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Sample records for incises duplex dna

  1. DNA Methylation Modulates Nociceptive Sensitization after Incision.

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    Yuan Sun

    Full Text Available DNA methylation is a key epigenetic mechanism controlling DNA accessibility and gene expression. Blockade of DNA methylation can significantly affect pain behaviors implicated in neuropathic and inflammatory pain. However, the role of DNA methylation with regard to postoperative pain has not yet been explored. In this study we sought to investigate the role of DNA methylation in modulating incisional pain and identify possible targets under DNA methylation and contributing to incisional pain. DNA methyltranferase (DNMT inhibitor 5-Aza-2'-deoxycytidine significantly reduced incision-induced mechanical allodynia and thermal sensitivity. Aza-2'-deoxycytidine also reduced hindpaw swelling after incision, suggesting an anti-inflammatory effect. Global DNA methylation and DNMT3b expression were increased in skin after incision, but none of DNMT1, DNMT3a or DNMT3b was altered in spinal cord or DRG. The expression of proopiomelanocortin Pomc encoding β-endorphin and Oprm1 encoding the mu-opioid receptor were upregulated peripherally after incision; moreover, Oprm1 expression was further increased under DNMT inhibitor treatment. Finally, local peripheral injection of the opioid receptor antagonist naloxone significantly exacerbated incision-induced mechanical hypersensitivity. These results suggest that DNA methylation is functionally relevant to incisional nociceptive sensitization, and that mu-opioid receptor signaling might be one methylation regulated pathway controlling sensitization after incision.

  2. Capturing a DNA duplex under near-physiological conditions

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    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.

  3. Thermal stability of DNA quadruplex-duplex hybrids.

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    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.

  4. The DNA Repair Repertoire of Mycobacterium smegmatis FenA Includes the Incision of DNA 5' Flaps and the Removal of 5' Adenylylated Products of Aborted Nick Ligation.

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    Uson, Maria Loressa; Ghosh, Shreya; Shuman, Stewart

    2017-09-01

    We characterize Mycobacterium smegmatis FenA as a manganese-dependent 5'-flap endonuclease homologous to the 5'-exonuclease of DNA polymerase I. FenA incises a nicked 5' flap between the first and second nucleotides of the duplex segment to yield a 1-nucleotide gapped DNA, which is then further resected in dinucleotide steps. Initial FenA cleavage at a Y-flap or nick occurs between the first and second nucleotides of the duplex. However, when the template 3' single strand is eliminated to create a 5'-tailed duplex, FenA incision shifts to between the second and third nucleotides. A double-flap substrate with a mobile junction (mimicking limited strand displacement synthesis during gap repair) is preferentially incised as the 1-nucleotide 3'-flap isomer, with the scissile phosphodiester shifted by one nucleotide versus a static double flap. FenA efficiently removes the 5' App(dN) terminus of an aborted nick ligation reaction intermediate, thereby highlighting FenA as an agent of repair of such lesions, which are formed under a variety of circumstances by bacterial NAD + -dependent DNA ligases and especially by mycobacterial DNA ligases D and C. IMPORTANCE Structure-specific DNA endonucleases are implicated in bacterial DNA replication, repair, and recombination, yet there is scant knowledge of the roster and catalytic repertoire of such nucleases in Mycobacteria This study identifies M. smegmatis FenA as a stand-alone endonuclease homologous to the 5'-exonuclease domain of mycobacterial DNA polymerase 1. FenA incises 5' flaps, 5' nicks, and 5' App(dN) intermediates of aborted nick ligation. The isolated N-terminal domain of M. smegmatis Pol1 is also shown to be a flap endonuclease. Copyright © 2017 American Society for Microbiology.

  5. Micromechanics of base pair unzipping in the DNA duplex

    International Nuclear Information System (INIS)

    Volkov, Sergey N; Paramonova, Ekaterina V; Yakubovich, Alexander V; Solov’yov, Andrey V

    2012-01-01

    All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G⋅C content and rather distinct for the parts with A⋅T content. It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork. (paper)

  6. DNA polymerase. beta. reaction with ultraviolet-irradiated DNA incised by correndonuclease

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    Nowak, R; Zarebska, Z [Instytut Onkologii, Warsaw (Poland); Zmudzka, B [Polska Akademia Nauk, Warsaw. Inst. Biochemii i Biofizyki

    1980-09-19

    Covalently closed circular Col E1 DNA was ultraviolet-irradiated with a dose of 60 J/m/sup 2/, thus introducing about 3.2 pyrimidine dimers per DNA molecule. Treatment of irradiated Col E1 DNA with Micrococcus luteus correndonuclease resulted, in the vicinity of pyrimidine dimers, in an average of 3.3 incisions per DNA molecule, and converted DNA to the open circular form. Incised Col E1 DNA stimulated no reaction with calf thymus DNA polymerase ..cap alpha.. but was recognized as a template by DNA polymerase ..beta... The latter enzyme incorporated about 1.6 molecules of dTMP (corresponding to 6 molecules of dNMP) per one correndonuclease incision. The length of the DNA polymerase ..beta.. product was comparable to the anticipated length of the DNA region within which the hydrogen bonds were disrupted owing to dimer formation. The enzyme required Mg/sup 2 +/ and four dNTPs for reaction and was resistant to N-ethylmaleimide or p-mercuribenzoate.

  7. Protein complexation with DNA phosphates as a cause for DNA duplex destabilization : a thermodynamic model

    NARCIS (Netherlands)

    Genderen, van M.H.P.; Buck, H.M.

    1989-01-01

    Complexation of positively charged sites in a protein with the negative DNA phosphate groups shields the phosphate charges. This diminishes interstrand electrostatic repulsions, which stabilizes the duplex. When phosphate shidlding is present in one DNA strand only, the conformation of this strand

  8. Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

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    Fabian Haß

    2017-10-01

    Full Text Available The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs, have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.

  9. Structure of DNA toroids and electrostatic attraction of DNA duplexes

    International Nuclear Information System (INIS)

    Cherstvy, A G

    2005-01-01

    DNA-DNA electrostatic attraction is considered as the driving force for the formation of DNA toroids in the presence of DNA condensing cations. This attraction comes from the DNA helical charge distribution and favours hexagonal toroidal cross-sections. The latter is in agreement with recent cryo-electron microscopy studies on DNA condensed with cobalt hexammine. We treat the DNA-DNA interactions within the modern theory of electrostatic interaction between helical macromolecules. The size and thickness of the toroids is calculated within a simple model; other models of stability of DNA toroids are discussed and compared

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

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    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.

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

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    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.

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

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    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.

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

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    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.

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

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    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.

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

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    Masashi Fujita

    Full Text Available 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.

  16. Human FAN1 promotes strand incision in 5'-flapped DNA complexed with RPA.

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    Takahashi, Daisuke; Sato, Koichi; Hirayama, Emiko; Takata, Minoru; Kurumizaka, Hitoshi

    2015-09-01

    Fanconi anaemia (FA) is a human infantile recessive disorder. Seventeen FA causal proteins cooperatively function in the DNA interstrand crosslink (ICL) repair pathway. Dual DNA strand incisions around the crosslink are critical steps in ICL repair. FA-associated nuclease 1 (FAN1) is a DNA structure-specific endonuclease that is considered to be involved in DNA incision at the stalled replication fork. Replication protein A (RPA) rapidly assembles on the single-stranded DNA region of the stalled fork. However, the effect of RPA on the FAN1-mediated DNA incision has not been determined. In this study, we purified human FAN1, as a bacterially expressed recombinant protein. FAN1 exhibited robust endonuclease activity with 5'-flapped DNA, which is formed at the stalled replication fork. We found that FAN1 efficiently promoted DNA incision at the proper site of RPA-coated 5'-flapped DNA. Therefore, FAN1 possesses the ability to promote the ICL repair of 5'-flapped DNA covered by RPA. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  17. Pyrrolo-dC modified duplex DNA as a novel probe for the sensitive assay of base excision repair enzyme activity.

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    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.

  18. Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA.

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    Odell, M; Shuman, S

    1999-05-14

    The 298-amino acid ATP-dependent DNA ligase of Chlorella virus PBCV-1 is the smallest eukaryotic DNA ligase known. The enzyme has intrinsic specificity for binding to nicked duplex DNA. To delineate the ligase-DNA interface, we have footprinted the enzyme binding site on DNA and the DNA binding site on ligase. The size of the exonuclease III footprint of ligase bound a single nick in duplex DNA is 19-21 nucleotides. The footprint is asymmetric, extending 8-9 nucleotides on the 3'-OH side of the nick and 11-12 nucleotides on the 5'-phosphate side. The 5'-phosphate moiety is essential for the binding of Chlorella virus ligase to nicked DNA. Here we show that the 3'-OH moiety is not required for nick recognition. The Chlorella virus ligase binds to a nicked ligand containing 2',3'-dideoxy and 5'-phosphate termini, but cannot catalyze adenylation of the 5'-end. Hence, the 3'-OH is important for step 2 chemistry even though it is not itself chemically transformed during DNA-adenylate formation. A 2'-OH cannot substitute for the essential 3'-OH in adenylation at a nick or even in strand closure at a preadenylated nick. The protein side of the ligase-DNA interface was probed by limited proteolysis of ligase with trypsin and chymotrypsin in the presence and absence of nicked DNA. Protease accessible sites are clustered within a short segment from amino acids 210-225 located distal to conserved motif V. The ligase is protected from proteolysis by nicked DNA. Protease cleavage of the native enzyme prior to DNA addition results in loss of DNA binding. These results suggest a bipartite domain structure in which the interdomain segment either comprises part of the DNA binding site or undergoes a conformational change upon DNA binding. The domain structure of Chlorella virus ligase inferred from the solution experiments is consistent with the structure of T7 DNA ligase determined by x-ray crystallography.

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

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    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

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

    Directory of Open Access Journals (Sweden)

    Yong Huang

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  2. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model.

    Science.gov (United States)

    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.

  3. 6-Thioguanine alters the structure and stability of duplex DNA and inhibits quadruplex DNA formation.

    Science.gov (United States)

    Marathias, V M; Sawicki, M J; Bolton, P H

    1999-07-15

    The ability to chemically synthesize biomolecules has opened up the opportunity to observe changes in structure and activity that occur upon single atom substitution. In favorable cases this can provide information about the roles of individual atoms. The substitution of 6-thioguanine (6SG) for guanine is a potentially very useful single atom substitution as 6SG has optical, photocrosslinking, metal ion binding and other properties of potential utility. In addition, 6-mercaptopurine is a clinically important pro-drug that is activated by conversion into 6SG by cells. The results presented here indicate that the presence of 6SG blocks the formation of quadruplex DNA. The presence of 6SG alters the structure and lowers the thermal stability of duplex DNA, but duplex DNA can be formed in the presence of 6SG. These results indicate that some of the cytotoxic activity of 6SG may be due to disruption of the quadruplex structures formed by telomere and other DNAs. This additional mode of action is consistent with the delayed onset of cytotoxicity.

  4. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies.

    Science.gov (United States)

    Kratochvílová, Irena; Vala, Martin; Weiter, Martin; Špérová, Miroslava; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    2013-01-01

    Oligonucleotides conduct electric charge via various mechanisms and their characterization and understanding is a very important and complicated task. In this work, experimental (temperature dependent steady state fluorescence spectroscopy, time-resolved fluorescence spectroscopy) and theoretical (Density Functional Theory) approaches were combined to study charge transfer processes in short DNA/DNA and RNA/DNA duplexes with virtually equivalent sequences. The experimental results were consistent with the theoretical model - the delocalized nature of HOMO orbitals and holes, base stacking, electronic coupling and conformational flexibility formed the conditions for more effective short distance charge transfer processes in RNA/DNA hybrids. RNA/DNA and DNA/DNA charge transfer properties were strongly connected with temperature affected structural changes of molecular systems - charge transfer could be used as a probe of even tiny changes of molecular structures and settings. © 2013. Published by Elsevier B.V. All rights reserved.

  5. NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite acyclic lesions

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Chang, Chienneng; Johnson, F.; Grollman, A.P.; Patel, D.J.

    1989-01-01

    Proton and phosphorus NMR studies are reported for two complementary nonanucleotide duplexes containing acyclic abasic sites. The first duplex, d(C-A-T-G-A-G-T-A-C)·d(G-T-A-C-P-C-A-T-G), contains an acyclic propanyl moiety, P, located opposite a deoxyadenosine at the center of the helix (designated AP P 9-mer duplex). The second duplex, d(C-A-T-G-A-G-T-A-C-)·d(G-T-A-C-E-C-A-T-G), contains a similarly located acyclic ethanyl moiety, E (designated AP E 9-mer duplex). The ethanyl moiety is one carbon shorter than the natural carbon-phosphodiester backbone of a single nucleotide unit of DNA. The majority of the exchangeable and nonexchangeable base and sugar protons in both the AP P 9-mer and AP E 9-mer duplexes, including those at the abasic site, have been assigned by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H 2 O and D 2 O solution between -5 and 5 degree C. These spectroscopic observations establish that A5 inserts into the helix opposite the abasic site (P14 and El14) and stacks between the flanking G4·C15 and G6·C13 Watson-Crick base pairs in both the AP P 9-mer and AP E 9-mer duplexes. Proton NMR parameters for the Ap P 9-mer and AP E 9-mer duplexes are similar to those reported previously. These proton NMR experiments demonstrate that the structures at abasic sites are very similar whether the five-membered ring is open or closed or whether the phosphodiester backbone is shortened by one carbon atom. Phosphorus spectra of the AP P 9-mer and AP E 9-mer duplexes (5 degree C) indicate that the backbone conformation is similarly perturbed at three phosphodiester backbone torsion angles

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  8. Templated Chemistry for Sequence-Specific Fluorogenic Detection of Duplex DNA

    Science.gov (United States)

    Li, Hao; Franzini, Raphael M.; Bruner, Christopher; Kool, Eric T.

    2015-01-01

    We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine, designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of ca. 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably, demonstrating high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and may allow detection of double stranded DNA, at least for homopurine-homopyrimidine target sites, under native, non-disturbing conditions. PMID:20859985

  9. Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs

    DEFF Research Database (Denmark)

    Izvolsky, K I; Demidov, V V; Nielsen, P E

    2000-01-01

    I restriction endonuclease and dam methylase. The pcPNA-assisted protection against enzymatic methylation is more efficient when the PNA-binding site embodies the methylase-recognition site rather than overlaps it. We conclude that pcPNAs may provide the robust tools allowing to sequence-specifically manipulate...... DNA duplexes in a virtually sequence-unrestricted manner....

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  12. Electron transfer in DNA duplexes containing 2-methyl-1,4-naphthoquinone

    OpenAIRE

    Bergeron, François; Houde, Daniel; Hunting, Darel J.; Wagner, J. Richard

    2004-01-01

    2-Methyl-1,4-naphthoquinone (menadione, MQ) was linked to synthetic oligonucleotides and exposed to near-UV light to generate base radical cations in DNA. This model system of electron transfer induced alkali-labile breaks at GG doublets, similar to anthraquinone and metallointercalators systems. In sharp contrast to other systems, the photolysis of MQ–DNA duplexes gave interstrand cross-links and alkali-labile breaks at bases on the complementary strand opposite the MQ moiety. For sequences ...

  13. DNA oligonucleotide duplexes containing intramolecular platinated cross-links: energetics, hydration, sequence, and ionic effects.

    Science.gov (United States)

    Kankia, Besik I; Soto, Ana Maria; Burns, Nicole; Shikiya, Ronald; Tung, Chang-Shung; Marky, Luis A

    2002-11-05

    The anticancer activity of cisplatin arises from its ability to bind covalently to DNA, forming primarily intrastrand cross-links to adjacent purine residues; the most common adducts involve d(GpG) (65%) and d(ApG) (25%) intrastrand cross-links. The incorporation of these platinum adducts in a B-DNA helix induces local distortions, causing bending and unwinding of the DNA. In this work, we used temperature-dependent UV spectroscopy to investigate the unfolding thermodynamics, and associated ionic effects, of two sets of DNA decamer duplexes containing either cis-[Pt(NH(3))(2)[d(GpG

  14. Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation.

    Science.gov (United States)

    Mekler, Vladimir; Minakhin, Leonid; Severinov, Konstantin

    2017-05-23

    The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (Cas9) endonuclease cleaves double-stranded DNA sequences specified by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for genome editing in various organisms. The RNA-programmed Cas9 locates the target site by scanning genomic DNA. We sought to elucidate the mechanism of initial DNA interrogation steps that precede the pairing of target DNA with guide RNA. Using fluorometric and biochemical assays, we studied Cas9/guide RNA complexes with model DNA substrates that mimicked early intermediates on the pathway to the final Cas9/guide RNA-DNA complex. The results show that Cas9/guide RNA binding to PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guide RNA. The duplex destabilization is mediated, in part, by Cas9/guide RNA affinity for unpaired segments of nontarget strand DNA close to PAM. Furthermore, our data indicate that the entry of double-stranded DNA beyond a short threshold distance from PAM into the Cas9/single-guide RNA (sgRNA) interior is hindered. We suggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proximal region during early steps of Cas9/guide RNA-DNA complex formation, thus additionally destabilizing the protospacer duplex. The mechanism that emerges from our analysis explains how the Cas9/sgRNA complex is able to locate the correct target sequence efficiently while interrogating numerous nontarget sequences associated with correct PAMs.

  15. Triple helical DNA in a duplex context and base pair opening

    Science.gov (United States)

    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

  16. 5' modification of duplex DNA with a ruthenium electron donor-acceptor pair using solid-phase DNA synthesis

    Science.gov (United States)

    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.

  17. Excision of thymine dimers from specifically incised DNA by extracts of xeroderma pigmentosum cells

    Energy Technology Data Exchange (ETDEWEB)

    Cook, K; Friedberg, E C; Slor, H; Cleaver, J E

    1975-07-17

    DNA repair defects as exhibited in fibroblasts from patients with xeroderma pigmentosa were studied. Five complementation groups for excision-repair defects were examined to test the hypothesis that a defective endonuclease or exonuclease may be the cause. No evidence was found to indicate that the enzyme activity functions in dimer excision. Since ultraviolet irradiated E. coli DNA incised with an endonuclease purified from phage-infected cells were used, it is possible that other factors may be involved in human UV endonuclease action. (JWP)

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  20. Pulsed IR Heating Studies of Single-Molecule DNA Duplex Dissociation Kinetics and Thermodynamics

    Science.gov (United States)

    Holmstrom, Erik D.; Dupuis, Nicholas F.; Nesbitt, David J.

    2014-01-01

    Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10−11 liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20–100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation. PMID:24411254

  1. Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Hobza, Pavel

    2008-01-01

    Roč. 73, č. 2 (2008), s. 161-174 ISSN 0010-0765 R&D Projects: GA MŠk LC512; GA ČR GA203/05/0009; GA ČR(CZ) GD203/05/H001 Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA duplex * interaction energy * stability Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.784, year: 2008

  2. Electrochemical single-molecule conductivity of duplex and quadruplex DNA

    DEFF Research Database (Denmark)

    Zhang, Ling; Zhang, Jingdong; Ulstrup, Jens

    2017-01-01

    Photoinduced and electrochemical charge transport in DNA (oligonucleotides, OGNs) and the notions “hopping”, superexchange, polaron, and vibrationally gated charge transport have been in focus over more than two decades. In recent years mapping of electrochemical charge transport of pure and redo...

  3. Effect of Radiofrequency Radiation on DNA Duplex Stability and Replication.

    Science.gov (United States)

    1983-08-01

    Ando, T. A nuclease specific for heat-denatured DNA isolated from a product of Aspergillus oryzae . Biochim Biophys Acta 114:158-168 (1966). Blakeley...metabolic acti- vation. Mutation Res 64:315-328 (1979). Vogt,. V.M. Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae . Eur J Biochem 33:192-200 (1973). 42

  4. Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  6. Unstable Hoogsteen base pairs adjacent to echinomycin binding sites within a DNA duplex

    International Nuclear Information System (INIS)

    Gilbert, D.E.; van der Marel, G.A.; van Boom, J.H.; Feigon, J.

    1989-01-01

    The bisintercalation complex present between the DNA octamer [d(ACGTACGT)] 2 and the cyclic octadepsipeptide antibiotic echinomycin has been studied by one- and two-dimensional proton NMR, and the results obtained have been compared with the crystal structures of related DNA-echinomycin complexes. Two echinomycins are found to bind cooperatively to each DNA duplex at the CpG steps, with the two quinoxaline rings of each echinomycin bisintercalating between the C·G and A·T base pairs. At low temperatures, the A·T base pairs on either side of the intercalation site adopt the Hoogsteen conformation, as observed in the crystal structures. However, as the temperature is raised, the Hoogsteen base pairs in the interior of the duplex are destabilized and are observed to be exchanging between the Hoogsteen base pair and either an open or a Watson-Crick base-paired state. The terminal A·T base pairs, which are not as constrained by the helix as the internal base pairs, remain stably Hoogsteen base-paired up to at least 45 degree C. The implications of these results for the biological role of Hoogsteen base pairs in echinomycin-DNA complexes in vivo are discussed

  7. Combined Triplex/Duplex Invasion of Double-Stranded DNA by "Tail-Clamp" Peptide Nucleic Acid

    DEFF Research Database (Denmark)

    Bentin, Thomas; Larsen, H. J.; Nielsen, Peter E.

    2003-01-01

    as determined by T-m measurements. Binding to double-stranded (ds) DNA occurred by combined triplex and duplex invasion as analyzed by permanganate probing. Furthermore, C-50 measurements revealed that tail-clamp PNAs consistently bound the dsDNA target more efficiently, and kinetics experiments revealed...

  8. Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA

    Science.gov (United States)

    Mielke, Steven P.; Grønbech-Jensen, Niels; Krishnan, V. V.; Fink, William H.; Benham, Craig J.

    2005-09-01

    The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and undertwist upstream from the site of transcription. The resulting superhelical stress is often sufficient to drive double-stranded DNA into a denatured state at locations such as promoters and origins of replication, where sequence-specific duplex opening is a prerequisite for biological function. In this way, transcription and other events that actively supercoil the DNA provide a mechanism for dynamically coupling genetic activity with regulatory and other cellular processes. Although computer modeling has provided insight into the equilibrium dynamics of DNA supercoiling, to date no model has appeared for simulating sequence-dependent DNA strand separation under the nonequilibrium conditions imposed by the dynamic introduction of torsional stress. Here, we introduce such a model and present results from an initial set of computer simulations in which the sequences of dynamically superhelical, 147 base pair DNA circles were systematically altered in order to probe the accuracy with which the model can predict location, extent, and time of stress-induced duplex denaturation. The results agree both with well-tested statistical mechanical calculations and with available experimental information. Additionally, we find that sites susceptible to denaturation show a propensity for localizing to supercoil apices, suggesting that base sequence determines locations of strand separation not only through the energetics of interstrand interactions, but also by influencing the geometry of supercoiling.

  9. Sequence distribution of acetaldehyde-derived N2-ethyl-dG adducts along duplex DNA.

    Science.gov (United States)

    Matter, Brock; Guza, Rebecca; Zhao, Jianwei; Li, Zhong-ze; Jones, Roger; Tretyakova, Natalia

    2007-10-01

    Acetaldehyde (AA) is the major metabolite of ethanol and may be responsible for an increased gastrointestinal cancer risk associated with alcohol beverage consumption. Furthermore, AA is one of the most abundant carcinogens in tobacco smoke and induces tumors of the respiratory tract in laboratory animals. AA binding to DNA induces Schiff base adducts at the exocyclic amino group of dG, N2-ethylidene-dG, which are reversible on the nucleoside level but can be stabilized by reduction to N2-ethyl-dG. Mutagenesis studies in the HPRT reporter gene and in the p53 tumor suppressor gene have revealed the ability of AA to induce G-->A transitions and A-->T transversions, as well as frameshift and splice mutations. AA-induced point mutations are most prominent at 5'-AGG-3' trinucleotides, possibly a result of sequence specific adduct formation, mispairing, and/or repair. However, DNA sequence preferences for the formation of acetaldehyde adducts have not been previously examined. In the present work, we employed a stable isotope labeling-HPLC-ESI+-MS/MS approach developed in our laboratory to analyze the distribution of acetaldehyde-derived N2-ethyl-dG adducts along double-stranded oligodeoxynucleotides representing two prominent lung cancer mutational "hotspots" and their surrounding DNA sequences. 1,7,NH 2-(15)N-2-(13)C-dG was placed at defined positions within DNA duplexes derived from the K-ras protooncogene and the p53 tumor suppressor gene, followed by AA treatment and NaBH 3CN reduction to convert N2-ethylidene-dG to N2-ethyl-dG. Capillary HPLC-ESI+-MS/MS was used to quantify N2-ethyl-dG adducts originating from the isotopically labeled and unlabeled guanine nucleobases and to map adduct formation along DNA duplexes. We found that the formation of N2-ethyl-dG adducts was only weakly affected by the local sequence context and was slightly increased in the presence of 5-methylcytosine within CG dinucleotides. These results are in contrast with sequence

  10. Duplex Interrogation by a Direct DNA Repair Protein in Search of Base Damage

    Science.gov (United States)

    Yi, Chengqi; Chen, Baoen; Qi, Bo; Zhang, Wen; Jia, Guifang; Zhang, Liang; Li, Charles J.; Dinner, Aaron R.; Yang, Cai-Guang; He, Chuan

    2012-01-01

    ALKBH2 is a direct DNA repair dioxygenase guarding mammalian genome against N1-methyladenine, N3-methylcytosine, and 1,N6-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 displays two novel features: i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability; ii) ALKBH2 does not have nor need a “damage-checking site”, which is critical for preventing spurious base-cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly. PMID:22659876

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

    Science.gov (United States)

    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

  12. Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

    Science.gov (United States)

    Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

    2016-01-01

    Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

  13. Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2014-01-25

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

  15. Visualizing Transient Watson-Crick Like Mispairs in DNA and RNA Duplexes

    Science.gov (United States)

    Kimsey, Isaac J.; Petzold, Katja; Sathyamoorthy, Bharathwaj; Stein, Zachary W.; Al-Hashimi, Hashim M.

    2015-01-01

    Rare tautomeric and anionic nucleobases are believed to play fundamental biological roles but their prevalence and functional importance has remained elusive because they exist transiently, in low-abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10−3-10−5) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases. PMID:25762137

  16. Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.

    Science.gov (United States)

    Kimsey, Isaac J; Petzold, Katja; Sathyamoorthy, Bharathwaj; Stein, Zachary W; Al-Hashimi, Hashim M

    2015-03-19

    Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show here that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick-like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10(-3) to 10(-5)) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases.

  17. Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA

    NARCIS (Netherlands)

    Etson, Candice M.; Hamdan, Samir M.; Richardson, Charles C.; Oijen, Antoine M. van; Richardson, Charles C.

    2010-01-01

    The DNA polymerases involved in DNA replication achieve high processivity of nucleotide incorporation by forming a complex with processivity factors. A model system for replicative DNA polymerases, the bacteriophage T7 DNA polymerase (gp5), encoded by gene 5, forms a tight, 1:1 complex with

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  20. Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics

    Science.gov (United States)

    Alvey, Heidi S.; Gottardo, Federico L.; Nikolova, Evgenia N.; Al-Hashimi, Hashim M.

    2015-01-01

    Hoogsteen base-pairing involves a 180 degree rotation of the purine base relative to Watson-Crick base-pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction, and replication. Here, using Nuclear Magnetic Resonance R1ρ relaxation dispersion, we show that transient Hoogsteen base-pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in Hoogsteen base-pair energetic stabilities that are comparable to variations in Watson-Crick base-pair stability, with Hoogsteen base-pairs being more abundant for energetically less favorable Watson-Crick base-pairs. Our results suggest that the variations in Hoogsteen stabilities and rates of formation are dominated by variations in Watson-Crick base pair stability, suggesting a late transition state for the Watson-Crick to Hoogsteen conformational switch. The occurrence of sequence and position-dependent Hoogsteen base-pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions. PMID:25185517

  1. Structural features of an exocyclic adduct positioned opposite an abasic site in a DNA duplex

    International Nuclear Information System (INIS)

    Kouchakdjian, M.; Patel, D.J.; Eisenberg, M.; Johnson, F.; Grollman, A.P.

    1991-01-01

    Structural studies have been extended to dual lesions where an exocyclic adduct is positioned opposite an abasic site in the center of a DNA oligomer duplex. NMR and energy minimization studies were performed on the 1,N 2 -propanodeoxyguanosine exocyclic adduct (X) positioned opposite a tetrahydrofuran abasic site (F) with the dual lesions located in the center of the (C1-A2-T3-G4-X5-G6-T7-A8-C9)·(G10-T11-A12-C13-F14-C15-A16-T17-G18) X·F 9-mer duplex. Two-dimensional NMR experiments establish that the X·F 9-mer helix is right-handed with Watson-Crick A·T and G·C base pairing on either side of the lesion site. NOEs are detected from the methylene protons of the exocyclic ring of X5 to the imino protons of G4·C15 and G6·C13 which flank the lesion site, as well as to the H1' and H1 double-prime protons of the cross strand F14 tetrahydrofuran moiety. These NMR results establish that the exocyclic adduct X5 is positioned between flanking G4·C15 and G6·C13 base pairs and directed toward the abasic lesion F14 on the partner strand. These studies establish that the exocyclic ring of the 1,N 2 -propanodeoxyguanosine adduct fits into the cavity generated by the abasic site

  2. High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

    International Nuclear Information System (INIS)

    Chou, Shanho; Flynn, P.; Wang, A.; Reid, B.

    1991-01-01

    Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies

  3. Electroporation and microinjection successfully deliver single-stranded and duplex DNA into live cells as detected by FRET measurements.

    Directory of Open Access Journals (Sweden)

    Rosemary A Bamford

    Full Text Available Förster resonance energy transfer (FRET technology relies on the close proximity of two compatible fluorophores for energy transfer. Tagged (Cy3 and Cy5 complementary DNA strands forming a stable duplex and a doubly-tagged single strand were shown to demonstrate FRET outside of a cellular environment. FRET was also observed after transfecting these DNA strands into fixed and live cells using methods such as microinjection and electroporation, but not when using lipid based transfection reagents, unless in the presence of the endosomal acidification inhibitor bafilomycin. Avoiding the endocytosis pathway is essential for efficient delivery of intact DNA probes into cells.

  4. DNA Duplex Length and Salt Concentration Dependence of Enthalpy−Entropy Compensation Parameters for DNA Melting

    KAUST Repository

    Starikov, E. B.; Nordén, Bengt

    2009-01-01

    of the DNA and their water-counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers of such a kind, the recent enthalpy-entropy compensation theory has been used. It is demonstrated

  5. DNA Duplex Length and Salt Concentration Dependence of Enthalpy−Entropy Compensation Parameters for DNA Melting

    KAUST Repository

    Starikov, E. B.

    2009-08-20

    Systematical differential calorimetry experiments on DNA oligomers with different lengths and placed in water solutions with various added salt concentrations may, in principle, unravel important information about the structure and dynamics of the DNA and their water-counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers of such a kind, the recent enthalpy-entropy compensation theory has been used. It is demonstrated that the application of the latter could enable direct estimation of thermodynamic parameters of the microphase transitions connected to the changes in DNA dynamical regimes versus the length of the biopolymers and the ionic strengths of their water solutions, and this calls for much more systematical experimental and theoretical studies in this field. © 2009 American Chemical Society.

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

    Science.gov (United States)

    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

  7. Hairpin and duplex formation in DNA fragments CCAATTTTGG, CCAATTTTTTGG, and CCATTTTTGG: a proton NMR study

    International Nuclear Information System (INIS)

    Pramanik, P.; Kanhouwa, N.; Kan, L.

    1988-01-01

    Three DNA fragments, CCAATTTTGG (1), CCAATTTTTTGG (2), AND CCATTTTTGG (3), were studied by proton NMR spectroscopy in aqueous solution. All these oligodeoxyribonucleotides contain common sequences at the 5' and 3' ends (5'-CCA and TGG-3'). 2 as well as 3 forms only hairpin structures with four unpaired thymidylyl units, four and three base pair stems, respectively, in neutral solution under low and high NaCl concentrations. At high salt concentration the oligomer 1 forms a duplex structure with -TT- internal loop. On the other hand, the same oligomer forms a stable hairpin structure at low salt and low strand concentrations at pH 7. The hairpin structure of 1 has a stem containing only three base pairs (CCA x TGG) and a loop containing four nucleotides (-ATTT-) that includes a dissociated A x T base pair. The two secondary structures of 1 coexist in an aqueous solution containing 0.1 M NaCl, at pH 7. The equilibrium shifts to the hairpin side when the temperature is raised. The stabilities and base-stacking modes of all three oligonucleotides in tow different structures are reported

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  10. Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

    Science.gov (United States)

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-01-01

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

  11. Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

    Science.gov (United States)

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-09-18

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. 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.

    Science.gov (United States)

    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.

  13. Benzene-derived N2-(4-hydroxyphenyl)-deoxyguanosine adduct: UvrABC incision and its conformation in DNA

    Energy Technology Data Exchange (ETDEWEB)

    Hang, Bo; Rodriguez, Ben; Yang, Yanu; Guliaev, Anton B.; Chenna, Ahmed

    2010-06-14

    Benzene, a ubiquitous human carcinogen, forms DNA adducts through its metabolites such as p-benzoquinone (p-BQ) and hydroquinone (HQ). N(2)-(4-Hydroxyphenyl)-2'-deoxyguanosine (N(2)-4-HOPh-dG) is the principal adduct identified in vivo by (32)P-postlabeling in cells or animals treated with p-BQ or HQ. To study its effect on repair specificity and replication fidelity, we recently synthesized defined oligonucleotides containing a site-specific adduct using phosphoramidite chemistry. We here report the repair of this adduct by Escherichia coli UvrABC complex, which performs the initial damage recognition and incision steps in the nucleotide excision repair (NER) pathway. We first showed that the p-BQ-treated plasmid was efficiently cleaved by the complex, indicating the formation of DNA lesions that are substrates for NER. Using a 40-mer substrate, we found that UvrABC incises the DNA strand containing N(2)-4-HOPh-dG in a dose- and time-dependent manner. The specificity of such repair was also compared with that of DNA glycosylases and damage-specific endonucleases of E. coli, both of which were found to have no detectable activity toward N(2)-4-HOPh-dG. To understand why this adduct is specifically recognized and processed by UvrABC, molecular modeling studies were performed. Analysis of molecular dynamics trajectories showed that stable G:C-like hydrogen bonding patterns of all three Watson-Crick hydrogen bonds are present within the N(2)-4-HOPh-G:C base pair, with the hydroxyphenyl ring at an almost planar position. In addition, N(2)-4-HOPh-dG has a tendency to form more stable stacking interactions than a normal G in B-type DNA. These conformational properties may be critical in differential recognition of this adduct by specific repair enzymes.

  14. Site-Directed Spin-Labeling of Nucleic Acids by Click Chemistry. Detection of Abasic Sites in Duplex DNA by EPR Spectroscopy

    DEFF Research Database (Denmark)

    Sigurdsson, Snorri; Vogel, Stefan; Shelke, Sandip

    2010-01-01

    and the nitroxide spin label. The spin label was used to detect, for the first time, abasic sites in duplex DNA by X-band CW-EPR spectroscopy and give information about other structural deformations as well as local conformational changes in DNA. For example, reduced mobility of the spin label in a mismatched pair...... label out of the duplex and toward the solution. Thus, reposition of the spin label, when acting as a mercury(II)-controlled mechanical lever, can be readily detected by EPR spectroscopy. The ease of incorporation and properties of the new spin label make it attractive for EPR studies of nucleic acids...

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

    Science.gov (United States)

    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

  16. Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

    International Nuclear Information System (INIS)

    Torigoe, Hidetaka; Miyakawa, Yukako; Ono, Akira; Kozasa, Tetsuo

    2012-01-01

    Highlights: ► Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio. ► The binding constant between Hg 2+ and the T:T mismatched base pair was 10 6 M −1 . ► The binding constant was larger than those for nonspecific metal–DNA interactions. ► The binding constant for the second Hg 2+ was larger than that for the first Hg 2+ . ► The positive cooperative binding was observed between Hg 2+ and multiple T:T. - Abstract: Metal-mediated base pairs by the interaction between metal ions and artificial bases in oligonucleotides have been developed for their potential applications in nanotechnology. We recently found that a natural T:T mismatched base pair bound with Hg 2+ ion to form a novel T–Hg–T base pair. Here, we examined the thermodynamic properties of the binding between Hg 2+ and each of the single and double T:T mismatched base pair duplex DNAs by isothermal titration calorimetry. Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio with 10 6 M −1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. In the Hg 2+ –double T:T mismatched base pair interaction, the affinity for the second Hg 2+ binding was significantly larger than that for the first Hg 2+ binding. The positively cooperative binding may be favorable to align multiple Hg 2+ in duplex DNA for the application of the metal-mediated base pairs in nanotechnology.

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

    Science.gov (United States)

    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.

  18. 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.

    Science.gov (United States)

    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

  19. Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures

    Directory of Open Access Journals (Sweden)

    Yogini P. Bhavsar

    2011-01-01

    Full Text Available Topological variants of single-strand DNA (ssDNA structures, referred to as “functional DNA,” have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analogs of deoxycytidine, Pyrrolo-dC (PdC and 1,3-diaza-2-oxophenoxazine (tC∘, can be incorporated into DNA. Here, we describe spectroscopic studies of both analogs to determine fluorescent properties that report on structural transitions from double-strand DNA (dsDNA to ssDNA, a common pathway in the transition to functional DNA structures. We obtained fluorescence-detected circular dichroism (FDCD spectra, steady-state fluorescence spectra, and fluorescence lifetimes of the fluorophores in DNA. Our results show that PdC is advantageous in fluorescence lifetime studies because of a distinct ~2 ns change between paired and unpaired bases. However, tC∘ is a better probe for FDCD experiments that report on the helical structure of DNA surrounding the fluorophore. Both fluorophores provide complementary data to measure DNA structural transitions.

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

    OpenAIRE

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

    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 electr...

  1. Capability of ds-DNA duplex structure in growing fluorescent silver nanoclusters

    International Nuclear Information System (INIS)

    Wu, Tao; Lin, Fan; Hu, Yuehua; Wang, Ying; Zhou, Xiaoshun; Shao, Yong

    2016-01-01

    Silver nanoclusters (AgNCs) have attracted wide interests in variant fields due to their easy synthesis and practical tunability in fluorescence properties. DNA has been generally used as the host to grow AgNCs due to the sequence-dependent fluorescence behavior. Actually, in such DNA, various ss-DNA segments that are structurally confined by the rigid ds-DNA counterparts have been used as the AgNCsГ—Ві growth sites. However, whether the ds-DNA structure plays somewhat role in AgNCsГ—Ві creation has not been well elucidated. Herein, we found that ds-DNA can also accommodate the growth of fluorescent AgNCs. The fluorescent AgNCs grown on ds-DNA should be separated each other and the G/C base pairs with right context sequences are the growth sites of fluorescent AgNCs. The intermediate A/T base pair among the continuous G/C ones seems to quench the growth of fluorescent AgNCs. For the repeat sequences, the fluorescence band position of AgNCs is not changed but the intensity is enhanced upon increasing the ds-DNA length, which is different from the results obtained with the previously reported ss-DNAs. AgNCs should be grown on the ds-DNA major groove, as convinced by the cytosine methylation experiment. Our work demonstrates that besides the ss-DNA role in defining AgNCs, one should also take into account the critical role of the ds-DNA segment in tuning the AgNCsГ—Ві fluorescence property.

  2. Recognition of base J in duplex DNA by J-binding protein

    NARCIS (Netherlands)

    Sabatini, Robert; Meeuwenoord, Nico; van Boom, Jacques H.; Borst, Piet

    2002-01-01

    beta-d-Glucosylhydroxymethyluracil, also called base J, is an unusual modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously found a J-binding

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

    Science.gov (United States)

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

    2018-01-25

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

  4. Structure of the DNA duplex d(ATTAAT2 with Hoogsteen hydrogen bonds.

    Directory of Open Access Journals (Sweden)

    Francisco J Acosta-Reyes

    Full Text Available The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT2, which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation. We conclude that any all-AT sequence might acquire this conformation under appropriate conditions. We also compare the detailed features of DNA in either the Hoogsteen or Watson-Crick conformations.

  5. Coupling of the nucleotide incision and 3' {yields} 5' exonuclease activities in Escherichia coli endonuclease IV: Structural and genetic evidences

    Energy Technology Data Exchange (ETDEWEB)

    Golan, Gali [Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Ishchenko, Alexander A. [Groupe Reparation de l' ADN, CNRS UMR 8126, Univ. Paris-Sud, Institut de Cancerologie Gustave Roussy, 39, rue Camille Desmoulins, F-94805 Villejuif Cedex (France); Khassenov, Bekbolat [National Center for Biotechnology, Astana (Kazakhstan); Shoham, Gil, E-mail: gil2@vms.huji.ac.il [Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Saparbaev, Murat K., E-mail: smurat@igr.fr [Groupe Reparation de l' ADN, CNRS UMR 8126, Univ. Paris-Sud, Institut de Cancerologie Gustave Roussy, 39, rue Camille Desmoulins, F-94805 Villejuif Cedex (France)

    2010-03-01

    Aerobic respiration generates reactive oxygen species (ROS) as a by-product of cellular metabolism which can damage DNA. The complex nature of oxidative DNA damage requires actions of several repair pathways. Oxidized DNA bases are substrates for two overlapping pathways: base excision repair (BER) and nucleotide incision repair (NIR). In the BER pathway a DNA glycosylase cleaves the N-glycosylic bond between the abnormal base and deoxyribose, leaving either an abasic site or single-stranded DNA break. Alternatively, in the NIR pathway, an apurinic/apyrimidinic (AP) endonuclease incises duplex DNA 5' next to oxidatively damaged nucleotide. The multifunctional Escherichia coli endonuclease IV (Nfo) is involved in both BER and NIR pathways. Nfo incises duplex DNA 5' of a damaged residue but also possesses an intrinsic 3' {yields} 5' exonuclease activity. Herein, we demonstrate that Nfo-catalyzed NIR and exonuclease activities can generate a single-strand gap at the 5' side of 5,6-dihydrouracil residue. Furthermore, we show that Nfo mutants carrying amino acid substitutions H69A and G149D are deficient in both NIR and exonuclease activities, suggesting that these two functions are genetically linked and governed by the same amino acid residues. The crystal structure of Nfo-H69A mutant reveals the loss of one of the active site zinc atoms (Zn1) and rearrangements of the catalytic site, but no gross changes in the overall enzyme conformation. We hypothesize that these minor changes strongly affect the DNA binding of Nfo. Decreased affinity may lead to a different kinking angle of the DNA helix and this in turn thwart nucleotide incision and exonuclease activities of Nfo mutants but to lesser extent of their AP endonuclease function. Based on the biochemical and genetic data we propose a model where nucleotide incision coupled to 3' {yields} 5' exonuclease activity prevents formation of lethal double-strand breaks when repairing bi

  6. Conformation and dynamics of nucleotides in bulges and symmetric internal loops in duplex DNA studied by EPR and fluorescence spectroscopies

    International Nuclear Information System (INIS)

    Cekan, Pavol; Sigurdsson, Snorri Th.

    2012-01-01

    Highlights: ► Bulges and loops were studied by both EPR and fluorescence spectroscopies using the probe Ç/Ç f . ► One-base bulge was in a temperature-dependent equilibrium between looped-out and stacked states. ► Bases in two- and three-base bulges were stacked at all temperatures, resulting in DNA bending. ► Bases were stacked in symmetrical two- to five-base internal loops, according to EPR data. ► Unexpectedly high fluorescence for the smaller loops indicated local structural perturbations. -- Abstract: The dynamics and conformation of base bulges and internal loops in duplex DNA were studied using the bifunctional spectroscopic probe Ç, which becomes fluorescent (Ç f ) upon reduction of the nitroxide functional group, along with EPR and fluorescence spectroscopies. A one-base bulge was in a conformational equilibrium between looped-out and stacked states, the former favored at higher temperature and the latter at lower temperature. Stacking of bulge bases was favored in two- and three-base bulges, independent of temperature, resulting in DNA bending as evidenced by increased fluorescence of Ç f . EPR spectra of Ç-labeled three-, four- and five-base symmetrical interior DNA bulges at 20 °C showed low mobility, indicating that the spin-label was stacked within the loop. The spin-label mobility at 37 °C increased as the loops became larger. A considerable variation in fluorescence between different loops was observed, as well as a temperature-dependence within constructs. Fluorescence unexpectedly increased as the size of the loop decreased at 2 °C. Fluorescence of the smallest loops, where a single T·T mismatch was located between the stem region and the probe, was even larger than for the single strand, indicating a considerable local structural deformation of these loops from regular B-DNA. These results show the value of combining EPR and fluorescence spectroscopy to study non-helical regions of nucleic acids.

  7. Simultaneous Binding of Hybrid Molecules Constructed with Dual DNA-Binding Components to a G-Quadruplex and Its Proximal Duplex.

    Science.gov (United States)

    Asamitsu, Sefan; Obata, Shunsuke; Phan, Anh Tuân; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

    2018-03-20

    A G-quadruplex (quadruplex) is a nucleic acid secondary structure adopted by guanine-rich sequences and is considered to be relevant to various pharmacological and biological contexts. Although a number of researchers have endeavored to discover and develop quadruplex-interactive molecules, poor ligand designability originating from topological similarity of the skeleton of diverse quadruplexes has remained a bottleneck for gaining specificity for individual quadruplexes. This work reports on hybrid molecules that were constructed with dual DNA-binding components, a cyclic imidazole/lysine polyamide (cIKP), and a hairpin pyrrole/imidazole polyamide (hPIP), with the aim toward specific quadruplex targeting by reading out the local duplex DNA sequence adjacent to designated quadruplexes in the genome. By means of circular dichroism (CD), fluorescence resonance energy transfer (FRET), surface plasmon resonance (SPR), and NMR techniques, we showed the dual and simultaneous recognition of the respective segment via hybrid molecules, and the synergistic and mutual effect of each binding component that was appropriately linked on higher binding affinity and modest sequence specificity. Monitoring quadruplex and duplex imino protons of the quadruplex/duplex motif titrated with hybrid molecules clearly revealed distinct features of the binding of hybrid molecules to the respective segments upon their simultaneous recognition. A series of the systematic and detailed binding assays described here showed that the concept of simultaneous recognition of quadruplex and its proximal duplex by hybrid molecules constructed with the dual DNA-binding components may provide a new strategy for ligand design, enabling targeting of a large variety of designated quadruplexes at specific genome locations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Sequence-selective targeting of duplex DNA by peptide nucleic acids

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    Sequence-selective gene targeting constitutes an attractive drug-discovery approach for genetic therapy, with the aim of reducing or enhancing the activity of specific genes at the transcriptional level, or as part of a methodology for targeted gene repair. The pseudopeptide DNA mimic peptide...

  9. 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

    Science.gov (United States)

    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

  10. Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

    Science.gov (United States)

    Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K; Al-Hashimi, Hashim M

    2017-05-19

    In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

    Science.gov (United States)

    Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K.

    2017-01-01

    Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. PMID:28369571

  12. Infrared Laser Heating Applied to Nanopore Sensing for DNA Duplex Analysis.

    Science.gov (United States)

    Angevine, Christopher E; Seashols-Williams, Sarah J; Reiner, Joseph E

    2016-03-01

    Temperature studies coupled with resistive-pulse nanopore sensing enable the quantification of a variety of important thermodynamic properties at the single-molecule limit. Previous demonstrations of nanopore sensing with temperature control have utilized bulk chamber heating methodologies. This approach makes it difficult to rapidly change temperatures and enable optical access for other analytical techniques (i.e., single-molecule fluorescence). To address these issues, researchers have explored laser-based methodologies through either direct infrared (IR) absorption or plasmonic assisted heating. In this paper, we demonstrate the use of IR-based direct absorption heating with the DNA sensing capabilities of a biological nanopore. The IR heating enables rapid changes of the temperature in and around an α-hemolysin pore, and we use this to explore melting properties for short (≤50 bp) double-stranded DNA homopolymers. We also demonstrate that the IR heating enables one to measure the percentage of different-sized DNA molecules in a binary mixture.

  13. Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

    Directory of Open Access Journals (Sweden)

    Masaru Tsunoda

    2010-01-01

    Full Text Available Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU, which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

  14. NMR and molecular modeling evidence for a G·A mismatch base pair in a purine-rich DNA duplex

    International Nuclear Information System (INIS)

    Li, Ying; Wilson, W.D.; Zon, G.

    1991-01-01

    1 H NMR experiments indicate that the oligomer 5'-d(ATGAGCGAATA) forms an unusual 10-base-pair duplex with 4 G·A base pairs and a 3' unpaired adenosine. NMR results indicate that guanoxine imino protons of the F·A mismatches are not hydrogen bonded but are stacked in the helix. A G→ I substitution in either G·A base pair causes a dramatic decrtease in duplex stability and indicates that hydrogen bonding of the guanosine amino group is critical. Nuclear Overhauser effect spectroscopy (NOESY) and two-dimensional correlated spectroscopy (COSY) results indicate that the overall duplex conformation is in the B-family. Cross-strand NOEs in two-dimensional NOESY spectra between a mismatched AH2 and an AH1' of the other mismatched base pair and between a mismatched GH8 and GNH1 of the other mismatch establish a purine-purine stacking pattern, adenosine over adenosine and guanosine over guanosine, which strongly stabilizes the duplex. A computer graphics molecular model of the ususual duplex was constructed with G·A base pairs containing A-NH 2 to GN3 and G-NH 2 to AN7 hydrogen bonds and B-form base pairs on both sides of the G·A pairs [5'-d(ATGAGC)]. The energy-minimized duplex satisfies all experimental constraints from NOESY and COSY results. A hydrogen bond from G-NH 2 of the mismatch to a phosphate oxygen is predicted

  15. Rolling replication of UV-irradiated duplex DNA in the phi X174 replicative-form----single-strand replication system in vitro

    International Nuclear Information System (INIS)

    Shavitt, O.; Livneh, Z.

    1989-01-01

    Cloning of the phi X174 viral origin of replication into phage M13mp8 produced an M13-phi X174 chimera, the DNA of which directed efficient replicative-form----single-strand rolling replication in vitro. This replication assay was performed with purified phi X174-encoded gene A protein, Escherichia coli rep helicase, single-stranded DNA-binding protein, and DNA polymerase III holoenzyme. The nicking of replicative-form I (RFI) DNA by gene A protein was essentially unaffected by the presence of UV lesions in the DNA. However, unwinding of UV-irradiated DNA by the rep helicase was inhibited twofold as compared with unwinding of the unirradiated substrate. UV irradiation of the substrate DNA caused a strong inhibition in its ability to direct DNA synthesis. However, even DNA preparations that contained as many as 10 photodimers per molecule still supported the synthesis of progeny full-length single-stranded DNA. The appearance of full-length radiolabeled products implied at least two full rounds of replication, since the first round released the unlabeled plus viral strand of the duplex DNA. Pretreatment of the UV-irradiated DNA substrate with purified pyrimidine dimer endonuclease from Micrococcus luteus, which converted photodimer-containing supercoiled RFI DNA into relaxed, nicked RFII DNA and thus prevented its replication, reduced DNA synthesis by 70%. Analysis of radiolabeled replication products by agarose gel electrophoresis followed by autoradiography revealed that this decrease was due to a reduction in the synthesis of progeny full-length single-stranded DNA. This implies that 70 to 80% of the full-length DNA products produced in this system were synthesized on molecules that carried photodimers

  16. Accurate and rapid modeling of iron–bleomycin-induced DNA damage using tethered duplex oligonucleotides and electrospray ionization ion trap mass spectrometric analysis

    OpenAIRE

    Harsch, Andreas; Marzilli, Lisa A.; Bunt, Richard C.; Stubbe, Joanne; Vouros, Paul

    2000-01-01

    Bleomycin B2 (BLM) in the presence of iron [Fe(II)] and O2 catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands were used in this investigation, allowing facile monitoring of all ss and ds cleavage events. A sequence for site-specific binding and cleavage by Fe–BLM was incorporated into each an...

  17. Excited-State Dynamics of a DNA Duplex in a Deep Eutectic Solvent Probed by Femtosecond Time-Resolved IR Spectroscopy.

    Science.gov (United States)

    de La Harpe, Kimberly; Kohl, Forrest R; Zhang, Yuyuan; Kohler, Bern

    2018-03-08

    To better understand how the solvent influences excited-state deactivation in DNA strands, femtosecond time-resolved IR (fs-TRIR) pump-probe measurements were performed on a d(AT) 9 ·d(AT) 9 duplex dissolved in a deep eutectic solvent (DES) made from choline chloride and ethylene glycol in a 1:2 mol ratio. This solvent, known as ethaline, is a member of a class of ionic liquids capable of solubilizing DNA with minimal disruption to its secondary structure. UV melting analysis reveals that the duplex studied here melts at 18 °C in ethaline compared to 50 °C in aqueous solution. Ethaline has an excellent transparency window that facilitates TRIR measurements in the double-bond stretching region. Transient spectra recorded in deuterated ethaline at room temperature indicate that photoinduced intrastrand charge transfer occurs from A to T, yielding the same exciplex state previously detected in aqueous solution. This state decays via charge recombination with a lifetime of 380 ± 10 ps compared to the 300 ± 10 ps lifetime measured earlier in D 2 O solution. The TRIR data strongly suggest that the long-lived exciplex forms exclusively in the solvated duplex, and not in the denatured single strands, which appear to have little, if any, base stacking. The longer lifetime of the exciplex state in the DES compared to aqueous solution is suggested to arise from reduced stabilization of the charge transfer state, resulting in slower charge recombination on account of Marcus inverted behavior.

  18. NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analog of 2-deoxyribose

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Chang, C.N.; Grollman, A.P.; Patel, D.J.

    1988-01-01

    Proton and phosphorus NMR studies are reported for the complementary d(C-A-T-G-A-G-T-A-C) x d(G-T-A-C-F-C-A-T-G) nonanucleotide duplex (designated AP/sub F/ 9-mer duplex) which contains a stable abasic site analog, F, in the center of the helix. This oligodeoxynucleotide contains a modified tetrahydrofuran moiety, isosteric with 2-deoxyribofuranose, which serves as a structural analog of a natural apurinic/apyrimidinic site. Exchangeable and nonexchangeable base and sugar protons, including those located at the abasic site, have been assigned in the complementary AP/sub F/ 9-mer duplex by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H 2 O and D 2 O solution at low temperature (0 0 C). These studies indicate that A5 inserts into the helix opposite the abasic site F14 and stacks with flanking G4 x C15 and G6 x C13 Watson-Crick base pairs. Base-sugar proton NOE connectivities were measured through G4-A5-G6 on the unmodified strand and between the base protons of C15 and the sugar protons of the 5'-flanking residue F14 on the modified strand. These studies establish that all glycosidic torsion angles are anti and that the helix is right-handed at and adjacent to the abasic site in the AP/sub F/ 9-mer duplex. Two of the 16 phosphodiester groups exhibit phosphorus resonances outside the normal spectral dispersion indicative of altered torsion angles at two of the phosphate groups in the backbone of the AP/sub F/ 9-mer duplex

  19. Targeting human c-Myc promoter duplex DNA with actinomycin D by use of multi-way analysis of quantum-dot-mediated fluorescence resonance energy transfer

    DEFF Research Database (Denmark)

    Gholami, Somayeh; Kompany Zare, Mohsen

    2013-01-01

    Actinomycin D (Act D), an oncogenic c-Myc promoter binder, interferes with the action of RNA polymerase. There is great demand for high-throughput technology able to monitor the activity of DNA-binding drugs. To this end, binding of 7-aminoactinomycin D (7AAD) to the duplex c-Myc promoter...... pairs resulted in efficient energy transfer from drug to QD via fluorescence resonance energy transfer (FRET). Multi-way analysis of the three-way data array obtained from titration experiments was performed by use of restricted Tucker3 and hard trilinear decomposition (HTD). These techniques enable...... the important advantage over univariate classical methods of enabling us to investigate the source of variance in the fluorescence signal of the DNA-drug complex. It was established that hard trilinear decomposition analysis of FRET-measured data overcomes the problem of rank deficiency, enabling calculation...

  20. Development and Evaluation of a Duplex Real-Time PCR Assay With a Novel Internal Standard for Precise Quantification of Plasma DNA.

    Science.gov (United States)

    Chen, Dan; Pan, Shiyang; Xie, Erfu; Gao, Li; Xu, Huaguo; Xia, Wenying; Xu, Ting; Huang, Peijun

    2017-01-01

    Circulating levels of cell-free DNA increase in many pathologic conditions. However, notable discrepancies in the quantitative analysis of cell-free DNA from a large number of laboratories have become a considerable pitfall, hampering its clinical application. We designed a novel recombinant DNA fragment that could be applied as an internal standard in a newly developed and validated duplex real-time PCR assay for the quantitative analysis of total cell-free plasma DNA, which was tested in 5,442 healthy adults and 200 trauma patients. Compared with two traditional methods, this novel assay showed a lower detection limit of 0.1 ng/mL, lower intra- and inter-assay CVs, and higher accuracy in the recovery test. The median plasma DNA concentration of healthy males (20.3 ng/mL, n=3,092) was significantly higher than that of healthy females (16.1 ng/mL, n=2,350) (Mann-Whitney two-sample rank sum test, PDNA concentration were 0-45.8 ng/mL and 0-52.5 ng/mL for healthy females and males, respectively. The plasma DNA concentrations of the majority of trauma patients (96%) were higher than the upper normal cutoff values and were closely related to the corresponding injury severity scores (R²=0.916, PDNA, showing promising application in clinical diagnosis.

  1. An exploration of sequence specific DNA-duplex/pyrene interactions for intercalated and surface-associated pyrene species. Final report, May 1, 1993--December 31, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Netzel, T.L.

    1997-03-01

    The broad objective of this DOE sponsored work on photoinduced electron transfer (ET) within covalently modified DNA was to learn about the rates of Et among various DNA bases and commonly used organic electron donor (D) and acceptor (A) molecules. This hypothesis driven, multidisciplinary project combined skills in modified nucleic acid synthesis and in continuous and time-resolved optical spectroscopies. Covalently modified DNA chemistry as investigated in this program had two specific long term goals. The first was to use experimental and theoretical insights into the mechanisms of electron transfer (ET) reactions to design supramolecular assemblies of redox-active chromophores that function as efficient vectorial ET engines. The second was to construct oligonucleotide probes for real-time monitoring of intracellular processes involving DNA and RNA such as m-RNA expression and translocation. This research project laid the groundwork for studying ET reactions within DNA duplexes by examining the photophysics of uridine nucleosides which are covalently labeled at the 5-position with 1-pyrenyl chromophores.

  2. Accurate and rapid modeling of iron-bleomycin-induced DNA damage using tethered duplex oligonucleotides and electrospray ionization ion trap mass spectrometric analysis.

    Science.gov (United States)

    Harsch, A; Marzilli, L A; Bunt, R C; Stubbe, J; Vouros, P

    2000-05-01

    Bleomycin B(2)(BLM) in the presence of iron [Fe(II)] and O(2)catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands were used in this investigation, allowing facile monitoring of all ss and ds cleavage events. A sequence for site-specific binding and cleavage by Fe-BLM was incorporated into each analyte. One of these core sequences, GTAC, is a known hot-spot for ds cleavage, while the other sequence, GGCC, is a hot-spot for ss cleavage. Incubation of each oligo-nucleotide under anaerobic conditions with Fe(II)-BLM allowed detection of the non-covalent ternary Fe-BLM/oligonucleotide complex in the gas phase. Cleavage studies were then performed utilizing O(2)-activated Fe(II)-BLM. No work-up or separation steps were required and direct MS and MS/MS analyses of the crude reaction mixtures confirmed sequence-specific Fe-BLM-induced cleavage. Comparison of the cleavage patterns for both oligonucleotides revealed sequence-dependent preferences for ss and ds cleavages in accordance with previously established gel electrophoresis analysis of hairpin oligonucleotides. This novel methodology allowed direct, rapid and accurate determination of cleavage profiles of model duplex oligonucleotides after exposure to activated Fe-BLM.

  3. Duplex Real-Time PCR Assay Distinguishes Aedes aegypti From Ae. albopictus (Diptera: Culicidae) Using DNA From Sonicated First-Instar Larvae.

    Science.gov (United States)

    Kothera, Linda; Byrd, Brian; Savage, Harry M

    2017-11-07

    Aedes aegypti (L.) and Ae. albopictus (Skuse) are important arbovirus vectors in the United States, and the recent emergence of Zika virus disease as a public health concern in the Americas has reinforced a need for tools to rapidly distinguish between these species in collections made by vector control agencies. We developed a duplex real-time PCR assay that detects both species and does not cross-amplify in any of the other seven Aedes species tested. The lower limit of detection for our assay is equivalent to ∼0.03 of a first-instar larva in a 60-µl sample (0.016 ng of DNA per real-time PCR reaction). The assay was sensitive and specific in mixtures of both species that reflected up to a 2,000-fold difference in DNA concentration. In addition, we developed a simple protocol to extract DNA from sonicated first-instar larvae, and used that DNA to test the assay. Because it uses real-time PCR, the assay saves time by not requiring a separate visualization step. This assay can reduce the time needed for vector control agencies to make species identifications, and thus inform decisions about surveillance and control. Published by Oxford University Press on behalf of Entomological Society of America 2017 This work is written by US Government employees and is in the public domain in the US.

  4. Quantification of Chemical and Mechanical Effects on the Formation of the G-Quadruplex and i-Motif in Duplex DNA.

    Science.gov (United States)

    Selvam, Sangeetha; Mandal, Shankar; Mao, Hanbin

    2017-09-05

    The formation of biologically significant tetraplex DNA species, such as G-quadruplexes and i-motifs, is affected by chemical (ions and pH) and mechanical [superhelicity (σ) and molecular crowding] factors. Because of the extremely challenging experimental conditions, the relative importance of these factors on tetraplex folding is unknown. In this work, we quantitatively evaluated the chemical and mechanical effects on the population dynamics of DNA tetraplexes in the insulin-linked polymorphic region using magneto-optical tweezers. By mechanically unfolding individual tetraplexes, we found that ions and pH have the largest effects on the formation of the G-quadruplex and i-motif, respectively. Interestingly, superhelicity has the second largest effect followed by molecular crowding conditions. While chemical effects are specific to tetraplex species, mechanical factors have generic influences. The predominant effect of chemical factors can be attributed to the fact that they directly change the stability of a specific tetraplex, whereas the mechanical factors, superhelicity in particular, reduce the stability of the competing species by changing the kinetics of the melting and annealing of the duplex DNA template in a nonspecific manner. The substantial dependence of tetraplexes on superhelicity provides strong support that DNA tetraplexes can serve as topological sensors to modulate fundamental cellular processes such as transcription.

  5. Single-Molecule Kinetics Reveal Cation-Promoted DNA Duplex Formation Through Ordering of Single-Stranded Helices

    Science.gov (United States)

    Dupuis, Nicholas F.; Holmstrom, Erik D.; Nesbitt, David J.

    2013-01-01

    In this work, the kinetics of short, fully complementary oligonucleotides are investigated at the single-molecule level. Constructs 6–9 bp in length exhibit single exponential kinetics over 2 orders of magnitude time for both forward (kon, association) and reverse (koff, dissociation) processes. Bimolecular rate constants for association are weakly sensitive to the number of basepairs in the duplex, with a 2.5-fold increase between 9 bp (k′on = 2.1(1) × 106 M−1 s−1) and 6 bp (k′on = 5.0(1) × 106 M−1 s−1) sequences. In sharp contrast, however, dissociation rate constants prove to be exponentially sensitive to sequence length, varying by nearly 600-fold over the same 9 bp (koff = 0.024 s−1) to 6 bp (koff = 14 s−1) range. The 8 bp sequence is explored in more detail, and the NaCl dependence of kon and koff is measured. Interestingly, konincreases by >40-fold (kon = 0.10(1) s−1 to 4.0(4) s−1 between [NaCl] = 25 mM and 1 M), whereas in contrast, koffdecreases by fourfold (0.72(3) s−1 to 0.17(7) s−1) over the same range of conditions. Thus, the equilibrium constant (Keq) increases by ≈160, largely due to changes in the association rate, kon. Finally, temperature-dependent measurements reveal that increased [NaCl] reduces the overall exothermicity (ΔΔH° > 0) of duplex formation, albeit by an amount smaller than the reduction in entropic penalty (−TΔΔS° duplex formation. PMID:23931323

  6. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.

    Energy Technology Data Exchange (ETDEWEB)

    Tsutakawa, Susan E.; Shin, David S.; Mol, Clifford D.; Izum, Tadahide; Arvai, Andrew S.; Mantha, Anil K.; Szczesny, Bartosz; Ivanov, Ivaylo N.; Hosfield, David J.; Maiti, Buddhadev; Pique, Mike E.; Frankel, Kenneth A.; Hitomi, Kenichi; Cunningham, Richard P.; Mitra, Sankar; Tainer, John A.

    2013-03-22

    Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair, AP sites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 ? resolution APE1-DNA product complex with Mg(2+) and a 0.92 Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg(2+). Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.

  7. Molecular Modeling of the Major DNA Adduct Formed from Food Mutagen Ochratoxin A in NarI Two-Base Deletion Duplexes: Impact of Sequence Context and Adduct Ionization on Conformational Preference and Mutagenicity.

    Science.gov (United States)

    Kathuria, Preetleen; Sharma, Purshotam; Manderville, Richard A; Wetmore, Stacey D

    2017-08-21

    Exposure to ochratoxin A (OTA), a possible human carcinogen, leads to many different DNA mutations. As a first step toward understanding the structural basis of OTA-induced mutagenicity, the present work uses a robust computational approach and a slipped mutagenic intermediate model previously studied for C 8 -dG aromatic amine adducts to analyze the conformational features of postreplication two-base deletion DNA duplexes containing OT-dG, the major OTA lesion at the C 8 position of guanine. Specifically, a total of 960 ns of molecular dynamics simulations (excluding trial simulations) were carried out on four OT-dG ionization states in three sequence contexts within oligomers containing the NarI recognition sequence, a known hotspot for deletion mutations induced by related adducts formed from known carcinogens. Our results indicate that the structural properties and relative stability of the competing "major groove" and "stacked" conformations of OTA adducted two-base deletion duplexes depend on both the OTA ionization state and the sequence context, mainly due to conformation-dependent deviations in discrete local (hydrogen-bonding and stacking) interactions at the lesion site, as well as DNA bending. When the structural characteristics of the OT-dG adducted two-base deletion duplexes are compared to those associated with previously studied C 8 -dG adducts, a greater understanding of the effects of the nucleobase-carcinogen linkage, and size of the carcinogenic moiety on the conformational preferences of damaged DNA is obtained. Most importantly, our work predicts key structural features for OT-dG-adducted deletion DNA duplexes, which in turn allow us to develop hypotheses regarding OT-dG replication outcomes. Thus, our computational results are valuable for the design and interpretation of future biochemical studies on the potentially carcinogenic OT-dG lesion.

  8. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    Science.gov (United States)

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. Copyright © 2012 Elsevier

  9. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA

    DEFF Research Database (Denmark)

    Moreno, Pedro M D; Geny, Sylvain; Pabon, Y Vladimir

    2013-01-01

    In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasi...

  10. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Byungchan, E-mail: bbccahn@mail.ulsan.ac.kr [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of); Bohr, Vilhelm A. [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  11. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA

    Directory of Open Access Journals (Sweden)

    Anna Aviñó

    2016-02-01

    Full Text Available Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide by ultraviolet (UV, circular dichroism (CD and nuclear magnetic resonance (NMR spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO is RNA. In addition, DNA triplexes (D:D·D are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions.

  12. Reversible Redox Activity by Ion-pH Dually Modulated Duplex Formation of i-Motif DNA with Complementary G-DNA

    Directory of Open Access Journals (Sweden)

    Soyoung Chang

    2018-04-01

    Full Text Available The unique biological features of supramolecular DNA have led to an increasing interest in biomedical applications such as biosensors. We have developed an i-motif and G-rich DNA conjugated single-walled carbon nanotube hybrid materials, which shows reversible conformational switching upon external stimuli such as pH (5 and 8 and presence of ions (Li+ and K+. We observed reversible electrochemical redox activity upon external stimuli in a quick and robust manner. Given the ease and the robustness of this method, we believe that pH- and ion-driven reversible DNA structure transformations will be utilized for future applications for developing novel biosensors.

  13. pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.

    Science.gov (United States)

    Bucek, Pavel; Jaumot, Joaquim; Aviñó, Anna; Eritja, Ramon; Gargallo, Raimundo

    2009-11-23

    Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.

  14. O6-ethylguanine carcinogenic lesions in DNA: An NMR study of O6etG·T pairing in dodecanucloetide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1989-01-01

    High-resolution two-dimensional NMR studies are reported on the self-complementary d-(C1-G2-C3-O 6 etG4-A5-G6-C7-T8-T9-G10-C11-G12) duplex (designated O 6 etG·T 12-mer) containing two symmetrically related O 6 etG·T lesion sites located four base pairs in from either end of the duplex. Parallel studies were undertaken on a related sequence containing O 6 meG·T lesion sites (designated O 6 meG·T 12-mer) in order to evaluate the influence of the size of the alkyl substituent on the structure of the duplex and were undertaken on a related sequence containing G·T mismatch sites (designated G·T 12-mer duplex), which served as the control duplex. The exchangeable and nonexchangeable proton and the phosphorus nuclei have been assigned from an analysis of two-dimensional nuclear Overhauser enhancement (NOE) and correlated spectra of the O 6 etG·T 12-mer, O 6 meG·T 12-mer, and G·T 12-mer duplexes in H 2 O and D 2 O solutions. The distance connectivities observed in the NOESY spectra of the O 6 alkG·T 12-mer duplexes establish that the helix is right-handed and all of the bases adopt an anti conformation of the glycosidic torsion angle including the O 6 alkG4 and T9 bases at the lesion site. These observations establish that the O 6 alkG4 and T9 residues are stacked into the duplex and that the O 6 CH 3 and O 6 CH 2 CH 3 groups of O 6 alkG4 adopt a syn orientation with respect to the N 1 of the alkylated guanine. Since the O 6 -alkyl group adopts a syn orientation, the separation between the O 6 of O 6 alkG4 and the O 4 of T9 in the major groove is increased, preventing the formation of a short hydrogen bond between the N 1 ring nitrogen of O 6 alkG4 and the imino proton of T9

  15. Mycobacterium smegmatis HelY Is an RNA-Activated ATPase/dATPase and 3'-to-5' Helicase That Unwinds 3'-Tailed RNA Duplexes and RNA:DNA Hybrids.

    Science.gov (United States)

    Uson, Maria Loressa; Ordonez, Heather; Shuman, Stewart

    2015-10-01

    Mycobacteria have a large and distinctive ensemble of DNA helicases that function in DNA replication, repair, and recombination. Little is known about the roster of RNA helicases in mycobacteria or their roles in RNA transactions. The 912-amino-acid Mycobacterium smegmatis HelY (MSMEG_3885) protein is a bacterial homolog of the Mtr4 and Ski2 helicases that regulate RNA 3' processing and turnover by the eukaryal exosome. Here we characterize HelY as an RNA-stimulated ATPase/dATPase and an ATP/dATP-dependent 3'-to-5' helicase. HelY requires a 3' single-strand RNA tail (a loading RNA strand) to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The findings that HelY ATPase is unresponsive to a DNA polynucleotide cofactor and that HelY is unable to unwind a 3'-tailed duplex in which the loading strand is DNA distinguish HelY from other mycobacterial nucleoside triphosphatases/helicases characterized previously. The biochemical properties of HelY, which resemble those of Mtr4/Ski2, hint at a role for HelY in mycobacterial RNA catabolism. RNA helicases play crucial roles in transcription, RNA processing, and translation by virtue of their ability to alter RNA secondary structure or remodel RNA-protein interactions. In eukarya, the RNA helicases Mtr4 and Ski2 regulate RNA 3' resection by the exosome. Mycobacterium smegmatis HelY, a bacterial homolog of Mtr4/Ski2, is characterized here as a unidirectional helicase, powered by RNA-dependent ATP/dATP hydrolysis, that tracks 3' to 5' along a loading RNA strand to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The biochemical properties of HelY suggest a role in bacterial RNA transactions. HelY homologs are present in pathogenic mycobacteria (e.g., M. tuberculosis and M. leprae) and are widely prevalent in Actinobacteria and Cyanobacteria but occur sporadically elsewhere in the bacterial domain. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. NMR studies of the exocyclic 1,N6-ethenodeoxyadenosine adduct (εdA) opposite thymidine in a DNA duplex. Nonplanar alignment of εdA(anti) and dT(anti) at the lesion site

    International Nuclear Information System (INIS)

    Kouchakdjian, M.; Patel, D.J.; Eisenberg, M.; Yarema, K.; Basu, A.; Essigmann, J.

    1991-01-01

    Two-dimensional proton NMR studies are reported on the complementary d(C-A-T-G-T-G-T-A-C)·d(G-T-A-C-εA-C-A-T-G) nonanucleotide duplex (designated εdA·dT 9-mer duplex) containing 1,N 6 -ethenodeoxyadenosine (εdA), a carcinogen-DNA adduct, positioned opposite thymidine in the center of the helix. The authors NMR studies have focused on the conformation of the εdA·dT 9-mer duplex at neutral pH with emphasis on defining the alignment at the dT5·εdA14 lesion site. The through-space NOE distance connectivities establish that both dT5 and εdA14 adopt anti glycosidic torsion angles, are directed into the interior of the helix, and stack with flanking Watson-Crick dG4·dC15 and dG6·dC13 pairs. Furthermore, the d(G4-T5-G6)·d(C13-εA14-C15) trinucleotide segment centered about the dT5·εdA14 lesion site adopts a right-handed helical conformation in solution. Energy minimization computations were undertaken starting from six different alignments of dT5(anti) and εdA14(anti) at the lesion site and were guided by distance constraints defined by lower and upper bounds estimated from NOESY data sets on the εdA·dT 9-mer duplex. The NMR data are consistent with a nonplanar alignment of εdA14(anti) and dT5(anti) with dT5 displaced toward the flanking dG4·dC15 base pair within the d(G4-T5-G6)·d(C13-εA14-C15) segment of the εdA·dT 9-mer duplex

  17. Detecting deletions, insertions, and single nucleotide substitutions in cloned β-globin genes and new polymorphic nucleotide substitutions in β-globin genes in a Japanese population using ribonuclease cleavage at mismatches in RNA: DNA duplexes

    International Nuclear Information System (INIS)

    Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-08-01

    The applicability of ribonuclease (RNase) cleavage at mismatches in RNA:DNA duplexes (the RNase cleavage method) for determining nucleotide variant rates was examined in a Japanese population. DNA segments of various lengths obtained from four different regions of one normal and three thalassemic cloned human β-globin genes were inserted into transcription vectors. Sense and antisense RNA probes uniformly labeled with 32 P were prepared. When RNA probes of 771 nucleotides (nt) or less were hybridized with cloned DNAs and the resulting duplexes were treated with a mixture of RNases A and T1, the length of products agreed with theoretical values. Twelve possible mismatches were examined. Since both sense and antisense probes were used, uncleavable mismatches such as G:T and G:G which were made from one combination of RNA and DNA strands could be converted to the cleavable C:A and C:C mismatches, respectively, by using the opposite combination. Deletions and insertions of one (G), four(TTCT), five (ATTTT), and 10 (ATTTTATTTT) nt were easily detected. A polymorphic substitution of T to C at position 666 of the second intervening sequence (IVS2-666) of the β-globin gene was detected using genomic DNAs from cell lines established from the peripheral B lymphocytes of 59 unrelated Japanese from Hiroshima or those amplified by polymerase chain reaction (PCR). The frequency of the gene with C at the IVS2-666 (allele C) was 0.48 and that of the gene with T (allene T) was 0.52. Two new polymorphic substitutions of C to A and A to T were detected at nucleotide positions 1789 and 1945 from the capping site, respectively, using genomic DNAs amplified by PCR. We conclude that it would be feasible to use the RNase cleavage method combined with PCR for large-scale screening of variation in chromosomal DNA. (J.P.N.)

  18. ATP-dependent partitioning of the DNA template into supercoiled domains by Escherichia coli UvrAB

    International Nuclear Information System (INIS)

    Koo, Hyeon-Sook; Liu, L.F.; Claassen, L.; Grossman, L.

    1991-01-01

    The helicase action of the Escherichia coli UvrAB complex on a covalently closed circular DNA template was monitored using bacterial DNA topoisomerase I, which specifically removes negative supercoils. In the presence of E. coli DNA topoisomerase I and ATP, the UvrAB complex gradually introduced positive supercoils into the input relaxed plasmid DNA template. Positive supercoils were not produced when E. coli DNA topoisomerase I was replaced by eukaryotic DNA topoisomerase I or when both E. coli and eukaryotic DNA topoisomerases I were added simultaneously. These results suggest that like other DNA helix-tracking processes, the ATP-dependent action of the UvrAM complex on duplex DNA simultaneously generates both positive and negative supercoils, which are not constrained by protein binding but are torsionally strained. The supercoiling activity of UvrAB on UV-damaged DNA was also studied using UV-damaged plasmid DNA and a mutant UvrA protein that lacks the 40 C-terminal amino acids and is defective in preferential binding to UV-damaged DNA. UvrAB was found to preferentially supercoil the UV-damaged DNA template, whereas the mutant protein supercoiled UV-damaged and undamaged DNA with equal efficiency. The authors results therefore suggest that the DNA helix-tracking activity of UvrAB may be involved in searching and/or prepriming the damaged DNA for UvrC incision. A possible role of supercoiled domains in the incision process is discussed

  19. Structural Properties of G,T-Parallel Duplexes

    Directory of Open Access Journals (Sweden)

    Anna Aviñó

    2010-01-01

    Full Text Available The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

  20. Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability

    KAUST Repository

    Tsutakawa, Susan E.

    2017-06-27

    DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5\\'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5\\'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5\\'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering\\', basic residues energetically steer an inverted ss 5\\'-flap through a gateway over FEN1\\'s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5\\'-flap specificity and catalysis, preventing genomic instability.

  1. New insights in the removal of the hydantoins, oxidation product of pyrimidines, via the base excision and nucleotide incision repair pathways.

    Directory of Open Access Journals (Sweden)

    Modesto Redrejo-Rodríguez

    Full Text Available BACKGROUND: Oxidative damage to DNA, if not repaired, can be both miscoding and blocking. These genetic alterations can lead to mutations and/or cell death, which in turn cause cancer and aging. Oxidized DNA bases are substrates for two overlapping repair pathways: base excision (BER and nucleotide incision repair (NIR. Hydantoin derivatives such as 5-hydroxyhydantoin (5OH-Hyd and 5-methyl-5-hydroxyhydantoin (5OH-5Me-Hyd, major products of cytosine and thymine oxidative degradation pathways, respectively, have been detected in cancer cells and ancient DNA. Hydantoins are blocking lesions for DNA polymerases and excised by bacterial and yeast DNA glycosylases in the BER pathway. However little is known about repair of pyrimidine-derived hydantoins in human cells. METHODOLOGY/PRINCIPAL FINDINGS: Here, using both denaturing PAGE and MALDI-TOF MS analyses we report that the bacterial, yeast and human AP endonucleases can incise duplex DNA 5' next to 5OH-Hyd and 5OH-5Me-Hyd thus initiating the NIR pathway. We have fully reconstituted the NIR pathway for these lesions in vitro using purified human proteins. Depletion of Nfo in E. coli and APE1 in HeLa cells abolishes the NIR activity in cell-free extracts. Importantly, a number of redundant DNA glycosylase activities can excise hydantoin residues, including human NTH1, NEIL1 and NEIL2 and the former protein being a major DNA glycosylase activity in HeLa cells extracts. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that both BER and NIR pathways can compete and/or back-up each other to remove hydantoin DNA lesions in vivo.

  2. Effect of point substitutions within the minimal DNA-binding domain of xeroderma pigmentosum group A protein on interaction with DNA intermediates of nucleotide excision repair.

    Science.gov (United States)

    Maltseva, E A; Krasikova, Y S; Naegeli, H; Lavrik, O I; Rechkunova, N I

    2014-06-01

    Xeroderma pigmentosum factor A (XPA) is one of the key proteins in the nucleotide excision repair (NER) process. The effects of point substitutions in the DNA-binding domain of XPA (positively charged lysine residues replaced by negatively charged glutamate residues: XPA K204E, K179E, K141E, and tandem mutant K141E/K179E) on the interaction of the protein with DNA structures modeling intermediates of the damage recognition and pre-incision stages in NER were analyzed. All these mutations decreased the affinity of the protein to DNA, the effect depending on the substitution and the DNA structure. The mutant as well as wild-type proteins bind with highest efficiency partly open damaged DNA duplex, and the affinity of the mutants to this DNA is reduced in the order: K204E > K179E > K141E = K141/179E. For all the mutants, decrease in DNA binding efficiency was more pronounced in the case of full duplex and single-stranded DNA than with bubble-DNA structure, the difference between protein affinities to different DNA structures increasing as DNA binding activity of the mutant decreased. No effect of the studied XPA mutations on the location of the protein on the partially open DNA duplex was observed using photoinduced crosslinking with 5-I-dUMP in different positions of the damaged DNA strand. These results combined with earlier published data suggest no direct correlation between DNA binding and activity in NER for these XPA mutants.

  3. The formation of double-strand breaks at multiply damaged sites is driven by the kinetics of excision/incision at base damage in eukaryotic cells

    International Nuclear Information System (INIS)

    Kozmin, S.G.; Sedletska, Y.; Reynaud-Angelin, A.; Sage, E.; Kozmin, S.G.; Sedletska, Y.; Reynaud-Angelin, A.; Sage, E.; Gasparutto, D.

    2009-01-01

    It has been stipulated that repair of clustered DNA lesions may be compromised, possibly leading to the formation of double-strand breaks (DSB) and, thus, to deleterious events. Using a variety of model multiply damaged sites (MDS), we investigated parameters that govern the formation of DSB during the processing of MDS. Duplexes carrying MDS were inserted into replicative or integrative vectors, and used to transform yeast Saccharomyces cerevisiae. Formation of DSB was assessed by a relevant plasmid survival assay. Kinetics of excision/incision and DSB formation at MDS was explored using yeast cell extracts. We show that MDS composed of two uracils or abasic sites, were rapidly incised and readily converted into DSB in yeast cells. In marked contrast, none of the MDS carrying opposed oG and hU separated by 38 bp gave rise to DSB, despite the fact that some of them contained preexisting single-strand break (a 1-nt gap). Interestingly, the absence of DSB formation in this case correlated with slow excision/incision rates of lesions. We propose that the kinetics of the initial repair steps at MDS is a major parameter that direct towards the conversion of MDS into DSB. Data provides clues to the biological consequences of MDS in eukaryotic cells. (authors)

  4. DNA incision evaluation, binding investigation and biocidal screening of Cu(II), Ni(II) and Co(II) complexes with isoxazole Schiff bases.

    Science.gov (United States)

    Ganji, Nirmala; Chityala, Vijay Kumar; Marri, Pradeep Kumar; Aveli, Rambabu; Narendrula, Vamsikrishna; Daravath, Sreenu; Shivaraj

    2017-10-01

    Two new series of binary metal complexes [M(L 1 ) 2 ] and [M(L 2 ) 2 ] where, M=Cu(II), Ni(II) & Co(II) and L 1 =4-((3,4-dimethylisoxazol-5-ylimino)methyl)benzene-1,3-diol; L 2 =2-((3,4-dimethylisoxazol-5-ylimino)methyl)-5-methoxyphenol were synthesized and characterized by elemental analysis, 1 H NMR, 13 C NMR, FT-IR, ESI mass, UV-Visible, magnetic moment, ESR, SEM and powder XRD studies. Based on these results, a square planar geometry is assigned for all the metal complexes where the Schiff base acts as uninegatively charged bidentate chelating agent via the hydroxyl oxygen and azomethine nitrogen atoms. DNA binding studies of all the complexes with calf thymus DNA have been comprehensively investigated using electronic absorption spectroscopy, fluorescence quenching and viscosity studies. The oxidative and photo cleavage affinity of metal complexes towards supercoiled pBR322 DNA has been ascertained by agarose gel electrophoresis assay. From the results, it is observed that all the metal complexes bind effectively to CT-DNA via an intercalative mode of binding and also cleave pBR322 DNA in a promising manner. Further the Cu(II) complexes have shown better binding and cleavage properties towards DNA. The antimicrobial activities of the Schiff bases and their metal complexes were studied on bacterial and fungal strains and the results denoted that the complexes are more potent than their Schiff base ligands. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Vesicoureteral Reflux and Duplex Systems

    OpenAIRE

    Thomas, John C.

    2008-01-01

    Vesicoureteral reflux (VUR) is the most common anomaly associated with duplex systems. In addition to an uncomplicated duplex system, reflux can also be secondary in the presence of an ectopic ureterocele with duplex systems. Controversy exists in regard to the initial and most definitive management of these anomalies when they coexist. This paper will highlight what is currently known about duplex systems and VUR, and will attempt to provide evidence supporting the various surgical approa...

  6. Increased Y-chromosome detection by SRY duplexing

    DEFF Research Database (Denmark)

    Hansen, Morten Høgh; Clausen, Frederik Banch; Dziegiel, Morten Hanefeld

    2012-01-01

    Determining fetal sex noninvasively is dependent of a robust assay. We designed a novel SRY assay and combined it with a SRY assay from literature forming a duplex assay with the same fluorescent dye to increase detection of Y-chromosome at low cell-free fetal DNA or chimeric DNA concentrations....

  7. The Duplex Society.

    Science.gov (United States)

    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)

  8. Duplex tab exhaust nozzle

    Science.gov (United States)

    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.

  9. Considerations in Duplex Investment.

    Science.gov (United States)

    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…

  10. The inverted Batman incision: a new incision in transcolumellar incision for open rhinoplasty.

    Science.gov (United States)

    Nakanishi, Yuji; Nagasao, Tomohisa; Shimizu, Yusuke; Miyamoto, Junpei; Fukuta, Keizo; Kishi, Kazuo

    2013-12-01

    Columellar and nostril shapes often present irregularity after transcolumellar incision for open rhinoplasty, because of the contracture of the incised wound. The present study introduces a new technique to prevent this complication, and verifies its efficacy in improving cosmetic appearance. In our new method, a zig-zag incision with three small triangular flaps is made on the columella and in the pericolumellar regions of the bilateral nostril rims. Since the shape of the incision resembles the contour of an inverted "batman", we term our new method the "Inverted Batman" incision. To verify the effectiveness of the Inverted Batman incision, aesthetic evaluation was conducted for 21 patients operated on using the conventional transcolumellar incision (Conventional Group) and 19 patients operated on using the Inverted Batman incision (Inverted Batman Group). The evaluation was performed by three plastic surgeons, using a four-grade scale to assess three separate items: symmetry of bilateral soft triangles, symmetry of bilateral margins of the columella, and evenness of the columellar surface. The scores of the two groups for these three items were compared using a non-parametric test (Mann-Whitney U-test). With all three items, the Inverted Batman group patients present higher scores than Conventional Group patients. The Inverted Batman incision is effective in preserving the correct anatomical structure of the columella, soft triangle, and nostril rims. Hence, we recommend the Inverted Batman incision as a useful technique for open rhinoplasty.

  11. Minimal abdominal incisions

    Directory of Open Access Journals (Sweden)

    João Carlos Magi

    2017-04-01

    Full Text Available Minimally invasive procedures aim to resolve the disease with minimal trauma to the body, resulting in a rapid return to activities and in reductions of infection, complications, costs and pain. Minimally incised laparotomy, sometimes referred to as minilaparotomy, is an example of such minimally invasive procedures. The aim of this study is to demonstrate the feasibility and utility of laparotomy with minimal incision based on the literature and exemplifying with a case. The case in question describes reconstruction of the intestinal transit with the use of this incision. Male, young, HIV-positive patient in a late postoperative of ileotiflectomy, terminal ileostomy and closing of the ascending colon by an acute perforating abdomen, due to ileocolonic tuberculosis. The barium enema showed a proximal stump of the right colon near the ileostomy. The access to the cavity was made through the orifice resulting from the release of the stoma, with a lateral-lateral ileo-colonic anastomosis with a 25 mm circular stapler and manual closure of the ileal stump. These surgeries require their own tactics, such as rigor in the lysis of adhesions, tissue traction, and hemostasis, in addition to requiring surgeon dexterity – but without the need for investments in technology; moreover, the learning curve is reported as being lower than that for videolaparoscopy. Laparotomy with minimal incision should be considered as a valid and viable option in the treatment of surgical conditions. Resumo: Procedimentos minimamente invasivos visam resolver a doença com o mínimo de trauma ao organismo, resultando em retorno rápido às atividades, reduções nas infecções, complicações, custos e na dor. A laparotomia com incisão mínima, algumas vezes referida como minilaparotomia, é um exemplo desses procedimentos minimamente invasivos. O objetivo deste trabalho é demonstrar a viabilidade e utilidade das laparotomias com incisão mínima com base na literatura e

  12. Craniosynostosis incision: scalpel or cautery?

    Science.gov (United States)

    Wood, Jeyhan S; Kittinger, Benjamin J; Perry, Victor L; Adenola, Adeyemi; van Aalst, John A

    2014-07-01

    There is an ongoing debate regarding the optimal instrument for scalp incisions: the scalpel or electrocautery. The argument generally focuses on improved healing after an incision made with a knife and decreased bleeding when using electrocautery. This study compares the use of scalpel and electrocautery in making coronal incisions for patients undergoing surgical correction of craniosynostosis. The outcome metric used is wound healing within 6 months after surgery. All patients presenting to the University of North Carolina Children's Hospital with craniosynostosis between July 1, 2007 and January 1, 2010 requiring a coronal incision for surgical correction were prospectively enrolled. In all of these patients, half of the coronal incision was made with knife; the other half, with needle tip cautery. Side of the incision was specified at the time of surgery in the operative report. Patients were excluded from the study if the instrument for incision was not specified or if only 1 modality was used for the entire incision. Sixty-eight patients underwent cranial vault reconstruction, of which 58 met inclusion criteria. Of the 58 matched pairs, 55 were analyzed statistically. The 3 excluded cases were those who had midline complications. There were 17 wound complications (15%): 8 in the knife group, 6 in the cautery group, and 3 at midline (with indeterminate side for the problem). We found no statistically significant difference in wound healing between incisions made with a knife or with electrocautery.

  13. O6-ethylguanine carcinogenic lesions in DNA: An NMR study of O6etG·C pairing in dodecanucleotide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1989-01-01

    The pairing of O 6 etG with C located four base pairs in from either end of the self-complementary d(C1-G2-C3-O 6 etG4-A5-G6-C7-T8-C9-G10-C11-G12) duplex (designated O 6 etG·C 12-mer) has been investigated from an analysis of proton and phosphorus two-dimensional NMR experiments. The structural consequences of increasing the alkyl group size were elucidated from a comparative study of the pairing of O 6 meG4 with C9 in a related sequence (designated O 6 meG·C 12-mer). The NMR parameters for both O 6 alkG-containing dodecanucleotides are also compared with those of the control sequence containing G4·C9 base pairs (designated G·C 12-mer). The NOE cross-peaks detected in the two-dimensional NOESY spectra of the O 6 alkG·C 12-mer duplexes in H 2 O solution establish that the O 6 etG4/O 6 meG4 and C9 bases at the lesion site stack into the helix between the flanking C3·G10 and A5·T8 Watson-Crick base pairs. The observed NOEs between the amino protons of C9 and the CH 3 protons of O 6 alkG4 establish a syn orientation of the O 6 -alkyl group with respect to the N 1 of alkylated guanine. A wobble alignment of the O 6 alkG4·C9 base pair stabilized by two hydrogen bonds, one between the amino group of C9 and N 1 of O 6 alkG and the other between the amino group of O 6 alkG and N 3 of C9, is tentatively proposed on the basis of the NOEs between the amino protons of C9 at the lesion site and the imino protons of flanking Watson-Crick base pairs

  14. The fourth incision: a cosmetic autopsy incision technique.

    Science.gov (United States)

    Patowary, Amarjyoti

    2010-03-01

    Autopsy procedure includes thorough external examination as well as internal examination including opening of all the body cavities for proper visualization of all the visceral organs. As such, there remains incision marks with stitches which harts the sentiment of the already traumatized relatives of the deceased. Moreover, it looks odd especially in cases of otherwise healthy dead bodies. So, autopsy incisions should be such that, we can get maximum possible visualization of the body cavities, particularly the thorax and abdomen, and at the same time the incision as well as the stitch marks are also hidden. This article is aimed to describe few modifications in the autopsy incisions for opening the thorax and abdomen and also proper visualization of the neck structures during autopsy where the incisions and the stitches are kept hidden.

  15. Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes

    DEFF Research Database (Denmark)

    Geny, Sylvain; Moreno, Pedro M D; Krzywkowski, Tomasz

    2016-01-01

    Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick binding. To improve the b...

  16. Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2-or 4-pyrenyl-functionalized O2 '-alkylated RNA monomers

    DEFF Research Database (Denmark)

    Karmakar, Saswata; Madsen, Andreas Stahl; Guenther, Dale C.

    2014-01-01

    '-alkylated uridine monomers X-Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA...

  17. Liquid in the major incision

    International Nuclear Information System (INIS)

    Herrera Jaramillo, Diego Alberto; Ortega Jaramillo, Hector

    2003-01-01

    We present the case of a patient with spill pleural extending in the left major incision. In the chest thorax PA, we could observe one of the complex radiographic appearances that take the reconfiguration of fluid in this localization, being this appearance dependent of the patient's position. Some points are also discussed on the anatomy of the major incisions and some of their radiographic characteristics

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

    Science.gov (United States)

    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.

  19. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  20. Single incision pediatric endoscopic surgery: advantages of relatively large incision

    International Nuclear Information System (INIS)

    Yilmaz, E.; Afsarlar, E.; Karaman, I.

    2015-01-01

    To describe Single Incision Pediatric Endoscopic Surgery (SIPES) performed on children with various diagnoses, emphasizing its advantages. Study Design: An observational case series. Place and Duration of Study: Department of Pediatric Surgery, Dr. Sami Ulus Maternity and Child Health Hospital, Ankara, Turkey, from January 2011 to November 2014. Methodology: A review of patient charts was conducted in which SIPES was preferred as the surgical procedure. Patient demographics, operative details, operative time, clinical outcomes, postoperative pain and cosmesis were analyzed. Results: SIPES was performed on 45 patients (21 girls, 24 boys). Thirty-three appendectomies, 5 varicocelectomies, 3 oophorectomies, 2 ovarian and one paratubal cyst excision, and one fallopian tube excision were performed. All except one procedures were performed through our standard 2cm umbilical vertical or smile incision. In 18 cases, abdominal irrigation/aspiration was easily performed through the existing larger incision, as is done with open surgical technique. None of the patients had early postoperative shoulder/back pain since complete disinflation of CO/sub 2/ could be ensured. All of the patients/parents were satisfied with the cosmesis. Conclusion: SIPES has the advantages of limiting the surgical scar to within the umbilicus and providing easy disinflation of CO/sub 2/, allowing intraabdominal cleaning and extraction of large volume tissue samples through a single large umbilical incision. (author)

  1. Maximizing synchronizability of duplex networks

    Science.gov (United States)

    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.

  2. A Dual-Specific Targeting Approach Based on the Simultaneous Recognition of Duplex and Quadruplex Motifs.

    Science.gov (United States)

    Nguyen, Thi Quynh Ngoc; Lim, Kah Wai; Phan, Anh Tuân

    2017-09-20

    Small-molecule ligands targeting nucleic acids have been explored as potential therapeutic agents. Duplex groove-binding ligands have been shown to recognize DNA in a sequence-specific manner. On the other hand, quadruplex-binding ligands exhibit high selectivity between quadruplex and duplex, but show limited discrimination between different quadruplex structures. Here we propose a dual-specific approach through the simultaneous application of duplex- and quadruplex-binders. We demonstrated that a quadruplex-specific ligand and a duplex-specific ligand can simultaneously interact at two separate binding sites of a quadruplex-duplex hybrid harbouring both quadruplex and duplex structural elements. Such a dual-specific targeting strategy would combine the sequence specificity of duplex-binders and the strong binding affinity of quadruplex-binders, potentially allowing the specific targeting of unique quadruplex structures. Future research can be directed towards the development of conjugated compounds targeting specific genomic quadruplex-duplex sites, for which the linker would be highly context-dependent in terms of length and flexibility, as well as the attachment points onto both ligands.

  3. Superficial parotidectomy via facelift incision

    NARCIS (Netherlands)

    Lohuis, Peter J. F. M.; Tan, M. Liane; Bonte, Katrien; van den Brekel, Michiel W. M.; Balm, Alfons J. M.; Vermeersch, Hubert B.

    2009-01-01

    The stigma of a visually prominent facial scar following parotid surgery can be distressing to a young patient. The surgical technique of parotidectomy via a facelift incision is described and evaluated. Thirty patients with a benign lesion of the parotid gland underwent a partial superficial

  4. Effects of post-treatment incubation on recombinogenesis in incision-proficient and incision-deficient strains of saccharomyces cerevisiae, 2

    International Nuclear Information System (INIS)

    Saeki, Tetsuya; Machida, Isamu

    1991-01-01

    After the photoaddition of mono- and bifunctional furocoumarins to G1 phase cells, most gene conversion and crossing-over occurred without post-irradiation incubation of these cells in incision-proficient strains. In contrast, incision-deficient cells showed marked induction of both recombinational events only after treated cells had been incubated for several hours before selection. These results indicate that when furocoumarins are photoadded to G1 cells, initiation of recombinational events occurs during the same G1 phase in the incision-proficient cells; whereas, it occurs only after post-irradiation DNA replication in incision-deficient cells. The action of the PSO2 gene product specific for the repair of DNA crosslinks in recombination induction is discussed and compared to the actions of the excision repair genes RAD1 and RAD2. (author)

  5. Welding of duplex and super-duplex stainless steels

    International Nuclear Information System (INIS)

    Van Nassau, L.; Meelker, H.; Hilkes, J.

    1994-01-01

    After a recall of the commercial designation of duplex or super-duplex steels (22-27% Cr, 4-8% Ni, 0.1-0.3% N with or without Mo (1.5-4%)) and of some metallurgical properties (phase diagrams, microstructure, ferrite determination, heat treatment and aging), welding technologies are synthetically presented (advantages-disadvantages of each process, metals filler, parameters of the welding processes, heat treatments after welding, cleaning, passivation, properties (mechanical, corrosion resistance) of the welded pieces). (A.B.). 28 refs. 5 figs., 15 tabs., 1 annexe

  6. Postoperative Granulomas at Liposuction Incision Sites.

    Science.gov (United States)

    Weniger, Frederick G; White, Peter F; Barrero Castedo, Carlos E

    2016-02-01

    Since most liposuction incisions heal uneventfully, difficult healing in such incisions must be investigated. In the cases of two gynecomastia liposuction patients in which a water-based lubricating gel was used on the liposuction incisions, the incisions failed to heal. For both patients, workup uncovered palisading granulomas at the lateral inframammary fold incision sites several months after otherwise successful surgeries. These two cases are presented and the previous literature is reviewed, with consideration given to the etiology and prevention of such granulomas. LEVEL OF EVIDENCE 5: Risk. © 2015 The American Society for Aesthetic Plastic Surgery, Inc. Reprints and permission: journals.permissions@oup.com.

  7. Base pair mismatches and carcinogen-modified bases in DNA: an NMR study of G x T and G x O4meT pairing in dodecanucleotide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Kouchakdjian, M.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1988-01-01

    High-resolution two-dimensional NMR studies have been completed on the self-complementary d(C-G-C-G-A-G-C-T-T-G-C-G) duplex (designated G x T 12-mer) and the self-complementary d(C-G-C-G-A-G-C-T-O 4 meT-G-C-G) duplex (designated G x O 4 meT 12-mer) containing G x T and G x O 4 meT pairs at identical positions four base pairs in from either end of the duplex. The exchangeable and nonexchangeable proton resonances have been assigned from an analysis of two-dimensional nuclear Overhauser enhancement (NOESY) spectra for the G x T 12-mer and G x O 4 meT 12-mer duplexes in H 2 O and D 2 O solution. The guanosine and thymidine imino protons in the G x T mismatch resonate at 10.57 and 11.98 ppm, respectively, and exhibit a strong NOE between themselves and to imino protons of flanking base pairs in the G x T 12-mer duplex. The large upfield chemical shift of this proton relative to that of the imino proton resonance of G in the G x T mismatch or in G x C base pairs indicates that hydrogen bonding to O 4 meT is either very weak or absent. This guanosine imino proton has an NOE to the OCH 3 group of O 4 meT across the pair and NOEs to the imino protons of flanking base pairs. Taken together with data from the NMR of nonexchangeable protons, this shows that both G and O 4 meT have anti-glycosidic torsion angles and are stacked into the duplex. Comparison of the intensity of the NOEs between the guanosine imino proton and the OCH 3 of O 4 meT as well as other protons in its vicinity demonstrates that the OCH 3 group of O 4 meT adopts the syn orientation with respect to N3 of the methylated thymidine. The authors propose an alternate base pairing mode stabilized by one short hydrogen bond between the 2-amino group of guanosine and the 2-carbonyl group of O 4 met

  8. Superimposed Code Theorectic Analysis of DNA Codes and DNA Computing

    Science.gov (United States)

    2010-03-01

    that the hybridization that occurs between a DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research...ssDNA single stranded DNA WC Watson – Crick A Adenine C Cytosine G Guanine T Thymine ... Watson - Crick (WC) duplex, e.g., TCGCA TCGCA . Note that non-WC duplexes can form and such a formation is called a cross-hybridization. Cross

  9. Achieving single channel, full duplex wireless communication

    KAUST Repository

    Choi, Jung Il; Jain, Mayank; Srinivasan, Kannan; Levis, Phil; Katti, Sachin

    2010-01-01

    This paper discusses the design of a single channel full-duplex wireless transceiver. The design uses a combination of RF and baseband techniques to achieve full-duplexing with minimal effect on link reliability. Experiments on real nodes show the full-duplex prototype achieves median performance that is within 8% of an ideal full-duplexing system. This paper presents Antenna Cancellation, a novel technique for self-interference cancellation. In conjunction with existing RF interference cancellation and digital baseband interference cancellation, antenna cancellation achieves the amount of self-interference cancellation required for full-duplex operation. The paper also discusses potential MAC and network gains with full-duplexing. It suggests ways in which a full-duplex system can solve some important problems with existing wireless systems including hidden terminals, loss of throughput due to congestion, and large end-to-end delays. Copyright 2010 ACM.

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

    Science.gov (United States)

    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

  11. Normalized cDNA libraries

    Science.gov (United States)

    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.

  12. Modified tubularized incised plate urethroplasty

    Directory of Open Access Journals (Sweden)

    Shivaji Mane

    2013-01-01

    Full Text Available Aim: To share our experience of doing tubularized incised plate urethroplasty with modifications. Materials and Methods: This is a single surgeon personal series from 2004 to 2009. One hundred patients of distal hypospadias were subjected for Snodgrass urethroplasty with preputioplasty. The age range was 1 to 5 year with mean age of 2.7 years. Selection criteria were good urethral plate, without chordee and torsion needing complete degloving. Main technical modification from original Snodgrass procedure was spongioplasty, preputioplasty, and dorsal slit when inability to retract prepuce during surgery. Results: Average follow-up period is 23 months. Seven (7% patients developed fistula and one patient had complete preputial dehiscence. Phimosis developed in three (3% patients and required circumcision. Dorsal slit was required in seven patients. One patient developed meatal stenosis in postoperative period. All other patients are passing single urinary stream and have cosmesis that is acceptable. Conclusions: Modified tubularized incised plate urethroplasty with preputioplasty effectively gives cosmetically normal looking penis with low complications.

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

    Science.gov (United States)

    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.

  14. Probabilistic Medium Access Control for Full-Duplex Networks with Half-Duplex Clients

    OpenAIRE

    Chen, Shih-Ying; Huang, Ting-Feng; Lin, Kate Ching-Ju; Hong, H. -W. Peter; Sabharwal, Ashutosh

    2016-01-01

    The feasibility of practical in-band full-duplex radios has recently been demonstrated experimentally. One way to leverage full-duplex in a network setting is to enable three-node full-duplex, where a full- duplex access point (AP) transmits data to one node yet simultaneously receives data from another node. Such three-node full-duplex communication however introduces inter-client interference, directly impacting the full-duplex gain. It hence may not always be beneficial to enable three-nod...

  15. Modified incision for maxillectomy: our experience.

    Science.gov (United States)

    Bhavana, Kranti; Tyagi, Isha; Ramani, Mukesh Kumar

    2012-06-01

    Radical maxillectomy has usually been done by the classical Weber Ferguson incision since age old times and still is being used widely due to its advantage of excellent exposure and minimal scarring as the incision follows the natural skin crease. In our modification of radical maxillectomy incision we avoid a scar on the midface by performing a midface degloving and combining it with a subconjunctival eye incision thus avoiding any cosmetic deformity and associated eye complication. It also avoids the late complication of cutaneous fistula following radiotherapy to these areas and due to early healing of the wound, early radiotherapy can be started.

  16. Thermodynamics of sequence-specific binding of PNA to DNA

    DEFF Research Database (Denmark)

    Ratilainen, T; Holmén, A; Tuite, E

    2000-01-01

    For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and seq......For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes...

  17. Nucleic acid nanomaterials: Silver-wired DNA

    Science.gov (United States)

    Auffinger, Pascal; Ennifar, Eric

    2017-10-01

    DNA double helical structures are supramolecular assemblies that are typically held together by classical Watson-Crick pairing. Now, nucleotide chelation of silver ions supports an extended silver-DNA hybrid duplex featuring an uninterrupted silver array.

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

    Science.gov (United States)

    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.

  19. Overall performance of the duplex Stirling refrigerator

    International Nuclear Information System (INIS)

    Erbay, L. Berrin; Ozturk, M. Mete; Doğan, Bahadır

    2017-01-01

    Highlights: • Overall performance coefficient of duplex Stirling refrigerator was investigated. • A definite region for the coefficient of performance of the refrigerator in duplex Stirling is identified. • A definite region for the thermal efficiency of the heat engine in duplex Stirling is identified. • Benchmark values and design bounds of the duplex Stirling refrigerator were obtained. - Abstract: The duplex Stirling refrigerator is an integrated refrigerator consists of Stirling cycle engine and Stirling cycle refrigerator used for cooling. The equality of the work generation of the heat engine to the work consumption of the refrigerator is the primary constraint of the duplex Stirling. The duplex Stirling refrigerator is investigated thermodynamically by considering the effects of constructional and operational parameters which are namely the temperature ratios for heat engine and refrigerator, and the compression ratios for both sides. The primary concern is given to the parametric effects on the overall coefficient of performance of the duplex Stirling refrigerator. The given diagrams provide a design bounds and benchmark results that allows seeing the big picture about the cooling load and heat input relation. Moreover they ease to determine the corresponding work rate to the target cooling load. As regard to the obtained results, a definite region for coefficient of performance of the refrigerator and a definite region for the thermal efficiency of the heat engine of the duplex Stirling are identified.

  20. Development of dansyl-modified oligonucleotide probes responding to structural changes in a duplex.

    Science.gov (United States)

    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.

  1. Duplex gall bladder: bystander or culprit.

    Science.gov (United States)

    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.

  2. Two-dimensional 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex and a quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex

    International Nuclear Information System (INIS)

    Powers, R.; Olsen, R.K.; Gorenstein, D.G.

    1989-01-01

    Assignment of the 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The 31P chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. While the 31P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine rules previously demonstrated. 31P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys3, MeCys7]TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small 31P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the 1H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a non-intercalative mode of association of the drug. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible

  3. Single Incision Laparoscopic Splenectomy: Our First Experiences

    Directory of Open Access Journals (Sweden)

    Umut Barbaros

    2011-06-01

    Full Text Available Objective: Most laparoscopic surgeons have attempted to reduce incisional morbidity and improve cosmetic outcomes by using less and smaller trocars. Single incision laparoscopic splenectomy is a new laparoscopic procedure. Herein we would like to present our experiences.Material and Methods: Between January 2009 and June 2009, data of the 7 patients who underwent single incision laparoscopic splenectomy were evaluated retrospectively.Results: There were 7 patients (5 females and 2 males with a mean age of 29.9 years. The most common splenectomy indication was idiopathic thrombocytopenic purpura. Single incision laparoscopic splenectomy was performed successfully in 6 patients. In one patient the operation was converted to an open procedure.Conclusion: With surgeons experienced in minimally invasive surgery, single incision laparoscopic splenectomy could be performed successfully. However, in order to demonstrate the differneces between standard laparoscopic splenectomy and SILS splenetomy, prospective randomized comparative studies are required.

  4. Single-incision total laparoscopic hysterectomy

    Directory of Open Access Journals (Sweden)

    Sinha Rakesh

    2011-01-01

    Full Text Available Single-incision laparoscopic surgery is an alternative to conventional multiport laparoscopy. Single-access laparoscopy using a transumbilical port affords maximum cosmetic benefits because the surgical incision is hidden in the umbilicus. The advantages of single-access laparoscopic surgery may include less bleeding, infection, and hernia formation and better cosmetic outcome and less pain. The disadvantages and limitations include longer surgery time, difficulty in learning the technique, and the need for specialized instruments. Ongoing refinement of the surgical technique and instrumentation is likely to expand its role in gynecologic surgery in the future. We perform single-incision total laparoscopic hysterectomy using three ports in the single transumbilical incision.

  5. Mast Quadrant-assisted Minimally Invasive Modified Transforaminal Lumbar Interbody Fusion: Single Incision Versus Double Incision

    Directory of Open Access Journals (Sweden)

    Xin-Lei Xia

    2015-01-01

    Full Text Available Background: The concept of minimally invasive techniques is to make every effort to reduce tissue damage. Certainly, reducing skin incision is an important part of these techniques. This study aimed to investigate the clinical feasibility of Mast Quadrant-assisted modified transforaminal lumbar interbody fusion (TLIF with a small single posterior median incision. Methods: During the period of March 2011 to March 2012, 34 patients with single-segment degenerative lumbar disease underwent the minimally invasive modified TLIF assisted by Mast Quadrant with a small single posterior median incision (single incision group. The cases in this group were compared to 37 patients with single-segment degenerative lumbar disease in the double incision group. The perioperative conditions of patients in these two groups were statistically analyzed and compared. The Oswestry Disability Index (ODI scores, Visual Analog Scale (VAS scores, and sacrospinalis muscle damage evaluation indicators before operation and 3, 12 months postoperation were compared. Results: A total of 31 and 35 cases in the single incision and double incision groups, respectively, completed at least 12 months of systemic follow-up. The differences in perioperative conditions between the two groups were not statistically significant. The incision length of the single incision group was significantly shorter than that of the double incision group (P < 0.01. The ODI and VAS scores of patients in both groups improved significantly at 3 and 12 months postoperation. However, these two indicators at 3 and 12 months postoperation and the sacrospinalis muscle damage evaluation indicators at 3 months postoperation did not differ significantly between the two groups (P ≥ 0.05. Conclusions: Mast Quadrant-assisted modified TLIF with a small single posterior median incision has excellent clinical feasibility compared to minimally invasive TLIF with a double paramedian incision.

  6. Single scrotal incision orchiopexy - a systematic review

    Directory of Open Access Journals (Sweden)

    Hugo Fabiano Fernandes Novaes

    2013-06-01

    Full Text Available Objective To conduct a systematic review on single scrotal incision orchiopexy. Materials and Methods A search was performed using Pubmed, through which 16 articles were selected out of a total of 133. The following conditions were considered exclusion criteria: other surgical methods such as an inguinal procedure or a laparoscopic approach, retractile testes, or patients with previous testicular or inguinal surgery. Results A total of 1558 orchiopexy surgeries initiated with a transcrotal incision were analyzed. Patients' ages ranged between 5 months and 21 years. Thirteen studies used high scrotal incisions, and low scrotal incisions were performed in the remainder of the studies. In 55 cases (3.53%, there was a need for inguinal incision. Recurrence was observed in 9 cases, testicular atrophy in 3, testicular hypotrophy in 2, and surgical site infections in 13 cases. High efficacy rates were observed, varying between 88% and 100%. Conclusions Single scrotal incision orchiopexy proved to be an effective technique and is associated with low rates of complications.

  7. A duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains.

    Science.gov (United States)

    Benacer, Douadi; Zain, Siti Nursheena Mohd; Lewis, John W; Khalid, Mohd Khairul Nizam Mohd; Thong, Kwai Lin

    2017-01-01

    This study aimed to develop a duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains. Primers were designed to target the rrs (LG1/LG2) and ligB (LP1/LP2) genes to confirm the presence of the Leptospira genus and the pathogenic species, respectively. The assay showed 100% specificity against 17 Leptospira strains with a limit of detection of 23.1pg/µl of leptospiral DNA and sensitivity of 103 leptospires/ml in both spiked urine and water. Our duplex endpoint PCR assay is suitable for rapid early detection of Leptospira with high sensitivity and specificity.

  8. Specificity of binding to four-way junctions in DNA by bacteriophage T7 endonuclease I.

    OpenAIRE

    Parsons, C A; West, S C

    1990-01-01

    T7 endonuclease I binds specifically to four-way junctions in duplex DNA and promotes their resolution into linear duplexes. Under conditions in which the nuclease activity is blocked by the absence of divalent cations, the enzyme forms a distinct protein-DNA complex with the junction, as detected by gel retardation and filter binding assays. The formation of this complex is structure-specific and contrasts with the short-lived binding complexes formed on linear duplex DNA. The binding comple...

  9. Prolonged CT urography in duplex kidney.

    Science.gov (United States)

    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.

  10. NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-oxo-7H-dG(syn)·dA(anti) alignment at lesion site

    International Nuclear Information System (INIS)

    Kouchakdjian, M.; Patel, D.J.; Bodepudi, V.; Shibutani, S.; Eisenberg, M.; Johnson, F.; Grollman, A.P.

    1991-01-01

    Proton NMR studies are reported on the complementary d(C1-C2-A3-C4-T5-A6-oxo-G7-T8-C9-A10-C11-C12)·d(G13-G14-T15-G16-A17-A18-T19-A20-G21-T22-G23-G24) dodecanucleotide duplex (designated 8-oxo-7H-dG·dA 12-mer), which contains a centrally located 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) residue, a group commonly found in DNA that has been exposed to ionizing radiation or oxidizing free radicals. From the NMR spectra it can be deduced that this moiety exists as two tautomers, or gives rise to two DNA conformations, that are in equilibrium and that exchange slowly. The present study focuses on the major component of the equilibrium that originates in the 6,8-dioxo tautomer of 8-oxo-7H-dG. The authors have assigned the exchangeable NH1, NH7, and NH 2 -2 base protons located on the Watson-Crick and Hoogsteen edges of 8-oxo-7H-dG7 in the 8-oxo-7H-dG·dA 12-mer duplex, using an analysis of one- and two-dimensional nuclear Overhauser enhancement (NOE) data in H 2 O solution. They were able to detect a set of intra- and interstrand NOEs between protons (exchangeable and nonexchangeable) on adjacent residues in the d(A6-oxo-G7-T8)·d(A17-A18-T19) trinucleotide segment centered about the lesion site that establishes stacking of the oxo-dG7(syn)·dA(anti) pair between stable Watson-Crick dA6·dT19 and dT8·A17 base pairs with minimal perturbation of the helix. The structural studies demonstrate that 8-oxo-7H-dG(syn)·dA(anti) forms a stable pair in the interior of the helix, providing a basis for the observed incorporation of dA opposite 8-oxo-7H-dG when readthrough occurs past this oxidized nucleoside base

  11. Screening of Modified RNA duplexes

    DEFF Research Database (Denmark)

    Schyth, Brian Dall; Bramsen, Jesper Bertram; Kjems, Jørgen

    protection against a fish pathogenic virus. This protection corresponded with an interferon response in the fish. Here we use this fish model to screen siRNAs containing various chemical modifications of the RNA backbone for their antiviral activity, the overall aim being identification of an siRNA form......Because of sequence specific gene targeting activity siRNAs are regarded as promising active compounds in gene medicine. But one serious problem with delivering siRNAs as treatment is the now well-established non-specific activities of some RNA duplexes. Cellular reactions towards double stranded...... RNAs include the 2´-5´ oligoadenylate synthetase system, the protein kinase R, RIG-I and Toll-like receptor activated pathways all resulting in antiviral defence mechanism. We have previously shown that antiviral innate immune reactions against double stranded RNAs could be detected in vivo as partial...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. Identification of a premature termination of DNA polymerization in ...

    Indian Academy of Sciences (India)

    2013-04-25

    Apr 25, 2013 ... strands to the 5′ end of the template strands, forming double- stranded DNA with ... duplex stem is important for high processive polymerization. HIV-1 reverse ... KF has been used as a model to study DNA polymerase.

  15. Full Duplex Emulation via Spatial Separation of Half Duplex Nodes in a Planar Cellular Network

    DEFF Research Database (Denmark)

    Thomsen, Henning; Kim, Dong Min; Popovski, Petar

    2016-01-01

    A Full Duplex Base Station (FD-BS) can be used to serve simultaneously two Half-Duplex (HD) Mobile Stations (MSs), one working in the uplink and one in the downlink, respectively. The same functionality can be realized by having two interconnected and spatially separated Half Duplex Base Stations...... (HD-BSs), which is a scheme termed CoMPflex (CoMP for In-Band Wireless Full Duplex). A FD-BS can be seen as a special case of CoMPflex with separation distance zero. In this paper we study the performance of CoMPflex in a two-dimensional cellular scenario using stochastic geometry and compare...

  16. Transconjunctival incision for total maxillectomy--an alternative for subciliary incision.

    Science.gov (United States)

    Goyal, Amit; Tyagi, Isha; Jain, Shilpa; Syal, Rajan; Singh, Alok Pratap; Kapila, Rajeev

    2011-09-01

    A subciliary incision may be associated with various complications of the lower eyelid when it is used during a total maxillectomy. The use of the transconjunctival incision instead is an alternative in suitable patients. The records of 17 patients were reviewed in whom a transconjunctival incision was used during total maxillectomy. These included 13 in whom the Weber-Ferguson incision was used, and 4 who had a sublabial incision. There was mild conjunctival oedema in all the cases during the immediate postoperative period but it did not last for more than two days. Four patients had mild to moderate oedema of the lid that resolved within two days. One had mild ectropion with transient epiphora, which was caused by early removal of the medial canthal sutures. We found the approach to be cosmetically acceptable as it avoids a scar in the subciliary region. The transconjunctival incision can be used in place of the subciliary incision for lateral exposure during total maxillectomy. There are few complications associated with the lower lid, and it has good cosmetic results; if it is combined with a sublabial incision in suitable patients, the maxillectomy is virtually scar-free. Copyright © 2010 British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  17. Comparison of surgically induced astigmatism in various incisions in manual small incision cataract surgery.

    Science.gov (United States)

    Jauhari, Nidhi; Chopra, Deepak; Chaurasia, Rajan Kumar; Agarwal, Ashutosh

    2014-01-01

    To determine the surgically induced astigmatism (SIA) in Straight, Frown and Inverted V shape (Chevron) incisions in manual small incision cataract surgery (SICS). A prospective cross sectional study was done on a total of 75 patients aged 40y and above with senile cataract. The patients were randomly divided into three groups (25 each). Each group received a particular type of incision (Straight, Frown or Inverted V shape incisions). Manual SICS with intraocular lens (IOL) implantation was performed. The patients were compared 4wk post operatively for uncorrected visual acuity (UCVA), best corrected visual acuity (BCVA) and SIA. All calculations were performed using the SIA calculator version 2.1, a free software program. The study was analyzed using SPSS version 15.0 statistical analysis software. The study found that 89.5% of patients in Straight incision group, 94.2% in Frown incision group and 95.7% in Inverted V group attained BCVA post-operatively in the range of 6/6 to 6/18. Mean SIA was minimum (-0.88±0.61D×90 degrees) with Inverted V incision which was statistically significant. Inverted V (Chevron) incision gives minimal SIA.

  18. Single incision laparoscopic colorectal resection: Our experience

    Directory of Open Access Journals (Sweden)

    Chinnusamy Palanivelu

    2012-01-01

    Full Text Available Background: A prospective case series of single incision multiport laparoscopic colorectal resections for malignancy using conventional laparoscopic trocars and instruments is described. Materials and Methods: Eleven patients (seven men and four women with colonic or rectal pathology underwent single incision multiport laparoscopic colectomy/rectal resection from July till December 2010. Four trocars were placed in a single transumblical incision. The bowel was mobilized laparoscopically and vessels controlled intracorporeally with either intra or extracorporeal anastomosis. Results: Three patients had carcinoma in the caecum, one in the hepatic flexure, two in the rectosigmoid, one in the descending colon, two in the rectum and two had ulcerative pancolitis (one with high grade dysplasia and another with carcinoma rectum. There was no conversion to standard multiport laparoscopy or open surgery. The median age was 52 years (range 24-78 years. The average operating time was 130 min (range 90-210 min. The average incision length was 3.2 cm (2.5-4.0 cm. There were no postoperative complications. The average length of stay was 4.5 days (range 3-8 days. Histopathology showed adequate proximal and distal resection margins with an average lymph node yield of 25 nodes (range 16-30 nodes. Conclusion: Single incision multiport laparoscopic colorectal surgery for malignancy is feasible without extra cost or specialized ports/instrumentation. It does not compromise the oncological radicality of resection. Short-term results are encouraging. Long-term results are awaited.

  19. Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: Two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum

    International Nuclear Information System (INIS)

    Banks, K.M.; Hare, D.R.; Reid, B.R.

    1989-01-01

    A three-dimensional solution structure for the self-complementary dodecanucleotide [(d-GCCTGATCAGGC)] 2 has been determined by distance geometry with further refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d(TGATCA)] 2 recognized and cut by the restriction endonuclease BclI, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences

  20. Primary closure of equine laryngotomy incisions

    DEFF Research Database (Denmark)

    Lindegaard, C.; Karlsson, L.; Ekstrøm, Claus Thorn

    2016-01-01

    incision between January 1995 and June 2012 were reviewed. Horses with a laryngotomy incision closed in three layers for primary healing were included. Descriptive data on healing characteristics and complications of laryngotomy wounds were collected from the medical records and via follow......The objective was to report healing characteristics and complications after primary closure of equine laryngotomies and analyse factors potentially associated with complications. This retrospective case series of the medical records of horses (n = 180) undergoing laryngoplasty and laryngotomy...... after primary closure of equine laryngotomy incisions are infrequent and considered of minimal severity and can be performed safely when paying careful attention to the closure of the cricothyroid membrane....

  1. Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

    Science.gov (United States)

    Wu, Xiangyang

    1999-07-01

    The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B-DNA

  2. Practical, real-time, full duplex wireless

    KAUST Repository

    Jain, Mayank; Choi, Jung Il; Kim, Taemin; Bharadia, Dinesh; Seth, Siddharth; Srinivasan, Kannan; Levis, Philip; Katti, Sachin; Sinha, Prasun

    2011-01-01

    This paper presents a full duplex radio design using signal inversion and adaptive cancellation. Signal inversion uses a simple design based on a balanced/unbalanced (Balun) transformer. This new design, unlike prior work, supports wideband and high power systems. In theory, this new design has no limitation on bandwidth or power. In practice, we find that the signal inversion technique alone can cancel at least 45dB across a 40MHz bandwidth. Further, combining signal inversion cancellation with cancellation in the digital domain can reduce self-interference by up to 73dB for a 10MHz OFDM signal. This paper also presents a full duplex medium access control (MAC) design and evaluates it using a testbed of 5 prototype full duplex nodes. Full duplex reduces packet losses due to hidden terminals by up to 88%. Full duplex also mitigates unfair channel allocation in AP-based networks, increasing fairness from 0.85 to 0.98 while improving downlink throughput by 110% and uplink throughput by 15%. These experimental results show that a re- design of the wireless network stack to exploit full duplex capability can result in significant improvements in network performance. © 2011 ACM.

  3. Energy balance and deformation mechanisms of duplexes

    Science.gov (United States)

    Mitra, Gautam; Boyer, Steven E.

    A duplex consists of a series of imbricate faults that are asymptotic to a roof thrust and a floor thrust. Depending on the final orientations of the imbricate faults and the final position of the branch lines, a duplex may be hinterland-dipping, foreland-dipping, or an antiformal stack. The exact geometry depends on various factors such as the initial dimensions of the individual slices (horses), their lithology, the amount of displacement (normalized to size of horse) on each fault, and the mechanics of movement along each fault. The energy required in duplex formation can be determined by calculating the total work involved in emplacing each horse: this is given by where W t=W p+W b+W g+W iWp is the work involved in initiating and propagating a fracture. Wb is the work involved in basal sliding, which may be frictional or some form of ductile flow, Wg is the work done against gravity during the emplacement of the horse, and Wi is the work involved in the internal deformation of the horse. By calculating and comparing these work terms it is possible to predict the conditions under which the different types of duplexes will form. Normally, the development of a hinterland-dipping duplex is most likely. However, if deformation conditions are favorable, displacements on individual imbricate faults may be very large compared to the size of the horses, leading to the formation of either antiformal stacks or foreland-dipping duplexes.

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

    Science.gov (United States)

    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.

  5. Small Incision Cataract Surgery (SICS with Clear Corneal Incision and SICS with Scleral Incision – A Comparative Study

    Directory of Open Access Journals (Sweden)

    Md Shafiqul Alam

    2014-01-01

    Full Text Available Background: Age related cataract is the leading cause of blindness and visual impairment throughout the world. With the advent of microsurgical facilities simple cataract extraction surgery has been replaced by small incision cataract surgery (SICS with posterior chamber intra ocular lens implant, which can be done either with clear corneal incision or scleral incision. Objective: To compare the post operative visual outcome in these two procedures of cataract surgery. Materials and method: This comparative study was carried out in the department of Ophthalmology, Delta Medical College & Hospital, Dhaka, Bangladesh, during the period of January 2010 to December 2012. Total 60 subjects indicated for age related cataract surgery irrespective of sex with the age range of 40-80 years with predefined inclusion and exclusion criteria were enrolled in the study. Subjects were randomly and equally distributed in 2 groups; Group A for SICS with clear corneal incision and group B for SICS with scleral incision. Post operative visual out come was evaluated by determining visual acuity and astigmatism in different occasions and was compared between groups. Statistical analysis was done by SPSS for windows version12. Results: The highest age incidence (43.3% was found between 61 to 70 years of age group. Among study subjects 40 were male and 20 were female. Preoperative visual acuity and astigmatism were evenly distributed between groups. Regarding postoperative unaided visual outcome, 6/12 or better visual acuity was found in 19.98% cases in group A and 39.6% cases in group B at 1st week. At 6th week 6/6 vision was found in 36.3% in Group A and 56.1% in Group B and 46.2% in group A and 66% in group B without and with correction respectively. With refractive correction, 6/6 vision was attained in 60% subjects of group A and 86.67% of group B at 8th week. Post operative visual acuity was statistically significant in all occasions. Postoperative astigmatism of

  6. Harvesting full-duplex rate gains in cellular networks with half-duplex user terminals

    KAUST Repository

    Alammouri, Ahmad; Elsawy, Hesham; Alouini, Mohamed-Slim

    2016-01-01

    Full-Duplex (FD) transceivers may be expensive in terms of complexity, power consumption, and price to be implemented in all user terminals. Therefore, techniques to exploit in-band full-duplex communication with FD base stations (BSs) and half

  7. Development of a duplex droplet digital PCR assay for absolute quantitative detection of "Candidatus Liberibacter asiaticus".

    Science.gov (United States)

    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.

  8. The boomerang incision for periareolar breast malignancies.

    Science.gov (United States)

    Tan, Mona P

    2007-11-01

    Breast-conservation surgery has been shown to be equivalent to mastectomy in terms of long-term survival for the treatment of breast cancer. Various techniques have been described on how to achieve clear margins and good cosmetic outcomes and therefore expand the indications for breast conservation. A novel incision is detailed to augment the options already available.

  9. Single scrotal incision orchidopexy for palpable undescended

    International Nuclear Information System (INIS)

    Ahmad, A.; Safdar, C.A.; Yasir, U.; Rasool, N.; Kanwal, S.; Boota, M.; Rehman, J.U.

    2014-01-01

    To retrospectively asses the results of single scrotal incision orchidopexy (SSIO) performed at our centre with ligation of the patent processus vaginalis in children having palpable undescended testes (UDT). Study Design: Quasi-experimental with retrospective data. Place and Duration of Study: Department of Paediatric surgery Military Hospital Rawalpindi, from April 2007 to December 2011. Patients and Methods: After making a single transverse incision at superior scrotal border, the testis was identified; gubernaculums and the sac were dissected to the highest level and divided. The testis was placed into the scrotum and fixed to the scrotal fascia/skin. All patients were assessed at 2 weeks, 2 months and 6 months post operatively, and then yearly. Results: A total of 38 orchidopexies were performed in 33 patients. The patients age ranged from 14 months to 7 years (mean:2.1 years). Bilateral UDT were found in 5 patients (15.1%). Operative time ranged from 20 to 45 minutes (mean: 36 minutes). The single scrotal incision technique was successful in all 38 cases (100%). All testes were easily fixed in the scrotum. Two patients (5.2%) developed scrotal haematoma and one patient (2.6%) developed stitch abscess. All showed good an atomical and cosmetic results up to a minimum of six months of follow-up. Conclusion: Single scrotal incision orchidopexy for palpable undescended testis is a simple and safe technique. It has shown to consume shorter time and give good cosmetic results. (author)

  10. Duplex kidney: not just a drooping lily.

    Science.gov (United States)

    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 (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.

  11. AUTENTIKASI DAGING AYAM SEGAR DARI KONTAMINASI DAGING BABI MENGGUNAKAN GEN CYT-B DENGAN ANALISIS DUPLEX- POLYMERASE CHAIN REACTION

    Directory of Open Access Journals (Sweden)

    Bayu Setya Hertanto

    2017-05-01

    Full Text Available Halal is one of important aspects in consumer protection. Meat and processed meat products are food that should be controlled strictly because those are prone to be adulterated by pork contamination. Therefore, it is necessary to provide detection technique which is accurate, fast and cheap. The objective of this research was to identify the presence of impurities of pork meat on raw chicken meat using gene Cyt-b with duplex-PCR analysis. This research used six samples of raw chicken meat and raw pork. Raw chicken meat was bought from supermarkets in the city of Surakarta and raw pork was obtained from pig slaughterhouse. The percentage of raw pork contamination on raw chicken meat was designed as much as 1, 5, 10, and 25%, respectively. The DNA genome was isolated according to DNA isolation protocol from Genomic DNA Mini Kit. In addition, duplex-PCR was performed based on protocol of KAPA2G Fast Multiplex PCR kit. The data was descriptively analyzed by directly looking the DNA bands on the gel documentation apparatus. The result showed that specific DNA bands for chicken and pig were completely appeared on 1.5% of agarose gels. Duplex-PCR detect contamination of pork on raw meat of chicken at all contamination levels. This research proved that the duplex-PCR detect the contamination of pork until the level of 1%.

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

    Directory of Open Access Journals (Sweden)

    Hilary A. McManus

    2017-05-01

    Full Text Available Background 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. Methods 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. Results 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. Discussion 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

  13. Radiological findings after endoscopic incision of ureterocele

    International Nuclear Information System (INIS)

    Cheon, Jung Eun; Kim, In One; Seok, Eul Hye; Cha, Joo Hee; Choi, Gook Myung; Kim, Woo Sun; Yeon, Kyung Mo; Kim, Kwang Myung; Choi, Hwang; Cheon, Jung Eun; Seok, Eul Hye; Cha, Joo Hee; Choi, Guk Myung

    2001-01-01

    Endoscopic incision of ureterocele is considered a simple and safe method for decompression of urinary tract obstruction above ureterocele. The purpose of this study was to evaluate the radiological findings after endoscopic incision of ureterocele. We retrospectively reviewed the radiological findings (ultrasonography (US), intravenous urography, and voiding cystourethrography(VCU)) in 16 patients with ureterocele who underwent endoscopic incision (mean age at surgery, 15 months; M:F 3:13; 18 ureteroceles). According to the postoperative results, treatment was classified as successful when medical treatment was still required, and second operation when additional surgical treatment was required. Postoperative US (n=10) showed that in all patients, urinary tract obstruction was relieved: the kidney parenchima was thicker and the ureterocele was smaller. Intravenous urography (n=8), demonstrated that in all patients, urinary tract obstruction and the excretory function of the kidney had improved. Postoperative VCU indicated that in 92% of patients (12 of 13), endoscopic incision of the ureterocele led to vesicoureteral reflux(VUR). Of these twelve, seven (58%) showed VUR of more than grade 3, while newly developed VUR was seen in five of eight patients (63%) who had preoperative VCU. Surgery was successful in four patients (25%), partially successful in three (19%), and a second operation-on account of recurrent urinary tract infection and VUR of more than grase 3 during the follow-up period-was required by nine (56%). Although endoscopic incision of a ureterocele is a useful way of relieving urinary tract obstruction, an ensuing complication may be VUR. Postoperative US and intravenous urography should be used to evaluate parenchymal change in the kidney and improvement of uronary tract obstructon, while to assess the extend of VUR during the follow-up period , postoperative VCU is required

  14. Synthesis and structural characterization of piperazino-modified DNA that favours hybridization towards DNA over RNA

    DEFF Research Database (Denmark)

    Skov, Joan; Bryld, Torsten; Lindegaard, Dorthe

    2011-01-01

    We report the synthesis of two C4'-modified DNA analogues and characterize their structural impact on dsDNA duplexes. The 4'-C-piperazinomethyl modification stabilizes dsDNA by up to 5°C per incorporation. Extension of the modification with a butanoyl-linked pyrene increases the dsDNA stabilizati...

  15. Duplex ultrasound surveillance after carotid artery endarterectomy.

    Science.gov (United States)

    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.

  16. Mycobacterium smegmatis RqlH defines a novel clade of bacterial RecQ-like DNA helicases with ATP-dependent 3'-5' translocase and duplex unwinding activities.

    Science.gov (United States)

    Ordonez, Heather; Unciuleac, Mihaela; Shuman, Stewart

    2012-05-01

    The Escherichia coli RecQ DNA helicase participates in a pathway of DNA repair that operates in parallel to the recombination pathway driven by the multisubunit helicase-nuclease machine RecBCD. The model mycobacterium Mycobacterium smegmatis executes homologous recombination in the absence of its helicase-nuclease machine AdnAB, though it lacks a homolog of E. coli RecQ. Here, we identify and characterize M. smegmatis RqlH, a RecQ-like helicase with a distinctive domain structure. The 691-amino acid RqlH polypeptide consists of a RecQ-like ATPase domain (amino acids 1-346) and tetracysteine zinc-binding domain (amino acids 435-499), separated by an RqlH-specific linker. RqlH lacks the C-terminal HRDC domain found in E. coli RecQ. Rather, the RqlH C-domain resembles bacterial ComF proteins and includes a phosphoribosyltransferase-like module. We show that RqlH is a DNA-dependent ATPase/dATPase that translocates 3'-5' on single-stranded DNA and has 3'-5' helicase activity. These functions inhere to RqlH-(1-505), a monomeric motor unit comprising the ATPase, linker and zinc-binding domains. RqlH homologs are distributed widely among bacterial taxa. The mycobacteria that encode RqlH lack a classical RecQ, though many other Actinobacteria have both RqlH and RecQ. Whereas E. coli K12 encodes RecQ but lacks a homolog of RqlH, other strains of E. coli have both RqlH and RecQ.

  17. Incision integrity and postoperative outcomes after microcoaxial phacoemulsification performed using 2 incision-dependent systems.

    Science.gov (United States)

    Vasavada, Vaishali; Vasavada, Abhay R; Vasavada, Viraj A; Srivastava, Samaresh; Gajjar, Devarshi U; Mehta, Siddharth

    2013-04-01

    To compare incision integrity and clinical outcomes of 2 microcoaxial phacoemulsification systems. Iladevi Cataract & IOL Research Centre, Ahmedabad, India. Prospective randomized clinical trial. Eyes were randomized to have phacoemulsification using a 1.8 mm clear corneal incision (CCI) system (Group 1, Stellaris system) or a 2.2 mm CCI system (Group 2, Intrepid Infiniti system). Incision enlargement at end of surgery was measured. At the conclusion of surgery, trypan blue was applied over the conjunctival surface, anterior chamber aspirate withdrawn, and ingress into anterior chamber measured. Postoperative observations included evaluation of the CCI using anterior segment optical coherence tomography (AS-OCT), change in central corneal thickness (CCT), and anterior segment inflammation at 1 day, 1 week, and 1 month and endothelial cell loss and surgically induced astigmatism (SIA) at 3 months. Incision enlargement (P.05). At the end of surgery, it is not the initial incision size alone but also the distortion of the incision during subsequent stages of surgery that determine the integrity of the CCI. Copyright © 2013 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  18. COMPARISON OF POSTOP SIA IN MSICS WITH STRAIGHT INCISION VERSUS FROWN INCISION

    Directory of Open Access Journals (Sweden)

    Shayana Bhumbla

    2017-05-01

    Full Text Available BACKGROUND Surgically-Induced Astigmatism (SIA is one of the commonest causes of poor postoperative vision even after uneventful cataract surgery. Recent advances have led to a newer concept of “refractive cataract surgery.” The aim of the study is to study the comparison of postop SIA in Manual Small Incision Cataract Surgery (MSICS with straight versus frown incision. MATERIALS AND METHODS 50 patients of cataract were divided into 2 groups (25 each - group A underwent MSICS with 6 mm straight incision, group B underwent MSICS with 6 mm frown incision. BCVA, keratometry readings were recorded with auto kerato-refractometer preop, at 1 week, 1 month, 3 months and SIA was calculated with SIA calculator version 2.1, a free software program. RESULTS Mean SIA in group A and B were - 1.14D versus 0.92D at 1 week; 1.26D versus 0.97D at 1 month; 1.29D versus 0.95D at 3 months. The difference was statistically significant at each follow up visit (p<0.05. CONCLUSION Frown incision gives lesser SIA than straight incision in MSICS.

  19. Buffer management in wireless full-duplex systems

    KAUST Repository

    Bouacida, Nader; Showail, Ahmad; Shihada, Basem

    2015-01-01

    , we address the problem of buffer management in full-duplex networks by using Wireless Queue Management (WQM), which is an active queue management technique for wireless networks. Our solution is based on Relay Full-Duplex MAC (RFD

  20. On full duplex Gaussian relay channels with self-interference

    KAUST Repository

    Behboodi, Arash; Chaaban, Anas; Mathar, Rudolf; Alouini, Mohamed-Slim

    2016-01-01

    Self interference (SI) in full duplex (FD) systems is the interference caused by the transmission stream on the reception stream. Being one of the main restrictive factors for performance of practical full duplex systems, however, not too much

  1. Molecular mechanism of DNA replication-coupled inactivation of the initiator protein in Escherichia coli: interaction of DnaA with the sliding clamp-loaded DNA and the sliding clamp-Hda complex.

    Science.gov (United States)

    Su'etsugu, Masayuki; Takata, Makoto; Kubota, Toshio; Matsuda, Yusaku; Katayama, Tsutomu

    2004-06-01

    In Escherichia coli, the ATP-DnaA protein initiates chromosomal replication. After the DNA polymerase III holoenzyme is loaded on to DNA, DnaA-bound ATP is hydrolysed in a manner depending on Hda protein and the DNA-loaded form of the DNA polymerase III sliding clamp subunit, which yields ADP-DnaA, an inactivated form for initiation. This regulatory DnaA-inactivation represses extra initiation events. In this study, in vitro replication intermediates and structured DNA mimicking replicational intermediates were first used to identify structural prerequisites in the process of DnaA-ATP hydrolysis. Unlike duplex DNA loaded with sliding clamps, primer RNA-DNA heteroduplexes loaded with clamps were not associated with DnaA-ATP hydrolysis, and duplex DNA provided in trans did not rescue this defect. At least 40-bp duplex DNA is competent for the DnaA-ATP hydrolysis when a single clamp was loaded. The DnaA-ATP hydrolysis was inhibited when ATP-DnaA was tightly bound to a DnaA box-bearing oligonucleotide. These results imply that the DnaA-ATP hydrolysis involves the direct interaction of ATP-DnaA with duplex DNA flanking the sliding clamp. Furthermore, Hda protein formed a stable complex with the sliding clamp. Based on these, we suggest a mechanical basis in the DnaA-inactivation that ATP-DnaA interacts with the Hda-clamp complex with the aid of DNA binding. Copyright Blackwell Publishing Limited

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

    Science.gov (United States)

    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.

  3. Current Status of Single-incision Laparoscopic Surgery

    DEFF Research Database (Denmark)

    Ahmed, Irfan; Ciancio, Fabio; Ferrara, Vincenzo

    2012-01-01

    Recent advances in minimally invasive surgery have centered on reducing the number of incisions required, which has led to the development of the single-incision laparoscopic technique. A panel of European single-incision laparoscopy experts met to discuss the current status of, and the future...

  4. Higher Incision at Upper Part of Lower Segment Caesarean Section

    Directory of Open Access Journals (Sweden)

    Yong Shao

    2014-06-01

    Conclusions: An incision at the upper part of the lower segment reduces blood loss, enhances uterine retraction, predisposes to fewer complications, is easier to repair, precludes bladder adhesion to the suture line and reduces operation time. Keywords: caesarean section; higher incision technique; traditional uterine incision technique.

  5. Full-Duplex Relay Selection in Cognitive Underlay Networks

    KAUST Repository

    Khafagy, Mohammad Galal; Alouini, Mohamed-Slim; Aissa, Sonia

    2017-01-01

    In this work, we analyze the performance of full-duplex relay selection (FDRS) in spectrum-sharing networks. Contrary to half-duplex relaying, full-duplex relaying (FDR) enables simultaneous listening/forwarding at the secondary relay(s), thereby

  6. Measuring secondary phases in duplex stainless steels

    Science.gov (United States)

    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.

  7. Full-duplex optical communication system

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  9. Quantitative structure of a complex between a minor-groove-specific drug and a bent DNA decamer duplex: Use of 2D NMR data and NOESY constrained energy minimization

    International Nuclear Information System (INIS)

    Sarma, M.H.; Gupta, G.; Garcia, A.E.; Umemoto, K.; Sarma, R.H.

    1990-01-01

    Two-dimensional nuclear magnetic resonance (2D NMR) studies on d(GA4T4C)2 and d(GT4A4C)2 showed that A.T pairs are propeller twisted. As a result, A/T tracts form a straight rigid structural block with an array of bifurcated inter base pair H bonds in the major groove. It was demonstrated (previous paper) that replacement of methyl group by hydrogen (changing from T to U) in the major groove does not disrupt the array of bifurcated H bonds in the major groove. In this article, we summarize results of 2D NMR and molecular mechanic studies on the effect of a minor-groove-binding A.T-specific drug on the structure d(GA4T4C)2. A distamycin analogue (Dst2) was used for this study. It is shown that Dst2 binds to the minor groove of d(GA4T4C)2 mainly driven by van der Waals interaction between A.T pairs and the drug; as a consequence, an array of bifurcated H bonds can be formed in the minor groove between amide/amino protons of Dst2 and A.T pairs of DNA. NOESY data suggest that Dst2 predominantly binds at the central 5 A.T pairs. NOESY data also reveal that, upon drug binding, d(GA4T4C)2 does not undergo any significant change in conformation from the free state; i.e., propeller-twisted A.T pairs are still present in DNA and hence the array of bifurcated H bonds must be preserved in the major groove. NOESY data for the A5-T6 sequence also indicate that there is little change in junction stereochemistry upon drug binding

  10. Small incision guarded hydroaspiration of iris lesions.

    Science.gov (United States)

    Singh, Arun D

    2017-11-01

    To describe the technique and results of a minimally invasive surgical technique for resection of small iris lesions. Consecutive case series of 22 patients with localised, small iris lesions that were resected using the described surgical technique that composed of multiple, small corneal incisions created to allow for internal iris resection with 23-gauge horizontal vitrectomy scissors, followed by guarded tumour aspiration through a clear plastic tubing (diameter 3.5 mm) primed with viscoelastic agent. The mean largest basal diameter was 3.0 mm (range 1.5-5.0 mm; median 3.0 mm) and mean thickness was 1.3 mm (range 0.5-2.5 mm; median 1.0 mm). Use of multiple (2-4) small corneal incisions (range 2.0-3.0 mm; mean 2.8 mm) allowed reduced postoperative morbidity (significant hyphema (0%), hypotony (0%), wound leak (0%), >2 line change in best corrected visual acuity at postoperative 1 week (4.5%) and mean corneal astigmatism of 1.0 D (range 0.14-2.99 D; median 0.8 D) at postoperative 4-12 weeks. The tumour could be resected with clear surgical margins in all neoplastic cases (benign (2), borderline (1) and malignant (16)). Local recurrence or metastases were not observed in any melanoma case over a mean follow-up of 33.0 months (range 1.0-90.0 months; median 33.5 months). Small incision guarded hydroaspiration is a minimally invasive surgical technique for resection of select small iris lesions. Use of multiple small corneal incisions avoids morbidity associated with a single large corneoscleral incision, and use of guarded aspiration may eliminate the risk of wound contamination by the malignant tumour. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

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

    Science.gov (United States)

    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.

  12. Ultra-short silicon MMI duplexer

    Science.gov (United States)

    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.

  13. Duplex Design Project: Science Pilot Test.

    Science.gov (United States)

    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…

  14. Duplex ultrasound for identifying renal artery stenosis

    DEFF Research Database (Denmark)

    Zachrisson, Karin; Herlitz, Hans; Lönn, Lars

    2017-01-01

    Background Renal artery duplex ultrasound (RADUS) is an established method for diagnosis of renal artery stenosis (RAS), but there is no consensus regarding optimal RADUS criteria. Purpose To define optimal cutoff values for RADUS parameters when screening for RAS using intra-arterial trans...

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

    Science.gov (United States)

    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

  16. Comparison of duplex PCR and phenotypic analysis in differentiating Candida dubliniensis from Candida albicans from oral samples.

    Science.gov (United States)

    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.

  17. Comparison of electrocautery incision with scalpel incision in midline abdominal surgery - A double blind randomized controlled trial.

    Science.gov (United States)

    Prakash, Lalgudi Dorairajan; Balaji, Nitesh; Kumar, Sathasivam Suresh; Kate, Vikram

    2015-07-01

    To compare the electrocautery incision with scalpel incision in patients undergoing abdominal surgery using a midline incision with respect to incision time, blood loss during incision, postoperative incision site pain and wound infection. Patients undergoing midline abdominal surgery were randomized into electrocautery and scalpel groups. The incision dimensions, incision time and blood loss during incision were noted intraoperatively. Postoperative pain and wound infection were recorded on every postoperative day for one week. 41 patients in each of the two groups were analyzed. Gender and age distribution was similar in both the groups. The mean incision time per unit wound area in the electrocautery group and scalpel group was 9.40 ± 3.37 s/cm(2) and 9.07 ± 3.40 s/cm(2) (p = 0.87) respectively. The mean blood loss per unit wound area was significantly lower in the electrocautery group at 6.46 ± 3.94 ml when compared to that of 23.40 ± 15.28 ml in the scalpel group (p= electrocautery and scalpel groups (14.63% vs. 12.19%; p = 0.347). With a comparable Postoperative incision site pain, wound infection rate and significantly lower blood loss with the equal time taken for the incision, electrocautery can be considered safe and effective in making skin incision in midline laparotomy compared to scalpel incision. Copyright © 2015 IJS Publishing Group Limited. Published by Elsevier Ltd. All rights reserved.

  18. Noncovalent DNA Binding Drives DNA Alkylation by Leinamycin. Evidence That the Z,E-5-(Thiazol-4-yl)-penta-2,4-dienone Moiety of the Natural Product Serves As An Atypical DNA Intercalator

    Science.gov (United States)

    Fekry, Mostafa I.; Szekely, Jozsef; Dutta, Sanjay; Breydo, Leonid; Zang, Hong; Gates, Kent S.

    2012-01-01

    Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 103 M−1. Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allows construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA. PMID:21954957

  19. Electrocautery skin incision for neurosurgery procedures--technical note.

    Science.gov (United States)

    Nitta, Naoki; Fukami, Tadateru; Nozaki, Kazuhiko

    2011-01-01

    The reluctance to incise skin with electrocautery is partly attributable to concerns about excessive scarring and poor wound healing. However, recently no difference was reported in wound complications between the cold scalpel and electrocautery scalpel. We assessed the safety and efficacy of electrocautery skin incision in 22 scalp incisions, including 4 cases of reoperation. Electrocautery skin incisions were created using a sharp needle electrode. The generator unit was set on cutting mode, with power of 6 W and 330 kHz sinusoid waveform. Subcutaneous dissections also used the sharp needle electrode, set on coagulating mode, with power of 10 W and 1 MHz pulse-modulated waveform. Galea incisions used a standard blade tip, set on coagulating mode, with power of 20 W and 1 MHz pulse-modulated waveform. Skin incision with the sharp needle electrode caused no charring of the wound. Little bleeding or oozing were observed and skin clips were not necessary. No wound complication such as necrosis or infection occurred. Electrocautery skin incisions for re-operations were also performed safely without complications. Electrocautery skin incision is sufficiently safe procedure not only for first operation but also for re-operation. Electrocautery skin incision is efficacious, especially for extended operation times, because of little blood loss from the edges of skin incision and possible avoidance of skin edge necrosis or alopecia caused by skin clips.

  20. A single incision transaxillary thoracoscopic sympathectomy

    Directory of Open Access Journals (Sweden)

    Marić Nebojša

    2014-01-01

    Full Text Available Background/Aim. Primary hyperhidrosis causes are unknown. The disorder begins in early childhood. It intensifies in puberty and maturity. It is equally present in both sexes. The symptoms exacerbate when the body temperature rises and due to emotional stimuli affecting the sympathetic nerve system. The aim of this study was to demonstrate that videoassisted thoracoscopic surgery (VATS sympathectomy is a method for primary focal hyperhidrosis permanent treatment. The single incision method in properly selected patients maximizes the intervention effectiveness and minimizes aesthetic side effects. Methods. This prospective study analysed the findings in patients who had been operated on due to primary focal hyperhidrosis (face, palms, and armpits using a single small transaxilarry incision in the third inter-rib space at the level of the anterior axillary line with two 5 mm flexible ports. All the patients, with T2-T5 thoracoscopic sympathectomy of the sympathetic chain using a single small incision in the third inter-rib space in the anterior axillary line, were analysed in the period from September 2009 to November 2010 regarding the postoperative morbidity and outcomes of the operation (clinical evaluation and visual analogue scale with a view to assessing the effectiveness of the surgery conducted in this manner. Results. A total of 47 patients (18 men, 29 women, 18 to 48 years old (29 on average had underwent 94 bilateral video-assisted thoracoscopic sympathectomies. The sympathectomy was indicated in cases of facial blushing and sweating (6.38%, palmary sweating (34.04%, axillary sweating (14.89% or both palmary and axillary sweating (44.68%. The largest percentage of patients (98.6% had left the hospital the following day. The postoperative 30 day’s mortality was 0 and the conversion into open surgery was not necessary. As for complications, there had been an occurrence of partial pneumothorax in two patients treated by means of

  1. Small-incision lenticule extraction (SMILE)

    DEFF Research Database (Denmark)

    Hansen, Rasmus Søgaard; Lyhne, Niels; Grauslund, Jakob

    2016-01-01

    surgery was 0.07 ± 0.03 (logMAR). However, 12 eyes (1.6 %) lost 2 or more lines of CDVA from before surgery to 3 months postoperatively. Simultaneous treatment of up to 3.00 D of astigmatism was not associated with less predictable refractive outcomes. CONCLUSIONS: In the short term, SMILE seemed......PURPOSE: To study the outcomes of small-incision lenticule extraction (SMILE) for treatment of myopia and myopic astigmatism. METHODS: Retrospective study of patients treated for myopia or myopic astigmatism with SMILE, using a VisuMax(®) femtosecond laser (Carl Zeiss Meditec, Jena, Germany...

  2. Development of duplex PCR for simultaneous detection of Theileria spp. and Anaplasma spp. in sheep and goats.

    Science.gov (United States)

    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.

  3. Flexible single-incision surgery: a fusion technique.

    Science.gov (United States)

    Noguera, José F; Dolz, Carlos; Cuadrado, Angel; Olea, José; García, Juan

    2013-06-01

    The development of natural orifice transluminal endoscopic surgery has led to other techniques, such as single-incision surgery. The use of the flexible endoscope for single-incision surgery paves the way for further refinement of both surgical methods. To describe a new, single-incision surgical technique, namely, flexible single-incision surgery. Assessment of the safety and effectiveness of endoscopic cholecystectomy in a series of 30 patients. This technique consists of a single umbilical incision through which a flexible endoscope is introduced and consists of 2 parallel entry ports that provide access to nonarticulated laparoscopic instruments. The technique was applied in all patients for whom it was prescribed. No general or surgical wound complications were noted. Surgical time was no longer than usual for single-port surgery. Flexible single-incision surgery is a new single-site surgical technique offering the same level of patient safety, with additional advantages for the surgeon at minimal cost.

  4. Single-incision laparoscopic bariatric surgery

    Directory of Open Access Journals (Sweden)

    Huang Chih-Kun

    2011-01-01

    Full Text Available Background: Bariatric surgery has been established as the best option of treatment for morbid obesity. In recent years single-incision laparoscopic surgery (SILS has emerged as another modality of carrying out the bariatric procedures. While SILS represents an advance, its application in morbid obesity at present is limited. In this article, we review the technique and results of SILS in bariatric surgery. Methods: The PubMed database was searched and totally 11 series reporting SILS in bariatric surgery were identified and analyzed. The case reports were excluded. Since 2008, 114 morbidly obese patients receiving SILS bariatric surgeries were reported. Results: The procedures performed included SILS gastric banding, sleeve gastrectomy and gastric bypass. No mortality was reported in the literatures. Sixteen patients (14.05% needed an additional incision for a liver retractor, a trocar or for conversion. Only one complication of wound infection was reported in these series. All the surgeons reported that the patients were highly satisfied with the scar. Conclusion: Because of abundant visceral and subcutaneous fat and multiple comorbidities in morbid obesity, it is more challenging for surgeons to perform the procedures with SILS. It is clear that extensive development of new instruments and technical aspects of these procedures as well as randomized studies to compare them with traditional laparoscopy are essential before these procedures can be utilized in day-to-day clinical practice.

  5. Enantiospecific kinking of DNA by a partially intercalating metal complex

    KAUST Repository

    Reymer, Anna; Nordé n, Bengt

    2012-01-01

    Opposite enantiomers of [Ru(phenanthroline) 3] 2+ affect the persistence length of DNA differently, a long speculated effect of helix kinking. Our molecular dynamics simulations confirm a substantial change of duplex secondary structure produced

  6. Two-Step Incision for Periarterial Sympathectomy of the Hand

    Directory of Open Access Journals (Sweden)

    Seung Bae Jeon

    2015-11-01

    Full Text Available BackgroundSurgical scars on the palmar surface of the hand may lead to functional and also aesthetic and psychological consequences. The objective of this study was to introduce a new incision technique for periarterial sympathectomy of the hand and to compare the results of the new two-step incision technique with those of a Koman incision by using an objective questionnaire.MethodsA total of 40 patients (17 men and 23 women with intractable Raynaud's disease or syndrome underwent surgery in our hospital, conducted by a single surgeon, between January 2008 and January 2013. Patients who had undergone extended sympathectomy or vessel graft were excluded. Clinical evaluation of postoperative scars was performed in both groups one year after surgery using the patient and observer scar assessment scale (POSAS and the Wake Forest University rating scale.ResultsThe total patient score was 8.59 (range, 6-15 in the two-step incision group and 9.62 (range, 7-18 in the Koman incision group. A significant difference was found between the groups in the total PS score (P-value=0.034 but not in the total observer score. Our analysis found no significant difference in preoperative and postoperative Wake Forest University rating scale scores between the two-step and Koman incision groups. The time required for recovery prior to returning to work after surgery was shorter in the two-step incision group, with a mean of 29.48 days in the two-step incision group and 34.15 days in the Koman incision group (P=0.03.ConclusionsCompared to the Koman incision, the new two-step incision technique provides better aesthetic results, similar symptom improvement, and a reduction in the recovery time required before returning to work. Furthermore, this incision allows the surgeon to access a wide surgical field and a sufficient exposure of anatomical structures.

  7. Renal duplex Doppler ultrasound findings in diabetics

    International Nuclear Information System (INIS)

    Shim, Hyang Yee; Kim, Young Geun; Kook, Cheol Keu; Yoon, Chong Hyun; Lee, Shin Hyung; Lee, Chang Joon

    1993-01-01

    The correlation between clinical-laboratory findings and renal duplex Doppler ultrasound findings was studied in 45 patients with diabetes mellitus to see the role of duplex Doppler ultrasound in the detection of diabetic nephropathy. The resistive indices in patients with elevated serum creatinine, BUN, proteinuria, and systolic blood pressure levels were statistically significantly higher than those in patients with normal levels (p<0.05). Also resistive indics in patients with retinopathy were higher than that in patients without retinopathy (p<0.05). But the ultrasound morphologic changes of kidney such as renal length, cortical eye-catching, and corticomedullarycontrast were not well correlated with clinical-laboratory data and resistive index. The resistive index of the kidney in conjunction with clinical-laboratory data in diabetics may be helpful in the evaluation of diabetic nephropathy

  8. Renal duplex Doppler ultrasound findings in diabetics

    Energy Technology Data Exchange (ETDEWEB)

    Shim, Hyang Yee; Kim, Young Geun; Kook, Cheol Keu; Yoon, Chong Hyun; Lee, Shin Hyung; Lee, Chang Joon [National Medical Center, Seoul (Korea, Republic of)

    1993-12-15

    The correlation between clinical-laboratory findings and renal duplex Doppler ultrasound findings was studied in 45 patients with diabetes mellitus to see the role of duplex Doppler ultrasound in the detection of diabetic nephropathy. The resistive indices in patients with elevated serum creatinine, BUN, proteinuria, and systolic blood pressure levels were statistically significantly higher than those in patients with normal levels (p<0.05). Also resistive indics in patients with retinopathy were higher than that in patients without retinopathy (p<0.05). But the ultrasound morphologic changes of kidney such as renal length, cortical eye-catching, and corticomedullarycontrast were not well correlated with clinical-laboratory data and resistive index. The resistive index of the kidney in conjunction with clinical-laboratory data in diabetics may be helpful in the evaluation of diabetic nephropathy

  9. Thermal ageing of duplex stainless steels

    International Nuclear Information System (INIS)

    Massoud, J.P.; Van Duysen, J.C.; Zacharie, G.; Auger, P.; Danoix, F.

    1992-03-01

    The evolution of the mechanical properties of Mobearing anf Mo-free cast duplex stainless steels, induced by long term ageing in the range 300-400 deg C, has been studied in relation with the evolution of their microstructure. The unmixing of the ferritic Fe-Cr-Ni, solid solution by three-dimensional (sponge-like) spinodal decomposition and the precipitation of intermetallic G-phase particles are the main characteristics of this microstructural evolution

  10. Development and Evaluation of a Single-Step Duplex PCR for Simultaneous Detection of Fasciola hepatica and Fasciola gigantica (Family Fasciolidae, Class Trematoda, Phylum Platyhelminthes)

    Science.gov (United States)

    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

  11. Development and evaluation of a single-step duplex PCR for simultaneous detection of Fasciola hepatica and Fasciola gigantica (family Fasciolidae, class Trematoda, phylum Platyhelminthes).

    Science.gov (United States)

    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.

  12. Development of a lean duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Liljas, M.; Johansson, P.; Liu Hui-Ping; Olsson, C.O.A. [Avesta Research Centre, Avesta (Sweden). Outokumpu Stainless

    2008-06-15

    The classic series of duplex stainless steels shows very high corrosion resistance and can be used for very demanding applications. A new lean duplex steel, LDX 2101 {sup registered} (EN 1.4162, UNS S32101), has been developed with corrosion resistance on a par with standard austenitic grades. Application areas include: structural components, chemical industry, tanks and containers. The steel was designed to have equal amounts of ferrite and austenite in annealed condition and with an austenite that is stable against strain-induced martensite. Thanks to its high nitrogen content, the steel has a fast austenite reformation when subjected to thermal cycling, e.g. welding. Unlike conventional duplex grades, the formation of intermetallic phase is very sluggish, although precipitation of nitrides and carbides has a certain impact on material properties after exposure in the temperature range 600 to 800 C. The precipitation behaviour after different isothermal treatments is described and its influence on different product properties is shown. A good agreement was found between impact toughness and corrosion resistance for a wide range of thermal treatments. (orig.)

  13. Joint duplex mode selection, channel allocation, and power control for full-duplex cognitive femtocell networks

    Directory of Open Access Journals (Sweden)

    Mingjie Feng

    2015-02-01

    Full Text Available In this paper, we aim to maximize the sum rate of a full-duplex cognitive femtocell network (FDCFN as well as guaranteeing the quality of service (QoS of users in the form of a required signal to interference plus noise ratios (SINR. We first consider the case of a pair of channels, and develop optimum-achieving power control solutions. Then, for the case of multiple channels, we formulate joint duplex model selection, power control, and channel allocation as a mixed integer nonlinear problem (MINLP, and propose an iterative framework to solve it. The proposed iterative framework consists of a duplex mode selection scheme, a near-optimal distributed power control algorithm, and a greedy channel allocation algorithm. We prove the convergence of the proposed iterative framework as well as a lower bound for the greedy channel allocation algorithm. Numerical results show that the proposed schemes effectively improve the sum rate of FDCFNs.

  14. Characterization of thermal aging of duplex stainless steel by SQUID

    International Nuclear Information System (INIS)

    Isobe, Y.; Kamimura, A.; Aoki, K.; Nakayasu, F.

    1995-01-01

    Thermal aging is a growing concern for long-term-aged duplex stainless steel piping in nuclear power plants. Superconducting QUantum Interference Device (SQUID) was used for the detection of thermal aging of SUS329 rolled duplex stainless steel and SCS16 cast duplex stainless steel. It was found that the SQUID output signal pattern in the presence of AC magnetic field applied to the specimen was sensitive to the changes in electromagnetic properties due to thermal aging

  15. Full-Duplex MIMO Small-Cell Networks: Performance Analysis

    OpenAIRE

    Atzeni, Italo; Kountouris, Marios

    2015-01-01

    Full-duplex small-cell relays with multiple antennas constitute a core element of the envisioned 5G network architecture. In this paper, we use stochastic geometry to analyze the performance of wireless networks with full-duplex multiple-antenna small cells, with particular emphasis on the probability of successful transmission. To achieve this goal, we additionally characterize the distribution of the self-interference power of the full-duplex nodes. The proposed framework reveals useful ins...

  16. Electron Beam Welding of Duplex Steels with using Heat Treatment

    Science.gov (United States)

    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.

  17. On the Performance of In-Band Full-Duplex Cooperative Communications

    KAUST Repository

    Khafagy, Mohammad Galal

    2016-01-01

    -duplex potentials. Full-duplex relaying (FDR), where intermediate nodes may now support source-destination communication via simultaneous listening/forwarding, represents one of two full-duplex settings currently recommended for deployment in future fifth

  18. Repair of Clustered Damage and DNA Polymerase Iota.

    Science.gov (United States)

    Belousova, E A; Lavrik, O I

    2015-08-01

    Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

  19. Detection of chicken contamination in beef meatball using duplex-PCR Cyt b gene

    Science.gov (United States)

    Sari, E. P.; Kartikasari, L. R.; Cahyadi, M.

    2017-04-01

    Beef is one of expensive animal protein sources compared to other meats, on the other hand, chicken is cheap animal protein source. Mixing of chicken into beef meatball is possibly performed to decrease production cost. The aim of this study was to detect chicken contamination in beef meatball using Cytochrome b (Cyt b) gene by duplex-PCR. Sample was designed and prepared as follows, 100% of chicken meatball, 100% of beef meatball and serial level of chicken contaminations in beef meatball (1, 5, 10 and 25%, respectively). Isolation of DNA genome from meatball was according to the guideline of gSYNCTM DNA Extraction Kit for animal tissue. The PCR reaction was carried out using KAPA2G Fast Multiplex Mix. This study found that the DNA genome was succesfully extracted. Moreover, chicken contamination in beef meatball was indicated by the presence of 227 bp DNA band on 2% of agarose gels. Current study revealed that duplex-PCR using Cyt b gene as a genetic marker was able to detect chicken contamination in beef meatball until 1% of chicken meat in the sample. It can be effectively used to identify contamination and also authenticate species origin in animal products to protect consumer from undesirable contents in the food.

  20. Temporal versus Superior Limbal Incision: Any difference in visual ...

    African Journals Online (AJOL)

    Aim: To compare the visual outcome of a superiorly placed limbal incision with a temporal limbal incision in extracapsular cataract surgery. The main outcome measures are visual acuity and the degree of stigmatism based on refraction. Method: A retrospective non randomized comparative study. Medical records of 40 ...

  1. Transurethral incision of urethral diverticulum in the female

    DEFF Research Database (Denmark)

    Miskowiak, J; Honnens de Lichtenberg, M

    1989-01-01

    A new technique of transurethral incision of urethral diverticulum was successfully used in two women. The method described is safe, simple and shortens operating time.......A new technique of transurethral incision of urethral diverticulum was successfully used in two women. The method described is safe, simple and shortens operating time....

  2. Mini transverse versus longitudinal incision in carpal tunnel syndrome

    International Nuclear Information System (INIS)

    Korkmaz, M.; Cepoglu, M.C.

    2013-01-01

    Objective: To evaluate the effectiveness of mini-transverse compared with mini-longitudinal incision for carpal tunnel release (CTR) with reference to postoperative functional capacity, symptom severity and complication rate. Study Design: Analytical study. Place and Duration of Study: Cumhuriyet University Medical Faculty, Department of Orthopaedics, Tokat State Hospital, Department of Orthopaedics and Medical Park Tokat Hospital, Department of Neurosurgery, from January 2007 to January 2009. Methodology: This study included 93 hands of 79 patients with carpal tunnel syndrome (CTS), which were operated between 2007 and 2009. Patients were divided according to incision types into Group-1 (undergoing mini-longitudinal incision) and Group-2 (undergoing mini-transverse incision). Patients were evaluated initially and at 3 weeks after treatment according to symptom severity and functional status of Boston Questionnaire (BQ). Demographic and clinical data were analyzed and compared statistically between two groups. Results: Statistically significant differences were observed in BQ symptom and functional scores between the pre- and postoperative period (p < 0.0001). BQ symptom and functional scores at postoperative period were better in Group-1 than Group-2 (p = 0.044 and p = 0.023 respectively). The scar hypersensitivity (p = 0.258) and tenderness (p = 1.00) associated with the incision sites were not statistically different. Conclusion: Longitudinal incision is more effective on symptom and functional conditions than transverse incision. However, there was less scar formation with transverse incision. (author)

  3. [Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

    Science.gov (United States)

    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

  4. Incisive canal deflation for correct implant placement: case report.

    Science.gov (United States)

    Spin-Neto, Rubens; Bedran, Telma Blanca Lombardo; de Paula, Wagner Nunes; de Freitas, Rubens Moreno; de Oliveira Ramalho, Lizeti Toledo; Marcantonio, Elcio

    2009-12-01

    This article is a case report of a patient in whom the prosthetic planning indicated the necessity of an incisive canal deflation for the correct installation of an implant that is to be osseointegrated. In the reopening phase after the bone graft installation, the incisive canal deflation (biopsy of its content) was done and titanium implants were installed with one of them invading the anatomical space occupied previously by the incisive canal. The biopsy analysis showed fragments of the incisive artery and nerve, which are responsible for the anterior upper-tooth pulp, the periodontium vascularization and the innervation. From the anastomosis present along with other structures allied with the absence of teeth in the region, there was no detriment to the patient caused by the deflation. Incisive canal deflation is a viable technique in implantology. It can permit ideal prosthetic planning with no detriment to the patient.

  5. Vertical compared with transverse incisions in abdominal surgery

    DEFF Research Database (Denmark)

    Grantcharov, T P; Rosenberg, J

    2001-01-01

    , and late complications (incisional hernia). RESULTS: Eleven randomised controlled trials and seven retrospective studies were identified. The transverse incision offers as good an access to most intra-abdominal structures as a vertical incision. The transverse incision results in significantly less......OBJECTIVE: To reach an evidence-based consensus on the relative merits of vertical and transverse laparotomy incisions. DESIGN: Review of all published randomised controlled trials that compared the postoperative complications after the two main types of abdominal incisions, vertical and transverse....... SETTING: Teaching hospital, Denmark. SUBJECTS: Patients undergoing open abdominal operations. INTERVENTIONS: For some of the variables (burst abdomen and incisional hernia) it was considered adequate to include retrospective studies. Studies were identified through Medline, Cochrane library, Embase...

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

    Science.gov (United States)

    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.

  7. Harvesting full-duplex rate gains in cellular networks with half-duplex user terminals

    KAUST Repository

    AlAmmouri, Ahmad

    2016-07-26

    Full-Duplex (FD) transceivers may be expensive in terms of complexity, power consumption, and price to be implemented in all user terminals. Therefore, techniques to exploit in-band full-duplex communication with FD base stations (BSs) and half-duplex (HD) users\\' equipment (UEs) are required. In this context, 3-node topology (3NT) has been recently proposed for FD BSs to reuse the uplink (UL) and downlink (DL) channels with HD terminals within the same cell. In this paper, we present a tractable mathematical framework, based on stochastic geometry, for 3NT in cellular networks. To this end, we propose a design paradigm via pulse-shaping and partial overlap between UL and DL channels to maximize the harvested rate gains in 3NT. The results show that 3NT achieves a close performance to networks with FD BSs and FD UEs, denoted by 2-node topology (2NT) networks. A maximum of 5% rate loss is reported when 3NT is compared to 2NT with efficient self-interference cancellation (SIC). If the SIC in 2NT is not efficient, 3NT highly outperforms 2NT. Consequently, we conclude that, irrespective to the UE duplexing scheme, it is sufficient to have FD BSs to harvest FD rate gains.

  8. Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation.

    Science.gov (United States)

    Banyasz, Akos; Ketola, Tiia; Martínez-Fernández, Lara; Improta, Roberto; Markovitsi, Dimitra

    2018-04-17

    There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.

  9. Influence of Incision Location on Transmitter Loss, Healing, Incision Lengths, Suture Retention, and Growth of Juvenile Chinook Salmon

    Energy Technology Data Exchange (ETDEWEB)

    Panther, Jennifer L.; Brown, Richard S.; Gaulke, Greggory L.; Woodley, Christa M.; Deters, Katherine A.

    2010-05-11

    In this study, conducted by Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers, Portland District, we measured differences in survival and growth, incision openness, transmitter loss, wound healing, and erythema among abdominal incisions on the linea alba, lateral and parallel to the linea alba (muscle-cutting), and following the underlying muscle fibers (muscle-sparing). A total of 936 juvenile Chinook salmon were implanted with both Juvenile Salmon Acoustic Tracking System transmitters (0.43 g dry) and passive integrated transponder tags. Fish were held at 12°C (n = 468) or 20°C (n = 468) and examined once weekly over 98 days. We found survival and growth did not differ among incision groups or between temperature treatment groups. Incisions on the linea alba had less openness than muscle-cutting and muscle-sparing incisions during the first 14 days when fish were held at 12°C or 20°C. Transmitter loss was not different among incision locations by day 28 when fish were held at 12°C or 20°C. However, incisions on the linea alba had greater transmitter loss than muscle-cutting and muscle-sparing incisions by day 98 at 12°C. Results for wound closure and erythema differed among temperature groups. Results from our study will be used to improve fish-tagging procedures for future studies using acoustic or radio transmitters.

  10. Duplex ultrasound: Indications and findings in a newly created ...

    African Journals Online (AJOL)

    Duplex ultrasound: Indications and findings in a newly created facility at the University of Calabar Teaching Hospital, Calabar. ... It is recommended that timely referrals be made, and mobile Doppler units be acquired to save more lives and limbs in the developing world. Keywords: Calabar, deep venous thrombosis, duplex ...

  11. Criteria for the Segmentation of Vowels on Duplex Oscillograms.

    Science.gov (United States)

    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…

  12. Zoster duplex: a clinical report and etiologic analysis.

    Science.gov (United States)

    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.

  13. Duplex tube steam reformer development program

    International Nuclear Information System (INIS)

    Lewe, C.K.; Nieto, J.M.; Papadopoulos, A.

    1978-09-01

    Work done in partial fulfillment of Task 7 of the Duplex Steam Reformer Development Program is described. The DSR concept acts as a double barrier between a process heat high temperature reactor plant (PNP) and a closed loop chemical heat pipe (CHP) for the long distance transport of chemical energy to a remote industrial user. The current state of the DSR design is described as well as related systems and equipment. The PNP concept presented is based upon work currently underway in the Federal Republic of Germany

  14. Duplex ultrasound evidence of fat embolism syndrome

    Directory of Open Access Journals (Sweden)

    Abdallah Naddaf, MD

    2016-12-01

    Full Text Available Fat embolism syndrome is a potentially fatal disease process most commonly associated with long-bone and pelvic fractures. Reports describing ultrasound evidence of fat emboli are restricted to echocardiography. We propose a new objective finding on venous duplex ultrasound imaging of the lower extremities as a useful diagnostic criterion by presenting the case reports of two patients with acute long-bone fractures, possibly leading to earlier orthopedic fixation and allocation of resources to those patients at higher risk of fat embolism syndrome.

  15. Timing, Coordination, and Rhythm : Acrobatics at the DNA Replication Fork

    NARCIS (Netherlands)

    Hamdan, Samir M.; Oijen, Antoine M. van

    2010-01-01

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In

  16. Assessment of corneal astigmatism following frown and straight incision forms in sutureless manual small incision cataract surgery

    Directory of Open Access Journals (Sweden)

    Amedo AO

    2016-04-01

    Full Text Available Angela Ofeibea Amedo, Kwadwo Amoah, Nana Yaa Koomson, David Ben Kumah, Eugene Appenteng Osae Department of Optometry and Visual Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana Abstract: To investigate which of two tunnel incision forms (frown versus straight in sutureless manual small incision cataract surgery creates more corneal astigmatism. Sixty eyes of 60 patients who had consented to undergo cataract surgery and to partake in this study were followed from baseline through >12-week postoperative period. Values of preoperative and postoperative corneal astigmatism for the 60 eyes, measured with a Bausch and Lomb keratometer, were extracted from the patients’ cataract surgery records. Residual astigmatism was computed as the difference between preoperative and postoperative keratometry readings. Visual acuity was assessed during the preoperative period and at each postoperative visit with a Snellen chart at 6 m. Fifty eyes of 50 patients were successfully followed-up on. Overall, the mean residual astigmatism was 0.75±0.12 diopters. The differences in mean residual astigmatism between the two different incision groups were statistically significant (t [48]=6.33, P<0.05; frown incision group recorded 1.00±0.12 diopters, whereas the straight incision group recorded 0.50±0.12 diopters. No significant difference was observed between male and female groups (t [48]=0.24, P>0.05. Residual corneal astigmatism in the frown incision group was significantly higher than in the straight incision group. Fisher’s exact test did not reveal a significant association between incision forms and visual acuity during the entire postoperative period (P>0.05. Keywords: cataract, residual corneal astigmatism, frown incision, straight incision

  17. Full Duplex Communications in 5G Small Cells

    DEFF Research Database (Denmark)

    Mahmood, Nurul Huda; Gatnau, Marta; Berardinelli, Gilberto

    2017-01-01

    Full duplex communication promises system performance improvement over conventional half duplex communication by allowing simultaneous transmission and reception. However, such concurrent communication results in strong self interference and an increase in the overall network interference, and can...... only be exploited when traffic is available in both directions. The potential throughput gains of full duplex communication over conventional half duplex transmission in a small cell network with asymmetric traffic conditions is investigated in this contribution. The throughput performance gains...... are analysed using tools from stochastic geometry, and further confirmed through extensive system level simulations. Our findings explicitly quantify how the gains from full duplex communication depend on the traffic profile and the inter-cell interference coupling. The demonstrated throughput gains and delay...

  18. Corrosion behavior of 2205 duplex stainless steel.

    Science.gov (United States)

    Platt, J A; Guzman, A; Zuccari, A; Thornburg, D W; Rhodes, B F; Oshida, Y; Moore, B K

    1997-07-01

    The corrosion of 2205 duplex stainless steel was compared with that of AISI type 316L stainless steel. The 2205 stainless steel is a potential orthodontic bracket material with low nickel content (4 to 6 wt%), whereas the 316L stainless steel (nickel content: 10 to 14 wt%) is a currently used bracket material. Both stainless steels were subjected to electrochemical and immersion (crevice) corrosion tests in 37 degrees C, 0.9 wt% sodium chloride solution. Electrochemical testing indicates that 2205 has a longer passivation range than 316L. The corrosion rate of 2205 was 0.416 MPY (milli-inch per year), whereas 316L exhibited 0.647 MPY. When 2205 was coupled to 316L with equal surface area ratio, the corrosion rate of 2205 reduced to 0.260 MPY, indicating that 316L stainless steel behaved like a sacrificial anode. When 316L is coupled with NiTi, TMA, or stainless steel arch wire and was subjected to the immersion corrosion test, it was found that 316L suffered from crevice corrosion. On the other hand, 2205 stainless steel did not show any localized crevice corrosion, although the surface of 2205 was covered with corrosion products, formed when coupled to NiTi and stainless steel wires. This study indicates that considering corrosion resistance, 2205 duplex stainless steel is an improved alternative to 316L for orthodontic bracket fabrication when used in conjunction with titanium, its alloys, or stainless steel arch wires.

  19. Electrolytic pickling of duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Ipek, N.; Holm, B.; Pettersson, R. [Swedish Institute for Metals Research, Drottning Kristinas vaeg 48, 11428 Stockholm (Sweden); Runnsjoe, G.; Karlsson, M. [Outokumpu Stainless AB, 77422 Avesta (Sweden)

    2005-08-01

    Pickling of duplex stainless steels has proved to be much more difficult than that of standard austenitic grades. Electrolytic pre-pickling is shown to be a key process towards facilitating the pickling process for material annealed both in the production-line and in laboratory experiments. The mechanism for the neutral electrolytic process on duplex 2205 and austenitic 316 steels has been examined and the oxide scale found to become thinner as a function of electrolytic pickling time. Spallation or peeling of the oxide induced by gas evolution did not play a decisive role. A maximum of about 20% of the current supplied to the oxidised steel surface goes to dissolution reactions whereas about 80% of the current was consumed in oxygen gas production. This makes the current utilisation very poor, particularly against the background of reports that in indirect electrolytic pickling only about 30% of the total current, supplied to the process, actually goes into the strip. A parametric study was therefore carried out to determine whether adjustment of process variables could improve the current utilisation. (Abstract Copyright [2005], Wiley Periodicals, Inc.)

  20. On phase equilibria in duplex stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Wessman, S. [Swerea KIMAB AB, Stockholm (Sweden); Pettersson, R. [Outokumpu Stainless AB, Avesta Research Centre, Avesta (Sweden); Hertzman, S. [Outokumpu Stainless Research Foundation, Stockholm (Sweden)

    2010-05-15

    The equilibrium conditions of four duplex stainless steels; Fe-23Cr-4.5Ni-0.1N, Fe-22Cr-5.5Ni-3Mo-0.17N, Fe-25Cr-7Ni-4Mo-0.27N and Fe-25Cr-7Ni-4Mo-1W-1.5Cu-0.27N were studied in the temperature region from 700 to 1000 C. Phase compositions were determined with SEM EDS and the phase fractions using image analysis on backscattered SEM images. The results showed that below 1000 C the steels develop an inverse duplex structure with austenite and sigma phase, of which the former is the matrix phase. With decreasing temperature, the microstructure will be more and more complex and finely dispersed. The ferrite is, for the higher alloyed steels, only stable above 1000 C and at lower temperatures disappears in favour of intermetallic phases. The major intermetallic phase is sigma phase with small amounts of chi phase, the latter primarily in high Mo and W grades. Nitrides, not a focus in this investigation, were present as rounded particles and acicular precipitates at lower temperatures. The results were compared to theoretical predictions using the TCFE5 and TCFE6 databases. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  1. Cosmetic effects of skin-crease camouflage incision versus longitudinal incision following carotid endarterectomy.

    Science.gov (United States)

    Kazimierczak, Arkadiusz; Rybicka, Anita; Rynio, Pawel; Gutowski, Piotr; Wiernicki, Ireneusz

    2018-03-01

    Despite the increasing use of carotid angioplasty and stenting (CAS), carotid endarterectomy (CEA) nonetheless remains a more medically beneficial method of treatment for carotid artery stenosis. Therefore, one possibility for progress within this procedure may be to use minimally invasive carotid surgery, especially when the scar is in plain sight: the use of the natural wrinkles (skin crease) as a camouflage of the skin incision provides significant cosmetic improvements. To compare the cosmetic effects of classic and trans-wrinkle CEA. To assess the distance between the carotid artery bifurcation (CAB) and the skin-crease incision whilst attempting CEA. It was a randomized prospective study with two groups: patients undergoing classic surgery (control group; n = 100) and skin-crease trans-wrinkle camouflaged CEA (study group; n = 100). Follow-up was at 2 months and 1 year. The medical results of the treatment were similar in both groups. The cumulative count of strokes and myocardial infarctions was 0.5% within 30 days, and after one year 3.5% (and 5.5% including cases of death). The superiority of the transverse crease being hidden compared to the conventional longitudinal technique was proven in the Patient and Observer Scar Assessment Scale (POSAS) score, respectively 11.4 ±1.0 vs. 14.1 ±3.4 (p = 0.0001) after 2 months and 13.5 ±2.8 vs. 14.1 ±3.4 (p = 0.039) after a year. Trans-wrinkle incision gives better cosmetic results, can be safely performed in most cases, and offers a comfortable approach during CEA.

  2. Charge transport through DNA/DNA duplexes and DNA/RNA hybrids: complex mechanism study

    Czech Academy of Sciences Publication Activity Database

    Kratochvílová, Irena; Vala, M.; Weiter, M.; Špérová, M.; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    2013-01-01

    Roč. 20, č. 1 (2013), s. 9-9 ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /11./. 14.03.2013-16.03.2013, Nové Hrady] Institutional support: RVO:61388963 ; RVO:68378271 ; RVO:86652036 Keywords : charge transport * fluorescence spectroscopy * DFT Subject RIV: CF - Physical ; Theoretical Chemistry

  3. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  4. Rietveld and impedance analysis of cold and hot rolled duplex and lean duplex steels for application in paper and pulp industry

    Energy Technology Data Exchange (ETDEWEB)

    Esteves, Luiza; Lins, Vanessa de Freitas Cunha, E-mail: luizaeq@yahoo.com.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Departamento de Engenharia Quimica; Paiva, Paulo Renato Perdigao [Centro Federal de Educacao Tecnologica de Minas Gerais (CEFET), Belo Horizonte, MG (Brazil); Viana, Adolfo Kalergis do Nascimento [APERAM South America, Timoteo, MG (Brazil)

    2017-01-15

    In this study, X-Ray Diffraction (XRD) and Rietveld Refinement were performed to identify and quantify the ferrite and austenite phase of cold and hot rolled duplex stainless steels (UNS S31803) and lean duplex stainless steels (UNS S32304). Electrochemical impedance spectroscopy (EIS) was applied to evaluate the chemical behavior of duplex and lean duplex stainless steels in white, green, and black liquors of paper and pulp industry. Rietveld analysis results showed a higher austenite content than the standard limit for duplex steels in the hot rolled condition. The hot rolling condition plays a major role in improving corrosion resistance in white liquor mainly for the lean duplex steel. (author)

  5. Rietveld and impedance analysis of cold and hot rolled duplex and lean duplex steels for application in paper and pulp industry

    International Nuclear Information System (INIS)

    Esteves, Luiza; Lins, Vanessa de Freitas Cunha; Viana, Adolfo Kalergis do Nascimento

    2017-01-01

    In this study, X-Ray Diffraction (XRD) and Rietveld Refinement were performed to identify and quantify the ferrite and austenite phase of cold and hot rolled duplex stainless steels (UNS S31803) and lean duplex stainless steels (UNS S32304). Electrochemical impedance spectroscopy (EIS) was applied to evaluate the chemical behavior of duplex and lean duplex stainless steels in white, green, and black liquors of paper and pulp industry. Rietveld analysis results showed a higher austenite content than the standard limit for duplex steels in the hot rolled condition. The hot rolling condition plays a major role in improving corrosion resistance in white liquor mainly for the lean duplex steel. (author)

  6. A skin abscess model for teaching incision and drainage procedures.

    Science.gov (United States)

    Fitch, Michael T; Manthey, David E; McGinnis, Henderson D; Nicks, Bret A; Pariyadath, Manoj

    2008-07-03

    Skin and soft tissue infections are increasingly prevalent clinical problems, and it is important for health care practitioners to be well trained in how to treat skin abscesses. A realistic model of abscess incision and drainage will allow trainees to learn and practice this basic physician procedure. We developed a realistic model of skin abscess formation to demonstrate the technique of incision and drainage for educational purposes. The creation of this model is described in detail in this report. This model has been successfully used to develop and disseminate a multimedia video production for teaching this medical procedure. Clinical faculty and resident physicians find this model to be a realistic method for demonstrating abscess incision and drainage. This manuscript provides a detailed description of our model of abscess incision and drainage for medical education. Clinical educators can incorporate this model into skills labs or demonstrations for teaching this basic procedure.

  7. Buffer management in wireless full-duplex systems

    KAUST Repository

    Bouacida, Nader

    2015-10-19

    Wireless full-duplex radios can simultaneously transmit and receive using the same frequency. In theory, this can double the throughput. In fact, there is only little work addressing aspects other than throughput gains in full-duplex systems. Over-buffering in today\\'s networks or the so-called “bufferbloat” phenomenon creates excessive end-to-end delays resulting in network performance degradation. Our analysis shows that full-duplex systems may suffer from high latency caused by bloated buffers. In this paper, we address the problem of buffer management in full-duplex networks by using Wireless Queue Management (WQM), which is an active queue management technique for wireless networks. Our solution is based on Relay Full-Duplex MAC (RFD-MAC), an asynchronous media access control protocol designed for relay full-duplexing. We compare the performance of WQM in full-duplex environment to Drop Tail mechanism over various scenarios. Our solution reduces the end-to-end delay by two orders of magnitude while achieving similar throughput in most of the cases.

  8. Morphodynamic Model of Submarine Canyon Incision by Sandblasting

    Science.gov (United States)

    Zhang, L.; Parker, G.; Izumi, N.; Cartigny, M.; Li, T.; Wang, G.

    2017-12-01

    Submarine canyons are carved by turbidity currents under the deep sea. As opposed to subaerial canyons, the relevant processes are not easy to observe directly. Turbidity currents are bottom-hugging sediment gravity flows of that can incise or deposit on the seafloor to create submarine canyons or fans. The triggers of turbidity currents can be storms, edge waves, internal waves, canyon wall sapping, delta failure, breaching and hyperpycnal flows. The formation and evolution mechanisms of submarine canyons are similar to those of subaerial canyons, but have substantial differences. For example, sandblasting, rather than wear due to colliding gravel clasts is more likely to be the mechanism of bedrock incision. Submarine canyons incise downward, and often develop meander bends and levees within the canyon, so defining "fairways". Here we propose a simple model for canyon incision. The starting point of our model is the Macro Roughness Saltation Abrasion Alluviation model of Zhang et al. [2015], designed for bedrock incision by gravel clasts in mixed bedrock-alluvial rivers. We adapt this formulation to consider sandblasting as a means of wear. We use a layer-averaged model for turbidity current dynamics. The current contains a mixture of mud, which helps drive the flow but which does not cause incision, and sand, which is the agent of incision. We show that the model can successfully model channel downcutting, and indeed illustrate the early formation of net incisional cyclic steps, i.e. upstream-migrating undulations on the bed associated with transcritical (in the Froude sense) flow. These steps can be expected to abet the process of incision.

  9. Diathermy versus scalpel incisions for open cholecystectomy comparative study

    International Nuclear Information System (INIS)

    Ali, M.A.; Niazi, W.A.K.

    2014-01-01

    The aim of the study was to make a comparison between skin incisions made with electrocautery versus scalpel in terms of their safety, efficacy and post-operative complications. Design: A randomized controlled study. Setting: The study was conducted in Combined Military Hospital (CMH) Kharian, Pakistan airforce (PAF) Hospital Sargodha. Duration of Study: May 2008 to August 2011. Patients and Methods: Ninety seven patients who underwent open cholecystectomy were randomly divided into two groups on the basis of the use of electrocautery versus steel scalpel for making skin incision and sub-cutaneous tissue dissection. Parameters recorded were, time taken from skin incision to full incising of the peritoneum, length of the wound, amount of blood loss during this step of surgery in each group. Post-operative pain scoring using visual analogue scale was done. Wound complications such as infection, haematoma/seroma and dehiscence were noted too. One month of follow up was recorded in each group. Subsequently a comparison of these findings was done. Results: Incision time (sec/cm/sub 2/) was longer in scalpel group than in diathermy group (p = 0.001), whereas, incision blood loss (ml/cm/sub 2/) was significantly less in diathermy group than in scalpel group (p = 0.03). There was no difference in post-operative pain perception as delineated by visual pain analogue scoring system between the two groups (p = 0.57). Post-operative wound complications and the final healing of wound at 01 month of follow-up were almost similar in both groups. Conclusion: Electrocautery may be used safely without any untoward complication in making skin incision and sub-cutaneous tissue dissection with an advantage of reduced incision time and and less blood loss. (author)

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

    Science.gov (United States)

    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.

  11. Iodination as a probe for small regions of disrupted secondary structure in double-stranded DNA

    DEFF Research Database (Denmark)

    Jensen, Kaj Frank; Nes, Ingolf F.; Wells, Robert D.

    1976-01-01

    Conditions were established where the thallium-catalyzed iodination of random coil DNA proceeded 100–200 times faster than for native DNA. This reaction was explored as a probe for localized regions of disrupted base pairs in duplex DNA. A heteroduplex was constructed between DNA fragments produced...

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

    Science.gov (United States)

    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.

  13. Racemic DNA crystallography.

    Science.gov (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Corrosion behavior of sensitized duplex stainless steel.

    Science.gov (United States)

    Torres, F J; Panyayong, W; Rogers, W; Velasquez-Plata, D; Oshida, Y; Moore, B K

    1998-01-01

    The present work investigates the corrosion behavior of 2205 duplex stainless steel in 0.9% NaCl solution after various heat-treatments, and compares it to that of 316L austenitic stainless steel. Both stainless steels were heat-treated at 500, 650, and 800 degrees C in air for 1 h, followed by furnace cooling. Each heat-treated sample was examined for their microstructures and Vickers micro-hardness, and subjected to the X-ray diffraction for the phase identification. Using potentiostatic polarization method, each heat-treated sample was corrosion-tested in 37 degrees C 0.9% NaCl solution to estimate its corrosion rate. It was found that simulated sensitization showed an adverse influence on both steels, indicating that corrosion rates increased by increasing the sensitization temperatures.

  15. Duplex stainless steel surface bay laser cladding

    International Nuclear Information System (INIS)

    Amigo, V.; Pineda, Y.; Segovia, F.; Vicente, A.

    2004-01-01

    Laser cladding is one of the most promising techniques to restore damaged surfaces and achieve properties similar to those of the base metal. In this work, duplex stainless steels have been cladded by a nickel alloy under different processing conditions. The influence of the beam speed and defocusing variables ha been evaluated in the microstructure both of the cladding and heat affected zone, HAZ. These results have been correlated to mechanical properties by means of microhardness measurements from cladding area to base metal through the interface. This technique has shown to be very appropriate to obtain controlled mechanical properties as they are determined by the solidification microstructure, originated by the transfer of mass and heat in the system. (Author) 21 refs

  16. Duplex quantum communication through a spin chain

    Science.gov (United States)

    Wang, Zhao-Ming; Bishop, C. Allen; Gu, Yong-Jian; Shao, Bin

    2011-08-01

    Data multiplexing within a quantum computer can allow for the simultaneous transfer of multiple streams of information over a shared medium thereby minimizing the number of channels needed for requisite data transmission. Here, we investigate a two-way quantum communication protocol using a spin chain placed in an external magnetic field. In our scheme, Alice and Bob each play the role of a sender and a receiver as two states, cos((θ1)/(2))0+sin((θ1)/(2))eiφ11 and cos((θ2)/(2))0+sin((θ2)/(2))eiφ21, are transferred through one channel simultaneously. We find that the transmission fidelity at each end of a spin chain can usually be enhanced by the presence of a second party. This is an important result for establishing the viability of duplex quantum communication through spin chain networks.

  17. Numerical Simulation of Duplex Steel Multipass Welding

    Directory of Open Access Journals (Sweden)

    Giętka T.

    2016-12-01

    Full Text Available Analyses based on FEM calculations have significantly changed the possibilities of determining welding strains and stresses at early stages of product design and welding technology development. Such an approach to design enables obtaining significant savings in production preparation and post-weld deformation corrections and is also important for utility properties of welded joints obtained. As a result, it is possible to make changes to a simulated process before introducing them into real production as well as to test various variants of a given solution. Numerical simulations require the combination of problems of thermal, mechanical and metallurgical analysis. The study presented involved the SYSWELD software-based analysis of GMA welded multipass butt joints made of duplex steel sheets. The analysis of the distribution of stresses and displacements were carried out for typical welding procedure as during real welding tests.

  18. APE1 incision activity at abasic sites in tandem repeat sequences.

    Science.gov (United States)

    Li, Mengxia; Völker, Jens; Breslauer, Kenneth J; Wilson, David M

    2014-05-29

    Repetitive DNA sequences, such as those present in microsatellites and minisatellites, telomeres, and trinucleotide repeats (linked to fragile X syndrome, Huntington disease, etc.), account for nearly 30% of the human genome. These domains exhibit enhanced susceptibility to oxidative attack to yield base modifications, strand breaks, and abasic sites; have a propensity to adopt non-canonical DNA forms modulated by the positions of the lesions; and, when not properly processed, can contribute to genome instability that underlies aging and disease development. Knowledge on the repair efficiencies of DNA damage within such repetitive sequences is therefore crucial for understanding the impact of such domains on genomic integrity. In the present study, using strategically designed oligonucleotide substrates, we determined the ability of human apurinic/apyrimidinic endonuclease 1 (APE1) to cleave at apurinic/apyrimidinic (AP) sites in a collection of tandem DNA repeat landscapes involving telomeric and CAG/CTG repeat sequences. Our studies reveal the differential influence of domain sequence, conformation, and AP site location/relative positioning on the efficiency of APE1 binding and strand incision. Intriguingly, our data demonstrate that APE1 endonuclease efficiency correlates with the thermodynamic stability of the DNA substrate. We discuss how these results have both predictive and mechanistic consequences for understanding the success and failure of repair protein activity associated with such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains. Published by Elsevier Ltd.

  19. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

    Science.gov (United States)

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

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

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

    2017-10-30

    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 monoclinicP21lattice of hexagonal metric. The various twinning criteria give somewhat 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.

  1. Comparison of the Keratometric Corneal Astigmatic Power after Phacoemulsification: Clear Temporal Corneal Incision versus Superior Scleral Tunnel Incision

    Directory of Open Access Journals (Sweden)

    Yongqi He

    2009-01-01

    Full Text Available Objective. This is prospective randomized control trial to compare the mean keratometric corneal astigmatism diopter power (not surgical induced astigmatism among preop and one-month and three-month postop phacoemulcification of either a clear temporal corneal incision or a superior scleral tunnel Incision, using only keratometric astigmatic power reading to evaluate the difference between the two cataract surgery incisions. Methods. 120 patients (134 eyes underwent phacoemulcification were randomly assigned to two groups: Group A, the clear temporal corneal incision group, and Group B, the superior scleral tunnel incision group. SPSS11.5 Software was used for statistical analysis to compare the postsurgical changes of cornea astigmatism on keratometry. Results. The changes of corneal astigmatic diopter in Groups A and B after 3 month postop from keratometric reading were 1.04 + 0.76 and 0.94 + 0.27, respectively (=.84>.05, which showed no statistic significance difference. Conclusion. The incision through either temporal clear cornea or superior scleral tunnel in phacoemulcification shows no statistic difference in astigmatism change on keratometry 3-month postop.

  2. Behaviour of UV-sensitive mutants of Proteus mirabilis to repair incision breaks

    International Nuclear Information System (INIS)

    Stoerl, K.; Mund, C.

    1977-01-01

    In U.V.-sensitive mutants of P. mirabilis with the phenotype HCR, REC and EXR single-strand breaks appeared immediately after UV-irradiation. The behaviour of REC- and EXR-mutants was similar to the wildtype. The number of incision breaks observed by sedimentation analysis in these strains was very low. They could be joined during the excision repair process. From the ability of REC- and EXR-strains to rejoin most of the induced single-strand breaks it can be concluded that these strains have approximately the same capacity for excision repair as the wildtype. HCR-mutants of P. mirabilis produced single-strand breaks after UV-irradiation in contrast to HCR-mutants of E. coli. Therefore we suggest that HCR-mutants of P. mirabilis are not completely inhibited in the incision step. The single-strand breaks introduced in the DNA at the beginning of the repair process were not rejoined during further incubation. Experiments with toluenized cells led to the same results. The newly synthesized daughter DNA-strands of UV-irradiated HCR-mutants were of low molecular weight in comparison with those from unirradiated control cells during the repair period. This result is in agreement with the incapability of HCR-mutants to remove the pyrimidine dimers from the parental template strand. (author)

  3. Initiation of the microgene polymerization reaction with non-repetitive homo-duplexes

    International Nuclear Information System (INIS)

    Itsko, Mark; Zaritsky, Arieh; Rabinovitch, Avinoam; Ben-Dov, Eitan

    2008-01-01

    Microgene Polymerization Reaction (MPR) is used as an experimental system to artificially simulate evolution of short, non-repetitive homo-duplex DNA into multiply-repetitive products that can code for functional proteins. Blunt-end ligation by DNA polymerase is crucial in expansion of homo-duplexes (HDs) into head-to-tail multiple repeats in MPR. The propagation mechanism is known, but formation of the initial doublet (ID) by juxtaposing two HDs and polymerization through the gap has been ambiguous. Initiation events with pairs of HDs using Real-Time PCR were more frequent at higher HD concentrations and slightly below the melting temperature. A process molecularity of about 3.1, calculated from the amplification efficiency and the difference in PCR cycles at which propagation was detected at varying HD concentrations, led to a simple mechanism for ID formation: the gap between two HDs is bridged by a third. Considering thermodynamic aspects of the presumed intermediate 'nucleation complex' can predict relative propensity for the process with other HDs

  4. Development of oxide dispersion strengthened 2205 duplex stainless steel composite

    Directory of Open Access Journals (Sweden)

    Oladayo OLANIRAN

    2015-05-01

    Full Text Available Composites of duplex stainless steel were produced by oxide dispersion strengthening with comparatively improved mechanical properties by hot press sintering of partially stabilized Zirconia (PSZ, 3% yttria, mole fraction dispersion in 2205 duplex stainless steels. Ceramic oxide was added as reinforcement, while chromium (Cr and Nickel (Ni were incorporated to maintain the austenitic/ferritic phase balance of the duplex stainless steel. The powders and sintered were characterized in detail using scanning electron microscopy (SEM and X-ray diffraction (XRD. The microstructural evolution and phase formation during oxide dispersion strengthening of duplex stainless steel composites were investigated. The influence of composition variation of the reinforcements on the microstructural and corrosion behaviour in simulated mine water of the composites were investigated. In this manuscript, it was established that composition has great influence on the structure/properties relationship of the composites developed.

  5. Improper Signaling for Virtual Full-Duplex Relay Systems

    KAUST Repository

    Gaafar, Mohamed

    2017-02-14

    Virtual full-duplex (VFD) is a powerful solution to compensate the rate loss of half-duplex relaying without the need to full-duplex capable nodes. Inter-relay interference (IRI) challenges the operation of VFD relaying systems. Recently, improper signaling is employed at both relays of the VFD to mitigate the IRI by imposing the same signal characteristics for both relays. To further boost the achievable rate performance, asymmetric time sharing VFD relaying system is adopted with different improper signals at the half-duplex relays. The joint tuning of the three design parameters improves the achievable rate performance at different ranges of IRI and different relays locations. Extensive simulation results are presented and analyzed to show the achievable rate gain of the proposed system and understand the system behavior.

  6. Improper Signaling for Virtual Full-Duplex Relay Systems

    KAUST Repository

    Gaafar, Mohamed; Amin, Osama; Schaefer, Rafael F.; Alouini, Mohamed-Slim

    2017-01-01

    Virtual full-duplex (VFD) is a powerful solution to compensate the rate loss of half-duplex relaying without the need to full-duplex capable nodes. Inter-relay interference (IRI) challenges the operation of VFD relaying systems. Recently, improper signaling is employed at both relays of the VFD to mitigate the IRI by imposing the same signal characteristics for both relays. To further boost the achievable rate performance, asymmetric time sharing VFD relaying system is adopted with different improper signals at the half-duplex relays. The joint tuning of the three design parameters improves the achievable rate performance at different ranges of IRI and different relays locations. Extensive simulation results are presented and analyzed to show the achievable rate gain of the proposed system and understand the system behavior.

  7. Aortoiliac reconstructive surgery based upon the results of duplex scanning

    NARCIS (Netherlands)

    van der Zaag, E. S.; Legemate, D. A.; Nguyen, T.; Balm, R.; Jacobs, M. J.

    1998-01-01

    OBJECTIVE: To evaluate whether duplex scanning can replace angiography in patients operated for aortoiliac obstructive disease. DESIGN: Retrospective. MATERIALS AND METHODS: Between January 1995 and October 1996, 44 patients underwent vascular surgery of the aortoiliac tract. The study population

  8. The role of duplex stainless steels for downhole tubulars

    International Nuclear Information System (INIS)

    Francis, R.

    1993-01-01

    In sour conditions there is an increasing trend to turn to corrosion resistant alloys for downhole tubulars. The most commonly used CRA tubular is 13Cr, and there are thousands of feet in service. However, there are limits to the use of 13Cr, ie., the risk of sulphide stress corrosion cracking at high H 2 S levels, and the possibility of pitting or high corrosion rates in waters with high chloride contents. Where the service conditions are felt to be too severe for 13Cr alloys it has been traditional to switch to nickel base alloys such as alloys 825 and C-276 (UNS N08825 and N10276). The alloys are much more expensive than 13Cr, and in recent years the duplex stainless steels have been selected as alloys with superior corrosion and SSCC resistance compared with 13Cr, and having lower cost than nickel alloys. Originally the 22Cr duplex alloy (UNS 31803) was used, but more recently the 25Cr super duplex alloys (UNS S32760 and S32750) have become more available. The present paper reviews the data available for 13Cr and the limits of applicability. Data is also presented for laboratory tests for both the 22Cr and 25Cr super duplex alloys. There is extensive service experience with both 22Cr and 25Cr super duplex in the North Sea, covering both downhole tubulars, manifold and post wellhead equipment. Data is presented showing some of the sour condition being experienced in the North Sea by super duplex alloys. These results show that there is a substantial gap between the limits of use for 13Cr and the 25Cr super duplex stainless steel alloys. This means that in many sour environments super duplex stainless steel provides a cost effective alternative to nickel-base alloys

  9. Magnetic resonance urography in duplex kidney with ectopic ureteral insertion

    Directory of Open Access Journals (Sweden)

    Conjeevaram Rajendrarao Thambidorai

    2011-01-01

    Full Text Available This is a report on the use of magnetic resonance urography (MRU in a 6-year-old girl who presented with urinary incontinence. She had a left duplex kidney with poorly functioning upper moiety and ectopic insertion of the dilated upper pole ureter. MRU has been shown to be superior to conventional imaging techniques in delineating poorly functioning moieties of duplex kidneys and ectopic ureters.

  10. Transcranial Duplex Sonography Predicts Outcome following an Intracerebral Hemorrhage.

    Science.gov (United States)

    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 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.

  11. Method for construction of normalized cDNA libraries

    Science.gov (United States)

    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.

  12. Lateral Erosion Encourages Vertical Incision in a Bimodal Alluvial River

    Science.gov (United States)

    Gran, K. B.

    2015-12-01

    Sand can have a strong impact on gravel transport, increasing gravel transport rates by orders of magnitude as sand content increases. Recent experimental work by others indicates that adding sand to an armored bed can even cause armor to break-up and mobilize. These two elements together help explain observations from a bimodal sand and gravel-bedded river, where lateral migration into sand-rich alluvium breaks up the armor layer, encouraging further incision into the bed. Detailed bedload measurements were coupled with surface and subsurface grain size analyses and cross-sectional surveys in a seasonally-incised channel carved into the upper alluvial fan of the Pasig-Potrero River at Mount Pinatubo, Philippines. Pinatubo erupted in 1991, filling valleys draining the flanks of the volcano with primarily sand-sized pyroclastic flow debris. Twenty years after the eruption, sand-rich sediment inputs are strongly seasonal, with most sediment input to the channel during the rainy season. During the dry season, flow condenses from a wide braided planform to a single-thread channel in most of the upper basin, extending several km onto the alluvial fan. This change in planform creates similar unit discharge ranges in summer and winter. Lower sediment loads in the dry season drive vertical incision until the bed is sufficiently armored. Incision proceeds downstream in a wave, with increasing sediment transport rates and decreasing grain size with distance downstream, eventually reaching a gravel-sand transition and return to a braided planform. Incision depths in the gravel-bedded section exceeded 3 meters in parts of a 4 km-long study reach, a depth too great to be explained by predictions from simple winnowing during incision. Instead, lateral migration into sand-rich alluvium provides sufficient fine sediment to break up the armor surface, allowing incision to start anew and increasing the total depth of the seasonally-incised valley. Lateral migration is recorded in a

  13. On the Secrecy Degrees of Freedom with Full-Duplex Communication

    DEFF Research Database (Denmark)

    Mahmood, Nurul Huda; Mogensen, Preben Elgaard

    2017-01-01

    of such an application. The potential of full duplex nodes in improving the physical layer security of a communication link is investigated in this contribution. We specifically derive the information theoretic secrecy degrees of freedom measure for a pair of nodes communicating in full duplex mode. Moreover, closed...... and the delay reduction of full duplex communication are somewhat limited in realistic network settings, leading researchers to study other possible applications of full duplex communication which can provide significantly higher gains over half duplex communication. Physical layer security is an example...... form expressions for the instantaneous and ergodic throughput gain of full duplex communication over conventional half duplex is derived. The secrecy degrees of freedom with full duplex is shown to be two as opposed to that of zero in half duplex mode....

  14. Effects of two different incision phacoemulsification on corneal astigmatism

    Directory of Open Access Journals (Sweden)

    Lu Huo

    2014-12-01

    Full Text Available AIM:To compare the effect of different incision in corneal astigmatism after phacoemulsification. METHODS: Totally 88 cases(122 eyeswith pure cataract were randomly divided into two groups. Forty cases(60 eyeswere clarity corneal incision in group A, and 48 cases(62 eyeswere sclera tunnel incision in group B. Mean corneal astigmatism, surgically induced astigmatism(SIA, uncorrected visual acuity(UCVAand best correct vision acuity(BCVAwere observed in pre- and post-operation at 1d; 1wk; 1mo.RESULTS: The mean astigmatism had statistically significant difference between two groups at 1d; 1wk; 1mo after operation(PPP>0.05. UCVA≥0.5 and BCVA≥0.8 had statistically significant difference at 1d; 1wk(PP>0.05.CONCLUSION: Phacoemulsification with scleral tunnel incision remove combined intraocular lens(IOLimplantation has small changes to corneal astigmatism. By selecting personalized corneal incision according to the corneal topography might be more beneficial.

  15. Accurate Detection of Methicillin-Resistant Staphylococcus aureus in Mixtures by Use of Single-Bacterium Duplex Droplet Digital PCR.

    Science.gov (United States)

    Luo, Jun; Li, Junhua; Yang, Hang; Yu, Junping; Wei, Hongping

    2017-10-01

    Accurate and rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is needed to screen MRSA carriers and improve treatment. The current widely used duplex PCR methods are not able to differentiate MRSA from coexisting methicillin-susceptible S. aureus (MSSA) or other methicillin-resistant staphylococci. In this study, we aimed to develop a direct method for accurate and rapid detection of MRSA in clinical samples from open environments, such as nasal swabs. The new molecular assay is based on detecting the cooccurrence of nuc and mecA markers in a single bacterial cell by utilizing droplet digital PCR (ddPCR) with the chimeric lysin ClyH for cell lysis. The method consists of (i) dispersion of an intact single bacterium into nanoliter droplets, (ii) temperature-controlled release of genomic DNA (gDNA) by ClyH at 37°C, and (iii) amplification and detection of the markers ( nuc and mecA ) using standard TaqMan chemistries with ddPCR. Results were analyzed based on MRSA index ratios used for indicating the presence of the duplex-positive markers in droplets. The method was able to achieve an absolute limit of detection (LOD) of 2,900 CFU/ml for MRSA in nasal swabs spiked with excess amounts of Escherichia coli , MSSA, and other mecA -positive bacteria within 4 h. Initial testing of 104 nasal swabs showed that the method had 100% agreement with the standard culture method, while the normal duplex qPCR method had only about 87.5% agreement. The single-bacterium duplex ddPCR assay is rapid and powerful for more accurate detection of MRSA directly from clinical specimens. Copyright © 2017 American Society for Microbiology.

  16. EFFECT OF INTERMETALLIC PHASES ON CORROSION BEHAVIOR AND MECHANICAL PROPERTIES OF DUPLEX STAINLESS STEEL AND SUPER-DUPLEX STAINLESS STEEL

    OpenAIRE

    Prabhu Paulraj; Rajnish Garg

    2015-01-01

    Duplex Stainless Steels (DSS) and Super Duplex Stainless Steel (SDSS) have excellent integration of mechanical and corrosion properties. However, the formation of intermetallic phases is a major problem in their usage. The mechanical and corrosion properties are deteriorated due to the presence of intermetallic phases. These phases are induced during welding, prolonged exposure to high temperatures, and improper heat treatments. The main emphasis of this review article is on intermetallic pha...

  17. Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA.

    Science.gov (United States)

    Hughesman, Curtis B; Turner, Robin F B; Haynes, Charles A

    2011-06-14

    Melting thermodynamic data obtained by differential scanning calorimetry (DSC) are reported for 43 duplexed oligonucleotides containing one or more locked nucleic acid (LNA) substitutions. The measured heat capacity change (ΔC(p)) for the helix-to-coil transition is used to compute the changes in enthalpy and entropy for melting of an LNA-bearing duplex at the T(m) of its corresponding isosequential unmodified DNA duplex to allow rigorous thermodynamic analysis of the stability enhancements provided by LNA substitutions. Contrary to previous studies, our analysis shows that the origin of the improved stability is almost exclusively a net reduction (ΔΔS° thermodynamics and the increased melting temperature (ΔT(m)) of heteroduplexes formed between an unmodified DNA strand and a complementary strand containing any number and configuration of standard LNA nucleotides A, T, C, and G. This single-base thermodynamic (SBT) model requires only four entropy-related parameters in addition to ΔC(p). Finally, DSC data for 20 duplexes containing the nucleobase-modified LNAs 2-aminoadenine (D) and 2-thiothymine (H) are reported and used to determine SBT model parameters for D and H. The data and model suggest that along with the greater stability enhancement provided by D and H bases relative to their corresponding A and T analogues, the unique pseudocomplementary properties of D-H base pairs may make their use appealing for in vitro and in vivo applications.

  18. Phase Transformations in Cast Duplex Stainless Steels

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yoon-Jun [Iowa State Univ., Ames, IA (United States)

    2004-01-01

    Duplex stainless steels (DSS) constitute both ferrite and austenite as a matrix. Such a microstructure confers a high corrosion resistance with favorable mechanical properties. However, intermetallic phases such as σ and χ can also form during casting or high-temperature processing and can degrade the properties of the DSS. This research was initiated to develop time-temperature-transformation (TTT) and continuous-cooling-transformation (CCT) diagrams of two types of cast duplex stainless steels, CD3MN (Fe-22Cr-5Ni-Mo-N) and CD3MWCuN (Fe-25Cr-7Ni-Mo-W-Cu-N), in order to understand the time and temperature ranges for intermetallic phase formation. The alloys were heat treated isothermally or under controlled cooling conditions and then characterized using conventional metallographic methods that included tint etching, and also using electron microscopy (SEM, TEM) and wavelength dispersive spectroscopy (WDS). The kinetics of intermetallic-phase (σ + χ) formation were analyzed using the Johnson-Mehl-Avrami (MA) equation in the case of isothermal transformations and a modified form of this equation in the case of continuous cooling transformations. The rate of intermetallic-phase formation was found to be much faster in CD3MWCuN than CD3MN due mainly to differences in the major alloying contents such as Cr, Ni and Mo. To examine in more detail the effects of these elements of the phase stabilities; a series of eight steel castings was designed with the Cr, Ni and Mo contents systematically varied with respect to the nominal composition of CD3MN. The effects of varying the contents of alloying additions on the formation of intermetallic phases were also studied computationally using the commercial thermodynamic software package, Thermo-Calc. In general, σ was stabilized with increasing Cr addition and χ by increasing Mo addition. However, a delicate balance among Ni and other minor elements such as N and Si also exists. Phase equilibria in DSS can be affected by

  19. Clinical utility of carotid duplex ultrasound prior to cardiac surgery.

    Science.gov (United States)

    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 (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

  20. Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus.

    Science.gov (United States)

    Fukui, Kenji; Iino, Hitoshi; Baba, Seiki; Kumasaka, Takashi; Kuramitsu, Seiki; Yano, Takato

    2017-09-01

    DNA mismatch repair (MMR) system corrects mismatched bases that are generated mainly by DNA replication errors. The repair system excises the error-containing single-stranded region and enables the re-synthesis of the strand. In the early reactions of MMR, MutL endonuclease incises the newly-synthesized/error-containing strand of the duplex to initiate the downstream excision reaction. MutL endonuclease consists of the N-terminal ATPase and C-terminal endonuclease domains. In this study, we report the crystal structure of the ATPase domain of MutL endonuclease from Aquifex aeolicus. The overall structure of the domain was similar to those of human MutL homologs and Escherichia coli MutL, although E. coli MutL has no endonuclease activity. The ATPase domain was comprised of two subdomains: the N-terminal ATP-binding subdomain and the C-terminal α-β sandwich subdomain. Site-directed mutagenesis experiment identified DNA-interacting eight basic amino acid residues, which were distributed across both the two subdomains and formed a DNA-binding cleft. Docking simulation between the structures of the ATPase and endonuclease domains generated a reliable model structure for the full-length A. aeolicus MutL, which satisfies our previous result of small-angle X-ray scattering analysis. On the basis of the model structure and further experimental results, we concluded that the two separate DNA-binding sites in the full-length A. aeolicus MutL simultaneously bind a dsDNA molecule. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Modification of the Nuss Procedure: The Single-incision Technique

    Directory of Open Access Journals (Sweden)

    Tetsushi Aizawa, MD

    2014-11-01

    Full Text Available Summary: The Nuss procedure is a prevalent minimally invasive surgery for pectus excavatum. Although the Nuss procedure has the advantage of leaving less obtrusive scars, the standard technique requires at least 3 skin incisions to insert several instruments. We experienced 7 cases of the modified Nuss procedure using a single incision during a 7-year period. To facilitate passing of the bar, a traction guide was created according to our unique method. There was no need for a bar stabilizer, and no severe intraoperative complications occurred. All patients exhibited satisfactory short-term results; however, 1 patient suffered from bar rotation and required repeat surgery for fixation. Two patients underwent bar removal via the same single incision without any difficulties.

  2. Enantiospecific kinking of DNA by a partially intercalating metal complex

    KAUST Repository

    Reymer, Anna

    2012-01-01

    Opposite enantiomers of [Ru(phenanthroline) 3] 2+ affect the persistence length of DNA differently, a long speculated effect of helix kinking. Our molecular dynamics simulations confirm a substantial change of duplex secondary structure produced by wedge-intercalation of one but not the other enantiomer. This effect is exploited by several classes of DNA operative proteins. © The Royal Society of Chemistry 2012.

  3. Superimposed Code Theoretic Analysis of Deoxyribonucleic Acid (DNA) Codes and DNA Computing

    Science.gov (United States)

    2010-01-01

    DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research addresses how the...Acid dsDNA double stranded DNA MOSAIC Mobile Stream Processing Cluster PCR Polymerase Chain Reaction RAM Random Access Memory ssDNA single stranded DNA WC Watson – Crick A Adenine C Cytosine G Guanine T Thymine ...are 5′→3′ and strands with strikethrough are 3′→5′. A dsDNA duplex formed between a strand and its reverse complement is called a

  4. Minimizing surgical skin incision scars with a latex surgical glove.

    Science.gov (United States)

    Han, So-Eun; Ryoo, Suk-Tae; Lim, So Young; Pyon, Jai-Kyung; Bang, Sa-Ik; Oh, Kap-Sung; Mun, Goo-Hyun

    2013-04-01

    The current trend in minimally invasive surgery is to make a small surgical incision. However, the excessive tensile stress applied by the retractors to the skin surrounding the incision often results in a long wound healing time and extensive scarring. To minimize these types of wound problems, the authors evaluated a simple and cost-effective method to minimize surgical incision scars based on the use of a latex surgical glove. The tunnel-shaped part of a powder-free latex surgical glove was applied to the incision and the dissection plane. It was fixed to the full layer of the dissection plane with sutures. The glove on the skin surface then was sealed with Ioban (3 M Health Care, St. Paul, MN, USA) to prevent movement. The operation proceeded as usual, with the retractor running through the tunnel of the latex glove. It was possible to complete the operation without any disturbance of the visual field by the surgical glove, and the glove was neither torn nor separated by the retractors. The retractors caused traction and friction during the operation, but the extent of damage to the postoperative skin incision margin was remarkably less than when the operation was performed without a glove. This simple and cost-effective method is based on the use of a latex surgical glove to protect the surgical skin incision site and improve the appearance of the postoperative scar. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

  5. Simulation of channel sandstone architecture in an incised valley

    Energy Technology Data Exchange (ETDEWEB)

    Frykman, P.; Johannessen, P.; Andsbjerg, J.

    1998-12-31

    The present report describes a geostatistical modelling study that is aimed at reflecting the architecture of the channel sandstones in an incised valley fill. The example used for this study is a part of the Middle Jurassic sandy succession of the Bryne Formation in the Danish central Graben. The succession consists mainly of fluvial sediments in the lower part, overlain by tidal influenced sediments, which again is overlain by shallow marine sediments. The modelling study has been performed on a sequence of incised valley sediments in the upper part of the Bryne Formation overlying fluvial sediments. (au) EFP-96. 19 refs.

  6. Better outcome from arthroscopic partial meniscectomy than skin incisions only?

    DEFF Research Database (Denmark)

    Roos, Ewa M; Hare, Kristoffer Borbjerg; Nielsen, Sabrina Mai

    2018-01-01

    . In total, nine participants experienced 11 adverse events; six in the surgery group and three in the skin-incisions-only group. CONCLUSION: We found greater improvement from arthroscopic partial meniscectomy compared with skin incisions only at 2 years, with the statistical uncertainty of the between......-group difference including what could be considered clinically relevant. Because of the study being underpowered, nearly half in the sham group being non-blinded and one-third crossing over to surgery, the results cannot be generalised to the greater patient population. TRIAL REGISTRATION NUMBER: NCT01264991....

  7. Corrosion behaviour of sintered duplex stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Utrilla, M. Victoria; Urena, Alejandro; Otero, Enrique; Munez, Claudio Jose [Escuela Superior de Ciencias Experimentales y Tecnologia, Universidad Rey Juan Carlos, C/ Tulipan s/n, 28933 Mostoles, Madrid (Spain)

    2004-07-01

    Duplex austenite-ferrite stainless steels were prepared by mixing austenitic (316L) and ferritic (434L) atomized powders. Although different 316L/434L ratios were prepared, present work centred its study on 50% ferrite - 50% austenite sintered steel. The powders were mixed and pressed at 700 MPa and sintered at 1250 deg. C for 30 min in vacuum. The cooling rate was 5 deg. C/min. Solution treatment was carried out to homogenize the microstructure at 1100 deg. C during 20 min. A microstructural study of the material in solution was performed, evaluating the microstructure, proportion and shape of porosity, and ferrite percentage. This last was measured by two methods, quantitative metallography and Fischer ferrito-metry. The materials were heat treated in the range of 700 to 1000 deg. C, for 10, 30 and 60 min and water quenched, to study the microstructural changes and the influence on the intergranular corrosion resistance. The method used to evaluate the sensitization to the intergranular corrosion was the electrochemical potentio-kinetic reactivation procedure (EPR). The test solution was 0.5 M H{sub 2}SO{sub 4} + 0,01 M KSCN at 30 deg. C. The criterion used to evaluate the sensitization was the ratio between the maximum reactivation density (Ir) and the maximum activation density (Ia). The results of the electrochemical tests were discussed in relation with the microstructures observed at the different heat treatments. (authors)

  8. Meta-analysis of the effectiveness of surgical scalpel or diathermy in making abdominal skin incisions.

    LENUS (Irish Health Repository)

    Ahmad, Nasir Zaheer

    2012-02-01

    BACKGROUND: Surgical scalpels are traditionally used to make skin incisions. Diathermy incisions on contrary are less popular among the surgeons. The aim of this meta-analysis was to compare the effectiveness of both techniques and address the common fallacies about diathermy incisions. METHODS: A literature search of MEDLINE and Cochrane databases was done, using the keywords diathermy, cold scalpel, and incisions. Eleven clinical trials comparing both methods of making skin incisions were selected for meta-analysis. The end points compared included postoperative wound infection, pain in first 24 hours after surgery, time taken to complete the incisions, and incision-related blood loss. RESULTS: Postoperative wound infection rate was comparable in both techniques (P = 0.147, odds ratio = 1.257 and 95% CI = 0.923-1.711). Postoperative pain was significantly less with diathermy incisions in first 24 hours (P = 0.031, weighted mean difference = 0.852 and 95% CI = 0.076-1.628). Similarly, the time taken to complete the incision and incision-related blood loss was significantly less with diathermy incisions (95% CI = 0.245-0.502 and 0.548-1.020, respectively). CONCLUSION: Diathermy incisions are equally prone to get wound infection, as do the incisions made with scalpel. Furthermore, lower incidence of early postoperative pain, swiftness of the technique, and a reduced blood loss are the encouraging facts supporting routine use of diathermy for abdominal skin incisions after taking careful precautions.

  9. C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA.

    Science.gov (United States)

    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.

  10. A Model of H-NS Mediated Compaction of Bacterial DNA

    NARCIS (Netherlands)

    Joyeux, M.; Vreede, J.

    2013-01-01

    The histone-like nucleoid structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA duplexes, or in cis, by binding to different sites on the same

  11. Minimal incision surgery in strabismus: Modified fornix-based approach.

    Science.gov (United States)

    Pérez-Flores, I

    2016-07-01

    To evaluate the modified fornix-based technique as an approach for minimal incision surgery in strabismus. The medical records of all consecutive patients that underwent strabismus surgery with fornix-based conjunctival incision between 2007 and 2012 were retrospectively reviewed. As a primary variable, an analysis was made of the wound size depending on the number of stitches. A descriptive study was performed on the variables related to patients and to the type of strabismus and surgery. Out of 153patients identified, 138 with 294 surgeries were included. In 200 (68%) interventions, the incision was sutured with one stitch, in 77 (26.2%) with 2, in 13 (4.4%) with 3, and in 4 (1.4%) with 4, with the mean number of stitches being 1.39±0.64. The mean age of the patients was 39years (2-80), and 36 (26.1%) had previous strabismus surgery, with topical anaesthesia being used in 35 (25.4%) cases. At 3months after surgery deviation was ≤10DP in 114 (82.6%) patients. There were no wound-related complications. The modified fornix-based technique is an effective and safe approach for minimal incision surgery in strabismus, in patients at all ages, with previous history of strabismus surgery and with topical anaesthesia. Copyright © 2015 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.

  12. Phenomenon of mucous retention in the incisive canal.

    Science.gov (United States)

    Keith, D A

    1979-11-01

    Mucous glands are rarely found in the anterior palate but may be observed in the incisive canal. A case history is presented of a lesion that resembled a nasopalatine cyst both clinically and radiographically but which was in fact an intra-bony extravasation phenomenon.

  13. Heterotopic ossification in abdominal incision : a case report

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Yoon Sik; Nam, Kung Sook; Hwang, Im Kyung; Kim, Heung Chul [College of Medicine, Hallym Univ., Chuncheon (Korea, Republic of)

    2001-08-01

    Heterotopic ossification in abdominal incision is a rare post-surgical sequala and a subtype of myositis ossificans traumatica. Recognition of this rare condition is important because it may be misinterpreted as a retained foreign body or incisional neoplastic recurrence. We report a case involving a 59-year-old man who presented with a palpable epigastric mass and pronounced fatigability.

  14. Tubularized incised plate technique for recurrent hypospadias: a ...

    African Journals Online (AJOL)

    management of recurrent hypospadias. Summary background ... The potential advantages of tubularized incised plate .... after a mean duration of 4.9 ± 3.1 years from the previous repair (Table 2). .... erection and the risk of infection, especially in patients older than 15 .... However, previous surgery often limits the availability ...

  15. Ultrasonic diagnosis and transurethral incision of ureterocele with hydronephrosis

    DEFF Research Database (Denmark)

    Waaddegaard, P; Miskowiak, J; Stage, P

    1991-01-01

    In a 65-year-old woman with right-sided loin pain, ultrasonography revealed a grossly dilated and obstructed right pyelogram due to a 50-mm ureterocele. After transurethral lateral incision of the ureterocele, there was complete recovery without vesicoureteric reflux. Ultrasonography is advantage...

  16. Single-incision laparoscopic cholecystectomy with needle graspers.

    Science.gov (United States)

    Sumiyoshi, Kinjiro; Sato, Norihiro; Akagawa, Shin; Hirano, Tatsuya; Koikawa, Kazuhiro; Horioka, Kohei; Ozono, Keigo; Fujiwara, Kenji; Tanaka, Masao; Sada, Masayuki

    2012-01-01

    Single-incision laparoscopic cholecystectomy (SILC) is a promising alternative to standard multi-incision laparoscopic cholecystectomy (LC). However, generalization of SILC is still hampered by technical difficulties mainly associated with the lack of trocars used for retraction of the gallbladder. We therefore developed a modified method of SILC with the use of needle graspers (SILC-N) for optimal retraction and exposure. In addition to two trocars inserted through a single transumbilical incision, two needle ports were placed on the right subcostal and lateral abdominal wall, through which needle graspers were used for retraction of the gallbladder. Since December, 2009, 12 patients with symptomatic cholelithiasis were treated by SILC-N. SILC-N was successfully performed in all but one patient requiring a conversion to the 4-port LC with a mean operative time of 71.5 (48-107) minutes. None of the patients experienced intraoperative or postoperative complications. The transumbilical incision and pinholes for needle graspers were almost invisible on discharge. Our preliminary results suggest that SILC-N is a simple, safe and feasible technique of cholecystectomy offering similar postoperative recovery and better cosmetic outcome as compared to conventional LC.

  17. Single-incision laparoscopic surgery for pyloric stenosis.

    Science.gov (United States)

    Kozlov, Yury; Novogilov, Vladimir; Podkamenev, Alexey; Rasputin, Andrey; Weber, Irina; Solovjev, Alexey; Yurkov, Pavel

    2012-04-01

    Laparoscopy is the most common procedure for correction of congenital pyloric stenosis. The standard laparoscopic approach is based on the three-port technique. In contrast to the standard laparoscopic technique, the single-incision laparoscopic surgery (SILS) requires only one incision. We report on our experience with this surgical approach. Between September 2009 and August 2010 a total of 24 children underwent a laparoscopic pyloromyotomy, 12 in SILS technique. The single incision was carried through the center of the umbilicus. The working instruments were introduced in a two-dimensional direction into the peritoneal cavity via the same umbilical incision. The two groups were compared for patients' demographics, operative report and early postoperative outcomes. All SILS procedures were performed successfully with no conversion rate. There were no differences in the preoperative parameters between the two groups regarding age before surgery and body weight at operation. Operative time and time of full enteral intake was similar to comparable procedures with usage of a standard laparoscopic approach. There were no operative or postoperative complications. The early experience described in this study confirms that SILS can be applied for treatment of pyloric stenosis with outcomes similar to the standard laparoscopic surgery.

  18. Cost assessment of instruments for single-incision laparoscopic cholecystectomy

    DEFF Research Database (Denmark)

    Henriksen, Nadia A; Al-Tayar, Haytham; Rosenberg, Jacob

    2012-01-01

    Specially designed surgical instruments have been developed for single-incision laparoscopic surgery, but high instrument costs may impede the implementation of these procedures. The aim of this study was to compare the cost of operative implements used for elective cholecystectomy performed...

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

    Directory of Open Access Journals (Sweden)

    Wilson Zoe A

    2008-06-01

    Full Text Available Abstract 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.

  20. THE INFLUENCE OF POSTHEAT TREATMENT ON FERRITE REDISTRIBUTION IN DUPLEX STEELS ELECTRON BEAM WELDS

    OpenAIRE

    Zita Iždinská; František Kolenič

    2009-01-01

    The duplex stainless steel is two-phase steel with the structure composed of austenite and ferrite with optimum austenite/ferrite proportion 50%. At present, classical arc processes for welding duplex steels are generally regarded as acceptable. On the other hand electron and laser beam welding is up to now considered less suitable for welding duplex steels. The submitted work presents the results of testing various thermal conditions at welding duplex stainless steel with electron beam. It w...

  1. [External periareolar incision for subdermal mastectomy in men with gynecomastia].

    Science.gov (United States)

    Montiel-Jarquín, Alvaro; Reyes-Páramo, Pedro; Ramos-Alvarez, Gloria; López-Colombo, Aurelio; Tinajero-Esquivel, Magdalena; Ruiz-León, Betzabé

    2007-01-01

    Gynecomastia describes a benign increase of the mammary gland in men. When medical treatment fails, symptoms and psychological alterations persist. Subdermal mastectomy is the definitive treatment and can be achieved by different incisions, each with potential complications. We undertook this study to present clinical characteristics of 11 patients with gynecomastia and the results obtained with subdermal mastectomy by means of external periareolar incision. A descriptive cohort study in male patients with gynecomastia was carried out in a third-level medical care hospital. Patients were treated with subdermal mastectomy by means of external periareolar incision. There were 11 male patients with an average age of 19 years (range: 11-60 years), 3 patients (27.2%) with bilateral gynecomastia and 8 patients (72.7%) with unilateral gynecomastia. Average time of evolution was 22 months (range: 16-48 months), 9 patients (81.8%) reported pain, 11 patients (100%) reported psychological alterations with cutaneous alteration, 11 patients (100%) had normal secondary sexual characteristics, 1 patient (9%) had supernumerary nipple development, and 11 patients (100%) had well-defined lesions. According to Simon's classification: seven patients (63.6%) were classified as grade 1, three patients (27.2%) as grade 2 and one patient (9.09%) as grade 3. Each patient had a subdermal mastectomy with external periareolar incision, 11 patients (100%) had a histopathological report of gynecomastia; 1 patient (9.09%) displayed keloid healing and none displayed complications inherent to the surgical procedure. Mastectomy by means of external periareolar incision is useful in the treatment of gynecomastia.

  2. Analysing Self Interference Cancellation in Full Duplex Radios

    DEFF Research Database (Denmark)

    Mahmood, Nurul Huda; Shafique Ansari, Imran; Berardinelli, Gilberto

    2016-01-01

    Full duplex communication promises a theoretical $100\\%$ throughput gain by doubling the number of simultaneous transmissions. Such compelling gains are conditioned on perfect cancellation of the self interference power resulting from simultaneous transmission and reception. Generally, self...... interference power is modelled as a noise-like constant level interference floor. However, experimental validations have shown that the self interference power is in practice a random variable depending on a number of factors such as the surrounding wireless environment and the degree of interference...... cancellation. In this study, we derive an analytical model for the residual self interference power, and demonstrate various applications of the derived model in analysing the performance of a Full Duplex radio. In general, full duplex communication is found to provide only modest throughput gains over half...

  3. CMOS serial link for fully duplexed data communication

    Science.gov (United States)

    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.

  4. Features of residual stresses in duplex stainless steel butt welds

    Science.gov (United States)

    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.

  5. DNA interactions with a Methylene Blue redox indicator depend on the DNA length and are sequence specific.

    Science.gov (United States)

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

    2010-06-01

    A DNA molecular beacon approach was used for the analysis of interactions between DNA and Methylene Blue (MB) as a redox indicator of a hybridization event. DNA hairpin structures of different length and guanine (G) content were immobilized onto gold electrodes in their folded states through the alkanethiol linker at the 5'-end. Binding of MB to the folded hairpin DNA was electrochemically studied and compared with binding to the duplex structure formed by hybridization of the hairpin DNA to a complementary DNA strand. Variation of the electrochemical signal from the DNA-MB complex was shown to depend primarily on the DNA length and sequence used: the G-C base pairs were the preferential sites of MB binding in the duplex. For short 20 nts long DNA sequences, the increased electrochemical response from MB bound to the duplex structure was consistent with the increased amount of bound and electrochemically readable MB molecules (i.e. MB molecules that are available for the electron transfer (ET) reaction with the electrode). With longer DNA sequences, the balance between the amounts of the electrochemically readable MB molecules bound to the hairpin DNA and to the hybrid was opposite: a part of the MB molecules bound to the long-sequence DNA duplex seem to be electrochemically mute due to long ET distance. The increasing electrochemical response from MB bound to the short-length DNA hybrid contrasts with the decreasing signal from MB bound to the long-length DNA hybrid and allows an "off"-"on" genosensor development.

  6. The width of the incisive canal and labial alveolar bone of the incisive canal: an assessment on CT images

    International Nuclear Information System (INIS)

    Roh, Yang Gyun; Jang, Hyun Seon; Kim, Byung Ock; Kim, Jin Soo

    2006-01-01

    To assess the width of the labial alveolar bone of the incisive canal and the width of the incisive canal on spiral computed tomographic images of the anterior portion of the maxilla. Study materials included 38 CT scans taken for preoperative planning of implant placement. Axial cross-sectioned image entirely showing the incisive canal at an orifice to the oral cavity, middle portion, and an orifice to the nasal cavity and the diameter of the incisive canal at the middle portion were determined by two specialist using Digora for Windows 2.1. The statistical analyses were carried out using SPSS 12.0.1. When the maxillary central incisors remained, the mean labial alveolar bone width were 6.81±1.41 mm, 6.46±1.33 mm, and 7.91±1.33 mm. When the maxillary central incisors were missed the mean width were 5.42±2.20 mm, 6.23±2.29 mm, and 7.89±2.13 mm. The labial alveolar bone width at middle portion and an orifice to the nasal cavity were of no statistical significant difference according to presence of the maxillary central incisors (P>0.05). The width between oral cavity and nasal cavity, middle portion and to masal cavity revealed statistically significant difference (P<0.05)

  7. Incisional hernia after upper abdominal surgery: A randomised controlled trial of midline versus transverse incision

    NARCIS (Netherlands)

    J.A. Halm (Jens); H. Lip (Harm); P.I.M. Schmitz (Paul); J. Jeekel (Hans)

    2009-01-01

    textabstractObjectives: To determine whether a transverse incision is an alternative to a midline incision in terms of incisional hernia incidence, surgical site infection, postoperative pain, hospital stay and cosmetics in cholecystectomy. Summary background data: Incisional hernias after midline

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

    Science.gov (United States)

    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.

  9. Comparison of simulated and measured quantities of a duplex reactor

    Energy Technology Data Exchange (ETDEWEB)

    Koskela, M.; Kajava, M. [ABB Marine, Helsinki (Finland)

    1997-12-31

    The purpose of this article is to illustrate the use of an analog simulator as a design tool when designing new power electric equipment. The purpose of simulation is to predict the functionality of electrical equipment to be constructed. Duplex reactor is an electromagnetic device designed to reduce voltage harmonics and short circuit currents in the ship electrical network. In this report a comparison between simulated and measured electrical quantities of a duplex reactor has been made. The purpose of the measurements was to show the correct functioning of the reactor. The simulation results and the measured waveforms corresponds well to each other. (orig.) 4 refs.

  10. Mechanical properties of welded joints of duplex steels

    International Nuclear Information System (INIS)

    Kawiak, M.; Nowacki, J.

    2003-01-01

    The paper presents the study results of mechanical properties of duplex steels UNS S31803 welded joints as well as duplex and NV A36 steels welded joints. They have ben welded by FCAW method in CO 2 using FCW 2205-H flux-cored wire. The joints have been subjected: tensile tests, impact tests, bending tests, hardness tests and metallographic investigations. The influence of welding parameters and mechanical properties of the joints was appreciated. The welding method assured high tensile strength of the joints (approximately 770 MPa) and high impact strength of the welds (approximately 770 J). All samples were broken outside of welds. (author)

  11. Duplex sonography of the near-surface leg veins

    International Nuclear Information System (INIS)

    Mendoza, E.

    2007-01-01

    The book contains the following contributions: The ultrasonograph, selection of the ultrasonic transducer, anatomy of the near-surface vein system, physiology of the near-surface vein system, varicose status classification, systematics of the duplex sonography of near-surface leg veins, provocational maneuver for the duplex sonographic varicose diagnostics, exploration of vena saphena parva, perforans veins, side branches, phlebitis, sonography for varicose therapy, postsurgical sonography, deep leg veins, examination of near-surface leg veins for the pathology of the deep vein system, differential diagnostic clarification of leg oedema from the phlebologic-lymphological view, diagnostic side features along the near-surface leg veins

  12. Reducing duplex examinations in patients with iatrogenic pseudoaneurysms.

    Science.gov (United States)

    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) (IPSAs (>2.5 cm). We evaluated the impact of a revised treatment algorithm that includes primary treatment of both small (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 (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

  13. In situ detection of tandem DNA repeat length

    Energy Technology Data Exchange (ETDEWEB)

    Yaar, R.; Szafranski, P.; Cantor, C.R.; Smith, C.L. [Boston Univ., MA (United States)

    1996-11-01

    A simple method for scoring short tandem DNA repeats is presented. An oligonucleotide target, containing tandem repeats embedded in a unique sequence, was hybridized to a set of complementary probes, containing tandem repeats of known lengths. Single-stranded loop structures formed on duplexes containing a mismatched (different) number of tandem repeats. No loop structure formed on duplexes containing a matched (identical) number of tandem repeats. The matched and mismatched loop structures were enzymatically distinguished and differentially labeled by treatment with S1 nuclease and the Klenow fragment of DNA polymerase. 7 refs., 4 figs.

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

    Science.gov (United States)

    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

  15. What can we learn from fluvial incision in high mountains?

    Science.gov (United States)

    Fuchs, Margret; Gloaguen, Richard; Krbetschek, Matthias

    2013-04-01

    High and actively deforming mountain ranges attract the attention of geoscientists as they provide natural laboratories of fast evolving process-response systems. Tectonic compressional settings, often linked to perpendicular extension, control the topographic growth and hence, erosion, transport pathways and sedimentation. High altitude differences within short horizontal distances promote material re-organisation and high rates of surface processes. Furthermore, high mountains constitute orographic barriers that affect atmospheric circulations as well as host different climate regimes similar to those of widely separated latitudinal belts. Both cause a high sensitivity of surface processes to changes in climatic conditions. However, feedbacks between climatic and tectonic forcing are complex. Additionally, the dominance of one or the other varies in space and also over time, inheriting various traces of the paleo-morphodynamic conditions to the subsequent process regimes. To unravel the forces driving the evolution of relief in active mountains, numerous studies employ the drainage network of the corresponding mountains as a proxy of landscape evolution. Especially the rates of river incision provide a powerful tool to characterize the surface response and infer causes behind it. Several parameters of river incision are available to describe the fluvial incision at individual sites (e.g. terrace incision rates), along the river course (e.g. longitudinal river profiles, Hack index) and in its perpendicular dimension (e.g. valley cross sections, valley shape ratios). But they require careful interpretation. They are sensitive to both, climatic and tectonic forcing. Therefore, the synopsis of such indices for fluvial incision is essential to evaluate the role of climatic versus tectonic forcing. Here, we use the Panj river system, the major river draining the Pamir mountains of Central Asia, as an example. The Panj experiences high altitude changes of more than 4000

  16. Channel incision and suspended sediment delivery at Caspar Creek, Mendocino County, California

    Science.gov (United States)

    Nicholas J. Dewey; Thomas E. Lisle; Leslie M. Reid

    2003-01-01

    Tributary and headwater valleys in the Caspar Creek watershed,in coastal Mendocino County, California,show signs of incision along much of their lengths.An episode of incision followed initial-entry logging which took place between 1860 and 1906. Another episode of incision cut into skid-trails created for second-entry logging in the 1970's.

  17. Enzymatic recognition of DNA replication origins

    International Nuclear Information System (INIS)

    Stayton, M.M.; Bertsch, L.; Biswas, S.

    1983-01-01

    In this paper we discuss the process of recognition of the complementary-strand origin with emphasis on RNA polymerase action in priming M13 DNA replication, the role of primase in G4 DNA replication, and the function of protein n, a priming protein, during primosome assembly. These phage systems do not require several of the bacterial DNA replication enzymes, particularly those involved in the regulation of chromosome copy number of the initiatiion of replication of duplex DNA. 51 references, 13 figures, 1 table

  18. Equilibrious Strand Exchange Promoted by DNA Conformational Switching

    Science.gov (United States)

    Wu, Zhiguo; Xie, Xiao; Li, Puzhen; Zhao, Jiayi; Huang, Lili; Zhou, Xiang

    2013-01-01

    Most of DNA strand exchange reactions in vitro are based on toehold strategy which is generally nonequilibrium, and intracellular strand exchange mediated by proteins shows little sequence specificity. Herein, a new strand exchange promoted by equilibrious DNA conformational switching is verified. Duplexes containing c-myc sequence which is potentially converted into G-quadruplex are designed in this strategy. The dynamic equilibrium between duplex and G4-DNA is response to the specific exchange of homologous single-stranded DNA (ssDNA). The SER is enzyme free and sequence specific. No ATP is needed and the displaced ssDNAs are identical to the homologous ssDNAs. The SER products and exchange kenetics are analyzed by PAGE and the RecA mediated SER is performed as the contrast. This SER is a new feature of G4-DNAs and a novel strategy to utilize the dynamic equilibrium of DNA conformations.

  19. Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xi; Ballin, Jeff D.; Della-Maria, Julie; Tsai, Miaw-Sheue; White, Elizabeth J.; Tomkinson, Alan E.; Wilson, Gerald M.

    2009-05-11

    The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIII{beta} and the hLigIII{alpha}/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.

  20. Penetrating and Intrastromal Corneal Arcuate Incisions in Rabbit and Human Cadaver Eyes: Manual Diamond Blade and Femtosecond Laser-Created Incisions.

    Science.gov (United States)

    Gray, Brad; Binder, Perry S; Huang, Ling C; Hill, Jim; Salvador-Silva, Mercedes; Gwon, Arlene

    2016-07-01

    To compare morphologic differences between freehand diamond or femtosecond laser-assisted penetrating and intrastromal arcuate incisions. Freehand diamond blade, corneal arcuate incisions (180° apart, 60° arc lengths) and 150 kHz femtosecond laser (80% scheimpflug pachymetry depth corneal thickness) arcuate incisions were performed in rabbits. Intrastromal arcuate incisions (100 μm above Descemet's membrane, 100 μm below epithelium) were performed in rabbit corneas (energy 1.2 μJ, spot line separation 3 × 3 μm, 90° side cut angle). Eyes were examined by slit lamp and light microscopy up to 47 days post-procedure. Freehand diamond blade penetrating incisions, and femtosecond laser penetrating and intrastromal arcuate incisions (energy 1.8 μJ, spot line separation 2 × 2 μm) were performed in cadaver eyes. Optical coherence tomography was performed immediately after surgery and the corneas were fixed for light scanning and transmission electron microscopy. The rabbit model showed anterior stromal inflammation with epithelial hyperplasia in penetrating blade and laser penetrating wounds. The laser intrastromal and penetrating incisions showed localized constriction of the stromal layers of the cornea near the wound. In cadaver eyes, penetrating wound morphology was similar between blade and laser whereas intrastromal wounds did not affect the cornea above or below incisions. Penetrating femtosecond laser arcuate incisions have more predictable and controlled outcomes shown by less post-operative scarring than incisions performed with a diamond blade. Intrastromal incisions do not affect uncut corneal layers as demonstrated by histopathology. The femtosecond laser has significant advantages in its ability to make intrastromal incisions which are not achievable by traditional freehand or mechanical diamond blades.

  1. DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae

    Science.gov (United States)

    Boiteux, Serge; Jinks-Robertson, Sue

    2013-01-01

    DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage. PMID:23547164

  2. Incisive papilla and positions of maxillary anterior teeth among ...

    African Journals Online (AJOL)

    Results: One hundred and twelve maxillary casts generated from participants aged 18-35 years (mean age 22.39±2.00 years), with well aligned arches were studied. The maxillary central incisor exhibited a mean of 14.93±1.52mm from the posterior limit of the incisive papilla while the inter-canine line scored a mean of ...

  3. Optimisation of welding procedures for duplex and superduplex stainless steels

    International Nuclear Information System (INIS)

    Westin, Elin M.

    2014-01-01

    Austenitic stainless steels are increasingly being replaced by duplex grades that can offer similar corrosion resistance with far higher strength. This increased strength makes it possible to reduce material consumption whilst also decreasing transport and construction costs. Although established welding methods used for austenitic steels can be used for duplex steels, modification of the procedures can lead to improved results. This paper reviews the welding of duplex stainless steel and examines precautions that may be required. The advantages and disadvantages of different welding methods are highlighted and some high productivity solutions are presented. The application of a more efficient process with a high deposition rate (e.g. flux- cored arc welding) can decrease labour costs. Further close control of heat input and interpass temperature can result in more favourable microstructures and final properties. Although welding adversely affects the corrosion resistance of austenitic and duplex stainless steels, particularly the pitting resistance, relative to the parent material, this problem can be minimised by proper backing gas protection and subsequent pickling.

  4. A most spectrum-efficient duplexing system: CDD

    Science.gov (United States)

    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.

  5. Full-Duplex Relay Selection in Cognitive Underlay Networks

    KAUST Repository

    Khafagy, Mohammad Galal

    2017-09-30

    In this work, we analyze the performance of full-duplex relay selection (FDRS) in spectrum-sharing networks. Contrary to half-duplex relaying, full-duplex relaying (FDR) enables simultaneous listening/forwarding at the secondary relay(s), thereby allowing for a higher spectral efficiency. However, since the source and relay simultaneously transmit in FDR, their superimposed signal at the primary receiver should now satisfy the existing interference constraint, which can considerably limit the secondary network throughput. In this regard, relay selection can offer an adequate solution to boost the secondary throughput while satisfying the imposed interference limit. We first analyze the performance of opportunistic FDRS with residual self-interference (RSI) by deriving the exact cumulative distribution function of its end-to-end signal-to-interference-plus-noise ratio under Nakagami-m fading. We also evaluate the offered diversity gain of relay selection for different full-duplex cooperation schemes in the presence/absence of a direct source-destination link. When the adopted RSI link gain model is sublinear in the relay power, which agrees with recent research findings, we show that remarkable diversity gain can be recovered even in the presence of an interfering direct link. Second, we evaluate the end-to-end performance of FDRS with interference constraints due to the presence of a primary receiver. Finally, the presented exact theoretical findings are verified by numerical simulations.

  6. ON SECURE FULL DUPLEX COMMUNICATION IN MOBILE AD HOC NETWORK

    OpenAIRE

    S. C. Dutta; Sudha Singh; D. K. Singh

    2013-01-01

    This paper is to establish Ad Hoc network in mobile phones and start fully secured full duplex communication in any situation. This type of communication will be cost effective and it will be fastest way of communication in case of any server failure or server error.

  7. Reliability Capacity of Half-Duplex Channels with Strict Deadlines

    DEFF Research Database (Denmark)

    Costa, Rui; Roetter, Daniel Enrique Lucani; Vinhoza, Tiago

    2015-01-01

    A fundamental characterization of a half-duplex wireless system with packet losses under traffic with hard deadlines is instrumental to understanding and developing efficient, coding aware policies for real-time applications. We set forth the concept of reliability capacity with a limited number ...

  8. Corrosion behavior of duplex and reference cladding in NPP Grohnde

    International Nuclear Information System (INIS)

    Besch, O.A.; Yagnik, S.K.; Eucken, C.M.; Bradley, E.R.

    1996-01-01

    The Nuclear Fuel Industry Research (NFIR) Group undertook a lead test assembly (LTA) program in NPP Grohnde PWR in Germany to assess the corrosion performance of duplex and reference cladding. Two identical 16 by 16 LTAs, each containing 32 peripheral test rods, completed four reactor cycles, reaching a peak rod burnup of 46 MWd/kgU. The results from poolside examinations performed at the end of each cycle, together with power histories and coolant chemistry, are reported. Five different cladding materials were characterized during fabrication. The corrosion performance of the cladding materials was tracked in long-term tests in high-pressure, high-temperature autoclaves. The relative ranking of corrosion behavior in such tests corresponded well with the in-reactor corrosion performance. The extent and distribution of hydriding in duplex and reference specimens during the autoclave testing has been characterized. The in-reactor corrosion data indicate that the low-tin Zircaloy-4 reference cladding, R2, had an improved corrosion resistance compared to high-tin Zircaloy-4 reference cladding, R1. Two types of duplex cladding, D1 (Zr-2.5% Nb) and D2 (Zr-0.4% Fe-0.5% Sn), showed an even further improvement in corrosion resistance compared to R2 cladding. The third duplex cladding, D3 (Zr-4 + 1.0% Nb), had significantly less corrosion resistance, which was inferior to R1. The in-reactor and out-reactor corrosion performances have been ranked

  9. Comprehensive Educational Assessment for the States: The Duplex Design.

    Science.gov (United States)

    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…

  10. Podiatry Ankle Duplex Scan: Readily Learned and Accurate in Diabetes.

    Science.gov (United States)

    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.

  11. Full-duplex wireless communications systems self-interference cancellation

    CERN Document Server

    Le-Ngoc, Tho

    2017-01-01

    This book introduces the development of self-interference (SI)-cancellation techniques for full-duplex wireless communication systems. The authors rely on estimation theory and signal processing to develop SI-cancellation algorithms by generating an estimate of the received SI and subtracting it from the received signal. The authors also cover two new SI-cancellation methods using the new concept of active signal injection (ASI) for full-duplex MIMO-OFDM systems. The ASI approach adds an appropriate cancelling signal to each transmitted signal such that the combined signals from transmit antennas attenuate the SI at the receive antennas. The authors illustrate that the SI-pre-cancelling signal does not affect the data-bearing signal. This book is for researchers and professionals working in wireless communications and engineers willing to understand the challenges of deploying full-duplex and practical solutions to implement a full-duplex system. Advanced-level students in electrical engineering and computer ...

  12. LNA effects on DNA binding and conformation

    DEFF Research Database (Denmark)

    Pabon-Martinez, Y Vladimir; Xu, You; Villa, Alessandra

    2017-01-01

    -substitution in the duplex pyrimidine strand alters the double helix structure, affecting x-displacement, slide and twist favoring triplex formation through enhanced TFO major groove accommodation. Collectively, these findings should facilitate the design of potent anti-gene ONs.......The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand invading oligonucleotides to modulate gene expression. To be efficient, the oligonucleotides (ONs) should target DNA selectively, with high affinity. Here we combined...... hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures. Particularly, we investigated the role played by the position and number of locked...

  13. Perancangan dan Implementasi Duplexer Mikrostrip untuk Frekuensi LTE pada band ke-7

    Directory of Open Access Journals (Sweden)

    ENCENG SULAEMAN

    2013-07-01

    The necessary of mobile communication has increased in technology, now it released the new of technology is Long Term Evolution (LTE. Type of duplex is Frequency Division Duplex (FDD, designed a duplexer which it is capable for transmitting and receiving process at the same time with the different of frequency between uplink and downlink. Research of designed and implemented a duplexer using Hybrid Coupler and Bandstop filters based on Split Ring Resonators for the frequency band 7th on LTE technology at Base Transceiver Station (BTS. Duplexer is made by combining two coupler and two bandstop filter. The results of duplexer measurements, when Tx port transmit the signal to antenna port with attenuation at the downlink frequency center at 3.168 dB. Attenuation from antenna port to Rx port about 6 dB. Isolation between Tx port and Rx port about 15 dB. Keywords: Duplexer, Bandstop Filter, Split Ring Resonator, Hybrid Coupler, and Long Term Evolution.

  14. An evaluation of nuclear design characteristics of duplex burnable poison rods for extended cycle core

    International Nuclear Information System (INIS)

    Lee, D. J.; Kim, M. H.; Song, K. W.

    2003-01-01

    Nuclear design characteristics of duplex burnable poison rod were evaluated for three integral type burnable absorbers; Gadolinia, Erbia and IFBA. Inter-comparison was done for both 12 and 24 month cycle for Korean Standard Nuclear Plant. Fuel assemblies with duplex BP was designed to the equivalent assembly with 8 and 16 gadolinia BP 2 . Duplex BP is composed of inner region of natural U-Gd 2 O 3 , and outer shell of, UO 2 -Er2O 3 . In order to evaluate the duplex BP, assemblies with erbia and IFBA were compared with alternative options. A sensitivity studies were performed to the size of region, compositions and location of duplex BPs. It was shown that duplex BP gave favorable k-infinite curve to burnup, but IFBA provided the least residual reactivity penalty as EOC. Erbia was good for more negative MTCs. IFBA and erbia had better neutronic performance than gadolinia od duplex BP in the aspect of pin power peaking

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

    Science.gov (United States)

    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.

  16. Manual small incision extracapsular cataract surgery in Australia.

    Science.gov (United States)

    van Zyl, Lourens; Kahawita, Shyalle; Goggin, Michael

    2014-11-01

    Examination of the results and describing the technique of manual small incision extracapsular cataract extraction on patients with advanced cataracts in urban Australia. A descriptive case series. Thirty-eight patients at three public hospitals, one tertiary and two secondary ophthalmic units in urban Australia. Forty eyes with dense mature cataracts with hand movement vision or worse underwent a planned manual small incision extracapsular cataract extraction instead of traditional phaco-emulsification. Postoperative visual aquity, surgically induced astigmatism and complications. Seventy-eight per cent of patients had an uncorrected visual acuity of 6/12 or better on the first postoperative day. Eighty-three per cent of patients had a distance corrected visual acuity of 6/9 or better 3 months postoperatively. One case was complicated by a posterior capsule rupture. No cases of endophthalmitis were reported. The summated vector mean of the surgically induced astigmatism was 0.089D at 93°. Manual small incision extracapsular cataract extraction is an efficacious cataract surgery technique with good visual outcome and is a safe alternative to phaco-emulsification in suitable cases in a first-world setting. © 2014 Royal Australian and New Zealand College of Ophthalmologists.

  17. Single incision thoracoscopic sympathectomy for palmar and axillary hyperhidrosis

    Directory of Open Access Journals (Sweden)

    Aram Baram

    2014-02-01

    Full Text Available Background: Primary hyperhidrosis is characterized by excessive sweating beyond physiological needs. It is a common disease (incidence 2.8% that causes intense discomfort for patients. In the last decade, advantages of Single-Incision Thoracoscopic Sympathectomy have become clear, particularly in decreasing morbidity of sympathectomy. Patients and methods: From January 2010 to December 2012, 39 patients (29 females and 10 males with primary palmar or axillary hyperhidrosis were treated by thoracoscopic sympathectomy. The age ranged from 18 to 40 years with a mean of 26.28 years. We used single incision thoracoscopic electrocoagulation through 10 mm incision for thoracic sympathetic chain (T2–T4. Results: The mean follow-up was 23.6 ± 14.2 months (range = 4–24 months. A total of 97.42% of patients were satisfied with the results. A total of 72.5% of patients had cure, one patient (2.5% and another patient (2.5% presented with recurrent axillary hyperhidrosis. The morbidity was 10.2% with no mortality. Percentage of compensatory sweating and gustatory sweating were 5.1% (p = .353 and 2.5% (p = .552, respectively. The result of sympathectomy in patients with both palmar and axillary hyperhidrosis was significantly better (17, 43.58% compared to palmar type (14, 35.89% or axillary type (7, 17.94%. Conclusion: Thoracoscopic sympathectomy is a simple, safe, and cost-effective therapy with good results and low complications.

  18. 6-Thioguanine alters the structure and stability of duplex DNA and inhibits quadruplex DNA formation.

    OpenAIRE

    Marathias, V M; Sawicki, M J; Bolton, P H

    1999-01-01

    The ability to chemically synthesize biomolecules has opened up the opportunity to observe changes in structure and activity that occur upon single atom substitution. In favorable cases this can provide information about the roles of individual atoms. The substitution of 6-thioguanine (6SG) for guanine is a potentially very useful single atom substitution as 6SG has optical, photocrosslinking, metal ion binding and other properties of potential utility. In addition, 6-mercaptopurine is a clin...

  19. Molecular mechanisms of DNA photodamage

    Energy Technology Data Exchange (ETDEWEB)

    Starrs, S.M

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA){sub n} and (GA){sub n}, and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a

  20. Molecular mechanisms of DNA photodamage

    International Nuclear Information System (INIS)

    Starrs, S.M.

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA) n and (GA) n , and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a dimeric

  1. Development of a one-step duplex RT-qPCR for the quantification of phocine distemper virus.

    Science.gov (United States)

    Bogomolni, Andrea L; Frasca, Salvatore; Matassa, Keith A; Nielsen, Ole; Rogers, Kara; De Guise, Sylvain

    2015-04-01

    Worldwide, stranded marine mammals and the network personnel who respond to marine mammal mortality have provided much of the information regarding marine morbillivirus infections. An assay to determine the amount of virus present in tissue samples would be useful to assist in routine surveying of animal health and for monitoring large-scale die-off events. False negatives from poor-quality samples prevent determination of the true extent of infection, while only small amounts of tissue samples or archived RNA may be available at the time of collection for future retrospective analysis. We developed a one-step duplex real-time reverse transcriptase-quantitative-PCR assay (RT-qPCR) based on Taqman probe technology to quantify phocine distemper virus (PDV) isolated from an outbreak in harbor (Phoca vitulina concolor) and gray seals (Halichoerus grypus) along the northeast US coast in 2006. The glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) gene was selected to assess RNA quality. This duplex assay is specific for PDV and sensitive through a range of 10(0) to 10(9) copies ds-plasmid DNA. For the GAPDH target, the reaction in duplex amplified 10(0) to 10(9) copies of ds-plasmid DNA and was detectable in multiple seal species. This assay reduced the likelihood of false negative results due to degradation of tissues and well-to-well variability while providing sensitive and specific detection of PDV, which would be applicable in molecular epidemiologic studies and pathogen detection in field and laboratory investigations involving a variety of seal species.

  2. Sensitivity of the green alga Pediastrum duplex Meyen to allelochemicals is strain-specific and not related to co-occurrence with allelopathic macrophytes.

    Directory of Open Access Journals (Sweden)

    Falk Eigemann

    Full Text Available Interspecific differences in the response of microalgae to stress have numerous ecological implications. However, little is known of intraspecific sensitivities and the potential role of local genetic adaptation of populations. We compared the allelochemical sensitivity of 23 Pediastrum duplex Meyen strains, a common component of the freshwater phytoplankton. In order to test for local genetic adaptation, strains were isolated from water bodies with and without the allelopathically-active submerged macrophyte Myriophyllum. Strains were assigned to P. duplex on the basis of cell shape and colony morphology and only P. duplex strains that belonged to the same lineage in an ITS rDNA phylogeny were used. Inhibition of strain growth rates and maximum quantum yields of photosystem II were measured after exposure to tannic acid (TA and co-culture with Myriophyllum spicatum. Growth rate inhibition varied over one order of magnitude between the P. duplex strains. There was no correlation between the presence of Myriophyllum in the source location and the sensitivity of the strains to TA or the presence of Myriophyllum, suggesting that at least strong unidirectional local adaptation to Myriophyllum had not taken place in the studied water bodies. The maximum quantum yield of photosystem II of TA exposed algae decreased, whereas the yield of algae exposed to M. spicatum was slightly higher than that of the controls. The ranking of P. duplex strain sensitivities differed between the types of exposure (single additions of TA versus co-existence with M. spicatum and the parameter measured (growth rate versus maximum quantum yield, emphasizing the importance of measuring multiple traits when analysing strain-specific sensitivities towards allelochemicals. The observation that sensitivities to allelochemicals vary widely among strains of a single freshwater algal species should be taken into account if evaluating ecological consequences of allelopathic

  3. In vivo architectural analysis of clear corneal incisions using anterior segment optical coherence tomography.

    Science.gov (United States)

    Dupont-Monod, Sylvère; Labbé, Antoine; Fayol, Nicolas; Chassignol, Alexis; Bourges, Jean-Louis; Baudouin, Christophe

    2009-03-01

    To use anterior segment optical coherence tomography (AS-OCT) to analyze the in vivo architecture of clear corneal incisions after phacoemulsification using different techniques. Department of Ophthalmology, Quinze-Vingts National Ophthalmology Hospital, Paris, France. This prospective observational study analyzed clear corneal incisions used in phacoemulsification. All wounds were evaluated 1 day and 8 days postoperatively by AS-OCT (Visante). Incision architecture and pachymetry at the wound level were analyzed. Thirty-five clear corneal incisions were analyzed. Six eyes had 2.75 mm coaxial phacoemulsification, 19 had 2.20 mm microincision coaxial phacoemulsification, and 10 had 1.30 mm bimanual microincision phacoemulsification. The 1.30 mm incision had a straight-line configuration. The 2.20 mm and 2.75 mm incisions had an arcuate configuration. The angles of incidence of 1.30 mm incisions were greater than those of 2.20 mm incisions (P<.001). All incisions had slight corneal edema limited to the incision area. The edema was slightly greater around 1.30 mm incisions (mean pachymetry 1143 microm +/- 140 [SD]) than around 2.20 mm incisions (mean 1012 +/- 101 microm) (P = .001). Bimanual procedures had satisfactory endothelial apposition in the enlarged areas, where stromal edema was less than that surrounding the unenlarged 1.30 mm incisions. The 3 phacoemulsification techniques induced gaping of the endothelial edge, minor inadequate endothelial apposition, and mild stromal edema in the area of the clear corneal incisions. Bimanual microincision sleeveless phacoemulsification may alter the wound slightly more than coaxial 2.75 mm and microcoaxial 2.20 mm sleeved-tip phacoemulsification.

  4. A Simultaneous Analytical Method for Duplex Identification of Porcine and Horse in the Meat Products by EvaGreen based Real-time PCR

    OpenAIRE

    Sakalar, Erg?n; Erg?n, Seyma ?z?irak; Akar, Emine

    2015-01-01

    A duplex real-time polymerase chain reaction (PCR) based assay for the detection of porcine and horse meat in sausages was designed by using EvaGreen fluorescent dye. Primers were selected from mitochondrial 12S rRNA and 16S rRNA genes which are powerful regions for identification of horse and porcine meat. DNA from reference samples and industrial products was successfully extracted using the GIDAGEN? Multi-Fast DNA Isolation Kit. Genomes were identified based on their specific melting peaks...

  5. Watson-Crick base pairing controls excited-state decay in natural DNA.

    Science.gov (United States)

    Bucher, Dominik B; Schlueter, Alexander; Carell, Thomas; Zinth, Wolfgang

    2014-10-13

    Excited-state dynamics are essential to understanding the formation of DNA lesions induced by UV light. By using femtosecond IR spectroscopy, it was possible to determine the lifetimes of the excited states of all four bases in the double-stranded environment of natural DNA. After UV excitation of the DNA duplex, we detected a concerted decay of base pairs connected by Watson-Crick hydrogen bonds. A comparison of single- and double-stranded DNA showed that the reactive charge-transfer states formed in the single strands are suppressed by base pairing in the duplex. The strong influence of the Watson-Crick hydrogen bonds indicates that proton transfer opens an efficient decay path in the duplex that prohibits the formation or reduces the lifetime of reactive charge-transfer states. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. DNA-repair measurements by use of the modified comet assay

    DEFF Research Database (Denmark)

    Godschalk, Roger W L; Ersson, Clara; Riso, Patrizia

    2013-01-01

    The measurement of DNA-repair activity by extracts from cells or tissues by means of the single-cell gel electrophoresis (comet) assay has a high potential to become widely used in biomonitoring studies. We assessed the inter-laboratory variation in reported values of DNA-repair activity...... on substrate cells that had been incubated with Ro19-8022 plus light to generate oxidatively damaged DNA. Eight laboratories assessed the DNA-repair activity of three cell lines (i.e. one epithelial and two fibroblast cell lines), starting with cell pellets or with cell extracts provided by the coordinating...... laboratory. There was a large inter-laboratory variation, as evidenced by the range in the mean level of repair incisions between the laboratory with the lowest (0.002incisions/10(6)bp) and highest (0.988incisions/10(6)bp) incision activity. Nevertheless, six out of eight laboratories reported the same cell...

  7. DNA translocation by human uracil DNA glycosylase: the case of single-stranded DNA and clustered uracils.

    Science.gov (United States)

    Schonhoft, Joseph D; Stivers, James T

    2013-04-16

    Human uracil DNA glycosylase (hUNG) plays a central role in DNA repair and programmed mutagenesis of Ig genes, requiring it to act on sparsely or densely spaced uracil bases located in a variety of contexts, including U/A and U/G base pairs, and potentially uracils within single-stranded DNA (ssDNA). An interesting question is whether the facilitated search mode of hUNG, which includes both DNA sliding and hopping, changes in these different contexts. Here we find that hUNG uses an enhanced local search mode when it acts on uracils in ssDNA, and also, in a context where uracils are densely clustered in duplex DNA. In the context of ssDNA, hUNG performs an enhanced local search by sliding with a mean sliding length larger than that of double-stranded DNA (dsDNA). In the context of duplex DNA, insertion of high-affinity abasic product sites between two uracil lesions serves to significantly extend the apparent sliding length on dsDNA from 4 to 20 bp and, in some cases, leads to directionally biased 3' → 5' sliding. The presence of intervening abasic product sites mimics the situation where hUNG acts iteratively on densely spaced uracils. The findings suggest that intervening product sites serve to increase the amount of time the enzyme remains associated with DNA as compared to nonspecific DNA, which in turn increases the likelihood of sliding as opposed to falling off the DNA. These findings illustrate how the search mechanism of hUNG is not predetermined but, instead, depends on the context in which the uracils are located.

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  9. Full-Duplex Communications in Large-Scale Cellular Networks

    KAUST Repository

    AlAmmouri, Ahmad

    2016-04-01

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization and efficiency. However, the penetration of FD communications to the cellular networks domain is challenging due to the imposed uplink/downlink interference. This thesis presents a tractable framework, based on stochastic geometry, to study FD communications in multi-tier cellular networks. Particularly, we assess the FD communications effect on the network performance and quantify the associated gains. The study proves the vulnerability of the uplink to the downlink interference and shows that the improved FD rate gains harvested in the downlink (up to 97%) comes at the expense of a significant degradation in the uplink rate (up to 94%). Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between the uplink and the downlink frequency bands. We derive the required conditions to harvest rate gains from the α-duplex scheme and show its superiority to both the FD and half-duplex (HD) schemes. In particular, we show that the α-duplex scheme provides a simultaneous improvement of 28% for the downlink rate and 56% for the uplink rate. We also show that the amount of the overlap can be optimized based on the network design objective. Moreover, backward compatibility is an essential ingredient for the success of new technologies. In the context of in-band FD communication, FD base stations (BSs) should support HD users\\' equipment (UEs) without sacrificing the foreseen FD gains. The results show that FD-UEs are not necessarily required to harvest rate gains from FD-BSs. In particular, the results show that adding FD-UEs to FD-BSs offers a maximum of 5% rate gain over FD-BSs and HD-UEs case, which is a marginal gain compared to the burden required to implement FD transceivers at the UEs\\' side. To this end, we shed light on practical scenarios where HD-UEs operation with FD-BSs outperforms the

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Elaine Ann Moore

    Full Text Available 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.

  12. Downlink Error Rates of Half-duplex Users in Full-duplex Networks over a Laplacian Inter-User Interference Limited and EGK fading

    KAUST Repository

    Soury, Hamza; Elsawy, Hesham; Alouini, Mohamed-Slim

    2017-01-01

    This paper develops a mathematical framework to study downlink error rates and throughput for half-duplex (HD) terminals served by a full-duplex (FD) base station (BS). The developed model is used to motivate long term pairing for users that have

  13. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    International Nuclear Information System (INIS)

    Swasey, Steven M; Gwinn, Elisabeth G

    2016-01-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson–Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag + , as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag + –DNA nanostructures. Our studies of Ag + -induced assembly of non-complementary DNA oligomers employ strands of 2–24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag + can be achieved by optimizing solution conditions. These Ag + -mediated duplexes are stable to at least 60 mM Mg 2+ , higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag + -mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag + -mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’. (paper)

  14. Rapid detection of Opisthorchis viverrini and Strongyloides stercoralis in human fecal samples using a duplex real-time PCR and melting curve analysis.

    Science.gov (United States)

    Janwan, Penchom; Intapan, Pewpan M; Thanchomnang, Tongjit; Lulitanond, Viraphong; Anamnart, Witthaya; Maleewong, Wanchai

    2011-12-01

    Human opisthorchiasis caused by the liver fluke Opisthorchis viverrini is an endemic disease in Southeast Asian countries including the Lao People's Democratic Republic, Cambodia, Vietnam, and Thailand. Infection with the soil-transmitted roundworm Strongyloides stercoralis is an important problem worldwide. In some areas, both parasitic infections are reported as co-infections. A duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis was developed for the rapid detection of O. viverrini and S. stercoralis in human fecal samples. Duplex real-time FRET PCR is based on fluorescence melting curve analysis of a hybrid of amplicons generated from two genera of DNA elements: the 162 bp pOV-A6 DNA sequence specific to O. viverrini and the 244 bp 18S rRNA sequence specific to S. stercoralis, and two pairs of specific fluorophore-labeled probes. Both O. viverrini and S. stercoralis can be differentially detected in infected human fecal samples by this process through their different fluorescence channels and melting temperatures. Detection limit of the method was as little as two O. viverrini eggs and four S. stercoralis larvae in 100 mg of fecal sample. The assay could distinguish the DNA of both parasites from the DNA of negative fecal samples and fecal samples with other parasite materials, as well as from the DNA of human leukocytes and other control parasites. The technique showed 100% sensitivity and specificity. The introduced duplex real-time FRET PCR can reduce labor time and reagent costs and is not prone to carry over contamination. The method is important for simultaneous detection especially in areas where both parasites overlap incidence and is useful as the screening tool in the returning travelers and immigrants to industrialized countries where number of samples in the diagnostic units will become increasing.

  15. Signatures of Late Pleistocene fluvial incision in an Alpine landscape

    Science.gov (United States)

    Leith, Kerry; Fox, Matthew; Moore, Jeffrey R.

    2018-02-01

    Uncertainty regarding the relative efficacy of fluvial and glacial erosion has hindered attempts to quantitatively analyse the Pleistocene evolution of alpine landscapes. Here we show that the morphology of major tributaries of the Rhone River, Switzerland, is consistent with that predicted for a landscape shaped primarily by multiple phases of fluvial incision following a period of intense glacial erosion after the mid-Pleistocene transition (∼0.7 Ma). This is despite major ice sheets reoccupying the region during cold intervals since the mid-Pleistocene. We use high-resolution LiDAR data to identify a series of convex reaches within the long-profiles of 18 tributary channels. We propose these reaches represent knickpoints, which developed as regional uplift raised tributary bedrock channels above the local fluvial baselevel during glacial intervals, and migrated upstream as the fluvial system was re-established during interglacial periods. Using a combination of integral long-profile analysis and stream-power modelling, we find that the locations of ∼80% of knickpoints in our study region are consistent with that predicted for a fluvial origin, while the mean residual error over ∼100 km of modelled channels is just 26.3 m. Breaks in cross-valley profiles project toward the elevation of former end-of-interglacial channel elevations, supporting our model results. Calculated long-term uplift rates are within ∼15% of present-day measurements, while modelled rates of bedrock incision range from ∼1 mm/yr for low gradient reaches between knickpoints to ∼6-10 mm/yr close to retreating knickpoints, typical of observed rates in alpine settings. Together, our results reveal approximately 800 m of regional uplift, river incision, and hillslope erosion in the lower half of each tributary catchment since 0.7 Ma.

  16. Tensile properties of duplex UNS S32205 and lean duplex UNS S32304 steels and the influence of short duration 475 ºC aging

    Directory of Open Access Journals (Sweden)

    Sérgio Souto Maior Tavares

    2012-12-01

    Full Text Available Duplex stainless steels are high strength and corrosion resistant steels extensively used in the petrochemical and chemical industries. The aging at 475 ºC for long periods of time provokes embrittlement and deterioration of corrosion resistance. However, short duration aging at 475 ºC may be used as heat treatment to improve mechanical resistance with small decrease in the other properties. In this work the flow stress curves of lean duplex UNS S32304 and duplex UNS S32205 steels were modeled with Hollomon's equation and work hardening exponents (n were determined. The analyses were conducted in specimens annealed and heat treated at 475 ºC for short periods of time. The aging at 475 ºC for 4 hours, 8 hours and 12 hours promoted significant hardening with small decrease of ductility. The work hardening exponents of both steels were compared, being higher in the duplex steel than in the lean duplex grade.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Marta Matvienko

    Full Text Available 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.

  19. The extended minimal incision approach to midface rejuvenation.

    Science.gov (United States)

    Pontius, Allison T; Williams, Edwin F

    2005-08-01

    Recent major advancements in comprehensive facial rejuvenation have focused on management of midfacial aging. Multiple techniques have been described to treat the aging midface; the mere nature of so many approaches is evidence that no one technique has prevailed. Although the nasolabial region remains a challenge to correct, the approach described herein provides comprehensive rejuvenation of the midface, lateral brow, and jawline. The technique is performed via a minimal incision brow-lift approach and has been performed (with minor modifications) by the senior author in more than 650 patients over the past 9 years. The technique has proven to be safe, reliable, and effective.

  20. Promotion of double-duplex invasion of peptide nucleic acids through conjugation with nuclear localization signal peptide.

    Science.gov (United States)

    Aiba, Yuichiro; Honda, Yuta; Komiyama, Makoto

    2015-03-02

    Pseudo-complementary peptide nucleic acid (pcPNA), as one of the most widely used synthetic DNA analogues, invades double-stranded DNA according to Watson-Crick rules to form invasion complexes. This unique mode of DNA recognition induces structural changes at the invasion site and can be used for a range of applications. In this paper, pcPNA is conjugated with a nuclear localization signal (NLS) peptide, and its invading activity is notably promoted both thermodynamically and kinetically. Thus, the double-duplex invasion complex is formed promptly at low pcPNA concentrations under high salt conditions, where the invasion otherwise never occurs. Furthermore, NLS-modified pcPNA is successfully employed for site-selective DNA scission, and the targeted DNA is selectively cleaved under conditions that are not conducive for DNA cutters using unmodified pcPNAs. This strategy of pcPNA modification is expected to be advantageous and promising for a range of in vitro and in vivo applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Solution structure of the luzopeptin-DNA complex

    International Nuclear Information System (INIS)

    Zhang, Xiaolu; Patel, D.J.

    1991-01-01

    The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. Once equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. The authors have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The formation of cis peptide bonds for luzopeptin in the complex results in an increased separation of the long sides of the rectangular cyclic depsipeptide backbone and reorients in the glycine amide proton so that it can form an intermolecular hydrogen bond with the 2-carbonyl of T3 in the complex. This observation explains, in part, the requirement for Watson-Crick A·T pairs to be sandwiched between the quinolines at the bisintercalation site in the luzopeptin-DNA complex. The NMR studies on the luzopeptin-d(C-A-T-G) complex unequivocally establish that antitumor agents can undergo conformational transitions on complex formation with DNA, and it is the conformation of the drug in the complex that should serve as the starting point for drug design studies. The above structural details on the solution structure of the luzopeptin-DNA complex also explain the sequence selectivity of luzopeptin for bisintercalation at d(C-A)·d(T-G) steps in the d(C-A-T-G) duplex in solution

  2. Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis

    NARCIS (Netherlands)

    Hamdan, Samir M.; Loparo, Joseph J.; Takahashi, Masateru; Richardson, Charles C.; Oijen, Antoine M. van

    2009-01-01

    In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to

  3. Effect of Temperature on the Intrinsic Flexibility of DNA and Its Interaction with Architectural Proteins

    NARCIS (Netherlands)

    Driessen, R.P.C.; Sitter, G.; Moolenaar, G.F.; Wuite, G.J.L.; Goosen, N.; Dame, R.T.

    2014-01-01

    The helical structure of double-stranded DNA is destabilized by increasing temperature. Above a critical temperature (the melting temperature), the two strands in duplex DNA become fully separated. Below this temperature, the structural effects are localized. Using tethered particle motion in a

  4. Mechanical Deformation Behavior of Lean Duplex 329LA Steel

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Byung-Jun [Research Institute of Industrial Science and Technology, Pohang (Korea, Republic of); Choi, Jeom-Yong [POSCO Technical Research Lab., Pohang (Korea, Republic of); Park, Kyung-Tae [Hanvat National University, Daejeon (Korea, Republic of); Lee, Ho Seong [Kyungpook National University, Daegu (Korea, Republic of)

    2015-09-15

    The tensile response of Lean Duplex 329LA stainless steel was investigated over various strain rates. It was observed that the mechanical response, including in particular the total elongation of the tested alloy, was strongly affected by the strain rate. As the strain rate decreased from 10-1 s-1 to 10-4 s-1, the elongation increased. As the strain rate increased, the deformation mode in an austenite phase was dominated by dislocation glide, resulting in deterioration of the elongation. The substructure of the ferritic phase showed a dislocation cell structure, independent of the applied strain rate. The optimum mechanical properties of lean duplex stainless steel thus can be obtained by controlling the deformation mode in the austenitic phase.

  5. Mechanical Deformation Behavior of Lean Duplex 329LA Steel

    International Nuclear Information System (INIS)

    Yoon, Byung-Jun; Choi, Jeom-Yong; Park, Kyung-Tae; Lee, Ho Seong

    2015-01-01

    The tensile response of Lean Duplex 329LA stainless steel was investigated over various strain rates. It was observed that the mechanical response, including in particular the total elongation of the tested alloy, was strongly affected by the strain rate. As the strain rate decreased from 10-1 s-1 to 10-4 s-1, the elongation increased. As the strain rate increased, the deformation mode in an austenite phase was dominated by dislocation glide, resulting in deterioration of the elongation. The substructure of the ferritic phase showed a dislocation cell structure, independent of the applied strain rate. The optimum mechanical properties of lean duplex stainless steel thus can be obtained by controlling the deformation mode in the austenitic phase.

  6. Duplex-tube sodium-indication steam generator

    International Nuclear Information System (INIS)

    Matal, O.; Martoch, J.

    1984-01-01

    The steam generator with duplex tubes and sodium indication is connected to the main sodium input and output via the inlet and outlet chambers and has indication spaces connected to the interspaces of the duplex tubes. The first indication space is linked with the auxiliary inlet pipe to the inlet chamber and the second indication space is connected with the auxiliary pipe to the outlet chamber. Mounted to the auxiliary inlet pipe is at least one closure, i.e., a valve or electromagnetic stop. Mounted on the auxiliary outlet pipe is an indication sensor, e.g., a sodium flow sensor. At least one indication space is provided with an alarm sensor, e.g., a thermocouple, a pressure gauge and one sensor to monitor the hydrogen content of sodium. (J.P.)

  7. Comments on process of duplex coatings on aluminum alloys

    Institute of Scientific and Technical Information of China (English)

    Samir H.A.; QIAN Han-cheng(钱翰城); XIA Bo-cai(夏伯才); WU Shi-ming(吴仕明)

    2004-01-01

    Despite the great achievements made in improvement of wear resistance properties of aluminum alloys,their applications in heavy surface load-bearing are limited. Single coating is insufficient to produce the desired combination of surface properties. These problems can be solved through the duplex coatings. The aim of the present study is to overview the research advances on processes of duplex coatings on aluminum alloys combined with micro plasma oxidation process and with other modern processes such as physical vapour deposition and plasma assisted chemical vapour deposition and also to evaluate the performance of micro plasma oxidation coatings in improving the load-bearing, friction and wear resistance properties of aluminum alloys in comparison with other coatings. Wherein, a more detailed presentation of the processes and their performances and disadvantages are given as well.

  8. Weld oxide formation on lean duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Westin, E.M. [Outokumpu Stainless, Avesta Research Centre, P.O. Box 74, SE-774 22 Avesta (Sweden)], E-mail: elin.westin@outokumpu.com; Olsson, C.-O.A. [Outokumpu Stainless, Avesta Research Centre, P.O. Box 74, SE-774 22 Avesta (Sweden); Hertzman, S. [Outokumpu Stainless Research Foundation, Brinellvaegen 23, SE-100 44 Stockholm (Sweden)

    2008-09-15

    Weld oxides have a strong influence on corrosion resistance, but have hitherto only been studied to a limited extent for duplex stainless steels. X-ray photoelectron spectroscopy (XPS) has here been used to study heat tint formed on gas tungsten arc (GTA) welds on the commercial duplex grades LDX 2101 (EN 1.4162/UNS S32101) and 2304 (EN 1.4362/UNS S32304) welded with and without nitrogen additions to the shielding gas. The process of heat tint formation is discussed in terms of transport phenomena to explain the effect of atmosphere, temperature and composition. The oxides formed were found to be enriched in manganese and corrosion testing shows that nitrogen has a strong influence on the weld oxide. A mechanism is proposed including evaporation from the weld pool and subsequent redeposition.

  9. Listen and talk full-duplex cognitive radio networks

    CERN Document Server

    Liao, Yun; Han, Zhu

    2016-01-01

    This brief focuses on the use of full-duplex radio in cognitive radio networks, presenting a novel spectrum sharing protocol that allows the secondary users to simultaneously sense and access the vacant spectrum. This protocol, called “Listen-and-talk” (LAT), is evaluated by both mathematical analysis and computer simulations in comparison with other existing protocols, including the listen-before-talk protocol. In addition to LAT-based signal processing and resource allocation, the brief discusses techniques such as spectrum sensing and dynamic spectrum access. The brief proposes LAT as a suitable access scheme for cognitive radio networks, which can support the quality-of-service requirements of these high priority applications. Fundamental theories and key techniques of cognitive radio networks are also covered. Listen and Talk: Full-duplex Cognitive Radio Networks is designed for researchers, developers, and professionals involved in cognitive radio networks. Advanced-level students studying signal pr...

  10. Standard test methods for characterizing duplex grain sizes

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2002-01-01

    1.1 These test methods provide simple guidelines for deciding whether a duplex grain size exists. The test methods separate duplex grain sizes into one of two distinct classes, then into specific types within those classes, and provide systems for grain size characterization of each type. 1.2 Units—The values stated in SI units are to be regarded as standard. No other units of measurement are included in this standard. 1.3 This standard may involve hazardous materials, operations, and equipment. This standard does not purport to address all of the safety concerns associated with its use. It is the responsibility of the user of this standard to consult appropriate safety and health practices and determine the applicability of regulatory limitations prior to its use.

  11. Weld oxide formation on lean duplex stainless steel

    International Nuclear Information System (INIS)

    Westin, E.M.; Olsson, C.-O.A.; Hertzman, S.

    2008-01-01

    Weld oxides have a strong influence on corrosion resistance, but have hitherto only been studied to a limited extent for duplex stainless steels. X-ray photoelectron spectroscopy (XPS) has here been used to study heat tint formed on gas tungsten arc (GTA) welds on the commercial duplex grades LDX 2101 (EN 1.4162/UNS S32101) and 2304 (EN 1.4362/UNS S32304) welded with and without nitrogen additions to the shielding gas. The process of heat tint formation is discussed in terms of transport phenomena to explain the effect of atmosphere, temperature and composition. The oxides formed were found to be enriched in manganese and corrosion testing shows that nitrogen has a strong influence on the weld oxide. A mechanism is proposed including evaporation from the weld pool and subsequent redeposition

  12. Rapid detection of SNP (c.309T>G in the MDM2 gene by the Duplex SmartAmp method.

    Directory of Open Access Journals (Sweden)

    Yasuaki Enokida

    Full Text Available BACKGROUND: Genetic polymorphisms in the human MDM2 gene are suggested to be a tumor susceptibility marker and a prognostic factor for cancer. It has been reported that a single nucleotide polymorphism (SNP c.309T>G in the MDM2 gene attenuates the tumor suppressor activity of p53 and accelerates tumor formation in humans. METHODOLOGY: In this study, to detect the SNP c.309T>G in the MDM2 gene, we have developed a new SNP detection method, named "Duplex SmartAmp," which enabled us to simultaneously detect both 309T and 309G alleles in one tube. To develop this new method, we introduced new primers i.e., nBP and oBPs, as well as two different fluorescent dyes that separately detect those genetic polymorphisms. RESULTS AND CONCLUSIONS: By the Duplex SmartAmp method, the genetic polymorphisms of the MDM2 gene were detected directly from a small amount of genomic DNA or blood samples. We used 96 genomic DNA and 24 blood samples to validate the Duplex SmartAmp by comparison with results of the conventional PCR-RFLP method; consequently, the Duplex SmartAmp results agreed totally with those of the PCR-RFLP method. Thus, the new SNP detection method is considered useful for detecting the SNP c.309T>G in the MDM2 gene so as to judge cancer susceptibility against some cellular stress in the clinical setting, and also to handle a large number of samples and enable rapid clinical diagnosis.

  13. Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction

    Science.gov (United States)

    Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

    2014-01-01

    DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag+-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.

  14. Implementation of real-time duplex synthetic aperture ultrasonography

    DEFF Research Database (Denmark)

    Hemmsen, Martin Christian; Larsen, Lee; Kjeldsen, Thomas

    2015-01-01

    This paper presents a real-time duplex synthetic aperture imaging system, implemented on a commercially available tablet. This includes real-time wireless reception of ultrasound signals and GPU processing for B-mode and Color Flow Imaging (CFM). The objective of the work is to investigate the im...... and that the required bandwidth between the probe and processing unit is within the current Wi-Fi standards....

  15. Internal stresses in an austeno-ferritic duplex stainless steel

    International Nuclear Information System (INIS)

    Verhaeghe, B.; Brechet, Y.; Louchet, F.; Massoud, J.P.; Touzeau, D.

    1996-04-01

    Austeno-ferritic duplex steels possess microstructures containing comparable volume fractions of hard and soft phases which are bi-percolated. They are therefore liable to develop large internal stresses during straining. The evolution and the relaxation of these stresses and the occurrence of damage are characterized using Bauschinger tests. Thermally aged and non-aged material behaviour are compared. Plastic flow in the hard phase is shown to be significantly efficient in releasing these internal stresses. (authors). 15 refs., 8 figs

  16. Investigation of hot cracking resistance of 2205 duplex steel

    Energy Technology Data Exchange (ETDEWEB)

    Adamiec, J; Scibisz, B, E-mail: janusz.adamiec@polsl.pl [Silesian University of Technology, Faculty of Materials Science and Metallurgy, ul. Krasinskiego 8, PL-40019 Katowice (Poland)

    2010-02-15

    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 R{sub f}parameter (R{sub f} = (T{sub liquidus} - 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 deg. 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 T{sub L} = 1465 deg. C and a solidus temperature of T{sub S} = 1454 deg. C were observed. For NST a mean value was assumed, in which the cracks appeared for six samples; the temperature was 1381 deg. C. As the value of the NDT temperature 1367 deg. C was applied while for DRT the assumed temperature was 1375 deg. 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.

  17. Investigation of hot cracking resistance of 2205 duplex steel

    Science.gov (United States)

    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.

  18. Investigation of hot cracking resistance of 2205 duplex steel

    International Nuclear Information System (INIS)

    Adamiec, J; Scibisz, B

    2010-01-01

    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 R f parameter (R f = (T liquidus - 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 deg. 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 T L = 1465 deg. C and a solidus temperature of T S = 1454 deg. C were observed. For NST a mean value was assumed, in which the cracks appeared for six samples; the temperature was 1381 deg. C. As the value of the NDT temperature 1367 deg. C was applied while for DRT the assumed temperature was 1375 deg. 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.

  19. Directed Formation of DNA Nanoarrays through Orthogonal Self-Assembly

    Directory of Open Access Journals (Sweden)

    Eugen Stulz

    2011-06-01

    Full Text Available We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II and Ni(II induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.

  20. On full duplex Gaussian relay channels with self-interference

    KAUST Repository

    Behboodi, Arash

    2016-08-15

    Self interference (SI) in full duplex (FD) systems is the interference caused by the transmission stream on the reception stream. Being one of the main restrictive factors for performance of practical full duplex systems, however, not too much is known about its effect on the fundamental limits of relaying systems. In this work, we consider the full duplex three-node relay channel with SI where SI is modeled as an additive Gaussian noise whose variance is dependent on instantaneous input power. The classical achievable rates and upper bounds for the single three-node relay channel no longer apply due to the structure of SI. Achievable rates for Decode-and-Forward (DF) and Compress-and-Forward (CF) and upper bounds on the capacity are derived assuming Gaussian inputs and SI. The deterministic model is also introduced and its capacity is characterized. The optimal joint source-relay distributions is discussed. Numerical results are provided comparing the achievable rates and upper bound. © 2016 IEEE.

  1. Duplex Schemes in Multiple Antenna Two-Hop Relaying

    Directory of Open Access Journals (Sweden)

    Anja Klein

    2008-04-01

    Full Text Available A novel scheme for two-hop relaying defined as space division duplex (SDD relaying is proposed. In SDD relaying, multiple antenna beamforming techniques are applied at the intermediate relay station (RS in order to separate downlink and uplink signals of a bi-directional two-hop communication between two nodes, namely, S1 and S2. For conventional amplify-and-forward two-hop relaying, there appears a loss in spectral efficiency due to the fact that the RS cannot receive and transmit simultaneously on the same channel resource. In SDD relaying, this loss in spectral efficiency is circumvented by giving up the strict separation of downlink and uplink signals by either time division duplex or frequency division duplex. Two novel concepts for the derivation of the linear beamforming filters at the RS are proposed; they can be designed either by a three-step or a one-step concept. In SDD relaying, receive signals at S1 are interfered by transmit signals of S1, and receive signals at S2 are interfered by transmit signals of S2. An efficient method in order to combat this kind of interference is proposed in this paper. Furthermore, it is shown how the overall spectral efficiency of SDD relaying can be improved if the channels from S1 and S2 to the RS have different qualities.

  2. Duplex geometry: an example from the Moine Thrust Belt

    Science.gov (United States)

    Bowler, S.

    1987-04-01

    The geometry and microstructure of a small duplex formed in one bed from the Moine Thrust Belt of northwest Scotland is reported. The structure is seen in oblique section, within the Cambrian Pipe-rock, in an area of low strain. A range of movement direction indicators are present in the structure. An early grain shape fabric developed close to the roof thrust is taken as the best estimate of the overall movement direction towards 287°. Slickensides in the gouge developed on movement planes within the duplex show varied orientations on a given plane, and are not considered useful indicators of thrust transport direction. Branch lines exposed converge and diverge, suggesting little lateral continuity of the exposed structure. The microstructures present within the structure indicate an increase in localised deformation, and in cataclastic behavior as the duplex evolved. Early layer parallel shear is ubiquitous, giving rise to an elongate grain shape fabric close to bedding surfaces. In early formed horses, a layer-parallel, oblate grain shape fabric, which shows localised slip zones, is overprinted by gouge formation. Later formed horses show only fracturing and gouge development. This sequence is attributed to stick-slip behavior in the propagation or displacement of the original fault, now the floor thrust.

  3. Microstructures and mechanical properties of duplex low carbon steel

    Science.gov (United States)

    Alfirano; Eben, U. S.; Hidayat, M.

    2018-04-01

    The microstructures behavior of duplex cold-rolled low carbon steel for automotive applications has been investigated. Intercritical annealing treatment is commonly used to develop a duplex low carbon steel containing ferrite and martensite. To get a duplex phase ferrite and martensite, the specimens were heated at inter-critical annealing temperature of 775°C - 825°C, for heating time up to 20 minutes, followed by water-quenched. The hardness of specimens was studied. The optical microscopy was used to analyze the microstructures. The optimal annealing conditions (martensite volume fraction approaching 20%) at 775°C with a heating time of 10 minutes was achieved. The highest hardness value was obtained in cold-rolled specimens of 41% in size reduction for intercritical annealing temperature of 825°C. In this condition, the hardness value was 373 HVN. The correlation between intercritical annealing temperature and time can be expressed in the transformation kinetics as fγ/fe = 1-exp(-Ktn) wherein K and n are grain growth rate constant and Avrami’s exponent, respectively. From experiment, the value of K = 0.15 and n = 0.461. Using the relationship between temperatures and heating time, activation energy (Q) can be calculated that is 267 kJ/mol.

  4. Development and test evaluation of duplex steam reformer tube

    International Nuclear Information System (INIS)

    Allen, D.C.; Meyer, D.J.; Pflasterer, G.R.

    1980-01-01

    For HTR applications involving a steam reformer (SR), it is uncertain whether an intermediate heat exchanger (IHX) is required. There are several system configurations that could be developed for the application of nuclear heat using the steam reformer reaction. The considerations (advantages vs. disadvantages) for each of the system configurations are summarized. The approach that technically and economically appears to be the most attractive, in studies conducted by General Electric, combines the SR process heat exchanger and the IHX in a single component using a duplex tube. A central question concerning the duplex tube concept is whether the design would provide adequate leak monitoring capability and significant reduction in tritium and hydrogen diffusion, while introducing only a small increase in overall temperature difference from the helium to the process gas. A cooperative GE-KFA effort was undertaken to develop, fabricate, test, and evaluate a duplex steam reformer tube. GE was responsible for the development and fabrication of the tube, and KFA was responsible for testing the tube in the EVA I facility at Juelich. Both GE and KFA are evaluating the thermochemical and metallurgical test data. Actual fabrication of the tube was performed by Foster-Wheeler in accordance with the GE design. This paper reviews the highlights of the fabrication development and preliminary evaluation of the test data

  5. Systematic review and meta-analysis of electrocautery versus scalpel for surgical skin incisions.

    Science.gov (United States)

    Aird, Lisa N F; Brown, Carl J

    2012-08-01

    The creation of surgical skin incisions has historically been performed using a cold scalpel. The use of electrocautery for this purpose has been controversial with respect to patient safety and surgical efficacy. A systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted to compare skin incisions made by electrocautery and a scalpel. A systematic electronic literature search was performed using 2 electronic databases (MEDLINE and PubMed), and the methodological quality of included publications was evaluated. Six RCTs were identified comparing electrocautery (n = 606) and a scalpel (n = 628) for skin incisions. No significant difference in wound infection rates or scar cosmesis was identified between the treatment groups. Electrocautery significantly reduced the incision time and postoperative wound pain. A trend toward less incisional blood loss from skin incisions made with electrocautery was noted. Electrocautery is a safe and effective method for performing surgical skin incisions. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Qualitative comparison of duplex Stirling and absorption refrigerators in domestic applications

    Energy Technology Data Exchange (ETDEWEB)

    Shao, H. [Global Cooling BV, Zutphen (Netherlands)

    2000-07-01

    A qualitative comparison has been carried out between the duplex Stirling and the absorption refrigerator for domestic applications. The duplex Stirling has many advantages over the absorption refrigerator on efficiency, modulation, suitability, operating costs, pollution reduction. Based on the state of the art of free-piston gas-bearing and linear-motor Stirling engines and coolers, it appears technically and economically feasible to develop the duplex Stirling to compete with the absorption refrigerator for heat-driven domestic refrigeration. (orig.)

  7. Characterization of duplex stainless steel weld metals obtained by hybrid plasma-gas metal arc welding

    OpenAIRE

    Yurtisik,Koray; Tirkes,Suha; Dykhno,Igor; Gur,C. Hakan; Gurbuz,Riza

    2013-01-01

    Despite its high efficiency, autogenous keyhole welding is not well-accepted for duplex stainless steels because it causes excessive ferrite in as-welded duplex microstructure, which leads to a degradation in toughness and corrosion properties of the material. Combining the deep penetration characteristics of plasma arc welding in keyhole mode and metal deposition capability of gas metal arc welding, hybrid plasma - gas metal arc welding process has considered for providing a proper duplex mi...

  8. Single incision laparoscopic liver resection (SILL – a systematic review

    Directory of Open Access Journals (Sweden)

    Benzing, Christian

    2015-12-01

    Full Text Available Background: Today, minimally invasive liver resections for both benign and malignant tumors are routinely performed. Recently, some authors have described single incision laparoscopic liver resection (SILL procedures. Since SILL is a relatively young branch of laparoscopy, we performed a systematic review of the current literature to collect data on feasibility, perioperative results and oncological outcome.Methods: A literature research was performed on Medline for all studies that met the eligibility criteria. Titles and abstracts were screened by two authors independently. A study was included for review if consensus was obtained by discussion between the authors on the basis of predefined inclusion criteria. A thorough quality assessment of all included studies was performed. Data were analyzed and tabulated according to predefined outcome measures. Synthesis of the results was achieved by narrative review. Results: A total of 15 eligible studies were identified among which there was one prospective cohort study and one randomized controlled trial comparing SILL to multi incision laparoscopic liver resection (MILL. The rest were retrospective case series with a maximum of 24 patients. All studies demonstrated convincing results with regards to feasibility, morbidity and mortality. The rate of wound complications and incisional hernia was low. The cosmetic results were good.Conclusions: This is the first systematic review on SILL including prospective trials. The results of the existing studies reporting on SILL are favorable. However, a large body of scientific evidence on the field of SILL is missing, further randomized controlled studies are urgently needed.

  9. Magnetic resonance imaging evaluation of incision healing after cesarean sections

    Energy Technology Data Exchange (ETDEWEB)

    Dicle, O. [Department of Radiodiagnosis, Dokuz Eyluel University, Izmir (Turkey); Kuecuekler, C. [Department of Radiodiagnosis, Dokuz Eyluel University, Izmir (Turkey); Pirnar, T. [Department of Radiodiagnosis, Dokuz Eyluel University, Izmir (Turkey); Erata, Y. [Department of Gynecology and Obstetrics, Dokuz Eyluel University, Izmir (Turkey); Posaci, C. [Department of Gynecology and Obstetrics, Dokuz Eyluel University, Izmir (Turkey)

    1997-02-01

    The purpose of this study was to examine the healing period of incision scar in myometrial wall and the normal pelvis after cesarean sections by means of MRI. In this study 17 voluntary women were examined after their first delivery with cesarean section in the early postpartum period (first 5 days), and following this, three more times in 3-month intervals. The MRI examinations were performed on a 1.0-T system (Magnetom, Siemens, Erlangen, Germany), and sagittal T1-weighted (550/17 TR/TE) and T2-weighted (2000/80 TR/TE) spin-echo (SE) images of the pelvis were obtained. During follow-up examinations incision scar tissues lost their signals within the first 3 months on both SE sequences, and little alteration was observed in the subsequent tests. Zonal anatomy of the uterus reappeared completely 6 months after cesarean sections. The time for the involution of the uterus was independent of the zonal anatomy recovery, and the maximum involution was inspected within the first 3 months. In conclusion, the maturation time of myometrial scar tissue in uncomplicated cesarean sections, which can be evaluated by the signal alterations in MRI, is approximately 3 months, whereas the complete involution and the recovery of the zonal anatomy need at least 6 months. (orig.). With 6 figs.

  10. Muscle sparing lateral thoracotomy: the standard incision for thoracic procedures

    Directory of Open Access Journals (Sweden)

    Mihai Dumitrescu

    2017-05-01

    Full Text Available Lateral thoracotomy is a versatile approach with many variations and is currently the most widely used incision in thoracic surgery. In the current article we are presenting the muscle-sparing lateral thoracotomy in the lateral decubitus position which we consider to be the “standard” for lateral thoracotomies. Indications, surgical technique and pitfalls are described alongside our experience with thoracic drainage. Although there is no consensus regarding the name of this incision, some authors call it “axillary thoracotomy” while others call it a “modified lateral thoracotomy”, they all agree on one aspect – the importance of muscle sparing – which makes it the go-to thoracotomy for both small and large procedures involving the lung. Lateral muscle sparing thoracotomy allows for good exposure of the pulmonary hilum, fissures, apex and diaphragm. The approach is easy and quick to perform while at the same time ensuring faster postoperative recovery by sparing the latissimus dorsi muscle, better cosmetics and lower postoperative pain score when compared to the posterolateral or classical lateral thoracotomies.

  11. Magnetic resonance imaging evaluation of incision healing after cesarean sections

    International Nuclear Information System (INIS)

    Dicle, O.; Kuecuekler, C.; Pirnar, T.; Erata, Y.; Posaci, C.

    1997-01-01

    The purpose of this study was to examine the healing period of incision scar in myometrial wall and the normal pelvis after cesarean sections by means of MRI. In this study 17 voluntary women were examined after their first delivery with cesarean section in the early postpartum period (first 5 days), and following this, three more times in 3-month intervals. The MRI examinations were performed on a 1.0-T system (Magnetom, Siemens, Erlangen, Germany), and sagittal T1-weighted (550/17 TR/TE) and T2-weighted (2000/80 TR/TE) spin-echo (SE) images of the pelvis were obtained. During follow-up examinations incision scar tissues lost their signals within the first 3 months on both SE sequences, and little alteration was observed in the subsequent tests. Zonal anatomy of the uterus reappeared completely 6 months after cesarean sections. The time for the involution of the uterus was independent of the zonal anatomy recovery, and the maximum involution was inspected within the first 3 months. In conclusion, the maturation time of myometrial scar tissue in uncomplicated cesarean sections, which can be evaluated by the signal alterations in MRI, is approximately 3 months, whereas the complete involution and the recovery of the zonal anatomy need at least 6 months. (orig.). With 6 figs

  12. EFFECT OF INTERMETALLIC PHASES ON CORROSION BEHAVIOR AND MECHANICAL PROPERTIES OF DUPLEX STAINLESS STEEL AND SUPER-DUPLEX STAINLESS STEEL

    Directory of Open Access Journals (Sweden)

    Prabhu Paulraj

    2015-08-01

    Full Text Available Duplex Stainless Steels (DSS and Super Duplex Stainless Steel (SDSS have excellent integration of mechanical and corrosion properties. However, the formation of intermetallic phases is a major problem in their usage. The mechanical and corrosion properties are deteriorated due to the presence of intermetallic phases. These phases are induced during welding, prolonged exposure to high temperatures, and improper heat treatments. The main emphasis of this review article is on intermetallic phases and their effects on corrosion and mechanical properties. First the effect of various alloying elements on DSS and SDSS has been discussed followed by formation of various intermetallic phases. The intermetallic phases affect impact toughness and corrosion resistance significantly. Their deleterious effect on weldments has also been reviewed.

  13. Discussion on the Relevant Factors of General Surgery Incision Infection and Prevention Methods

    Directory of Open Access Journals (Sweden)

    Jin Baotao

    2017-01-01

    Full Text Available There are many reasons that can lead to incision infection of general surgical patients. The main reasons include weight, age, body albumin level, surgical time, observation ward, etc. This paper analyzes the clinic data of patients with incision infection after general surgery based on clinic practice and study on the reasons that have impact on general surgical incision infection and gives relevant prevention countermeasures.

  14. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

    DEFF Research Database (Denmark)

    Räschle, Markus; Smeenk, Godelieve; Hansen, Rebecca K

    2015-01-01

    DNA interstrand cross-links (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. We devised ...

  15. Characterization of microstructure and texture across dissimilar super duplex/austenitic stainless steel weldment joint by super duplex filler metal

    Energy Technology Data Exchange (ETDEWEB)

    Eghlimi, Abbas, E-mail: a.eghlimi@ma.iut.ac.ir [Department of Materials Engineering, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Shamanian, Morteza [Department of Materials Engineering, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Eskandarian, Masoomeh [Department of Materials Engineering, Shiraz University, Shiraz 71348-51154 (Iran, Islamic Republic of); Zabolian, Azam [Department of Natural Resources, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Szpunar, Jerzy A. [Department of Mechanical Engineering, University of Saskatchewan, Saskatoon SK S7N 5A9 (Canada)

    2015-08-15

    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 decreased 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.

  16. THE INFLUENCE OF POSTHEAT TREATMENT ON FERRITE REDISTRIBUTION IN DUPLEX STEELS ELECTRON BEAM WELDS

    Directory of Open Access Journals (Sweden)

    Zita Iždinská

    2009-04-01

    Full Text Available The duplex stainless steel is two-phase steel with the structure composed of austenite and ferrite with optimum austenite/ferrite proportion 50%. At present, classical arc processes for welding duplex steels are generally regarded as acceptable. On the other hand electron and laser beam welding is up to now considered less suitable for welding duplex steels. The submitted work presents the results of testing various thermal conditions at welding duplex stainless steel with electron beam. It was shown, that application of suitable postheat made possible to reduce the ferrite content in weld metal.

  17. DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain.

    Science.gov (United States)

    Northall, Sarah J; Buckley, Ryan; Jones, Nathan; Penedo, J Carlos; Soultanas, Panos; Bolt, Edward L

    2017-09-01

    Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities. When isolated from the rest of Hel308, the WHD protein alone bound to duplex DNA but not ssDNA, and DNA binding by WHD protein was abolished by the same mutations as were analyzed in full-length Hel308. Isolated WHD from a human Hel308 homologue (HelQ) also bound to duplex DNA. By disrupting the interface between the Hel308 WHD and a RecA-like domain, a topology typical of Ski2 helicases, we show that this is crucial for ATPase and helicase activities. The data suggest a model in which the WHD promotes activity of Hel308 directly, through binding to duplex DNA that is distinct from ssDNA binding by core helicase, and indirectly through interaction with the RecA-like domain. We propose how the WHD may contribute to ssDNA translocation, resulting in DNA helicase activity or in removal of other DNA bound proteins by "reeling" ssDNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Residual stresses and fatigue in a duplex stainless steel

    International Nuclear Information System (INIS)

    Johansson, Johan

    1999-01-01

    Duplex stainless steels, consisting of approximately equal amounts of austenite and ferrite, often combine the best features of austenitic and ferritic stainless steels. They generally have good mechanical properties, including high strength and ductility, and the corrosion resistance is often better than conventional austenitic grades. This has lead to a growing use of duplex stainless steels as a material in mechanically loaded constructions. However, detailed knowledge regarding its mechanical properties and deformation mechanisms are still lacking. In this thesis special emphasis has been placed on the residual stresses and their influence on mechanical behaviour of duplex stainless steels. Due to the difference in coefficient of thermal expansion between the two phases, tensile microstresses are found in the austenitic phase and balancing compressive microstresses in the ferritic phase. The first part of this thesis is a literature survey, which will give an introduction to duplex stainless steels and review the fatigue properties of duplex stainless steels and the influence of residual stresses in two-phase material. The second part concerns the evolution of the residual stress state during uniaxial loading. Initial residual stresses were found to be almost two times higher in the transverse direction compared to the rolling direction. During loading the absolute value of the microstresses increased in the macroscopic elastic regime but started to decrease with increasing load in the macroscopic plastic regime. A significant increase of the microstresses was also found to occur during unloading. Finite element simulations also show stress variation within one phase and a strong influence of both the elastic and plastic anisotropy of the individual phases on the simulated stress state. In the third part, the load sharing between the phases during cyclic loading is studied. X-ray diffraction stress analysis and transmission electron microscopy show that even if

  19. Residual stresses and fatigue in a duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Johansson, Johan

    1999-05-01

    Duplex stainless steels, consisting of approximately equal amounts of austenite and ferrite, often combine the best features of austenitic and ferritic stainless steels. They generally have good mechanical properties, including high strength and ductility, and the corrosion resistance is often better than conventional austenitic grades. This has lead to a growing use of duplex stainless steels as a material in mechanically loaded constructions. However, detailed knowledge regarding its mechanical properties and deformation mechanisms are still lacking. In this thesis special emphasis has been placed on the residual stresses and their influence on mechanical behaviour of duplex stainless steels. Due to the difference in coefficient of thermal expansion between the two phases, tensile microstresses are found in the austenitic phase and balancing compressive microstresses in the ferritic phase. The first part of this thesis is a literature survey, which will give an introduction to duplex stainless steels and review the fatigue properties of duplex stainless steels and the influence of residual stresses in two-phase material. The second part concerns the evolution of the residual stress state during uniaxial loading. Initial residual stresses were found to be almost two times higher in the transverse direction compared to the rolling direction. During loading the absolute value of the microstresses increased in the macroscopic elastic regime but started to decrease with increasing load in the macroscopic plastic regime. A significant increase of the microstresses was also found to occur during unloading. Finite element simulations also show stress variation within one phase and a strong influence of both the elastic and plastic anisotropy of the individual phases on the simulated stress state. In the third part, the load sharing between the phases during cyclic loading is studied. X-ray diffraction stress analysis and transmission electron microscopy show that even if

  20. Long-Term Incisal Relationships After Palatoplasty in Patients With Isolated Cleft Palate.

    Science.gov (United States)

    Odom, Elizabeth B; Woo, Albert S; Mendonca, Derick A; Huebener, Donald V; Nissen, Richard J; Skolnick, Gary B; Patel, Kamlesh B

    2016-06-01

    Various palatoplasty techniques have limited incisions in the hard palate due to concerns that these incisions may limit maxillary growth. There is little convincing long-term evidence to support this. Our purpose is to determine incisal relationships, an indicator for future orthognathic procedure, in patients after repair of an isolated cleft of the secondary palate. Our craniofacial database was used to identify patients aged 10 years or greater with an isolated cleft of the secondary palate who underwent palatoplasty between 1985 and 2002. Data collected included age at palatoplasty and follow-up, cleft type, associated syndrome, Robin sequence, surgeon, repair technique, number of operations, and occlusion. Incisal relationship was determined through clinical observation by a pediatric dentist and orthodontist. Seventy eligible patients operated on by 9 surgeons were identified. Class III incisal relationship was seen in 5 patients (7.1%). Palatoplasty techniques over the hard palate (63 of 70 patients) included 2-flap palatoplasty, VY-pushback, and Von Langenbeck repair. There was an association between class III incisal relationship and syndromic diagnosis (P <0.001). Other study variables were not associated with class III incisal relationships. In patients with an isolated cleft of the secondary palate, there was no association between class III incisal relationship and surgeon, age at repair, cleft type, palatoplasty technique, or number of operations. Increased likelihood of class III incisal relationship was associated primarily with syndromic diagnosis.

  1. Midline versus transverse incision for cesarean delivery in low-income countries

    DEFF Research Database (Denmark)

    Maaløe, Nanna; Aabakke, Anna J M; Secher, Niels J

    2014-01-01

    While transverse incision is the recommended entry technique for cesarean delivery in high-income countries, it is our experience that midline incision is still used routinely in many low-income settings. Accordingly, international guidelines lack uniformity on this matter. Although evidence...... is limited, the literature suggests important advantages of the transverse incision, with lower risk of long-term disabilities such as wound disruption and hernia. Also, potential extra time spent on this incision appears not to impact neonatal outcome. Therefore, we suggest that it is time for a change...

  2. Diathermy vs. scalpel skin incisions in general surgery: double-blind, randomized, clinical trial.

    Science.gov (United States)

    Shamim, Muhammad

    2009-08-01

    This prospective, double-blind, randomized, controlled trial was designed to compare the outcome of diathermy incisions versus scalpel incisions in general surgery. A total of 369 patients who underwent diathermy incision (group A: 185 patients) or scalpel incision (group B: 184 patients) were analyzed. Variables analyzed were: surgical wound classification, length and depth of incision, incision time, duration of operation, incisional blood loss, postoperative pain, duration of hospital stay, duration of healing, and postoperative complications. The inclusion criteria were all patients who underwent elective or emergency general surgery. The exclusion criteria were only cases with incomplete patients' data and patients who were lost to follow-up. This study was conducted at Fatima Hospital-Baqai Medical University and Shamsi Hospital (Karachi), from January 2006 to December 2007. Incision time was significantly longer for patients in group B (p = 0.001). Incisional blood loss also was more for patients in group B (p = 0.000). Pain perception was found to be markedly reduced during the first 48 h in group A (p = 0.000). Total period of hospital stay (p = 0.129) and time for complete wound healing (p = 0.683) were almost the same for both groups. Postoperative complication rate by wound classification did not differ markedly between the two groups (p = 0.002 vs. p = 0.000). Diathermy incision has significant advantages compared with the scalpel because of reduced incision time, less blood loss, & reduced early postoperative pain.

  3. DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

    NARCIS (Netherlands)

    Taghavi, Amirhossein; van der Schoot, Paul; Berryman, Joshua T

    2017-01-01

    Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNADNA) as a possible

  4. Advantages of the modified double ring areolar incision over the traditional areolar incision in multicentric breast fibroadenoma surgery.

    Science.gov (United States)

    Zhang, Mingliang; Shen, Gongjin; Zhang, Song; Cui, Zhen; Qian, Jun

    2017-09-01

    This study was conducted to investigate the clinical advantages of modified double ring areola incision (MDRAI) compared to ordinary areola incision (OAI) in multicentric breast fibroadenoma in women. Sixty cases of multicentric benign breast tumor were recruited from the First Affiliated Hospital of Bengbu Medical College from January to December 2016. The cases were divided into two groups according to surgical approach: MDRAI (n = 20) and OAI (n = 40). The operation duration, intraoperative blood loss, drainage time, and postoperative recurrence rate in the first six months were compared. The mean age and tumor locations were not statistically different between the groups (P > 0.05). However, more lesions and larger tumor diameter were found in the MDRAI group than in the OAI group, with statistical difference (P  0.05). However, the intraoperative blood loss was statistically different between the two groups (P < 0.05). All 60 cases received six months of follow-up. Eight recurrent cases were found in the OAI group, but none in the MDRAI group. The recurrence rate was significantly different (χ 2  = 4.62, P < 0.05). Compared with OAI, MDRAI offers greater advantages in the aspects of blood loss and recurrence for the treatment of breast benign tumor, especially for multicentric larger lesions. © 2017 The Authors. Thoracic Cancer published by China Lung Oncology Group and John Wiley & Sons Australia, Ltd.

  5. Prevalence of and risk factors for symptomatic urinary tract infection after endoscopic incision for the treatment of ureterocele in children.

    Science.gov (United States)

    Moriya, Kimihiko; Nakamura, Michiko; Nishimura, Yoko; Kanno, Yukiko; Kitta, Takeya; Kon, Masafumi; Shinohara, Nobuo

    2017-09-01

    To clarify the impact of endoscopic incision (EI) for ureterocele as an initial procedure, by performing a retrospective chart review, focusing on the prevalence of and risk factors for symptomatic urinary tract infection (UTI) after EI. In the present study we included children with ureterocele, managed between September 1994 and April 2016, who were observed conservatively without additional surgical management after EI. Ureterocele was categorized as intravesical or ectopic. Symptomatic UTI was defined as either recurrent non-febrile or febrile UTI. The prevalence of and risk factors for symptomatic UTI were analysed using Cox proportional hazard models or Kaplan-Meier curves, and the log-rank test. A total of 36 children met the inclusion criteria. The median age of the participants at EI was 8.9 months. Eleven children had symptomatic UTIs (febrile, n = 9; recurrent non-febrile, n = 2) during the median follow-up of 75.5 months. Initial symptomatic UTI in each child occurred UTI-free rate after EI was 65.6%. The risk factors for symptomatic UTI were female gender, duplex system, ectopic ureterocele, and unchanged hydronephrosis after EI. The present study determined the critical period and risk factors for symptomatic UTI after EI for the treatment of ureterocele. The results suggest that when conservative management is indicated after EI, patients, especially those with risk factors, should be followed carefully at least for 25 months after EI for symptomatic UTI. © 2017 The Authors BJU International © 2017 BJU International Published by John Wiley & Sons Ltd.

  6. Outcomes of small incision lenticule extraction (SMILE) in low myopia.

    Science.gov (United States)

    Reinstein, Dan Z; Carp, Glenn I; Archer, Timothy J; Gobbe, Marine

    2014-12-01

    To report the visual and refractive outcomes of small incision lenticule extraction for low myopia using the VisuMax femtosecond laser (Carl Zeiss Meditec, Jena, Germany). A retrospective analysis of 120 consecutive small incision lenticule extraction procedures was performed for low myopia. Inclusion criteria were preoperative spherical equivalent refraction up to -3.50 diopters (D), cylinder up to 1.50 D, and corrected distance visual acuity of 20/20 or better. Outcomes analysis was performed for all eyes with 1-year follow-up according to the Standard Graphs for Reporting Refractive Surgery, and also including mesopic contrast sensitivity. One-year data were available for 110 eyes (92%). Preoperatively, mean spherical equivalent refraction was -2.61 ± 0.54 D (range: -1.03 to -3.50 D) and mean cylinder was 0.55 ± 0.38 D (range: 0.00 to 1.50 D). Postoperatively, mean spherical equivalent refraction was -0.05 ± 0.36 D (range: -0.94 to +1.25 D) and mean cylinder was ± 0.50 D in 84% and ± 1.00 D in 99% of eyes. Uncorrected distance visual acuity was 20/20 or better in 96% of eyes and 20/25 or better in 100% of eyes. One line of corrected distance visual acuity was lost in 9%, but no eyes lost two or more lines. There was an initial overcorrection in mean spherical equivalent refraction on day 1 (+0.37 D) as expected, which regressed to +0.10 D at 1 month and -0.05 D at 3 months, after which stability was reached (mean spherical equivalent refraction was -0.05 D at 1 year). Contrast sensitivity at 1 year was slightly increased at 3, 6, 12, and 18 cycles per degree (P < .05). Small incision lenticule extraction for low myopia was found to be safe and effective with outcomes similar to those previously reported for LASIK. Copyright 2014, SLACK Incorporated.

  7. Complex DNA structures and structures of DNA complexes

    International Nuclear Information System (INIS)

    Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J.

    1994-01-01

    Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe 1 H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful

  8. Complex DNA structures and structures of DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J. [Scripps Research Institute, La Jolla, CA (United States)

    1994-12-01

    Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe {sup 1}H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful.

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

    Science.gov (United States)

    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 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.

  10. Mouse preferential incising force orientation changes during jaw closing muscle hyperalgesia and is sex dependent.

    Science.gov (United States)

    Widmer, C G; Morris-Wiman, J

    2016-12-01

    Mouse incising is controlled by a central pattern generator and this activity can change in the presence of pain. The incising frequency and maximum force generation decreases with pain. In this study, we used repetitive acidic injections in the left masseter muscle of male and female mice to determine differences between baseline and jaw muscle pain conditions and the effect of sex on preferential incising direction. A within subject design was used to evaluate data previously acquired using multi-axis force data (X, Y and Z) from the 4th baseline recording day and day 7 post-injection (day of maximal pain response) for each mouse of each sex. A total of 34 female and male (age 3-9months) CD-1 mice were evaluated. After mathematically rotating the X and Y axes to align the Y axis to be parallel to the wire struts of the cage top, data were analyzed to determine incising direction preference during baseline (non-pain) and pain (day 7) conditions and between sex. Radar plots of X-Y, X-Z and Y-Z axes depicted the average direction of incising preference between baseline and pain conditions for each sex. Statistical differences among groups were tested using a mixed model ANOVA. Similar to previous findings, female mice had a more robust difference in incising direction preference when comparing male and female pain conditions and this was most evident in the X-Z axes. The incising frequencies most commonly affected were 5.3, 6.2 and 7.6Hz. Male mice varied little in their incising direction preference between the baseline and pain conditions. In addition, statistical comparison of ratios of the percent of time spent incising in the Z versus X axes for each incising frequency found that the incising preference was not different when comparing 5.3 and 7.6Hz frequencies. Finally, female mice used a novel approach to minimize pain while incising by rotating their head and body nearly 180 degrees while males did not use this strategy as frequently. The preferred incising

  11. Clear corneal incision leakage after phacoemulsification--detection using povidone iodine 5%.

    Science.gov (United States)

    Chee, Soon-Phaik

    2005-01-01

    The purpose of this work was to study the incidence of clear corneal wound leakage at the conclusion of standard co-axial phacoemulsification in a prospective observational series of 100 consecutive cataract cases in a single surgeon's institutional practice. At the conclusion of standard co-axial phacoemulsification using a 2.75 mm temporal single plane clear corneal incision with a 1 mm clear corneal side-port incision, the wounds were hydrated and checked for water-tightness. Povidone iodine 5% (P-I) was then evenly dripped over the cornea and the wounds were inspected visually. Any leakage of aqueous observed was recorded. The amount of leakage was graded as small or large from each wound. Leaky wounds were further hydrated and retested with P-I until sealed. Wound integrity was reassessed on the first postoperative day by use of fluorescein. Of the 100 cases, wound leakage was observed for 31 eyes (31%)-ten main incisions, nineteen side-port incisions, and both incisions in two cases. Wound leakage was easily detected as a ribbon of clear fluid streaming from the incision amid a pool of brown solution. Povidone iodine was not observed within the tract in any incision. All wound leakage was small except for one from the main incision and two from the side-port incision. None of the eyes developed wound leakage the day after surgery and none developed endophthalmitis. In conclusion, leakage from clear corneal incisions at the conclusion of phacoemulsification occurs in almost a third of cases, predominantly from the side incision. It is easily detected by use of the P-I test.

  12. Improved quantification accuracy for duplex real-time PCR detection of genetically modified soybean and maize in heat processed foods

    Directory of Open Access Journals (Sweden)

    CHENG Fang

    2013-04-01

    Full Text Available Real-time PCR technique has been widely used in quantitative GMO detection in recent years.The accuracy of GMOs quantification based on the real-time PCR methods is still a difficult problem,especially for the quantification of high processed samples.To develop the suitable and accurate real-time PCR system for high processed GM samples,we made ameliorations to several real-time PCR parameters,including re-designed shorter target DNA fragment,similar lengths of amplified endogenous and exogenous gene targets,similar GC contents and melting temperatures of PCR primers and TaqMan probes.Also,one Heat-Treatment Processing Model (HTPM was established using soybean flour samples containing GM soybean GTS 40-3-2 to validate the effectiveness of the improved real-time PCR system.Tested results showed that the quantitative bias of GM content in heat processed samples were lowered using the new PCR system.The improved duplex real-time PCR was further validated using processed foods derived from GM soybean,and more accurate GM content values in these foods was also achieved.These results demonstrated that the improved duplex real-time PCR would be quite suitable in quantitative detection of high processed food products.

  13. Median sternotomy - gold standard incision for cardiac surgeons

    Directory of Open Access Journals (Sweden)

    Radu Matache

    2016-05-01

    Full Text Available Sternotomy is the gold standard incision for cardiac surgeons but it is also used in thoracic surgery especially for mediastinal, tracheal and main stem bronchus surgery. The surgical technique is well established and identification of the correct anatomic landmarks, midline tissue preparation, osteotomy and bleeding control are important steps of the procedure. Correct sternal closure is vital for avoiding short- and long-term morbidity and mortality. The two sternal halves have to be well approximated to facilitate healing of the bone and to avoid instability, which is a risk factor for wound infection. New suture materials and techniques would be expected to be developed to further improve the patients evolution, in respect to both immediate postoperative period and long-term morbidity and mortality

  14. Mandibular incisive canal in relation to periapical surgery

    Directory of Open Access Journals (Sweden)

    Kani Bilginaylar

    2016-01-01

    Full Text Available The aim of the present paper is to emphasize the importance of the mandibular interforaminal neurovascular bundle with a case and make a warning to dentists and surgeons during oral and maxillofacial surgeries, such as implant replacement, bone harvesting, genioplasty, open reduction of a mandibular fracture, and cyst enucleations at this region. In this paper, we present a 58-year-old male who referred with pain and a tingling sensation on the left lower lip. After radiographical, extraoral and intraoral examinations, findings indicated the lesion to be a cyst which was related with a periapical lesion of the canine tooth and extracted socket of first premolar tooth. After removal of a cyst, the mandibular incisive nerve was documented which was in relation to cyst cavity.

  15. Incisiones verticales en SARPE Vertical incisions in SARPE

    Directory of Open Access Journals (Sweden)

    J. Gonzalez Lagunas

    2005-06-01

    Full Text Available La expansión rápida de paladar asistida quirúrgicamente (SARPE es una de las opciones terapeuticas de los transtornos transversales del maxilar superior. Presentamos nuestra experiencia inicial con una variante técnica consistente en una corticotomía de la pared lateral del maxilar combinada con una osteotomía palatina media transincisal, y efectuadas a través de tres pequeñas incisiones verticales.Surgically assisted rapid palatal expansion (SARPE is one of the therapeutic options for the correction of transverse maxillary collapse. We present our initial experience with a technique consisting in a lateral corticotomy of the maxilla plus a transincisal midpalatal osteotomy, both performed through minimal vertical incisions.

  16. A case of bifocal endometriosis involving a pfannenstiel incision.

    Science.gov (United States)

    Evsen, Mehmet Sidik; Sak, Muhammet Erdal; Yalinkaya, Ahmet; Firat, Ugur; Caca, Fatma Nur

    2011-01-01

    A 25-year-old woman was referred to our clinic for atypical cyclic pain and masses at both ends of a Pfannenstiel incision scar. Ultrasound of the anterior abdominal wall showed two masses. Both masses were hypoechoic, heterogeneous lesions located at opposite ends of the scar. The lesions were surgically excised with. Microscopic examination revealed endometrial gland structures with endometrial stroma in fibroadipose tissue in sections of both specimens indicative of endometriosis. Incisional endometriosis (IE) is a form of extrapelvic endometriosis especially in scars of obstetric or gynecologic surgery IE may be multifocal at surgical scars. We report the a case of bifocal incisional endometriosis in Pfannesteil scar. Whole scar evaluation should be done for incisional endometriosis and surgical excision should be performed for treatment.

  17. Processing of free radical damaged DNA bases

    International Nuclear Information System (INIS)

    Wallace, S.

    2003-01-01

    Free radicals produced during the radiolysis of water gives rise to a plethora of DNA damages including single strand breaks, sites of base loss and a wide variety of purine and pyrimidine base lesions. All these damages are processed in cells by base excision repair. The oxidative DNA glycosylases which catalyze the first step in the removal of a base damage during base excision repair evolved primarily to protect the cells from the deleterious mutagenic effects of single free radical-induced DNA lesions arising during oxidative metabolism. This is evidenced by the high spontaneous mutation rate in bacterial mutants lacking the oxidative DNA glycosylases. However, when a low LET photon transverses the DNA molecule, a burst of free radicals is produced during the radiolysis of water that leads to the formation of clustered damages in the DNA molecule, that are recognized by the oxidative DNA glycosylases. When substrates containing two closely opposed sugar damages or base and sugar damages are incubated with the oxidative DNA glycosylases in vitro, one strand is readily incised by the lyase activity of the DNA glycosylase. Whether or not the second strand is incised depends on the distance between the strand break resulting from the incised first strand and the remaining DNA lesion on the other strand. If the lesions are more than two or three base pairs apart, the second strand is readily cleaved by the DNA glycosylase, giving rise to a double strand break. Even if the entire base excision repair system is reconstituted in vitro, whether or not a double strand break ensues depends solely upon the ability of the DNA glycosylase to cleave the second strand. These data predicted that cells deficient in the oxidative DNA glycosylases would be radioresistant while those that overproduce an oxidative DNA glycosylase would be radiosensitive. This prediction was indeed borne in Escherichia coli that is, mutants lacking the oxidative DNA glycosylases are radioresistant

  18. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies

    Czech Academy of Sciences Publication Activity Database

    Kratochvílová, Irena; Vala, M.; Weiter, M.; Špérová, M.; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    180-181, Oct-Nov (2013), s. 127-134 ISSN 0301-4622 R&D Projects: GA TA ČR TA01011165; GA ČR(CZ) GAP304/10/1951; GA ČR GA13-27676S; GA ČR GA202/09/0193 Institutional support: RVO:68378271 ; RVO:86652036 ; RVO:61388963 Keywords : charge transfer in oligonucleotides * temperature dependent steady state fluorescence spectroscopy * time-resolved fluorescence spectroscopy Subject RIV: JJ - Other Materials; CC - Organic Chemistry (UOCHB-X) Impact factor: 2.319, year: 2013

  19. 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.

    Science.gov (United States)

    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.

  20. Mycobacterium smegmatis Lhr Is a DNA-dependent ATPase and a 3'-to-5' DNA translocase and helicase that prefers to unwind 3'-tailed RNA:DNA hybrids.

    Science.gov (United States)

    Ordonez, Heather; Shuman, Stewart

    2013-05-17

    We are interested in the distinctive roster of helicases of Mycobacterium, a genus of the phylum Actinobacteria that includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis Lhr as the exemplar of a novel clade of superfamily II helicases, by virtue of its biochemical specificities and signature domain organization. Lhr is a 1507-amino acid monomeric nucleic acid-dependent ATPase that uses the energy of ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single strand DNA and to unwind duplexes en route. The ATPase is more active in the presence of calcium than magnesium. ATP hydrolysis is triggered by either single strand DNA or single strand RNA, yet the apparent affinity for a DNA activator is 11-fold higher than for an RNA strand of identical size and nucleobase sequence. Lhr is 8-fold better at unwinding an RNA:DNA hybrid than it is at displacing a DNA:DNA duplex of identical nucleobase sequence. The truncated derivative Lhr-(1-856) is an autonomous ATPase, 3'-to-5' translocase, and RNA:DNA helicase. Lhr-(1-856) is 100-fold better RNA:DNA helicase than DNA:DNA helicase. Lhr homologs are found in bacteria representing eight different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis) and Proteobacteria (including Escherichia coli).

  1. Detection of Ultra-Rare Mitochondrial Mutations in Breast Stem Cells by Duplex Sequencing.

    Directory of Open Access Journals (Sweden)

    Eun Hyun Ahn

    Full Text Available Long-lived adult stem cells could accumulate non-repaired DNA damage or mutations that increase the risk of tumor formation. To date, studies on mutations in stem cells have concentrated on clonal (homoplasmic mutations and have not focused on rarely occurring stochastic mutations that may accumulate during stem cell dormancy. A major challenge in investigating these rare mutations is that conventional next generation sequencing (NGS methods have high error rates. We have established a new method termed Duplex Sequencing (DS, which detects mutations with unprecedented accuracy. We present a comprehensive analysis of mitochondrial DNA mutations in human breast normal stem cells and non-stem cells using DS. The vast majority of mutations occur at low frequency and are not detectable by NGS. The most prevalent point mutation types are the C>T/G>A and A>G/T>C transitions. The mutations exhibit a strand bias with higher prevalence of G>A, T>C, and A>C mutations on the light strand of the mitochondrial genome. The overall rare mutation frequency is significantly lower in stem cells than in the corresponding non-stem cells. We have identified common and unique non-homoplasmic mutations between non-stem and stem cells that include new mutations which have not been reported previously. Four mutations found within the MT-ND5 gene (m.12684G>A, m.12705C>T, m.13095T>C, m.13105A>G are present in all groups of stem and non-stem cells. Two mutations (m.8567T>C, m.10547C>G are found only in non-stem cells. This first genome-wide analysis of mitochondrial DNA mutations may aid in characterizing human breast normal epithelial cells and serve as a reference for cancer stem cell mutation profiles.

  2. Intersegmental interactions in supercoiled DNA: atomic force microscope study

    Energy Technology Data Exchange (ETDEWEB)

    Shlyakhtenko, Luda S.; Miloseska, Lela; Potaman, Vladimir N.; Sinden, Richard R.; Lyubchenko, Yuri L

    2003-10-15

    Intersegmental interactions in DNA facilitated by the neutralization of electrostatic repulsion was studied as a function of salt concentration and DNA supercoiling. DNA samples with defined superhelical densities were deposited onto aminopropyl mica at different ionic conditions and imaged in air after drying of the samples. Similar to hydrodynamic data, we did not observe a collapse of supercoiled DNA, as proposed earlier by cryo-EM studies. Instead, the formation of the contacts between DNA helices within supercoiled loops with no visible space between the duplexes was observed. The length of such close contacts increased upon increasing NaCl concentration. DNA supercoiling was a critical factor for the stabilization of intersegmental contacts. Implications of the observed effect for understanding DNA compaction in the cell and for regulation DNA transactions via interaction of distantly separated DNA regions are discussed.

  3. Performance of fast-absorbable suture and histo-glue in closing incisions in Brown trout

    DEFF Research Database (Denmark)

    Jepsen, Niels; Larsen, Martin Hage; Aarestrup, Kim

    2017-01-01

    , growth, tag expulsion rate and incision healing was compared among three groups of dummy transmitter-tagged wild brown trout Salmo trutta where incisions were closed with two types of suture material (absorbable vs. fast absorbable) and Histo-glue. The tagged fish were kept in semi-natural ponds for 20...

  4. Numerical modeling and optimization of machining duplex stainless steels

    Directory of Open Access Journals (Sweden)

    Rastee D. Koyee

    2015-01-01

    Full Text Available The shortcomings of the machining analytical and empirical models in combination with the industry demands have to be fulfilled. A three-dimensional finite element modeling (FEM introduces an attractive alternative to bridge the gap between pure empirical and fundamental scientific quantities, and fulfill the industry needs. However, the challenging aspects which hinder the successful adoption of FEM in the machining sector of manufacturing industry have to be solved first. One of the greatest challenges is the identification of the correct set of machining simulation input parameters. This study presents a new methodology to inversely calculate the input parameters when simulating the machining of standard duplex EN 1.4462 and super duplex EN 1.4410 stainless steels. JMatPro software is first used to model elastic–viscoplastic and physical work material behavior. In order to effectively obtain an optimum set of inversely identified friction coefficients, thermal contact conductance, Cockcroft–Latham critical damage value, percentage reduction in flow stress, and Taylor–Quinney coefficient, Taguchi-VIKOR coupled with Firefly Algorithm Neural Network System is applied. The optimization procedure effectively minimizes the overall differences between the experimentally measured performances such as cutting forces, tool nose temperature and chip thickness, and the numerically obtained ones at any specified cutting condition. The optimum set of input parameter is verified and used for the next step of 3D-FEM application. In the next stage of the study, design of experiments, numerical simulations, and fuzzy rule modeling approaches are employed to optimize types of chip breaker, insert shapes, process conditions, cutting parameters, and tool orientation angles based on many important performances. Through this study, not only a new methodology in defining the optimal set of controllable parameters for turning simulations is introduced, but also

  5. Identification of sigma and chi phases in duplex stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Llorca-Isern, Núria, E-mail: nullorca@ub.edu [Departament de Ciència dels Materials i Enginyeria Metallurgica, Facultat de Química, Universitat de Barcelona, Marti-Franqués 1, 08028 Barcelona (Spain); López-Luque, Héctor, E-mail: hlopezlu7@alumnes.ub.edu [Departament de Ciència dels Materials i Enginyeria Metallurgica, Facultat de Química, Universitat de Barcelona, Marti-Franqués 1, 08028 Barcelona (Spain); López-Jiménez, Isabel, E-mail: ilopezji9@alumnes.ub.edu [Departament de Ciència dels Materials i Enginyeria Metallurgica, Facultat de Química, Universitat de Barcelona, Marti-Franqués 1, 08028 Barcelona (Spain); Biezma, Maria Victoria, E-mail: maria.biezma@unican.es [Department of Earth, Materials Science and Engineering, University of Cantabria - UC, Gamazo, 1, 39004 Santander (Spain)

    2016-02-15

    The aim of this work is to find out the most suitable method for detecting and analyzing accurately the formation conditions of secondary phases, particularly Sigma-phase (σ-phase) and Chi-phase (χ-phase) in duplex stainless steels (UNS S32205 and UNS S32750). The microstructure was characterized after a solution annealing at 1080 °C followed by an isothermal heating at 830 °C for different time ranges, ranging from 1 min to 9 h, in order to enlighten the controversial point concerning the mechanism of χ-phase nucleation in relation with the σ-phase. Etched samples were observed using optical microscopy (MO), and scanning electron microscopy (FESEM) with a backscattered electron detector (BSE) was used on unetched samples. Compositional microanalysis (EDS) was carried out for identifying the different phases present in the steels. Sigma phase was easily observed using different etching procedures, whereas χ-phase was only clearly detected with FESEM–BSE on unetched samples. The compositional analyses showed that the molybdenum content in χ-phase almost doubles the content of this element in σ-phase, and as a result the kinetics of nucleation and growth were also found to be remarkably faster when the alloy content in the steel is higher. In addition, chromium nitrides and carbides were also observed to precipitate as a result of the heat treatments and, in the case of the chromium nitrides, they act as a favorable site for the nucleation of σ-phase and χ-phase. - Highlights: • Microscopy was used on heat treated duplex steels for microstructure identification. • FESEM–BSE observation on unetched samples provided the best contrast between phases. • Analyses of carbides, nitrides, chi and sigma phases were possible by EDS and WDS. • Chromium nitrides act as favorable site for the nucleation of chi and sigma phases. • Secondary phases nucleation kinetics are faster in superduplex than in duplex steels.

  6. Surveillance Duplex Ultrasonography of Stent Grafts for Popliteal Aneurysms.

    Science.gov (United States)

    Pineda, Danielle M; Troutman, Douglas A; Dougherty, Matthew J; Calligaro, Keith D

    2016-05-01

    Stent grafts, also known as covered stents, have become an increasingly acceptable treatment for popliteal artery aneurysms. However, endovascular exclusion confers lower primary patency compared to traditional open bypass and exclusion. The purpose of this study was to evaluate whether duplex ultrasonography (DU) can reliably diagnose failing stent grafts placed for popliteal artery aneurysms prior to occlusion. Between June 5, 2007, and March 11, 2014, 21 stent grafts (Viabahn; Gore, Flagstaff, Arizona) were placed in 19 patients for popliteal artery aneurysms. All patients had at least 1 follow-up duplex scan postoperatively. Mean follow-up was 28.9 months (9-93 months). Postoperative DU surveillance was performed in our Intersocietal Accreditation Commission noninvasive vascular laboratory at 1 week postprocedure and every 6 months thereafter. Duplex ultrasonography measured peak systolic velocities (PSVs) and ratio of adjacent PSVs (Vr) every 5 cm within the stent graft and adjacent arteries. We retrospectively classified the following factors as "abnormal DU findings": focal PSV > 300 cm/s, uniform PSVs 3.0. These DU criteria were derived from laboratory-specific data that we previously published on failing stent grafts placed for lower extremity occlusive disease. Four of the 21 stent grafts presented with symptomatic graft thrombosis within 6 months of a normal DU. Three of these 4 patients presented with rest pain and underwent thrombectomy (2) or vein bypass (1), and 1 elected for nonintervention for claudication. Our results suggest that surveillance DU using criteria established for grafts placed for occlusive disease may not be useful for predicting stent graft failure in popliteal artery aneurysms. © The Author(s) 2016.

  7. Toughness and other mechanical properties of the duplex stainless steel 2205

    International Nuclear Information System (INIS)

    Sieurin, H.; Sandstroem, R.

    2003-01-01

    The use and range of potential applications of duplex stainless steel continuously increase. An overview of the mechanical properties of duplex stainless steel 2205 is presented with focus on toughness properties. Impact and fracture toughness as well as strength results from the European research project, EcoPress, are presented. (orig.)

  8. Interference alignment for degrees of freedom improvement in 3-relay half-duplex systems

    KAUST Repository

    Park, Seongho; Ko, Youngchai; Park, Kihong; Alouini, Mohamed-Slim

    2011-01-01

    In a half-duplex relaying, the capacity pre-log factor is a major drawback in spectral efficiency. This paper proposes a linear precoding scheme and an alternate relaying protocol in a dual-hop half-duplex system where three relays help

  9. Importance of diastolic velocities in the detection of celiac and mesenteric artery disease by duplex ultrasound

    DEFF Research Database (Denmark)

    Perko, M J; Just, S; Schroeder, T V

    1997-01-01

    To assess the predictive value of ultrasound duplex scanning in the detection of superior mesenteric artery (SMA) and celiac artery (CA) occlusive disease.......To assess the predictive value of ultrasound duplex scanning in the detection of superior mesenteric artery (SMA) and celiac artery (CA) occlusive disease....

  10. Four-Tap RF Canceller Evaluation for Indoor In-Band Full-Duplex Wireless Operation

    Science.gov (United States)

    2016-07-24

    I. INTRODUCTION In-band full-duplex (IBFD) wireless operation can help alleviate the frequency spectrum congestion issues faced by current system...Valkama, “Wideband self-adaptive rf cancellation circuit for full- duplex radio: Operating principle and measurements,” in 2015 IEEE 81st Vehicular

  11. Value of Duplex scanning in the selection of patients for percutaneous transluminal angioplasty

    NARCIS (Netherlands)

    van der Heijden, F. H.; Legemate, D. A.; van Leeuwen, M. S.; Mali, W. P.; Eikelboom, B. C.

    1993-01-01

    Duplex scanning is becoming increasingly important in the diagnosis and follow-up of arterial lesions, though most surgeons and radiologists currently still prefer diagnostic angiography prior to percutaneous transluminal angioplasty (PTA). We performed PTA based on Duplex scanning alone in 31

  12. Can duplex Doppler ultrasound replace computerized tomography in staging patients with renal cell carcinoma?

    NARCIS (Netherlands)

    Bos, SD; Mensink, HJA

    The purpose of this study was to evaluate the accuracy and reliability of duplex Doppler ultrasound (US) and computerized tomography (CT) in staging patients with renal cell carcinoma (RCC). Sixty-six patients were evaluated pre-operatively with duplex Doppler ultrasound and CT. The results were

  13. Optimization of welding variables for duplex stainless steel by GTAW and SMAW

    International Nuclear Information System (INIS)

    Ajmal, M.; Anwar, M.Y.; Nawaz, A.

    2006-01-01

    The main problems faced during the welding of duplex stainless steels are cleanliness and slag inclusions. In the present work the methods to eliminate these problems were studied during the welding of duplex stainless steel by Gas Tungsten Arc Welding (GTAW) and Shielded Metal Arc Welding (SMAW). Since the duplex stainless steel is an expensive material, the initial experiments for optimization of welding variables were. carried out on low carbon steel (CS) plates with duplex consumables. Welding of butt groove joints on CS plates was carried with various sets of welding variables i.e. current, voltage and arc energy using duplex consumables. The. radiographic inspection, micro-structural observations and hardness testing of the welds suggested the welding variables that will produce a sound weld on CS plate. These optimized variables were then used for the welding of edge groove joint and T -joint on duplex stainless steel by GTAW and SMAW processes. The hardness and micro-structural study of the joints produced on duplex stainless steel by GTAW and SMAW with duplex consumables were also studied. No slag inclusions and porosity were observed in the microstructure of these weldments and their properties were found similar to the parent metal. (author)

  14. Full-duplex MIMO system based on antenna cancellation technique

    DEFF Research Database (Denmark)

    Foroozanfard, Ehsan; Franek, Ondrej; Tatomirescu, Alexandru

    2014-01-01

    The performance of an antenna cancellation technique for a multiple-input– multiple-output (MIMO) full-duplex system that is based on null-steering beamforming and antenna polarization diversity is investigated. A practical implementation of a symmetric antenna topology comprising three dual......-polarized patch antennas operating at 2.4 GHz is described. The measurement results show an average of 60 dB self-interference cancellation over 200 MHz bandwidth. Moreover, a decoupling level of up to 22 dB is achieved for MIMO multiplexing using antenna polarization diversity. The performance evaluation...

  15. Design of a Microwave Duplexer without Ferrite and without Magnet

    Directory of Open Access Journals (Sweden)

    F. Mejri

    2018-06-01

    Full Text Available In this paper we present the design, realization and characterization of a microwave duplexer, compact, easy to realize and integrate into systems such as ground penetrating radars. It is made without the use of ferrite or magnet. This device is designed in the S band and made in micro-ribbon technology. It consists of a power divider and two RF amplifiers, low gain, using a BFR91 bipolar transistor. The latter is frequently available and inexpensive. Measurements made on a vector network analyzer have shown a low insertion loss with insulation considered satisfactory – for low power applications - between the transmitter (Tx and the receiver (Rx circuits.

  16. Thermal study of bare tips with various system parameters and incision sizes.

    Science.gov (United States)

    Osher, Robert H; Injev, Valentine P

    2006-05-01

    To identify major and minor surgeon-controlled parameters that affect incision temperature when performing microincision lens removal using the Alcon Infiniti Vision System. In vitro research and development laboratory, Alcon Research, Irvine, California, USA. Phacoemulsification was performed in eye-bank cadaver eyes and the following parameters evaluated: incision, duty cycle, ultrasound (US) power, aspiration flow rate (AFR), vacuum, pulse, bottle height and balanced salt solution temperature, and tip design/size. Each parameter was varied while the others remained constant. The resulting temperature of the incision and US tip was measured using a thermal camera. Major contributors to elevated incision temperature included incision size, US power, duty cycle, AFR, vacuum setting, tip design, and presence of an ophthalmic viscosurgical device (OVD). Minor contributors included pulse frequency, bottle height, and temperature of the infusate. Microincision lens removal can be performed at safe temperatures with the knowledgeable selection of surgeon-controlled parameters.

  17. Single-incision laparoscopic surgery through an ostomy site: a natural approach by an unnatural orifice.

    Science.gov (United States)

    Lopez, Nicole E; Peterson, Carrie Y; Ramamoorthy, Sonia L; McLemore, Elisabeth C; Sedrak, Michael F; Lowy, Andrew M; Horgan, Santiago; Talamini, Mark A; Sicklick, Jason K

    2015-02-01

    Single-incision laparoscopic surgery (SILS) is gaining popularity for a wide variety of surgical operations and capitalizes on the benefits of traditional laparoscopic surgery without incurring multiple incision sites. Traditionally, SILS is performed by a midline periumbilical approach. However, such a minimally invasive approach may be utilized in patients who already have an abdominal incision. Our series retrospectively reviews 7 cases in which we utilized the fascial defect at the time of after ostomy reversal as our SILS incision site. In turn, we performed a variety of concurrent intra-abdominal procedures with excellent technical success and outcomes. Our study is the largest single-institution case series of this novel approach and suggests that utilizing an existing ostomy-site abdominal incision is a safe and effective location for SILS port placement and should be considered in patients undergoing concurrent procedures.

  18. Physical-Layer Security of a Buffer-Aided Full-Duplex Relaying System

    KAUST Repository

    El Shafie, Ahmed

    2016-07-07

    This letter proposes a novel hybrid half-/full-duplex relaying scheme to enhance the relay channel security. A source node (Alice) communicates with her destination node (Bob) in the presence of a buffer-aided full-duplex relay node (Rooney) and a potential eavesdropper (Eve). Rooney adopts two different relaying, namely randomize-and-forward and decode-andforward relaying strategies, to improve the security of the legitimate system. In the first relaying strategy, Rooney uses a codebook different from that used at Alice. In the second relaying strategy, Rooney and Alice use the same codebooks. In addition, Rooney switches between half-duplex and full-duplex modes to further enhance the security of the legitimate system. The numerical results demonstrate that our proposed scheme achieves a significant average secrecy end-to-end throughput improvement relative to the conventional bufferless full-duplex relaying scheme.

  19. Analyzing the Potential of Full Duplex in 5G Ultra-Dense Small Cell Networks

    DEFF Research Database (Denmark)

    Gatnau, Marta; Berardinelli, Gilberto; Mahmood, Nurul Huda

    2016-01-01

    Full duplex technology has become an attractive solution for future 5th Generation (5G) systems for accommodating the exponentially growing mobile traffic demand. Full duplex allows a node to transmit and receive simultaneously in the same frequency band, thus, theoretically, doubling the system...... throughput over conventional half duplex systems. A key limitation in building a feasible full duplex node is the self-interference, i.e., the interference generated by the transmitted signal to the desired signal received on the same node. This constraint has been overcome given the recent advances...... in the self-interference cancellation technology. However, there are other limitations in achieving the theoretical full duplex gain: residual self-interference, traffic constraints and inter-cell and intra-cell interference. The contribution of this article is twofold. Firstly, achievable levels of self...

  20. On the Potential of Full Duplex Performance in 5G Ultra-Dense Small Cell Networks

    DEFF Research Database (Denmark)

    Gatnau, Marta; Fleischer, Marko; Berardinelli, Gilberto

    2016-01-01

    inter-cell interference and traffic constraints. In this paper, we first study the self-interference cancellation capabilities by using a real demonstrator. Results show that achieving ~110 dB of cancellation is already possible with the current available technology, thus providing the required level...... of isolation to build an operational full duplex node. Secondly, we investigate the inter-cell interference and traffic constraints impact on the full duplex performance in 5th generation systems. System level results show that both the traffic and the inter-cell interference can significantly reduce...... the potential gain of full duplex with respect to half duplex. However, for large traffic asymmetry, full duplex can boost the performance of the lightly loaded link....

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

    Science.gov (United States)

    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.

  2. Physical-Layer Security of a Buffer-Aided Full-Duplex Relaying System

    KAUST Repository

    El Shafie, Ahmed; Salem, Ahmed Sultan; Al-Dhahir, Naofal

    2016-01-01

    This letter proposes a novel hybrid half-/full-duplex relaying scheme to enhance the relay channel security. A source node (Alice) communicates with her destination node (Bob) in the presence of a buffer-aided full-duplex relay node (Rooney) and a potential eavesdropper (Eve). Rooney adopts two different relaying, namely randomize-and-forward and decode-andforward relaying strategies, to improve the security of the legitimate system. In the first relaying strategy, Rooney uses a codebook different from that used at Alice. In the second relaying strategy, Rooney and Alice use the same codebooks. In addition, Rooney switches between half-duplex and full-duplex modes to further enhance the security of the legitimate system. The numerical results demonstrate that our proposed scheme achieves a significant average secrecy end-to-end throughput improvement relative to the conventional bufferless full-duplex relaying scheme.

  3. Recent, climate-driven river incision rate fluctuations in the Mercantour crystalline massif, southern French Alps

    Science.gov (United States)

    Petit, C.; Goren, L.; Rolland, Y.; Bourlès, D.; Braucher, R.; Saillard, M.; Cassol, D.

    2017-06-01

    We present a new geomorphological analysis of the Tinée River tributaries in the southern French Alps based on numerical inverse and forward modelling of their longitudinal profiles. We model their relative uplift history with respect to the main channel, hence the incision rate history of this channel. Inverse models show that all tributaries have consistent incision rate histories with alternating high and low values. A comparison with global temperature curves shows that these variations correlate with quaternary climate changes. We suggest that during warm periods, a wave of regressive erosion propagates in the Tinée River, while its tributaries deeply incise their substratum to catch up with the falling base-level. We also show that the post 140 ka history of this landscape evolution is dominated by fluvial incision. We then perform forward models of river incision and simulate the incision of the Tinée River system over a time span of 600 ka. This model allows us to extract time and space incision rate variations of the Tinée River. With a background of a few mm.yr-1, incision rate can increase up to more than 1 cm yr-1 during short periods of time due to climatic oscillations. This result is compatible with published cosmogenic nuclide based dating, which evidenced incision rates from 0.2 to 24 mm yr-1. The part of the channel located between 12 and 20 km downstream from the source has undergone several periods of rapid incision rates, which could explain the steep hillslopes and the triggering of a landslide ∼10 ka ago.

  4. Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  6. Duplex PCR for differentiation of the vaccine strain Brucella suis S2 and B. suis biovar 1 from other strains of Brucella spp.

    Science.gov (United States)

    Nan, Wenlong; Tan, Pengfei; Wang, Yong; Xu, Zouliang; Mao, Kairong; Peng, Daxin; Chen, Yiping

    2014-09-01

    Immunisation with attenuated Brucella spp. vaccines prevents brucellosis, but may also interfere with diagnosis. In this study, a duplex PCR was developed to distinguish Brucella suis vaccine strain S2 from field strains of B. suis biovar 1 and other Brucella spp. The PCR detected 60 fg genomic DNA of B. suis S2 or biovar 1 field strains and was able to distinguish B. suis S2 and wild-type strains of B. suis biovar 1 among 76 field isolates representing all the common species and biovars, as well as four vaccine strains, of Brucella. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Fluorescent Oligonucleotides Containing a 2-Ethynylfluorene-or 2-Ethynylfluorenone-labeled 2'-Deoxyguanosine Unit: Fluorescence Changes upon Duplex Formation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Min Ji; Hwang, Gil Tae [Kyungpook National University, Daegu (Korea, Republic of)

    2016-08-15

    Two new DNA probes bearing a fluorescent deoxyguanosine unit labeled with 2-ethynylfluorene (G{sup FL} )or 2-ethynylfluorenone (G{sup FO}) were synthesized and examined for their efficiency as quencher-free linear beacon probes. Oligodeoxynucleotides (ODNs) containing a G{sup FL} or G{sup FO} unit exhibit low thermal selectivity and few distinctive fluorescence changes upon duplex formation due to the syn conformation about the glycosidic bond. An exciplex emission was observed when the G{sup FL} unit of ODNs bearing adenine flanking bases was positioned opposite to the adenine nucleobases.

  8. High-temperature fracture toughness of duplex microstructures

    International Nuclear Information System (INIS)

    French, J.D.; Chan, H.M.; Harmer, M.P.; Miller, G.A.

    1996-01-01

    The temperature dependence of the fracture toughness of ceramics exhibiting duplex microstructures was studied relative to their single-phase constituents using two test methods: bend testing of chevron-notched beams, and the indentation-crack-length technique. The two materials systems studied were Al 2 O 3 :c-ZrO 2 (Y) and Al 2 O 3 :Y 3 Al 5 O 12 (YAG), and the testing temperature ranged from room temperature to 1,200 C. The study showed that in both systems the duplex materials showed higher toughness values than their single-phase constituents above 800 C. This result was attributed to the contribution of low-energy interphase boundaries to the overall composite toughness. Indentation crack length measurements gave toughness values and trends comparable to those determined by the chevron-notched beam method. By comparing the results of the two test methods it was possible to demonstrate that the indentation calibration constant (ξ) shows no significant temperature or material dependence. For the zirconia-containing materials, however, indentation at elevated temperatures is accompanied by significant localized plasticity, which suppressed the radial cracking. Under such conditions, some caution is warranted, since localized plasticity can lead to an overestimation of the fracture toughness

  9. Tribological behavior of duplex coating improved by ion implantation

    International Nuclear Information System (INIS)

    Kakas, D.; Skoric, B.; Rakita, M.

    2004-01-01

    In the present paper the tribological behavior of the coatings are discussed. Duplex coatings were applied on cold working steel 100Cr6. Samples were plasma nitrided at different thickness of plasma surface layers. TiN was deposited with a classic BALZERS PVD equipment and subsequent ion implantation. Ion implantation was provided with N 5+ ions. The other samples were produced with IBAD technology in DANFYSIK chamber. Wear resistance and exchanges of friction coefficient were measured with on-line test using special designed tribology equipment. Following the tests, the wear zone morphology and characteristics of surface layer structure as well as important properties were investigated by scanning electron microscopy (SEM) and X-ray diffraction analysis (XRD). Scratch adhesion testing was performed using commercially available equipment. Energy dispersive X-ray analysis (EDAX) of the wear-scars on pins provided essential information on the wear characteristics. In this paper some results related to influence of duplex coating production methodology on tribological behavior for cold working steel was presented

  10. Unusual Presentation of Duplex Kidneys: Ureteropelvic Junction Obstruction

    Directory of Open Access Journals (Sweden)

    Cemile Başdaş

    2016-01-01

    Full Text Available Aim. Ureteropelvic junction obstruction (UPJO is rarely associated with a duplex collecting system. We review this unusual anomaly in terms of presentation, diagnostic evaluation, and surgical management. Method. We retrospectively reviewed the medical records of patients diagnosed with a duplex system with UPJO. Result. Sixteen patients (6 girls, 10 boys with 18 moieties were treated surgically and four patients were treated conservatively. The median age at surgery was two years (range, 2 months to 7 years. The lower pole and upper moiety were affected in 12 and two kidneys, respectively, and both were affected in two patients. The anomaly was right-sided in 12 moieties and left-sided in six. The duplication was incomplete in seven patients and complete in nine. The mean renal pelvis diameter at the time of surgery was 25.6 (range 11–48 mm mm by USG. The mean renal function of the involved moiety was 28.3% before surgery. Management included pyelopyelostomy or ureteropyelostomy in six moieties, dismembered pyeloplasty in eight moieties, heminephrectomy in four cases, and simultaneous upper heminephrectomy and lower pole ureteropyelostomy in one patient. Conclusion. There is no standard approach for these patients and treatment should be individualized according to physical presentation, detailed anatomy, and severity of obstruction.

  11. Microstructural characterization of thermally-aged duplex stainless steels

    International Nuclear Information System (INIS)

    Nomoto, A.; Hamaoka, T.; Nishida, K.; Dohi, K.; Soneda, N.

    2011-01-01

    The embrittlement of duplex stainless steels is of concern for the long term operation of light water reactors. The objectives of this work was to characterize solute atom distribution in ferrite phase of thermally aged duplex stainless steels by using atom tomography probe and to measure the hardness of ferrite phase by using nano-indentation technique. This series of slides highlights 4 main conclusions. First, phase separation quickly evolves and then slows down during the thermal ageing. Secondly, precipitates are formed after ageing for 1000 hr at 400 C and 2000 hr at 350 C. The clusters become larger with time at 400 C. Chemical composition of the clusters do not change very much with cluster size and ageing time at 400 C. Thirdly, no cluster formation is observed in the materials aged at 450 C. It is likely that precipitation occurs faster than phase separation at lower temperatures. Fourthly, hardness changes are well described by combining the contributions of phase separation and G phase formation. 'Variation' is a good parameter to describe hardness change due to phase separation. Contribution of G-phase needs to be considered separately

  12. Duplex-imprinted nano well arrays for promising nanoparticle assembly

    Science.gov (United States)

    Li, Xiangping; Manz, Andreas

    2018-02-01

    A large area nano-duplex-imprint technique is presented in this contribution using natural cicada wings as stamps. The glassy wings of the cicada, which are abundant in nature, exhibit strikingly interesting nanopillar structures over their membrane. This technique, with excellent performance despite the nonplanar surface of the wings, combines both top-down and bottom-up nanofabrication techniques. It transitions micro-nanofabrication from a cleanroom environment to the bench. Two different materials, dicing tape with an acrylic layer and a UV optical adhesive, are used to make replications at the same time, thus achieving duplex imprinting. The promise of a large volume of commercial manufacturing of these nanostructure elements can be envisaged through this contribution to speeding up the fabrication process and achieving a higher throughput. The contact angle of the replicated nanowell arrays before and after oxygen plasma was measured. Gold nanoparticles (50 nm) were used to test how the nanoparticles behaved on the untreated and plasma-treated replica surface. The experiments show that promising nanoparticle self-assembly can be obtained.

  13. Study of Sigma Phase in Duplex SAF 2507

    Science.gov (United States)

    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.

  14. Duplex Identification of Staphylococcus aureus by Aptamer and Gold Nanoparticles.

    Science.gov (United States)

    Chang, Tianjun; Wang, Libo; Zhao, Kexu; Ge, Yu; He, Meng; Li, Gang

    2016-06-01

    Staphylococcus aureus is the top common pathogen causing infections and food poisoning. Identification of S. aureus is crucial for the disease diagnosis and regulation of food hygiene. Herein, we report an aptamer-AuNPs based method for duplex identification of S. aureus. Using AuNPs as an indicator, SA23, an aptamer against S. aureus, can well identify its target from Escherichia coli, Listeria monocytogenes and Pseudomonas aeruginosa. Furthermore, we find citrate-coated AuNPs can strongly bind to S. aureus, but not bind to Salmonella enterica and Proteus mirabilis, which leads to different color changes in salt solution. This colorimetric response is capable of distinguishing S. aureus from S. enteritidis and P. mirabilis. Thus, using the aptasensor and AuNPs together, S. aureus can be accurately identified from the common pathogens. This duplex identification system is a promising platform for simple visual identification of S. aureus. Additionally, in the aptasensing process, bacteria are incubated with aptamers and then be removed before the aptamers adding to AuNPs, which may avoid the interactions between bacteria and AuNPs. This strategy can be potentially applied in principle to detect other cells by AuNPs-based aptasensors.

  15. STUDY OF VARIOUS MODALITIES IN MANAGEMENT OF INCISION HERNIA REPAIR

    Directory of Open Access Journals (Sweden)

    Raghu Rachha

    2018-03-01

    Full Text Available BACKGROUND Incisional hernias are a major problem following abdominal surgery and their repairs are among the common surgeries done by a general surgeon.1 Besides the preoperative factors such as anaemia, BMI over 25 kg/m2 and smoking which are leading causes contributing to the development of Incisional hernia, laparotomy performed through the abdominal incision doubles the risk of IH.2 In addition, wound infection, increases the risk of IH formation by 1.9 times.3 If left unattended they may attain large size therefore cause discomfort and lead to the complications like Obstruction, Strangulation, Incarceration increasing the risk of morbidity and mortality.4 Treatment of IH involves further major surgery and the results may be poor, with the recurrence rates of up to 49% reported.5 A wide spectrum of surgical techniques have been developed and recommended ranging from sutured techniques to the various types of prosthetic mesh. MATERIALS AND METHODS 30 patients were studied who presented to emergency department with incisional hernias during August 2014 – September 2016 at Gandhi Medical College and Hospital. All patients underwent definitive treatment. RESULTS From our study it is observed that 1. The maximum cases of incisional hernias presenting to the emergency surgical department were found to be in 51-60 years age group. 2. There was female preponderance. 3. Obstruction is the most common presenting symptom found in 60% of cases followed by irreducibility (33.3% and strangulation (6.67%. 4. The onset of incisional hernias is more after 10 years following previous surgery. 5. Among 30 patients, bowel was viable in 18 patients (60% and mesh repair was done in 13 patients. Bowel was gangrenous in 12 patients (40% and anatomical repair was done in 17 patients. 6. Out of 30, women got infected in 11 patients (36.67% wound dehiscence noted in 5 patients (16.67%. 7. The recurrence rate was 6.67% with 6 months follow up. CONCLUSION 1. The mean

  16. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  17. Stress corrosion cracking of duplex stainless steels in caustic solutions

    Science.gov (United States)

    Bhattacharya, Ananya

    Duplex stainless steels (DSS) with roughly equal amount of austenite and ferrite phases are being used in industries such as petrochemical, nuclear, pulp and paper mills, de-salination plants, marine environments, and others. However, many DSS grades have been reported to undergo corrosion and stress corrosion cracking in some aggressive environments such as chlorides and sulfide-containing caustic solutions. Although stress corrosion cracking of duplex stainless steels in chloride solution has been investigated and well documented in the literature but the SCC mechanisms for DSS in caustic solutions were not known. Microstructural changes during fabrication processes affect the overall SCC susceptibility of these steels in caustic solutions. Other environmental factors, like pH of the solution, temperature, and resulting electrochemical potential also influence the SCC susceptibility of duplex stainless steels. In this study, the role of material and environmental parameters on corrosion and stress corrosion cracking of duplex stainless steels in caustic solutions were investigated. Changes in the DSS microstructure by different annealing and aging treatments were characterized in terms of changes in the ratio of austenite and ferrite phases, phase morphology and intermetallic precipitation using optical micrography, SEM, EDS, XRD, nano-indentation and microhardness methods. These samples were then tested for general and localized corrosion susceptibility and SCC to understand the underlying mechanisms of crack initiation and propagation in DSS in the above-mentioned environments. Results showed that the austenite phase in the DSS is more susceptible to crack initiation and propagation in caustic solutions, which is different from that in the low pH chloride environment where the ferrite phase is the more susceptible phase. This study also showed that microstructural changes in duplex stainless steels due to different heat treatments could affect their SCC

  18. 2'β-Fluoro-Tricyclo Nucleic Acids (2'F-tc-ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation.

    Science.gov (United States)

    Istrate, Alena; Katolik, Adam; Istrate, Andrei; Leumann, Christian J

    2017-08-01

    We describe the synthesis, thermal stability, structural and RNase H activation properties of 2'β-fluoro-tricyclo nucleic acids (2'F-tc-ANA). Three 2'F-tc-ANA nucleosides (T, 5Me C and A) were synthesized starting from a previously described fluorinated tricyclo sugar intermediate. NMR analysis and quantum mechanical calculations indicate that 2'F-tc-ANA nucleosides prefer sugar conformations in the East and South regions of the pseudorotational cycle. UV-melting experiments revealed that non-consecutive insertions of 2'F-tc-ANA units in DNA reduce the affinity to DNA and RNA complements. However, an oligonucleotide with five contiguous 2'F-tc-ANA-T insertions exhibits increased affinity to complementary RNA. Moreover, a fully modified 10-mer 2'F-tc-ANA oligonucleotide paired to both DNA (+1.6 °C/mod) and RNA (+2.5 °C/mod) with significantly higher affinity compared to corresponding unmodified DNA, and similar affinity compared to corresponding tc-DNA. In addition, CD spectroscopy and molecular dynamics simulations indicate that the conformation of the 2'F-tc-ANA/RNA duplex is similar to that of a DNA/RNA duplex. Moreover, in some sequence contexts, 2'F-tc-ANA promotes RNase H-mediated cleavage of a complementary RNA strand. Taken together, 2'F-tc-ANA represents a nucleic acid analogue that offers the advantage of high RNA affinity while maintaining the ability to activate RNase H, and can be considered a prospective candidate for gene silencing applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. A new general model for predicting melting thermodynamics of complementary and mismatched B-form duplexes containing locked nucleic acids: application to probe design for digital PCR detection of somatic mutations.

    Science.gov (United States)

    Hughesman, Curtis; Fakhfakh, Kareem; Bidshahri, Roza; Lund, H Louise; Haynes, Charles

    2015-02-17

    Advances in real-time polymerase chain reaction (PCR), as well as the emergence of digital PCR (dPCR) and useful modified nucleotide chemistries, including locked nucleic acids (LNAs), have created the potential to improve and expand clinical applications of PCR through their ability to better quantify and differentiate amplification products, but fully realizing this potential will require robust methods for designing dual-labeled hydrolysis probes and predicting their hybridization thermodynamics as a function of their sequence, chemistry, and template complementarity. We present here a nearest-neighbor thermodynamic model that accurately predicts the melting thermodynamics of a short oligonucleotide duplexed either to its perfect complement or to a template containing mismatched base pairs. The model may be applied to pure-DNA duplexes or to duplexes for which one strand contains any number and pattern of LNA substitutions. Perturbations to duplex stability arising from mismatched DNA:DNA or LNA:DNA base pairs are treated at the Gibbs energy level to maintain statistical significance in the regressed model parameters. This approach, when combined with the model's accounting of the temperature dependencies of the melting enthalpy and entropy, permits accurate prediction of T(m) values for pure-DNA homoduplexes or LNA-substituted heteroduplexes containing one or two independent mismatched base pairs. Terms accounting for changes in solution conditions and terminal addition of fluorescent dyes and quenchers are then introduced so that the model may be used to accurately predict and thereby tailor the T(m) of a pure-DNA or LNA-substituted hydrolysis probe when duplexed either to its perfect-match template or to a template harboring a noncomplementary base. The model, which builds on classic nearest-neighbor thermodynamics, should therefore be of use to clinicians and biologists who require probes that distinguish and quantify two closely related alleles in either a

  20. Dideoxynucleoside triphosphate-sensitive DNA polymerase from rice is involved in base excision repair and immunologically similar to mammalian DNA pol beta.

    Science.gov (United States)

    Sarkar, Sailendra Nath; Bakshi, Sankar; Mokkapati, Sanath K; Roy, Sujit; Sengupta, Dibyendu N

    2004-07-16

    A single polypeptide with ddNTP-sensitive DNA polymerase activity was purified to near homogeneity from the shoot tips of rice seedlings and analysis of the preparations by SDS-PAGE followed by silver staining showed a polypeptide of 67 kDa size. The DNA polymerase activity was found to be inhibitory by ddNTP in both in vitro DNA polymerase activity assay and activity gel analysis. Aphidicolin, an inhibitor of other types of DNA polymerases, had no effect on plant enzyme. The 67 kDa rice DNA polymerase was found to be recognized by the polyclonal antibody (purified IgG) made against rat DNA polymerase beta (pol beta) both in solution and also on Western blot. The recognition was found to be very specific as the activity of Klenow enzyme was unaffected by the antibody. The ability of rice nuclear extract to correct G:U mismatch of oligo-duplex was observed when oligo-duplex with 32P-labeled lower strand containing U (at 22nd position) was used as substrate. Differential appearance of bands at 21-mer, 22-mer, and 51-mer position in presence of dCTP was visible only with G:U mismatch oligo-duplex, but not with G:C oligo-duplex. While ddCTP or polyclonal antibody against rat-DNA pol beta inhibits base excision repair (BER), aphidicolin had no effect. These results for the first time clearly demonstrate the ability of rice nuclear extract to run BER and the involvement of ddNTP-sensitive pol beta type DNA polymerase. Immunological similarity of the ddNTP-sensitive DNA polymerase beta of rice and rat and its involvement in BER revealed the conservation of structure and function of ddNTP-sensitive DNA pol beta in plant and animal.

  1. De Qeurvian Tenosynovitis: Clinical Outcomes of Surgical Treatment with Longitudinal and Transverse Incision

    Directory of Open Access Journals (Sweden)

    Arefah Dehghani Tafti

    2011-03-01

    Full Text Available AbstractObjectives: De Quervain disease is a mechanical tenosynovitis due to inadequacy volume between abductor pollicis longus, extensor pollicis brevis and their tunnel. Treatment methods include immobilization, steroid injections, and operation. For the first time Fritz De Quervain described surgical treatment of this disease. Since then, various ways of treatment have been reported. The purpose of this study is to compare the clinical outcomes of a longitudinal incision with a transverse incision in De Quervain disease.Methods: This was a randomized controlled clinical trial conducted in three hospitals in Iran, Yazd from March 2003 to September 2008. One hundred-twenty patients with De Quervain disease who did not respond to conservative treatment were operated with two different incisions. The patients were followed for three months to compare the surgical outcomes.Results: During a three month follow-up, a significant difference was shown between the two methods (p=0.03. Results of surgical treatment with longitudinal incision were excellent (only 5 hypertrophic scars, but there were 13 postoperative complaints with transverse incision.Conclusion: According to our findings, longitudinal incision in surgical treatment of De Quervain disease is better than transverse incision.

  2. Nuclear management in manual small incision cataract surgery by snare technique

    Directory of Open Access Journals (Sweden)

    Bhattacharya Debasish

    2009-01-01

    Full Text Available Manual small incision cataract surgery has evolved into a popular method of cataract surgery in India. However, in supra hard cataract, bringing out the whole nucleus through the sclerocorneal flap valve incision becomes difficult. A bigger incision required in such cataracts loses its value action, as the internal incision and corneal valve slips beyond the limbus into sclera. Struggling with the supra hard cataracts through a regular small incision. Phacofracture in the anterior chamber becomes a useful option in these cases. In the snare technique, a stainless steel wire loop when lassoed around the nucleus in the anterior chamber constricts from the equator, easily dividing the hardest of the nuclei into two halves. The wire loop constricts in a controlled way when the second cannula of snare is pulled. The divided halves can easily be brought out by serrated crocodile forceps. This nuclear management can be safely performed through a smaller sclerocorneal flap valve incision where the corneal valve action is retained within the limbus without sutures, and the endothelium or the incision is not disturbed. However, the technique requires space in the anterior chamber to maneuver the wire loop and anterior chamber depth more than 2.5 mm is recommended. Much evidence to this wonderful technique is not available in literature, as its popularity grew through live surgical workshops and small interactive conferences.

  3. Complications of femtosecond laser corneal small incision lenticule extraction

    Directory of Open Access Journals (Sweden)

    Qing-Hong Lin

    2017-07-01

    Full Text Available AIM:To investigate the safety and complications of femtosecond laser corneal small incision lenticule extraction(SMILEprocedure and discuss the prevention and treatment.METHODS: We retrospectively studied the complications of 403 patients(799 eyeswith myopia and myopic astigmatism treated by SMILE.RESULTS: All the patients underwent the operation successfully. Only 1 case(1 eyesuffered from dark spot and changed to femtosecond laser-assisted LASIK(FS-LASIK, 5 cases(5 eyes, 0.6%suffered from the suction loss, 11 cases(17 eyes, 2.1%developed opaque bubble layer. All patients gained perfect uncorrected visual acuity(UCVA(20/20. The best corrected visual acuity(BCVAdid not decrease after operations. The incidence of haze and diffuse lamellar keratitis was low(0.3% and 0.4%, respectivelyand no other complications were observed. There was 9 eyes in 6 patients(1.1%found regression of refraction at 6mo after surgery, while the UCVA of rest patients reached 1.0 at 3mo after surgery.CONCLUSION: The SMILE procedure has high safety for myopia and myopic astigmatism. Effective prevention and management of the complications is the key to achieve the satisfactory visual acuity.

  4. Single-Incision Laparoscopic Sterilization of the Cheetah (Acinonyx jubatus).

    Science.gov (United States)

    Hartman, Marthinus J; Monnet, Eric; Kirberger, Robert M; Schmidt-Küntzel, Anne; Schulman, Martin L; Stander, Jana A; Stegmann, George F; Schoeman, Johan P

    2015-07-01

    To describe laparoscopic ovariectomy and salpingectomy in the cheetah (Acinonyx jubatus) using single-incision laparoscopic surgery (SILS). Prospective cohort. Female cheetahs (Acinonyx jubatus) (n = 21). Cheetahs were randomly divided to receive either ovariectomy (n = 11) or salpingectomy (n = 10). The use and complications of a SILS port was evaluated in all of cheetahs. Surgery duration and insufflation volumes of carbon dioxide (CO2 ) were recorded and compared across procedures. Laparoscopic ovariectomy and salpingectomy were performed without complications using a SILS port. The poorly-developed mesosalpinx and ovarian bursa facilitated access to the uterine tube for salpingectomy in the cheetah. The median surgery duration for ovariectomy was 24 minutes (interquartile range 3) and for salpingectomy was 19.5 minutes (interquartile range 3) (P = .005). The median volume of CO2 used for ovariectomy was 11.25 L (interquartile range 3.08) and for salpingectomy was 4.90 L (interquartile range 2.52), (P = .001) CONCLUSIONS: Laparoscopic ovariectomy and salpingectomy can be performed in the cheetah using SILS without perioperative complications. Salpingectomy is faster than ovariectomy and requires less total CO2 for insufflation. © Copyright 2015 by The American College of Veterinary Surgeons.

  5. Half-Duplex and Full-Duplex AF and DF Relaying with Energy-Harvesting in Log-Normal Fading

    KAUST Repository

    Rabie, Khaled M.

    2017-08-15

    Energy-harvesting (EH) and wireless power transfer in cooperative relaying networks have recently attracted a considerable amount of research attention. Most of the existing work on this topic however focuses on Rayleigh fading channels, which represent outdoor environments. In contrast, this paper is dedicated to analyze the performance of dual-hop relaying systems with EH over indoor channels characterized by log-normal fading. Both half-duplex (HD) and full-duplex (FD) relaying mechanisms are studied in this work with decode-and-forward (DF) and amplify-and-forward (AF) relaying protocols. In addition, three EH schemes are investigated, namely, time switching relaying, power splitting relaying and ideal relaying receiver which serves as a lower bound. The system performance is evaluated in terms of the ergodic outage probability for which we derive accurate analytical expressions. Monte Carlo simulations are provided throughout to validate the accuracy of our analysis. Results reveal that, in both HD and FD scenarios, AF relaying performs only slightly worse than DF relaying which can make the former a more efficient solution when the processing energy cost at the DF relay is taken into account. It is also shown that FD relaying systems can generally outperform HD relaying schemes as long as the loop-back interference in FD is relatively small. Furthermore, increasing the variance of the log-normal channel has shown to deteriorate the performance in all the relaying and EH protocols considered.

  6. Evidence that novobiocin and nalidixic acid do not inhibit excision repair in u.v.-irradiated human skin fibroblasts at a pre-incision

    International Nuclear Information System (INIS)

    Keyse, S.M.; Tyrrell, R.M.

    1985-01-01

    The effects of novobiocin and nalidixic acid on the specific toxicity of aphidicolin towards u.v. irradiated arrested human skin fibroblasts have been determined. Contrary to the result expected if either drug were causing inhibition of excision repair at a pre-incision step the sector of toxicity due to a combined treatment of 300 μg ml -1 nalidixic acid and 1.0 μg ml -1 aphidicolin is unchanged when compared with that due to treatment with 1.0 μg ml -1 aphidicolin alone, while that for 150 μg ml -1 novobiocin + 1.0 μg ml -1 aphidicolin was slightly increased. In parallel measurements of the inhibition of u.v.-induced DNA repair synthesis in arrested fibroblasts by these drugs, 150 μg ml -1 novobiocin inhibited repair synthesis by approx.60% over the fluence range employed. Nalidixic acid (300 μg ml -1 ) caused no detectable inhibition of repair synthesis. It was concluded that the mode of action of novobiocin in the inhibition of DNA excision repair is not via the inhibition of a pre-incision step and the data do not support the hypothesis that a type II topoisomerase mediated change in DNA supercoiling is an essential early step in excision repair of u.v.-induced damage. (author)

  7. Evidence that novobiocin and nalidixic acid do not inhibit excision repair in u.v.-irradiated human skin fibroblasts at a pre-incision step

    International Nuclear Information System (INIS)

    Keyse, S.M.; Tyrrell, R.M.

    1985-01-01

    The effects of novobiocin and nalidixic acid on the specific toxicity of aphidicolin towards u.v. irradiated arrested (nondividing) human skin fibroblasts have been determined. Contrary to the result expected if either drug were causing inhibition of excision repair at a pre-incision step the sector of toxicity due to a combined treatment of 300 micrograms ml -1 nalidixic acid and 1.0 micrograms ml -1 aphidicolin is unchanged when compared with that due to treatment with 1.0 micrograms ml -1 aphidicolin alone, while that for 150 micrograms ml -1 novobiocin + 1.0 micrograms ml -1 aphidicolin was slightly increased. In parallel measurements of the inhibition of u.v.-induced DNA repair synthesis in arrested fibroblasts by these drugs, 150 micrograms ml -1 novobiocin inhibited repair synthesis by approximately 60% over the fluence range employed. Nalidixic acid at a concentration of 300 micrograms ml -1 caused no detectable inhibition of repair synthesis. The authors conclude that the mode of action of novobiocin in the inhibition of DNA excision repair is not via the inhibition of a pre-incision step and the data do not support the hypothesis that a type II topoisomerase mediated change in DNA supercoiling is an essential early step in excision repair of u.v.-induced damage

  8. General method of preparation of uniformly 13C, 15N-labeled DNA fragments for NMR analysis of DNA structures

    International Nuclear Information System (INIS)

    Rene, Brigitte; Masliah, Gregoire; Zargarian, Loussine; Mauffret, Olivier; Fermandjian, Serge

    2006-01-01

    Summary 13 C, 15 N labeling of biomolecules allows easier assignments of NMR resonances and provides a larger number of NMR parameters, which greatly improves the quality of DNA structures. However, there is no general DNA-labeling procedure, like those employed for proteins and RNAs. Here, we describe a general and widely applicable approach designed for preparation of isotopically labeled DNA fragments that can be used for NMR studies. The procedure is based on the PCR amplification of oligonucleotides in the presence of labeled deoxynucleotides triphosphates. It allows great flexibility thanks to insertion of a short DNA sequence (linker) between two repeats of DNA sequence to study. Size and sequence of the linker are designed as to create restriction sites at the junctions with DNA of interest. DNA duplex with desired sequence and size is released upon enzymatic digestion of the PCR product. The suitability of the procedure is validated through the preparation of two biological relevant DNA fragments

  9. An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Takahashi, Norio; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-05-01

    We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32 P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

  10. Selection of patients with infrainguinal arterial occlusive disease for percutaneous transluminal angioplasty with duplex scanning

    International Nuclear Information System (INIS)

    Bostroem Ardin, A.; Hellberg, A.; Ljungman, C.; Logason, K.; Karacagil, S.; Loefberg, A.M.; Andren, B.

    2002-01-01

    Aim: To evaluate the role of duplex scanning in the selection of patients with infrainguinal arterial occlusive disease for percutaneous transluminal angioplasty (PTA). Material and Methods: From January 1995 through May 2000, 702 patients (952 limbs), with chronic lower extremity ischemia due to infrainguinal atherosclerotic disease diagnosed by duplex scanning, were retrospectively studied. Diagnostic angiography (130 limbs) or infrainguinal PTA (108 limbs) was performed in 238 limbs. Two investigators retrospectively analyzed the duplex examinations and angiographies in a blinded manner and used similar criteria for the interpretation of lesions suitable or not suitable for PTA. Results: The superficial femoral, popliteal and crural artery lesions were correctly selected for PTA in 85%, 66% and 32%, respectively. The accuracy, sensitivity, specificity, negative predictive value and positive predictive value of duplex scanning to appropriately categorize femoropopliteal lesions as suitable or unsuitable for PTA were 89%, 83%, 92%, 94% and 78%, respectively. The accuracy of duplex scanning for predicting the performance of infrainguinal PTA was 83%. Conclusion: Duplex scanning has an important impact on the selection of treatment modalities in limbs with infrainguinal arterial occlusive disease. Femoropopliteal lesions can be reliably selected to PTA according to duplex scan findings

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  13. Ultrasonographic evaluation of the healing of ventral midline abdominal incisions in the horse.

    Science.gov (United States)

    Wilson, D A; Badertscher, R R; Boero, M J; Baker, G J; Foreman, J H

    1989-06-01

    Ultrasonography was used to evaluate the ventral midline incisions of 21 ponies following exploratory laparotomy. The incisions were evaluated before surgery and at weekly intervals from one to seven weeks after surgery. Both 5.0 and 7.5 MHz linear array and 7.5 MHz sector transducers were used for the evaluations. The incisional complications observed were drainage, oedema, suture sinus formation, suture abscess, superficial dehiscence and incisional hernia. Ultrasonographic imaging of the ventral midline incision was an easy, reliable and objective method for detecting and monitoring the progression of incisional complications in a non-invasive manner.

  14. Towards achieving small-incision cataract surgery 99.8% of the time.

    Directory of Open Access Journals (Sweden)

    Thomas R

    2000-01-01

    Full Text Available A surgical approach designed to reliably attain the modern goal of small incision cataract surgery 99.8% of the time is described. Phacoemulsification as well as a manual small incision technique is utilised to achieve the desired outcome as often as possible and for all types of cataracts. The logic, and required surgical steps are described and illustrated. This surgical technique allows the advantages of small incision surgery to be reliably achieved. The method is flexible and allows decisions and steps to be modified depending on the skill and comfort zone of the individual surgeon.

  15. Techniques for creating inconspicuous face-lift scars: avoiding visible incisions and loss of temporal hair.

    Science.gov (United States)

    Kridel, Russell W H; Liu, Edmund S

    2003-01-01

    Patients seeking rhytidectomy desire an improved neckline, jawline, and midface, but rarely at the price of signs that betray a face-lift, namely, visible incisions. We describe our face-lift incisional planning and the rationale behind specific surgical maneuvers for preventing unwanted sequelae. The telltale signs of poorly placed incisions include temporal hair loss, conspicuous scars, an unnatural appearance to the tragus, and a posterior hairline distorsion. Special considerations are given to the male patient and to the salvage of readily visible incision lines from previous surgery.

  16. Transverse versus Longitudinal Incisions for Femoral Artery Exposure in Treating Patients with Peripheral Vascular Disease.

    Science.gov (United States)

    Parikh, Punam P; Rubio, Gustavo A; Patel, Kunal; Gupta, Kapil; Jones, Keith; Rey, Jorge; Robinson, Handel

    2018-02-01

    This study evaluates differences in wound complication rate when transverse versus longitudinal incision is utilized to expose femoral vessels in managing patients with peripheral vascular disease. A retrospective review from 2013 to 2015 was conducted of 150 patients undergoing 156 lower extremity revascularizations with femoral artery exposure through a groin incision. Patients were stratified into 2 groups, transverse versus longitudinal groin incision. Data were reviewed for 3 surgeons that utilize either transverse or longitudinal groin incision in patients undergoing common or iliofemoral endarterectomies, or where femoral artery was used as inflow and/or outflow vessel for limb revascularization. Each group had a comparative outcomes analysis based on incision type. The primary outcome was wound complication, defined as any wound infection, lymphocele, hematoma, dehiscence, pseudoaneurysm, or necrosis. Other outcomes studied included unplanned return to operating room for wound complication, wound vacuum therapy, and soft-tissue flap closure. Data were analyzed using 2-tailed chi-squared test and Student's t-test. Patients in the transverse (n = 85 cases) versus longitudinal (n = 71 cases) cohorts were similar in relation to demographics and comorbidities. Overall mean follow-up was 220 days. Patients with a transverse as compared to longitudinal incision had a significantly lower overall wound complication rate, 7% vs. 42%, respectively (P transverse incisions were associated with lower incidence of unplanned return to the operating room to manage wound complications than patients with a longitudinal incision (5% vs. 23%, respectively; P Transverse versus longitudinal incisions were also associated with significantly lower need for wound vacuum therapy (6% vs. 15%, respectively; P Transverse groin incisions for femoral artery exposure may offer a lower risk of wound complications for open procedures as compared to a longitudinal incision

  17. Determination of the major tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA adduct by 1H and 15N NMR studies

    International Nuclear Information System (INIS)

    Lin, Chin Hsiung; Hurley, L.H.

    1990-01-01

    (+)-CC-1065 is an extremely potent antitumor antibiotic produced by Streptomyces zelensis. The potent cytotoxic effects of the drug are thought to be due to the formation of a covalent adduct with DNA through N3 of adenine. Although the covalent linkage sites between (+)-CC-1065 and DNA have been determined, the tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA duplex adduct was not defined. The [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct was then studied by 1 H and 15 N NMR. One-dimensional NOE difference and two-dimensional NOESY 1 H NMR experiments on the nonisotopically labeled 12-mer duplex adduct demonstrate that the 6-amino protons of the covalently modified adenine exhibit two signals at 9.19 and 9.08 ppm. Proton NMR experiments on the [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct show that the two resonance signals for adenine H6 observed on the nonisotopically labeled duplex adduct were split into doublets by the 15 N nucleus with coupling constants of 91.3 Hz for non-hydrogen-bonded and 86.8 Hz for hydrogen-bonded amino protons. The authors conclude that the covalently modified adenine N6 of the (+)-CC-1065-12-mer duplex adduct is predominantly in the doubly protonated form, in which calculations predict that the C6-N6 bond is shortened and the positive charge is delocalized over the entire adenine molecule

  18. Renal damage in vesicoureteral reflux associated to duplex systems

    International Nuclear Information System (INIS)

    Orellana, P.; Velasquez, C.; Baquedano, P.

    2002-01-01

    Duplex system (DS) is a common occurrence and it can be associated to a range of ureteral and renal anomalies draining the two poles of the duplex kidneys, as vesicoureteral reflux (VUR) in the lower moiety and ureterocele in the upper moiety. The VUR in a duplex system can be primary or secondary (associated to an ureterocele). The assessment of parenchymal uptake and function of the whole and separate parts of the kidneys is important for therapeutical decisions. Objective: To determine the presence of renal damage, by dimercaptosuccinic acid (DMSA) scintigraphy in children with a refluxing DS and if there any difference between primary and secondary reflux. Patients and Methods: 36 children; 23 girls and 13 boys, with VUR into completely duplicated collecting systems was studied retrospectively (37 RU with DS, 35 unilateral and 1 bilateral), with a mean age of 2.43 y.o. (range: 1 month-11y.o.). All of the children underwent ultrasonography, voiding cystourethrogram and renal static scintigraphy. Among the 37 RU with VUR, 25 had primary VUR and 12 had VUR secondary to the presence of an ureterocele. Ten out of the 36 children (27.8%) were evaluated due to antenatal diagnosis and the remaining 26 (72.2%) after urinary tract infection (UTI). Results: Seventy percent of the 37 RU with VUR into completely duplicated collecting systems had renal damage demonstrated by renal static scintigraphy. Among the 25 RU with primary VUR, 19 (76%) had renal damage, 6 with a complete absence of function in the lower moiety. In this group, 80% of children was studied due to an UTI at a mean age of 3.3 y.o. In the group of children with secondary VUR, we observed a lower moiety with renal damage in 6/12 (50%), in 4 of them associated with an abnormal upper moiety. 7 out of 12 children (58.3%) had an abnormal upper moiety, 4 of them with a damage in lower moiety too. One children presented with renal exclusion. Half of these children were studied due to UTI, at a mean age of 1 y

  19. Perancangan dan Implementasi Duplexer Mikrostrip untuk Frekuensi LTE pada band ke-7

    Directory of Open Access Journals (Sweden)

    ENCENG SULAEMAN

    2017-06-01

    Full Text Available ABSTRAK Kebutuhan akan komunikasi bergerak semakin mengalami peningkatan dalam dunia teknologi yang ada saat ini, maka hadirlah teknologi terbaru yaitu Long Term Evolution (LTE. Dengan teknik duplex jenis Frequency Division Duplex (FDD, dirancanglah duplexer yang mampu melakukan proses pengiriman dan penerimaan dalam satu waktu dengan frekuensi yang berbeda antara uplink dan downlink. Pada penelitian ini dirancang dan diimplementasikan sebuah duplekser dengan menggunakan metoda Hybrid Coupler dan Bandstop Filter berbasis Split Ring Resonator untuk band frekuensi ke-7 pada teknologi LTE di sisi Base Transceiver Station (BTS. Duplekser dibuat dengan menggabungkan dua buah hybrid Coupler dan dua buah Bandstop Filter. Hasil pengukuran duplexer saat port Tx mengirimkan sinyal ke antena dengan nilai redaman pada frekuensi tengah downlink sebesar 3.168 dB. Lalu pada saat antena menerima sinyal untuk diteruskan ke Rx terdapat redaman di frekuensi tengah uplink sebesar 6 dB. Sedangkan untuk isolasi dari port Tx-port Rx dihasilkan sebesar 15 dB. Kata kunci: Duplexer, Bandstop Filter, Split Ring Resonator, Hybrid Coupler, dan Long Term Evolution. ABSTRACT The necessary of mobile communication has increased in technology, now it released the new of technology is Long Term Evolution (LTE. Type of duplex is Frequency Division Duplex (FDD, designed a duplexer which it is capable for transmitting and receiving process at the same time with the different of frequency between uplink and downlink. Research of designed and implemented a duplexer using Hybrid Coupler and Bandstop filters based on Split Ring Resonators for the frequency band 7th on LTE technology at Base Transceiver Station (BTS. Duplexer is made by combining two coupler and two bandstop filter. The results of duplexer measurements, when Tx port transmit the signal to antenna port with attenuation at the downlink frequency center at 3.168 dB. Attenuation from antenna port to Rx port about 6 d

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

    Science.gov (United States)

    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.