprising confining light sensitive fluid to a surface and exposing the light-sensitive fluid to a light pattern. This causes the fluid exposed to the light to coalesce into discrete units and adhere to the surface. This places each of the units in contact with a set of different oligonucleotide molecules so as to allow the molecules to disperse into the units. 13 figs.

Duplex evaluation following femoropopliteal angioplasty and stenting: criteria and utility of surveillance.

PubMed

Baril, Donald T; Marone, Luke K

2012-07-01

Surveillance following lower extremity bypass, carotid endarterectomy, and endovascular aortic aneurysm repair has become the standard of care at most institutions. Conversely, surveillance following lower extremity endovascular interventions is performed somewhat sporadically in part because the duplex criteria for recurrent stenoses have been ill defined. It appears that duplex surveillance after peripheral endovascular interventions, as with conventional bypass, is beneficial in identifying recurrent lesions which may preclude failure and occlusion. In-stent stenosis following superficial femoral artery angioplasty and stenting can be predicted by both peak systolic velocity and velocity ratio data as measured by duplex ultrasound. Duplex criteria have been defined to determine both ≥50% in-stent stenosis and ≥80% in-stent stenosis. Although not yet well studied, it appears that applying these criteria during routine surveillance may assist in preventing failure of endovascular interventions.

Preparation of 13C/15N-labeled oligomers using the polymerase chain reaction

DOEpatents

Chen, Xian; Gupta, Goutam; Bradbury, E. Morton

2001-01-01

Preparation of .sup.13 C/.sup.15 N-labeled DNA oligomers using the polymerase chain reaction (PCR). A PCR based method for uniform (.sup.13 C/.sup.15 N)-labeling of DNA duplexes is described. Multiple copies of a blunt-ended duplex are cloned into a plasmid, each copy containing the sequence of interest and restriction Hinc II sequences at both the 5' and 3' ends. PCR using bi-directional primers and uniformly .sup.13 C/.sup.15 N-labeled dNTP precursors generates labeled DNA duplexes containing multiple copies of the sequence of interest. Twenty-four cycles of PCR, followed by restriction and purification, gave the uniformly .sup.13 C/.sup.15 N-labeled duplex sequence with a 30% yield. Such labeled duplexes find significant applications in multinuclear magnetic resonance spectroscopy.

Effect of heat input on dissimilar welds of ultra high strength steel and duplex stainless steel: Microstructural and compositional analysis

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

Tasalloti, H., E-mail: hamed.tasalloti.kashani@stu

The effect of heat input on the microstructure and compositional heterogeneity of welds of direct-quenched ultra high strength steel (Optim 960 QC) and duplex stainless steel (UNS S32205) was studied. The dissimilar welds were made using GMAW with a fully austenitic filler wire. In addition to grain coarsening in the heat affected zone (HAZ) of the ferritic side, it was found that an increase in heat input correlatively increased the proportional volume of bainitic to martensitic phases. Coarse ferritic grains were observed in the duplex HAZ. Higher heat input, however, had a beneficial effect on the nucleation of austenite inmore » the HAZ. Heat input had a regulatory effect on grain growth within the austenitic weld and more favorable equiaxed austenite was obtained with higher heat input. On the ferritic side of the welds, macrosegregation in the form of a martensitic intermediate zone was observed for all the cooling rates studied. However, on the duplex side, macrosegregation in the fusion boundary was only noticed with higher cooling rates. Microstructural observations and compositional analysis suggest that higher heat input could be beneficial for the structural integrity of the weld despite higher heat input increasing the extent of adverse coarse grains in the HAZ, especially on the ferritic side. - Highlights: •The effect of heat input on dissimilar welds of UHSS and DSS was studied. •Transmutation of the microstructure was discussed in detail. •The influence of heat input on compositional heterogeneity of welds was described. •Higher heat input enhanced bainitic transformation on the ferritic side. •Macrosegregation was affected by the amount of heat input on the DSS side.« less

Microstructure, Hardness, and Corrosion Behavior of TiC-Duplex Stainless Steel Composites Fabricated by Spark Plasma Sintering

NASA Astrophysics Data System (ADS)

Han, Ying; Zhang, Wei; Sun, Shicheng; Chen, Hua; Ran, Xu

2017-08-01

Duplex stainless steel composites with various weight fractions of TiC particles are prepared by spark plasma sintering. Ferritic 434L and austenitic 316L stainless steel powders are premixed in a 50:50 weight ratio and added with 3-9 wt.% TiC. The compacts are sintered in the solid state under vacuum conditions at 1223 K for 5 min. The effects of TiC content on the microstructure, hardness, and corrosion resistance of duplex stainless steel composites fabricated by powder metallurgy are evaluated. The results indicate that the TiC particulates as reinforcements can be distributed homogeneously in the steel matrix. Densification of sintered composites decreases with increasing TiC content. M23C6 carbide precipitates along grain boundary, and its neighboring Cr-Mo-depleted region is formed in the sintered microstructure, which can be eliminated subsequently with appropriate heat treatment. With the addition of TiC, the hardness of duplex stainless steel fabricated by powder metallurgy can be markedly enhanced despite increased porosity in the composites. However, TiC particles increase the corrosion rate and degrade the passivation capability, particularly for the composite with TiC content higher than 6 wt.%. Weakened metallurgical bonding in the composite with high TiC content provides the preferred sites for pitting nucleation and/or dissolution.

Geometry of an outcrop-scale duplex in Devonian flysch, Maine

USGS Publications Warehouse

Bradley, D.C.; Bradley, L.M.

1994-01-01

We describe an outcrop-scale duplex consisting of 211 exposed repetitions of a single bed. The duplex marks an early Acadian (Middle Devonian) oblique thrust zone in the Lower Devonian flysch of northern Maine. Detailed mapping at a scale of 1:8 has enabled us to measure accurately parameters such as horse length and thickness, ramp angles and displacements; we compare these and derivative values with those of published descriptions of duplexes, and with theoretical models. Shortening estimates based on line balancing are consistently smaller than two methods of area balancing, suggesting that layer-parallel shortening preceded thrusting. ?? 1994.

Capturing a DNA duplex under near-physiological conditions

NASA Astrophysics Data System (ADS)

Zhang, Huijuan; Xu, Wei; Liu, Xiaogang; Stellacci, Francesco; Thong, John T. L.

2010-10-01

We report in situ trapping of a thiolated DNA duplex with eight base pairs into a polymer-protected gold nanogap device under near-physiological conditions. The double-stranded DNA was captured by electrophoresis and covalently attached to the nanogap electrodes through sulfur-gold bonding interaction. The immobilization of the DNA duplex was confirmed by direct electrical measurements under near-physiological conditions. The conductance of the DNA duplex was estimated to be 0.09 μS. We also demonstrate the control of DNA dehybridization by heating the device to temperatures above the melting point of the DNA.

Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function

PubMed Central

Liu, Zhi; Ding, Shuang; Kropachev, Konstantin; Lei, Jia; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E.

2015-01-01

The nucleotide excision repair of certain bulky DNA lesions is abrogated in some specific non-canonical DNA base sequence contexts, while the removal of the same lesions by the nucleotide excision repair mechanism is efficient in duplexes in which all base pairs are complementary. Here we show that the nucleotide excision repair activity in human cell extracts is moderate-to-high in the case of two stereoisomeric DNA lesions derived from the pro-carcinogen benzo[a]pyrene (cis- and trans-B[a]P-N 2-dG adducts) in a normal DNA duplex. By contrast, the nucleotide excision repair activity is completely abrogated when the canonical cytosine base opposite the B[a]P-dG adducts is replaced by an abasic site in duplex DNA. However, base excision repair of the abasic site persists. In order to understand the structural origins of these striking phenomena, we used NMR and molecular spectroscopy techniques to evaluate the conformational features of 11mer DNA duplexes containing these B[a]P-dG lesions opposite abasic sites. Our results show that in these duplexes containing the clustered lesions, both B[a]P-dG adducts adopt base-displaced intercalated conformations, with the B[a]P aromatic rings intercalated into the DNA helix. To explain the persistence of base excision repair in the face of the opposed bulky B[a]P ring system, molecular modeling results suggest how the APE1 base excision repair endonuclease, that excises abasic lesions, can bind productively even with the trans-B[a]P-dG positioned opposite the abasic site. We hypothesize that the nucleotide excision repair resistance is fostered by local B[a]P residue—DNA base stacking interactions at the abasic sites, that are facilitated by the absence of the cytosine partner base in the complementary strand. More broadly, this study sets the stage for elucidating the interplay between base excision and nucleotide excision repair in processing different types of clustered DNA lesions that are substrates of nucleotide excision repair or base excision repair mechanisms. PMID:26340000

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

PubMed

Paiva, Anthony M; Sheardy, Richard D

2005-04-20

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

Duplex recombinase polymerase amplification assays incorporating competitive internal controls for bacterial meningitis detection.

PubMed

Higgins, Owen; Clancy, Eoin; Forrest, Matthew S; Piepenburg, Olaf; Cormican, Martin; Boo, Teck Wee; O'Sullivan, Nicola; McGuinness, Claire; Cafferty, Deirdre; Cunney, Robert; Smith, Terry J

2018-04-01

Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification technology that provides rapid and robust infectious disease pathogen detection, ideal for point-of-care (POC) diagnostics in disease-prevalent low-resource countries. We have developed and evaluated three duplex RPA assays incorporating competitive internal controls for the detection of leading bacterial meningitis pathogens. Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae singleplex RPA assays were initially developed and evaluated, demonstrating 100% specificity with limits of detection of 4.1, 8.5 and 3.9 genome copies per reaction, respectively. Each assay was further developed into internally controlled duplex RPA assays via the incorporation of internal amplification control templates. Clinical performance of each internally controlled duplex RPA assay was evaluated by testing 64 archived PCR-positive clinical samples. Compared to real-time PCR, all duplex RPA assays demonstrated 100% diagnostic specificity, with diagnostic sensitivities of 100%, 86.3% and 100% for the S. pneumoniae, N. meningitidis and H. influenzae assays, respectively. This study details the first report of internally controlled duplex RPA assays for the detection of bacterial meningitis pathogens: S. pneumoniae, N. meningitidis and H. influenzae. We have successfully demonstrated the clinical diagnostic utility of each duplex RPA assay, introducing effective diagnostic technology for POC bacterial meningitis identification in disease-prevalent developing countries. Copyright © 2018 Elsevier Inc. All rights reserved.

Analysis of features of stainless steels in dissimilar welded joints in chloride inducted corrosion

NASA Astrophysics Data System (ADS)

Topolska, S.; Łabanowski, J.

2017-08-01

Stainless steels of femtic-austenitic microstructure that means the duplex Cr-Ni-Mo steels, in comparison with austenitic steel includes less expensive nickel and has much better mechanical properties with good formability and corrosion resistance, even in environments containing chloride ions. Similar share of high chromium ferrite and austenite, which is characterized by high ductility, determines that the duplex steels have good crack resistance at temperatures up to approximately -40°C. The steels containing approximately 22% Cr, 5% Ni, 3% Mo and 0.2% N crystallizes as a solid solution δ, partially transforming from the temperature of about 1200°C to 850°C into the phase α. The stable structure of considered steels, at temperatures above 850°C, is ferrite, and at lower temperatures the mixture of phase γ+α +σ. The two-phase structure α+γ the duplex steel obtains after hyperquenching at the temperature of stability of the mixture of α+γ phases, and the share of the phases depends on the hyper quenching attributes. Hyperquenching in water, with a temperature close to 1200°C, ensures the instance in the microstructure of the steel a large share of ferrite and a small share of the high chromium austenite. This causes the increase of strength properties and reducing the plasticity of the steel and its resistance ability to cracking and corrosion. Slower cooling from the mentioned temperature, for example in the air, enables the partial transformation of the a phase into the γ one (α → γ) and increasing the share of austenite in the steel structure. It leads to improvement of plasticity properties. In the paper are presented the results of investigations of heteronymous welded joints of duplex steel and austenitic one. The results include the relation between the chemical composition of steels and their weldability.

Using small RNA deep sequencing data to detect siRNA duplexes induced by plant viruses

USDA-ARS?s Scientific Manuscript database

Small interfering RNA (siRNA) duplexes are produced in plants during virus infection, which are short (usually 21 to 24-base pair) double-stranded RNAs (dsRNAs) with several overhanging nucleotides on the 5' end and 3' end. The investigation of the siRNA duplexes is useful to better understand the R...

Molecular dynamics analysis of stabilities of the telomeric Watson-Crick duplex and the associated i-motif as a function of pH and temperature.

PubMed

Panczyk, Tomasz; Wolski, Pawel

2018-06-01

This work deals with a molecular dynamics analysis of the protonated and deprotonated states of the natural sequence d[(CCCTAA) 3 CCCT] of the telomeric DNA forming the intercalated i-motif or paired with the sequence d[(CCCTAA) 3 CCCT] and forming the Watson-Crick (WC) duplex. By utilizing the amber force field for nucleic acids we built the i-motif and the WC duplex either with native cytosines or using their protonated forms. We studied, by applying molecular dynamics simulations, the role of hydrogen bonds between cytosines or in cytosine-guanine pairs in the stabilization of both structures in the physiological fluid. We found that hydrogen bonds exist in the case of protonated i-motif and in the standard form of the WC duplex. They, however, vanish in the case of the deprotonated i-motif and protonated form of the WC duplex. By determining potentials of mean force in the enforced unwrapping of these structures we found that the protonated i-motif is thermodynamically the most stable. Its deprotonation leads to spontaneous and observed directly in the unbiased calculations unfolding of the i-motif to the hairpin structure at normal temperature. The WC duplex is stable in its standard form and its slight destabilization is observed at the acidic pH. However, the protonated WC duplex unwraps very slowly at 310 K and its decomposition was not observed in the unbiased calculations. At higher temperatures (ca. 400 K or more) the WC duplex unwraps spontaneously. Copyright © 2018. Published by Elsevier B.V.

Duplex unwinding and ATPase activities of the DEAD-box helicase eIF4A are coupled by eIF4G and eIF4B

PubMed Central

Özeş, Ali R.; Feoktistova, Kateryna; Avanzino, Brian C.; Fraser, Christopher S.

2011-01-01

Eukaryotic initiation factor 4A (eIF4A) is a DEAD-box helicase that stimulates translation initiation by unwinding mRNA secondary structure. The accessory proteins, eIF4G, eIF4B, and eIF4H enhance the duplex unwinding activity of eIF4A, but the extent to which they modulate eIF4A activity is poorly understood. Here, we use real time fluorescence assays to determine the kinetic parameters of duplex unwinding and ATP hydrolysis by these initiation factors. To ensure efficient duplex unwinding, eIF4B and eIF4G cooperatively activate the duplex unwinding activity of eIF4A. Our data reveal that eIF4H is much less efficient at stimulating eIF4A unwinding activity than eIF4B, implying that eIF4H is not able to completely substitute for eIF4B in duplex unwinding. By monitoring unwinding and ATPase assays using identical conditions, we demonstrate that eIF4B couples the ATP hydrolysis cycle of eIF4A with strand separation, thereby minimizing non-productive unwinding events. Using duplex substrates with altered GC contents, but with similar predicted thermal stabilities, we further show that the rate of formation of productive unwinding complexes is strongly influenced by the local stability per base pair in addition to the stability of the entire duplex. This finding explains how a change in the GC content of a hairpin while maintaining overall predicted thermal stability is able to influence translation initiation. PMID:21840318

Maximizing synchronizability of duplex networks

NASA Astrophysics Data System (ADS)

Wei, Xiang; Emenheiser, Jeffrey; Wu, Xiaoqun; Lu, Jun-an; D'Souza, Raissa M.

2018-01-01

We study the synchronizability of duplex networks formed by two randomly generated network layers with different patterns of interlayer node connections. According to the master stability function, we use the smallest nonzero eigenvalue and the eigenratio between the largest and the second smallest eigenvalues of supra-Laplacian matrices to characterize synchronizability on various duplexes. We find that the interlayer linking weight and linking fraction have a profound impact on synchronizability of duplex networks. The increasingly large inter-layer coupling weight is found to cause either decreasing or constant synchronizability for different classes of network dynamics. In addition, negative node degree correlation across interlayer links outperforms positive degree correlation when most interlayer links are present. The reverse is true when a few interlayer links are present. The numerical results and understanding based on these representative duplex networks are illustrative and instructive for building insights into maximizing synchronizability of more realistic multiplex networks.

Full-duplex bidirectional data transmission link using twisted lights multiplexing over 1.1-km orbital angular momentum fiber

PubMed Central

Chen, Shi; Liu, Jun; Zhao, Yifan; Zhu, Long; Wang, Andong; Li, Shuhui; Du, Jing; Du, Cheng; Mo, Qi; Wang, Jian

2016-01-01

We present a full-duplex bidirectional data transmission link using twisted lights multiplexing over 1.1-km orbital angular momentum (OAM) fiber. OAM+1 and OAM−1 modes carrying 20-Gbit/s quadrature phase-shift keying (QPSK) signals are employed in the downlink and uplink transmission experiments. The observed mode crosstalks are less than −15.2 dB, and the full-duplex crosstalks are less than −12.7 dB. The measured full-duplex optical signal-to-noise ratio (OSNR) penalties at a bit-error rate (BER) of 2 × 10−3 are ~2.4 dB in the downlink transmission and ~2.3 dB in the uplink transmission. The obtained results show favorable full-duplex twisted lights multiplexing data transmission performance in a km-scale OAM fiber link. PMID:27901082

Consequences of Normalizing Transcriptomic and Genomic Libraries of Plant Genomes Using a Duplex-Specific Nuclease and Tetramethylammonium Chloride

PubMed Central

Froenicke, Lutz; Lavelle, Dean; Martineau, Belinda; Perroud, Bertrand; Michelmore, Richard

2013-01-01

Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce. PMID:23409088

Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

PubMed

Matvienko, Marta; Kozik, Alexander; Froenicke, Lutz; Lavelle, Dean; Martineau, Belinda; Perroud, Bertrand; Michelmore, Richard

2013-01-01

Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.

Improvement of localised corrosion resistance of AISI 2205 Duplex Stainless Steel joints made by gas metal arc welding under electromagnetic interaction of low intensity

NASA Astrophysics Data System (ADS)

García-Rentería, M. A.; López-Morelos, V. H.; García-Hernández, R.; Dzib-Pérez, L.; García-Ochoa, E. M.; González-Sánchez, J.

2014-12-01

The resistance to localised corrosion of AISI 2205 duplex stainless steel plates joined by Gas Metal Arc Welding (GMAW) under the effect of electromagnetic interaction of low intensity (EMILI) was evaluated with sensitive electrochemical methods. Welds were made using two shielding gas mixtures: 98% Ar + 2% O2 (M1) and 97% Ar + 3% N2 (M2). Plates were welded under EMILI using the M1 gas with constant welding parameters. The modified microstructural evolution in the high temperature heat affected zone and at the fusion zone induced by application of EMILI during welding is associated with the increase of resistance to localised corrosion of the welded joints. Joints made by GMAW using the shielding gas M2 without the application of magnetic field presented high resistance to general corrosion but high susceptibility to undergo localised attack.

Norovirus in feces and nasopharyngeal swab of children with and without acute gastroenteritis symptoms: First report of GI.5 in Brazil and GI.3 in nasopharyngeal swab.

PubMed

Dábilla, Nathânia; Nunes Vieira Almeida, Tâmera; Carvalho Rebouças Oliveira, Anniely; Kipnis, André; Neres Silva, Thairiny; Souza Fiaccadori, Fabíola; Teixeira de Sousa, Teresinha; de Paula Cardoso, Divina das Dôres; Souza, Menira

2017-02-01

Noroviruses (NoVs) are an important cause of acute gastroenteritis (AGE), worldwide. To evaluate the frequency, viral load and molecular profile of NoV in fecal and nasopharyngeal swab samples from hospitalized children, and to determine children's secretor status. From May 2014 to May 2015, 219 children were included in the study, 96 with gastroenteric symptoms and 123 without gastroenteric symptoms. All fecal and nasopharyngeal swab samples were screened by TaqMan RT-qPCR duplex (GI/GII NoV) and quality samples were characterized by genomic sequencing. Norovirus positivity rate in feces was 15.4% in asymptomatic and 18.8% in the symptomatic group. The median viral loads in feces were 2.69×10 8 GC/g and 4.32×10 7 GC/g from children with or without AGE symptoms, respectively. In nasopharyngeal swab samples, the NoV positivity was 11.4% in symptomatic children, with a median viral load of 2.20×10 7 GC/mL and 6.5% in asymptomatic children, with an average viral load of 1.73×10 6 GC/mL. In only two cases NoV was detected in both samples. A considerable genomic variability was observed in feces, with six genotypes being detected, as follows: GII.4, GII.6, GI.3 and GII.3, GI.2 and GI.5. Two GI.3 was detected in nasopharyngeal swab. Our data reveal considerable NoV frequencies in both nasopharyngeal and fecal samples from symptomatic and asymptomatic children. Higher viral loads were detected in samples from AGE symptomatic children, when compared to asymptomatic children. High genomic variability was observed, with this being the first report of GI.5 NoV in Brazil and of GI.3 in nasopharyngeal swab samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanical characteristics of welded joints between different stainless steels grades

NASA Astrophysics Data System (ADS)

Topolska, S.; Łabanowski, J.

2017-08-01

Investigation of mechanical characteristics of welded joints is one of the most important tasks that allow determining their functional properties. Due to the very high, still rising, cost of some stainless steels it is justified, on economic grounds, welding austenitic stainless steel with steels that are corrosion-resistant like duplex ones. According to forecasts the price of corrosion resistant steels stil can increase by 26 ÷ 30%. For technical reasons welded joints require appropriate mechanical properties such as: tensile strength, bending, ductility, toughness, and resistance to aggressive media. Such joints are applied in the construction of chemical tankers, apparatus and chemical plants and power steam stations. Using the proper binder makes possible the welds directly between the elements of austenitic stainless steels and duplex ones. It causes that such joits behave satisfactorily in service in such areas like maritime constructions and steam and chemical plants. These steels have high mechanical properties such as: the yield strength, the tensile strength and the ductility as well as the resistance to general corrosion media. They are resistant to both pitting and stress corrosions. The relatively low cost of production of duplex steels, in comparison with standard austenitic steels, is inter alia, the result of a reduced amount of scarce and expensive Nickel, which is seen as a further advantage of these steels.

Development and validation of a duplex real-time PCR assay for the diagnosis of equine piroplasmosis.

PubMed

Lobanov, Vladislav A; Peckle, Maristela; Massard, Carlos L; Brad Scandrett, W; Gajadhar, Alvin A

2018-03-02

Equine piroplasmosis (EP) is an economically significant infection of horses and other equine species caused by the tick-borne protozoa Theileria equi and Babesia caballi. The long-term carrier state in infected animals makes importation of such subclinical cases a major risk factor for the introduction of EP into non-enzootic areas. Regulatory testing for EP relies on screening of equines by serological methods. The definitive diagnosis of EP infection in individual animals will benefit from the availability of sensitive direct detection methods, for example, when used as confirmatory assays for non-negative serological test results. The objectives of this study were to develop a real-time quantitative polymerase chain reaction (qPCR) assay for simultaneous detection of both agents of EP, perform comprehensive evaluation of its performance and assess the assay's utility for regulatory testing. We developed a duplex qPCR targeting the ema-1 gene of T. equi and the 18S rRNA gene of B. caballi and demonstrated that the assay has high analytical sensitivities for both piroplasm species. Validation of the duplex qPCR on samples from 362 competitive enzyme-linked immunosorbent assay (cELISA)-negative horses from Canada and the United States yielded no false-positive reactions. The assay's performance was further evaluated using samples collected from 430 horses of unknown EP status from a highly endemic area in Brazil. This set of samples was also tested by a single-target 18S rRNA qPCR for T. equi developed at the OIE reference laboratory for EP in Japan, and a previously published single-target 18S rRNA qPCR for B. caballi whose oligonucleotides we adopted for use in the duplex qPCR. Matching serum samples were tested for antibodies to these parasites using cELISA. By the duplex qPCR, T. equi-specific 18S rRNA qPCR and cELISA, infections with T. equi were detected in 87.9% (95% confidence interval, CI: 84.5-90.7%), 90.5% (95% CI: 87.3-92.3%) and 87.4% (95% CI: 84.0-90.2%) of the horses, respectively. The B. caballi prevalence estimates were 9.3% (95% CI: 6.9-12.4%) by the duplex qPCR and 7.9% (95% CI: 5.7-10.9%) by the respective single-target qPCR assay. These values were markedly lower compared to the seroprevalence of 58.6% (95% CI: 53.9-63.2%) obtained by B. caballi-specific cELISA. The relative diagnostic sensitivity of the duplex qPCR for T. equi was 95.5%, as 359 of the 376 horses with exposure to T. equi confirmed by cELISA had parasitemia levels above the detection limit of the molecular assay. In contrast, only 39 (15.5%) of the 252 horses with detectable B. caballi-specific antibodies were positive for this piroplasm species by the duplex qPCR. The duplex qPCR described here performed comparably to the existing single-target qPCR assays for T. equi and B. caballi and will be more cost-effective in terms of results turnaround time and reagent costs when both pathogens are being targeted for disease control and epidemiological investigations. These validation data also support the reliability of the ema-1 gene-specific oligonucleotides developed in this study for confirmatory testing of non-negative serological test results for T. equi by qPCR. However, the B. caballi-specific qPCR cannot be similarly recommended as a confirmatory assay for routine regulatory testing due to the low level of agreement with serological test results demonstrated in this study. Further studies are needed to determine the transmission risk posed by PCR-negative equines with detectable antibodies to B. caballi.

47 CFR 80.374 - Provisions for frequencies in the 4000-4063 and the 8100-8195 kHz bands shared with the fixed...

Code of Federal Regulations, 2010 CFR

2010-10-01

... ship-to-shore duplex operations with coast stations assigned the frequencies described in § 80.371(b... shore-to-ship simplex operations; or (iv) Duplex operations with coast stations assigned in the band... coast stations for: (i) Supplementary ship-to-shore duplex operations with coast stations assigned the...

A Commentary on "Updating the Duplex Design for Test-Based Accountability in the Twenty-First Century"

ERIC Educational Resources Information Center

Brandt, Steffen

2010-01-01

This article presents the author's commentary on "Updating the Duplex Design for Test-Based Accountability in the Twenty-First Century," in which Isaac I. Bejar and E. Aurora Graf propose the application of a test design--the duplex design (which was proposed in 1988 by Bock and Mislevy) for application in current accountability assessments.…

50. Photocopy of copy of original Officers' Duplex Quarters drawing ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

50. Photocopy of copy of original Officers' Duplex Quarters drawing by Turner, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University. Detail of front entrance and of gable dormer - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

48. Photocopy of copy of original Officers' Duplex Quarters drawing ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

48. Photocopy of copy of original Officers' Duplex Quarters drawing by Turner, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Attic and roof, basement, first floor, and second floor plans - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

49. Photocopy of copy of original Officers' Duplex Quarters drawing ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

49. Photocopy of copy of original Officers' Duplex Quarters drawing by Turner, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Front, rear, and side elevations, and cross-section - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

An Arabidopsis ATP-dependent, DEAD-box RNA helicase loses activity upon iosAsp formation but is restored by Protein Isoaspartyl Methltransferase

USDA-ARS?s Scientific Manuscript database

Arabidopsis thaliana PLANT RNA HELICASE75 (AtPRH75) demonstrated an ATP-dependent, RNA duplex unwinding capacity and an ATP-independent, RNA duplex reforming ability. It is known to accumulate isoAsp, but the consequences of isoAsp formation in AtPRH75 are unknown. Duplex unwinding was abolished by ...

The effects of laser welding parameters on the microstructure of ferritic and duplex stainless steels welds

NASA Astrophysics Data System (ADS)

Pekkarinen, J.; Kujanpää, V.

This study is focused to determine empirically, which microstructural changes occur in ferritic and duplex stainless steels when heat input is controlled by welding parameters. Test welds were done autogenously bead-on-plate without shielding gas using 5 kW fiber laser. For comparison, some gas tungsten arc welds were made. Used test material were 1.4016 (AISI 430) and 1.4003 (low-carbon ferritic) type steels in ferritic steels group and 1.4162 (low-alloyed duplex, LDX2101) and 1.4462 (AISI 2205) type steels in duplex steels group. Microstructural changes in welds were identified and examined using optical metallographic methods.

Concurrent infections of pseudorabies virus and porcine bocavirus in China detected by duplex nanoPCR.

PubMed

Luo, Yakun; Liang, Lin; Zhou, Ling; Zhao, Kai; Cui, Shangjin

2015-07-01

Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for the simple, rapid, and specific amplification of DNA and has been used to detect viruses. A duplex nanoPCR molecular detection system was developed to detect pseudorabies virus (PRV) and porcine bocavirus (PBoV). Primers were selected to target conserved regions within the PRV gE gene and the PBoV NS1 gene. Under optimized nanoPCR reaction conditions, two specific fragments of 316 bp (PRV) and 996 bp (PBoV) were amplified by the duplex nanoPCR with a detection limit of 6 copies for PRV and 95 copies for PBoV; no fragments were amplified when other porcine viruses were used as template. When used to test 550 clinical samples, the duplex nanoPRC assay and a conventional duplex PCR assay provided very similar results (98.1% consistency); single PRV infections, single PBoV infections, and concurrent PRV and PBoV infections were detected in 37%, 15%, and 9% of the samples, respectively. The results indicate that the novel duplex nanoPCR assay is useful for the rapid detection of PRV and PBoV in pigs. Copyright © 2015 Elsevier B.V. All rights reserved.

A sensitive duplex nanoparticle-assisted PCR assay for identifying porcine epidemic diarrhea virus and porcine transmissible gastroenteritis virus from clinical specimens.

PubMed

Zhu, Yu; Liang, Lin; Luo, Yakun; Wang, Guihua; Wang, Chunren; Cui, Yudong; Ai, Xia; Cui, Shangjin

2017-02-01

In this study, a novel duplex nanoparticle-assisted polymerase chain reaction (nanoPCR) assay was developed to detect porcine epidemic diarrhea virus (PEDV) and porcine transmissible gastroenteritis virus (TGEV). Two pairs of primers were designed based on the conserved region within the N gene of PEDV and TGEV. In a screening of 114 clinical samples from four provinces in China for PEDV and TGEV, 48.2 and 3.5 % of the samples, respectively, tested positive. Under optimized conditions, the duplex nanoPCR assay had a detection limit of 7.6 × 10 1 and 8.5 × 10 1 copies μL -1 for PEDV and TGEV, respectively. The sensitivity of the duplex nanoPCR assay was ten times higher than that of a conventional PCR assay. Moreover, no fragments were amplified when the duplex nanoPCR assay was used to test samples containing other porcine viruses. Our results indicate that the duplex nanoPCR assay described here is useful for the rapid detection of PEDV and TGEV and can be applied in clinical diagnosis.

Effects of chitosan inhibitor on the electrochemical corrosion behavior of 2205 duplex stainless steel

NASA Astrophysics Data System (ADS)

Yang, Se-fei; Wen, Ying; Yi, Pan; Xiao, Kui; Dong, Chao-fang

2017-11-01

The effects of chitosan inhibitor on the corrosion behavior of 2205 duplex stainless steel were studied by electrochemical measurements, immersion tests, and stereology microscopy. The influences of immersion time, temperature, and chitosan concentration on the corrosion inhibition performance of chitosan were investigated. The optimum parameters of water-soluble chitosan on the corrosion inhibition performance of 2205 duplex stainless steel were also determined. The water-soluble chitosan showed excellent corrosion inhibition performance on the 2205 duplex stainless steel. Polarization curves demonstrated that chitosan acted as a mixed-type inhibitor. When the stainless steel specimen was immersed in the 0.2 g/L chitosan solution for 4 h, a dense and uniform adsorption film covered the sample surface and the inhibition efficiency (IE) reached its maximum value. Moreover, temperature was found to strongly influence the corrosion inhibition of chitosan; the inhibition efficiency gradually decreased with increasing temperature. The 2205 duplex stainless steel specimen immersed in 0.4 g/L water-soluble chitosan at 30°C displayed the best corrosion inhibition among the investigated specimens. Moreover, chitosan decreased the corrosion rate of the 2205 duplex stainless steel in an FeCl3 solution.

Geometry and kinematics of the fold-thrust belt and structural evolution of the major Himalayan fault zones in the Darjeeling -- Sikkim Himalaya, India

NASA Astrophysics Data System (ADS)

Bhattacharyya, Kathakali

The Darjeeling-Sikkim Himalaya lies in the eastern part of the Himalayan fold-thrust belt (FTB) in a zone of high arc-perpendicular convergence between the Indian and Eurasian plates. In this region two distinct faults form the Main Central thrust (MCT), the structurally higher MCT1 and the lower MCT2; both these faults have translated the Greater Himalayan hanging wall rocks farther towards the foreland than in the western Himalaya. The width of the sub-MCT Lesser Himalayan rocks progressively decreases from the western Himalaya to this part of the eastern Himalaya, and as a result, the width of the FTB is narrower in this region compared to the western Himalaya. Our structural analysis shows that in the Darjeeling-Sikkim Himalaya the sub-MCT Lesser Himalayan duplex is composed of two duplex systems and has a more complex geometry than in the rest of the Himalayan fold-thrust belt. The structurally higher Dating duplex is a hinterland-dipping duplex; the structurally lower Rangit duplex varies in geometry from a hinterland-dipping duplex in the north to an antiformal stack in the middle and a foreland-dipping duplex in the south. The MCT2 is the roof thrust of the Daling duplex and the Ramgarh thrust is the roof thrust of the Rangit duplex. In this region, the Ramgarh thrust has a complex structural history with continued reactivation during footwall imbrication. The foreland-dipping component of the Rangit duplex, along with the large displacement associated with the reactivation of the Ramgarh thrust accounts for the large translation of the MCT sheets in the Darjeeling-Sikkim Himalaya. The growth of the Lesser Himalayan duplex modified the final geometry of the overlying MCT sheets, resulting in a plunge culmination that manifests itself as a broad N-S trending "anticline" in the Darjeeling-Sikkim Himalaya. This is not a "river anticline" as its trace lies west of the Teesta river. A transport parallel balanced cross section across this region has accommodated a total minimum shortening of ˜502 km (˜82%) south of the South Tibetan Detachment system (STDS). Based on this shortening, the average long-term shortening rate is estimated to be ˜22mm/yr in this region. The available shortening estimates from different parts of the Himalayan arc show significant variations in shortening, but based on the present available data, it is difficult to evaluate the primary cause for this variation. The shortening in the Himalayan fold-thrust belt (FTB) is highest in the middle of the Himalayan arc (western Nepal) and progressively decreases towards the two syntaxes. Although the width of the Lesser Himalayan belt decreases in the eastern Himalaya, the Lesser Himalayan shortening percentage remains approximately similar to that in the Nepal Himalaya. In addition, the shortening accommodated within the Lesser Himalayan duplex progressively increases from the western to the eastern Himalaya where it accommodates nearly half of the total shortening. The regional restorations suggest that the width of the original Lesser Himalayan basin may have played an important role in partitioning the shortening in the Himalayan FTB. In addition, the retrodeformed cross section in the Darjeeling-Sikkim Himalaya provides insights into the palinspastic reconstruction of the Gondwana basin of Peninsular India, suggesting that this basin extended ˜150 km northward of its present northernmost exposure in this region. The balanced cross section suggests that each of the MCT sheets has undergone translation of ≥100km in this region. Although a regional scale flat-on-flat relationship is seen in the MCT sheets, there is a significant variation in overburden from the trailing portion to the leading edge of the MCT due to the geometry of the tapered crystalline orogenic wedge. Microstructural studies from three segments of the MCT2 fault zone suggest that the MCT2 zone has undergone strain softening by different mechanisms along different portions of its transport-parallel length, mainly as a result of changing overburden conditions. This regional strain softening provides a suitable explanation for the large translation of ≥100 km along a relatively thin MCT2 fault zone in the Darjeeling-Sikkim Himalaya.

Quality assurance of lower limb venous duplex scans performed by vascular surgeons.

PubMed

Kordowicz, A; Ferguson, G; Salaman, R; Onwudike, M

2015-02-01

Duplex scanning is the gold standard for investigating venous reflux; increasingly surgeons perform these scans themselves. There has been no data published analysing the accuracy of Duplex scans performed by vascular surgeons. We aimed to evaluate an objective method of comparing the results of lower limb Duplex scans performed by one consultant vascular surgeon with those performed by a vascular technologist. We assessed 100 legs with symptomatic varicose veins. Each patient underwent two lower limb venous Duplex scans; one performed by a consultant vascular surgeon and one by a vascular technologist. Scan results were randomised and sent to two consultant vascular surgeons blinded to the identity and experience of the sonographer. They were asked to recommend treatment. A k score was calculated in each case to assess the level of agreement between the scans performed by the consultant and the technologist. Eighty-one patients were studied (53 females). The kappa score for assessor 1 was 0.60 (95%CI:0.44-0.75) and for assessor 2 was 0.62 (95%CI:0.48-0.75). k scores >0.60 represent a substantial strength of agreement. Duplex scans performed by this surgeon were comparable to those performed by a vascular technologist. It is possible to quality-assure duplex performed by vascular surgeons without directly observing the scanning process or reviewing digitally recorded images. We propose standardisation of training, assessment and quality assurance for vascular surgeons wishing to perform ultrasound scans.

Response of duplex Cr(N)/S and Cr(C)/S coatings on 316L stainless steel to tribocorrosion in 0.89% NaCl solution under plastic contact conditions.

PubMed

Sun, Y; Dearnley, P A; Mallia, Bertram

2017-08-01

Two duplex coatings, Cr(N)/S and Cr(C)/S, were deposited on 316 L stainless steel by magnetron sputtering. The effectiveness of these duplex coatings in improving the tribocorrosion behavior of medical alloys under elastic contact conditions has been demonstrated in a recent publication. The present work focused on the response of these duplex coatings to tribocorrosion under plastic contact conditions. Tribocorrosion tests were conducted in 0.89% NaCl solution at 37°C at an initial contact pressure of 740 MPa and under unidirectional sliding conditions for sliding duration up to 24 h. The results showed that during sliding in the corrosive solution, the duplex coatings were plastically deformed into the substrate to a depth about 1 μm. The Cr(C)/S duplex coating had sufficient ductility to accommodate the deformation without cracking, such that it was worn through gradually, leading to the gradual increase in open circuit potential (OCP) and coefficient of friction (COF). On the other hand, the Cr(N)/S duplex coating suffered from cracking at all tested potentials, leading to coating blistering after prolonged sliding at OCP and stable pit formation in the substrate beneath the coating at applied anodic potentials. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1503-1513, 2017. © 2016 Wiley Periodicals, Inc.

The value and economic analysis of routine postoperative carotid duplex ultrasound surveillance after carotid endarterectomy.

PubMed

AbuRahma, Ali F; Srivastava, Mohit; AbuRahma, Zachary; Jackson, Will; Mousa, Albeir; Stone, Patrick A; Dean, L Scott; Green, Jason

2015-08-01

Several studies have reported on the role of postoperative duplex ultrasound surveillance after carotid endarterectomy (CEA) with varying results. Most of these studies had a small sample size or did not analyze cost-effectiveness. We analyzed 489 of 501 CEA patients with patch closure. All patients had immediate postoperative duplex ultrasound examination and were routinely followed up both clinically and with duplex ultrasound at regular intervals of 1 month, 6 months, 12 months, and every 12 months thereafter. A Kaplan-Meier analysis was used to estimate the rate of ≥50% and ≥80% post-CEA restenosis over time and the time frame of progression from normal to ≥50% or ≥80% restenosis. The cost of post-CEA duplex surveillance was also estimated. Overall, 489 patients with a mean age of 68.5 years were analyzed. Ten of these had residual postoperative ≥50% stenosis, and 37 did not undergo a second duplex ultrasound examination and therefore were not included in the final analysis. The mean follow-up was 20.4 months (range, 1-63 months), with a mean number of duplex ultrasound examinations of 3.6 (range, 1-7). Eleven of 397 patients (2.8%) with a normal finding on immediate postoperative duplex ultrasound vs 4 of 45 (8.9%) with mild stenosis on immediate postoperative duplex ultrasound progressed to ≥50% restenosis (P = .055). Overall, 15 patients (3.1%) had ≥50% restenosis, 9 with 50% to <80% and 4 with 80% to 99% (2 of these had carotid artery stenting reintervention), and 2 had late carotid occlusion. All of these were asymptomatic, except for one who had a transient ischemic attack. The mean time to ≥50% to <80% restenosis was 14.7 months vs 19.8 months for ≥80% restenosis after the CEA. Freedom from restenosis rates were 98%, 96%, 94%, 94%, and 94% for ≥50% restenosis and 99%, 98%, 97%, 97%, and 97% for ≥80% restenosis at 1 year, 2 years, 3 years, 4 years, and 5 years, respectively. Freedom from myocardial infarction, stroke, and deaths was not significantly different between patients with and without restenosis (100%, 93%, 83%, and 83% vs 94%, 91%, 86%, and 79% at 1 year, 2 years, 3 years, and 4 years, respectively; P = .951). The estimated charge of this surveillance was 3.6 × 489 (number of CEAs) × $800 (charge for carotid duplex ultrasound), which equals $1,408,320, to detect only four patients with ≥80% to 99% restenosis who may have been potential candidates for reintervention. This study shows that the value of routine postoperative duplex ultrasound surveillance after CEA with patch closure may be limited, particularly if the finding on immediate postoperative duplex ultrasound is normal or shows minimal disease. Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Comparison of monoplex and duplex RT-PCR assays for the detection of measles virus.

PubMed

Binkhamis, Khalifa; Gillis, Hayley; Lafreniere, Joseph Daniel; Hiebert, Joanne; Mendoza, Lillian; Pettipas, Janice; Severini, Alberto; Hatchette, Todd F; LeBlanc, Jason J

2017-01-01

Rapid and accurate detection of measles virus is important for case diagnosis and public health management. This study compared the performance of two monoplex RT-PCR reactions targeting the H and N genes to a duplex RT-PCR targeting both genes simultaneously. The duplex simplified processing without compromising assay performance characteristic. Copyright © 2016 Elsevier B.V. All rights reserved.

NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.

PubMed

Lee, Joon-Hwa; Park, Chin-Ju; Shin, Jae-Sun; Ikegami, Takahisa; Akutsu, Hideo; Choi, Byong-Seok

2004-01-01

The cis-syn cyclobutane pyrimidine dimer (CPD) is a cytotoxic, mutagenic and carcinogenic DNA photoproduct and is repaired by the nucleotide excision repair (NER) pathway in mammalian cells. The XPC-hHR23B complex as the initiator of global genomic NER binds to sites of certain kinds of DNA damage. Although CPDs are rarely recognized by the XPC-hHR23B complex, the presence of mismatched bases opposite a CPD significantly increased the binding affinity of the XPC-hHR23B complex to the CPD. In order to decipher the properties of the DNA structures that determine the binding affinity for XPC-hHR23B to DNA, we carried out structural analyses of the various types of CPDs by NMR spectroscopy. The DNA duplex which contains a single 3' T*G wobble pair in a CPD (CPD/GA duplex) induces little conformational distortion. However, severe distortion of the helical conformation occurs when a CPD contains double T*G wobble pairs (CPD/GG duplex) even though the T residues of the CPD form stable hydrogen bonds with the opposite G residues. The helical bending angle of the CPD/GG duplex was larger than those of the CPD/GA duplex and properly matched CPD/AA duplex. The fluctuation of the backbone conformation and significant changes in the widths of the major and minor grooves at the double T*G wobble paired site were also observed in the CPD/GG duplex. These structural features were also found in a duplex that contains the (6-4) adduct, which is efficiently recognized by the XPC-hHR23B complex. Thus, we suggest that the unique structural features of the DNA double helix (that is, helical bending, flexible backbone conformation, and significant changes of the major and/or minor grooves) might be important factors in determining the binding affinity of the XPC-hHR23B complex to DNA.

Genetic Heterogeneity in Streptococcus mutans1

PubMed Central

Coykendall, Alan L.

1971-01-01

The genetic homogeneity among eight cariogenic strains of Streptococcus mutans was assessed by deoxyribonucleic acid (DNA)-DNA reassociation experiments. DNA species were extracted from strains GS5, Ingbritt, 10449, FAl, BHT, E49, SLl, and KlR. Labeled DNA (14C-DNA) was extracted from strains 10449, FAl, and SLl. Denatured 14C-DNA fragments were allowed to reassociate, i.e., form hybrid duplexes, with denatured DNA immobilized on membrane filters incubated in 0.45 m NaCl-0.045 m sodium citrate at 67 or 75 C. At 67 C, 10449 14C-DNA reassociated extensively only with GS5 and Ingbritt DNA. FAl 14C-DNA hybridized extensively only with BHT DNA, and SLl 14C-DNA reassociated with KlR and E49 DNA. DNA which hybridized extensively at 67 C also reassociated to a high degree at 75 C. Thermal elution of 14C-FAl-BHT duplexes showed that the hybrid duplexes were thermostable. The results indicate that S. mutans is a genetically heterogeneous species. The strains studied can be divided into three (possibly four) genetic groups, and these groups closely parallel antigenic groups. PMID:5551636

[Quality standards for duplex ultrasonographic assessment (duplex us) of abdominal aortic stent grafts].

PubMed

Diard, A; Becker, F; Pichot, O

2017-05-01

The quality standards of the French Society of Vascular Medicine for the ultrasound assessment of lower limb arteries in vascular medicine practice are based on the principle that these examinations have to meet two requirements: technical know-how (knowledge of devices and methodologies); medical know-how (level of examination matching the indication and purpose of the examination, interpretation and critical analysis of results). To describe an optimal level of examination adjusted to the indication or clinical hypothesis; to establish harmonious practices, methodologies, terminologies, results description and report; to provide good practice reference points and to promote a high quality process. The three levels of examination, indications and objectives for each level; the reference standard examination (level 2) and its variants according to indications; the minimal content of the exam report, the medical conclusion letter to the corresponding physician (synthesis, conclusion and management suggestions); commented glossary (anatomy, hemodynamics, signs and symptoms); technical basis; device settings. Here, we discuss duplex ultrasound for the supervision of the aortic stent grafts. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Routine preoperative colour Doppler duplex ultrasound scanning in anterolateral thigh flaps.

PubMed

Lichte, Johanna; Teichmann, Jan; Loberg, Christina; Kloss-Brandstätter, Anita; Bartella, Alexander; Steiner, Timm; Modabber, Ali; Hölzle, Frank; Lethaus, Bernd

2016-10-01

The anterolateral thigh flap (ALT) is often used to reconstruct the head and neck and depends on one or more skin perforators, which often present with variable anatomy. The aim of this study was to localise and evaluate the precise position of these perforators preoperatively with colour Doppler duplex ultrasound scanning (US). We detected 74 perforators in 30 patients. The mean duration of examination with colour Doppler was 29 (range 13-51) minutes. Adequate perforators and their anatomical course could be detected preoperatively extremely accurately (p<0.001). The mean difference between the preoperatively marked, and the real, positions was 6.3 (range 0-16) mm. There was a highly significant correlation between the accuracy of the prediction and the body mass index of the patient (0.75; p<0.001). Neither the age nor the sex of the patient correlated with the accuracy of the prediction. Colour Doppler duplex US used preoperatively to localise perforators in ALT flaps is reliable and could be adopted as standard procedure. Copyright © 2016 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Influence of Sintering Temperature on Hardness and Wear Properties of TiN Nano Reinforced SAF 2205

NASA Astrophysics Data System (ADS)

Oke, S. R.; Ige, O. O.; E Falodun, O.; Obadele, B. A.; Mphalele, M. R.; Olubambi, P. A.

2017-12-01

Conventional duplex stainless steel degrade in wear and mechanical properties at high temperature. Attempts have been made by researchers to solve this problems leading to the dispersion of second phase particles into duplex matrix. Powder metallurgy methods have been used to fabricate dispersion strengthened steels with a challenge of obtaining fully dense composite and grain growth. This could be resolved by appropriate selection of sintering parameters especially temperature. In this research, spark plasma sintering was utilized to fabricate nanostructured duplex stainless steel grade SAF 2205 with 5 wt.% nano TiN addition at different temperatures ranging from 1000 °C to 1200 °C. The effect of sintering temperature on the microstructure, density, hardness and wear of the samples was investigated. The results showed that the densities and grain sizes of the sintered nanocomposites increased with increasing the sintering temperature. The microstructures reveal ferrite and austenite grains with fine precipitates within the ferrite grains. The study of the hardness and wear behaviors, of the samples indicated that the optimum properties were obtained for the sintering temperature of 1150 °C.

Microstructural evolution during aging at 800 °C and its effect on the magnetic behavior of UNS S32304 lean duplex stainless steel

NASA Astrophysics Data System (ADS)

Dille, J.; Areiza, M. C. L.; Tavares, S. S. M.; Pereira, G. R.; De Almeida, L. H.; Rebello, J. M. A.

2017-03-01

Duplex stainless steels are high strength and corrosion resistant alloys extensively used in chemical and petrochemical industries. However, exposition to temperatures in the range 300-1000 °C leads to precipitation of different phases having a detrimental effect on the mechanical properties and on the corrosion resistance of the alloy. In this work, the microstructural evolution during aging of a UNS S32304 lean duplex stainless steel was investigated by scanning electron microscopy, transmission electron microscopy and magnetic force microscopy. Formation of secondary austenite as well as Cr2N and Cr23C6 precipitation and, consequently, a decrease of ferrite volume fraction were observed. EDX analysis indicated that secondary austenite is depleted in chromium which is detrimental to the corrosion resistance of the alloy. A variation of magnetic properties and Eddy current measurement parameters during aging was simultaneously detected and can be explained by the decrease of ferrite volume content. Therefore, Eddy current non-destructive testing can be successfully applied to detect the formation of deleterious phases during aging.

Structural studies of the 5'-phenazinium-tethered matched and G-A-mismatched DNA duplexes by NMR spectroscopy.

PubMed

Maltseva, T; Sandström, A; Ivanova, I M; Sergeyev, D S; Zarytova, V F; Chattopadhyaya, J

1993-05-01

The mechanism through which modified oligo-DNA analogues act as antisense repressors at the transcriptional and translational level of gene expression is based on the information content in the nucleotide sequence which is determined by the specific base pairing. The efficiency of such action is largely determined by the stability of the duplex formed between the oligonucleotide reagent and the target sequence and also by the mismatched base pairing, such as G-A, that occurs during replication or recombination. We herein report that the phenazinium (Pzn)-tethered matched duplex p(d(TGTTTGGC)):(Pzn)-p(d(CCAAACA)) (III) (Tm = 50 degrees C) has a much larger stability than the parent matched duplex p(d(TGTTTGGC)):p(d(CCAAACA)) (I) (Tm = 30 degrees C). On the other hand, the Pzn-tethered G-A-mismatched duplex p(d(TGTTTGGC)):(Pzn)-p(d(ACAAACA)) (IV) (Tm = 34 degrees C) is only slightly more stable than its parent mismatched duplex p(d(TGTTTGGC)):p(d(ACAAACA)) (Tm = 25 degrees C). A detailed 500 MHz NMR study and constrained MD refinements of NMR-derived structures have been undertaken for the DNA duplexes (I), (II), (III) and (IV) in order to understand the structural basis of stabilization of Pzn-tethered matched DNA duplex (delta Tm = 20 degrees C) compared to mismatched duplex (delta Tm = 9 degrees C). Assignment of the 1H-NMR (500 MHz) spectra of the duplexes has been carried out by 2D NOESY, HOHAHA and DQF-COSY experiments. The torsion angles have been extracted from the J-coupling constants obtained by simulation of most of the DQF-COSY cross-peaks using program SMART. The solution structure of the duplexes were assessed by an iterative hybride relaxation matrix method (MORASS) combined with NOESY distances and torsion angles restrained molecular dynamics (MD) using program Amber 4.0. The standard Amber 4.0 force-field parameters were used for the oligonucleotide in conjunction with the new parameters for Pzn residue which was obtained by full geometry optimization using ab initio program (3-21G basis set). It has been shown that mismatched G-A bases are in the anti-anti conformation. The mismatched 7G-1A form stable base pairs through inter-strand hydrogen bonds (N7(A)...HN2(G) (1.92 A) with a subtended angle of 176 degrees and N3(G)...HN6(A) (2.01 A) with a subtended angle of 153 degrees (the 'amino-type' hydrogen bond)) and a propeller twist of 36 degrees for 7G-1A residues.(ABSTRACT TRUNCATED AT 400 WORDS)

Duplex ultrasound

MedlinePlus

Vascular ultrasound; Peripheral vascular ultrasound ... A duplex ultrasound combines: Traditional ultrasound: This uses sound waves that bounce off blood vessels to create pictures. Doppler ultrasound: This ...

Nitride alloy layer formation of duplex stainless steel using nitriding process

NASA Astrophysics Data System (ADS)

Maleque, M. A.; Lailatul, P. H.; Fathaen, A. A.; Norinsan, K.; Haider, J.

2018-01-01

Duplex stainless steel (DSS) shows a good corrosion resistance as well as the mechanical properties. However, DSS performance decrease as it works under aggressive environment and at high temperature. At the mentioned environment, the DSS become susceptible to wear failure. Surface modification is the favourable technique to widen the application of duplex stainless steel and improve the wear resistance and its hardness properties. Therefore, the main aim of this work is to nitride alloy layer on the surface of duplex stainless steel by the nitriding process temperature of 400°C and 450°C at different time and ammonia composition using a horizontal tube furnace. The scanning electron microscopy and x-ray diffraction analyzer are used to analyse the morphology, composition and the nitrided alloy layer for treated DSS. The micro hardnesss Vickers tester was used to measure hardness on cross-sectional area of nitrided DSS. After nitriding, it was observed that the hardness performance increased until 1100 Hv0.5kgf compared to substrate material of 250 Hv0.5kgf. The thickness layer of nitride alloy also increased from 5μm until 100μm due to diffusion of nitrogen on the surface of DSS. The x-ray diffraction results showed that the nitride layer consists of iron nitride, expanded austenite and chromium nitride. It can be concluded that nitride alloy layer can be produced via nitriding process using tube furnace with significant improvement of microstructural and hardness properties.

G-quadruplexes Significantly Stimulate Pif1 Helicase-catalyzed Duplex DNA Unwinding*

PubMed Central

Duan, Xiao-Lei; Liu, Na-Nv; Yang, Yan-Tao; Li, Hai-Hong; Li, Ming; Dou, Shuo-Xing; Xi, Xu-Guang

2015-01-01

The evolutionarily conserved G-quadruplexes (G4s) are faithfully inherited and serve a variety of cellular functions such as telomere maintenance, gene regulation, DNA replication initiation, and epigenetic regulation. Different from the Watson-Crick base-pairing found in duplex DNA, G4s are formed via Hoogsteen base pairing and are very stable and compact DNA structures. Failure of untangling them in the cell impedes DNA-based transactions and leads to genome instability. Cells have evolved highly specific helicases to resolve G4 structures. We used a recombinant nuclear form of Saccharomyces cerevisiae Pif1 to characterize Pif1-mediated DNA unwinding with a substrate mimicking an ongoing lagging strand synthesis stalled by G4s, which resembles a replication origin and a G4-structured flap in Okazaki fragment maturation. We find that the presence of G4 may greatly stimulate the Pif1 helicase to unwind duplex DNA. Further studies reveal that this stimulation results from G4-enhanced Pif1 dimerization, which is required for duplex DNA unwinding. This finding provides new insights into the properties and functions of G4s. We discuss the observed activation phenomenon in relation to the possible regulatory role of G4s in the rapid rescue of the stalled lagging strand synthesis by helping the replicator recognize and activate the replication origin as well as by quickly removing the G4-structured flap during Okazaki fragment maturation. PMID:25627683

Teleneurosonology: a novel application of transcranial and carotid ultrasound.

PubMed

Rubin, Mark N; Barrett, Kevin M; Freeman, W David; Lee Iannotti, Joyce K; Channer, Dwight D; Rabinstein, Alejandro A; Demaerschalk, Bart M

2015-03-01

To demonstrate the technical feasibility of interfacing transcranial Doppler (TCD) and carotid "duplex" ultrasonography (CUS) peripherals with telemedicine end points to provide real-time spectral waveform and duplex imaging data for remote review and interpretation. We performed remote TCD and CUS examinations on a healthy, volunteer employee from our institution without known cerebrovascular disease. The telemedicine end point was stationed in our institution's hospital where the neurosonology examinations took place and the control station was in a dedicated telemedicine room in a separate building. The examinations were performed by a postgraduate level neurohospitalist trainee (M.N.R.) and interpreted by an attending vascular neurologist, both with experience in the performance and interpretation of TCD and CUS. Spectral waveform and duplex ultrasound data were successfully transmitted from TCD and CUS instruments through a telemedicine end point to a remote reviewer at a control station. Image quality was preserved in all cases, and technical failures were not encountered. This proof-of-concept study demonstrates the technical feasibility of interfacing TCD and CUS peripherals with a telemedicine end point to provide real-time spectral waveform and duplex imaging data for remote review and interpretation. Medical diagnostic and telemedicine devices should be equipped with interfaces that allow simple transmission of high-quality audio and video information from the medical devices to the telemedicine technology. Further study is encouraged to determine the clinical impact of teleneurosonology. Copyright © 2015 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Ift25 is not a cystic kidney disease gene but is required for early steps of kidney development.

PubMed

Desai, Paurav B; San Agustin, Jovenal T; Stuck, Michael W; Jonassen, Julie A; Bates, Carlton M; Pazour, Gregory J

2018-06-01

Eukaryotic cilia are assembled by intraflagellar transport (IFT) where large protein complexes called IFT particles move ciliary components from the cell body to the cilium. Defects in most IFT particle proteins disrupt ciliary assembly and cause mid gestational lethality in the mouse. IFT25 and IFT27 are unusual components of IFT-B in that they are not required for ciliary assembly and mutant mice survive to term. The mutants die shortly after birth with numerous organ defects including duplex kidneys. Completely duplex kidneys result from defects in ureteric bud formation at the earliest steps of metanephric kidney development. Ureteric bud initiation is a highly regulated process involving reciprocal signaling between the ureteric epithelium and the overlying metanephric mesenchyme with regulation by the peri-Wolffian duct stroma. The finding of duplex kidney in Ift25 and Ift27 mutants suggests functions for these genes in regulation of ureteric bud initiation. Typically the deletion of IFT genes in the kidney causes rapid cyst growth in the early postnatal period. In contrast, the loss of Ift25 results in smaller kidneys, which show only mild tubule dilations that become apparent in adulthood. The smaller kidneys appear to result from reduced branching in the developing metanephric kidney. This work indicates that IFT25 and IFT27 are important players in the early development of the kidney and suggest that duplex kidney is part of the ciliopathy spectrum. Copyright © 2018 Elsevier B.V. All rights reserved.

Detection of imminent vein graft occlusion: what is the optimal surveillance program?

PubMed

Tinder, Chelsey N; Bandyk, Dennis F

2009-12-01

The prediction of infrainguinal vein bypass failure remains an inexact judgment. Patient demographics, technical factors, and vascular laboratory graft surveillance testing are helpful in identifying a high-risk graft cohort. The optimal surveillance program to detect the bypass at risk for imminent occlusion continues to be developed, but required elements are known and include clinical assessment for new or changes in limb ischemia symptoms, measurement of ankle and/or toe systolic pressure, and duplex ultrasound imaging of the bypass graft. Duplex ultrasound assessment of bypass hemodynamics may be the most accurate method to detect imminent vein graft occlusion. The finding of low graft flow during intraoperative assessment or at a scheduled surveillance study predicts failure; and if associated with an occlusive lesion, a graft revision can prolong patency. The most common abnormality producing graft failure is conduit stenosis caused by myointimal hyperplasia; and the majority can be repaired by an endovascular intervention. Frequency of testing to detect the failing bypass should be individualized to the patient, the type of arterial bypass, and prior duplex ultrasound scan findings. The focus of surveillance is on identification of the low-flow arterial bypass and timely repair of detected critical stenosis defined by duplex velocity spectra criteria of a peak systolic velocity 300 cm/s and peak systolic velocity ratio across the stenosis >3.5-correlating with >70% diameter-reducing stenosis. When conducted appropriately, a graft surveillance program should result in an unexpected graft failure rate of <3% per year.

Electromagnetic non-destructive technique for duplex stainless steel characterization

NASA Astrophysics Data System (ADS)

Rocha, João Vicente; Camerini, Cesar; Pereira, Gabriela

2016-02-01

Duplex stainless steel (DSS) is a two-phase (ferrite and austenite) material, which exhibits an attractive combination of mechanical properties and high corrosion resistance, being commonly employed for equipment of petrochemical plants, refining units and oil & gas platforms. The best properties of DSS are achieved when the phases are in equal proportions. However, exposition to high temperatures (e.g. welding process) may entail undesired consequences, such as deleterious phases precipitation (e.g. sigma, chi) and different proportion of the original phases, impairing dramatically the mechanical and corrosion properties of the material. A detailed study of the magnetic behavior of DSS microstructure with different ferrite austenite ratios and deleterious phases content was accomplished. The non destructive method evaluates the electromagnetic properties changes in the material and is capable to identify the presence of deleterious phases into DSS microstructure.

Four human Plasmodium species quantification using droplet digital PCR.

PubMed

Srisutham, Suttipat; Saralamba, Naowarat; Malleret, Benoit; Rénia, Laurent; Dondorp, Arjen M; Imwong, Mallika

2017-01-01

Droplet digital polymerase chain reaction (ddPCR) is a partial PCR based on water-oil emulsion droplet technology. It is a highly sensitive method for detecting and delineating minor alleles from complex backgrounds and provides absolute quantification of DNA targets. The ddPCR technology has been applied for detection of many pathogens. Here the sensitive assay utilizing ddPCR for detection and quantification of Plasmodium species was investigated. The assay was developed for two levels of detection, genus specific for all Plasmodium species and for specific Plasmodium species detection. The ddPCR assay was developed based on primers and probes specific to the Plasmodium genus 18S rRNA gene. Using ddPCR for ultra-sensitive P. falciparum assessment, the lower level of detection from concentrated DNA obtained from a high volume (1 mL) blood sample was 11 parasites/mL. For species identification, in particular for samples with mixed infections, a duplex reaction was developed for detection and quantification P. falciparum/ P. vivax and P. malariae/ P. ovale. Amplification of each Plasmodium species in the duplex reaction showed equal sensitivity to singleplex single species detection. The duplex ddPCR assay had higher sensitivity to identify minor species in 32 subpatent parasitaemia samples from Cambodia, and performed better than real-time PCR. The ddPCR assay shows high sensitivity to assess very low parasitaemia of all human Plasmodium species. This provides a useful research tool for studying the role of the asymptomatic parasite reservoir for transmission in regions aiming for malaria elimination.

Tribological behavior of CrN-coated Cr-Mo-V steels used as die materials

NASA Astrophysics Data System (ADS)

Çelik, Gülşah Aktaş; Polat, Şeyda; Atapek, Ş. Hakan

2017-12-01

DIN 1.2343 and 1.2367 steels are commonly used as die materials in aluminum extrusion, and single/duplex/multi-coatings enhance their surface properties. The design of an appropriate substrate/coating system is important for improving the tribological performance of these steels under service conditions because the load-carrying capacity of the system can be increased by decreasing the plastic deformation of the substrate. In this study, the tribological behavior of CrN-coated Cr-Mo-V steels (DIN 1.2343, 1.2367, and 1.2999 grades) was investigated using different setups and tribological pairs at room and elevated temperatures. The aim of this study was to reveal the wear resistance of a suggested system (1.2999/CrN) not yet studied and to understand both the wear and the failure characteristics of coated systems. The results showed that (i) among the steels studied, the DIN 1.2999 grade steel exhibited the lowest friction coefficient because it had the highest load-carrying capacity as a result of secondary hardening at elevated temperatures; (ii) at room temperature, both abrasive tracks and adhesive layers were observed on the worn surfaces; and (iii) a combination of chemical reactions and progressive oxidation caused aluminum adhesion on the worn surface, and the detachment of droplets and microcracking were the characteristic damage mechanisms at high temperatures.

Preoperative Duplex Scanning is a Helpful Diagnostic Tool in Neurogenic Thoracic Outlet Syndrome.

PubMed

Orlando, Megan S; Likes, Kendall C; Mirza, Serene; Cao, Yue; Cohen, Anne; Lum, Ying Wei; Freischlag, Julie A

2016-01-01

To evaluate the diagnostic role of venous and arterial duplex scanning in neurogenic thoracic outlet syndrome (NTOS). Retrospective review of patients who underwent duplex ultrasonography prior to first rib resection and scalenectomy (FRRS) for NTOS from 2005 to 2013. Abnormal scans included ipsilateral compression (IC) with abduction of the symptomatic extremity (>50% change in subclavian vessel flow), contralateral (asymptomatic side) compression (CC) or bilateral compression (BC). A total of 143 patients (76% female, average age 34, range 13-59) underwent bilateral preoperative duplex scanning. Ipsilateral compression was seen in 44 (31%), CC in 12 (8%), and BC in 14 (10%). Seventy-three (51%) patients demonstrated no compression. Patients with IC more often experienced intraoperative pneumothoraces (49% vs. 25%, P < .05) and had positive Adson tests (86% vs. 61%, P < .02). Compression of the subclavian vein or artery on duplex ultrasonography can assist in NTOS diagnosis. Ipsilateral compression on abduction often correlates with Adson testing. © The Author(s) 2016.

A most spectrum-efficient duplexing system: CDD

NASA Astrophysics Data System (ADS)

Lee, William C. Y.

2001-10-01

The game to play in wireless communications when it comes to increasing spectrum efficiency is to eliminate interference. Currently, all cellular systems use FDD (Frequency Division Duplexing) in an attempt to eliminate the interference from the adjacent cells. Through the use of many technologies only one type of interference remains and that is the adjacent base-tohome mobile interference. TDD (Time Division Duplexing) has not been used for mobile cellular systems, not only because of the adjacent base-to-home mobile interference, but also because of the additional adjacent base-to-home base interference, and adjacent mobile-to-home mobile interference. Therefore, TDD can only be used for small, confined area systems. CDD (Code Division Duplexing) can eliminate all three kinds of interference; the adjacent base-to-home mobile, the adjacent baseto-home base, and the adjacent mobile- to- home in cellular systems. Eliminating each of these interferences makes CDD the most spectrum efficient duplexing system. This talk will elaborate on a set of smart codes, which will make an efficient CDD system a reality.

G-quadruplex and G-rich sequence stimulate Pif1p-catalyzed downstream duplex DNA unwinding through reducing waiting time at ss/dsDNA junction

PubMed Central

Zhang, Bo; Wu, Wen-Qiang; Liu, Na-Nv; Duan, Xiao-Lei; Li, Ming; Dou, Shuo-Xing; Hou, Xi-Miao; Xi, Xu-Guang

2016-01-01

Alternative DNA structures that deviate from B-form double-stranded DNA such as G-quadruplex (G4) DNA can be formed by G-rich sequences that are widely distributed throughout the human genome. We have previously shown that Pif1p not only unfolds G4, but also unwinds the downstream duplex DNA in a G4-stimulated manner. In the present study, we further characterized the G4-stimulated duplex DNA unwinding phenomenon by means of single-molecule fluorescence resonance energy transfer. It was found that Pif1p did not unwind the partial duplex DNA immediately after unfolding the upstream G4 structure, but rather, it would dwell at the ss/dsDNA junction with a ‘waiting time’. Further studies revealed that the waiting time was in fact related to a protein dimerization process that was sensitive to ssDNA sequence and would become rapid if the sequence is G-rich. Furthermore, we identified that the G-rich sequence, as the G4 structure, equally stimulates duplex DNA unwinding. The present work sheds new light on the molecular mechanism by which G4-unwinding helicase Pif1p resolves physiological G4/duplex DNA structures in cells. PMID:27471032

The energetic basis of the DNA double helix: a combined microcalorimetric approach

PubMed Central

Vaitiekunas, Paulius; Crane-Robinson, Colyn; Privalov, Peter L.

2015-01-01

Microcalorimetric studies of DNA duplexes and their component single strands showed that association enthalpies of unfolded complementary strands into completely folded duplexes increase linearly with temperature and do not depend on salt concentration, i.e. duplex formation results in a constant heat capacity decrement, identical for CG and AT pairs. Although duplex thermostability increases with CG content, the enthalpic and entropic contributions of an AT pair to duplex formation exceed that of a CG pair when compared at the same temperature. The reduced contribution of AT pairs to duplex stabilization comes not from their lower enthalpy, as previously supposed, but from their larger entropy contribution. This larger enthalpy and particularly the greater entropy results from water fixed by the AT pair in the minor groove. As the increased entropy of an AT pair exceeds that of melting ice, the water molecule fixed by this pair must affect those of its neighbors. Water in the minor groove is, thus, orchestrated by the arrangement of AT groups, i.e. is context dependent. In contrast, water hydrating exposed nonpolar surfaces of bases is responsible for the heat capacity increment on dissociation and, therefore, for the temperature dependence of all thermodynamic characteristics of the double helix. PMID:26304541

Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson–Crick terminal base pairs

PubMed Central

O'Toole, Amanda S.; Miller, Stacy; Haines, Nathan; Zink, M. Coleen; Serra, Martin J.

2006-01-01

Thermodynamic parameters are reported for duplex formation of 48 self-complementary RNA duplexes containing Watson–Crick terminal base pairs (GC, AU and UA) with all 16 possible 3′ double-nucleotide overhangs; mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest-neighbor analysis, the addition of a second dangling nucleotide to a single 3′ dangling nucleotide increases stability of duplex formation up to 0.8 kcal/mol in a sequence dependent manner. Results from this study in conjunction with data from a previous study [A. S. O'Toole, S. Miller and M. J. Serra (2005) RNA, 11, 512.] allows for the development of a refined nearest-neighbor model to predict the influence of 3′ double-nucleotide overhangs on the stability of duplex formation. The model improves the prediction of free energy and melting temperature when tested against five oligomers with various core duplex sequences. Phylogenetic analysis of naturally occurring miRNAs was performed to support our results. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent upon the identity of the 3′ double-nucleotide overhang. Thermodynamic parameters for 3′ single terminal overhangs adjacent to a UA pair are also presented. PMID:16820533

Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe

PubMed Central

Ding, Yuan; Zhang, Xiaojun; Tham, Kenneth W.; Qin, Peter Z.

2014-01-01

Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes. PMID:25092920

Control of the photocatalytic activity of bimetallic complexes of pyropheophorbide-a by nucleic acids.

PubMed

Arian, Dumitru; Kovbasyuk, Larisa; Mokhir, Andriy

2011-12-05

Photocatalytic activity of a photosensitizer (PS) in an oligodeoxyribonucleotide duplex 5'-PS~ODN1/ODN2~Q-3' is inhibited because of close proximity of a quencher Q. The ODN2 in this duplex is selected to be longer than the ODN1. Therefore, in the presence of a nucleic acid (analyte), which is fully complementary to the ODN2 strand, the duplex is decomposed with formation of an analyte/ODN2~Q duplex and a catalytically active, single stranded PS~ODN1. In this way the catalytic activity of the PS can be controlled by the specific nucleic acids. We applied this reaction earlier for the amplified detection of ribonucleic acids in live cells (Arian, D.; Cló, E.; Gothelf, K.; Mokhir, A. Chem.-Eur. J.2010, 16(1), 288). As a photosensitizer (PS) we used In(3+)(pyropheophorbide-a)chloride and as a quencher (Q)--Black-Hole-Quencher-3 (BHQ-3). The In(3+) complex is a highly active photocatalyst in aqueous solution. However, it can coordinate additional ligands containing thiols (e.g., proteins, peptides, and aminoacids), that modulate properties of the complex itself and of the corresponding bio- molecules. These possible interactions can lead to undesired side effects of nucleic acid controlled photocatalysts (PS~ODN1/ODN2∼Q) in live cells. In this work we explored the possibility to substitute the In(3+) complex for those ones of divalent metal ions, Zn(2+) and Pd(2+), which exhibit lower or no tendency to coordinate the fifth ligand. We found that one of the compounds tested (Pd(pyropheophorbide-a) is as potent and as stable photosensitizer as its In(3+) analogue, but does not coordinate additional ligands that makes it more suitable for cellular applications. When the Pd complex was introduced in the duplex PS~ODN1/ODN2~Q as a PS, its photocatalytic activity could be controlled by nucleic acids as efficiently as that of the corresponding In(3+) complex.

Tricriticality in the q-neighbor Ising model on a partially duplex clique.

PubMed

Chmiel, Anna; Sienkiewicz, Julian; Sznajd-Weron, Katarzyna

2017-12-01

We analyze a modified kinetic Ising model, a so-called q-neighbor Ising model, with Metropolis dynamics [Phys. Rev. E 92, 052105 (2015)PLEEE81539-375510.1103/PhysRevE.92.052105] on a duplex clique and a partially duplex clique. In the q-neighbor Ising model each spin interacts only with q spins randomly chosen from its whole neighborhood. In the case of a duplex clique the change of a spin is allowed only if both levels simultaneously induce this change. Due to the mean-field-like nature of the model we are able to derive the analytic form of transition probabilities and solve the corresponding master equation. The existence of the second level changes dramatically the character of the phase transition. In the case of the monoplex clique, the q-neighbor Ising model exhibits a continuous phase transition for q=3, discontinuous phase transition for q≥4, and for q=1 and q=2 the phase transition is not observed. On the other hand, in the case of the duplex clique continuous phase transitions are observed for all values of q, even for q=1 and q=2. Subsequently we introduce a partially duplex clique, parametrized by r∈[0,1], which allows us to tune the network from monoplex (r=0) to duplex (r=1). Such a generalized topology, in which a fraction r of all nodes appear on both levels, allows us to obtain the critical value of r=r^{*}(q) at which a tricriticality (switch from continuous to discontinuous phase transition) appears.

Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler's murine encephalomyelitis virus and rat theilovirus.

PubMed

Yuan, Wen; Wang, Jing; Xu, Fengjiao; Huang, Bihong; Lian, Yuexiao; Rao, Dan; Yin, Xueqin; Wu, Miaoli; Zhu, Yujun; Zhang, Yu; Huang, Ren; Guo, Pengju

2016-10-01

Theiler's murine encephalomyelitis virus (TMEV) and rat theilovirus (RTV), the member of the genus Cardiovirus, are widespread in laboratory mice and rats, and are potential contaminants of biological materials. Cardioviruses infection may cause serious complications in biomedical research. To improve the efficiency of routine screening for Cardioviruses infection, a duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed for simultaneous detection and differentiation of TMEV and RTV. The duplex assay was specific for reference strains of TMEV and RTV, and no cross-reaction was found with seven other rodent viruses. The limits of detection of both TMEV and RTV were 4×10(1) copies RNA/reaction. Reproducibility was estimated using standard dilutions, with coefficients of variation <3.1%. 439 clinical samples were evaluated by both duplex real-time RT-PCR and conventional RT-PCR. For 439 clinical samples，95 samples were positive for TMEV and 72 samples were positive for RTV using duplex real-time RT-PCR approach, whereas only 77 samples were positive for TMEV and 66 samples were positive for RTV when conventional RT-PCR was applied. Mixed infections were found in 20 samples when analyzed by conventional RT-PCR whereas 30 samples were found to be mixed infection when duplex real-time RT-PCR was applied. This duplex assay provides a useful tool for routine health monitoring and screening of contaminated biological materials of these two viruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection and prevalence of pathogenic Yersinia enterocolitica in refrigerated and frozen dairy products by duplex PCR and dot hybridization targeting the virF and ail genes.

PubMed

Ye, Y W; Ling, N; Han, Y J; Wu, Q P

2014-11-01

Pathogenic Yersinia enterocolitica is involved in yersiniosis through expression of chromosome-borne or plasmid-borne virulence factors. Yersinia enterocolitica is a cold-tolerant pathogen frequently isolated from refrigerated or frozen foods. However, little attention has been focused on the prevalence of pathogenic Y. enterocolitica in refrigerated or frozen dairy samples in China. In this study, we developed a new duplex PCR targeting the plasmid-borne virF gene and chromosome-borne ail gene for detection of pathogenic Y. enterocolitica isolates. We established a detection limit for the duplex PCR of 6.5 × 10(2)cfu/mL in artificially contaminated dairy samples. In addition, the duplex PCR could detect directly 4.5 to 5.7 cfu of Y. enterocolitica in 5 mL of brain heart infusion broth after 6 h of enrichment at 28 °C. A newly developed dot hybridization assay further confirmed specificity of the duplex PCR for detection of virulent Y. enterocolitica. Furthermore, 13 Y. enterocolitica and 5 pathogenic strains, from 88 commercial frozen or refrigerated dairy products, were detected successfully by the China National Standard method (GB/T4789.8-2008) and the duplex PCR, respectively. Finally, biotypes and serotypes of pathogenic Y. enterocolitica strains were further characterized. The duplex PCR developed here is reliable for large-scale screening, routine monitoring, and risk assessment of pathogenic Y. enterocolitica in refrigerated or frozen dairy products. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The morphology and treatment of coexisting ureteropelvic junction obstruction in lower moiety of duplex kidney.

PubMed

Liu, Wei; Zhang, Liujuan; Ma, Rui; Wu, Rongde

2016-10-01

Duplex kidney is a common congenital anomaly of the urinary tract, while ureteropelvic junction obstruction (UPJO) in lower unit of duplex kidney is rare. Surgical treatment can be challenging in such cases. The aim was to report our experience in managements of UPJO in lower moiety of duplex kidney. Among the pediatric patients with duplex system from 2007 to 2013, 7 children were diagnosed with UPJO in lower moiety. Their medical records were retrospectively analyzed, mainly focused on anatomic aspects and operation details. The lower pole UPJO associated with incomplete duplex systems were identified in 6 patients on the left side and 1 on the right side. Median patient age at surgery was 11 months (range 6-84 months). Prenatal hydronephrosis was detected in 4 patients, and 3 had intermittent abdominal pain. Hydronephrosis, thin parenchyma and presence of UPJO in lower moiety could be shown on computed tomography urogram (CTU). The ureters were fused in a "Y" shape without any dilation. Based on the length between UPJO to the confluence in retrograde ureteropyelography, patients were classified into group 1 (5 cases,≤3 cm) and group 2 (2 cases, >3 cm). In group 1, surgical procedure involved end-to-side pyeloureterostomy of the lower pelvis to the ureteral confluence in 4 cases and laparoscopic pyeloureterostomy in one case. The two patients in group 2 underwent laparoscopic pyeloplasty of lower moiety. In all of these patients hydronephrosis gradually improved and no complications were detected during follow-up. UPJO in a duplex kidney requires careful evaluation and treatment should be individualized. Ureteropyeloanastomosis is a feasible treatment for duplex kidneys associated to a functioning lower moiety with UPJO. With the technical improvements in laparoscopic pyeloplasty, this procedure can be performed using laparoscopy. Copyright © 2016 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Effect of structure variation of the aptamer-DNA duplex probe on the performance of displacement-based electrochemical aptamer sensors.

PubMed

Pang, Jie; Zhang, Ziping; Jin, Haizhu

2016-03-15

Electrochemical aptamer-based (E-AB) sensors employing electrode-immobilized, redox-tagged aptamer probes have emerged as a promising platform for the sensitive and quick detection of target analytes ranging from small molecules to proteins. Signal generation in this class of sensor is linked to change in electron transfer efficiency upon binding-induced change in flexibility/conformation of the aptamer probe. Because of this signaling mechanism, signal gains of these sensors can be improved by employing a displacement-based recognition system, which links target binding with a large-scale flexibility/conformation shift from the aptamer-DNA duplex to the single-stranded DNA or the native aptamer. Despite the relatively large number of displacement-based E-AB sensor samples, little attention has been paid to the structure variation of the aptamer-DNA duplex probe. Here we detail the effects of complementary length and position of the aptamer-DNA duplex probe on the performance of a model displacement-based E-AB sensor for ATP. We find that, greater background suppression and signal gain are observed with longer complementary length of the aptamer-DNA duplex probe. However, sensor equilibration time slows monotonically with increasing complementary length; and with too many target binding sites in aptamer sequence being occupied by the complementary DNA, the aptamer-target binding does not occur and no signal gain observed. We also demonstrate that signal gain of the displacement-based E-AB sensor is strongly dependent on the complementary position of the aptamer-DNA duplex probe, with complementary position located at the electrode-attached or redox-tagged end of the duplex probe, larger background suppression and signal increase than that of the middle position are observed. These results highlight the importance of rational structure design of the aptamer-DNA duplex probe and provide new insights into the optimization of displacement-based E-AB sensors. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of one novel multiple-target plasmid for duplex quantitative PCR analysis of roundup ready soybean.

PubMed

Zhang, Haibo; Yang, Litao; Guo, Jinchao; Li, Xiang; Jiang, Lingxi; Zhang, Dabing

2008-07-23

To enforce the labeling regulations of genetically modified organisms (GMOs), the application of reference molecules as calibrators is becoming essential for practical quantification of GMOs. However, the reported reference molecules with tandem marker multiple targets have been proved not suitable for duplex PCR analysis. In this study, we developed one unique plasmid molecule based on one pMD-18T vector with three exogenous target DNA fragments of Roundup Ready soybean GTS 40-3-2 (RRS), that is, CaMV35S, NOS, and RRS event fragments, plus one fragment of soybean endogenous Lectin gene. This Lectin gene fragment was separated from the three exogenous target DNA fragments of RRS by inserting one 2.6 kb DNA fragment with no relatedness to RRS detection targets in this resultant plasmid. Then, we proved that this design allows the quantification of RRS using the three duplex real-time PCR assays targeting CaMV35S, NOS, and RRS events employing this reference molecule as the calibrator. In these duplex PCR assays, the limits of detection (LOD) and quantification (LOQ) were 10 and 50 copies, respectively. For the quantitative analysis of practical RRS samples, the results of accuracy and precision were similar to those of simplex PCR assays, for instance, the quantitative results were at the 1% level, the mean bias of the simplex and duplex PCR were 4.0% and 4.6%, respectively, and the statistic analysis ( t-test) showed that the quantitative data from duplex and simplex PCR had no significant discrepancy for each soybean sample. Obviously, duplex PCR analysis has the advantages of saving the costs of PCR reaction and reducing the experimental errors in simplex PCR testing. The strategy reported in the present study will be helpful for the development of new reference molecules suitable for duplex PCR quantitative assays of GMOs.

Effects of Polymer Conjugation on Hybridization Thermodynamics of Oligonucleic Acids.

PubMed

Ghobadi, Ahmadreza F; Jayaraman, Arthi

2016-09-15

In this work, we perform coarse-grained (CG) and atomistic simulations to study the effects of polymer conjugation on hybridization/melting thermodynamics of oligonucleic acids (ONAs). We present coarse-grained Langevin molecular dynamics simulations (CG-NVT) to assess the effects of the polymer flexibility, length, and architecture on hybridization/melting of ONAs with different ONA duplex sequences, backbone chemistry, and duplex concentration. In these CG-NVT simulations, we use our recently developed CG model of ONAs in implicit solvent, and treat the conjugated polymer as a CG chain with purely repulsive Weeks-Chandler-Andersen interactions with all other species in the system. We find that 8-100-mer linear polymer conjugation destabilizes 8-mer ONA duplexes with weaker Watson-Crick hydrogen bonding (WC H-bonding) interactions at low duplex concentrations, while the same polymer conjugation has an insignificant impact on 8-mer ONA duplexes with stronger WC H-bonding. To ensure the configurational space is sampled properly in the CG-NVT simulations, we also perform CG well-tempered metadynamics simulations (CG-NVT-MetaD) and analyze the free energy landscape of ONA hybridization for a select few systems. We demonstrate that CG-NVT-MetaD simulation results are consistent with the CG-NVT simulations for the studied systems. To examine the limitations of coarse-graining in capturing ONA-polymer interactions, we perform atomistic parallel tempering metadynamics simulations at well-tempered ensemble (AA-MetaD) for a 4-mer DNA in explicit water with and without conjugation to 8-mer poly(ethylene glycol) (PEG). AA-MetaD simulations also show that, for a short DNA duplex at T = 300 K, a condition where the DNA duplex is unstable, conjugation with PEG further destabilizes DNA duplex. We conclude with a comparison of results from these three different types of simulations and discuss their limitations and strengths.

Mechanisms and regulation of DNA replication initiation in eukaryotes

PubMed Central

Parker, Matthew W.; Botchan, Michael R.; Berger, James M.

2017-01-01

Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a given cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the Origin Recognition Complex (ORC), and subsequent activation of the helicase by incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here we review the molecular mechanisms that underpin eukaryotic DNA replication initiation – from selecting replication start sites to replicative helicase loading and activation – and describe how these events are often distinctly regulated across different eukaryotic model organisms. PMID:28094588

Mechanisms and regulation of DNA replication initiation in eukaryotes.

PubMed

Parker, Matthew W; Botchan, Michael R; Berger, James M

2017-04-01

Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.

The use of ultrasound for postoperative monitoring of cerebral bypass grafts: A technical report.

PubMed

Morton, Ryan P; Abecassis, Isaac Joshua; Moore, Anne E; Kelly, Cory M; Levitt, Michael R; Kim, Louis J; Sekhar, Laligam N

2017-06-01

Duplex ultrasound and transcranial Doppler are valuable tools for post-operative monitoring of extracranial-intracranial cerebral bypass grafts. Here we describe our technique for the evaluation of both high-flow and low-flow cerebral bypass grafts over a nine year period. 186 bypass grafts were studied daily during the inpatient period between Jan 2005 and Dec 2014 after surgery for various cerebrovascular pathologies. There was a technical success rate of 97%. Duplex ultrasonographic flow measurements had excellent interobserver reliability with an intraclass correlation coefficient (ICC) of 0.89 (p=0.009). Technical nuances are highlighted and a brief discussion of pathology is undertaken. Copyright © 2017 Elsevier Ltd. All rights reserved.

Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes.

PubMed

Zhu, Lizhe; Jiang, Hanlun; Sheong, Fu Kit; Cui, Xuefeng; Wang, Yanli; Gao, Xin; Huang, Xuhui

2017-09-01

At the core of RNA interference, the Argonaute proteins (Ago) load and utilize small guide nucleic acids to silence mRNAs or cleave foreign nucleic acids in a sequence specific manner. In recent years, based on extensive structural studies of Ago and its interaction with the nucleic acids, considerable progress has been made to reveal the dynamic aspects of various Ago-mediated processes. Here we review these novel insights into the guide-strand loading, duplex unwinding, and effects of seed mismatch, with a focus on two representative Agos, the human Ago 2 (hAgo2) and the bacterial Thermus thermophilus Ago (TtAgo). In particular, comprehensive molecular simulation studies revealed that although sharing similar overall structures, the two Agos have vastly different conformational landscapes and guide-strand loading mechanisms because of the distinct rigidity of their L1-PAZ hinge. Given the central role of the PAZ motions in regulating the exposure of the nucleic acid binding channel, these findings exemplify the importance of protein motions in distinguishing the overlapping, yet distinct, mechanisms of Ago-mediated processes in different organisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: Comparison of single base mismatches and base bulges

PubMed Central

Naiser, Thomas; Ehler, Oliver; Kayser, Jona; Mai, Timo; Michel, Wolfgang; Ott, Albrecht

2008-01-01

Background The high binding specificity of short 10 to 30 mer oligonucleotide probes enables single base mismatch (MM) discrimination and thus provides the basis for genotyping and resequencing microarray applications. Recent experiments indicate that the underlying principles governing DNA microarray hybridization – and in particular MM discrimination – are not completely understood. Microarrays usually address complex mixtures of DNA targets. In order to reduce the level of complexity and to study the problem of surface-based hybridization with point defects in more detail, we performed array based hybridization experiments in well controlled and simple situations. Results We performed microarray hybridization experiments with short 16 to 40 mer target and probe lengths (in situations without competitive hybridization) in order to systematically investigate the impact of point-mutations – varying defect type and position – on the oligonucleotide duplex binding affinity. The influence of single base bulges and single base MMs depends predominantly on position – it is largest in the middle of the strand. The position-dependent influence of base bulges is very similar to that of single base MMs, however certain bulges give rise to an unexpectedly high binding affinity. Besides the defect (MM or bulge) type, which is the second contribution in importance to hybridization affinity, there is also a sequence dependence, which extends beyond the defect next-neighbor and which is difficult to quantify. Direct comparison between binding affinities of DNA/DNA and RNA/DNA duplexes shows, that RNA/DNA purine-purine MMs are more discriminating than corresponding DNA/DNA MMs. In DNA/DNA MM discrimination the affected base pair (C·G vs. A·T) is the pertinent parameter. We attribute these differences to the different structures of the duplexes (A vs. B form). Conclusion We have shown that DNA microarrays can resolve even subtle changes in hybridization affinity for simple target mixtures. We have further shown that the impact of point defects on oligonucleotide stability can be broken down to a hierarchy of effects. In order to explain our observations we propose DNA molecular dynamics – in form of zipping of the oligonucleotide duplex – to play an important role. PMID:18477387

Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion

PubMed Central

Cai, Yuqin; Kropachev, Konstantin; Xu, Rong; Tang, Yijin; Kolbanovskii, Marina; Kolbanovskii, Alexander; Amin, Shantu; Patel, Dinshaw J.; Broyde, Suse; Geacintov, Nicholas E.

2010-01-01

Summary The effects of non-nearest base sequences, beyond the nucleotides flanking a DNA lesion on either side, on nucleotide excision repair (NER) in extracts from human cells were investigated. We constructed two duplexes containing the same minor groove-aligned 10S (+)-trans-anti-B[a]P-N2-dG (G*) DNA adduct, derived from the environmental carcinogen benzo[a]pyrene (B[a]P): 5′-C-C-A-T-C-G*-C-T-A-C-C-3′ (CG*C-I), and 5′-C-A-C3-A4-C5-G*-C-A-C-A-C-3′ (CG*C-II). We utilized gel electrophoresis to compare the extent of DNA bending, and molecular dynamics (MD) simulations to analyze the structural characteristics of these two DNA duplexes. The NER efficiencies are 1.6 ± 0.2 times greater in the case of the CG*C-II than the CG*C-I sequence context in 135-mer duplexes. Gel electrophoresis and self-ligation circularization experiments revealed that the CG*C-II duplex is more bent than the CG*C-I duplex, while MD simulations showed that the unique -C3-A4-C5- segment in the CG*C-II duplex plays a key role. The presence of a minor groove-positioned guanine amino group, namely, the Watson-Crick partner to C3, acts as a wedge; facilitated by a highly deformable local -C3-A4- base step, this amino group allows the B[a]P ring system to produce a more enlarged minor groove in CG*C-II than in CG*C-I, as well as a local untwisting and enlarged and flexible Roll only in the CG*C-II sequence. These structural properties fit well with our prior findings that in the case of the family of minor groove 10S (+)-trans-anti-B[a]P-N2-dG lesions, flexible bends and enlarged minor groove widths (Cai et al. (2009) J. Mol. Biol., 385: 30–44) constitute NER recognition signals, and extend our understanding of sequence context effects on NER to the neighbors that are distant to the lesion. PMID:20399214

Explicit ions/implicit water generalized Born model for nucleic acids

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

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model, and utilizes a non-standard approach to defining the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes – disconnected dielectric boundary around the solute-ion or ion-ion pairs. Fully analytical description of all energymore » components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force (PMF) for Na+-Cl− ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of DNA duplex; these differences in the counterion binding patters were shown earlier to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native Thymine bases are used to explore the physics behind CoHex-Thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-Thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range, and may be important to consider in the context of methylation effects on DNA condensation.« less

Explicit ions/implicit water generalized Born model for nucleic acids

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

2018-05-01

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

The Origins of Microtexture in Duplex Ti Alloys (Preprint)

DTIC Science & Technology

2008-06-01

To) June 2008 Journal Article Preprint 4 . TITLE AND SUBTITLE THE ORIGINS OF MICROTEXTURE IN DUPLEX Ti ALLOYS (PREPRINT) 5a. CONTRACT NUMBER In...house 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 62102F 6 . AUTHOR(S) M.G. Glavic (UES, Inc.) B.B. Bartha (United Technologies Corporation...applicable to duplex alpha/beta titanium microstructures. The crystallographic coherency of the primary and secondary alpha phase with the prior beta

Approximation methods for the stability analysis of complete synchronization on duplex networks

NASA Astrophysics Data System (ADS)

Han, Wenchen; Yang, Junzhong

2018-01-01

Recently, the synchronization on multi-layer networks has drawn a lot of attention. In this work, we study the stability of the complete synchronization on duplex networks. We investigate effects of coupling function on the complete synchronization on duplex networks. We propose two approximation methods to deal with the stability of the complete synchronization on duplex networks. In the first method, we introduce a modified master stability function and, in the second method, we only take into consideration the contributions of a few most unstable transverse modes to the stability of the complete synchronization. We find that both methods work well for predicting the stability of the complete synchronization for small networks. For large networks, the second method still works pretty well.

Features of residual stresses in duplex stainless steel butt welds

NASA Astrophysics Data System (ADS)

Um, Tae-Hwan; Lee, Chin-Hyung; Chang, Kyong-Ho; Nguyen Van Do, Vuong

2018-04-01

Duplex stainless steel finds increasing use as an alternative to austenitic stainless steel, particularly where chloride or sulphide stress corrosion cracking is of primary concern, due to the excellent combination of strength and corrosion resistance. During welding, duplex stainless steel does not create the same magnitude or distribution of weld-induced residual stresses as those in welded austenitic stainless steel due to the different physical and mechanical properties between them. In this work, an experimental study on the residual stresses in butt-welded duplex stainless steel is performed utilizing the layering technique to investigate the characteristics of residual stresses in the weldment. Three-dimensional thermos-mechanical-metallurgical finite element analysis is also performed to confirm the residual stress measurements.

High frequency of hepatitis E virus infection in swine from South Brazil and close similarity to human HEV isolates.

PubMed

Passos-Castilho, Ana Maria; Granato, Celso Francisco Hernandes

Hepatitis E virus is responsible for acute and chronic liver infections worldwide. Swine hepatitis E virus has been isolated in Brazil, and a probable zoonotic transmission has been described, although data are still scarce. The aim of this study was to investigate the frequency of hepatitis E virus infection in pigs from a small-scale farm in the rural area of Paraná State, South Brazil. Fecal samples were collected from 170 pigs and screened for hepatitis E virus RNA using a duplex real-time RT-PCR targeting a highly conserved 70nt long sequence within overlapping parts of ORF2 and ORF3 as well as a 113nt sequence of ORF2. Positive samples with high viral loads were subjected to direct sequencing and phylogenetic analysis. hepatitis E virus RNA was detected in 34 (20.0%) of the 170 pigs following positive results in at least one set of screening real-time RT-PCR primers and probes. The swine hepatitis E virus strains clustered with the genotype hepatitis E virus-3b reference sequences in the phylogenetic analysis and showed close similarity to human hepatitis E virus isolates previously reported in Brazil. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Reducing duplex examinations in patients with iatrogenic pseudoaneurysms.

PubMed

Stone, Patrick A; Aburahma, Ali F; Flaherty, Sarah K

2006-06-01

Ultrasound-guided thrombin injection has become the initial treatment of choice for femoral access-related pseudoaneurysms. Patients typically undergo serial duplex examinations to assess for spontaneous resolution of small iatrogenic pseudoaneurysms (IPSAs) (<2.5 cm), or may require repeated diagnostic, therapeutic, and follow-up studies for larger IPSAs (>2.5 cm). We evaluated the impact of a revised treatment algorithm that includes primary treatment of both small (<2.5 cm) and larger pseudoaneurysms (>2.5 cm), rather than observation of smaller ones, and attempts to establish a single duplex examination via a point-of-care treatment strategy. We reviewed 105 consecutive patients treated with ultrasound-guided thrombin injection from July 2001 through September 2004. Patient, IPSAs, characteristics, and treatment methods were examined. The number of duplex examinations per patient was evaluated over the treatment interval. Also, published cost data were used to compare primary treatment of small ISPAs vs observation with serial duplex examinations. Successful thrombosis occurred in 103 (98.1%) of 105 treated pseudoaneurysms. No minor or major complications occurred after thrombin injection in either small or large ISPAs, and both failures requiring operation were in the large aneurysm group. The recurrence rate for the series was 1.9% (2/105), and both recurrences were successfully treated with an additional thrombin injection. A single injection was successful in treating 43 (97.7%) of 44 small (<2.5 cm) IPSAs, and one required a second injection. Patients had an average of 3.3 duplex examinations in our first year of treatment experience, which declined to 1.5 by our third year with the institution of a point-of-care service model for all pseudoaneurysms. Based on this decreased use of duplex examination and an average treatment cohort of 35 IPSA patients per year our institution, we determined this results in a reduction of 35 hours of laboratory time and nearly 70 ultrasounds per year. Similarly for small pseudoaneurysms, a point-of-service primary treatment program rather than observation results in an estimated cost savings of $12,000, based on treating 15 small IPSAs per year. Ultrasound-guided thrombin injection is safe and effective for the treatment of nearly all iatrogenic pseudoaneurysms. We recommend primary treatment of small pseudoaneurysms by ultrasound-guided thrombin injection rather than observation with serial duplex scans. A point-of-care treatment algorithm can result in cost savings by reducing the number of necessary duplex examinations.

Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae).

PubMed

McManus, Hilary A; Sanchez, Daniel J; Karol, Kenneth G

2017-01-01

Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex . Genomic DNA from Hydrodictyon reticulatum and Pediastrum duplex was subjected to Illumina paired-end sequencing and the complete plastomes were assembled for each. Plastome size and gene content were characterized and compared with other plastomes from the Sphaeropleales. Homology searches using BLASTX were used to characterize introns and open reading frames (orfs) ≥ 300 bp. A phylogenetic analysis of gene order across the Sphaeropleales was performed. The plastome of Hydrodictyon reticulatum is 225,641 bp and Pediastrum duplex is 232,554 bp. The plastome structure and gene order of H. reticulatum and P. duplex are more similar to each other than to other members of the Sphaeropleales. Numerous unique open reading frames are found in both plastomes and the plastome of P. duplex contains putative viral protein genes, not found in other Sphaeropleales plastomes. Gene order analyses support the monophyly of the Hydrodictyaceae and their sister relationship to the Neochloridaceae. The complete plastomes of Hydrodictyon reticulatum and Pediastrum duplex , representing the largest of the Sphaeropleales sequenced thus far, once again highlight the variability in size, architecture, gene order and content across the Chlorophyceae. Novel intron insertion sites and unique orfs indicate recent, independent invasions into each plastome, a hypothesis testable with an expanded plastome investigation within the Hydrodictyaceae.

A two-dimensional 1H-NMR study of the dam methylase site: comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence. The sequence dependence of methylation upon base-pair lifetimes.

PubMed

Fazakerley, G V; Quignard, E; Teoule, R; Guy, A; Guschlbauer, W

1987-09-15

We report two-dimensional NOE (NOESY) spectra on the sequence d(GCGATCATGG).d(CCATGATCGC) which contains the unmethylated dam site. As expected the DNA adopts a B-form conformation but appears to be distorted at the TG step of the second strand. This distorsion, probably bending, is not seen on the opposite strand. When the first strand is methylated on adenine in the GATC or CATG sequence the NOESY spectra indicate little or no change in the conformation. However the single strand-duplex exchange is slowed down to the slow-exchange region on a proton NMR time scale. We have assigned the exchangeable imino and cytidine amino resonances of the three duplexes. From the imino linewidths as a function of temperature, we observe that the unmethylated and the hemimethylated Gm6ATC duplexes melt normally from the ends. However, this is not so for the hemimethylated Cm6ATG duplex which, apart from the terminal base pairs, melts cooperatively and at higher temperature. In spectra recorded in H2O a second duplex is observed, for the Gm6ATC sequence, which we have not been able to identify. It is however unlikely to be a hairpin structure. Ultraviolet-melting curves also indicate the presence of two transitions for this duplex. The effect of methylation upon base-pair lifetimes has been studied by comparing the above three duplexes. Little effect is observed upon methylation in the GATC sequence but a drastic increase in the lifetimes of all base pairs is observed upon methylation in the CATG sequence.

Sequence specificity of mutagen-nucleic acid complexes in solution: intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes.

PubMed

Patel, D J; Canuel, L L

1977-07-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex.

Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

PubMed Central

Patel, Dinshaw J.; Canuel, Lita L.

1977-01-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex. PMID:268613

Synthesis of 2',4'-propylene-bridged (carba-ENA) thymidine and its analogues: the engineering of electrostatic and steric effects at the bottom of the minor groove for nuclease and thermodynamic stabilities and elicitation of RNase H.

PubMed

Liu, Yi; Xu, Jianfeng; Karimiahmadabadi, Mansoureh; Zhou, Chuanzheng; Chattopadhyaya, Jyoti

2010-11-05

2',4'-Propylene-bridged thymidine (carba-ENA-T) and five 8'-Me/NH(2)/OH modified carba-ENA-T analogues have been prepared through intramolecular radical addition to C═N of the tethered oxime-ether. These carba-ENA nucleosides have been subsequently incorporated into 15mer oligodeoxynucleotides (AON), and their affinity toward cDNA and RNA, nuclease resistance, and RNase H recruitment capability have been investigated in comparison with those of the native and ENA counterparts. These carba-ENAs modified AONs are highly RNA-selective since all of them led to slight thermal stabilization effect for the AON:RNA duplex, but quite large destabilization effect for the AON:DNA duplex. It was found that different C8' substituents (at the bottom of the minor groove) on carba-ENA-T only led to rather small variation of thermal stability of the AON:RNA duplexes. We, however, observed that the parent carba-ENA-T modified AONs exhibited higher nucleolytic stability than those of the ENA-T modified counterparts. The nucleolytic stability of carba-ENA-T modified AONs can be further modulated by C8' substituent to variable extents depending on not only the chemical nature but also the stereochemical orientation of the C8' substituents: Thus, (1) 8'S-Me on carba-ENA increases the nucleolytic stability but 8'R-Me leads to a decreased effect; (2) 8'R-OH on carba-ENA had little, if any, effect on nuclease resistance but 8'S-OH resulted in significantly decreased nucleolytic stability; and (3) 8'-NH(2) substituted carba-ENA leads to obvious loss in the nuclease resistance. The RNA strand in all of the carba-ENA derivatives modified AON:RNA hybrid duplexes can be digested by RNase H1 with high efficiency, even at twice the rate of those of the native and ENA modified counterpart.

Recent Developments in Assessing Microstructure-Sensitive Early Stage Fatigue of Polycrystals (Postprint)

DTIC Science & Technology

2014-04-01

can strongly affect formation of fatigue cracks. El Bartali et al. [7] quantified plastic strain at the grain scale in a duplex stainless steel and mea... Fatigue Fract Eng Mater Struct 2013. [7] El Bartali A, Aubin V, Degallaix S. Fatigue damage analysis in a duplex stainless steel by digital image...S. Surface observation and measurement techniques to study the fatigue damage micromechanisms in a duplex stainless steel . Int J Fatigue 2009;31:2049

Surgical retroperitoneoscopic and transperitoneoscopic access in varicocelectomy: duplex scan results in pediatric population.

PubMed

Mancini, Stefano; Bulotta, Anna Lavinia; Molinaro, Francesco; Ferrara, Francesco; Tommasino, Giulio; Messina, Mario

2014-12-01

This is a retrospective study to compare duplex scan results of laparoscopic Palomo's technique through retroperitoneal and transperitoneal approach for varicocelectomy in children. We statistically analyzed recurrence, testicular volume growth and complications. Surgical intervention was performed utilizing transperitoneoscopic (group A) or retroperitoneoscopic access (group B). Duplex scan control was performed after 12 months (T1), after 2 years (T2) and the last one at 18 years old in most patients. Statistical analysis was performed using the t-test for parametric data. Differences in proportions were evaluated using χ2 or Fisher's exact test. We treated 120 children (age range 10-17 years) who presented an asymptomatic IV grade of reflux, Coolsaet 1, associated with a left testicular hypotrophy in 36.6% of the cases (44 patients). No post-operative complications were verified. Duplex scan exam showed an increase of left testicular growth in both groups, with complete hypotrophy disappear in patients in both groups after 24 months. Hydrocele, diagnosed clinically and confirmed with duplex scan, was the most frequent post-operative complication (22/120 cases; 18.3%). This study showed the importance of duplex scan at all steps of this vascular pathology in children, and that there is no significantly difference in results between the two surgical techniques except for hydrocele in transperitoneoscopic access. Copyright © 2014 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

Comparison of the severity of lower extremity arterial disease in smokers and patients with diabetes using a novel duplex Doppler scoring system.

PubMed

Hiremath, Rudresh; Gowda, Goutham; Ibrahim, Jebin; Reddy, Harish T; Chodiboina, Haritha; Shah, Rushit

2017-07-01

The aim of this study was to validate the diagnostic feasibility of a novel scoring system of peripheral arterial disease (PAD) in smokers and patients with diabetes depending on duplex Doppler sonographic features. Patients presenting with the symptomatology of PAD were divided into three groups: diabetes only, smoking only, and smokers with diabetes. The patients were clinically examined, a clinical severity score was obtained, and the subjects were categorized into the three extrapolated categories of mild, moderate, and severe. All 106 subjects also underwent a thorough duplex Doppler examination, and various aspects of PAD were assessed and tabulated. These components were used to create a novel duplex Doppler scoring system. Depending on the scores obtained, each individual was categorized as having mild, moderate, or severe illness. The Cohen kappa value was used to assess interobserver agreement between the two scoring systems. Interobserver agreement between the traditional Rutherford clinical scoring system and the newly invented duplex Doppler scoring system showed a kappa value of 0.83, indicating significant agreement between the two scoring systems (P<0.001). Duplex Doppler imaging is an effective screening investigation for lower extremity arterial disease, as it not only helps in its diagnosis, but also in the staging and grading of the disease, providing information that can be utilized for future management and treatment planning.

Validation of a novel venous duplex ultrasound objective structured assessment of technical skills for the assessment of venous reflux.

PubMed

Jaffer, Usman; Normahani, Pasha; Lackenby, Kimberly; Aslam, Mohammed; Standfield, Nigel J

2015-01-01

Duplex ultrasound measurement of reflux time is central to the diagnosis of venous incompetence. We have developed an assessment tool for Duplex measurement of venous reflux for both simulator and patient-based training. A novel assessment tool, Venous Duplex Ultrasound Assessment of Technical Skills (V-DUOSATS), was developed. A modified DUOSATS was used for simulator training. Participants of varying skill level were invited to viewed an instructional video and were allowed ample time to familiarize with the Duplex equipment. Attempts made by the participants were recorded and independently assessed by 3 expert assessors and 5 novice assessors using the modified V-DUOSATS. "Global" assessment was also done by expert assessors on a 4-point Likert scale. Content, construct, and concurrent validities as well as reliability were evaluated. Content and construct validity as well as reliability were demonstrated. Receiver operator characteristic analysis-established cut points of 19/22 and 21/30 were most appropriate for simulator and patient-based assessment, respectively. We have validated a novel assessment tool for Duplex venous reflux measurement. Further work is required to establish transference validity of simulator training to improve skill in scanning patients. We have developed and validated V-DUOSATS for simulator training. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Transvaginal duplex ultrasonography appears to be the gold standard investigation for the haemodynamic evaluation of pelvic venous reflux in the ovarian and internal iliac veins in women.

PubMed

Whiteley, M S; Dos Santos, S J; Harrison, C C; Holdstock, J M; Lopez, A J

2015-12-01

To assess the suitability of transvaginal duplex ultrasonography to identify pathological reflux in the ovarian and internal iliac veins in women. A retrospective study of patients treated in 2011 and 2012 was performed in a specialised vein clinic. Diagnostic transvaginal duplex ultrasonography in women presenting with symptoms or signs of pelvic vein reflux were compared with the outcomes of treatment from pelvic vein embolisation. A repeat transvaginal duplex ultrasonography was performed 6 weeks later by a blinded observer and any residual reflux was identified. Results from 100 sequential patients were analysed. Mean age 44.2 years (32-69) with mode average parity of 3 (0-5 deliveries). Pre-treatment, 289/400 veins were refluxing (ovarian - 29 right, 81 left; internal iliac - 93 right, 86 left). Coil embolisation was successful in 86/100 patients and failed partially in 14/100 - 5 due to failure to cannulate the target vein. One false-positive diagnosis was made. Currently there is no accepted gold standard for pelvic vein incompetence. Comparing transvaginal duplex ultrasonography with the outcome from selectively treating the veins identified as having pathological reflux with coil embolisation, there were no false-negative diagnoses and only one false-positive. This study suggests that transvaginal duplex ultrasonography could be the gold standard in assessing pelvic vein reflux. © The Author(s) 2014.

The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide

PubMed Central

Jolley, Elizabeth A.

2017-01-01

Abstract Non-standard nucleotides are ubiquitous in RNA. Thermodynamic studies with RNA duplexes containing non-standard nucleotides, whether incorporated naturally or chemically, can provide insight into the stability of Watson–Crick pairs and the role of specific functional groups in stabilizing a Watson–Crick pair. For example, an A-U, inosine•U and pseudouridine•A pair each form two hydrogen bonds. However, an RNA duplex containing a central I•U pair or central Ψ•A pair is 2.4 kcal/mol less stable or 1.7 kcal/mol more stable, respectively, than the corresponding duplex containing an A-U pair. In the non-standard nucleotide purine, hydrogen replaces the exocyclic amino group of A. This replacement results in a P•U pair containing only one hydrogen bond. Optical melting studies were performed with RNA duplexes containing P•U pairs adjacent to different nearest neighbors. The resulting thermodynamic parameters were compared to RNA duplexes containing A-U pairs in order to determine the contribution of the hydrogen bond involving the exocyclic amino group. Results indicate a loss of 1.78 kcal/mol, on average, when an internal P•U replaces A-U in an RNA duplex. This value is compared to the thermodynamics of a hydrogen bond determined by similar methods. Nearest neighbor parameters were derived for use in free energy and secondary structure prediction software. PMID:28180321

High-efficient full-duplex WDM-RoF system with sub-central station

NASA Astrophysics Data System (ADS)

Liu, Anliang; Yin, Hongxi; Wu, Bin

2018-05-01

With an additional sub-central station (S-CS), a high-efficient full-duplex radio-over-fiber (RoF) system compatible with the wavelength-division-multiplexing technology is proposed and experimentally demonstrated in this paper. To improve the dispersion tolerance of the RoF system, the baseband data format for the downlink and an all-optical down-conversion approach for the uplink are employed. In addition, this RoF system can not only make full use of the fiber link resources but also realize the upstream transmission without any local light sources at remote base stations (BSs). A 10-GHz RoF experimental system with a 1.25-Gb/s rate bidirectional transmission is established based on the S-CS structure. The feasibility and reliability of this RoF system are verified through eye diagrams and bit error rate (BER) curves experimentally obtained.

Yb-fibre Laser Welding of 6 mm Duplex Stainless Steel 2205

NASA Astrophysics Data System (ADS)

Bolut, M.; Kong, C. Y.; Blackburn, J.; Cashell, K. A.; Hobson, P. R.

Duplex stainless steel (DSS) is one of the materials of choice for structural and nuclear applications, having high strength and good corrosion resistance when compared with other grades of stainless steel. The welding process used to join these materials is critical as transformation of the microstructure during welding directly affects the material properties. High power laser welding has recently seen an increase in research interest as it offers both speed and flexibility. This paper presents an investigation into the important parameters affecting laser welding of DSS grade 2205, with particular focus given to the critical issue of phase transformation during welding. Bead-on-plate melt-run trials without filler material were performed on 6mm thick plates using a 5 kW Yb-fibre laser. The laser beam was characterized and a Design of Experiment approach was used to quantify the impact of the process parameters. Optical metallographic methods were used to examine the resulting microstructures.

Impact deformation behavior of duplex and superaustenitic stainless steels welds by split Hopkinson pressure bar

NASA Astrophysics Data System (ADS)

Wang, Shing-Hoa; Huang, Chih-Sheng; Lee, Woei-Shyan; Chen, Tao-Hsing; Wu, Chia-Chang; Lien, Charles; Tsai, Hung-Yin

2009-12-01

A considerable volume of γ phase increases in the fusion zone (weld metal) for two duplex stainless steels after a high-strain-rate impact. The strain-induced γ phase formation in the fusion zone results in local hardness variation depending on the strain rate. The α phase content in the fusion zone decreases as the impact strain rate increases for SAF 2205 DSS and SAF 2507 DSS. The results of the two-phase content measured by Ferritoscope correspond to that assessed by image analyses. In contrast, superaustenite stainless steel is unaffected by such an impact owing to its fully stable austenization. Impacted welds at a high strain rate of 5 × 103 s-1 reveal feather-like surface creases along the solidified curved columnar grain boundaries. The apparent surface creases are formed due to the presence of diffuse Lüders bands, which are caused by heavy plastic deformation in coarse-grain materials.

Toehold-Mediated Displacement of an Adenosine-Binding Aptamer from a DNA Duplex by its Ligand.

PubMed

Monserud, Jon H; Macri, Katherine M; Schwartz, Daniel K

2016-10-24

DNA is increasingly used to engineer dynamic nanoscale circuits, structures, and motors, many of which rely on DNA strand-displacement reactions. The use of functional DNA sequences (e.g., aptamers, which bind to a wide range of ligands) in these reactions would potentially confer responsiveness on such devices, and integrate DNA computation with highly varied molecular stimuli. By using high-throughput single-molecule FRET methods, we compared the kinetics of a putative aptamer-ligand and aptamer-complement strand-displacement reaction. We found that the ligands actively disrupted the DNA duplex in the presence of a DNA toehold in a similar manner to complementary DNA, with kinetic details specific to the aptamer structure, thus suggesting that the DNA strand-displacement concept can be extended to functional DNA-ligand systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and validation of a duplex real-time PCR assay for the simultaneous detection of three mustard species (Sinapis alba, Brassica nigra and Brassica juncea) in food.

PubMed

Palle-Reisch, Monika; Cichna-Markl, Margit; Hochegger, Rupert

2014-06-15

The paper presents a duplex real-time PCR assay for the simultaneous detection of three potentially allergenic mustard species commonly used in food: white mustard (Sinapis alba), black mustard (Brassica nigra) and brown mustard (Brassica juncea). White mustard is detected in the "green" and black/brown mustard in the "yellow" channel. The duplex real-time PCR assay does not show cross-reactivity with other Brassicaceae species including broccoli, cauliflower, radish and rapeseed. Low cross-reactivities (difference in the Ct value ⩾ 11.91 compared with the positive control) were obtained with cumin, fenugreek, ginger, rye and turmeric. When applying 500 ng DNA per PCR tube, the duplex real-time PCR assay allowed the detection of white, black and brown mustard in brewed model sausages down to a concentration of 5mg/kg in 10 out of 10 replicates. The duplex real-time PCR assay was applied to verify correct labelling of commercial foodstuffs. Copyright © 2013 Elsevier Ltd. All rights reserved.

Duplex investigations in children: Are clinical signs in children with venous disorders relevant?

PubMed

Birgitte Maessen-Visch, M; Smeets, L; van Vleuten, C

2015-12-01

Ultra sound colored duplex sonography is the preferred method in diagnosing chronic venous disease. Data in children on incidence, indications, and results are lacking. From the total of 9180 duplex investigations performed in our hospital from 2009 to 2012, data on indication and results of the investigation as well as patient characteristics were evaluated retrospectively for the proportion of pediatric patients. Duplex investigations were performed 49 times in 38 children (6-18 years), with an average of 1.3 times (1-6 times) per child. Forty percent showed abnormalities: 17 times deep venous thrombosis was suspected; deep venous thrombosis was objectified in 18%. In the 21 investigations performed for varicosis-related complaints, varicose veins or venous malformations were objectified in 57%. Edema was never a symptom of chronic venous disease. Duplex investigation is not often performed in children. In children with established deep venous thrombosis, a family history with deep venous thrombosis is common. In general, edema was not seen in children with varicose veins and, therefore, does not seem a reliable clinical sign at young age. © The Author(s) 2014.

Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs.

PubMed

Kondo, Jiro; Yamada, Tom; Hirose, Chika; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2014-02-24

The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

NDI and DAN DNA: nucleic acid-directed assembly of NDI and DAN.

PubMed

Ikkanda, Brian A; Samuel, Stevan A; Iverson, Brent L

2014-03-07

Two novel DNA base surrogate phosphoramidites 1 and 2, based upon relatively electron-rich 1,5-dialkoxynaphthalene (DAN) and relatively electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI), respectively, were designed, synthesized, and incorporated into DNA oligonucleotide strands. The DAN and NDI artificial DNA bases were inserted within a three-base-pair region within the interior of a 12-mer oligonucleotide duplex in various sequential arrangements and investigated with CD spectroscopy and UV melting curve analysis. The CD spectra of the modified duplexes indicated B-form DNA topology. Melting curve analyses revealed trends in DNA duplex stability that correlate with the known association of DAN and NDI moieties in aqueous solution as well as the known favorable interactions between NDI and natural DNA base pairs. This demonstrates that DNA duplex stability and specificity can be driven by the electrostatic complementarity between DAN and NDI. In the most favorable case, an NDI-DAN-NDI arrangement in the middle of the DNA duplex was found to be approximately as stabilizing as three A-T base pairs.

Development of internally controlled duplex real-time NASBA diagnostics assays for the detection of microorganisms associated with bacterial meningitis.

PubMed

Clancy, Eoin; Coughlan, Helena; Higgins, Owen; Boo, Teck Wee; Cormican, Martin; Barrett, Louise; Smith, Terry J; Reddington, Kate; Barry, Thomas

2016-08-01

Three duplex molecular beacon based real-time Nucleic Acid Sequence Based Amplification (NASBA) assays have been designed and experimentally validated targeting RNA transcripts for the detection and identification of Haemophilus influenzae, Neisseria meningitidis and Streptococcus pneumoniae respectively. Each real-time NASBA diagnostics assay includes an endogenous non-competitive Internal Amplification Control (IAC) to amplify the splice variant 1 mRNA of the Homo sapiens TBP gene from human total RNA. All three duplex real-time NASBA diagnostics assays were determined to be 100% specific for the target species tested for. Also the Limits of Detection (LODs) for the H. influenzae, N. meningitidis and S. pneumoniae duplex real-time NASBA assays were 55.36, 0.99, and 57.24 Cell Equivalents (CE) respectively. These robust duplex real-time NASBA diagnostics assays have the potential to be used in a clinical setting for the rapid (<60min) specific detection and identification of the most prominent microorganisms associated with bacterial meningitis in humans. Copyright © 2016 Elsevier B.V. All rights reserved.

Mapping the miRNA interactome by crosslinking ligation and sequencing of hybrids (CLASH)

PubMed Central

Helwak, Aleksandra; Tollervey, David

2014-01-01

RNA-RNA interactions play critical roles in many cellular processes but studying them is difficult and laborious. Here, we describe an experimental procedure, termed crosslinking ligation and sequencing of hybrids (CLASH), which allows high-throughput identification of sites of RNA-RNA interaction. During CLASH, a tagged bait protein is UV crosslinked in vivo to stabilise RNA interactions and purified under denaturing conditions. RNAs associated with the bait protein are partially truncated, and the ends of RNA-duplexes are ligated together. Following linker addition, cDNA library preparation and high-throughput sequencing, the ligated duplexes give rise to chimeric cDNAs, which unambiguously identify RNA-RNA interaction sites independent of bioinformatic predictions. This protocol is optimized for studying miRNA targets bound by Argonaute proteins, but should be easily adapted for other RNA-binding proteins and classes of RNA. The protocol requires around 5 days to complete, excluding the time required for high-throughput sequencing and bioinformatic analyses. PMID:24577361

Duplex System with Ectopic Ureter Opens into the Posterior Urethra: Case Report.

PubMed

Milicevic, Snjezana; Bijelic, Radojka; Krivokuca, Vladimir; Jakovljevic, Branislava

2018-04-01

Duplicated ureter or Duplex Collecting System is a congenital condition in which the ureteric bud, the embryological origin of the ureter, arises twice, resulting in two ureters draining a single kidney. This congenital anomaly is rare, and even rarer when the duplex system with ectopic ureter is present. This type of congenital anomaly is even more rarely diagnosed and surgically treated in adulthood. This case report presents a case of a 32-year-old male, who had a duplex collecting system with two ureters on the left side. Ectopic ureter, draining the upper pole of the left kidney, opened into the posterior urethra. In our patient, taking into account the clinical perspective, the renal tissue damaging of the upper pole which was not functional, partial nephrectomy and ureterectomy was successfully performed.

Direct Determination of the Equilibrium Unbinding Potential Profile for a Short DNA Duplex from Force Spectroscopy Data

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

Noy, A

2004-05-04

Modern force microscopy techniques allow researchers to use mechanical forces to probe interactions between biomolecules. However, such measurements often happen in non-equilibrium regime, which precludes straightforward extraction of the equilibrium energy information. Here we use the work averaging method based on Jarzynski equality to reconstruct the equilibrium interaction potential from the unbinding of a complementary 14-mer DNA duplex from the results of non-equilibrium single-molecule measurements. The reconstructed potential reproduces most of the features of the DNA stretching transition, previously observed only in equilibrium stretching of long DNA sequences. We also compare the reconstructed potential with the thermodynamic parameters of DNAmore » duplex unbinding and show that the reconstruction accurately predicts duplex melting enthalpy.« less

2'-modified nucleosides for site-specific labeling of oligonucleotides

NASA Technical Reports Server (NTRS)

Krider, Elizabeth S.; Miller, Jeremiah E.; Meade, Thomas J.

2002-01-01

We report the synthesis of 2'-modified nucleosides designed specifically for incorporating labels into oligonucleotides. Conversion of these nucleosides to phosphoramidite and solid support-bound derivatives proceeds in good yield. Large-scale synthesis of 11-mer oligonucleotides possessing the 2'-modified nucleosides is achieved using these derivatives. Thermal denaturation studies indicate that the presence of 2'-modified nucleosides in 11-mer duplexes has minimal destabilizing effects on the duplex structure when the nucleosides are placed at the duplex termini. The powerful combination of phosphoramidite and support-bound derivatives of 2'-modified nucleosides affords the large-scale preparation of an entirely new class of oligonucleotides. The ability to synthesize oligonucleotides containing label attachment sites at 3', intervening, and 5' locations of a duplex is a significant advance in the development of oligonucleotide conjugates.

RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

PubMed

NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

2016-12-27

Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

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.

Considerations for Isochronous Data Services over the Proximity-1 Space Link

NASA Technical Reports Server (NTRS)

Gao, Jay L.

2006-01-01

Future mission concepts for robotic and human explorations will involve a high level of real time control/monitoring operations such as tele-operation for spacecraft rendezvous and surface mobile platforms carrying life-support equipments. The timely dissemination of voice, command, and real-time telemetry for monitoring and coordination purposes is critical for mission success. It is envisioned that future missions will require a network infrastructure capable of supporting isochronous data services. The CCSDS Proximity-1 Space Link Protocol1 could be used to provide isochronous service over the surface-to-Earth relay as well as "beyond-the-horizon" communications between distant Lunar or Mars surface elements. This paper will analyze the latency, jitter, and throughput performance of the Proximity-1 protocol for isochronous applications. In particular we will focus on constrained scenarios where the protocol operates in full-duplex mode, carrying isochronous traffic in one direction and error-controlled traffic in the other direction. We analyze the impact of the strict priority scheme in Proximity-1 on delay jitter and the impact of the isochronous traffic on the efficiency of the reliable data transfer in the other direction, and discuss methods for performance optimization. In general, jitter performance is driving by relative loading of isochronous traffic on the forward link compared to the acknowledgement traffic. Under light loading condition, the upper-bound of the delay jitter is the transmission duration of an acknowledgement frame on the forward link; for higher loading scenarios, the maximum jitter is scaled up by the inverse of the residual bandwidth, i.e., the spare capacity available in the forward link to carry isochronous traffic.

Distributed Topology Organization and Transmission Scheduling in Wireless Ad Hoc Networks

DTIC Science & Technology

2004-01-01

slot consists of two mini -slots that support that support full-duplex transfer–one for master-to-slave transmission and the other from slave-to-master...protocol storage requirement would only be 208 bits in this case. 111 Communication requirements Each half-duplex mini -slot can be used by either a data or...either a data or control packet, eq. (4.2) sets the minimum half-duplex mini -slot size in the system or equivalently, the maximum system period

Normalized cDNA libraries

DOEpatents

Soares, Marcelo B.; Efstratiadis, Argiris

1997-01-01

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

Normalized cDNA libraries

DOEpatents

Soares, M.B.; Efstratiadis, A.

1997-06-10

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3{prime} noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

A Synchronous Digital Duplexing Technique for OFDMA-Based Indoor Communications

NASA Astrophysics Data System (ADS)

Park, Chang-Hwan; Ko, Yo-Han; Kim, Yeong-Jun; Park, Kyung-Won; Jeon, Won-Gi; Paik, Jong-Ho; Lee, Seok-Pil; Cho, Yong-Soo

In this paper, we propose a new digital duplexing scheme, called synchronous digital duplexing (SDD), which can increase data efficiency and flexibility of resource by transmitting uplink signal and downlink signal simultaneously in wireless communication. In order to transmit uplink and downlink signals simultaneously, the proposed SDD obtains mutual information among subscriber stations (SSs) with a mutual ranging symbol. This information is used for selection of transmission time, decision on cyclic suffix (CS) insertion, determination of CS length, and re-establishment of FFT starting point.

Measuring secondary phases in duplex stainless steels

NASA Astrophysics Data System (ADS)

Calliari, I.; Brunelli, K.; Dabalà, M.; Ramous, E.

2009-01-01

The use of duplex stainless steels is limited by their susceptibility to the formation of dangerous intermetallic phases resulting in detrimental effects on impact toughness and corrosion resistance. This precipitation and the quantitative determinations of the phases have received considerable attention and different precipitation sequences (σ phase, χ phase, and carbides) have been suggested. This study investigates the phase transformation during continuous cooling and isothermal treatments in commercial duplex stainless steel grades and the effects on alloy properties, and compares the most common techniques of analysis.

Effect of caffeine on superior mesenteric artery blood flow velocities in preterm neonates.

PubMed

Abdel Wahed, Mohamed A; Issa, Hanan M; Khafagy, Soha M; Abdel Raouf, Shaimaa M

2017-09-22

To investigate the effect of caffeine infusion on superior mesenteric artery (SMA) blood flow velocities (BFV) in preterm infants. Prospective observational study on 38 preterm neonates 28-33 +6 weeks gestation, who developed apnea on their first day of life, and caffeine citrate infusion was initiated at a loading dose of 20 mg/kg, followed by a maintenance dose of 5-10 mg/kg/day. Duplex ultrasound measurements of SMA BFV were recorded: peak systolic velocity (PSV), end diastolic velocity (EDV) and resistive index (RI), at 15 min before, 1-, 2- and 6-h after caffeine loading dose, and 2 h after two maintenance doses. There was a significant reduction in PSV 1-h (p = .008), a significant decrease in EDV 1- and 2-h (p = .000 and p = .005, respectively) and a significant increase in RI 1- and 2-h (p = .003 and p = .005, respectively) following caffeine loading dose, as compared to values before caffeine infusion. No significant effect of caffeine maintenance doses on SMA BFV was observed (p > .05). Blood flow in SMA is significantly reduced after caffeine citrate infusion at a loading dose of 20 mg/kg. This effect continues for at least 2 h. Meanwhile, SMA BFV seems not affected by maintenance doses.

Sex determination in goat by amplification of the HMG box using duplex PCR.

PubMed

Shi, Lei; Yue, Wenbin; Ren, Youshe; Lei, Fulin; Zhao, Junxing

2008-05-01

The objective of this study was to obtain a fast, accurate and reliable method of determining the sex of goat embryos prior to implantation through amplification of the high-motility-group (HMG) box of the sex-determining region of the Y chromosome (SRY) gene of the goats. Goat specific primers were designed for duplex polymerase chain reaction (PCR). As an internal control gene, the goat beta-action gene sequence was simultaneously amplified together with the HMG box of goat SRY gene. Males showed both 1 SRY band and 1 beta-action band, but only 1 beta-action band was present in the agarose gel electrophoresis of females. The result indicated that the goat HMG-box sequence motif of SRY was male specific. Afterward, the optimized PCR procedure was applied in 30 embryo biopsies and the biopsied embryos were transferred into 30 recipient female goats. The sex of the 13 kids proved anatomically corresponded to the sex determined by PCR (100% accuracy). Thus, this study showed that this duplex PCR method can be applied to sex the goat pre-implantation embryos and to manipulate the sex ratio of offspring in goat breeding programs.

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

Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri

Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the basesmore » and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.« less

77 FR 53212 - Federal Property Suitable as Facilities To Assist the Homeless

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-31

... Buildings Duplex Cabins Yosemite CA 95389 Landholding Agency: Interior Property Number: 61201230009 Status... details 33 Buildings Duplex Cabins Yosemite CA 95389 Landholding Agency: Interior Property Number...

There is no benefit to universal carotid artery duplex screening before a major cardiac surgical procedure.

PubMed

Adams, Brian C; Clark, Ross M; Paap, Christina; Goff, James M

2014-01-01

Perioperative stroke is a devastating complication after cardiac surgery. In an attempt to minimize this complication, many cardiac surgeons routinely preoperatively order carotid artery duplex scans to assess for significant carotid stenosis. We hypothesize that the routine screening of preoperative cardiac surgery patients with carotid artery duplex scans detects few patients who would benefit from carotid intervention or that a significant carotid stenosis reliably predicts stroke risk after cardiac surgery. A retrospective review identified 1,499 patients who underwent cardiac surgical procedures between July 1999 and September 2010. Data collected included patient demographics, comorbidities, history of previous stroke, preoperative carotid artery duplex scan results, location of postoperative stroke, and details of carotid endarterectomy (CEA) procedures before, in conjunction with, or after cardiac surgery. Statistical methods included univariate analysis and Fisher's exact test. Twenty-six perioperative strokes were identified (1.7%). In the 21 postoperative stroke patients for whom there is complete carotid artery duplex scan data, 3 patients had a hemodynamically significant lesion (>70%) and 1 patient underwent unilateral carotid CEA for bilateral disease. Postoperative strokes occurred in the anterior cerebral circulation (69.2%), posterior cerebral circulation (15.4%), or both (15.4%). Patient comorbidities, preoperative carotid artery duplex scan screening velocities, or types of cardiac surgical procedure were not predictive for stroke. Thirteen patients (0.86%) underwent CEA before, in conjunction with, or after cardiac surgery. Two of these patients had symptomatic disease, 1 of whom underwent CEA before and the other after his cardiac surgery. Of the 11 asymptomatic patients, 2 underwent CEA before, 3 concurrently, and 6 after cardiac surgery. Left main disease (≥50% stenosis), previous stroke, and peripheral vascular disease were found to be statistically significant predictors of carotid revascularization. A cost analysis of universal screening resulted in an estimated net cost of $378,918 during the study period. The majority of postoperative strokes after cardiac surgery are not related to extracranial carotid artery disease and they are not predicted by preoperative carotid artery duplex scan screening. Consequently, universal carotid artery duplex scan screening cannot be recommended and a selective approach should be adopted. Published by Elsevier Inc.

Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis.

PubMed

Gupta, Sharad K; Sur, Souvik; Prasad Ojha, Rajendra; Tandon, Vibha

2013-07-01

This paper describes the synthesis of a novel 8-aza-7-deazapurin-2,6-diamine (DPP)-containing peptide nucleic acid (PNA) monomer and Boc protecting group-based oligomerization of PNA, replacing adenine (A) with DPP monomers in the PNA strand. The PNA oligomers were synthesized against the biologically relevant SV40 promoter region (2494-AATTTTTTTTATTTA-2508) of pEGFP-N3 plasmid. The DPP-PNA·DNA duplex showed enhanced stability as compared to normal duplex (A-PNA·DNA). The electronic distribution of DPP monomer suggested that DPP had better electron donor properties over 2,6-diamino purine. UV melting and thermodynamic analysis revealed that the PNA oligomer containing a diaminopyrazolo(3,4-d)pyrimidine moiety (DPP) stabilized the PNA·DNA hybrids compared to A-PNA·DNA. DPP-PNA·DNA duplex showed higher water activity (Δnw = 38.5) in comparison to A-PNA·DNA duplex (Δnw = 14.5). The 50 ns molecular dynamics simulations of PNA·DNA duplex containing DPP or unmodified nucleobase-A showed average H-bond distances in the DPP-dT base pair of 2.90 Å (OH-N bond) and 2.91 Å (NH-N bond), which were comparably shorter than in the A-dT base pair, in which the average distances were 3.18 Å (OH-N bond) and 2.97 Å (NH-N bond), and there was one additional H-bond in the DPP-dT base pair of around 2.98 Å (O2H-N2 bond), supporting the higher stability of DPP-PNA·DNA. The analysis of molecular dynamics simulation data showed that the system binding free energy increased at a rate of approximately -4.5 kcal mol(-1) per DPP base of the PNA·DNA duplex. In summary, increased thermal stability, stronger hydrogen bonding and more stable conformation in the DPP-PNA·DNA duplex make it a better candidate as antisense/antigene therapeutic agents.

Very-High-Frequency Aerosat Airborne Terminal

DOT National Transportation Integrated Search

1977-12-01

This report summarizes the result of a study aimed at defining the airborne VHF terminal for the experimental AEROSAT program. The system consists of a 22-channel VHF transceiver for full-duplex operation. Provisions are made for voice, data, and sur...

NASA's K/Ka-Band Broadband Aeronautical Terminal for Duplex Satellite Video Communications

NASA Technical Reports Server (NTRS)

Densmore, A.; Agan, M.

1994-01-01

JPL has recently begun the development of a Broadband Aeronautical Terminal (BAT) for duplex video satellite communications on commercial or business class aircraft. The BAT is designed for use with NASA's K/Ka-band Advanced Communications Technology Satellite (ACTS). The BAT system will provide the systems and technology groundwork for an eventual commercial K/Ka-band aeronautical satellite communication system. With industry/government partnerships, three main goals will be addressed by the BAT task: 1) develop, characterize and demonstrate the performance of an ACTS based high data rate aeronautical communications system; 2) assess the performance of current video compression algorithms in an aeronautical satellite communication link; and 3) characterize the propagation effects of the K/Ka-band channel for aeronautical communications.

Fail-Safe Operation of a High-Temperature Magnetic Bearing Investigated for Gas Turbine Engine Applications

NASA Technical Reports Server (NTRS)

Choi, Benjamin B.; Montague, Gerald T.

2002-01-01

The Structural Mechanics and Dynamics Branch at the NASA Glenn Research Center has developed a three-axis high-temperature magnetic bearing suspension rig to enhance the safety of the bearing system up to 1000 F. This test rig can accommodate thrust and radial bearings up to a 22.84 cm (9 in.) diameter with a maximum axial loading of 22.25 kN (5000 lb) and a maximum radial loading up to 4.45 kN (1000 lb). The test facility was set up to test magnetic bearings under high-temperature (1100 F) and high-speed (20,000 rpm) conditions. The magnetic bearing is located at the center of gravity of the rotor between two high-temperature grease-packed mechanical ball bearings. The drive-end duplex angular contact ball bearing, which is in full contact, acts as a moment release and provides axial stability. The outboard end ball bearing has a 0.015-in. radial clearance between the rotor to act as a backup bearing and to compensate for axial thermal expansion. There is a 0.020-in. radial air gap between the stator pole and the rotor. The stator was wrapped with three 1-kW band heaters to create a localized hot section; the mechanical ball bearings were outside this section. Eight threaded rods supported the stator. These incorporated a plunger and Bellville washers to compensate for radial thermal expansion and provide rotor-to-stator alignment. The stator was instrumented with thermocouples and a current sensor for each coil. Eight air-cooled position sensors were mounted outside the hot section to monitor the rotor. Another sensor monitored this rotation of the outboard backup bearing. Ground fault circuit interrupts were incorporated into all power amplifier loops for personnel safety. All instrumentation was monitored and recorded on a LabView-based data acquisition system. Currently, this 12-pole heteropolar magnetic bearing has 13 thermal cycles and over 26 hr of operation at 1000 F.

Novel 1.5 GPa-strength with 50%-ductility by transformation-induced plasticity of non-recrystallized austenite in duplex steels.

PubMed

Sohn, Seok Su; Song, Hyejin; Jo, Min Chul; Song, Taejin; Kim, Hyoung Seop; Lee, Sunghak

2017-04-28

Needs for steel designs of ultra-high strength and excellent ductility have been an important issue in worldwide automotive industries to achieve energy conservation, improvement of safety, and crashworthiness qualities. Because of various drawbacks in existing 1.5-GPa-grade steels, new development of formable cold-rolled ultra-high-strength steels is essentially needed. Here we show a plausible method to achieve ultra-high strengths of 1.0~1.5 GPa together with excellent ductility above 50% by actively utilizing non-recrystallization region and TRansformation-Induced Plasticity (TRIP) mechanism in a cold-rolled and annealed Fe-Mn-Al-C-based steel. We adopt a duplex microstructure composed of austenite and ultra-fine ferrite in order to overcome low-yield-strength characteristics of austenite. Persistent elongation up to 50% as well as ultra-high yield strength over 1.4 GPa are attributed to well-balanced mechanical stability of non-crystallized austenite with critical strain for TRIP. Our results demonstrate how the non-recrystallized austenite can be a metamorphosis in 1.5-GPa-grade steel sheet design.

Aptamer-loaded Gold Nanoconstructs for Targeted Cancer Therapy

NASA Astrophysics Data System (ADS)

Dam, Duncan Hieu Minh

Traditional cancer treatments, including chemotherapy, often cause severe side effects in patients. Targeted therapy where tumor cells are targeted via biomarkers overexpressed on the cell surface has been shown to reduce such adverse effects. Monoclonal antibodies (mAbs) are currently the most common chemotherapeutic agents that bind with high affinity to these cancer markers. However, poor intratumoral uptake of mAb and release of drugs from mAb carriers have been the biggest challenge for this delivery method. As a result, recent work has focused on other strategies to improve the efficacy of drug delivery in targeted therapy. Among potential carriers for drug delivery, gold nanoparticles (AuNPs) have emerged as one of the most promising vehicles. This thesis describes the development of a drug delivery nanoconstruct that can both target cancer cells and induce therapeutic effects. The nanoconstructs are composed of gold nanostars (AuNS) as delivery vehicles loaded with the DNA aptamer AS1411 that can target the ubiquitous shuttle protein nucleolin (NCL) in various cancer cell types. The gold nanocarrier stabilizes the oligonucleotides for intracellular delivery and promotes high loading densities of the oligonucleotide drugs. We have investigated the interactions of the nanoconstruct with different subcellular compartments of the cancer cells. This physical phenomenon has shown to correlate with the biological activities such as apoptosis and cell death that happen in the cancer cells after incubation with the nanoconstructs. A thorough screening of the nanoconstructs in 13 different cancer cell lines is conducted to narrow down the potential targets for in vivo study. Before testing the in vivo efficacy, we evaluate the toxicity of the nanoconstructs in non-tumor animals, which confirms its safety for further in vivo applications. The accumulation of the nanoconstructs in two different cancerous tumors, however, suggests that further optimization of the design is required. Thus, we introduced an improved nanoconstruct with higher loading of AS1411 on the surface of AuNS. The significant enhancement in the loading of the Apt increases the cellular uptake as well as the in vitro efficacy of the nanoconstruct in both fibrosarcoma and pancreatic cancer cells. To further optimize the design of the nanoconstruct, we create a conjugation method in which the loading of AS1411 can be effectively controlled at various pH conditions. This method can potentially be applied for any DNA or RNA; however, the stability of oligonucleotides is unknown as a function of pH. Therefore, we also evaluate how pH conditions can affect the loading densities and structural integrity of a range of different oligonucleotides (single stranded DNA, hairpin DNA, duplexes, quadruplexes) on AuNS. The ultimate goal of this process is to identify a set of design principles to optimize oligonucleotide loading based on the local chemical environment around the nanoparticle.

Rapid method to detect duplex formation in sequencing by hybridization methods

DOEpatents

Mirzabekov, Andrei Darievich; Timofeev, Edward Nikolaevich; Florentiev, Vladimer Leonidovich; Kirillov, Eugene Vladislavovich

1999-01-01

A method for determining the existence of duplexes of oligonucleotide complementary molecules is provided whereby a plurality of immobilized oligonucleotide molecules, each of a specific length and each having a specific base sequence, is contacted with complementary, single stranded oligonucleotide molecules to form a duplex so as to facilitate intercalation of a fluorescent dye between the base planes of the duplex. The invention also provides for a method for constructing oligonucleotide matrices comprising confining light sensitive fluid to a surface, exposing said light-sensitive fluid to a light pattern so as to cause the fluid exposed to the light to coalesce into discrete units and adhere to the surface; and contacting each of the units with a set of different oligonucleotide molecules so as to allow the molecules to disperse into the units.

Development of a One-Step Duplex RT-PCR Method for the Simultaneous Detection of VP3/VP1 and VP1/P2B Regions of the Hepatitis A Virus.

PubMed

Kim, Mi-Ju; Lee, Shin-Young; Kim, Hyun-Joong; Lee, Jeong Su; Joo, In Sun; Kwak, Hyo Sun; Kim, Hae-Yeong

2016-08-28

The simultaneous detection and accurate identification of hepatitis A virus (HAV) is critical in food safety and epidemiological studies to prevent the spread of HAV outbreaks. Towards this goal, a one-step duplex reverse-transcription (RT)-PCR method was developed targeting the VP1/P2B and VP3/VP1 regions of the HAV genome for the qualitative detection of HAV. An HAV RT-qPCR standard curve was produced for the quantification of HAV RNA. The detection limit of the duplex RT-PCR method was 2.8 × 10(1) copies of HAV. The PCR products enabled HAV genotyping analysis through DNA sequencing, which can be applied for epidemiological investigations. The ability of this duplex RT-PCR method to detect HAV was evaluated with HAV-spiked samples of fresh lettuce, frozen strawberries, and oysters. The limit of detection of the one-step duplex RT-PCR for each food model was 9.4 × 10(2) copies/20 g fresh lettuce, 9.7 × 10(3) copies/20 g frozen strawberries, and 4.1 × 10(3) copies/1.5 g oysters. Use of a one-step duplex RT-PCR method has advantages such as shorter time, decreased cost, and decreased labor owing to the single amplification reaction instead of four amplifications necessary for nested RT-PCR.

Structural model of the p14/SF3b155 · branch duplex complex.

PubMed

Schellenberg, Matthew J; Dul, Erin L; MacMillan, Andrew M

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14 · bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein-RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14 · duplex interaction must be disrupted before the first step of splicing.

Structural model of the p14/SF3b155·branch duplex complex

PubMed Central

Schellenberg, Matthew J.; Dul, Erin L.; MacMillan, Andrew M.

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14•bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein–RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14•duplex interaction must be disrupted before the first step of splicing. PMID:21062891

High strength, high ductility low carbon steel

DOEpatents

Koo, Jayoung; Thomas, Gareth

1978-01-01

A high strength, high ductility low carbon steel consisting essentially of iron, 0.05-0.15 wt% carbon, and 1-3 wt% silicon. Minor amounts of other constituents may be present. The steel is characterized by a duplex ferrite-martensite microstructure in a fibrous morphology. The microstructure is developed by heat treatment consisting of initial austenitizing treatment followed by annealing in the (.alpha. + .gamma.) range with intermediate quenching.

Podiatry Ankle Duplex Scan: Readily Learned and Accurate in Diabetes.

PubMed

Normahani, Pasha; Powezka, Katarzyna; Aslam, Mohammed; Standfield, Nigel J; Jaffer, Usman

2018-03-01

We aimed to train podiatrists to perform a focused duplex ultrasound scan (DUS) of the tibial vessels at the ankle in diabetic patients; podiatry ankle (PodAnk) duplex scan. Thirteen podiatrists underwent an intensive 3-hour long simulation training session. Participants were then assessed performing bilateral PodAnk duplex scans of 3 diabetic patients with peripheral arterial disease. Participants were assessed using the duplex ultrasound objective structured assessment of technical skills (DUOSATS) tool and an "Imaging Score". A total of 156 vessel assessments were performed. All patients had abnormal waveforms with a loss of triphasic flow. Loss of triphasic flow was accurately detected in 145 (92.9%) vessels; the correct waveform was identified in 139 (89.1%) cases. Participants achieved excellent DUOSATS scores (median 24 [interquartile range: 23-25], max attainable score of 26) as well as "Imaging Scores" (8 [8-8], max attainable score of 8) indicating proficiency in technical skills. The mean time taken for each bilateral ankle assessment was 20.4 minutes (standard deviation ±6.7). We have demonstrated that a focused DUS for the purpose of vascular assessment of the diabetic foot is readily learned using intensive simulation training.

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

Triple helical DNA in a duplex context and base pair opening

PubMed Central

Esguerra, Mauricio; Nilsson, Lennart; Villa, Alessandra

2014-01-01

It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region. PMID:25228466

Follow-up of renal and mesenteric artery revascularization with duplex ultrasonography

PubMed Central

Taylor, David C.; Houston, Gordon T.M.; Anderson, Caroline; Jameson, Margot; Popatia, Shelley

1996-01-01

Objective To evaluate the long-term anatomic results of renal revascularization procedures using duplex ultrasonography. Design A case series. Setting A university-affiliated hospital. Patients Twenty-five patients who had undergone renal percutaneous transluminal angioplasty (PTA) (18 arteries), renal bypass (10 arteries) and mesenteric bypass (6 arteries). The mean follow-up was 22 months (range from 3 to 48 months) for those who underwent renal PTA, 23 months (range from 1.5 to 70 months) for those who underwent renal bypass and 34 months (range from 8 to 144 months) for those who underwent mesenteric bypass. Main Outcome Measures Patency rates for the three procedures as assessed by duplex ultrasonography. Results Duplex ultrasonography demonstrated patency without stenosis after renal and mesenteric artery revascularization in 14 arteries subjected to renal PTA, 9 arteries subjected to renal bypass and 6 arteries subjected to mesenteric bypass. Three arteries that had renal PTA had recurrent vessel stenosis and one had occlusion. One artery that had renal bypass showed occlusion. Conclusions Renal PTA, renal bypass and mesenteric bypass are durable procedures at 2 years of follow-up, and duplex ultrasonography is a valuable method for assessing the patency of arteries after renal and mesenteric revascularization. PMID:8599785

Effects of Hypoxanthine Substitution in Peptide Nucleic Acids Targeting KRAS2 Oncogenic mRNA Molecules: Theory and Experiment

PubMed Central

Sanders, Jeffrey M.; Wampole, Matthew E.; Chen, Chang-Po; Sethi, Dalip; Singh, Amrita; Dupradeau, François-Yves; Wang, Fan; Gray, Brian D.; Thakur, Mathew L.; Wickstrom, Eric

2013-01-01

Genetic disorders can arise from single base substitutions in a single gene. A single base substitution for wild type guanine in the twelfth codon of KRAS2 mRNA occurs frequently to initiate lung, pancreatic, and colon cancer. We have observed single base mismatch specificity in radioimaging of mutant KRAS2 mRNA in tumors in mice by in vivo hybridization with radiolabeled peptide nucleic acid (PNA) dodecamers. We hypothesized that multi-mutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick basepairs with adenine, cytosine, thymine, and uracil. Using molecular dynamics simulations and free energy calculations, we show that hypoxanthine substitutions in PNAs are tolerated in KRAS2 RNA-PNA duplexes where wild type guanine is replaced by mutant uracil or adenine in RNA. To validate our predictions, we synthesized PNA dodecamers with hypoxanthine, and then measured the thermal stability of RNA-PNA duplexes. Circular dichroism thermal melting results showed that hypoxanthine-containing PNAs are more stable in duplexes where hypoxanthine-adenine and hypoxanthine-uracil base pairs are formed than single mismatch duplexes or duplexes containing hypoxanthine-guanine opposition. PMID:23972113

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

47 CFR 80.701 - Scope of service.

Code of Federal Regulations, 2010 CFR

2010-10-01

... the paired duplex channels listed in subpart H of this part. Alaska-private fixed stations may operate... fixed stations or with ship stations, and on duplex frequencies listed in subpart H of this part when...

Full-duplex optical communication system

NASA Technical Reports Server (NTRS)

Shay, Thomas M. (Inventor); Hazzard, David A. (Inventor); Horan, Stephen (Inventor); Payne, Jason A. (Inventor)

2004-01-01

A method of full-duplex electromagnetic communication wherein a pair of data modulation formats are selected for the forward and return data links respectively such that the forward data electro-magnetic beam serves as a carrier for the return data. A method of encoding optical information is used wherein right-hand and left-hand circular polarizations are assigned to optical information to represent binary states. An application for an earth to low earth orbit optical communications system is presented which implements the full-duplex communication and circular polarization keying modulation format.

Method for construction of normalized cDNA libraries

DOEpatents

Soares, Marcelo B.; Efstratiadis, Argiris

1996-01-01

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

Method for construction of normalized cDNA libraries

DOEpatents

Soares, M.B.; Efstratiadis, A.

1996-01-09

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form. The method comprises: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

Surface modification of 17-4PH stainless steel by DC plasma nitriding and titanium nitride film duplex treatment

NASA Astrophysics Data System (ADS)

Qi, F.; Leng, Y. X.; Huang, N.; Bai, B.; Zhang, P. Ch.

2007-04-01

17-4PH stainless steel was modified by direct current (DC) plasma nitriding and titanium nitride film duplex treatment in this study. The microstructure, wear resistance and corrosion resistance were characterized by X-ray diffraction (XRD), pin-on-disk tribological test and polarization experiment. The results revealed that the DC plasma nitriding pretreatment was in favor of improving properties of titanium nitride film. The corrosion resistance and wear resistance of duplex treatment specimen was more superior to that of only coated titanium nitride film.

Evaluation of two singleplex reverse transcription-Insulated isothermal PCR tests and a duplex real-time RT-PCR test for the detection of porcine epidemic diarrhea virus and porcine deltacoronavirus.

PubMed

Zhang, Jianqiang; Tsai, Yun-Long; Lee, Pei-Yu Alison; Chen, Qi; Zhang, Yan; Chiang, Cheng-Jen; Shen, Yu-Han; Li, Fu-Chun; Chang, Hsiao-Fen Grace; Gauger, Phillip C; Harmon, Karen M; Wang, Hwa-Tang Thomas

2016-08-01

Recent outbreaks of porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) in multiple countries have caused significant economic losses and remain a serious challenge to the swine industry. Rapid diagnosis is critical for the implementation of efficient control strategies before and during PEDV and PDCoV outbreaks. Insulated isothermal PCR (iiPCR) on the portable POCKIT™ device is user friendly for on-site pathogen detection. In the present study, a singleplex PEDV RT-iiPCR, a singleplex PDCoV RT-iiPCR, and a duplex PEDV/PDCoV real-time RT-PCR (rRT-PCR) commercial reagents targeting the M gene were compared to an N gene-based PEDV rRT-PCR and an M gene-based PDCoV rRT-PCR that were previously published and used as reference PCRs. All PCR assays were highly specific and did not cross react with other porcine enteric pathogens. Analytical sensitivities of the PEDV RT-iiPCR, PDCoV RT-iiPCR and duplex PEDV/PDCoV rRT-PCR were determined using in vitro transcribed RNA as well as viral RNA extracted from ten-fold serial dilutions of PEDV and PDCoV cell culture isolates. Performance of each PCR assay was further evaluated using 170 clinical samples (86 fecal swabs, 24 feces, 19 intestines, and 41 oral fluids). Compared to the reference PEDV rRT-PCR, the sensitivity, specificity and accuracy of the PEDV RT-iiPCR were 97.73%, 98.78%, and 98.24%, respectively, and those of the duplex PEDV/PDCoV rRT-PCR were 98.86%, 96.34%, and 97.65%, respectively. Compared to the reference PDCoV rRT-PCR, the sensitivity, specificity and accuracy of the PDCoV RT-iiPCR were 100%, 100%, and 100%, respectively, and those of the PEDV/PDCoV duplex rRT-PCR were 96.34%, 100%, and 98.24%, respectively. Overall, all three new PCR assays were comparable to the reference rRT-PCRs for detection of PEDV and/or PDCoV. The PEDV and PDCoV RT-iiPCRs are potentially useful tools for on-site detection and the duplex PEDV/PDCoV rRT-PCR provides a convenient method to simultaneously detect the two viruses and differentiate PEDV from PDCoV. Copyright © 2016 Elsevier B.V. All rights reserved.

Pitting and stress corrosion cracking of stainless steel

NASA Astrophysics Data System (ADS)

Saithala, Janardhan R.

An investigation has been performed to determine the pitting resistance of stainless steels and stress corrosion cracking of super duplex stainless steels in water containing chloride ions from 25 - 170°C. The steels studied are 12% Cr, FV520B, FV566, 304L, Uranus65, 2205, Ferallium Alloy 255, and Zeron 100. All these commercial materials used in very significant industrial applications and suffer from pitting and stress corrosion failures. The design of a new experimental setup using an autoclave enabled potentiodynamic polarisation experiments and slow strain rate tests in dilute environments to be conducted at elevated temperatures. The corrosion potentials were controlled using a three electrode cell with computer controlled potentiostat.The experimental programme to determine pitting potentials was designed to simulate the service conditions experienced in most industrial plants and develop mathematical model equations to help a design engineer in material selection decision. Stress corrosion resistance of recently developed Zeron100 was evaluated in dilute environments to propose a mechanism in chloride solutions at high' temperatures useful for the nuclear and power generation industry. Results have shown the significance of the composition of alloying elements across a wide range of stainless steels and its influence on pitting. Nitrogen and molybdenum added to modern duplex stainless steels was found to be unstable at higher temperatures. The fractographic results obtained using the scanning electron microscope (SEM) has given insight in the initiation of pitting in modem duplex and super duplex stainless steels. A mathematical model has been proposed to predict pitting in stainless steels based on the effect of environmental factors (temperature, chloride concentration, and chemical composition). An attempt has been made to identify the mechanism of SCC in Zeron100 super duplex stainless steel.The proposed empirical models have shown good correlation between predicted pitting potential values with experimental results. It has been shown that the SCC mechanism in Zeron100 supports the slip assisted anodic dissolution model of SCC. The relationship between pitting and stress corrosion in dilute environments is established and empirical equations have been proposed to determine the damage region for wide range of stainless steels.

Analytical Validation of Quantitative Real-Time PCR Methods for Quantification of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients

PubMed Central

Ramírez, Juan Carlos; Cura, Carolina Inés; Moreira, Otacilio da Cruz; Lages-Silva, Eliane; Juiz, Natalia; Velázquez, Elsa; Ramírez, Juan David; Alberti, Anahí; Pavia, Paula; Flores-Chávez, María Delmans; Muñoz-Calderón, Arturo; Pérez-Morales, Deyanira; Santalla, José; Guedes, Paulo Marcos da Matta; Peneau, Julie; Marcet, Paula; Padilla, Carlos; Cruz-Robles, David; Valencia, Edward; Crisante, Gladys Elena; Greif, Gonzalo; Zulantay, Inés; Costales, Jaime Alfredo; Alvarez-Martínez, Miriam; Martínez, Norma Edith; Villarroel, Rodrigo; Villarroel, Sandro; Sánchez, Zunilda; Bisio, Margarita; Parrado, Rudy; Galvão, Lúcia Maria da Cunha; da Câmara, Antonia Cláudia Jácome; Espinoza, Bertha; de Noya, Belkisyole Alarcón; Puerta, Concepción; Riarte, Adelina; Diosque, Patricio; Sosa-Estani, Sergio; Guhl, Felipe; Ribeiro, Isabela; Aznar, Christine; Britto, Constança; Yadón, Zaida Estela; Schijman, Alejandro G.

2015-01-01

An international study was performed by 26 experienced PCR laboratories from 14 countries to assess the performance of duplex quantitative real-time PCR (qPCR) strategies on the basis of TaqMan probes for detection and quantification of parasitic loads in peripheral blood samples from Chagas disease patients. Two methods were studied: Satellite DNA (SatDNA) qPCR and kinetoplastid DNA (kDNA) qPCR. Both methods included an internal amplification control. Reportable range, analytical sensitivity, limits of detection and quantification, and precision were estimated according to international guidelines. In addition, inclusivity and exclusivity were estimated with DNA from stocks representing the different Trypanosoma cruzi discrete typing units and Trypanosoma rangeli and Leishmania spp. Both methods were challenged against 156 blood samples provided by the participant laboratories, including samples from acute and chronic patients with varied clinical findings, infected by oral route or vectorial transmission. kDNA qPCR showed better analytical sensitivity than SatDNA qPCR with limits of detection of 0.23 and 0.70 parasite equivalents/mL, respectively. Analyses of clinical samples revealed a high concordance in terms of sensitivity and parasitic loads determined by both SatDNA and kDNA qPCRs. This effort is a major step toward international validation of qPCR methods for the quantification of T. cruzi DNA in human blood samples, aiming to provide an accurate surrogate biomarker for diagnosis and treatment monitoring for patients with Chagas disease. PMID:26320872

Postcategorical auditory distraction in short-term memory: Insights from increased task load and task type.

PubMed

Marsh, John E; Yang, Jingqi; Qualter, Pamela; Richardson, Cassandra; Perham, Nick; Vachon, François; Hughes, Robert W

2018-06-01

Task-irrelevant speech impairs short-term serial recall appreciably. On the interference-by-process account, the processing of physical (i.e., precategorical) changes in speech yields order cues that conflict with the serial-ordering process deployed to perform the serial recall task. In this view, the postcategorical properties (e.g., phonology, meaning) of speech play no role. The present study reassessed the implications of recent demonstrations of auditory postcategorical distraction in serial recall that have been taken as support for an alternative, attentional-diversion, account of the irrelevant speech effect. Focusing on the disruptive effect of emotionally valent compared with neutral words on serial recall, we show that the distracter-valence effect is eliminated under conditions-high task-encoding load-thought to shield against attentional diversion whereas the general effect of speech (neutral words compared with quiet) remains unaffected (Experiment 1). Furthermore, the distracter-valence effect generalizes to a task that does not require the processing of serial order-the missing-item task-whereas the effect of speech per se is attenuated in this task (Experiment 2). We conclude that postcategorical auditory distraction phenomena in serial short-term memory (STM) are incidental: they are observable in such a setting but, unlike the acoustically driven irrelevant speech effect, are not integral to it. As such, the findings support a duplex-mechanism account over a unitary view of auditory distraction. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Detection of common carotid artery stenosis using duplex ultrasonography: a validation study with computed tomographic angiography.

PubMed

Slovut, David P; Romero, Javier M; Hannon, Kathleen M; Dick, James; Jaff, Michael R

2010-01-01

Severe stenosis of the common carotid artery (CCA), while uncommon, is associated with increased risk of transient ischemic attack and stroke. To date, no validated duplex ultrasound criteria have been established for grading the severity of CCA stenosis. The goal of this study was to use receiver-operating curve (ROC) analysis with computed tomographic angiography as the reference standard to establish duplex ultrasound criteria for diagnosing >or=50% CCA stenosis. The study cohort included 64 patients (42 men, 22 women) with a mean age of 65 +/- 12 years (range, 16-89 years) who had CCA peak systolic velocity (PSV) >or=150 cm/sec and underwent computed tomographic angiography (CTA) of the cervical and intracerebral vessels within 1 month of the duplex examination. One study was excluded because the CTA was technically inadequate, whereas another was excluded because the patient underwent bilateral CCA stenting. The CCA ipsilateral to any of the following was excluded from the analysis: innominate artery occlusion (n = 1), previous stenting of the ICA or CCA (n = 7), carotid endarterectomy (n = 1), or carotid-to-carotid bypass (n = 1). Thus, the data set included 62 patients and 115 vessels. Bland-Altman analysis was used to examine the agreement between two measures of luminal reduction measured by CTA: percent diameter stenosis and percent area stenosis. Receiver operating characteristic (ROC) analysis was used to determine optimal PSV and EDV thresholds for diagnosing >or=50% CCA stenosis. Severity of CCA stenosis was <50% in 76 vessels, 50%-59% in eight, 60%-69% in eight, 70%-79% in nine, 80%-89% in three, 90%-99% in five, and occluded in six. Duplex ultrasonography identified six of six (100%) patients with 100% CCA occlusion by CTA. Bland-Altman analysis showed poor agreement between percent stenosis determined by vessel diameter compared with percent stenosis determined by reduction in lumen area. Therefore, subsequent analysis was performed using percent stenosis by area. ROC analysis of different PSV thresholds for detecting stenosis >or=50% showed that >182 cm/sec was the most accurate with a sensitivity of 64% and specificity of 88% (P < .0001). Sensitivity, specificity, and accuracy of carotid duplex were higher when the stenosis was located in the mid or distal aspects of the CCA (sensitivity 76%, specificity 89%, area under curve 0.84, P < .001) than in the intrathoracic and proximal segment of the artery (P = NS). ROC analysis of different EDV thresholds for detecting CCA stenosis >or=50% showed that >30 cm/sec was the most accurate with a sensitivity of 54% and a specificity of 74% (P < .0239). Duplex ultrasonography is highly sensitive, specific, and accurate for detecting CCA lesions in the mid and distal CCA. Use of peak systolic velocity may lead to improved detection of CCA disease and initiation of appropriate therapy to reduce the risk of stroke. Copyright 2010 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

Tectonic controls of transient landscapes in the Bhutan Himalaya

NASA Astrophysics Data System (ADS)

Adams, B. A.; Whipple, K. X.; Hodges, K. V.; Van Soest, M. C.; Heimsath, A. M.

2013-12-01

Previous research has identified many landscapes within the Himalaya that are not easily explained by classical critical taper models of orogenic wedges. One of the most striking examples is the sharp physiographic transition between the more subdued landforms of the Lower Himalayan ranges and the Higher Himalayan ranges to the north in Nepal. This transition has been attributed to several potential causes: changes in the rheology of rocks at depth, a ramp in the basal detachment of the orogenic wedge, a blind duplex, or a north-dipping, surface-breaking thrust fault. A similar, but more subdued transition marks the northern margin of perched, low-relief landscape patches found at ca. 3000 m in Bhutan. These low-relief surfaces, characterized by bogs and thick saprolites at the surface, overlie piggyback basins within the evolving orogenic wedge, filled with hundreds of meters of colluvial and alluvial deposits. The southern boundaries of the low-relief surfaces are less regular than the physiographic transition at their northern boundaries. The surfaces occur at similar elevations but are not continuous geographically, having been dissected by a series of river systems draining southward from the crest of the range. Pronounced knickpoints have formed at the southern margins of the low-relief surfaces. Our work suggests that there is a young (Pliocene-Pleistocene) fault system coincident with the physiographic transition in Bhutan. This high-angle, north-dipping structure, the Lhuentse fault, has minor normal-sense offset and could not have been responsible for differential uplift of the rugged terrain (in the hanging wall) relative to the low-relief landscape (in the footwall). The Lhuentse fault is coincident with the back limb of a previously inferred blind duplex at depth, and thus may be associated with active deformation on a rotated horse within the duplex. This duplex may also be responsible for the creation of the low-relief landscapes to the south of the Lhuentse fault due to upstream tilting in the back limb of the antiformal rock uplift pattern. Erosion patterns modeled on the basis of newly acquired 40Ar/39Ar and (U-Th)/He thermochronometric data as well as basin-average erosion rates from detrital cosmogenic nuclide concentrations are consistent with this hypothesis. We used a landscape evolution model (CHILD) to track landscape response to an imposed antiformal rock uplift gradient produced by an active duplex at depth. Rotation associated with the back limb of such a duplex causes aggradation, surface uplift, and headward migration of knickpoints. The wedge of sediment deposited during fluvial aggradation migrates northward beyond the back limb where uplift lessens. At this position in the landscape, a subdued physiographic transition develops in the model, similar to the one observed in Bhutan. Our modeling suggests that the presence and juxtaposition of low-relief landscapes and a physiographic transition, and our observed distribution of erosion rates can be explained by a single, simple mechanism related to the growth of a blind duplex.

Relationships between duplex findings and quality of life in long-term follow-up of patients treated for chronic venous disease.

PubMed

Huang, Ying; Gloviczki, Peter

2016-03-01

Relationships between duplex findings and data on health-related quality of life (QoL) to assess long-term results of treatment of varicose veins and chronic venous insufficiency (CVI) are not well known. The goal of this review was to correlate duplex findings and QoL assessments in clinical studies with long-term follow-up. A review of the English language literature on PUBMED revealed 17 clinical studies, including 9 randomized controlled trials (RCTs), 6 prospective, and 2 retrospective studies that included patients with at least 5-year follow-up after endovenous laser ablation (EVLA), radiofrequency ablation (RFA), ultrasound-guided foam sclerotherapy (UGFS), and traditional superficial venous surgery. At 5 years, great saphenous vein (GSV) occlusion rate on duplex ultrasound ranged from 66% to 82% for EVLA, from 62% to 92% for RFA, from 41% to 58% for UGFS and from 54% to 85% for surgery. Freedom from GSV reflux rates were 82% and 84%, respectively for EVLA and surgery, and ranged between 84% and 95% for RFA. Significant improvements were observed in several domains of generic QoL and in most domains of venous disease-specific QoL, irrespective of the treatment. In at least one RCT, CIVIQ scores correlated well with abnormal duplex findings in patients who underwent treatment with UGFS. In another RCT, long-term AVVQ was significantly better after surgery as compared with UGFS similar to results of duplex findings. Analysis of the available literature confirmed that all four techniques were effective in the abolishment of reflux or obliteration of the GSV. Moreover, well-designed RCTs with large sample size are needed to produce robust long-term data on clinical outcome after treatment of varicose veins and CVI and to better understand the relationships between duplex-derived data and QoL assessments. © The Author(s) 2016.

Synthesis and structures of a pincer-type rhodium(iii) complex: reactivity toward biomolecules.

PubMed

Milutinović, Milan M; Bogojeski, Jovana V; Klisurić, Olivera; Scheurer, Andreas; Elmroth, Sofi K C; Bugarčić, Živadin D

2016-10-04

A novel rhodium(iii) complex [Rh III (H 2 L tBu )Cl 3 ] (1) (H 2 L tBu = 2,6-bis(5-tert-butyl-1H-pyrazol-3-yl)pyridine) containing a pincer type, tridentate nitrogen-donor chelate system was synthesized. Single crystal X-ray structure analysis revealed that 1 crystallizes in the orthorhombic space group Pbcn with a = 20.7982(6), b = 10.8952(4), c = 10.9832(4) Å, V = 2488.80(15) Å 3 , and eight molecules in the unit cell. The rhodium center in the complex [Rh III (H 2 L tBu )Cl 3 ] (1) is coordinated in a slightly distorted octahedral geometry by the tridentate N,N,N-donor and three chloro ligands, adopting a mer arrangement with an essentially planar ligand skeleton. Due to the tridentate coordination of the N,N,N-donor, the central nitrogen atom N1 is located closer to the Rh III center. The reactivity of the synthesized complex toward small biomolecules (l-methionine (l-Met), guanosine-5'-monophosphate (5'-GMP), l-histidine (l-His) and glutathione (GSH)) and to a series of duplex DNAs and RNA was investigated. The order of reactivity of the studied small biomolecules is: 5'-GMP > GSH > l-Met > l-His. Duplex RNA reacts faster with the [Rh III (H 2 L tBu )Cl 3 ] complex than duplex DNA, while shorter duplex DNA (15mer GG) reacts faster compared with 22mer GG duplex DNA. In addition, a higher reactivity is achieved with a DNA duplex with a centrally located GG-sequence than with a 22GTG duplex DNA, in which the GG-sequence is separated by a T base. Furthermore, the interaction of this metal complex 1 with calf thymus DNA (CT-DNA) and bovine serum albumin (BSA) was examined by absorption (UV-Vis) and emission spectral studies (EthBr displacement studies). Overall, the studied complex exhibited good DNA and BSA interaction ability.

Thermoacoustic Duplex Technology for Cooling and Powering a Venus Lander

NASA Astrophysics Data System (ADS)

Walker, A. R.; Haberbusch, M. S.; Sasson, J.

2015-04-01

A Thermoacoustic Stirling Heat Engine (TASHE) is directly coupled to a Pulse Tube Refrigerator (PTR) in a duplex configuration, providing simultaneous cooling and electrical power, thereby suiting the needs of a long-lived Venus lander.

43. View of station from southwest side with duplex keepers' ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

43. View of station from southwest side with duplex keepers' dwelling to the left. USLHB photo by Herbert Bamber, June 9, 1893. - Bodie Island Light Station, Off Highway 12, Nags Head, Dare County, NC

Insight into a conformation of the PNA-PNA duplex with (2‧R,4‧R)- and (2‧R,4‧S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbones

NASA Astrophysics Data System (ADS)

Maitarad, Amphawan; Poomsuk, Nattawee; Vilaivan, Chotima; Vilaivan, Tirayut; Siriwong, Khatcharin

2018-04-01

Suitable conformations for peptide nucleic acid (PNA) self-hybrids with (2‧R,4‧R)- and (2‧R,4‧S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbones (namely, acpcPNA and epi-acpcPNA, respectively) were investigated based on molecular dynamics simulations. The results revealed that hybridization of the acpcPNA was observed only in the parallel direction, with a conformation close to the P-type structure. In contrast, self-hybrids of the epi-acpcPNA were formed in the antiparallel and parallel directions; the antiparallel duplex adopted the B-form conformation, and the parallel duplex was between B- and P-forms. The calculated binding energies and the experimental data indicate that the antiparallel epi-acpcPNA self-hybrid was more stable than the parallel duplex.

Development of dansyl-modified oligonucleotide probes responding to structural changes in a duplex.

PubMed

Suzuki, Yoshio; Kowata, Keiko; Komatsu, Yasuo

2013-11-15

We have synthesized a nonnucleoside amidite block of dansyl fluorophore to prepare dansyl-modified oligonucleotides (ONTs). The fluorescence intensities of dansyl-ONT specifically increased by the presence of adjacent guanosine residues but, significantly reduced in a dansyl-flipping duplex. These changes were caused by solvatochromism effect due to the number of guanine which is hydrophobic functional group and the external environment of dansyl group. The fluorescence intensities could be plotted as a function of the ONTs concentrations and the increase in the fluorescence was observed to equimolar concentrations of target DNA. This duplex exhibited higher melting temperature relative to the corresponding duplexes containing other base pairs. Similar changes in fluorescence could be detected upon hybridization with complementary RNAs. Thus, the dansyl-modified ONTs provide sequence specific fluorescent probe of DNA and RNA. Copyright © 2013 Elsevier Ltd. All rights reserved.

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

DOE PAGES

Manthei, Kelly A.; Hill, Morgan C.; Burke, Jordan E.; ...

2015-03-23

RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. In this paper, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3' single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ~90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATPmore » hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. Finally, this bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.« less

Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization.

PubMed

Sheng, Jia; Hassan, Abdalla E A; Zhang, Wen; Zhou, Jianfeng; Xu, Bingqian; Soares, Alexei S; Huang, Zhen

2011-05-01

We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNA duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation. © The Author(s) 2011. Published by Oxford University Press.

Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization

PubMed Central

Sheng, Jia; Hassan, Abdalla E. A.; Zhang, Wen; Zhou, Jianfeng; Xu, Bingqian; Soares, Alexei S.; Huang, Zhen

2011-01-01

We report here the first synthesis of 5-phenyl–telluride–thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNA duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation. PMID:21245037

Synthesis Structure and Imaging of Oligodeoxyribonucleotides with Tellurium-nucleobase Derivatization

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

J Sheng; A Hassan; W Zhang

2011-12-31

We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNAmore » duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation.« less

Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization

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

Sheng, J.; Soares, A.; Hassan, A. E. A.

2011-05-01

We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNAmore » duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation.« less

Rapid method to detect duplex formation in sequencing by hybridization methods, a method for constructing containment structures for reagent interaction

DOEpatents

Mirzabekov, Andrei Darievich; Yershov, Gennadiy Moiseyevich; Guschin, Dmitry Yuryevich; Gemmell, Margaret Anne; Shick, Valentine V.; Proudnikov, Dmitri Y.; Timofeev, Edward N.

2002-01-01

A method for determining the existence of duplexes of oligonucleotide complementary molecules is provided whereby a plurality of immobilized oligonucleotide molecules, each of a specific length and each having a specific base sequence, is contacted with complementary, single stranded oligonucleotide molecules to form a duplex so as to facilitate intercalation of a fluorescent dye between the base planes of the duplex. The invention also provides for a method for constructing oligonucleotide matrices comprising confining light sensitive fluid to a surface, exposing said light-sensitive fluid to a light pattern so as to cause the fluid exposed to the light to polymerize into discrete units and adhere to the surface; and contacting each of the units with a set of different oligonucleotide molecules so as to allow the molecules to disperse into the units.

Insights into the structural features and stability of peptide nucleic acid with a D-prolyl-2-aminocyclopentane carboxylic acid backbone that binds to DNA and RNA.

PubMed

Poomsuk, Nattawee; Vilaivan, Tirayut; Siriwong, Khatcharin

2018-06-12

Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system. Copyright © 2018 Elsevier Inc. All rights reserved.

Defined presentation of carbohydrates on a duplex DNA scaffold.

PubMed

Schlegel, Mark K; Hütter, Julia; Eriksson, Magdalena; Lepenies, Bernd; Seeberger, Peter H

2011-12-16

A new method for the spatially defined alignment of carbohydrates on a duplex DNA scaffold is presented. The use of an N-hydroxysuccinimide (NHS)-ester phosphoramidite along with carbohydrates containing an alkylamine linker allows for on-column labeling during solid-phase oligonucleotide synthesis. This modification method during solid-phase synthesis only requires the use of minimal amounts of complex carbohydrates. The covalently attached carbohydrates are presented in the major groove of the B-form duplex DNA as potential substrates for murine type II C-type lectin receptors mMGL1 and mMGL2. CD spectroscopy and thermal melting revealed only minimal disturbance of the overall helical structure. Surface plasmon resonance and cellular uptake studies with bone-marrow-derived dendritic cells were used to assess the capability of these carbohydrate-modified duplexes to bind to mMGL receptors. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prenatal complicated duplex collecting system and ureterocele-Important risk factors for urinary tract infection.

PubMed

Visuri, Sofia; Jahnukainen, Timo; Taskinen, Seppo

2018-04-01

To evaluate the risk of urinary tract infections (UTIs) in infants with prenatally detected complicated duplex collecting system (CDS) or ureterocele. All patients with prenatally detected CDS (n=34) or single system ureterocele (n=7) who were admitted to our institution between 2003 and 2013 were enrolled in this retrospective analysis. Duplex collecting systems with ureterocele (n=13), vesicoureteral reflux (VUR) (n=20) or nonrefluxing megaureter without ureterocele (n=7) were determined as complicated. Twenty-six (63%) patients were females. The prevalence of UTI was compared to 66 controls. The median follow-up time was 5.5 (1.7-12.2) years. Eighteen (44%) patients and 3 (5%) controls had at least one UTI (p<0.001) at the median age of 0.8 and 0.4years, respectively (p=0.481). Fifty-seven percent of the UTIs were breakthrough infections and 82% of those were non-Escherichia coli infections. UTIs occurred prior to any surgical intervention in 4/13 (31%) patients with ureterocele, in 2/14 (14%) patients with VUR, in 4/7 (57%) patients with both ureterocele and VUR, and in 3/7 (43%) patients with nonrefluxing megaureter without VUR or ureterocele (p-values 0.012, 0.209, 0.001 and 0.010, respectively, compared to controls). Postoperative UTIs were observed in 29% of the girls and in none of the 11 boys (p=0.072). The incidence of UTI after perforation of ureterocele was only 14%. Children with prenatally detected ureterocele or duplex collecting system associated with nonrefluxing megaureter are at high risk of UTI despite prophylactic antibiotics. In case of prenatally detected ureterocele we suggest to consider early endoscopic perforation. III. Copyright © 2017 Elsevier Inc. All rights reserved.

Full duplex fiber link for alternative wired and wireless access based on SSB optical millimeter-wave with 4-PAM signal

NASA Astrophysics Data System (ADS)

Ma, Jianxin; Zhang, Junjie

2015-03-01

A novel full-duplex fiber-wireless link based on single sideband (SSB) optical millimeter (mm)-wave with 10 Gbit/s 4-pulse amplitude modulation (PAM) signal is proposed to provide alternative wired and 40 GHz wireless accesses for the user terminals. The SSB optical mm-wave with 4-PAM signal consists of two tones: one bears the 4-PAM signal and the other is unmodulated with high power. After transmission over the fiber to the hybrid optical network unit (HONU), the SSB optical mm-wave signal can be decomposed by fiber Bragg gratings (FBGs) as the SSB optical mm-wave signal with reduced carrier-to-sideband ratio (the baseband 4-PAM optical signal) and the uplink optical carrier for the wireless (wired) access. This makes the HONU free from the laser source. For the uplink, since the wireless access signal is converted to the baseband by power detection, both the transmitter in the HONU and the receiver in optical line terminal (OLT) are co-shared for both wireless and wired accesses, which makes the full duplex link much simpler. In our scheme, the optical electrical field of the square-root increment level 4-PAM signal assures an equal level spacing receiving for both the downlink wired and wireless accesses. Since the downlink wireless signal is down-converted to the baseband by power detection, RF local oscillator is unnecessary. To confirm the feasibility of our proposed scheme, a simulation full duplex link with 40 GHz SSB optical mm-wave with 10 Gbit/s 4-PAM signal is built. The simulation results show that both down- and up-links for either wired or wireless access can keep good performance even if the link length of the SSMF is extended to 40 km.

Ultrasensitive sensing platform for platelet-derived growth factor BB detection based on layered molybdenum selenide-graphene composites and Exonuclease III assisted signal amplification.

PubMed

Huang, Ke-Jing; Shuai, Hong-Lei; Zhang, Ji-Zong

2016-03-15

A highly sensitive and ultrasensitive electrochemical aptasensor for platelet-derived growth factor BB (PDGF-BB) detection is fabricated based on layered molybdenum selenide-graphene (MoSe2-Gr) composites and Exonuclease III (Exo III)-aided signal amplification. MoSe2-Gr is prepared by a simple hydrothermal method and used as a promising sensing platform. Exo III has a specifical exo-deoxyribonuclease activity for duplex DNAs in the direction from 3' to 5' terminus, however its activity is limited on the duplex DNAs with more than 4 mismatched terminal bases at 3' ends. Herein, aptamer and complementary DNA (cDNA) sequences are designed with four thymine bases on 3' ends. In the presence of target protein, the aptamer associates with it and facilitates the formation of duplex DNA between cDNA and signal DNA. The duplex DNA then is digested by Exo III and releases cDNA, which hybridizes with signal DNA to perform a new cleavage process. Nevertheless, in the absence of target protein, the aptamer hybridizes with cDNA will inhibit the Exo III-assisted nucleotides cleavage. The signal DNA then hybridizes with capture DNA on the electrode. Subsequently, horse radish peroxidase is fixed on electrode by avidin-biotin reaction and then catalyzes hydrogen peroxide and hydroquinone to produce electrochemical response. Therefore, a bridge can be established between the concentration of target protein and the degree of the attenuation of the obtained signal, providing a quantitative measure of target protein with a broad detection range of 0.0001-1 nM and a detection limit of 20 fM. Copyright © 2015 Elsevier B.V. All rights reserved.

Angle selective fiber coupler.

PubMed

Barnoski, M K; Morrison, R J

1976-01-01

Angle selective input coupling through the side of a slightly tapered section of Corning highly multimode fiber has been experimentally demonstrated for the first time. This coupling technique allows the possibility of fabricating bidirectional (duplex) couplers for systems employing single strands of multimode, low loss fiber.

Tertiary thrust systems and fluid flow beneath the Beaufort coastal plain (1002 area), Arctic National Wildlife Refuge, Alaska, U.S.A.

USGS Publications Warehouse

Potter, Christopher J.; Grow, John A.; Perry, William J.; Moore, Thomas E.; O'Sullivan, Paul B.; Phillips, Jeffrey D.; Saltus, Richard W.

2004-01-01

In the eastern part of the 1002 area, a northward-younging pattern of thin-skinned deformation is apparent. Converging patterns of Paleocene reflectors on the north flank of the Sabbath syncline indicate that the Aichilik high and the Sabbath syncline formed as a passive-roof duplex and piggyback basin, respectively, just behind the Paleocene deformation front. During the Eocene and possibly the Oligocene, thin-skinned thrusting advanced northward over the present location of the Niguanak high. A passive-roof duplex occupied the frontal part of this system. The Kingak and Hue shales exposed above the Niguanak high were transported into their present structural position during the Eocene to Oligocene motion on the long thrust ramps above the present south flank of the Niguanak high. Broad, basement-cored subsurface domes (Niguanak high and Aurora dome) formed near the deformation front in the Oligocene, deforming the overlying thin-skinned structures and feeding a new increment of displacement into thin-skinned structures directly to the north. Deformation continued through the Miocene above a detachment in the basement. Offshore seismicity and Holocene shortening documented by previous workers may indicate that contractional deformation continues to the present day.

Multistory duplexes with forward dipping roofs, north central Brooks Range, Alaska

USGS Publications Warehouse

Wallace, W.K.; Moore, Thomas E.; Plafker, G.

1997-01-01

The Endicott Mountains allochthon has been thrust far northward over the North Slope parautochthon in the northern Brooks Range. Progressively younger units are exposed northward within the allochthon. To the south, the incompetent Hunt Fork Shale has thickened internally by asymmetric folds and thrust faults. Northward, the competent Kanayut Conglomerate forms a duplex between a floor thrust in Hunt Fork and a roof thrust in the Kayak Shale. To the north, the competent Lisburne Group forms a duplex between a floor thrust in Kayak and a roof thrust in the Siksikpuk Formation. Both duplexes formed from north vergent detachment folds whose steep limbs were later truncated by south dipping thrust faults that only locally breach immediately overlying roof thrusts. Within the parautochthon, the Kayak, Lisburne, and Siksikpuk-equivalent Echooka Formation form a duplex identical to that in the allochthon. This duplex is succeeded abruptly northward by detachment folds in Lisburne. These folds are parasitic to an anticlinorium interpreted to reflect a fault-bend folded horse in North Slope "basement," with a roof thrust in Kayak and a floor thrust at depth. These structures constitute two northward tapered, internally deformed wedges that are juxtaposed at the base of the allochthon. Within each wedge, competent units have been shortened independently between detachments, located mainly in incompetent units. The basal detachment of each wedge cuts upsection forward (northward) to define a wedge geometry within which units dip regionally forward. These dips reflect forward decrease in internal structural thickening by forward vergent folds and hindward dipping thrust faults. Copyright 1997 by the American Geophysical Union.

5' modification of duplex DNA with a ruthenium electron donor-acceptor pair using solid-phase DNA synthesis

NASA Technical Reports Server (NTRS)

Frank, Natia L.; Meade, Thomas J.

2003-01-01

Incorporation of metalated nucleosides into DNA through covalent modification is crucial to measurement of thermal electron-transfer rates and the dependence of these rates with structure, distance, and position. Here, we report the first synthesis of an electron donor-acceptor pair of 5' metallonucleosides and their subsequent incorporation into oligonucleotides using solid-phase DNA synthesis techniques. Large-scale syntheses of metal-containing oligonucleotides are achieved using 5' modified phosporamidites containing [Ru(acac)(2)(IMPy)](2+) (acac is acetylacetonato; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (3) and [Ru(bpy)(2)(IMPy)](2+) (bpy is 2,2'-bipyridine; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (4). Duplexes formed with the metal-containing oligonucleotides exhibit thermal stability comparable to the corresponding unmetalated duplexes (T(m) of modified duplex = 49 degrees C vs T(m) of unmodified duplex = 47 degrees C). Electrochemical (3, E(1/2) = -0.04 V vs NHE; 4, E(1/2) = 1.12 V vs NHE), absorption (3, lambda(max) = 568, 369 nm; 4, lambda(max) = 480 nm), and emission (4, lambda(max) = 720 nm, tau = 55 ns, Phi = 1.2 x 10(-)(4)) data for the ruthenium-modified nucleosides and oligonucleotides indicate that incorporation into an oligonucleotide does not perturb the electronic properties of the ruthenium complex or the DNA significantly. In addition, the absence of any change in the emission properties upon metalated duplex formation suggests that the [Ru(bpy)(2)(IMPy)](2+)[Ru(acac)(2)(IMPy)](2+) pair will provide a valuable probe for DNA-mediated electron-transfer studies.

Synthesis and conformational properties of oligonucleotides incorporating 2'-O-phosphorylated ribonucleotides as structural motifs of pre-tRNA splicing intermediates.

PubMed

Tsuruoka, H; Shohda, K; Wada, T; Sekine, M

2000-11-03

To synthesize oligonucleotides containing 2'-O-phosphate groups, four kinds of ribonucleoside 3'-phosphoramidite building blocks 6a-d having the bis(2-cyano-1,1-dimethylethoxy)thiophosphoryl (BCMETP) group were prepared according to our previous phosphorylation procedure. These phosphoramidite units 6a-d were not contaminated with 3'-regioisomers and were successfully applied to solid-phase synthesis to give oligodeoxyuridylates 15, 16 and oligouridylates 21, 22. Self-complementary Drew-Dickerson DNA 12mers 24-28 replaced by a 2'-O-phosphorylated ribonucleotide at various positions were similarly synthesized. In these syntheses, it turned out that KI(3) was the most effective reagent for oxidative desulfurization of the initially generated thiophosphate group to the phosphate group on polymer supports. Without using this conversion step, a tridecadeoxyuridylate 17 incorporating a 2'-O-thiophosphorylated uridine derivative was also synthesized. To investigate the effect of the 2'-phosphate group on the thermal stability and 3D-structure of DNA(RNA) duplexes, T(m) measurement of the self-complementary oligonucleotides obtained and MD simulation of heptamer duplexes 33-36 were carried out. According to these analyses, it was suggested that the nucleoside ribose moiety phosphorylated at the 2'-hydroxyl function predominantly preferred C2'-endo to C3'-endo conformation in DNA duplexes so that it did not significantly affect the stability of the DNA duplex. On the other hand, the 2'-modified ribose moiety was expelled to give a C3'-endo conformation in RNA duplexes so that the RNA duplexes were extremely destabilized.

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

NASA Technical Reports Server (NTRS)

Egli, M.; Usman, N.; Rich, A.

1993-01-01

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

Materials selection for kraft batch digesters

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

Wensley, A.; Moskal, M.; Wilton, W.

1997-08-01

Several candidate materials were evaluated by corrosion testing in autoclaves containing white and black liquors for batch digesters. The relationship between corrosion rate and corrosion potential was determined for ASTM SA516-Grade 70 carbon steel, UNS S30403 (Type 304L) austenitic stainless steel, UNS S31803 (2205) and UNS S32550 (2605) duplex stainless steels, and two stainless steel weld overlays, applied by the GMAW (gas metal arc welding) and SAW (submerged arc welding) processes. The tests revealed that SA516-Grade 70 carbon steel and type 304L stainless steel can experience high rates of corrosion. For the duplex stainless steels and weld overlays, corrosion resistancemore » improved with chromium content. A chromium content of at least 25% was found to be necessary for good corrosion resistance.« less

A novel high-speed PLC communication modem

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

Abraham, K.C.; Roy, S.

1992-10-01

In this paper an innovative design for power line carrier (PLC) communication using digitally modulated signals is presented. The major contribution consists of a new signal coupler to the power line that achieves a stable transmission bandwidth of 4 KHz on distribution lines over long distances. Preliminary field tests achieved half-duplex operation at 1.2 Kbaud over a distribution power line to the 120V network and back with a symbol error rate of about 2% using less than about 10 W of average transmitted power, which is considerably superior to the present state-of-the-art PLC modems. Full-duplex operation over 120/240V intra-building wiringmore » has also been field tested at 9.6 Kbaud over distances of 3000 ft. using 1W of average transmitted power.« less

The effects of insulation defects on the corrosion of sub-sea super duplex stainless steel process pipes

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

Francis, R.; Irwin, J.; Byrne, G.

1995-10-01

There is an increasing use of CRAs (corrosion resistant alloys) for subsea flowlines. These pipes carry corrosive fluids at high temperatures and pressures, and insulation is usually, applied to prevent excessive cooling of the process fluids. The present tests were undertaken to investigate the effect of insulation defects on the susceptibility to localized corrosion of a super duplex stainless steel at different internal temperatures. Four different commercial coating systems were tested, Neoprene, EPDM, Polyurethane and Polyurethane foam. The results show that pitting occurred at an average temperature of 55 C for neoprene and EPDM, and at lower temperatures for themore » other two coatings. The reasons for this are discussed, and the implications for service applications.« less

Development of a duplex rapid assay for immunoglobulins M and G to evaluate the parvoviral immune status of clinically healthy dogs.

PubMed

Palma, Marco; de la Roja, Nuria; Montón, Mercedes; Sastre, Patricia; Ramírez, Susana; Barreiro, Belén; Venteo, Angel; Rueda, Paloma

2016-05-01

A duplex rapid assay for detection of serum antibodies to canine parvovirus (CPV) was developed. Canine immunoglobulin (Ig)M or IgG were captured in immunotubes with anti-canine IgM or IgG and detected with parvovirus VP2 recombinant protein followed by an anti-VP2 monoclonal antibody. The assay was tested using a collection of sera from dogs that were vaccinated against CPV on arrival at an animal shelter in Madrid, Spain. Results were compared with those of 2 commercial enzyme-linked immunosorbent assays (ELISAs) considered as reference techniques. A high correlation was found between the duplex rapid assay and the ELISAs, presenting an accuracy of 98% and 100% for IgG and IgM, respectively. According to the IgG and IgM levels at days 0-3 postvaccination, the samples were divided into 2 groups. One group of dogs showed high IgG and low IgM values at the first sampling post-vaccination and during the following 14 days, indicating that they had previously been in contact with the virus, either by vaccination or infection before arrival at the animal shelter. A second group of dogs appeared to be unvaccinated or uninfected before arrival at the animal shelter because they had negative IgM and IgG values soon after vaccination. These animals responded to vaccination, as demonstrated by seroconversion of both isotypes of immunoglobulins. The developed assay appears to be useful in determining the unknown immune status of dogs to CPV, especially in kennels and shelters where the rate of infection by CPV is relatively high. © 2016 The Author(s).

A novel high-throughput format assay for HIV-1 integrase strand transfer reaction using magnetic beads.

PubMed

He, Hong-qiu; Ma, Xiao-hui; Liu, Bin; Chen, Wei-zu; Wang, Cun-xin; Cheng, Shao-hui

2008-03-01

To develop a novel high-throughput format assay to monitor the integrase (IN) strand transfer (ST) reaction in vitro and apply it to a reaction character study and the identification of antiviral drugs. The donor DNA duplex, with a sequence identical to the U5 end of HIV-1 long terminal repeats, is labeled at its 5' end with biotin (BIO). The target DNA duplex is labeled at its 3' end with digoxin (DIG). IN mediates the integration of donor DNA into target DNA and results in a 5' BIO and 3' DIG-labeled duplex DNA product. Streptavidin-coated magnetic beads were used to capture the product, and the amount of DIG was measured as the ST reaction product. The assay was optimized in 96-well microplate format for high-throughput screening purpose. Moreover, the assay was applied in a ST reaction character study, and the efficiency of the assay in the identification of antiviral compounds was tested. The end-point values, measured as absorbance at 405 nm was approximately 1.5 for the IN-mediated ST reaction as compared with no more than 0.05 of background readings. The ST reaction character and the half maximal inhibitory concentration (IC50) values of 2 known IN inhibitors obtained in our assay were similar to previously reported results using other assays. The evaluation parameter Z' factor for this assay ranged from 0.6 to 0.9. The assay presented here has been proven to be rapid, sensitive, and specific for the detection of IN ST activity, the reaction character study, as well as for the identification of antiviral drugs targeting IN.

1. VIEW OF STAFF HOUSE (FEATURE 10), FACING SOUTHWEST. DUPLEX ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. VIEW OF STAFF HOUSE (FEATURE 10), FACING SOUTHWEST. DUPLEX (FEATURE 7) IS VISIBLE IN THE BACKGROUND AT RIGHT. - Copper Canyon Camp of the International Smelting & Refining Company, Staff House, Copper Canyon, Battle Mountain, Lander County, NV

A conserved MCM single-stranded DNA binding element is essential for replication initiation.

PubMed

Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

2014-04-01

The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001.

A conserved MCM single-stranded DNA binding element is essential for replication initiation

PubMed Central

Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

2014-01-01

The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001 PMID:24692448

How to control hydrogen level in (super) duplex stainless steel weldments using the GTAW or GMAW process

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

Mee, V.V.D.; Meelker, H.; Schelde, R.V.D.

1999-01-01

In this investigation, an attempt is made to further the understanding of factors influencing the hydrogen content in duplex stainless steel gas tungsten arc (GTA) and gas metal arc (GMA) welds as well as to what extent it affects hydrogen-induced cracking susceptibility. The results indicated that susceptibility to hydrogen cracking using the GTA or GMA process appears to be limited. In practice, maintaining a moisture level below 10 ppm in the shielding gas is of less importance than the choice of welding parameters. Even a moisture level of 1000 ppm in the shielding gas, in combination with the correct weldingmore » parameters, will result in a sufficient low hydrogen content in the weld. Similarly, a moisture level in the shielding gas below 10 ppm does not necessarily result in low hydrogen content in the weld metal. Although very high ferrite levels were combined with high restrain and high hydrogen content, none of the GMA and GTA welds cracked. Susceptibility to hydrogen cracking is concluded to be limited.« less

Corrosion-free precast prestressed concrete piles made with stainless steel reinforcement : construction, test and evaluation.

DOT National Transportation Integrated Search

2015-03-01

The use of duplex high-strength stainless steel (HSSS) grade 2205 prestressing strand and : austenitic stainless steel (SS) grade 304 spiral wire reinforcement is proposed as a replacement of : conventional prestressing steel, in order to provide a 1...

Experimental and numerical researches of duplex burnishing process in aspect of achieved productive quality of the product

NASA Astrophysics Data System (ADS)

Patyk, Radoslaw; Kukielka, Leon; Kaldunski, Pawel; Bohdal, Lukasz; Chodor, Jaroslaw; Kulakowska, Agnieszka; Kukielka, Krzysztof; Nagnajewicz, Slawomir

2018-05-01

The paper presents the results of experimental researches and numerical simulations of the duplex burnishing process. During duplex burnishing process the treatment is carry out in two stages. In the first stage - on the semi-fabrication surface, the regular asperities are embossed with triangular, symmetrical, periodic outline. In the second stage the asperities are burnished (smooth burnishing) till the needed asperities equalized, resulting in a smooth and strengthened surface layer. The implementation of such technology results in receiving of a new surface layer characterized by favorable functional properties, particularly increased resistance to fatigue wear.

Microstructure and corrosion behavior of shielded metal arc-welded dissimilar joints comprising duplex stainless steel and low alloy steel

NASA Astrophysics Data System (ADS)

Srinivasan, P. Bala; Muthupandi, V.; Sivan, V.; Srinivasan, P. Bala; Dietzel, W.

2006-12-01

This work describes the results of an investigation on a dissimilar weld joint comprising a boiler-grade low alloy steel and duplex stainless steel (DSS). Welds produced by shielded metal arc-welding with two different electrodes (an austenitic and a duplex grade) were examined for their microstructural features and properties. The welds were found to have overmatching mechanical properties. Although the general corrosion resistance of the weld metals was good, their pitting resistance was found to be inferior when compared with the DSS base material.

Atomistic Simulations of Complex DNA DSBs and the Interactions with Ku70/80 Heterodimer

NASA Technical Reports Server (NTRS)

Hu, Shaowen; Cucinotta, Francis A.

2011-01-01

Compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex. Binding of Ku drastically reduces the structural disruption and flexibility caused by the complex lesions. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. Binding of Ku promotes the rigidity of DNA duplexes, due to the clamp structure of the inner surface of the rings of Ku70/80.

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.

Recruitment of Rod Photoreceptors from Short-Wavelength-Sensitive Cones during the Evolution of Nocturnal Vision in Mammals.

PubMed

Kim, Jung-Woong; Yang, Hyun-Jin; Oel, Adam Phillip; Brooks, Matthew John; Jia, Li; Plachetzki, David Charles; Li, Wei; Allison, William Ted; Swaroop, Anand

2016-06-20

Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinas. In mice, we discovered genetic and epigenetic vestiges of short-wavelength cones in developing rods, and cell-lineage tracing validated the genesis of rods from S cones. Curiously, rods did not derive from S cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Published by Elsevier Inc.

Evaluation of present thermal barrier coatings for potential service in electric utility gas turbines

NASA Technical Reports Server (NTRS)

Bratton, R. J.; Lau, S. K.; Lee, S. Y.

1982-01-01

The resistance of present-day thermal barrier coatings to combustion gases found in electric utility turbines was assessed. The plasma sprayed coatings, both duplex and graded types, were primarily zirconia-based, although a calcium silicate was also evaluated. Both atmospheric burner rig tests and high pressure tests (135 psig) showed that several present-day thermal barrier coatings have a high potential for service in gas turbines burning the relatively clean GT No. 2 fuel. However, coating improvements are needed for use in turbines burning lower grade fuel such as residual oil. The duplex ZrO2.8Y2O3/NiCrA1Y coating was ranked highest and selected for near-term field testing, with Ca2SiO4/NiCrA1Y ranked second. Graded coatings show potential for corrosive turbine operating conditions and warrant further development. The coating degradation mechanisms for each coating system subjected to the various environmental conditions are also described.

Comparison of duplex PCR and phenotypic analysis in differentiating Candida dubliniensis from Candida albicans from oral samples.

PubMed

Sampath, Asanga; Weerasekera, Manjula; Dilhari, Ayomi; Gunasekara, Chinthika; Bulugahapitiya, Uditha; Fernando, Neluka; Samaranayake, Lakshman

2017-12-01

Candida dubliniensis shares a wide range of phenotypic characteristics with Candida albicans including a common trait called germ tube positivity. Hence, laboratory differentiation of these two species is cumbersome. Duplex PCR analyses for C. albicans and C. dubliniensis was performed directly on DNA extracted from a total of 122 germ tube positive isolates derived from 100 concentrated oral rinse samples from a random cohort of diabetics attending a clinic in Sri Lanka. These results were confirmed by DNA sequencing of internal transcribed spacer (ITS) region of rDNA of the yeasts. Performance efficacy of duplex PCR was then compared with phenotypic identification using a standard battery of phenotypic tests. Of the 122 germ tube positive isolates three were identified by duplex PCR as C. dubliniensis and the remainder as C. albicans. On the contrary, when the standard phenotypic tests, sugar assimilation and chlamydospore formation, were used to differentiate the two species 13 germ tube positive isolates were erroneously identified as C. dubliniensis. Duplex PCR was found to be rapid, sensitive and more specific than phenotypic identification methods in discriminating C. dubliniensis from C. albicans. This is also the first report on the oral carriage of C. dubliniensis in a Sri Lankan population.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase

PubMed Central

Aarattuthodiyil, Suja; Byrd, Alicia K.; Raney, Kevin D.

2014-01-01

Interactions between helicases and the tracking strand of a DNA substrate are well-characterized; however, the role of the displaced strand is a less understood characteristic of DNA unwinding. Dda helicase exhibited greater processivity when unwinding a DNA fork compared to a ss/ds DNA junction substrate. The lag phase in the unwinding progress curve was reduced for the forked DNA compared to the ss/ds junction. Fewer kinetic steps were required to unwind the fork compared to the ss/ds junction, suggesting that binding to the fork leads to disruption of the duplex. DNA footprinting confirmed that interaction of Dda with a fork leads to two base pairs being disrupted whereas no disruption of base pairing was observed with the ss/ds junction. Neutralization of the phosphodiester backbone resulted in a DNA-footprinting pattern similar to that observed with the ss/ds junction, consistent with disruption of the interaction between Dda and the displaced strand. Several basic residues in the 1A domain which were previously proposed to bind to the incoming duplex DNA were replaced with alanines, resulting in apparent loss of interaction with the duplex. Taken together, these results suggest that Dda interaction with the tracking strand, displaced strand and duplex coordinates DNA unwinding. PMID:25249618

Influence of 5-N-carboxamide modifications on the thermodynamic stability of oligonucleotides

PubMed Central

Wolk, Steven K.; Shoemaker, Richard K.; Mayfield, Wes S.; Mestdagh, Andrew L.; Janjic, Nebojsa

2015-01-01

We have recently shown that the incorporation of modified nucleotides such as 5-N-carboxamide-deoxyuridines into random nucleic acid libraries improves success rates in SELEX experiments and facilitates the identification of ligands with slow off-rates. Here we report the impact of these modifications on the thermodynamic stability of both duplexes and intramolecular ‘single-stranded’ structures. Within duplexes, large, hydrophobic naphthyl groups were destabilizing relative to the all natural DNA duplex, while the hydrophilic groups exhibited somewhat improved duplex stability. All of the significant changes in stability were driven by opposing contributions from the enthalpic and entropic terms. In contrast, both benzyl and naphthyl modifications stabilized intramolecular single-stranded structures relative to their natural DNA analogs, consistent with the notion that intramolecular folding allows formation of novel, stabilizing hydrophobic interactions. Imino proton NMR data provided evidence that elements of the folded structure form at temperatures well below the Tm, with a melting transition that is distinctly less cooperative when compared to duplex DNA. Although there are no data to suggest that the unmodified DNA sequences fold into structures similar to their modified analogs, this still represents clear evidence that these modifications impart thermodynamic stability to the folded structure not achievable with unmodified DNA. PMID:26438535

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

Evaluation of a duplex reverse-transcription real-time PCR assay for the detection of encephalomyocarditis virus.

PubMed

Qin, Shaomin; Underwood, Darren; Driver, Luke; Kistler, Carol; Diallo, Ibrahim; Kirkland, Peter D

2018-06-01

We evaluated a fluorogenic probe-based assay for the detection of encephalomyocarditis virus (EMCV) by comparing a set of published primers and probe to a new set of primers and probe. The published reagents failed to amplify a range of Australian isolates and an Italian reference strain of EMCV. In contrast, an assay based on 2 new sets of primers and probes that were run in a duplex reverse-transcription real-time PCR (RT-rtPCR) worked well, with high amplification efficiency. The analytical sensitivity was ~100-fold higher than virus isolation in cell culture. The intra-assay variation was 0.21-4.90%. No cross-reactivity was observed with a range of other porcine viruses. One hundred and twenty-two clinical specimens were tested simultaneously by RT-rtPCR and virus isolation in cell culture; 72 specimens gave positive results by RT-rtPCR, and 63 of these were also positive by virus isolation. Of 245 archived cell culture isolates of EMCV that were tested in the RT-rtPCR, 242 samples were positive. The new duplex RT-rtPCR assay is a reliable tool for the detection of EMCV in clinical specimens and for use in epidemiologic investigations.

Spermine Condenses DNA, but Not RNA Duplexes

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

Katz, Andrea M.; Tolokh, Igor S.; Pabit, Suzette A.

Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA, and some RNAs such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA, but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA and compare our findings with predictions of molecular dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence, containing a mixture of 14 GC pairs and 11 AU pairs, resists condensation relative to DNA of an equivalent sequence or to 25 basemore » pair poly(rA):poly(rU) RNA. Comparison of wide-angle x-ray scattering profiles with simulation suggests that spermine is sequestered deep within the major groove of mixed sequence RNA, preventing condensation by limiting opportunities to bridge to other molecules as well as stabilizing the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds external to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble, and available for interaction with other molecules in the cell, despite the presence of spermine at concentrations high enough to precipitate DNA.« less

Planck-Benzinger thermal work function: Monoclonal antibody-DNA duplex binding interactions

NASA Astrophysics Data System (ADS)

Chun, Paul W.

We have reexamined the van't Hoff plots and delineation of thermodynamic data of the monoclonal antibodies of Jel 274 and Jel 241 binding to DNA duplex at high ionic strength using fluorescein-labeled oligonucleotide titration with increasing concentrations of the antibody as reported by Tanha and Lee (Nucleic Acid Res, 1997, 25, 1442). To compare the thermodynamic parameters from data over the experimental temperature range of 277-312.5 K, the binding constant from van't Hoff plots is used to evaluate ΔGo(T) from 0 to 400 K using our general linear T3 model, ΔGo(T) = α +βT2+γT3. The limited information provided by the van't Hoff plots and their extensions is not sufficient to describe the variations in the Gibbs free energy change as a function of temperature and other thermodynamic functions observed in these and other biological interactions. Rather, it is necessary to determine a number of thermodynamic parameters, including the heat of reaction, (Th), (Tm), and (TCp), and the thermal set point, (TS), all of which can be precisely assessed using our general linear T3 model. To date, no experimental measurement offers this degree of accuracy. In evaluating the thermodynamic parameters in the binding interaction of monoclonal IgG Jel 241-d[AT]20DNA duplex, it is apparent that at a high NaCl concentration, the range of the compensatory temperatures, (Th) = 155 K and (Tm) = 450 K, is much broader than observed in any other sample, whereas the thermal set points, (TS) = 330 K, is 20-30 K higher. The inherent chemical bond energy ΔHo(T0) is much lower in this sample. The values of thermal agitation energy (heat capacity integrals) are of similar magnitude for all the samples tested. It appears that increasing the NaCl concentration to 130 mM will greatly enhance the binding interaction between the monoclonal antibody and DNA duplex. It is not clear, however, from the limited data available, whether the binding interaction is sequence specific, although logic would suggest it is.

Targeting Prostate Cancer with Multifunctional Nanoparticles

DTIC Science & Technology

2015-10-01

duplexes using Lipofectamine RNAiMAX (Invitrogen) as well as the appropriate controls including vehicle, non-targeting siRNA (siSC5) (negative...independent claudin-3 and claudin-4 siRNA duplexes using Lipofectamine RNAiMAX (Invitrogen). For these experiments we also included the appropriate

View west along Marine Barracks Way at rear of Marine ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View west along Marine Barracks Way at rear of Marine Corps Officers' Housing, with carports on left and duplex on right - U.S. Naval Base, Pearl Harbor, Marine Corps Officers' Duplex Quarters, Salvor Street & Russell Avenue, Pearl City, Honolulu County, HI

Internal Carotid Artery Hypoplasia: Role of Color-Coded Carotid Duplex Sonography.

PubMed

Chen, Pei-Ya; Liu, Hung-Yu; Lim, Kun-Eng; Lin, Shinn-Kuang

2015-10-01

The purpose of this study was to determine the role of color-coded carotid duplex sonography for diagnosis of internal carotid artery hypoplasia. We retrospectively reviewed 25,000 color-coded carotid duplex sonograms in our neurosonographic database to establish more diagnostic criteria for internal carotid artery hypoplasia. A definitive diagnosis of internal carotid artery hypoplasia was made in 9 patients. Diagnostic findings on color-coded carotid duplex imaging include a long segmental small-caliber lumen (52% diameter) with markedly decreased flow (13% flow volume) in the affected internal carotid artery relative to the contralateral side but without intraluminal lesions. Indirect findings included markedly increased total flow volume (an increase of 133%) in both vertebral arteries, antegrade ipsilateral ophthalmic arterial flow, and a reduced vessel diameter with increased flow resistance in the ipsilateral common carotid artery. Ten patients with distal internal carotid artery dissection showed a similar color-coded duplex pattern, but the reductions in the internal and common carotid artery diameters and increase in collateral flow from the vertebral artery were less prominent than those in hypoplasia. The ipsilateral ophthalmic arterial flow was retrograde in 40% of patients with distal internal carotid artery dissection. In addition, thin-section axial and sagittal computed tomograms of the skull base could show the small diameter of the carotid canal in internal carotid artery hypoplasia and help distinguish hypoplasia from distal internal carotid artery dissection. Color-coded carotid duplex sonography provides important clues for establishing a diagnosis of internal carotid artery hypoplasia. A hypoplastic carotid canal can be shown by thin-section axial and sagittal skull base computed tomography to confirm the final diagnosis. © 2015 by the American Institute of Ultrasound in Medicine.

Development of a duplex droplet digital PCR assay for absolute quantitative detection of "Candidatus Liberibacter asiaticus".

PubMed

Selvaraj, Vijayanandraj; Maheshwari, Yogita; Hajeri, Subhas; Chen, Jianchi; McCollum, Thomas Greg; Yokomi, Raymond

2018-01-01

Huanglongbing (HLB, citrus greening) is a devastating citrus disease affecting citrus production worldwide. It is associated with the bacterium "Candidatus Liberibacter asiaticus" (CLas) and is vectored by the Asian citrus psyllid (ACP). Currently, diagnosis of CLas in regulatory samples is based on real-time quantitative polymerase chain reaction (qPCR) using 16S rRNA gene specific primers/probe. The detection of CLas using qPCR is challenging due to low pathogen titer and uneven distribution in infected plants and exacerbated by sampling issues and presence of inhibitors. This study evaluated a duplex droplet digital polymerase chain reaction (ddPCR) using multi-copy gene targets, 16S and RNR, to simultaneously detect CLas DNA targets in the same sample for unambiguous detection of the HLB pathogen in DNA extracts from citrus leaves and ACP. Standard curve analyses on tenfold dilution series with plasmid, citrus leaf and ACP DNA showed that both ddPCR and qPCR exhibited good linearity and efficiency in the duplex assay. CLas-infected low titer samples were used to validate the duplex ddPCR and qPCR performance and demonstrated that detection rate is higher when both 16S and RNR primers were used in duplex assay. However, the receiver operating characteristic analysis indicated that area under the curve for RNR primer was significantly broader, compared to 16S primers for CLas detection at low target titer. The absolute quantification of CLas at variable titers was reproducible and repeatable for both primer sets and the ddPCR showed higher resilience to PCR inhibitors with citrus leaf and ACP extracts. Hence, the resultant duplex ddPCR assay resulted in a significantly improved detection platform for diagnosis of CLas in samples with low pathogen titer.

Development of duplex PCR for simultaneous detection of Theileria spp. and Anaplasma spp. in sheep and goats.

PubMed

Cui, Yanyan; Zhang, Yan; Jian, Fuchun; Zhang, Longxian; Wang, Rongjun; Cao, Shuxuan; Wang, Xiaoxing; Yan, Yaqun; Ning, Changshen

2017-05-01

Theileria spp. and Anaplasma spp., which are important tick-borne pathogens (TBPs), impact the health of humans and animals in tropical and subtropical areas. Theileria and Anaplasma co-infections are common in sheep and goats. Following alignment of the relevant DNA sequences, two primer sets were designed to specifically target the Theileria spp. 18S rRNA and Anaplasma spp. 16S rRNA gene sequences. Genomic DNA from the two genera was serially diluted tenfold for testing the sensitivities of detection of the primer sets. The specificities of the primer sets were confirmed when DNA from Anaplasma and Theileria (positive controls), other related hematoparasites (negative controls) and ddH 2 O were used as templates. Fifty field samples were also used to evaluate the utility of single PCR and duplex PCR assays, and the detection results were compared with those of the PCR methods previously published. An optimized duplex PCR assay was established from the two primer sets based on the relevant genes from the two TBPs, and this assay generated products of 298-bp (Theileria spp.) and 139-bp (Anaplasma spp.). The detection limit of the assay was 29.4 × 10 -3  ng per μl, and there was no cross-reaction with the DNA from other hematoparasites. The results showed that the newly developed duplex PCR assay had an efficiency of detection (P > 0.05) similar to other published PCR methods. In this study, a duplex PCR assay was developed that can simultaneously identify Theileria spp. and Anaplasma spp. in sheep and goats. This duplex PCR is a potentially valuable assay for epidemiological studies of TBPs in that it can detect cases of mixed infections of the pathogens. Copyright © 2017 Elsevier Inc. All rights reserved.

Development of a duplex droplet digital PCR assay for absolute quantitative detection of "Candidatus Liberibacter asiaticus"

PubMed Central

Hajeri, Subhas; Chen, Jianchi; McCollum, Thomas Greg

2018-01-01

Huanglongbing (HLB, citrus greening) is a devastating citrus disease affecting citrus production worldwide. It is associated with the bacterium “Candidatus Liberibacter asiaticus” (CLas) and is vectored by the Asian citrus psyllid (ACP). Currently, diagnosis of CLas in regulatory samples is based on real-time quantitative polymerase chain reaction (qPCR) using 16S rRNA gene specific primers/probe. The detection of CLas using qPCR is challenging due to low pathogen titer and uneven distribution in infected plants and exacerbated by sampling issues and presence of inhibitors. This study evaluated a duplex droplet digital polymerase chain reaction (ddPCR) using multi-copy gene targets, 16S and RNR, to simultaneously detect CLas DNA targets in the same sample for unambiguous detection of the HLB pathogen in DNA extracts from citrus leaves and ACP. Standard curve analyses on tenfold dilution series with plasmid, citrus leaf and ACP DNA showed that both ddPCR and qPCR exhibited good linearity and efficiency in the duplex assay. CLas-infected low titer samples were used to validate the duplex ddPCR and qPCR performance and demonstrated that detection rate is higher when both 16S and RNR primers were used in duplex assay. However, the receiver operating characteristic analysis indicated that area under the curve for RNR primer was significantly broader, compared to 16S primers for CLas detection at low target titer. The absolute quantification of CLas at variable titers was reproducible and repeatable for both primer sets and the ddPCR showed higher resilience to PCR inhibitors with citrus leaf and ACP extracts. Hence, the resultant duplex ddPCR assay resulted in a significantly improved detection platform for diagnosis of CLas in samples with low pathogen titer. PMID:29772016

The minute virus of mice (MVM) nonstructural protein NS1 induces nicking of MVM DNA at a unique site of the right-end telomere in both hairpin and duplex conformations in vitro.

PubMed

Willwand, K; Baldauf, A Q; Deleu, L; Mumtsidu, E; Costello, E; Beard, P; Rommelaere, J

1997-10-01

The right-end telomere of replicative form (RF) DNA of the autonomous parvovirus minute virus of mice (MVM) consists of a sequence that is self-complementary except for a three nucleotide loop around the axis of symmetry and an interior bulge of three unpaired nucleotides on one strand (designated the right-end 'bubble'). This right-end inverted repeat can exist in the form of a folded-back strand (hairpin conformation) or in an extended form, base-paired to a copy strand (duplex conformation). We recently reported that the right-end telomere is processed in an A9 cell extract supplemented with the MVM nonstructural protein NS1. This processing is shown here to result from the NS1-dependent nicking of the complementary strand at a unique position 21 nt inboard of the folded-back genomic 5' end. DNA species terminating in duplex or hairpin configurations, or in a mutated structure that has lost the right-end bulge, are all cleaved in the presence of NS1, indicating that features distinguishing these structures are not prerequisites for nicking under the in vitro conditions tested. Cleavage of the hairpin structure is followed by strand-displacement synthesis, generating the right-end duplex conformation, while processing of the duplex structure leads to the release of free right-end telomeres. In the majority of molecules, displacement synthesis at the right terminus stops a few nucleotides before reaching the end of the template strand, possibly due to NS1 which is covalently bound to this end. A fraction of the right-end duplex product undergoes melting and re-folding into hairpin structures (formation of a 'rabbit-ear' structure).

Characterization of microstructure and texture across dissimilar super duplex/austenitic stainless steel weldment joint by super duplex filler metal

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

Eghlimi, Abbas, E-mail: a.eghlimi@ma.iut.ac.ir; Shamanian, Morteza; Eskandarian, Masoomeh

In the present paper, microstructural changes across an as-welded dissimilar austenitic/duplex stainless steel couple welded by a super duplex stainless steel filler metal using gas tungsten arc welding process is characterized with optical microscopy and electron back-scattered diffraction techniques. Accordingly, variations of microstructure, texture, and grain boundary character distribution of base metals, heat affected zones, and weld metal were investigated. The results showed that the weld metal, which was composed of Widmanstätten austenite side-plates and allotriomorphic grain boundary austenite morphologies, had the weakest texture and was dominated by low angle boundaries. The welding process increased the ferrite content but decreasedmore » the texture intensity at the heat affected zone of the super duplex stainless steel base metal. In addition, through partial ferritization, it changed the morphology of elongated grains of the rolled microstructure to twinned partially transformed austenite plateaus scattered between ferrite textured colonies. However, the texture of the austenitic stainless steel heat affected zone was strengthened via encouraging recrystallization and formation of annealing twins. At both interfaces, an increase in the special character coincident site lattice boundaries of the primary phase as well as a strong texture with <100> orientation, mainly of Goss component, was observed. - Graphical abstract: Display Omitted - Highlights: • Weld metal showed local orientation at microscale but random texture at macroscale. • Intensification of <100> orientated grains was observed adjacent to the fusion lines. • The austenite texture was weaker than that of the ferrite in all duplex regions. • Welding caused twinned partially transformed austenites to form at SDSS HAZ. • At both interfaces, the ratio of special CSL boundaries of the primary phase increased.« less

Development and Evaluation of a Single-Step Duplex PCR for Simultaneous Detection of Fasciola hepatica and Fasciola gigantica (Family Fasciolidae, Class Trematoda, Phylum Platyhelminthes)

PubMed Central

Nguyen, Khue Thi; Nguyen, Nga Thi Bich; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Hoang, Chau Thi Minh; De, Nguyen Van

2012-01-01

A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap. PMID:22692744

Development and evaluation of a single-step duplex PCR for simultaneous detection of Fasciola hepatica and Fasciola gigantica (family Fasciolidae, class Trematoda, phylum Platyhelminthes).

PubMed

Le, Thanh Hoa; Nguyen, Khue Thi; Nguyen, Nga Thi Bich; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Hoang, Chau Thi Minh; De, Nguyen Van

2012-08-01

A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap.

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.

76 FR 64924 - Updating State Residential Building Energy Efficiency Codes

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-19

...) considers high-rise (greater than three stories) multifamily residential buildings and hotel, motel, and..., duplexes, townhouses, row houses, and low-rise multifamily buildings (not greater than three stories) such... pumps as compared to other electric heating technologies, this code change is expected to increase the...

Duplex tab exhaust nozzle

NASA Technical Reports Server (NTRS)

Gutmark, Ephraim Jeff (Inventor); Martens, Steven (nmn) (Inventor)

2012-01-01

An exhaust nozzle includes a conical duct terminating in an annular outlet. A row of vortex generating duplex tabs are mounted in the outlet. The tabs have compound radial and circumferential aft inclination inside the outlet for generating streamwise vortices for attenuating exhaust noise while reducing performance loss.

Computer Maintenance Operations Center (CMOC), showing duplexed cyber 170174 computers ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Computer Maintenance Operations Center (CMOC), showing duplexed cyber 170-174 computers - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

Specific DNA duplex formation at an artificial lipid bilayer: towards a new DNA biosensor technology.

PubMed

Werz, Emma; Korneev, Sergei; Montilla-Martinez, Malayko; Wagner, Richard; Hemmler, Roland; Walter, Claudius; Eisfeld, Jörg; Gall, Karsten; Rosemeyer, Helmut

2012-02-01

A novel technique is described which comprises a base-specific DNA duplex formation at a lipid bilayer-H(2) O-phase boundary layer. Two different probes of oligonucleotides both carrying a double-tailed lipid at the 5'-terminus were incorporated into stable artificial lipid bilayers separating two compartments (cis/trans-channel) of an optically transparent microfluidic sample carrier with perfusion capabilities. Both the cis- and trans-channels are filled with saline buffer. Injection of a cyanine-5-labeled target DNA sequence, which is complementary to only one of the oligonucleotide probes, into the cis-channel, followed by a thorough perfusion, leads to an immobilization of the labeled complementary oligonucleotide on the membrane as detected by single-molecule fluorescence spectroscopy and microscopy. In the case of fluorescent but non-complementary DNA sequences, no immobilized fluorescent oligonucleotide duplex could be detected on the membrane. This clearly verifies a specific duplex formation at the membrane interface. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

PubMed

Hithell, Gordon; Shaw, Daniel J; Donaldson, Paul M; Greetham, Gregory M; Towrie, Michael; Burley, Glenn A; Parker, Anthony W; Hunt, Neil T

2016-05-05

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.

Effect of C(60) fullerene on the duplex formation of i-motif DNA with complementary DNA in solution.

PubMed

Jin, Kyeong Sik; Shin, Su Ryon; Ahn, Byungcheol; Jin, Sangwoo; Rho, Yecheol; Kim, Heesoo; Kim, Seon Jeong; Ree, Moonhor

2010-04-15

The structural effects of fullerene on i-motif DNA were investigated by characterizing the structures of fullerene-free and fullerene-bound i-motif DNA, in the presence of cDNA and in solutions of varying pH, using circular dichroism and synchrotron small-angle X-ray scattering. To facilitate a direct structural comparison between the i-motif and duplex structures in response to pH stimulus, we developed atomic scale structural models for the duplex and i-motif DNA structures, and for the C(60)/i-motif DNA hybrid associated with the cDNA strand, assuming that the DNA strands are present in an ideal right-handed helical conformation. We found that fullerene shifted the pH-induced conformational transition between the i-motif and the duplex structure, possibly due to the hydrophobic interactions between the terminal fullerenes and between the terminal fullerenes and an internal TAA loop in the DNA strand. The hybrid structure showed a dramatic reduction in cyclic hysteresis.

Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations

PubMed Central

Makiguchi, Wataru; Tanabe, Junki; Yamada, Hidekazu; Iida, Hiroki; Taura, Daisuke; Ousaka, Naoki; Yashima, Eiji

2015-01-01

Self-recognition and self-discrimination within complex mixtures are of fundamental importance in biological systems, which entirely rely on the preprogrammed monomer sequences and homochirality of biological macromolecules. Here we report artificial chirality- and sequence-selective successive self-sorting of chiral dimeric strands bearing carboxylic acid or amidine groups joined by chiral amide linkers with different sequences through homo- and complementary-duplex formations. A mixture of carboxylic acid dimers linked by racemic-1,2-cyclohexane bis-amides with different amide sequences (NHCO or CONH) self-associate to form homoduplexes in a completely sequence-selective way, the structures of which are different from each other depending on the linker amide sequences. The further addition of an enantiopure amide-linked amidine dimer to a mixture of the racemic carboxylic acid dimers resulted in the formation of a single optically pure complementary duplex with a 100% diastereoselectivity and complete sequence specificity stabilized by the amidinium–carboxylate salt bridges, leading to the perfect chirality- and sequence-selective duplex formation. PMID:26051291

A model of EcoRII restriction endonuclease action: the active complex is most likely formed by one protein subunit and one DNA recognition site

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Kubareva, E. A.; Shabarova, Z. A.

1999-01-01

To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'. All binding substrate or substrate analogues tested could be divided into two major groups: (i) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type of complex, observed both in the presence and absence of Mg2+. Unlike the latter, duplexes under the first group can be hydrolyzed by endonuclease. Data obtained suggest that the active complex is most likely formed by one protein subunit and one DNA recognition sequence. A model of EcoRII endonuclease action is presented.

Recombinant DHX33 Protein Possesses Dual DNA/RNA Helicase Activity.

PubMed

Wang, Xingshun; Ge, Wei; Zhang, Yandong

2018-06-13

RNA helicase DHX33 has been shown to participate in a variety of cellular activities, including ribosome biogenesis, protein translation, and gene transcription. We and others further discovered that DHX33 is strongly expressed in several types of human cancers and plays important roles in promoting cancer cell proliferation. To better understand the molecular mechanism for DHX33 in exerting its biological functions, we purified recombinant DHX33 and performed biochemical studies in vitro. DHX33 protein was found to have ATPase activity that is dependent on DNA or RNA duplexes. The ATPase activity of DHX33 is coupled with its RNA/DNA unwinding activity. If a key residue in the ATP binding site were mutated, the mutant DHX33 could not unwind DNA/RNA duplexes. Furthermore, a deletion mutant of a RKK motif previously identified to be involved in ribosome DNA binding could still unwind DNA duplexes, albeit with reduced efficiency. In summary, our study reveals that purified DHX33 protein possesses unwinding activity toward DNA and RNA duplexes.

Detection of 12 respiratory viruses by duplex real time PCR assays in respiratory samples.

PubMed

Arvia, Rosaria; Corcioli, Fabiana; Ciccone, Nunziata; Della Malva, Nunzia; Azzi, Alberta

2015-12-01

Different viruses can be responsible for similar clinical manifestations of respiratory infections. Thus, the etiological diagnosis of respiratory viral diseases requires the detection of a large number of viruses. In this study, 6 duplex real-time PCR assays, using EvaGreen intercalating dye, were developed to detect 12 major viruses responsible for respiratory diseases: influenza A and B viruses, enteroviruses (including enterovirus spp, and rhinovirus spp), respiratory syncytial virus, human metapneumovirus, coronaviruses group I (of which CoV 229E and CoV NL63 are part) and II (including CoV OC43 and CoV HKU1), parainfluenza viruses type 1, 2, 3 and 4, human adenoviruses and human bocaviruses. The 2 target viruses of each duplex reaction were distinguishable by the melting temperatures of their amplicons. The 6 duplex real time PCR assays were applied for diagnostic purpose on 202 respiratory samples from 157 patients. One hundred fifty-seven samples were throat swabs and 45 were bronchoalveolar lavages. The results of the duplex PCR assays were confirmed by comparison with a commercial, validated, assay; in addition, the positive results were confirmed by sequencing. The analytical sensitivity of the duplex PCR assays varied from 10(3) copies/ml to 10(4) copies/ml. For parainfluenza virus 2 only it was 10(5) copies/ml. Seventy clinical samples (35%) from 55 patients (30 children and 25 adults) were positive for 1 or more viruses. In adult patients, influenza A virus was the most frequently detected respiratory virus followed by rhinoviruses. In contrast, respiratory syncytial virus was the most common virus in children, followed by enteroviruses, influenza A virus and coronavirus NL63. The small number of samples/patients does not allow us to draw any epidemiological conclusion. Altogether, the results of this study indicate that the 6 duplex PCR assays described in this study are sensitive, specific and cost-effective. Thus, this assay could be particularly useful to identify the main respiratory viruses directly from clinical samples, after nucleic acid extraction, and, also, to screen a large number of patients for epidemiological studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development of a Duplex Ultrasound Simulator and Preliminary Validation of Velocity Measurements in Carotid Artery Models.

PubMed

Zierler, R Eugene; Leotta, Daniel F; Sansom, Kurt; Aliseda, Alberto; Anderson, Mark D; Sheehan, Florence H

2016-07-01

Duplex ultrasound scanning with B-mode imaging and both color Doppler and Doppler spectral waveforms is relied upon for diagnosis of vascular pathology and selection of patients for further evaluation and treatment. In most duplex ultrasound applications, classification of disease severity is based primarily on alterations in blood flow velocities, particularly the peak systolic velocity (PSV) obtained from Doppler spectral waveforms. We developed a duplex ultrasound simulator for training and assessment of scanning skills. Duplex ultrasound cases were prepared from 2-dimensional (2D) images of normal and stenotic carotid arteries by reconstructing the common carotid, internal carotid, and external carotid arteries in 3 dimensions and computationally simulating blood flow velocity fields within the lumen. The simulator displays a 2D B-mode image corresponding to transducer position on a mannequin, overlaid by color coding of velocity data. A spectral waveform is generated according to examiner-defined settings (depth and size of the Doppler sample volume, beam steering, Doppler beam angle, and pulse repetition frequency or scale). The accuracy of the simulator was assessed by comparing the PSV measured from the spectral waveforms with the true PSV which was derived from the computational flow model based on the size and location of the sample volume within the artery. Three expert examiners made a total of 36 carotid artery PSV measurements based on the simulated cases. The PSV measured by the examiners deviated from true PSV by 8% ± 5% (N = 36). The deviation in PSV did not differ significantly between artery segments, normal and stenotic arteries, or examiners. To our knowledge, this is the first simulation of duplex ultrasound that can create and display real-time color Doppler images and Doppler spectral waveforms. The results demonstrate that an examiner can measure PSV from the spectral waveforms using the settings on the simulator with a mean absolute error in the velocity measurement of less than 10%. With the addition of cases with a range of pathologies, this duplex ultrasound simulator will be a useful tool for training health-care providers in vascular ultrasound applications and for assessing their skills in an objective and quantitative manner. © The Author(s) 2016.

Molecular basis for methoxyamine initiated mutagenesis. 1H nuclear magnetic resonance studies of base-modified oligodeoxynucleotides.

PubMed

Stone, M J; Nedderman, A N; Williams, D H; Lin, P K; Brown, D M

1991-12-05

In order to reach a more detailed understanding of the mechanism of the mutagenic action of methoxyamine and of N4-methoxycytidine and its 2'-deoxyribo-analogue, the solution structures of the self-complementary octanucleotide, d(CGAATTCG) and its analogues, d(CGAATCCG), d(CGAATMCG) and d(CGAATPCG) (designated 8mer-AT, 8mer-AC, 8mer-AM, and 8mer-AP, respectively), were investigated by 1H nuclear magnetic resonance spectroscopy; M is N4-methoxycytosine (mo4C) and P is an analogue, the bicyclic dihydropyrimido[4,5-c][1,2]oxazin-7-one, in which the N-O bond is held in the anti configuration with respect to N3 of the cytosine ring. Correlated spectroscopy and nuclear Overhauser spectroscopy allowed assignment of the base, anomeric and H2'/H2" protons in 8mers-AT, -AM and -AP, and showed that all three had features consistent with a regular B-DNA duplex structure. Duplex-to-coil transition temperatures were determined to be 52(+/- 2) degrees C (8mer-AT), 51(+/- 2) degrees C (8mer-AP), 32(+/- 2) degrees C (8mer-AM); on the chemical shift timescale, the melting transition was fast for 8mer-AT and 8mer-AP, but slow for 8mer-AM. Imino proton spectra were indicative of Watson-Crick base-pairing in 8mers-AT, -AP and -AM. The 8mer-AP duplex had a structure and melting characteristics virtually identical with those of the 8mer-AT duplex. The preferred syn configuration of the methoxyl group in M had a destabilising effect on the 8mer-AM duplex. At low temperatures, the A.M base-pair was in fast equilibrium between Watson-Crick and wobble configurations, with the methoxyl function anti-oriented, but the melting transition was accompanied by isomerization of the methoxyl group to the syn conformation. This syn-anti isomerization was the rate-determining step in the duplex-to-coil transition. The 8mer-AC oligomer did not form a stable duplex.

C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA.

PubMed

Aschenbrenner, Daniela; Baumann, Fabian; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

2015-07-20

Increased thermal or mechanical stability of DNA duplexes is desired for many applications in nanotechnology or -medicine where DNA is used as a programmable building block. Modifications of pyrimidine bases are known to enhance thermal stability and have the advantage of standard base-pairing and easy integration during chemical DNA synthesis. Through single-molecule force spectroscopy experiments with atomic force microscopy and the molecular force assay we investigated the effect of pyrimidines harboring C-5 propynyl modifications on the mechanical stability of double-stranded DNA. Utilizing these complementary techniques, we show that propynyl bases significantly increase the mechanical stability if the DNA is annealed at high temperature. In contrast, modified DNA complexes formed at room temperature and short incubation times display the same stability as non-modified DNA duplexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fault Injection Campaign for a Fault Tolerant Duplex Framework

NASA Technical Reports Server (NTRS)

Sacco, Gian Franco; Ferraro, Robert D.; von llmen, Paul; Rennels, Dave A.

2007-01-01

Fault tolerance is an efficient approach adopted to avoid or reduce the damage of a system failure. In this work we present the results of a fault injection campaign we conducted on the Duplex Framework (DF). The DF is a software developed by the UCLA group [1, 2] that uses a fault tolerant approach and allows to run two replicas of the same process on two different nodes of a commercial off-the-shelf (COTS) computer cluster. A third process running on a different node, constantly monitors the results computed by the two replicas, and eventually restarts the two replica processes if an inconsistency in their computation is detected. This approach is very cost efficient and can be adopted to control processes on spacecrafts where the fault rate produced by cosmic rays is not very high.

Effect of Secondary Phase Precipitation on the Corrosion Behavior of Duplex Stainless Steels.

PubMed

Chan, Kai Wang; Tjong, Sie Chin

2014-07-22

Duplex stainless steels (DSSs) with austenitic and ferritic phases have been increasingly used for many industrial applications due to their good mechanical properties and corrosion resistance in acidic, caustic and marine environments. However, DSSs are susceptible to intergranular, pitting and stress corrosion in corrosive environments due to the formation of secondary phases. Such phases are induced in DSSs during the fabrication, improper heat treatment, welding process and prolonged exposure to high temperatures during their service lives. These include the precipitation of sigma and chi phases at 700-900 °C and spinodal decomposition of ferritic grains into Cr-rich and Cr-poor phases at 350-550 °C, respectively. This article gives the state-of the-art review on the microstructural evolution of secondary phase formation and their effects on the corrosion behavior of DSSs.

Development of Weld Metal Microstructures in Pulsed Laser Welding of Duplex Stainless Steel

NASA Astrophysics Data System (ADS)

Mirakhorli, F.; Malek Ghaini, F.; Torkamany, M. J.

2012-10-01

The microstructure of the weld metal of a duplex stainless steel made with Nd:YAG pulsed laser is investigated at different travel speeds and pulse frequencies. In terms of the solidification pattern, the weld microstructure is shown to be composed of two distinct zones. The presence of two competing heat transfer channels to the relatively cooler base metal and the relatively hotter previous weld spot is proposed to develop two zones. At high overlapping factors, an array of continuous axial grains at the weld centerline is formed. At low overlapping factors, in the zone of higher cooling rate, a higher percentage of ferrite is transformed to austenite. This is shown to be because with extreme cooling rates involved in pulsed laser welding with low overlapping, the ferrite-to-austenite transformation can be limited only to the grain boundaries.

Duplex scanning diagnosis of internal carotid artery dissections. A case control study.

PubMed

Alecu, C; Fortrat, J O; Ducrocq, X; Vespignani, H; de Bray, J M

2007-01-01

The reliability of duplex scanning (DS) for the diagnosis of internal carotid artery dissections (ICAD) is not clear. Nine DS signs known to be suggestive for the diagnosis of ICAD were compared between 70 patients with ICAD and 70 matched patients without dissection. Visible internal tapering occlusion, regular eccentric narrowing channel, ectasia beyond the carotid bulb, resistive index asymmetry, blood flow slowdown, ophthalmic artery blood flow inversion, and biphasic flow are more frequent in cases than in controls (p < 0.001). Atheroma plaques were absent in 80% of ICAD. When DS direct signs and hemodynamic signs were studied, sensitivity was 90% and specificity 60%. Diagnosis of ICAD by DS could be improved if direct signs were combined with hemodynamic signs, giving a high sensitivity and a rather good specificity. Copyright 2007 S. Karger AG, Basel.

Preliminary Results from Duplex Procedure for Obtain of Fe Based Materials for Automotive Applications

NASA Astrophysics Data System (ADS)

Crăciun, R. C.; Stanciu, S.; Geantă, V.; Voiculescu, I.; Manole, V.; Gârneţ, I. A.; Alexandru, A.; Cimpoesu, N.; Săndulache, F.

2017-06-01

Abstract Iron based materials still represent a high percentage from metallic materials used in industry, in general, and in automotive industry, in particular. In this case we used a duplex process in order to obtain the FeMnSiAl experimental alloy for a more efficient use of various units. In the first stage iron, manganese, silicon and aluminum were melted and mixed together using arc melting technology and for the second stage the alloy was re-melt for homogeneity in an induction furnace. Chemical composition, after each melting step, was analyzed using EDS Bruker detector for various areas and microstructural characterization using SEM, VegaTescan LMH II with SE detector, equipment. This alloy is proposed as a metallic approach of mechanical dumpers used in automotive industry for low and medium impact contacts.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects

NASA Astrophysics Data System (ADS)

Whitley, Kevin D.; Comstock, Matthew J.; Chemla, Yann R.

2018-02-01

Despite their importance in biology and use in nanotechnology, the elastic behavior of nucleic acids on "ultrashort" (<15 nt ) length scales remains poorly understood. Here, we use optical tweezers combined with fluorescence imaging to observe directly the hybridization of oligonucleotides (7-12 nt) to a complementary strand under tension and to measure the difference in end-to-end extension between the single-stranded and duplex states. Data are consistent with long-polymer models at low forces (<8 pN ) but smaller than predicted at higher forces (>8 pN ), the result of the sequence-dependent duplex edge effects.

Method for construction of normalized cDNA libraries

DOEpatents

Soares, Marcelo B.; Efstratiadis, Argiris

1998-01-01

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries.

Method for construction of normalized cDNA libraries

DOEpatents

Soares, M.B.; Efstratiadis, A.

1998-11-03

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries. 19 figs.

Color-coded duplex sonography for diagnosis of testicular torsion.

PubMed

Zoeller, G; Ringert, R H

1991-11-01

By color-coded duplex sonography moving structures are visualized as red or blue colors within a normal gray-scale B-mode ultrasound image. Thus, blood flow even within small vessels can be visualized clearly. Color-coded duplex sonographic examination was performed in 11 patients who presented with scrotal pain. This method proved to be reliable to differentiate between testicular torsion and testicular inflammation. By clearly demonstrating a lack of intratesticular blood flow in testicular torsion, while avoiding flow in scrotal skin vessels being misinterpreted as intratesticular blood flow, this method significantly decreases the number of patients in whom surgical evaluation is necessary to exclude testicular torsion.

The Duplex Society.

ERIC Educational Resources Information Center

Schorr, Alvin L.

1984-01-01

The duplex society, in which the poor live in close proximity to others but in a separate compartment, is already with us. Unless something deeply changes about family income, more than one-third of future generations will come to adulthood having spent a portion of their childhood in official poverty. (RM)

Value of delayed duplex ultrasound assessment after endothermal ablation of the great saphenous vein.

PubMed

Ryer, Evan J; Elmore, James R; Garvin, Robert P; Cindric, Matthew C; Dove, James T; Kekulawela, Stephanie; Franklin, David P

2016-08-01

Endothermal ablation (ETA) of the great saphenous vein (GSV) is associated with a small but definite risk of endothermal heat-induced thrombosis (EHIT) extending into the common femoral vein. Follow-up duplex ultrasound imaging to detect EHIT after ETA is considered standard of care, although the exact timing of duplex ultrasound imaging to detect EHIT after ETA remains unclear. We hypothesized that an additional duplex ultrasound assessment 1 week after ETA would not identify a significant number of patients with EHIT and would significantly increase health care costs. This was a retrospective review of consecutive ETA GSV procedures from 2007 to 2014. All patients were evaluated with duplex ultrasound imaging on postprocedure day 1, and 79% of patients underwent a second ultrasound assessment 1 week postprocedure. EHIT was considered present when proximal GSV closure progressed to level ≥4, based on a six-tier classification system. From January 1, 2007, until December 31, 2014, 842 patients underwent GSV ETA. Patients with EHIT were more likely to have had a prior deep venous thrombosis (DVT; P = .002) and a larger GSV (P = .006). Forty-three procedures (5.1%) were classified as having EHIT requiring anticoagulation, based on a level ≥4 proximal closure level. Of the 43 patients with EHIT, 20 (47%) were found on the initial ultrasound assessment performed 24 hours postprocedure, but 19 patients (44%) with EHIT would not have been identified with a single postoperative ultrasound scan performed 24 hours after intervention. These 19 patients had a level ≤3 closure level at the duplex ultrasound scan performed 24 hours postprocedure and progressed to EHIT on the delayed duplex ultrasound scan. Lastly, thrombotic complications in four patients (9%), representing three late DVT and one DVT/pulmonary embolism presenting to another hospital, would not have been identified regardless of the postoperative surveillance strategy. Maximum GSV diameter was the only significant predictor of progression to EHIT on multivariate analysis (P = .007). Based on 2014 United States dollars, the two-ultrasound surveillance paradigm is associated with health care charges of $31,109 per identified delayed venous thromboembolism event. Delayed duplex ultrasound assessment after ETA of the GSV comes with associated health care costs but does yield a significant number of patients with progression to EHIT. Better understanding of the timing, risk factors, and significance of EHIT is needed to cost-effectively care for patients after ETA for varicose veins. Copyright © 2016 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

[Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

PubMed

Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A

2016-01-01

It is generally accepted that the important characteristic features of the Watson-Crick duplex originate from the molecular structure of its subunits. However, it still remains to elucidate what properties of each subunit are responsible for the significant characteristic features of the DNA structure. The computations of desoxydinucleoside monophosphates complexes with Na-ions using density functional theory revealed a pivotal role of DNA conformational properties of single-chain minimal fragments in the development of unique features of the Watson-Crick duplex. We found that directionality of the sugar-phosphate backbone and the preferable ranges of its torsion angles, combined with the difference between purines and pyrimidines. in ring bases, define the dependence of three-dimensional structure of the Watson-Crick duplex on nucleotide base sequence. In this work, we extended these density functional theory computations to the minimal' fragments of DNA duplex, complementary desoxydinucleoside monophosphates complexes with Na-ions. Using several computational methods and various functionals, we performed a search for energy minima of BI-conformation for complementary desoxydinucleoside monophosphates complexes with different nucleoside sequences. Two sequences are optimized using ab initio method at the MP2/6-31++G** level of theory. The analysis of torsion angles, sugar ring puckering and mutual base positions of optimized structures demonstrates that the conformational characteristic features of complementary desoxydinucleoside monophosphates complexes with Na-ions remain within BI ranges and become closer to the corresponding characteristic features of the Watson-Crick duplex crystals. Qualitatively, the main characteristic features of each studied complementary desoxydinucleoside monophosphates complex remain invariant when different computational methods are used, although the quantitative values of some conformational parameters could vary lying within the limits typical for the corresponding family. We observe that popular functionals in density functional theory calculations lead to the overestimated distances between base pairs, while MP2 computations and the newer complex functionals produce the structures that have too close atom-atom contacts. A detailed study of some complementary desoxydinucleoside monophosphate complexes with Na-ions highlights the existence of several energy minima corresponding to BI-conformations, in other words, the complexity of the relief pattern of the potential energy surface of complementary desoxydinucleoside monophosphate complexes. This accounts for variability of conformational parameters of duplex fragments with the same base sequence. Popular molecular mechanics force fields AMBER and CHARMM reproduce most of the conformational characteristics of desoxydinucleoside monophosphates and their complementary complexes with Na-ions but fail to reproduce some details of the dependence of the Watson-Crick duplex conformation on the nucleotide sequence.

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

PubMed Central

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.

2015-01-01

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s2U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s2U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s2U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s2U:A and s2U:U pairs and their native counterparts. These results indicate that s2U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s2U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s2U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s2U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying. PMID:26240387

The usefulness of Duplex Doppler ultrasound in the angiological and dermatological diagnosis of patients with blue toe syndrome.

PubMed

Pawlaczyk, Katarzyna; Gabriel, Marcin; Strzelecka-Węklar, Daria A; Krasiński, Zbigniew; Stanisic, Michal; Gabriel, Zofia; Dzieciuchowicz, Łukasz; Adamski, Zygmunt

2017-10-01

Peripheral microembolism is one of the most frequent causes of acute limb ischemia. In order to effectively prevent relapses it is essential to localize and eliminate the source of embolism. To evaluate the role of Duplex Doppler ultrasound examination in identifying the causes of blue toe syndrome (BTS). The group of 165 patients with clinical symptoms of BTS on their upper limbs ( n = 16) and lower limbs ( n = 149) was investigated. They all underwent Duplex Doppler ultrasound of the major arteries of the extremities, where ischemic changes occurred. Morphological and functional changes which might be potential sources of microembolism were identified in 146 patients. These changes included significant short-length stenoses or unstable atherosclerotic plaque ( n = 73), true aneurysms ( n = 42) and pseudoaneurysms ( n = 17). In 11 cases, pathology of vascular prostheses in the form of anastomotic aneurysms, infection and residual thrombi after fibrinolysis was detected. In all cases, Duplex diagnosis was confirmed by other imaging and intraoperative tests. Duplex Doppler ultrasound of the arteries in the affected limb with a full length view should be the first-line examination in diagnosing patients with BTS. In the absence of hemodynamic blood flow disturbances in the major arteries in patients with symptoms of BTS, it is advisable to start haematological tests to identify/exclude congenital or acquired thrombophilia.

A tectonic model for the spatial occurrence of porphyry copper and polymetallic vein deposits - applications to Central Europe

USGS Publications Warehouse

Drew, Lawrence J.

2006-01-01

A structural-tectonic model, which was developed to assess the occurrence of undiscovered porphyry copper deposits and associated polymetallic vein systems for the Matra Mountains, Hungary, has been expanded here and applied to other parts of central Europe. The model explains how granitoid stocks are emplaced and hydrothermal fluids flow within local strain features (duplexes) within strike-slip fault systems that develop in continental crust above subducting plates. Areas of extension that lack shear at the corners and along the edges of the fault duplexes are structural traps for the granitoid stocks associated with porphyry copper deposits. By contrast, polymetallic vein deposits are emplaced where shear and extension are prevalent in the interior of the duplexes. This model was applied to the Late Cretaceous-age porphyry copper and polymetallic vein deposits in the Banat-Timok-Srednogorie region of Romania-Serbia-Bulgaria and the middle Miocene-age deposits in Romania and Slovakia. In the first area, porphyry copper deposits are most commonly located at the corners, and occasionally along the edges, of strike-slip fault duplexes, and the few polymetallic vein deposits identified are located at interior sites of the duplexes. In the second area, the model accounts for the preferred sites of porphyry copper and polymetallic vein deposits in the Apuseni Mountains (Romania) and central Slovakian volcanic field (Slovakia).

Ultra-short silicon MMI duplexer

NASA Astrophysics Data System (ADS)

Yi, Huaxiang; Huang, Yawen; Wang, Xingjun; Zhou, Zhiping

2012-11-01

The fiber-to-the-home (FTTH) systems are growing fast these days, where two different wavelengths are used for upstream and downstream traffic, typically 1310nm and 1490nm. The duplexers are the key elements to separate these wavelengths into different path in central offices (CO) and optical network unit (ONU) in passive optical network (PON). Multimode interference (MMI) has some benefits to be a duplexer including large fabrication tolerance, low-temperature dependence, and low-polarization dependence, but its size is too large to integrate in conventional case. Based on the silicon photonics platform, ultra-short silicon MMI duplexer was demonstrated to separate the 1310nm and 1490nm lights. By studying the theory of self-image phenomena in MMI, the first order images are adopted in order to keep the device short. A cascaded MMI structure was investigated to implement the wavelength splitting, where both the light of 1310nm and 1490nm was input from the same port, and the 1490nm light was coupling cross the first MMI and output at the cross-port in the device while the 1310nm light was coupling through the first and second MMI and output at the bar-port in the device. The experiment was carried on with the SOI wafer of 340nm top silicon. The cascaded MMI was investigated to fold the length of the duplexer as short as 117μm with the extinct ratio over 10dB.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands.

PubMed

Shen, Zhanhang; Mulholland, Kelly A; Zheng, Yujun; Wu, Chun

2017-09-01

DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge. Daunomycin and doxorubicin, two commonly used anticancer drugs, are examples of non-selective DNA ligands. In this study, we extended our early all-atom binding simulation studies between doxorubicin and a DNA duplex (d(CGATCG) 2 ) to probe the binding between daunomycin and a parallel DNA quadruplex (d(TGGGGT) 4 ) and DNA duplex. In addition to the end stacking mode, which mimics the mode in the crystal structure, a pure groove binding mode was observed in our free binding simulations. The dynamic and energetic properties of these two binding modes are thoroughly examined, and a detailed comparison is made between DNA quadruplex binding modes and DNA duplex binding modes. Implications on the design of more selective DNA quadruplex ligands are also discussed. Graphical abstract Top stacking and groov binding modes from the MD simulations.

Electronic coupling between Watson-Crick pairs for hole transfer and transport in desoxyribonucleic acid

NASA Astrophysics Data System (ADS)

Voityuk, Alexander A.; Jortner, Joshua; Bixon, M.; Rösch, Notker

2001-04-01

Electronic matrix elements for hole transfer between Watson-Crick pairs in desoxyribonucleic acid (DNA) of regular structure, calculated at the Hartree-Fock level, are compared with the corresponding intrastrand and interstrand matrix elements estimated for models comprised of just two nucleobases. The hole transfer matrix element of the GAG trimer duplex is calculated to be larger than that of the GTG duplex. "Through-space" interaction between two guanines in the trimer duplexes is comparable with the coupling through an intervening Watson-Crick pair. The gross features of bridge specificity and directional asymmetry of the electronic matrix elements for hole transfer between purine nucleobases in superstructures of dimer and trimer duplexes have been discussed on the basis of the quantum chemical calculations. These results have also been analyzed with a semiempirical superexchange model for the electronic coupling in DNA duplexes of donor (nuclobases)-acceptor, which incorporates adjacent base-base electronic couplings and empirical energy gaps corrected for solvation effects; this perturbation-theory-based model interpretation allows a theoretical evaluation of experimental observables, i.e., the absolute values of donor-acceptor electronic couplings, their distance dependence, and the reduction factors for the intrastrand hole hopping or trapping rates upon increasing the size of the nucleobases bridge. The quantum chemical results point towards some limitations of the perturbation-theory-based modeling.

A heat treatment procedure to produce fine-grained lamellar microstructures in a P/M titanium aluminide alloy

NASA Astrophysics Data System (ADS)

Au, Peter

A process for fabricating advanced aerospace titanium aluminide alloys starting from metal powders (the hot isostatically consolidated P/M process) is presented in this thesis. This process does not suffer the difficulties of chemical inhomogeneities and coarse grain structure of castings. In addition heat treatments which take advantage of the refined structure of HIP processed materials are developed to achieve microstructure control and subsequent mechanical property control. It is shown that a better "property balance" is possible after the heat treatment of HIP consolidated materials than it is with alternative processing. It is well understood that the standard microstructures (near-gamma, duplex, nearly lamellar, and fully lamellar) do not have the balanced mechanical properties (tensile, yield, creep and fatigue strength, ductility and fracture toughness) necessary for optimal performance in aero engine and automotive applications. In this work a fine-grained fully lamellar (FGFL) microstructure is developed for property control and in particular for achieving a much improved property balance. A heat treatment procedure for this purpose which consists of cyclic processing in the alpha transus temperature region to achieve an FGFL structure with grain sizes in the range of 50 mum to 150 mum is presented. Compared with conventional duplex structured materials, the minimum creep rate is an order of magnitude lower with only a 10% loss in tensile yield strength. Moreover, a three-fold increase in tensile elongation is possible by converting to an FGFL structure with only a 30% loss in minimum creep rate. These are attractive trade-offs when considering the use of these alloys for aerospace purposes. A thorough literature review of the mechanisms of formation of standard microstructures and their deformation under mechanical loading is contained in the thesis. In addition, conventional techniques to produce FGFL microstructures in wrought and cast materials are discussed in detail. Beyond the review, the results of experiments are described for determining the alpha transus temperature, the phase transformation kinetics in this region and the effects of heat treatment time and cooling rate on microstructure. Based on this preliminary work, a heat treatment to achieve a FGFL microstructure with grain sizes in the range of 50 mum to 150 mum is proposed and confirmed. The room temperature and high temperature mechanical properties of these materials are compared with those of conventional duplex and fully lamellar structures. The results of this experimentation are discussed in terms of the fundamental mechanisms for controlling microstructure and mechanical properties in these materials. The potential for applying cyclic heat treatments to cast and wrought materials to improve the mechanical property balance in engineering practice is discussed.

Considerations in Duplex Investment.

ERIC Educational Resources Information Center

Wright, Arthur; Goen, Tom

Problems of duplex investment are noted in the introduction to this booklet designed to provide a technique by which the investment decision can be approached, develop estimates of typical costs and returns under differing conditions, and encourage investors to analyze objectives and conditions before the decision to buy or build is made. A…

Project: Toward a National Educational Testing Network. Final Report.

ERIC Educational Resources Information Center

Bock, Darrell R.

Three fiscal year 1987 deliverables due for the "Toward a National Educational Testing Network: Feasibility Study of Duplex Design" are presented. The study is concerned with implementation of statewide and interstate testing of student attainment. The report includes: (1) a duplex design (DD) review paper discussing the means by which…

Comprehensive Educational Assessment for the States: The Duplex Design.

ERIC Educational Resources Information Center

Bock, R. Darrell; Mislevy, Robert J.

1988-01-01

The duplex design is proposed for educational assessment within a state school system. For individual students, scaled proficiency measures that are suitable for guidance and certification at various levels of attainment are provided. For classrooms or larger units, the design can supply group level measures for evaluation and research. (SLD)

2,6-Diaminopurine to TNA: Effect on Duplex Stabilities and on the Efficiency of Template-Controlled Ligations

NASA Technical Reports Server (NTRS)

Wu, Xiaolin; Delgado, Guillermo; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

2003-01-01

Replacement of adenine by 2,6-diaminopurine-two nucleobases to be considered equivalent from an etlological point of view-strongly enhances the stability of TNA/TNA, TNA/RNA, or TNA/DNA duplexes and efficiently accelerates template-directed ligation of TNA ligands.

47 CFR 27.50 - Power limits and duty cycle.

Code of Federal Regulations, 2011 CFR

2011-10-01

... supporting frequency division duplex (FDD) mobile and portable operations are restricted to transmitting in... duty cycle must not exceed 38 percent; for WCS CPE using FDD technology, the duty cycle must not exceed... stations using frequency division duplex (FDD) technology, the duty cycle must not exceed 12.5 percent in...

47 CFR 27.50 - Power limits and duty cycle.

Code of Federal Regulations, 2012 CFR

2012-10-01

... supporting frequency division duplex (FDD) mobile and portable operations are restricted to transmitting in... duty cycle must not exceed 38 percent; for WCS CPE using FDD technology, the duty cycle must not exceed... stations using frequency division duplex (FDD) technology, the duty cycle must not exceed 12.5 percent in...

The first example of a Hoogsteen base-paired DNA duplex in dynamic equilibrium with a Watson-Crick base-paired duplex--a structural (NMR), kinetic and thermodynamic study.

PubMed

Isaksson, J; Zamaratski, E; Maltseva, T V; Agback, P; Kumar, A; Chattopadhyaya, J

2001-06-01

A single-point substitution of the O4' oxygen by a CH2 group at the sugar residue of A6 (i.e. 2'-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5'-d(C1G2C3G4A5A6T7T8C9G10C11G12)2(-3), has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A), akin to the native counterpart, to a doubly A6:T7 Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A)<==>(1B): Keq = k1/k(-1) = 0.56+/-0.08. The dynamic conversion of the fully Watson-Crick basepaired (1A) to the partly Hoogsteen basepaired (1B) structure is marginally kinetically and thermodynamically disfavoured [k1 (298K) = 3.9 0.8 sec(-1); deltaHdegrees++ = 164+/-14 kJ/mol; -TdeltaS degrees++ (298K) = -92 kJ/mol giving a deltaG degrees++ 298 of 72 kJ/mol. Ea (k1) = 167 14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0 0.6 sec-1, deltaH degrees++ = 153 13 kJ/mol; -TdeltaSdegrees++ (298K) = -82 kJ/mol giving a deltaGdegrees++(298) of 71 kJ/mol. Ea (k-1) = 155 13 kJ/mol]. Acomparison of deltaGdegrees++(298) of the forward (k1) and backward (k-1) conversions, (1A)<==>(1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex. The chemical environments of the two interconverting DNA duplexes are very different as evident from their widely separated sets of chemical shifts connected by temperature-dependent exchange peaks in the NOESY and ROESY spectra. The fully Watson-Crick basepaired structure (1A) is based on a total of 127 intra, 97 inter and 17 cross-strand distance constraints per strand, whereas the double A6:T7 Hoogsteen basepaired (1B) structure is based on 114 intra, 92 inter and 15 cross-strand distance constraints, giving an average of 22 and 20 NOE distance constraints per residue and strand, respectively. In addition, 55 NMR-derived backbone dihedral constraints per strand were used for both structures. The main effect of the Hoogsteen basepairs in (1B) on the overall structure is a narrowing of the minor groove and a corresponding widening of the major groove. The Hoogsteen basepairing at the central A6:T7 basepairs in (1B) has enforced a syn conformation on the glycosyl torsion of the 2'-deoxyaristeromycin moiety, A6, as a result of substitution of the endocyclic 4'-oxygen in the natural sugar with a methylene group in A6. A comparison of the Watson-Crick basepaired duplex (1A) to the Hoogsteen basepaired duplex (1B) shows that only a few changes, mainly in alpha, sigma and gamma torsions, in the sugar-phosphate backbone seem to be necessary to accommodate the Hoogsteen basepair.

Impact Analysis of Flow Shaping in Ethernet-AVB/TSN and AFDX from Network Calculus and Simulation Perspective

PubMed Central

He, Feng; Zhao, Lin; Li, Ershuai

2017-01-01

Ethernet-AVB/TSN (Audio Video Bridging/Time-Sensitive Networking) and AFDX (Avionics Full DupleX switched Ethernet) are switched Ethernet technologies, which are both candidates for real-time communication in the context of transportation systems. AFDX implements a fixed priority scheduling strategy with two priority levels. Ethernet-AVB/TSN supports a similar fixed priority scheduling with an additional Credit-Based Shaper (CBS) mechanism. Besides, TSN can support time-triggered scheduling strategy. One direct effect of CBS mechanism is to increase the delay of its flows while decreasing the delay of other priority ones. The former effect can be seen as the shaping restriction and the latter effect can be seen as the shaping benefit from CBS. The goal of this paper is to investigate the impact of CBS on different priority flows, especially on the intermediate priority ones, as well as the effect of CBS bandwidth allocation. It is based on a performance comparison of AVB/TSN and AFDX by simulation in an automotive case study. Furthermore, the shaping benefit is modeled based on integral operation from network calculus perspective. Combing with the analysis of shaping restriction and shaping benefit, some configuration suggestions on the setting of CBS bandwidth are given. Results show that the effect of CBS depends on flow loads and CBS configurations. A larger load of high priority flows in AVB tends to a better performance for the intermediate priority flows when compared with AFDX. Shaping benefit can be explained and calculated according to the changing from the permitted maximum burst. PMID:28531158

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.

Exo-Dye-based assay for rapid, inexpensive, and sensitive detection of DNA-binding proteins.

PubMed

Chen, Zaozao; Ji, Meiju; Hou, Peng; Lu, Zuhong

2006-07-07

We reported herein a rapid, inexpensive, and sensitive technique for detecting sequence-specific DNA-binding proteins. In this technique, the common exonuclease III (ExoIII) footprinting assay is coupled with simple SYBR Green I staining for monitoring the activities of DNA-binding proteins. We named this technique as ExoIII-Dye-based assay. In this assay, a duplex probe was designed to detect DNA-binding protein. One side of the probe contains one protein-binding site, and another side of it contains five protruding bases at 3' end for protection from ExoIII digestion. If a target protein is present, it will bind to binding sites of probe and produce a physical hindrance to ExoIII, which protects the duplex probe from digestion of ExoIII. SYBR Green I will bind to probe, which results in high fluorescence intensity. On the contrary, in the absence of the target protein, the naked duplex probe will be degraded by ExoIII. SYBR Green I will be released, which results in a low fluorescence intensity. In this study, we employed this technique to successfully detect transcription factor NF-kappaB in crude cell extracts. Moreover, it could also be used to evaluate the binding affinity of NF-kappaB. This technique has therefore wide potential application in research, medical diagnosis, and drug discovery.

Effect of welding process on the microstructure and properties of dissimilar weld joints between low alloy steel and duplex stainless steel

NASA Astrophysics Data System (ADS)

Wang, Jing; Lu, Min-xu; Zhang, Lei; Chang, Wei; Xu, Li-ning; Hu, Li-hua

2012-06-01

To obtain high-quality dissimilar weld joints, the processes of metal inert gas (MIG) welding and tungsten inert gas (TIG) welding for duplex stainless steel (DSS) and low alloy steel were compared in this paper. The microstructure and corrosion morphology of dissimilar weld joints were observed by scanning electron microscopy (SEM); the chemical compositions in different zones were detected by energy-dispersive spectroscopy (EDS); the mechanical properties were measured by microhardness test, tensile test, and impact test; the corrosion behavior was evaluated by polarization curves. Obvious concentration gradients of Ni and Cr exist between the fusion boundary and the type II boundary, where the hardness is much higher. The impact toughness of weld metal by MIG welding is higher than that by TIG welding. The corrosion current density of TIG weld metal is higher than that of MIG weld metal in a 3.5wt% NaCl solution. Galvanic corrosion happens between low alloy steel and weld metal, revealing the weakness of low alloy steel in industrial service. The quality of joints produced by MIG welding is better than that by TIG welding in mechanical performance and corrosion resistance. MIG welding with the filler metal ER2009 is the suitable welding process for dissimilar metals jointing between UNS S31803 duplex stainless steel and low alloy steel in practical application.

DNA triplex structure, thermodynamics, and destabilisation: insight from molecular simulations.

PubMed

Boehm, Belinda J; Whidborne, Charles; Button, Alexander L; Pukala, Tara L; Huang, David M

2018-05-23

Molecular dynamics simulations are used to elucidate the structure and thermodynamics of DNA triplexes associated with the neurodegenerative disease Friedreich's ataxia (FRDA), as well as complexes of these triplexes with the small molecule netropsin, which is known to destabilise triplexes. The ability of molecular simulations in explicit solvent to accurately capture triplex thermodynamics is verified for the first time, with the free energy to dissociate a 15-base antiparallel purine triplex-forming oligomer (TFO) from the duplex found to be slightly higher than reported experimentally. The presence of netropsin in the minor groove destabilises the triplex as expected, reducing the dissociation free energy by approximately 50%. Netropsin binding is associated with localised narrowing of the minor groove near netropsin, an effect that has previously been under contention. This leads to localised widening of the major groove, weakening hydrogen bonds between the TFO and duplex. Consequently, destabilisation is found to be highly localised, occurring only when netropsin is bound directly opposite the TFO. The simulations also suggest that near saturation of the minor groove with ligand is required for complete triplex dissociation. A structural analysis of the DNA triplexes that can form with the FRDA-related duplex sequence indicates that the triplex with a parallel homopyrimidine TFO is likely to be more stable than the antiparallel homopurine-TFO triplex, which may have implications for disease onset and treatment.

Detection of secondary phases in duplex stainless steel by magnetic force microscopy and scanning Kelvin probe force microscopy

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

Ramírez-Salgado, J.; Domínguez-Aguilar, M.A., E-mail: madoming@imp.mx; Castro-Domínguez, B.

2013-12-15

The secondary phase transformations in a commercial super duplex stainless steel were investigated by micro-chemical analyses and high resolution scanning probe microscopy. Energy dispersive X-ray and electron probe detected ferrite and austenite as well as secondary phases in unetched aged duplex stainless steel type 25Cr-7Ni-3Mo. Volta potential indicated that nitride and sigma appeared more active than ferrite, while secondary austenite and austenite presented a nobler potential. Reversal order in nobility is thought to be attributable to the potential ranking provided by oxide nature diversity as a result of secondary phase surface compositions on steel. After eutectoid transformation, secondary austenite wasmore » detected by electron probe microanalysis, whereas atomic force microscopy distinguished this phase from former austenite by image contrast. Magnetic force microscopy revealed a “ghosted” effect on the latter microstructure probably derived from metal memory reminiscence of mechanical polishing at passivity and long range magnetic forces of ferrite phase. - Highlights: • Nobility detection of secondary phases by SKPFM in DSS particles is not a straightforward procedure. • As Volta potential and contrast are not always consistent SKPFM surface oxides is thought played an important role in detection. • AFM distinguished secondary austenite from former austenite by image contrast though SEM required EPMA.« less

Label-free liquid crystal biosensor based on specific oligonucleotide probes for heavy metal ions.

PubMed

Yang, Shengyuan; Wu, Chao; Tan, Hui; Wu, Yan; Liao, Shuzhen; Wu, Zhaoyang; Shen, Guoli; Yu, Ruqin

2013-01-02

In this study, to enhance the capability of metal ions disturbing the orientation of liquid crystals (LCs), we designed a new label-free LC biosensor for the highly selective and sensitive detection of heavy metal ions. This strategy makes use of the target-induced DNA conformational change to enhance the disruption of target molecules for the orientation of LC leading to an amplified optical signal. The Hg(2+) ion, which possesses a unique property to bind specifically to two DNA thymine (T) bases, is used as a model heavy metal ion. In the presence of Hg(2+), the specific oligonucleotide probes form a conformational reorganization of the oligonucleotide probes from hairpin structure to duplex-like complexes. The duplex-like complexes are then bound on the triethoxysilylbutyraldehyde/N,N-dimethyl-N-octadecyl (3-aminopropyl) trimethoxysilyl chloride (TEA/DMOAP)-coated substrate modified with capture probes, which can greatly distort the orientational profile of LC, making the optical image of LC cell birefringent as a result. The optical signal of LC sensor has a visible change at the Hg(2+) concentration of low to 0.1 nM, showing good detection sensitivity. The cost-effective LC sensing method can translate the concentration signal of heavy metal ions in solution into the presence of DNA duplexes and is expected to be a sensitive detection platform for heavy metal ions and other small molecule monitors.

Yeast Pif1 Accelerates Annealing of Complementary DNA Strands

PubMed Central

2015-01-01

Pif1 is a helicase involved in the maintenance of nuclear and mitochondrial genomes in eukaryotes. Here we report a new activity of Saccharomyces cerevisiae Pif1, annealing of complementary DNA strands. We identified preferred substrates for annealing as those that generate a duplex product with a single-stranded overhang relative to a blunt end duplex. Importantly, we show that Pif1 can anneal DNA in the presence of ATP and Mg2+. Pif1-mediated annealing also occurs in the presence of single-stranded DNA binding proteins. Additionally, we show that partial duplex substrates with 3′-single-stranded overhangs such as those generated during double-strand break repair can be annealed by Pif1. PMID:25393406

Spermine moiety attached to the C-5 position of deoxyuridine enhances the duplex stability of the phosphorothioate DNA/complementary DNA and shows the susceptibility of the substrate to RNase H.

PubMed

Moriguchi, Tomohisa; Sakai, Hideaki; Suzuki, Hideo; Shinozuka, Kazuo

2008-09-01

Novel phosphorothioate-modified oligodeoxynucleotides (S-ODNs) containing a deoxyuridine derivative bearing a spermine moiety at the C-5 position were synthesized. The study of the thermal stability and the thermodynamic stability showed that the modified S-ODNs have been able to form the stable duplexes with the complementary DNA. It was also found that the duplex composed of the modified S-ODN and its complementary RNA strand is the substrate for Escherichia coli RNase H, and the cleavage of the RNA strand by the enzyme was almost similar as in the case of the unmodified one.

Yeast Pif1 accelerates annealing of complementary DNA strands.

PubMed

Ramanagoudr-Bhojappa, Ramanagouda; Byrd, Alicia K; Dahl, Christopher; Raney, Kevin D

2014-12-09

Pif1 is a helicase involved in the maintenance of nuclear and mitochondrial genomes in eukaryotes. Here we report a new activity of Saccharomyces cerevisiae Pif1, annealing of complementary DNA strands. We identified preferred substrates for annealing as those that generate a duplex product with a single-stranded overhang relative to a blunt end duplex. Importantly, we show that Pif1 can anneal DNA in the presence of ATP and Mg(2+). Pif1-mediated annealing also occurs in the presence of single-stranded DNA binding proteins. Additionally, we show that partial duplex substrates with 3'-single-stranded overhangs such as those generated during double-strand break repair can be annealed by Pif1.

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

PubMed

Sakuraba, Shun; Asai, Kiyoshi; Kameda, Tomoshi

2015-11-05

The dimerization free energies of RNA-RNA duplexes are fundamental values that represent the structural stability of RNA complexes. We report a comparative analysis of RNA-RNA duplex dimerization free-energy changes upon mutations, estimated from a molecular dynamics simulation and experiments. A linear regression for nine pairs of double-stranded RNA sequences, six base pairs each, yielded a mean absolute deviation of 0.55 kcal/mol and an R(2) value of 0.97, indicating quantitative agreement between simulations and experimental data. The observed accuracy indicates that the molecular dynamics simulation with the current molecular force field is capable of estimating the thermodynamic properties of RNA molecules.

Effect of solution treatment on microstructure and properties of duplex stainless steel

NASA Astrophysics Data System (ADS)

Wang, X. Y.; Luo, J. M.; Huang, L. Q.; Wang, H. B.; Ma, C. W.

2017-09-01

The influence of solution treatment on microstructure and properties of 2205 duplex stainless steel (DSS) was studied. The microstructure, precipitates and corrosion resisting property were observed and analyzed by means of optical microscopy (OM), scanning electron microscopy (SEM) and electrochemical methods. The results showed that a large number of brittle σ-phase precipitates, which deteriorate the plasticity and corrosion resistance of the material, were easy to produce in the duplex stainless steel under the low temperature. The precipitation of σ-phase can be decreased and the plasticity and corrosion resistance can be improved by increasing solution temperature. In addition, the ferrite content increases with the increase of solution temperature, while less affected by cooling rate.

Design under Constraints: The Case of Large-Scale Assessment Systems

ERIC Educational Resources Information Center

Mislevy, Robert J.

2010-01-01

In "Updating the Duplex Design for Test-Based Accountability in the Twenty-First Century," Bejar and Graf (2010) propose extensions to the duplex design for large-scale assessment presented in Bock and Mislevy (1988). Examining the range of people who use assessment results--from students, teachers, administrators, curriculum designers,…

Comprehensive Educational Assessment for the States: The Duplex Design.

ERIC Educational Resources Information Center

Bock, R. Darrell; Mislevy, Robert

State testing programs often attempt to provide annual information for use in student guidance and qualification, school and program evaluation, and broad policy decisions. With the development of a new type of assessment instrument, the "duplex design," the several functions of state testing programs can be served in a single test…

Interstrand disulfide crosslinking of DNA bases supports a double nucleotide unpairing mechanism for flap endonucleases.

PubMed

Beddows, Amanda; Patel, Nikesh; Finger, L David; Atack, John M; Williams, David M; Grasby, Jane A

2012-09-14

Flap endonucleases (FENs) are proposed to select their target phosphate diester by unpairing the two terminal nucleotides of duplex. Interstrand disulfide crosslinks, introduced by oxidation of thiouracil and thioguanine bases, abolished the specificity of human FEN1 for hydrolysis one nucleotide into the 5'-duplex.

Pyrrolo-dC modified duplex DNA as a novel probe for the sensitive assay of base excision repair enzyme activity.

PubMed

Lee, Chang Yeol; Park, Ki Soo; Park, Hyun Gyu

2017-12-15

We develop a novel approach to determine formamidopyrimidine DNA glycosylase (Fpg) activity by taking advantage of the unique fluorescence property of pyrrolo-dC (PdC) positioned opposite to 8-oxoguanine (8-oxoG) in duplex DNA. In its initial state, PdC in duplex DNA undergoes the efficient stacking and collisional quenching interactions, showing the low fluorescence signal. In contrast, the presence of Fpg, which specifically removes 8-oxoG and incises resulting apurinic (AP) site, transforms duplex DNA into single-stranded (ss) DNAs. As a result, the intrinsic fluorescence signal of PdC in ssDNA is recovered to exhibit the significantly enhanced fluorescence signal. Based on this Fpg-dependent fluorescence response of PdC, we could reliably determine Fpg activity down to 1.25U/ml with a linear response from 0 to 50U/ml. In addition, the diagnostic capability of this strategy was successfully demonstrated by reliably assaying Fpg activity in human blood serum, showing its great potential in the practical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Human CST has independent functions during telomere duplex replication and C-strand fill-in

PubMed Central

Wang, Feng; Stewart, Jason A.; Kasbek, Christopher; Zhao, Yong; Wright, Woodring E.; Price, Carolyn M.

2012-01-01

Summary Human CST (CTC1-STN1-TEN1) is an RPA-like complex that is needed for efficient replication through the telomere duplex and genome-wide replication restart after fork stalling. Here we show that STN1/CST has a second function in telomere replication during G-overhang maturation. Analysis of overhang structure after STN1 depletion revealed normal kinetics for telomerase-mediated extension in S-phase but a delay in subsequent overhang shortening. This delay resulted from a defect in C-strand fill-in. Short telomeres exhibited the fill-in defect but normal telomere duplex replication, indicating that STN1/CST functions independently in these processes. Our work also indicates that the requirement for STN1/CST in telomere duplex replication correlates with increasing telomere length and replication stress. Our results provide the first direct evidence that STN1/CST participates in C-strand fill-in. They also demonstrate that STN1/CST participates in two mechanistically separate steps during telomere replication and identify CST as a novel replication factor that solves diverse replication-associated problems. PMID:23142664

Direct duplex real-time loop mediated isothermal amplification assay for the simultaneous detection of cow and goat species origin of milk and yogurt products for field use.

PubMed

Kim, Mi-Ju; Kim, Hae-Yeong

2018-04-25

A multiple loop-mediated isothermal amplification (LAMP) method was developed to detect cow and goat milk in the field using a portable fluorescence device. For rapid on-site detection, this duplex LAMP assay was used in combination with direct amplification, without DNA extraction. The cow- and goat-specific LAMP primer sets were designed based on the mitochondrial cytochrome b gene, and showed specificity against 13 other animal species in the reactions. The sensitivity of the duplex LAMP assay for cow and goat was 0.1 and 1 pg, respectively. The detection limit for both target species in milk mixtures was 2%. This assay successfully amplified and identified the two target species in 24 samples of commercial milk and yogurt products, with 30 min sampling-to-result analysis time. Therefore, this direct duplex real-time LAMP assay is useful for on-site simultaneous detection of cow and goat milk in commercial products, a capability needed to confirm accurate labeling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability.

PubMed

Moreira, Bernardo G; You, Yong; Behlke, Mark A; Owczarzy, Richard

2005-02-11

Single and dual-labeled fluorescent oligodeoxynucleotides are used in many molecular biology applications. We investigated the effects of commonly used fluorescent dyes and quenchers on the thermodynamic stability of a model probe-target DNA duplex. We demonstrate that those effects can be significant. Fluorescent dyes and quenchers were attached to the probe ends. In certain combinations, these groups stabilized the duplex up to 1.8kcal/mol and increased T(m) up to 4.3 degrees C. None of the groups tested significantly destabilized the duplex. Rank order of potency was, starting with the most stabilizing group: Iowa Black RQ approximately Black Hole 2>Cy5 approximately Cy3>Black Hole 1>QSY7 approximately Iowa Black FQ>Texas Red approximately TAMRA>FAM approximately HEX approximately Dabcyl>TET. Longer linkers decreased stabilizing effects. Hybridizations to targets with various dangling ends were also studied and were found to have only minor effects on thermodynamic stability. Depending on the dye/quencher combination employed, it can be important to include thermodynamic contributions from fluorophore and quencher when designing oligonucleotide probe assays.