WorldWideScience

Sample records for incises duplex dna

  1. DNA Methylation Modulates Nociceptive Sensitization after Incision.

    Directory of Open Access Journals (Sweden)

    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. Spermine Condenses DNA, but Not RNA Duplexes

    Energy Technology Data Exchange (ETDEWEB)

    Katz, Andrea M.; Tolokh, Igor S.; Pabit, Suzette A.; Baker, Nathan; Onufriev, Alexey V.; Pollack, Lois

    2017-01-01

    Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA, and some RNAs such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA, but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA and compare our findings with predictions of molecular dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence, containing a mixture of 14 GC pairs and 11 AU pairs, resists condensation relative to DNA of an equivalent sequence or to 25 base pair poly(rA):poly(rU) RNA. Comparison of wide-angle x-ray scattering profiles with simulation suggests that spermine is sequestered deep within the major groove of mixed sequence RNA, preventing condensation by limiting opportunities to bridge to other molecules as well as stabilizing the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds external to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble, and available for interaction with other molecules in the cell, despite the presence of spermine at concentrations high enough to precipitate DNA.

  3. Highly mutagenic exocyclic DNA adducts are substrates for the human nucleotide incision repair pathway.

    Directory of Open Access Journals (Sweden)

    Paulina Prorok

    Full Text Available BACKGROUND: Oxygen free radicals induce lipid peroxidation (LPO that damages and breaks polyunsaturated fatty acids in cell membranes. LPO-derived aldehydes and hydroxyalkenals react with DNA leading to the formation of etheno(ε-bases including 1,N(6-ethenoadenine (εA and 3,N(4-ethenocytosine (εC. The εA and εC residues are highly mutagenic in mammalian cells and eliminated in the base excision repair (BER pathway and/or by AlkB family proteins in the direct damage reversal process. BER initiated by DNA glycosylases is thought to be the major pathway for the removal of non-bulky endogenous base damage. Alternatively, in the nucleotide incision repair (NIR pathway, the apurinic/apyrimidinic (AP endonucleases can directly incise DNA duplex 5' to a damaged base in a DNA glycosylase-independent manner. METHODOLOGY/PRINCIPAL FINDINGS: Here we have characterized the substrate specificity of human major AP endonuclease 1, APE1, towards εA, εC, thymine glycol (Tg and 7,8-dihydro-8-oxoguanine (8oxoG residues when present in duplex DNA. APE1 cleaves oligonucleotide duplexes containing εA, εC and Tg, but not those containing 8oxoG. Activity depends strongly on sequence context. The apparent kinetic parameters of the reactions suggest that APE1 has a high affinity for DNA containing ε-bases but cleaves DNA duplexes at an extremely slow rate. Consistent with this observation, oligonucleotide duplexes containing an ε-base strongly inhibit AP site nicking activity of APE1 with IC(50 values in the range of 5-10 nM. MALDI-TOF MS analysis of the reaction products demonstrated that APE1-catalyzed cleavage of εA•T and εC•G duplexes generates, as expected, DNA fragments containing 5'-terminal ε-base residue. CONCLUSIONS/SIGNIFICANCE: The fact that ε-bases and Tg in duplex DNA are recognized and cleaved by APE1 in vitro, suggests that NIR may act as a backup pathway to BER to remove a large variety of genotoxic base lesions in human cells.

  4. Conserved guanine-guanine stacking in tetraplex and duplex DNA

    Czech Academy of Sciences Publication Activity Database

    Kypr, Jaroslav; Fialová, Markéta; Chládková, Jana; Tůmová, Marcela; Vorlíčková, Michaela

    2001-01-01

    Roč. 30, č. 7 (2001), s. 555-558 ISSN 0175-7571 R&D Projects: GA AV ČR IAA5004802 Institutional research plan: CEZ:AV0Z5004920 Keywords : tetraplex DNA * duplex DNA * circular dichroism spectra Subject RIV: BO - Biophysics Impact factor: 1.917, year: 2001

  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. 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.

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Hole Transport in A-form DNA/RNA Hybrid Duplexes

    Science.gov (United States)

    Wong, Jiun Ru; Shao, Fangwei

    2017-01-01

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

  9. 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 redox...... marked single- and double-strand OGNs has reached the single-molecule level based i.a. on electrochemical in situ scanning tunnelling microscopy (STM) and break-junction (B-J) STM. There are much fewer such reports on “non-canonical” OGN structures such as G-quadruplexes. We discuss first single......-molecule electrochemical conductivity of pure and redox marked duplex OGNs, and address next electrochemistry and electrochemical conductivity in the few reported monolayer and single-molecule G-quadruplex studies. Facile electrochemical electron transfer of iron protoporphyrin IX stacked onto three-quartet 12-guanine...

  10. Enhanced H-bonding and pi-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue

    DEFF Research Database (Denmark)

    Lou, Chenguang; Dallmann, Andre; Marafini, Pietro

    2014-01-01

    X-pyrene is a new nucleic acid duplex stabilizing cytosine analogue that combines enhanced pi-stacking, hydrogen bonding and electrostatic interactions to greatly increase the stability of bulged DNA duplexes and DNA/RNA hybrids. X-pyrene is highly selective for guanine as a partner and duplex...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    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.

  14. 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.

  15. 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.

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

    Science.gov (United States)

    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

  17. Comparing Charge Transport in Oligonucleotides: RNA:DNA Hybrids and DNA Duplexes.

    Science.gov (United States)

    Li, Yuanhui; Artés, Juan M; Qi, Jianqing; Morelan, Ian A; Feldstein, Paul; Anantram, M P; Hihath, Joshua

    2016-05-19

    Understanding the electronic properties of oligonucleotide systems is important for applications in nanotechnology, biology, and sensing systems. Here the charge-transport properties of guanine-rich RNA:DNA hybrids are compared to double-stranded DNA (dsDNA) duplexes with identical sequences. The conductance of the RNA:DNA hybrids is ∼10 times higher than the equivalent dsDNA, and conformational differences are determined to be the primary reason for this difference. The conductance of the RNA:DNA hybrids is also found to decrease more rapidly than dsDNA when the length is increased. Ab initio electronic structure and Green's function-based density of states calculations demonstrate that these differences arise because the energy levels are more spatially distributed in the RNA:DNA hybrid but that the number of accessible hopping sites is smaller. These combination results indicate that a simple hopping model that treats each individual guanine as a hopping site is insufficient to explain both a higher conductance and β value for RNA:DNA hybrids, and larger delocalization lengths must be considered.

  18. 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

  19. Detection of base pair mismatches in duplex DNA and RNA oligonucleotides using electrospray mass spectrometry

    Science.gov (United States)

    Griffey, Richard H.; Greig, Michael J.

    1997-05-01

    The identify and location of base pair mismatches in non- covalent DNA:RNA duplexes are established using MS and MS-MS on a quadruple ion trap with electrospray ionization (ESI). MS-MS experiments on a 14mer duplex (D) with a single C:A base pair mismatch using lower activation energy results in selective cleavage of the mismatched A nucleobase, even in the presence of the wild-type duplex. The location of the mismatch base pair can be discerned via presence of the wild-type duplex. The location of the mismatch base pair can be discerned via selection of the (D-5H)5- ion and fragmentation of the backbone at that location in a n additional MS-MS experiment. Selective fragmentation is observed for C in a C-C mismatched base pair, which is very difficult to detect using chemical cleavage or E. coli mismatch binding protein. In an RNA:DNA duplex with a single base pair mismatch, the DNA base is removed without fragmentation of the RNA strand, greatly simplifying the interpretation of the resulting MS spectrum. A method is presented for detecting two DNA strands, for example a point mutation which generates an oncogenic phenotype, and the wild-type message. The results suggest that ESI-MS-MS may provide a rapid and selective method to identify and locate genetic mutations without the need for chemical degradation or protein binding followed by gel electrophoresis.

  20. 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.

  1. Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid.

    NARCIS (Netherlands)

    Pohjoismaki, J.L.; Holmes, J.B.; Wood, S.R.; Yang, M.Y.; Yasukawa, T.; Reyes, A.; Bailey, L.J.; Cluett, T.J.; Goffart, S.; Willcox, S.; Rigby, R.E.; Jackson, A.P.; Spelbrink, J.N.; Griffith, J.D.; Crouch, R.J.; Jacobs, H.T.; Holt, I.J.

    2010-01-01

    We demonstrate, using transmission electron microscopy and immunopurification with an antibody specific for RNA/DNA hybrid, that intact mitochondrial DNA replication intermediates are essentially duplex throughout their length but contain extensive RNA tracts on one strand. However, the extent of

  2. Is transurethral incision better than upper pole partial nephrectomy for management of duplex system ureterocoele diagnosed in the first year of life?

    Directory of Open Access Journals (Sweden)

    Amr Hodhod

    2017-12-01

    Full Text Available Objective: To compare the outcomes of transurethral incision (TUI and upper pole partial nephrectomy (PN in patients with duplex system ureterocoele (DSU. Patients and methods: We retrospectively reviewed the medical charts of patients who presented with DSU in the first-year of life and were managed with either TUI or PN. Patients’ demographics, ultrasonography examinations, voiding cystourethrogram studies, and dimercaptosuccinic acid scans were reviewed. Also, the postoperative vesico-ureteric reflux status and febrile urinary tract infection occurrences, and subsequent surgical interventions were identified. The outcomes for the DSU location (intravesical vs extravesical were compared. Results: Between January 1995 and September 2015, 44 patients underwent TUI (31 patients or PN (13. The TUI patients presented at a median age of 1.1 months and were followed-up for a median of 47.4 months, whilst those who underwent PN presented at a median age of 1.06 months and were followed-up for a median of 44.23 months. Postoperatively, in the TUI group, four of 15 units had improved renal function and 11 units had stable function. In the PN group, five of nine units had stable renal function and the remaining four had worsened function (P = 0.019. Furthermore, 15 of the 31 patients (48% in the TUI group required second interventions compared with one of 13 patients in the PN group (P = 0.01. There was no significant difference between the outcomes of intravesical and extravesical DSUs after TUI and PN. Conclusion: This study shows significant renal function preservation with TUI compared to PN. However, secondary surgical interventions were higher with TUI. Keywords: Ureterocoele, Duplex system, Nephrectomy, Transurethral incision

  3. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.

    Science.gov (United States)

    Zhou, Huiqing; Hintze, Bradley J; Kimsey, Isaac J; Sathyamoorthy, Bharathwaj; Yang, Shan; Richardson, Jane S; Al-Hashimi, Hashim M

    2015-04-20

    Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. 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....

  5. Comparison of positively charged DNG with DNA duplexes: a computational approach.

    Science.gov (United States)

    Toporowski, Joseph W; Reddy, Swarnalatha Y; Bruice, Thomas C

    2005-06-01

    Molecular dynamics is used to investigate the structural properties of the cationic DNA analogue deoxynucleic guanidine (DNG), in which a guanidinium group replaces the phosphate moiety of DNA. This study examines the DNG duplex dodecamers d(Ag)(12).d(Tg)(12) and d(Gg)(12).d(Cg)(12), as well as their DNA counterparts. Watson-Crick base-pairing is maintained in the solvated DNG duplex models during the 5ns simulations. The idealized DNG dodecamers assume many parameters characteristic of the corresponding native DNA, assuming B-DNA conformations. Several helical parameters are rather unique to DNG, including buckle, slide, inclination, propeller, and X-displacement. Fewer transitions in backbone torsions occur in the DNG duplexes compared to those of the DNA, which may result from the greater rigidity of the sp(2) hybridized guanidinium group verses the flexible sp(3) phosphate group. The DNG helices have exceptionally shallow major grooves and very deep minor grooves. The major and minor groove widths of DNG are narrower than those of the respective DNA counterparts.

  6. Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

    Science.gov (United States)

    Egli, M.; Usman, N.; Rich, A.

    1993-01-01

    We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

  7. 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 ...

  8. ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid.

    Science.gov (United States)

    Birrento, Monica L; Bryan, Tracy M; Samosorn, Siritron; Beck, Jennifer L

    2015-07-01

    Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine (1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of (1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand (1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism.

  9. 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.

  10. Impact of bistrand abasic sites and proximate orientation on DNA global structure and duplex energetics.

    Science.gov (United States)

    Minetti, Conceição A; Sun, Jeffrey Y; Jacobs, Daniel P; Kang, Inkoo; Remeta, David P; Breslauer, Kenneth J

    2018-01-11

    Bistrand lesions embedded within a single helical turn of tridecameric deoxyoligonucleotide duplexes represent a model system for exploring the impact of clustered lesions that occur in vivo and pose a significant challenge to cellular repair machineries. Such investigations are essential for understanding the forces that dictate lesion-induced mutagenesis, carcinogenesis, and cytotoxicity within a context that mimics local helical perturbations caused by an ionizing radiation event. This study characterizes the structural and energy profiles of DNA duplexes harboring synthetic abasic sites (tetrahydrofuran, F) as models of clustered bistrand abasic (AP) lesions. The standard tridecameric dGCGTACCCATGCG·dCGCATGGGTACGC duplex is employed to investigate the energetic impact of single and bistrand AP sites by strategically replacing one or two bases within the central CCC/GGG triplet. Our combined analysis of temperature-dependent UV and circular dichroism (CD) profiles reveals that the proximity and relative orientation of AP sites within bistrand-damaged duplexes imparts a significant thermodynamic impact. Specifically, 3'-staggered lesions (CCF/GFG) exert a greater destabilizing effect when compared with their 5'-counterpart (FCC/GFG). Moreover, a duplex harboring the central bistrand AP lesion (CFC/GFG) is moderately destabilized yet exhibits distinct properties relative to both the 3' and 5'-orientations. Collectively, our energetic data are consistent with structural studies on bistrand AP-duplexes of similar sequence in which a 3'-staggered lesion exerts the greatest perturbation, a finding that provides significant insight regarding the impact of orientation on lesion repair processing efficiency. © 2018 The Authors Biopolymers Published by Wiley Periodicals, Inc.

  11. 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.

  12. Dual daughter strand incision is processive and increases the efficiency of DNA mismatch repair.

    Science.gov (United States)

    Hermans, Nicolaas; Laffeber, Charlie; Cristovão, Michele; Artola-Borán, Mariela; Mardenborough, Yannicka; Ikpa, Pauline; Jaddoe, Aruna; Winterwerp, Herrie H K; Wyman, Claire; Jiricny, Josef; Kanaar, Roland; Friedhoff, Peter; Lebbink, Joyce H G

    2016-08-19

    DNA mismatch repair (MMR) is an evolutionarily-conserved process responsible for the repair of replication errors. In Escherichia coli, MMR is initiated by MutS and MutL, which activate MutH to incise transiently-hemimethylated GATC sites. MMR efficiency depends on the distribution of these GATC sites. To understand which molecular events determine repair efficiency, we quantitatively studied the effect of strand incision on unwinding and excision activity. The distance between mismatch and GATC site did not influence the strand incision rate, and an increase in the number of sites enhanced incision only to a minor extent. Two GATC sites were incised by the same activated MMR complex in a processive manner, with MutS, the closed form of MutL and MutH displaying different roles. Unwinding and strand excision were more efficient on a substrate with two nicks flanking the mismatch, as compared to substrates containing a single nick or two nicks on the same side of the mismatch. Introduction of multiple nicks by the human MutLα endonuclease also contributed to increased repair efficiency. Our data support a general model of prokaryotic and eukaryotic MMR in which, despite mechanistic differences, mismatch-activated complexes facilitate efficient repair by creating multiple daughter strand nicks. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. 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

  14. 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

  15. QCM-based rupture force measurement as a tool to study DNA dehybridization and duplex stability.

    Science.gov (United States)

    Dultsev, Fedor N; Kolosovsky, Eugeny A; Lomzov, Alexander A; Pyshnyi, Dmitrii V

    2017-02-01

    The stability of double-stranded DNA (dsDNA) was assessed on the basis of unwinding force measurement. Unwinding force was measured directly with a quartz crystal microbalance (QCM). The amplitude of its surface oscillations was controlled by supplying variable alternate voltage. Under smoothly increasing amplitude of QCM surface oscillations, dsDNA fixed on QCM surface through one of its ends got unwound. This procedure allows reliable measurement of rupture force as small as 5-10 pN. It was demonstrated that oscillations of the surface, with dsDNA bound through one of its ends to this surface, at a frequency of 14 MHz, cause helix unwinding to form two complementary parts due to viscous forces of the liquid medium. Unwinding starts at the upper end. This was proven using oligonucleotide duplexes containing mismatches in different positions. For duplexes containing complementary 20 base pairs, the helix unwinding force is equal to 30-40 pN, which is in agreement with the data obtained by means of atomic-force microscopy (AFM) for the case of unzipping mode. Graphical Abstract Rupture force depending on mismatch position in dsDNA.

  16. Highly selective DNA biosensor based on the long-range electron transfer of indigo carmine through DNA duplex

    International Nuclear Information System (INIS)

    Wang, Q.; Ding, Y.; Wang, L.; Gao, C.; Gao, F.; Gao, F.

    2012-01-01

    We have developed a highly selective DNA biosensor. It was based on the long-range electron transfer (LRET) from the electroactive dye indigo carmine (IC) through the DNA duplex on a glassy carbon electrode. Voltammetric experiments showed that IC interacts with dsDNA through a typical intercalative mode with a relatively strong affinity of 2.3(±0.6) x 10 6 M -1 . If incubated with DNA in IC solution, no response was observed with the ssDNA-modified probe electrode. However, a pair of well-defined redox peak was observed with a DNA-hybridized electrode, proving the presence of LRET on the biosensor. The biosensor also can differentiate complementary sequences, non-complementary sequences, and even the mutated sequences with single-base mismatches at different sites. (author)

  17. Studies of DNA dumbbells VII: evaluation of the next-nearest-neighbor sequence-dependent interactions in duplex DNA.

    Science.gov (United States)

    Owczarzy, R; Vallone, P M; Goldstein, R F; Benight, A S

    1999-01-01

    Melting experiments were conducted on 22 DNA dumbbells as a function of solvent ionic strength from 25-115 mM Na(+). The dumbbell molecules have short duplex regions comprised of 16-20 base pairs linked on both ends by T(4) single-strand loops. Only the 4-8 central base pairs of the dumbbell stems differ for different molecules, and the six base pairs on both sides of the central sequence and adjoining loops on both ends are the same in every molecule. Results of melting analysis on the 22 new DNA dumbbells are combined with our previous results on 17 other DNA dumbbells, with stem lengths containing from 14-18 base pairs, reported in the first article of this series (Doktycz, Goldstein, Paner, Gallo, and Benight, Biopoly 32, 1992, 849-864). The combination of results comprises a database of optical melting parameters for 39 DNA dumbbells in ionic strengths from 25-115 mM Na(+). This database is employed to evaluate the thermodynamics of singlet, doublet, and triplet sequence-dependent interactions in duplex DNA. Analysis of the 25 mM Na(+) data reveals the existence of significant sequence-dependent triplet or next-nearest-neighbor interactions. The enthalpy of these interactions is evaluated for all possible triplets. Some of the triplet enthalpy values are less than the uncertainty in their evaluation, indicating no measurable interaction for that particular sequence. This finding suggests that the thermodynamic stability of duplex DNA depends on solvent ionic strength in a sequence-dependent manner. As a part of the analysis, the nearest-neighbor (base pair doublet) interactions in 55, 85, and 115 mM Na(+) are also reevaluated from the larger database. Copyright 2000 John Wiley & Sons, Inc.

  18. 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

  19. 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

    "Tail-clamp" PNAs composed of a short (hexamer) homopyrimidine triplex forming domain and a (decamer) mixed sequence duplex forming extension have been designed. Tail-clamp PNAs display significantly increased binding to single-stranded DNA compared with PNAs lacking a duplex-forming extension...... 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...... to five residues was feasible, but four bases were not sufficient to yield detectable dsDNA binding. The results validate the tail-clamp PNA concept and expand the applications of the P-loop technology....

  20. Structural insights into 5‧ flap DNA unwinding and incision by the human FAN1 dimer

    Science.gov (United States)

    Zhao, Qi; Xue, Xiaoyu; Longerich, Simonne; Sung, Patrick; Xiong, Yong

    2014-12-01

    Human FANCD2-associated nuclease 1 (FAN1) is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). FAN1 maintains genomic stability and prevents tissue decline in multiple organs, yet it confers ICL-induced anti-cancer drug resistance in several cancer subtypes. Here we report three crystal structures of human FAN1 in complex with a 5‧ flap DNA substrate, showing that two FAN1 molecules form a head-to-tail dimer to locate the lesion, orient the DNA and unwind a 5‧ flap for subsequent incision. Biochemical experiments further validate our model for FAN1 action, as structure-informed mutations that disrupt protein dimerization, substrate orientation or flap unwinding impair the structure-specific nuclease activity. Our work elucidates essential aspects of FAN1-DNA lesion recognition and a unique mechanism of incision. These structural insights shed light on the cellular mechanisms underlying organ degeneration protection and cancer drug resistance mediated by FAN1.

  1. Optimizing anti-gene oligonucleotide 'Zorro-LNA' for improved strand invasion into duplex DNA

    DEFF Research Database (Denmark)

    Zaghloul, Eman M; Madsen, Andreas S; Moreno, Pedro M D

    2011-01-01

    established a method, which conclusively demonstrates that an LNA ON can strand invade into duplex DNA. To make Zorros smaller in size and easier to design, we synthesized 3'-5'-5'-3' single-stranded Zorro-LNA (ssZorro) by using both 3'- and 5'-phosphoramidites. With ssZorro, a significantly greater extent......Zorro-LNA (Zorro) is a newly developed, oligonucleotide (ON)-based, Z-shaped construct with the potential of specific binding to each strand of duplex DNA. The first-generation Zorros are formed by two hybridized LNA/DNA mixmers (2-ON Zorros) and was hypothesized to strand invade. We have now...... and rate of double-strand invasion (DSI) was obtained than with conventional 2-ON Zorros. Introducing hydrophilic PEG-linkers connecting the two strands did not significantly change the rate or extent of DSI as compared to ssZorro with a nucleotide-based linker, while the longest alkyl-chain linker tested...

  2. Interaction of anticancer Ru(III) complexes with single stranded and duplex DNA model systems.

    Science.gov (United States)

    Musumeci, Domenica; Rozza, Lucia; Merlino, Antonello; Paduano, Luigi; Marzo, Tiziano; Massai, Lara; Messori, Luigi; Montesarchio, Daniela

    2015-08-21

    The interaction of the anticancer Ru(iii) complex AziRu - in comparison with its analogue NAMI-A, currently in advanced clinical trials as an antimetastatic agent - with DNA model systems, both single stranded and duplex oligonucleotides, was investigated using a combined approach, including absorption UV-vis spectroscopy, circular dichroism (CD) and electrospray mass spectrometry (ESI-MS) techniques. UV-vis absorption spectra of the Ru complexes were recorded at different times in a pseudo-physiological solution, to monitor the ligand exchange processes in the absence and in the presence of the examined oligonucleotides. CD experiments provided information on the overall conformational changes of the DNA model systems induced by these metal complexes. UV- and CD-monitored thermal denaturation studies were performed to analyse the effects of AziRu and NAMI-A on the stability of the duplex structures. ESI-MS experiments, carried out on the oligonucleotide/metal complex mixtures under investigation, allowed us to detect the formation of stable adducts between the guanine-containing oligomers and the ruthenium complexes. These data unambiguously demonstrate that both AziRu and NAMI-A can interact with the DNA model systems. Although very similar in their structures, the two metal compounds manifest a markedly different reactivity with the examined sequences, respectively, with either a naked Ru(3+) ion or a Ru(Im)(3+) (Im = imidazole) fragment being incorporated into the oligonucleotide structure via stable linkages.

  3. Cytosolic RNA:DNA Duplexes Generated by Endogenous Reverse Transcriptase Activity as Autonomous Inducers of Skin Inflammation in Psoriasis.

    Science.gov (United States)

    Molès, Jean-Pierre; Griez, Anthony; Guilhou, Jean-Jacques; Girard, Céline; Nagot, Nicolas; Van de Perre, Philippe; Dujols, Pierre

    2017-01-01

    Psoriasis is a chronic skin disease of unknown ætiology. Recent studies suggested that a large amount of cytosolic DNA (cyDNA) in keratinocytes is breaking keratinocytes DNA tolerance and promotes self-sustained inflammation in the psoriatic lesion. We investigated the origin of this cyDNA. We show that, amongst all the possible DNA structures, the cyDNA could be present as RNA:DNA duplexes in keratinocytes. We further show that endogenous reverse transcriptase activities generate such duplexes and consequently activate the production of Th1-inflammatory cytokines. These observations open a new research avenue related to endogenous retroelements for the aetiology of psoriasis and probably of other human chronic inflammatory diseases.

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

    Science.gov (United States)

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

    1995-01-01

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

  5. Parallel-stranded DNA and RNA duplexes - structural features and potential applications.

    Science.gov (United States)

    Szabat, Marta; Kierzek, Ryszard

    2017-12-01

    Nowadays, decades after the discovery of the right-handed B form of DNA, it is well known that nucleic acids have great conformational flexibility, exhibiting a large degree of variation in their structure. In nature, DNA and RNA exist in an antiparallel orientation, stabilized by Watson-Crick base pairs. However, in some cases, nucleic acid fragments with specific nucleotide sequences can adopt a parallel orientation involving non-canonical base pairing. Interestingly, parallel-stranded duplexes have been found in specific chromosome regions. Furthermore, parallel oriented regions have also been found in bacterial (Escherichia coli, Listeria innocua) and insect genomes (Drosophila melanogaster). These unusual structures could have a remarkable evolutionary role, as well as significant impact on biological processes. For example, parallel stretches were shown to be involved in processing the 3' ends of mRNAs and in specific gene silencing. Moreover, certain types of parallel-stranded duplexes may be useful tools, with several practical applications. They can constitute excellent templates for the formation of other structures and for the development of antigene and antisense approaches. © 2017 Federation of European Biochemical Societies.

  6. Optimized quantification of fragmented, free circulating DNA in human blood plasma using a calibrated duplex real-time PCR.

    Directory of Open Access Journals (Sweden)

    Martin Horlitz

    Full Text Available BACKGROUND: Duplex real-time PCR assays have been widely used to determine amounts and concentrations of free circulating DNA in human blood plasma samples. Circulatory plasma DNA is highly fragmented and hence a PCR-based determination of DNA concentration may be affected by the limited availability of full-length targets in the DNA sample. This leads to inaccuracies when counting PCR target copy numbers as whole genome equivalents. METHODOLOGY/PRINCIPAL FINDINGS: A model system was designed allowing for assessment of bias in a duplex real-time PCR research assay. We collected blood plasma samples from male donors in pools of 6 to 8 individuals. Circulatory plasma DNA was extracted and separated by agarose gel electrophoresis. Separated DNA was recovered from the gel in discrete size fractions and analyzed with different duplex real-time PCR Taqman assays detecting a Y chromosome-specific target and an autosomal target. The real-time PCR research assays used differed significantly in their ability to determine the correct copy number ratio of 0.5 between Y chromosome and autosome targets in DNA of male origin. Longer PCR targets did not amplify quantitatively in circulatory DNA, due to limited presence of full-length target sequence in the sample. CONCLUSIONS: PCR targets of the same small size are preferred over longer targets when comparing fractional circulatory DNA concentrations by real-time PCR. As an example, a DYS14/18S duplex real-time PCR research assay is presented that correctly measures the fractional concentration of male DNA in a male/female mixture of circulatory, fragmented DNA.

  7. Linker dependent intercalation of bisbenzimidazole-aminosugars in an RNA duplex; selectivity in RNA vs. DNA binding.

    Science.gov (United States)

    Ranjan, Nihar; Arya, Dev P

    2016-12-15

    Neomycin and Hoechst 33258 are two well-known nucleic acid binders that interact with RNA and DNA duplexes with high affinities respectively. In this manuscript, we report that covalent attachment of bisbenzimidazole unit derived from Hoechst 33258 to neomycin leads to intercalative binding of the bisbenzimidazole unit (oriented at 64-74° with respected to the RNA helical axis) in a linker length dependent manner. The dual binding and intercalation of conjugates were supported by thermal denaturation, CD, LD and UV-Vis absorption experiments. These studies highlight the importance of linker length in dual recognition by conjugates, for effective RNA recognition, which can lead to novel ways of recognizing RNA structures. Additionally, the ligand library screens also identify DNA and RNA selective compounds, with compound 9, containing a long linker, showing a 20.3°C change in RNA duplex T m with only a 13.0°C change in T m for the corresponding DNA duplex. Significantly, the shorter linker in compound 3 shows almost the reverse trend, a 23.8°C change in DNA T m , with only a 9.1°C change in T m for the corresponding RNA duplex. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Structural and Dynamical Impact of a Universal Fluorescent Nucleoside Analogue Inserted Into a DNA Duplex.

    Science.gov (United States)

    Zargarian, Loussiné; Ben Imeddourene, Akli; Gavvala, Krishna; Barthes, Nicolas P F; Michel, Benoit Y; Kenfack, Cyril A; Morellet, Nelly; René, Brigitte; Fossé, Philippe; Burger, Alain; Mély, Yves; Mauffret, Olivier

    2017-12-21

    Recently, a 3-hydroxychromone based nucleoside 3HCnt has been developed as a highly environment-sensitive nucleoside surrogate to investigate protein-DNA interactions. When it is incorporated in DNA, the probe is up to 50-fold brighter than 2-aminopurine, the reference fluorescent nucleoside. Although the insertion of 3HCnt in DNA was previously shown to not alter the overall DNA structure, the possibility of the probe inducing local effects cannot be ruled out. Hence, a systematic structural and dynamic study is required to unveil the 3HCnt's limitations and to properly interpret the data obtained with this universal probe. Here, we investigated by NMR a 12-mer duplex, in which a central adenine was replaced by 3HCnt. The chemical shifts variations and nOe contacts revealed that the 3HCnt is well inserted in the DNA double helix with extensive stacking interactions with the neighbor base pairs. These observations are in excellent agreement with the steady-state and time-resolved fluorescence properties indicating that the 3HCnt fluorophore is protected from the solvent and does not exhibit rotational motion. The 3HCnt insertion in DNA is accompanied by the extrusion of the opposite nucleobase from the double helix. Molecular dynamics simulations using NMR-restraints demonstrated that 3HCnt fluorophore exhibits only translational dynamics. Taken together, our data showed an excellent intercalation of 3HCnt in the DNA double helix, which is accompanied by localized perturbations. This confirms 3HCnt as a highly promising tool for nucleic acid labeling and sensing.

  9. 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

  10. 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.

  11. Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method

    International Nuclear Information System (INIS)

    Konerding, David E.; Cheatham, Thomas E.; Kollman, Peter A.; James, Thomas L.

    1999-01-01

    Restrained and unrestrained aqueous solution molecular dynamics simulations applying the particle mesh Ewald (PME) method to DNA duplex structures previously determined via in vacuo restrained molecular dynamics with NMR-derived restraints are reported. Without experimental restraints, the DNA decamer, d(CATTTGCATC).d(GATGCAAATG) and trisdecamer, d(AGCTTGCCTTGAG).d(CTCAAGGCAAGCT), structures are stable on the nanosecond time scale and adopt conformations in the B-DNA family. These free DNA simulations exhibit behavior characteristic of PME simulations previously performed on DNA sequences, including a low helical twist, frequent sugar pucker transitions, BI- BII(ε-ζ) transitions and coupled crankshaft (α-γ) motion. Refinement protocols similar to the original in vacuo restrained molecular dynamics (RMD) refinements but in aqueous solution using the Cornell et al. force field [Cornell et al. (1995) J. Am. Chem. Soc., 117, 5179-5197] and a particle mesh Ewald treatment produce structures which fit the restraints very well and are very similar to the original in vacuo NMR structure, except for a significant difference in the average helical twist. Figures of merit for the average structure found in the RMD PME decamer simulations in solution are equivalent to the original in vacuo NMR structure while the figures of merit for the free MD simulations are significantly higher. The free MD simulations with the PME method, however, lead to some sequence-dependent structural features in common with the NMR structures, unlike free MD calculations with earlier force fields and protocols. There is some suggestion that the improved handling of electrostatics by PME improves long-range structural aspects which are not well defined by the short-range nature of NMR restraints

  12. 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

  13. Different models for phosphate anion shielding in DNA duplexes: An elaboration with ab initio and molecular mechanics calculations

    Science.gov (United States)

    Buck, Henk

    In an effort to overcome a significant difference between high-level ab initio calculations and X-ray data of DNA duplexes, Fonseca Guerra et al. 9-11 studied a number of model systems for A-T and G-C basepairs at various levels of nonlocal Density Functional Theory. There was an excellent agreement with the gas-phase experimental bond enthalpies for the A-T and G-C basepairs. On the other hand the hydrogen bond lengths between the bases differ from the X-ray results. After introduction of a molecular environment as local water and Na+ ions, the agreement between theory and experiment was excellent. However, careful analysis shows that this picture is far from correct. In fact, the model was constructed as a backbone-modified DNA duplex in which the nonbonding oxygens of the phosphate linkages are completely shielded by proton addition. Experimental results with respect to backbone-modified DNAs clearly show that changes in the backbone focused on phosphate shielding result in DNA duplexes with a variety in conformational behavior. In addition to an analysis of the aforementioned contradiction, we also give molecular mechanics calculations which show that the A-T and G-C bond enthalpies are of the same order as the corresponding results of Fonseca Guerra et al. under the condition of complete anionic shielding of the nonbonded oxygens in the phosphate linkages.

  14. 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.

  15. Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods.

    Science.gov (United States)

    Taverniers, Isabel; Van Bockstaele, Erik; De Loose, Marc

    2004-03-01

    Analytical real-time PCR technology is a powerful tool for implementation of the GMO labeling regulations enforced in the EU. The quality of analytical measurement data obtained by quantitative real-time PCR depends on the correct use of calibrator and reference materials (RMs). For GMO methods of analysis, the choice of appropriate RMs is currently under debate. So far, genomic DNA solutions from certified reference materials (CRMs) are most often used as calibrators for GMO quantification by means of real-time PCR. However, due to some intrinsic features of these CRMs, errors may be expected in the estimations of DNA sequence quantities. In this paper, two new real-time PCR methods are presented for Roundup Ready soybean, in which two types of plasmid DNA fragments are used as calibrators. Single-target plasmids (STPs) diluted in a background of genomic DNA were used in the first method. Multiple-target plasmids (MTPs) containing both sequences in one molecule were used as calibrators for the second method. Both methods simultaneously detect a promoter 35S sequence as GMO-specific target and a lectin gene sequence as endogenous reference target in a duplex PCR. For the estimation of relative GMO percentages both "delta C(T)" and "standard curve" approaches are tested. Delta C(T) methods are based on direct comparison of measured C(T) values of both the GMO-specific target and the endogenous target. Standard curve methods measure absolute amounts of target copies or haploid genome equivalents. A duplex delta C(T) method with STP calibrators performed at least as well as a similar method with genomic DNA calibrators from commercial CRMs. Besides this, high quality results were obtained with a standard curve method using MTP calibrators. This paper demonstrates that plasmid DNA molecules containing either one or multiple target sequences form perfect alternative calibrators for GMO quantification and are especially suitable for duplex PCR reactions.

  16. Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding.

    Science.gov (United States)

    Davis, Ryan R; Shaban, Nadine M; Perrino, Fred W; Hollis, Thomas

    2015-01-01

    RNA-DNA hybrids play essential roles in a variety of biological processes, including DNA replication, transcription, and viral integration. Ribonucleotides incorporated within DNA are hydrolyzed by RNase H enzymes in a removal process that is necessary for maintaining genomic stability. In order to understand the structural determinants involved in recognition of a hybrid substrate by RNase H we have determined the crystal structure of a dodecameric non-polypurine/polypyrimidine tract RNA-DNA duplex. A comparison to the same sequence bound to RNase H, reveals structural changes to the duplex that include widening of the major groove to 12.5 Å from 4.2 Å and decreasing the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H. This structure allows a direct comparison to be made about the conformational changes induced in RNA-DNA hybrids upon binding to RNase H and may provide insight into how dysfunction in the endonuclease causes disease.

  17. Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation.

    Science.gov (United States)

    Lomzov, Alexander A; Vorobjev, Yury N; Pyshnyi, Dmitrii V

    2015-12-10

    A molecular dynamics simulation approach was applied for the prediction of the thermal stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA complex formation could be calculated using this approach. We have studied the influence of various simulation parameters on the secondary structure and the hybridization enthalpy value of Dickerson-Drew dodecamer. The optimal simulation parameters for the most reliable prediction of the enthalpy values were determined. The thermodynamic parameters (enthalpy and entropy changes) of a duplex formation were obtained experimentally for 305 oligonucleotides of various lengths and GC-content. The resulting database was studied with molecular dynamics (MD) simulation using the optimized simulation parameters. Gibbs free energy changes and the melting temperatures were evaluated using the experimental correlation between enthalpy and entropy changes of the duplex formation and the enthalpy values calculated by the MD simulation. The average errors in the predictions of enthalpy, the Gibbs free energy change, and the melting temperature of oligonucleotide complexes were 11%, 10%, and 4.4 °C, respectively. We have shown that the molecular dynamics simulation gives a possibility to calculate the thermal stability of native DNA/DNA complexes a priori with an unexpectedly high accuracy.

  18. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory.

    Science.gov (United States)

    Chu, Vincent B; Bai, Yu; Lipfert, Jan; Herschlag, Daniel; Doniach, Sebastian

    2007-11-01

    Poisson-Boltzmann (PB) theory is among the most widely applied electrostatic theories in biological and chemical science. Despite its reasonable success in explaining a wide variety of phenomena, it fails to incorporate two basic physical effects, ion size and ion-ion correlations, into its theoretical treatment. Recent experimental work has shown significant deviations from PB theory in competitive monovalent and divalent ion binding to a DNA duplex. The experimental data for monovalent binding are consistent with a hypothesis that attributes these deviations to counterion size. To model the observed differences, we have generalized an existing size-modified Poisson-Boltzmann (SMPB) theory and developed a new numerical implementation that solves the generalized theory around complex, atomistic representations of biological molecules. The results of our analysis show that good agreement to data at monovalent ion concentrations up to approximately 150 mM can be attained by adjusting the ion-size parameters in the new size-modified theory. SMPB calculations employing calibrated ion-size parameters predict experimental observations for other nucleic acid structures and salt conditions, demonstrating that the theory is predictive. We are, however, unable to model the observed deviations in the divalent competition data with a theory that only accounts for size but neglects ion-ion correlations, highlighting the need for theoretical descriptions that further incorporate ion-ion correlations. The accompanying numerical solver has been released publicly, providing the general scientific community the ability to compute SMPB solutions around a variety of different biological structures with only modest computational resources.

  19. Cisplatin adducts on a GGG sequence within a DNA duplex studied by NMR spectroscopy and molecular dynamics simulations.

    Science.gov (United States)

    Téletchéa, Stéphane; Skauge, Tormod; Sletten, Einar; Kozelka, Jirí

    2009-11-16

    The antitumor drug cisplatin(cis-[PtCl2(NH3)2]) reacts with cellular DNA to form GG intrastrand adducts between adjacent guanines as predominant lesions. GGG sites have been shown to be hotspots of platination. To study the structural perturbation induced by binding of cisplatin to two adjacent guanines of a GGG trinucleotide,we examined here the decanucleotide duplex d[(G1C2C3G*4 G*5 G6T7-C8G9C10).d(G11C12G13A14C15C16C17G18-G19C20)] (dsCG*G*G) intrastrand cross-linked at the G* guanines by cis-{Pt(NH3)2}2+ using NMR spectroscopy and molecular dynamics (MD) simulations.The NMR spectra of dsCG*G*G were found to be similar to those of previously characterized DNA duplexes cross-linked by cisplatin at apyG*G*X site (py=pyrimidine; X=C,T, A). This similarity of NMR spectra indicates that the base at the 3'-side of the G*G*-Pt cross-link does not affect the structure to a large extent. An unprecedented reversible isomerization between the duplex dsCG*G*G (bearing a G*4 G*5 -Pt chelate) and duplex dsGG*G*T (bearing a G*5 G*6 -Pt chelate)was observed, which yielded a 40:60 equilibrium between the two intrastrand GG-Pt cross-links. No formation of interstrand cross-links was observed.NMR spectroscopic data of dsCG*G*G indicated that the deoxyribose of the 5'-G* adopts an N-type conformation, and the cytidines C3, C15,and C16 have average phase angles intermediate between S and N. The NMR spectroscopic chemical shifts of dsGG*G*T showed some fundamental differences to those of pyG*G*-platinum adducts but were in agreement with the NMR spectra reported previously for the DNA duplexes crosslinked at an AG*G*C sequence by cisplatin or oxaliplatin. The presence of apurine instead of a pyrimidine at the 5'-side of the G*G* cross-link seems therefore to affect the structure of the XG* step significantly.

  20. 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.

  1. Stability and Mismatch Discrimination of Locked Nucleic Acid–DNA Duplexes

    Science.gov (United States)

    2011-01-01

    Locked nucleic acids (LNA; symbols of bases, +A, +C, +G, and +T) are introduced into chemically synthesized oligonucleotides to increase duplex stability and specificity. To understand these effects, we have determined thermodynamic parameters of consecutive LNA nucleotides. We present guidelines for the design of LNA oligonucleotides and introduce free online software that predicts the stability of any LNA duplex oligomer. Thermodynamic analysis shows that the single strand–duplex transition is characterized by a favorable enthalpic change and by an unfavorable loss of entropy. A single LNA modification confines the local conformation of nucleotides, causing a smaller, less unfavorable entropic loss when the single strand is restricted to the rigid duplex structure. Additional LNAs adjacent to the initial modification appear to enhance stacking and H-bonding interactions because they increase the enthalpic contributions to duplex stabilization. New nearest-neighbor parameters correctly forecast the positive and negative effects of LNAs on mismatch discrimination. Specificity is enhanced in a majority of sequences and is dependent on mismatch type and adjacent base pairs; the largest discriminatory boost occurs for the central +C·C mismatch within the +T+C+C sequence and the +A·G mismatch within the +T+A+G sequence. LNAs do not affect specificity in some sequences and even impair it for many +G·T and +C·A mismatches. The level of mismatch discrimination decreases the most for the central +G·T mismatch within the +G+G+C sequence and the +C·A mismatch within the +G+C+G sequence. We hypothesize that these discrimination changes are not unique features of LNAs but originate from the shift of the duplex conformation from B-form to A-form. PMID:21928795

  2. 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

    This paper describes a spin label that can detect and identify local structural deformations in duplex DNA, in particular abasic sites. The spin label was incorporated into DNA by a new postsynthetic approach using click-chemistry on a solid support, which simplified both the synthesis...

  3. DNA duplex stability as discriminative characteristic for Escherichia coli σ(54)- and σ(28)- dependent promoter sequences.

    Science.gov (United States)

    de Avila e Silva, Scheila; Forte, Franciele; T S Sartor, Ivaine; Andrighetti, Tahila; J L Gerhardt, Günther; Longaray Delamare, Ana Paula; Echeverrigaray, Sergio

    2014-01-01

    The advent of modern high-throughput sequencing has made it possible to generate vast quantities of genomic sequence data. However, the processing of this volume of information, including prediction of gene-coding and regulatory sequences remains an important bottleneck in bioinformatics research. In this work, we integrated DNA duplex stability into the repertoire of a Neural Network (NN) capable of predicting promoter regions with augmented accuracy, specificity and sensitivity. We took our method beyond a simplistic analysis based on a single sigma subunit of RNA polymerase, incorporating the six main sigma-subunits of Escherichia coli. This methodology employed successfully re-discovered known promoter sequences recognized by E. coli RNA polymerase subunits σ(24), σ(28), σ(32), σ(38), σ(54) and σ(70), with highlighted accuracies for σ(28)- and σ(54)- dependent promoter sequences (values obtained were 80% and 78.8%, respectively). Furthermore, the discrimination of promoters according to the σ factor made it possible to extract functional commonalities for the genes expressed by each type of promoter. The DNA duplex stability rises as a distinctive feature which improves the recognition and classification of σ(28)- and σ(54)- dependent promoter sequences. The findings presented in this report underscore the usefulness of including DNA biophysical parameters into NN learning algorithms to increase accuracy, specificity and sensitivity in promoter beyond what is accomplished based on sequence alone. Copyright © 2013 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  4. Structural effects of internucleotide linkage modification at mismatch site in DNA/RNA duplex: Raman study

    Czech Academy of Sciences Publication Activity Database

    Kříž, M.; Němeček, D.; Turpin, P. Y.; Rosenberg, Ivan; Štěpánek, J.

    2008-01-01

    Roč. 48, č. 1 (2008), s. 148-152 ISSN 0924-2031 R&D Projects: GA ČR GA203/05/0827 Institutional research plan: CEZ:AV0Z40550506 Keywords : nucleic acid * mismatch * hybrid duplex * Raman spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 1.810, year: 2008

  5. 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.

  6. 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.

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

    Science.gov (United States)

    Karmakar, Saswata; Madsen, Andreas S; Guenther, Dale C; Gibbons, Bradley C; Hrdlicka, Patrick J

    2014-10-21

    Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and--more recently--engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2'-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 hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔT(m)/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics.

  8. An enzyme system for replication of duplex circular DNA: the replicative form of phage phi X174.

    Science.gov (United States)

    Eisenberg, S; Scott, J F; Kornberg, A

    1976-05-01

    Viral single strands (SS) are converted to the duplex from (RF) by a soluble enzyme fraction uninfected Escherichia coli [Schekman et al. (1975) J. Biol. Chem. 250, 5859-5865]. When reactions were supplemented with a soluble enzyme fraction from phi X174-infected cells, replication of phi X174 superhelical RF I DNA was observed. The activity supplied by infected cells was absent in cells treated with chloramphenicol or in cells infected with a phi X174 phage mutant in cistron A (cis A). A host function coded by the rep gene, essential in vivo for RF replication (but not for SS leads to RF), was supplied by enzyme fractions from either infected or uninfected cells. Based on complementation assays, the cisA-dependent and the rep-dependent proteins have each been purified about 1000-fold. The synthetic products of the enzymatic reaction were identified as RF I and RF II in which viral (+) and complementary (-) strands were newly synthesized.

  9. Structure of the 1,N2-etheno-2'-deoxyguanosine adduct in duplex DNA at pH 8.6.

    Science.gov (United States)

    Shanmugam, Ganesh; Goodenough, Angela K; Kozekov, Ivan D; Guengerich, F Peter; Rizzo, Carmelo J; Stone, Michael P

    2007-11-01

    The structure of the 1,N(2)-etheno-2'-deoxyguanosine (1,N(2)-epsilondG) adduct, arising from the reaction of vinyl chloride with dG, was determined in the oligonucleotide duplex 5'-d(CGCATXGAATCC)-3'.5'-d(GGATTCCATGCG)-3' (X=1,N(2)-epsilondG) at pH 8.6 using high resolution NMR spectroscopy. The exocyclic lesion prevented Watson-Crick base-pairing capability at the adduct site and resulted in an approximately 17 degrees C decrease in Tm of the oligodeoxynucleotide duplex. At neutral pH, conformational exchange resulted in spectral line broadening near the adducted site, and it was not possible to determine the structure. However, at pH 8.6, it was possible to obtain well-resolved (1)H NMR spectra. This enabled a total of 385 NOE-based distance restraints to be obtained, consisting of 245 intra- and 140 inter-nucleotide distances. The (31)P NMR spectra exhibited two downfield-shifted resonances, suggesting a localized perturbation of the DNA backbone. The two downfield (31)P resonances were assigned to G(7) and C(19). The solution structure was refined by molecular dynamics calculations restrained by NMR-derived distance and dihedral angle restraints, using a simulated annealing protocol. The generalized Born approximation was used to simulate solvent. The emergent structures indicated that the 1,N(2)-epsilondG-induced structural perturbation was localized at the X(6).C(19) base pair, and its 5'-neighbor T(5).A(20). Both 1,N(2)-epsilondG and the complementary dC adopted the anti conformation about the glycosyl bonds. The 1,N (2)-epsilondG adduct was inserted into the duplex but was shifted towards the minor groove as compared to dG in a normal Watson-Crick C.G base pair. The complementary cytosine was displaced toward the major groove. The 5'-neighbor T(5).A(20) base pair was destabilized with respect to Watson-Crick base pairing. The refined structure predicted a bend in the helical axis associated with the adduct site.

  10. 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.

  11. G4-Tetra DNA Duplex Induce Lung Cancer Cell Apoptosis in A549 Cells

    Science.gov (United States)

    Xu, Xiaobo; Zhao, YiZhuo; Lu, Hu; Fu, Cuiping; Li, Xiao; Jiang, Liyan; Li, Shanqun

    2016-10-01

    The specific DNA is typically impermeable to the plasma membrane due to its natural characters, but DNA tetra structures (DTNs) can be readily uptake by cells in the absence of transfection agents, providing a new strategy to deliver DNA drugs. In this research, the delivery efficiency of tetrahedral DNA nanostructures was measured on adenocarcinomic human alveolar basal epithelial (A549) cells via delivering AS1411 (G4). The DNA tetra-AS1411 complex was rapidly and abundantly uptake by A549 cells, and the induced apoptosis was enhanced. Furthermore, biodistribution in mouse proved the rapid clearance from non-targeted organs in vivo. This study improved the understanding of potential function in DNA-based drug delivery and proved that DTNs-AS1411 could be potentially useful for the treatment of lung cancer.

  12. Human RAD52 Captures and Holds DNA Strands, Increases DNA Flexibility, and Prevents Melting of Duplex DNA: Implications for DNA Recombination

    Directory of Open Access Journals (Sweden)

    Ineke Brouwer

    2017-03-01

    Full Text Available Human RAD52 promotes annealing of complementary single-stranded DNA (ssDNA. In-depth knowledge of RAD52-DNA interaction is required to understand how its activity is integrated in DNA repair processes. Here, we visualize individual fluorescent RAD52 complexes interacting with single DNA molecules. The interaction with ssDNA is rapid, static, and tight, where ssDNA appears to wrap around RAD52 complexes that promote intra-molecular bridging. With double-stranded DNA (dsDNA, interaction is slower, weaker, and often diffusive. Interestingly, force spectroscopy experiments show that RAD52 alters the mechanics dsDNA by enhancing DNA flexibility and increasing DNA contour length, suggesting intercalation. RAD52 binding changes the nature of the overstretching transition of dsDNA and prevents DNA melting, which is advantageous for strand clamping during or after annealing. DNA-bound RAD52 is efficient at capturing ssDNA in trans. Together, these effects may help key steps in DNA repair, such as second-end capture during homologous recombination or strand annealing during RAD51-independent recombination reactions.

  13. 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

  14. Solution structure of the DNA decamer duplex containing a 3′-T·T base pair of the cis–syn cyclobutane pyrimidine dimer: implication for the mutagenic property of the cis–syn dimer

    OpenAIRE

    Lee, Joon-Hwa; Choi, Yun-Jeong; Choi, Byong-Seok

    2000-01-01

    The cis–syn dimer is the major DNA photoproduct produced by UV irradiation. In order to determine the origin of the mutagenic property of the cis–syn dimer, we used NMR restraints and molecular dynamics to determine the solution structure of a DNA decamer duplex containing a wobble pair between the 3′-T of the cis–syn dimer and the opposite T residue (CS/TA duplex). The solution structure of the CS/TA duplex revealed that the 3′-T·T base pair of the cis–syn dimer had base pair geometry that w...

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

    Science.gov (United States)

    Karmakar, Saswata; Madsen, Andreas S.; Guenther, Dale C.; Gibbons, Bradley C.; Hrdlicka, Patrick J.

    2014-01-01

    Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and - more recently - engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2′-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 hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔTm/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics. PMID:25144705

  16. Structural Insights into Conformation Differences between DNA/TNA and RNA/TNA Chimeric Duplexes.

    Science.gov (United States)

    Anosova, Irina; Kowal, Ewa A; Sisco, Nicholas J; Sau, Sujay; Liao, Jen-Yu; Bala, Saikat; Rozners, Eriks; Egli, Martin; Chaput, John C; Van Horn, Wade D

    2016-09-15

    Threose nucleic acid (TNA) is an artificial genetic polymer capable of heredity and evolution, and is studied in the context of RNA chemical etiology. It has a four-carbon threose backbone in place of the five-carbon ribose of natural nucleic acids, yet forms stable antiparallel complementary Watson-Crick homoduplexes and heteroduplexes with DNA and RNA. TNA base-pairs more favorably with RNA than with DNA but the reason is unknown. Here, we employed NMR, ITC, UV, and CD to probe the structural and dynamic properties of heteroduplexes of RNA/TNA and DNA/TNA. The results indicate that TNA templates the structure of heteroduplexes, thereby forcing an A-like helical geometry. NMR measurement of kinetic and thermodynamic parameters for individual base pair opening events reveal unexpected asymmetric "breathing" fluctuations of the DNA/TNA helix. The results suggest that DNA is unable to fully adapt to the conformational constraints of the rigid TNA backbone and that nucleic acid breathing dynamics are determined from both backbone and base contributions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. 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

    of decameric pcPNAs block an access of RNA polymerase to the corresponding promoter. Here, we show that this type of PNAs protects selected DNA sites containing all four nucleobases from the action of restriction enzymes and DNA methyltransferases. We have found that pcPNAs as short as octamers form stable......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...

  18. Thermodynamic stability and energetics of DNA duplexes containing major intrastrand cross-links of second-generation antitumor dinuclear Pt(II) complexes.

    Science.gov (United States)

    Florian, Jakub; Kasparkova, Jana; Farrell, Nicholas P; Brabec, Viktor

    2012-02-01

    The effects of major DNA intrastrand cross-links of antitumor dinuclear Pt(II) complexes [{trans-PtCl(NH(3))(2)}(2)-μ-{trans-(H(2)N(CH(2))(6)NH(2)(CH(2))(2)NH(2)(CH(2))(6)NH(2))}](4+) (1) and [{PtCl(DACH)}(2)-μ-{H(2)N(CH(2))(6)NH(2)(CH(2))(2)NH(2)(CH(2))(6)NH(2))}](4+) (2) (DACH is 1,2-diaminocyclohexane) on DNA stability were studied with emphasis on thermodynamic origins of that stability. Oligodeoxyribonucleotide duplexes containing the single 1,2, 1,3, or 1,5 intrastrand cross-links at guanine residues in the central TGGT, TGTGT, or TGTTTGT sequences, respectively, were prepared and analyzed by differential scanning calorimetry. The unfolding of the platinated duplexes was accompanied by unfavorable free energy terms. The efficiency of the cross-links to thermodynamically destabilize the duplex depended on the number of base pairs separating the platinated bases. The trend was 1,5→1,2→1,3 cross-link of 1 and 1,5→1,3→1,2 cross-link of 2. Interestingly, the results showed that the capability of the cross-links to reduce the thermodynamic stability of DNA (ΔG(298)(0)) correlated with the extent of conformational distortions induced in DNA by various types of intrastrand cross-links of 1 or 2 determined by chemical probes of DNA conformation. We also examined the efficiency of the mammalian nucleotide excision repair systems to remove from DNA the intrastrand cross-links of 1 or 2. The efficiency of the excinucleases to remove the cross-links from DNA depended on the length of the cross-link; the trend was identical to that observed for the efficiency of the intrastrand cross-links to thermodynamically destabilize the duplex. Thus, the results are consistent with the thesis that an important factor that determines the susceptibility of the intrastrand cross-links of dinuclear platinum complexes 1 and 2 to be removed from DNA by nucleotide excision repair is the efficiency of these lesions to thermodynamically destabilize DNA.

  19. NMR spectroscopic studies on metallo-base-pair in DNA duplex

    Czech Academy of Sciences Publication Activity Database

    Tanaka, Y.; Okamoto, I.; Furuita, K.; Šebera, Jakub; Kondo, J.; Torigoe, H.; Urata, H.; Dairaku, T.; Ono, A.; Kojima, C.; Sychrovský, Vladimír

    2014-01-01

    Roč. 19, Suppl 2 (2014), S732-S733 ISSN 0949-8257. [European Biological Inorganic Chemistry Conference /12./. 24.08.2014-28.08.2014, Zurich] Institutional support: RVO:61388963 Keywords : NMR * DNA * mercury * thymine Subject RIV: CF - Physical ; Theoretical Chemistry

  20. Thermal stability and energetics of 15-mer DNA duplex interstrand crosslinked by trans-diamminedichloroplatinum(II)

    Czech Academy of Sciences Publication Activity Database

    Hofr, Ctirad; Brabec, Viktor

    2005-01-01

    Roč. 77, č. 4 (2005), s. 222-229 ISSN 0006-3525 R&D Projects: GA ČR(CZ) GP202/01/D110; GA ČR(CZ) GA305/02/1552; GA AV ČR(CZ) LZ1K03010 Institutional research plan: CEZ:AV0Z50040507 Keywords : DNA * interstrand cross-link * transplatin Subject RIV: BO - Biophysics Impact factor: 2.545, year: 2005

  1. 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.

  2. Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

    Science.gov (United States)

    Pan, Feng; Roland, Christopher; Sagui, Celeste

    2014-01-01

    The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5′-CGCGCGCGCGCG-3′)2 dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na+, K+ and Mg2 +, with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H2O)6]2+ ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H2O)6]2+ to distant phosphates, resulting in acute bending of A-RNA; tight ‘ion traps’ in Z-RNA between C-O2 and the C-O2′ atoms in GpC steps; and others. PMID:25428372

  3. Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes.

    Science.gov (United States)

    Wang, Rui; Ranganathan, Srivathsan V; Valsangkar, Vibhav A; Magliocco, Stephanie M; Shen, Fusheng; Chen, Alan; Sheng, Jia

    2015-11-25

    5-Hydroxylmethylcytosine (5hmC) has been recognized as the sixth base with important biological functions in many tissues and cell types. We present here the high-resolution crystal structures and molecular simulation studies of both A-form and B-form DNA duplexes containing 5hmC. We observed that 5hmC interacts with its 3'-neighboring bases through water-bridged hydrogen bonds and these interactions may affect the further oxidation of 5hmC.

  4. Structural basis for replication origin unwinding by an initiator primase of plasmid ColE2-P9: duplex DNA unwinding by a single protein.

    Science.gov (United States)

    Itou, Hiroshi; Yagura, Masaru; Shirakihara, Yasuo; Itoh, Tateo

    2015-02-06

    Duplex DNA is generally unwound by protein oligomers prior to replication. The Rep protein of plasmid ColE2-P9 (34 kDa) is an essential initiator for plasmid DNA replication. This protein binds the replication origin (Ori) in a sequence-specific manner as a monomer and unwinds DNA. Here we present the crystal structure of the DNA-binding domain of Rep (E2Rep-DBD) in complex with Ori DNA. The structure unveils the basis for Ori-specific recognition by the E2Rep-DBD and also reveals that it unwinds DNA by the concerted actions of its three contiguous structural modules. The structure also shows that the functionally unknown PriCT domain, which forms a compact module, plays a central role in DNA unwinding. The conservation of the PriCT domain in the C termini of some archaeo-eukaryotic primases indicates that it probably plays a similar role in these proteins. Thus, this is the first report providing the structural basis for the functional importance of the conserved PriCT domain and also reveals a novel mechanism for DNA unwinding by a single protein. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Complex structure of the DNA-binding domain of AdpA, the global transcription factor in Streptomyces griseus, and a target duplex DNA reveals the structural basis of its tolerant DNA sequence specificity.

    Science.gov (United States)

    Yao, Ming Dong; Ohtsuka, Jun; Nagata, Koji; Miyazono, Ken-Ichi; Zhi, Yuehua; Ohnishi, Yasuo; Tanokura, Masaru

    2013-10-25

    AdpA serves as the global transcription factor in the A-factor regulatory cascade, controlling the secondary metabolism and morphological differentiation of the filamentous bacterium Streptomyces griseus. AdpA binds to over 500 operator regions with the consensus sequence 5'-TGGCSNGWWY-3' (where S is G or C, W is A or T, Y is T or C, and N is any nucleotide). However, it is still obscure how AdpA can control hundreds of genes. To elucidate the structural basis of this tolerant DNA recognition by AdpA, we focused on the interaction between the DNA-binding domain of AdpA (AdpA-DBD), which consists of two helix-turn-helix motifs, and a target duplex DNA containing the consensus sequence 5'-TGGCGGGTTC-3'. The crystal structure of the AdpA-DBD-DNA complex and the mutant analysis of AdpA-DBD revealed its unique manner of DNA recognition, whereby only two arginine residues directly recognize the consensus sequence, explaining the strict recognition of G and C at positions 2 and 4, respectively, and the tolerant recognition of other positions of the consensus sequence. AdpA-DBD confers tolerant DNA sequence specificity to AdpA, allowing it to control hundreds of genes as a global transcription factor.

  6. Fluorescent duplex allele-specific PCR and amplicon melting for rapid homogeneous mtDNA haplogroup H screening and sensitive mixture detection.

    Directory of Open Access Journals (Sweden)

    Harald Niederstätter

    Full Text Available BACKGROUND: For large scale studies aiming at a better understanding of mitochondrial DNA (mtDNA, sequence variation in particular mt haplogroups (hgs and population structure, reliable low-cost high-throughput genotyping assays are needed. Furthermore, methods facilitating sensitive mixture detection and relative quantification of allele proportions are indispensable for the study of heteroplasmy, mitochondrial sequence evolution, and mitochondrial disorders. Here the properties of a homogeneous competitive duplex allele specific PCR (ARMS assay were scrutinized in the light of these requirements. METHODOLOGY/PRINCIPAL FINDINGS: A duplex ARMS assay amplifying either the ancestral mtDNA 2706G allele (non-hg H samples or the derived 7028C allele (hg H samples in the presence of SYBR Green fluorescent reporter dye was developed and characterized. Product detection, allele calling, and hg inference were based on the amplicon-characteristic melting-point temperatures obtained with on-line post-PCR fluorescent dissociation curve analysis (DCA. The analytical window of the assay covered at least 5 orders of magnitude of template DNA input with a detection limit in the low picogram range of genomic DNA. A set of forensically relevant test specimens was analyzed successfully. The presence of mtDNA mixtures was detected over a broad range of input DNA amounts and mixture ratios, and the estimation of allele proportions in samples with known total mtDNA content was feasible with limitations. A qualified DNA analyst successfully analyzed approximately 2,200 DNA extracts within three regular working days, without using robotic lab-equipment. By performing the amplification on-line, the assay also facilitated absolute mtDNA quantification. CONCLUSIONS: Although this assay was developed just for a particular purpose, the approach is general in that it is potentially suitable in a broad variety of assay-layouts for many other applications, including the

  7. Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.

    Science.gov (United States)

    Redrejo-Rodríguez, Modesto; Vigouroux, Armelle; Mursalimov, Aibek; Grin, Inga; Alili, Doria; Koshenov, Zhanat; Akishev, Zhiger; Maksimenko, Andrei; Bissenbaev, Amangeldy K; Matkarimov, Bakhyt T; Saparbaev, Murat; Ishchenko, Alexander A; Moréra, Solange

    2016-01-01

    Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 5' to an oxidized base. The majority of characterized AP endonucleases possess classic BER activities, and approximately a half of them can also have a NIR activity. At present, the molecular mechanism underlying DNA substrate specificity of AP endonucleases remains unclear mainly due to the absence of a published structure of the enzyme in complex with a damaged base. To identify critical residues involved in the NIR function, we performed biochemical and structural characterization of Bacillus subtilis AP endonuclease ExoA and compared its crystal structure with the structures of other AP endonucleases: Escherichia coli exonuclease III (Xth), human APE1, and archaeal Mth212. We found conserved amino acid residues in the NIR-specific enzymes APE1, Mth212, and ExoA. Four of these positions were studied by means of point mutations in APE1: we applied substitution with the corresponding residue found in NIR-deficient E. coli Xth (Y128H, N174Q, G231S, and T268D). The APE1-T268D mutant showed a drastically decreased NIR activity and an inverted Mg(2+) dependence of the AP site cleavage activity, which is in line with the presence of an aspartic residue at the equivalent position among other known NIR-deficient AP endonucleases. Taken together, these data show that NIR is an evolutionarily conserved function in the Xth family of AP endonucleases. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  8. 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.

  9. Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines

    Energy Technology Data Exchange (ETDEWEB)

    Diop-Frimpong, Benjamin; Prakash, Thazha P.; Rajeev, Kallanthottathil G.; Manoharan, Muthiah; Egli, Martin (Isis Pharm.); (Alnylam Pharm.); (Vanderbilt)

    2010-03-05

    Substitution of oxygen atoms by sulfur at various locations in the nucleic acid framework has led to analogs such as the DNA phosphorothioates and 4'-thio RNA. The phosphorothioates are excellent mimics of DNA, exhibit increased resistance to nuclease degradation compared with the natural counterpart, and have been widely used as first-generation antisense nucleic acid analogs for applications in vitro and in vivo. The 4'-thio RNA analog exhibits significantly enhanced RNA affinity compared with RNA, and shows potential for incorporation into siRNAs. 2-Thiouridine (s{sup 2}U) and 5-methyl-2-thiouridine (m{sup 5}s{sup 2}U) are natural nucleotide analogs. s{sup 2}U in tRNA confers greater specificity of codon-anticodon interactions by discriminating more strongly between A and G compared with U. 2-Thio modification preorganizes the ribose and 2'-deoxyribose sugars for a C3'-endo conformation, and stabilizes heteroduplexes composed of modified DNA and complementary RNA. Combination of the 2-thio and sugar 2'-O-modifications has been demonstrated to boost both thermodynamic stability and nuclease resistance. Using the 2'-O-[2-(methoxy)ethyl]-2-thiothymidine (m{sup 5}s{sup 2}Umoe) analog, we have investigated the consequences of the replacement of the 2-oxygen by sulfur for base-pair geometry and duplex conformation. The crystal structure of the A-form DNA duplex with sequence GCGTAT*ACGC (T* = m{sup 5}s{sup 2}Umoe) was determined at high resolution and compared with the structure of the corresponding duplex with T* = m{sup 5}Umoe. Notable changes as a result of the incorporation of sulfur concern the base-pair parameter 'opening', an improvement of stacking in the vicinity of modified nucleotides as measured by base overlap, and a van der Waals interaction between sulfur atoms from adjacent m{sup 5}s{sup 2}Umoe residues in the minor groove. The structural data indicate only minor adjustments in the water structure as a result of

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

    OpenAIRE

    Olimpo, Jeffrey T.; DeStefano, Jeffrey J.

    2010-01-01

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

  11. 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.

  12. Duplex real-time PCR method for the detection of sesame (Sesamum indicum) and flaxseed (Linum usitatissimum) DNA in processed food products.

    Science.gov (United States)

    López-Calleja, Inés María; de la Cruz, Silvia; Martín, Rosario; González, Isabel; García, Teresa

    2015-01-01

    The development of a duplex real-time polymerase chain reaction (PCR) method allowing the simultaneous detection of sesame and flaxseed DNA in commercial food products is described. This duplex real-time PCR technique is based in the design of sesame- and flaxseed-specific primers based on the ITS1 region and two TaqMan fluorescent probes. The method was positive for sesame and flaxseed, and showed no cross-reactivity for all other heterologous plant and animal species tested. Sesame and flaxseed could be detected in a series of model samples with defined raw and heat-treated sesame in flaxseed, and flaxseed in sesame, respectively, with detection limits of 1.3 mg kg(-1) for sesame and 1.4 mg kg(-1) for flaxseed. The applicability of the assay for determining sesame and flaxseed in different food matrices was investigated by analysing a total of 238 commercial foodstuffs. This PCR method is useful for highly selective and sensitive detection of traces of sesame and flaxseed in commercial food products.

  13. The effects of a neutral cosolute on the B to Z transition for DNA duplexes incorporating both CG and CA steps.

    Science.gov (United States)

    Phromsiri, Pakinee; Gerling, Rebecca R; Blose, Joshua M

    2017-11-02

    In the cell, nearly 40% of the volume is occupied by macromolecular crowding agents and smaller osmolytes accumulate in response to environmental stresses. Of particular interest is the influence of osmolytes on the transition of the right-handed B-DNA to the left-handed Z-DNA. Due to the correlation between Z-DNA formation potential and regions of active transcription, Z-DNA is believed to serve a vital role in the transcription process, and changes in osmolyte concentration may influence transcription as a part of the stress response. We utilized circular dichroism spectroscopy to monitor changes in conformation of DNA duplexes containing a full-turn of Z-DNA in the presence and absence of PEG 200. We used PEG 200 as a model neutral cosolute. Sodium ion titrations revealed that PEG 200 influenced the folding of Z-DNA compared to dilute solution conditions by decreasing the free energy of folding, increasing folding cooperativity, and decreasing the in vitro [Na + ] and Δn required for folding for all sequences tested, even those that included 40% CA steps instead of the classic CG repeats. Moreover, the presence of 40% PEG 200 induced the Z-form conformation in sequences that would not fully adopt the Z-form structure even in 5 M NaCl. These results suggest that osmolytes may play a significant role in supporting the transient formation of Z-DNA in vivo, and that sequences containing a significant amounts of CA instead of CG repeats may more favorably adopt the Z-conformation as a part of binding and regulatory processes than had been previously considered.

  14. 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.

  15. NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription

    International Nuclear Information System (INIS)

    Szyperski, Thomas; Goette, Matthias; Billeter, Martin; Perola, Emanuele; Cellai, Luciano; Heumann, Hermann; Wuethrich, Kurt

    1999-01-01

    A high-quality NMR solution structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) was determined using the program DYANA with its recently implemented new module FOUND, which performs exhaustive conformational grid searches for dinucleotides. To ensure conservative data interpretation, the use of 1H-1H lower distance limit constraints was avoided. The duplex comprises the tRNA-DNA junction formed during the initiation of HIV-1 reverse transcription. It forms an A-type double helix that exhibits distinct structural deviations from a standard A-conformation. In particular, the minor groove is remarkably narrow, and its width decreases from about 7.5 A in the RNA/RNA stem to about 4.5 A in the RNA/DNA segment. This is unexpected, since minor groove widths for A-RNA and RNA/DNA hybrid duplexes of ∼11 A and ∼8.5 A, respectively, were previously reported. The present, new structure supports that reverse transcriptase-associated RNaseH specificity is related primarily to conformational adaptability of the nucleic acid in 'induced-fit'-type interactions, rather than the minor groove width of a predominantly static nucleic acid duplex

  16. 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.

  17. 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.

  18. Amino acids attached to 2'-amino-LNA: Synthesis of DNA mixmer oligonucleotides with increased duplex stability

    DEFF Research Database (Denmark)

    Johannsen, Marie Willaing; Wengel, Jesper; Wamberg, Michael Chr.

    2010-01-01

    -LNA nucleosides derivatized with amino acids have been synthesized and incorporated into DNA oligonucleotides. Following oligonucleotide synthesis, peptides have been added using solid phase peptide coupling chem. Modification of oligonucleotides with pos. charged residues greatly improves thermal stability....

  19. 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

  20. 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.

  1. Thermodynamic and kinetic characterization of duplex formation between 2'-O, 4'-C-methylene-modified oligoribonucleotides, DNA and RNA

    DEFF Research Database (Denmark)

    Christensen, Ulla

    2007-01-01

    2'-O,4'-C-methylene-linked ribonucleotide derivatives, named LNA (locked nucleic acid) and BNA (bridged nucleic acid) are nucleic acid analogoues that have shown high-affinity recognition of DNA and RNA, and the employment of LNA oligomers for antisense activity, gene regulation and nucleic acid...

  2. 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.

  3. Energetics, conformation, and recognition of DNA duplexes modified by monodentate Ru(II) complexes containing terphenyl arenes

    Czech Academy of Sciences Publication Activity Database

    Nováková, Olga; Malina, Jaroslav; Suchánková, T.; Kašpárková, Jana; Bugarcic, T.; Sadler, P.J.; Brabec, Viktor

    2010-01-01

    Roč. 16, č. 19 (2010), s. 5744-5754 ISSN 0947-6539 R&D Projects: GA ČR(CZ) GD301/09/H004; GA MŠk(CZ) LC06030; GA MŠk(CZ) ME08017; GA MŠk(CZ) ME10066; GA MŠk(CZ) OC08003; GA AV ČR(CZ) KAN200200651 Grant - others:GA MŠk(CZ) OC09018 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : calorimetry * ruthenium * DNA recognition Subject RIV: BO - Biophysics Impact factor: 5.476, year: 2010

  4. Study of Photochemical Cytosine to Uracil Transition via Ultrafast Photo-Cross-Linking Using Vinylcarbazole Derivatives in Duplex DNA.

    Science.gov (United States)

    Sethi, Siddhant; Nakamura, Shigetaka; Fujimoto, Kenzo

    2018-04-04

    Gene therapies, including genome editing, RNAi, anti-sense technology and chemical DNA editing are becoming major methods for the treatment of genetic disorders. Techniques like CRISPR-Cas9, zinc finger nuclease (ZFN) and transcription activator-like effector-based nuclease (TALEN) are a few such enzymatic techniques. Most enzymatic genome editing techniques have their disadvantages. Thus, non-enzymatic and non-invasive technologies for nucleic acid editing has been reported in this study which might possess some advantages over the older methods of DNA manipulation. 3-cyanovinyl carbazole ( CNV K) based nucleic acid editing takes advantage of photo-cross-linking between a target pyrimidine and the CNV K to afford deamination of cytosine and convert it to uracil. This method previously required the use of high temperatures but, in this study, it has been optimized to take place at physiological conditions. Different counter bases (inosine, guanine and cytosine) complementary to the target cytosine were used, along with derivatives of CNV K ( NH2V K and OHV K) to afford the deamination at physiological conditions.

  5. Study of Photochemical Cytosine to Uracil Transition via Ultrafast Photo-Cross-Linking Using Vinylcarbazole Derivatives in Duplex DNA

    Directory of Open Access Journals (Sweden)

    Siddhant Sethi

    2018-04-01

    Full Text Available Gene therapies, including genome editing, RNAi, anti-sense technology and chemical DNA editing are becoming major methods for the treatment of genetic disorders. Techniques like CRISPR-Cas9, zinc finger nuclease (ZFN and transcription activator-like effector-based nuclease (TALEN are a few such enzymatic techniques. Most enzymatic genome editing techniques have their disadvantages. Thus, non-enzymatic and non-invasive technologies for nucleic acid editing has been reported in this study which might possess some advantages over the older methods of DNA manipulation. 3-cyanovinyl carbazole (CNVK based nucleic acid editing takes advantage of photo-cross-linking between a target pyrimidine and the CNVK to afford deamination of cytosine and convert it to uracil. This method previously required the use of high temperatures but, in this study, it has been optimized to take place at physiological conditions. Different counter bases (inosine, guanine and cytosine complementary to the target cytosine were used, along with derivatives of CNVK (NH2VK and OHVK to afford the deamination at physiological conditions.

  6. 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

    was investigated by use of 2D-photoluminescence emission (2D-PLE), and the resulting data were subjected to analysis by use of convenient and powerful multi-way approaches. Fluorescence measurements were performed by use of the quantum dot (QD)-conjugated c-Myc promoter. Intercalation of 7AAD within duplex base...

  7. 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

  8. 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.

  9. LNA units present in the (2'-OMe)-RNA strand stabilize parallel duplexes (2'-OMe)-RNA/[All-R(P)-PS]-DNA and parallel triplexes (2'-OMe)-RNA/[All-R(P)-PS]-DNA/RNA. An improved tool for the inhibition of reverse transcription.

    Science.gov (United States)

    Maciaszek, Anna; Krakowiak, Agnieszka; Janicka, Magdalena; Tomaszewska-Antczak, Agnieszka; Sobczak, Milena; Mikołajczyk, Barbara; Guga, Piotr

    2015-02-28

    Homopurine phosphorothioate analogs of DNA, possessing all phosphorus atoms of RP configuration ([All-RP-PS]-DNA), when interact with appropriate complementary RNA or (2'-OMe)-RNA templates, form parallel triplexes or parallel duplexes of very high thermodynamic stability. The present results show that T-LNA or 5-Me-C-LNA units introduced into the parallel Hoogsteen-paired (2'-OMe)-RNA strands (up to four units in the oligomers of 9 or 12 nt in length) stabilize these parallel complexes. At neutral pH, dodecameric parallel duplexes have Tm values of 62-68 °C, which are by 4-10 °C higher than Tm for the reference duplex (with no LNA units present), while for the corresponding triplexes, Tm values exceeded 85 °C. For nonameric parallel duplexes, melting temperatures of 38-62 °C were found and (2'-OMe)-RNA oligomers containing 5-Me-C-LNA units stabilized the complexes more efficiently than the T-LNA containing congeners. In both series the stability of the parallel complexes increased with an increasing number of LNA units present. The same trend was observed in experiments of reverse transcription RNA→DNA (using AMV RT reverse transcriptase) where the formation of parallel triplexes (consisting of an RNA template, [All-RP-PS]-DNA nonamer and Hoogsteen-paired (2'-OMe)-RNA strands containing the LNA units) led to the efficient inhibition of the process. Under the best conditions checked (four 5-Me-C-LNA units, three-fold excess over the RNA template) the inhibition was 94% effective, compared to 71% inhibition observed in the reference system with the Hoogsteen-paired (2'-OMe)-RNA strand carrying no LNA units. This kind of complexation may "arrest" harmful RNA oligomers (e.g., viral RNA or mRNA of unwanted proteins) and, beneficially, exclude them from enzymatic processes, otherwise leading to viral or genetic diseases.

  10. 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.)

  11. Alopecia Following Bicoronal Incisions.

    Science.gov (United States)

    Kadakia, Sameep; Badhey, Arvind; Ashai, Sara; Lee, Thomas S; Ducic, Yadranko

    2017-05-01

    Multiple techniques may be used to perform bicoronal incisions, and alopecia is a known postoperative complication of this procedure. To date, no large studies exist comparing alopecia outcomes among bicoronal incision techniques with and without the use of Raney clips. To determine (1) whether postoperative alopecia is more common when bicoronal incisions are performed with monopolar cautery, Colorado microdissection tip cautery, or traditional cold steel and (2) whether this outcome is affected by the use of Raney clips. This retrospective study of postoperative alopecia included 505 patients undergoing bicoronal incisions in a single head and neck surgery practice from 1997 to 2015 with a minimum follow-up of 1 year. Patients with preexisting baldness as well as patients not following up for the minimum period were excluded. All data analysis took place between 1997 and 2015. Maximum alopecia width was measured in the postoperative period and compared among the technique groups both with and without Raney clip use. Raney clip duration as a product of surgery length was also compared. A total of 505 patients (301 male, 204 female) ranging in age from 3 to 97 years were included in the study (median age, 53.9 years). Of these, 236 underwent bicoronal incisions to approach the skull base, 78 to treat chronic frontal sinusitis unresponsive to endoscopic management or frontal sinus mucocele, 143 for trauma, and 48 for craniofacial surgery. For 173 patients, the cold steel technique was used for both skin and subcutaneous incision, 102 of whom needed Raney clips. For 161 patients, cold steel technique was used for skin incisions and monopolar cautery for subcutaneous incision; 81 of these patients required Raney clips. For 171 patients, Colorado tip microdissection cautery was used for both skin and subcutaneous incision, with Raney clips used in 66 of these patients. Incisions made with cold steel for both skin and subcutaneous tissue, regardless of Raney clip use

  12. 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....

  13. 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

  14. 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.

  15. The mandibular incisive foramen.

    OpenAIRE

    Serman, N J

    1989-01-01

    An anatomical variant in the region of the mental foramen is discussed. In these cases the inferior alveolar nerve divides into its two terminal branches only after it has exited through the mental foramen. The incisive nerve thus commences outside the mandible, and has a short extra-osseous course before it enters the mandible through a separate foramen on the same horizontal plane. For the distance between these two foramina there is no nerve supply within the mandible. The groove between t...

  16. Energetics, conformation, and recognition of DNA duplexes containing a major adduct of an anticancer azolato-bridged dinuclear PtII complex

    Czech Academy of Sciences Publication Activity Database

    Mlčoušková, J.; Malina, Jaroslav; Novohradský, V.; Kašpárková, J.; Komeda, S.; Brabec, Viktor

    2012-01-01

    Roč. 1820, č. 10 (2012), s. 1502-1511 ISSN 0304-4165 R&D Projects: GA ČR(CZ) GAP205/11/0856 Institutional research plan: CEZ:AV0Z50040702 Keywords : DNA * platinum * DNA repair Subject RIV: BO - Biophysics Impact factor: 3.848, year: 2012

  17. Site-specific interactions of JBP with base and sugar moieties in duplex J-DNA. Evidence for both major and minor groove contacts

    NARCIS (Netherlands)

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

    2002-01-01

    Beta-D-Glucosyl-hydroxymethyluracil, also called base J, is an unusually 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 identified a

  18. Oligopyridine-ruthenium(II)-amino acid conjugates: synthesis, characterization, DNA binding properties and interactions with the oligonucleotide duplex d(5'-CGCGCG-3')2

    Czech Academy of Sciences Publication Activity Database

    Triantafillidi, K.; Karidi, K.; Malina, Jaroslav; Garoufis, A.

    -, č. 32 (2009), s. 6403-6415 ISSN 1477-9226 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : oligopyridine- ruthenium (II)-amino acid conjugates * diastereomeric DNA binding * DNA photocleavage Subject RIV: BO - Biophysics Impact factor: 4.081, year: 2009

  19. 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

    Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and more recently engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating......'-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...

  20. 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.

  1. 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.

  2. 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.

  3. NMR analysis of duplex d(CGCGATCGCG)2 modified by lambda- and delta-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study

    Czech Academy of Sciences Publication Activity Database

    Myari, A.; Hadjiliadis, N.; Garoufis, A.; Malina, Jaroslav; Brabec, Viktor

    2007-01-01

    Roč. 12, č. 3 (2007), s. 279-292 ISSN 0949-8257 R&D Projects: GA ČR(CZ) GA305/05/2030; GA AV ČR(CZ) KJB400040601; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) KAN200200651; GA MŠk(CZ) LC06030; GA MŠk(CZ) 1P05OC072 Institutional research plan: CEZ:AV0Z50040702 Keywords : Ru(II) * peptide * DNA photocleavage Subject RIV: BO - Biophysics Impact factor: 3.325, year: 2007

  4. 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

  5. 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...

  6. Studies of DNA dumbbells. VI. Analysis of optical melting curves of dumbbells with a sixteen-base pair duplex stem and end-loops of variable size and sequence.

    Science.gov (United States)

    Paner, T M; Riccelli, P V; Owczarzy, R; Benight, A S

    1996-12-01

    Optical melting curves of 22 DNA dumbbells with the 16-base pair duplex sequence 5'-G-C-A-T-C-A-T-C-G-A-T-G-A-T-G-C-3' linked on both ends by single-strand loops of A, or C, sequences (iota = 2, 3, 4, 6, 8, 10, 14). T sequences (iota = 2, 3, 4, 6, 8, 10), and G iota sequences (iota = 2, 4) were measured in phosphate buffered solvents containing 30, 70, and 120 mM Na+. For dumbbells with loops comprised of at least three nucleotides, stability is inversely proportional to end-loop size. Dumbbells with loops comprised of only two nucleotide bases generally have lower stabilities than dumbbells with three base nucleotide loops. Experimental melting curves were analyzed in terms of the numerically exact (multistate) statistical thermodynamic model of DNA dumbbell melting previously described (T. M. paner, M. Amaratunga & A. S. Benight (1992), Biopolymers 32, 881). Theoretically calculated melting curves were fitted to experimental curves by simultaneously adjusting model parameters representing statistical weights of intramolecular hairpin loop and single-strand circle states. The systematically determined empirical parameters provided evaluations of the energetics of hairpin loop formation as a function of loop size, sequence, and salt environment. Values of the free energies of hairpin loop formation delta Gloop(n > iota) and single-strand circles, delta Gcir(N) as a function of end-loop size, tau = 2-14, circle size, N = 32 + 2 iota, and loop sequence were obtained. These quantities were found to depend on end-loop size but not loop sequence. Their empirically determined values also varied with solvent ionic strength. Analytical expressions for the partition function Q(T) of the dumbbells were evaluated using the empirically evaluated best-fit loop parameters. From Q(T), the melting transition enthalpy delta H, entropy delta S, and free energy delta G, were evaluated for the dumbbells as a function of end-loop size, sequence, and [Na+]. Since the multistate analysis

  7. 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)

  8. Achieving single channel, full duplex wireless communication

    KAUST Repository

    Choi, Jung Il

    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.

  9. 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

  10. 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)

  11. Incision for pleural tissue biopsy (image)

    Science.gov (United States)

    ... open pleural biopsy, a small piece of the pleural tissue is removed through a surgical incision in the chest. After the sample is obtained, a chest tube is placed and the incision is closed with ...

  12. 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.

  13. 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.

  14. Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

    OpenAIRE

    Pande, Vineet; Nilsson, Lennart

    2008-01-01

    Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3′-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA–DNA, LNA–LNA, LNA–RNA, RNA–DNA and RNA–RNA) in order to characterize their structure, dynamics and hydration. Structurally, the LNA–DNA and LNA–RNA duplexes are found to be similar to regular RNA–D...

  15. 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.

  16. Three versus four radial keratotomy incisions.

    Science.gov (United States)

    Melles, G R; Go, A T; Beekhuis, W H; van Rij, G; Binder, P S

    1992-01-01

    Radial keratotomy (RK) is currently performed with four or eight semi-radial incisions. To evaluate the effect of a theoretically more stable three-incision RK pattern, centripetal incisions were made in 16 human donor eyes (eight pairs), using a double-edged diamond blade set to 90% of central pachymetry and a 3.5 mm optical clear zone. Intraocular pressure was maintained at 15 mm Hg during surgery and while keratometry readings were made. One randomly selected eye of each pair had three radial incisions made at 12, 4 and 8 o'clock; the other eye had four radial incisions at 12, 3, 6, and 9 o'clock. Corneal flattening was 6.08 diopters (D) with four incisions and 4.84 D with three incisions (P less than .05). Astigmatism increased 0.44 D and 0.69 D, respectively (P greater than .1). Histologically measured mean incision depth (77.4%) did not differ significantly between the groups (P greater than .1). This study shows that 80% of the effect of a four-incision RK pattern can be obtained with a theoretically more stable three-incision pattern.

  17. 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.

  18. Is thymidine glycol containing DNA a substrate of E. coli DNA mismatch repair system?

    Directory of Open Access Journals (Sweden)

    Svetlana A Perevozchikova

    Full Text Available The DNA mismatch repair (MMR system plays a crucial role in the prevention of replication errors and in the correction of some oxidative damages of DNA bases. In the present work the most abundant oxidized pyrimidine lesion, 5,6-dihydro-5,6-dihydroxythymidine (thymidine glycol, Tg was tested for being recognized and processed by the E. coli MMR system, namely complex of MutS, MutL and MutH proteins. In a partially reconstituted MMR system with MutS-MutL-MutH proteins, G/Tg and A/Tg containing plasmids failed to provoke the incision of DNA. Tg residue in the 30-mer DNA duplex destabilized double helix due to stacking disruption with neighboring bases. However, such local structural changes are not important for E. coli MMR system to recognize this lesion. A lack of repair of Tg containing DNA could be due to a failure of MutS (a first acting protein of MMR system to interact with modified DNA in a proper way. It was shown that Tg in DNA does not affect on ATPase activity of MutS. On the other hand, MutS binding affinities to DNA containing Tg in G/Tg and A/Tg pairs are lower than to DNA with a G/T mismatch and similar to canonical DNA. Peculiarities of MutS interaction with DNA was monitored by Förster resonance energy transfer (FRET and fluorescence anisotropy. Binding of MutS to Tg containing DNAs did not result in the formation of characteristic DNA kink. Nevertheless, MutS homodimer orientation on Tg-DNA is similar to that in the case of G/T-DNA. In contrast to G/T-DNA, neither G/Tg- nor A/Tg-DNA was able to stimulate ADP release from MutS better than canonical DNA. Thus, Tg residue in DNA is unlikely to be recognized or processed by the E. coli MMR system. Probably, the MutS transformation to active "sliding clamp" conformation on Tg-DNA is problematic.

  19. Is thymidine glycol containing DNA a substrate of E. coli DNA mismatch repair system?

    Science.gov (United States)

    Perevozchikova, Svetlana A; Trikin, Roman M; Heinze, Roger J; Romanova, Elena A; Oretskaya, Tatiana S; Friedhoff, Peter; Kubareva, Elena A

    2014-01-01

    The DNA mismatch repair (MMR) system plays a crucial role in the prevention of replication errors and in the correction of some oxidative damages of DNA bases. In the present work the most abundant oxidized pyrimidine lesion, 5,6-dihydro-5,6-dihydroxythymidine (thymidine glycol, Tg) was tested for being recognized and processed by the E. coli MMR system, namely complex of MutS, MutL and MutH proteins. In a partially reconstituted MMR system with MutS-MutL-MutH proteins, G/Tg and A/Tg containing plasmids failed to provoke the incision of DNA. Tg residue in the 30-mer DNA duplex destabilized double helix due to stacking disruption with neighboring bases. However, such local structural changes are not important for E. coli MMR system to recognize this lesion. A lack of repair of Tg containing DNA could be due to a failure of MutS (a first acting protein of MMR system) to interact with modified DNA in a proper way. It was shown that Tg in DNA does not affect on ATPase activity of MutS. On the other hand, MutS binding affinities to DNA containing Tg in G/Tg and A/Tg pairs are lower than to DNA with a G/T mismatch and similar to canonical DNA. Peculiarities of MutS interaction with DNA was monitored by Förster resonance energy transfer (FRET) and fluorescence anisotropy. Binding of MutS to Tg containing DNAs did not result in the formation of characteristic DNA kink. Nevertheless, MutS homodimer orientation on Tg-DNA is similar to that in the case of G/T-DNA. In contrast to G/T-DNA, neither G/Tg- nor A/Tg-DNA was able to stimulate ADP release from MutS better than canonical DNA. Thus, Tg residue in DNA is unlikely to be recognized or processed by the E. coli MMR system. Probably, the MutS transformation to active "sliding clamp" conformation on Tg-DNA is problematic.

  20. Screening of Modified RNA duplexes

    DEFF Research Database (Denmark)

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

    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...... 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...

  1. 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.

  2. Thermal stabilisation of RNA·RNA duplexes and G-quadruplexes by phosphorothiolate linkages.

    Science.gov (United States)

    Piperakis, Michael M; Gaynor, James W; Fisher, Julie; Cosstick, Richard

    2013-02-14

    The effect of 3'-S-phosphorothiolate linkages on the stability of RNA·RNA duplexes and G-quadruplex structures has been studied. 3'-Thio-2'-deoxyuridine was incorporated into RNA duplexes and thermal melting studies revealed that the resulting 3'-S-phosphorothiolate linkages increased the stability of the duplex to thermal denaturation. Additionally, and contrary to expectation, a similar effect on duplex stability was observed when the same thionucleoside was incorporated into the RNA strand of a RNA·DNA duplex. A suitably protected derivative of 3'-thio-2'-deoxyguanosine was prepared using an oxidation-reduction strategy and this residue also increased the thermal stability the [d(TGGGGT)](4) G-quadruplex when positioned centrally. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and imply that the previously noted high thermal stability of parallel RNA quadruplexes is not derived from H-bonding interactions of the 2'-hydroxyl group, but can be attributed to conformational effects.

  3. Detection method for genetically modified papaya using duplex PCR.

    Science.gov (United States)

    Yamaguchi, Akihiro; Shimizu, Kaori; Mishima, Takashi; Aoki, Nobutaro; Hattori, Hideki; Sato, Hidetaka; Ueda, Nobuo; Watanabe, Takahiro; Hino, Akihiro; Akiyama, Hiroshi; Maitani, Tamio

    2006-08-01

    A simple and rapid method for the identification of genetically modified (GM) papaya, derived from Line 55-1, was developed by modifying the Japanese official PCR method. Genomic DNA was directly extracted from the fresh fruit without the lyophilization step, using a commercial silica-based kit. To develop a duplex PCR method which simultaneously detects the GM papaya-specific gene and the intrinsic papain gene, the papain 2-5'/3' (amplicon size; 184 bp) primer pair for the detection of the papain gene was newly designed within the region of the products (211 bp) amplified using the papain 1-5'/-3' primer pair adopted in the Japanese official PCR method. To detect the GM papaya-specific gene, the primer pair Nos C-5'/CaM N-3' described in the Japanese official method was used. The DNA sequences of the GM papaya gene and the intrinsic papain gene were co-amplified using the PCR method in a single tube. The developed duplex PCR method allows the simultaneous detection of the products by means of agarose gel electrophoresis or microchip electrophoresis. The proposed method for GM papaya identification is simple and rapid.

  4. Practical, real-time, full duplex wireless

    KAUST Repository

    Jain, Mayank

    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.

  5. 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.

  6. 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...

  7. UV-induced DNA incision and proliferating cell nuclear antigen recruitment to repair sites occur independently of p53-replication protein A interaction in p53 wild type and mutant ovarian carcinoma cells

    NARCIS (Netherlands)

    Riva, F.; Zuco, V.; Vink, A.A.; Supino, R.; Prosperi, E.

    2001-01-01

    The tumour suppressor gene TP53 plays an important role in the regulation of DNA repair, and particularly of nucleotide excision repair. The influence of p53 status on the efficiency of the principal steps of this repair pathway was investigated after UV-C irradiation in the human ovarian carcinoma

  8. Real-Time Duplex Applications of Loop-Mediated AMPlification (LAMP by Assimilating Probes

    Directory of Open Access Journals (Sweden)

    Ryo Kubota

    2015-03-01

    Full Text Available Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field.

  9. 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.

  10. 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.

  11. 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.

  12. Isolation, characterization and molecular cloning of Duplex-Specific Nuclease from the hepatopancreas of the Kamchatka crab

    Directory of Open Access Journals (Sweden)

    Vagner Laura L

    2008-05-01

    Full Text Available Abstract Background Nucleases, which are key components of biologically diverse processes such as DNA replication, repair and recombination, antiviral defense, apoptosis and digestion, have revolutionized the field of molecular biology. Indeed many standard molecular strategies, including molecular cloning, studies of DNA-protein interactions, and analysis of nucleic acid structures, would be virtually impossible without these versatile enzymes. The discovery of nucleases with unique properties has often served as the basis for the development of modern molecular biology methods. Thus, the search for novel nucleases with potentially exploitable functions remains an important scientific undertaking. Results Using degenerative primers and the rapid amplification of cDNA ends (RACE procedure, we cloned the Duplex-Specific Nuclease (DSN gene from the hepatopancreas of the Kamchatka crab and determined its full primary structure. We also developed an effective method for purifying functional DSN from the crab hepatopancreas. The isolated enzyme was highly thermostable, exhibited a broad pH optimum (5.5 – 7.5 and required divalent cations for activity, with manganese and cobalt being especially effective. The enzyme was highly specific, cleaving double-stranded DNA or DNA in DNA-RNA hybrids, but not single-stranded DNA or single- or double-stranded RNA. Moreover, only DNA duplexes containing at least 9 base pairs were effectively cleaved by DSN; shorter DNA duplexes were left intact. Conclusion We describe a new DSN from Kamchatka crab hepatopancreas, determining its primary structure and developing a preparative method for its purification. We found that DSN had unique substrate specificity, cleaving only DNA duplexes longer than 8 base pairs, or DNA in DNA-RNA hybrids. Interestingly, the DSN primary structure is homologous to well-known Serratia-like non-specific nucleases structures, but the properties of DSN are distinct. The unique substrate

  13. 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.

  14. A small incision technique facilitates pterygium removal

    Directory of Open Access Journals (Sweden)

    Shu Zhang

    2015-09-01

    Full Text Available AIM: To verify the advantages of an improved protocol for pterygium surgery(small incision removalover a conventional protocol of this surgery.METHODS: Totally 40 primary pterygium cases were divided into two groups(n=20 eachaccording to the protocols: small incision removal versus conventional removal. In our small incision removal, group 1, the pterygium body was cut open with a small incision firstly, through which the conjunctiva was separated from the underlying degenerated Tenon's layer; while in the conventional protocol, group 2, the whole head of pterygium was taken down before the separation. Then the head of pterygium was torn down in our protocol using a forceps instead of cutting it down with a blade, which was facilitated by a special corneal epithelial flap formation method. Surgery time, pain score and corneal wound healing were measured to provide objective comparison of outcome between the two protocols. RESULTS: In the group using small incision removal, the average surgery time was 7.72min(or 48.9%shorter than that of the control group using conventional protocol(PPCONCLUSION: The small incision pterygium removal protocol was easier to perform and resulted in a better outcome than the conventional protocol.

  15. 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

  16. 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 ca...

  17. Properties of 5- and/or 2-modified 2'-O-cyanoethyl uridine residue: 2'-O-cyanoethyl-5-propynyl-2-thiouridine as an efficient duplex stabilizing component.

    Science.gov (United States)

    Masaki, Yoshiaki; Miyasaka, Ryuta; Hirai, Kunihiro; Kanamori, Takashi; Tsunoda, Hirosuke; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

    2014-02-21

    We systematically synthesized eight types of 5- and/or 2-modified uridine derivatives and evaluated their effect on duplex stability. The incorporation of 2'-O-cyanoethyl-2-thio-5-propynyluridine (p(5)s(2)UOCE) into RNA was significantly effective for stabilization of RNA/RNA (+8.5 °C) and DNA/RNA (+10.4 °C) duplexes. These striking effects were maintained in oligonucleotides with different sequences or multiple incorporations. In addition, p(5)s(2)UOCE increased selectivity toward the correct AU Watson-Crick base pair over the most stable mismatched base pair in both RNA/RNA and DNA/RNA duplexes. Hence, p(5)s(2)UOCE could be useful for various applications of modified oligonucleotides that need high duplex stability and base pairing selectivity.

  18. Identification of Clinical Isolates of Candida using Duplex PCR

    Directory of Open Access Journals (Sweden)

    Homeyra Babaei

    2016-11-01

    Full Text Available Abstract Background: Candida albicans is still the main etiologic agent of candidiasis. However, infections of non-albicans Candida species are increasing. Candida dubliniensis is similar to C. albicans phenotypically and must be identified due to the better management of infection. The aim of the present study is to defferentiate and identify Candida species by Duplex PCR for get-ting an epidemiological data of Candida species among clinical specimens. Materials and Methods: DNA was extracted using phenol-chloroform method from fresh colonies. Internal Transcribed Spacer region was amplified by polymerase chain reaction using specific primers. Based on differences of bands sizes on agarose gel electrophoresis, species were identified. Results: Ninety four out of 100 patients (49 males and 51 females had predisposing fac-tors in the present study. Diabetes (73.4%, use of antibiotic (6.3%, vitamin deficiency (4.3% were the main predisposing factors. The most specimens belonged to mouth (75%, vagina (5%, and blood (4%. All isolates were identified as C. albicans. Conclusion: Duplex PCR is a rapid and precise method for the detection and differentia-tion of Candida species carefully, and in this method, phenotypic tests like germ-tube and chla-mydoconidia production, as well as biochemical tests are not required for clinical laboratories that have limited resources and time for response to the patients, and it can replace with the traditional methods.

  19. Abdominal incisions in General Surgery: a review | Ajao | Annals of ...

    African Journals Online (AJOL)

    There is this wrong notion that the only standard abdominal incision is the midline incision. Cases have been seen in which an abdominal incision extends from the xyphoid process to the symphysis pubis just to remove a perforated appendix! It is also not unusual to see a groin incision together with a lower abdominal ...

  20. Duplex scanning using sparse data sequences

    DEFF Research Database (Denmark)

    Møllenbach, S. K.; Jensen, Jørgen Arendt

    2008-01-01

    The velocity distribution in vessels can be displayed using duplex scanning where B-mode acquisitions are interspaced with the velocity data. This gives an image for orientation, but lowers the maximum detectable velocity by a factor of two. Other pulse sequences either omits the B-mode image...... is scaled by the factor A/T. The approach has been investigated using in vivo RF data from the Hepatic vein, Carotid artery and Aorta from a 33 year old healthy male. A B-K Medical 3535 ultrasound scanner has been used in Duplex mode with a BK 8556, 3.2 MHz linear array probe. The sampling frequency...

  1. 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.

  2. Color coded duplex sonography. Interdisciplinary vascular ultrasonography

    International Nuclear Information System (INIS)

    Kubale, R.; Stiegler, H.

    2002-01-01

    An interdisciplinary team of experts impart the state of the art in color coded duplex sonography applied for examination of all anatomic areas. Detailed information is given for every vascular area, describing the examination procedure, possible origins of mistakes or faults, and means to avoid them. In addition to the classical applications, eg. for examination of the extra- and intracranial vessels, vessels of the limbs, visceral vessels and the vessels of liver and kidney, there are chapters devoted to: haemodialysis shunts, arteriovenous malformations, duplex sonography of the penis, tumor vascularisation. (orig./CB) [de

  3. Laparoscopic cholecystectomy with two mini cosmetic incisions.

    Science.gov (United States)

    Tavassoli, Alireza; Noorshafiee, Sajad

    2017-12-18

    Minimally invasive surgery gained popularity between general surgeons especially laparoscopic four-port cholecystectomy. By introducing different methods such as NOTES and SILS, the costs elevated with its cosmetics. We aim to study a new technique of laparoscopic cholecystectomy by two incisions with best cosmetics, and same quality and lower cost as conventional four-port laparoscopic cholecystectomy and make a comparison between them. In a double-blind clinical trial from December 2012 to September 2014, patients with cholelithiasis who presented to general surgery clinic and candidate for laparoscopic cholecystectomy were studied. Half of patients underwent double-incision laparoscopic cholecystectomy and other half underwent conventional four-port laparoscopic cholecystectomy. The mean age and BMI were higher in double-incision and four-port group, respectively, but not statistically different. Also male to female ratio was 6:1 in double-incision group and 9:1 in four-port group, and they were not statistically different. The mean operation time was about 2 min more in double-incision group, but it is trivial to consider a significant difference at level of 5%. The mean pain score (0-10) was significantly lower in double incision group in comparison with four-port group (p < 0.0001). Patients in double incision group reported higher satisfaction and were sooner in return to work than in four-port group (p < 0.0001). It seems that DILS for uncomplicated cholelithiasis is safe. By reducing port number, we succeed in reducing the pain and need for analgesics, reducing hospital staying and sooner return to work. By taking into account using conventional CLS instrument and lowering the hospital charges, it could be a good alternative to SILS.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Nidhi Jauhari

    2014-12-01

    Full Text Available AIM:To determine the surgically induced astigmatism (SIA in Straight, Frown and Inverted V shape (Chevron incisions in manual small incision cataract surgery (SICS.METHODS: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.RESULTS: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.CONCLUSION:Inverted V (Chevron incision gives minimal SIA.

  6. The Modular Construction of DNA Double Helix

    Indian Academy of Sciences (India)

    DNA or the left-handed double helix,. Z- DNA. Construction of the Module .... 12. DNA, namely, replication and transcription. In the former case, Figure 3. 8 would represent a DNA single strand-generated by splitting of the mother duplex ...

  7. 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.

  8. 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.

  9. Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes.

    Science.gov (United States)

    Wons, Ewa; Mruk, Iwona; Kaczorowski, Tadeusz

    2015-11-01

    RNA/DNA hybrid duplexes regularly occur in nature, for example in transcriptional R loops. Their susceptibility to modification by DNA-specific or RNA-specific enzymes is, thus, a biologically relevant question, which, in addition, has possible biotechnological implications. In this study, we investigated the activity of four isospecific DNA methyltransferases (M.EcoVIII, M.LlaCI, M.HindIII, M.BstZ1II) toward an RNA/DNA duplex carrying one 5'-AAGCUU-3'/3'-TTCGAA-5' target sequence. The analyzed enzymes belong to the β-group of adenine N6-methyltransferases and recognize the palindromic DNA sequence 5'-AAGCTT-3'/3'-TTCGAA-5'. Under standard conditions, none of these isospecific enzymes could detectibly methylate the RNA/DNA duplex. However, the addition of agents that generally relax specificity, such as dimethyl sulfoxide (DMSO) and glycerol, resulted in substantial methylation of the RNA/DNA duplex by M.EcoVIII and M.LlaCI. Only the DNA strand of the RNA/DNA duplex was methylated. The same was not observed for M.HindIII or M.BstZ1II. This is, to our knowledge, the first report that demonstrates such activity by prokaryotic DNA methyltransferases. Possible applications of these findings in a laboratory practice are also discussed.

  10. Comparison of primary total hip replacements performed with a standard incision or a mini-incision.

    Science.gov (United States)

    Woolson, Steven T; Mow, Christopher S; Syquia, Jose Fernando; Lannin, John V; Schurman, David J

    2004-07-01

    Primary total hip replacement performed through an incision that is a minimally invasive technique. Proponents have claimed that mini-incision techniques reduce blood loss, transfusion requirements, postoperative pain, and the length of the hospital stay compared with standard techniques through a longer incision. However, we are aware of no well-designed comparison study that supports these claims. The purpose of the present study was to compare the short-term results of a mini-incision with a standard incision technique for total hip replacement. A consecutive series of patients who underwent 135 primary unilateral total hip replacements (fifty with use of a mini-incision [a standard incision) by three surgeons at one hospital were studied. Each surgeon selected patients to have a mini-incision procedure and performed a standard approach in the remaining patients. A posterior approach was used for all procedures. In-hospital data were collected retrospectively, and the initial postoperative radiographs were analyzed. Because of the selection process, the patients who had a mini-incision had both a significantly lower average body-mass index (p = 0.008) and a lower average score on the American Society of Anesthesiologists rating (p = 0.006), indicating that they were thinner and healthier than the patients who had a standard incision. With the numbers of patients available, no significant differences were found between the groups with respect to the average surgical time, intraoperative blood loss, in-hospital transfusion rate, length of hospital stay, or the patients' disposition after discharge. The mini-incision group was found to have a significantly higher risk of a wound complication (p = 0.02), a higher percentage of acetabular component malposition (p = 0.04), and poor fit and fill of femoral components inserted without cement (p = 0.0036). There was no evidence that the mini-incision technique resulted in less bleeding or less trauma to the soft tissues

  11. 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

  12. 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

  13. DOES TUBULARIZED INCISED PLATE URETHROPLASTY FIT ...

    African Journals Online (AJOL)

    Objective To evaluate prospectively our experience using tubularized incised plate (TIP) urethroplasty in primary and repeat penile shaft hypospadias. Patients and Methods Thirty-two boys with penile shaft hypospadias were selected to undergo TIP procedure. Their age ranged from 22 months to 9 years. Twenty-two cases ...

  14. 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)

  15. 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

  16. Dúplex telefónico - Duplex telephonic

    Directory of Open Access Journals (Sweden)

    Santos López, Pascual

    2006-12-01

    Full Text Available Only 19 years after a timid introduction of telephony in Spain and seven years before the founding of the National Telephonic Company of Spain, Pascual Salmerón Gómez records his two patents: "Duplex telephonic" and "Simultaneous duplex telephonic with telegraph machines". Two high technical complexity patents, registered in 1917 in the town of Arucas, province of Gran Canaria analyzed to our readers.Nephew of the inventor of the "Float Salmerón," José Salmerón Rojas and brother of Gerónimo Gómez Salmerón, inventor of "Cerealémetro" and owner of the theater Borras and with which we ended the saga Salmerón.

  17. Diffraction study on aging duplex stainless steel

    International Nuclear Information System (INIS)

    Ishigaki, Toru; Miura, Takayuki; Kuwano, Hisashi; Torii, Syuuki; Kamiyama, Takashi

    2001-01-01

    SUS329J2L duplex stainless steels exhibit high strength and resistance to corrosion, so widely used in piping of industrial plants. However, it is known that they are brought deterioration of strength using for long time. This reason of this deterioration is that ferrite decomposes to Fe-rich α phase and Cr-rich α' phase and, Cr-rich α' phase decreases mechanical properties and resistance for corrosion. In this experiment, we made neutron diffraction experiments on long time aging (625 K, 16000 h) duplex stainless steel to observe the behavior for α phase and α' phase, using Sirius diffractometer at KENS. The result shows, the lattice parameters in α phase were decreased. In contrast to, its in austenite (γ phase) were slightly increased. (author)

  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. 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.

  20. A duplex PCR for rapid and simultaneous detection of Brucella spp. in human blood samples.

    Science.gov (United States)

    Mirnejad, Reza; Mohamadi, Mozafar; Piranfar, Vahbeh; Mortazavi, Seied Mojtaba; Kachuei, Reza

    2013-06-01

    To design a duplex PCR for rapid and simultaneous detection of Brucella species. in human blood samples. Fifty-two peripheral bloods samples were collected from suspicious patients with brucellosis. Following DNA extraction, PCR assay were performed, using three primers that could simultaneously identify and differentiate three major species of pathogenic Brucella in humans and animals. Of the 52 peripheral bloods samples tested, 25 sample (48%) showed positive reactions in PCR. Twelve samples were positive for Brucella abortus 39 (B. abortus 39) (23%), 13 for Brucella melitensis 39 (B. melitensis 39) (25%) and 0 for Brucella ovis 39 (B. ovis 39) (0%). This work demonstrates that in case where specific primers were utilized, duplex PCR has proved to be a simple, fast, and relatively inexpensive method for simultaneous detection of important species of Brucella in clinical samples. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  1. Full Duplex Prototype of OFDM on GNURadio and USRPs

    OpenAIRE

    Zhou , Wei; Villemaud , Guillaume; Risset , Tanguy

    2014-01-01

    International audience; Full-duplex is a technology in telecommunication domain that can perform transmitting and receiving at the same time and in the same frequency band. The major obstacle of full-duplex is the self-interference (SI). Some previous works have focused on the SI cancellation in radio frequency (RF), and generally on a narrowband signal model. We have implemented a full-duplex prototype with orthogonal frequency-division multiplexing (OFDM) technology on GNURadio and Universa...

  2. 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

  3. Analysis of single-incision versus dual-incision fasciotomy for tibial fractures with acute compartment syndrome.

    Science.gov (United States)

    Bible, Jesse E; McClure, D Jake; Mir, Hassan R

    2013-11-01

    To analyze the rate of postoperative infection and nonunion after tibial fractures in patients treated for acute compartment syndrome (ACS) using (1) single-incision versus (2) dual-incision fasciotomy technique. Retrospective. Level I trauma center. Review of all adult tibial fractures operatively treated (n = 2756) over a 12-year period identified 175 patients with concurrent ACS requiring fasciotomy. Of 60 patients treated with intramedullary nails, 36 patients had single-incision fasciotomy and 24 had dual-incision fasciotomy. Of 81 patients treated with plate fixation, 59 patients had single-incision fasciotomy and 22 had dual-incision fasciotomy. Tibial fixation with fasciotomy for ACS. Occurrence of postoperative infection and nonunion. Both fasciotomy groups were similar across recorded patient and treatment characteristics. Need for skin graft was similar between fasciotomy groups. For patients treated with intramedullary nail (n = 60), 1 infection (2.8%) occurred in single-incision group versus 2 (8.3%) in dual-incision group (P = 0.558). Seven nonunions (19.4%) occurred in single-incision group versus 3 (12.5%) in dual-incision group (P = 0.726). For plate fixation patients (n = 81), 15 infections (25.4%) occurred with single-incision fasciotomy versus 5 infections (22.7%) with dual-incision fasciotomy (P = 1.000). Seven nonunions (11.9%) occurred with single-incision group versus 4 nonunions (18.2%) with dual-incision group (P = 0.479). This is the first study to compare a single-incision fasciotomy technique to a dual-incision technique in the setting of tibial fractures with ACS, with similar infection and nonunion rates with either technique. The choice of fasciotomy technique can be based on surgeon experience or patient condition as opposed to a suspected elevated infection or nonunion risk with either technique. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

  4. The Origins of Microtexture in Duplex Ti Alloys (Preprint)

    National Research Council Canada - National Science Library

    Glavic, M. G; Bartha, B. B; Jha, S. K; Szczepanski, C. J

    2008-01-01

    .... In addition, for a homogeneous duplex microstructures, all of the secondary alpha phase and the majority of the primary alpha grains retain crystallographic coherency, according to the Burgers...

  5. Drainage basins and channel incision on Mars

    Science.gov (United States)

    Aharonson, Oded; Zuber, Maria T.; Rothman, Daniel H.; Schorghofer, Norbert; Whipple, Kelin X.

    2002-02-01

    Measurements acquired by the Mars Orbiter Laser Altimeter on board the Mars Global Surveyor indicate that large drainage systems on Mars have geomorphic characteristics inconsistent with prolonged erosion by surface runoff. We find the topography has not evolved to an expected equilibrium terrain form, even in areas where runoff incision has been previously interpreted. By analogy with terrestrial examples, groundwater sapping may have played an important role in the incision. Longitudinally flat floor segments may provide a direct indication of lithologic layers in the bedrock, altering subsurface hydrology. However, it is unlikely that floor levels are entirely due to inherited structures due to their planar cross-cutting relations. These conclusions are based on previously unavailable observations, including extensive piece-wise linear longitudinal profiles, frequent knickpoints, hanging valleys, and small basin concavity exponents.

  6. Primary closure of equine laryngotomy incisions

    DEFF Research Database (Denmark)

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

    2016-01-01

    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....

  7. 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

  8. 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.

  9. Right Kocher’s incision: a feasible and effective incision for right hemicolectomy: a retrospective study

    Directory of Open Access Journals (Sweden)

    Theodosopoulos Theodosios

    2012-06-01

    Full Text Available Abstract Background The choice of surgical incision is determined by access to the surgical field, particularly when an oncological resection is required. Special consideration is also given to other factors, such as postoperative pain and its sequelae, fewer complications in the early postoperative period and a lower occurrence of incisional hernias. The purpose of this study is to compare the right Kocher’s and the midline incision, for patients undergoing right hemicolectomy, by focusing on short- and longterm results. Methods Between 1995 and 2009, hospital records for 213 patients that had undergone a right hemicolectomy for a right- sided adenocarcinoma were retrospectively studied. 113 patients had been operated via a Kocher’s and 100 via a midline incision. Demographic details, operative data (explorative access to the peritoneal cavity, time of operation, recovery parameters (time with IV analgesic medication, time to first oral fluid intake, time to first solid meal, time to discharge, and oncological parameters (lymph node harvest, TNM stage and resection margins were analyzed. Postoperative complications were also recorded. The two groups were retrospectively well matched with respect to demographic parameters and oncological status of the tumor. Results The median length of the midline incision was slightly longer (12 vs. 10 cm, p  Conclusions The Kocher’s incision approach for right- sided colon cancer is technically feasible, safe and overall very well tolerated. It can achieve the same standards of tumor resection and surgical field accessibility as the midline approach, while reducing postoperative recovery.

  10. 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

  11. 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

    (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...

  12. 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.

  13. Scaffolding along Nucleic Acid Duplexes Using 2'-Amino-Locked Nucleic Acids

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Wengel, Jesper

    2014-01-01

    depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing...... of clinically important single-nucleotide polymorphisms (SNPs) and imaging of nucleic acids in vitro, in cell culture, and in vivo. According to our studies, 2'-amino-LNA scaffolds are efficient within diagnostic probes for DNA and RNA targets and as therapeutics, whereas both 2'-amino- and isomeric 2'-α......-l-amino-LNA scaffolds have promising properties for stabilization and detection of DNA nanostructures. Attachment of fluorescent groups to the 2'-amino group results in very high fluorescent quantum yields of the duplexes and remarkable sensitivity of the fluorescence signal to target binding. Notably, fluorescent LNA...

  14. 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.

  15. Duplex tube steam reformer development program

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. 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

  17. 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 ...

  18. Acoustical and perceptual influence of duplex stringing in grand pianos.

    Science.gov (United States)

    Öberg, Fredrik; Askenfelt, Anders

    2012-01-01

    This study investigates the acoustical and perceptual influence of the string parts outside the speaking length in grand pianos (front and rear duplex strings). Acoustical measurements on a grand piano in concert condition were conducted, measuring the fundamental frequencies of all main and duplex strings in the four octaves D4-C8. Considerable deviations from the nominal harmonic relations between the rear duplex and main string frequencies, as described by the manufacturer in a patent, were observed. Generally the rear duplex strings were tuned higher than the nominal harmonic relations with average and median deviations approaching +50 cent. Single keys reached +190 and -100 cent. The spread in deviation from harmonic relations within trichords was also substantial with average and median values around 25 cent, occasionally reaching 60 cent. Contributions from both front and rear duplex strings were observed in the bridge motion and sound. The audibility of the duplex strings was studied in an ABX listening test. Complete dampening of the front duplex was clearly perceptible both for an experiment group consisting of musicians and a control group with naive subjects. The contribution from the rear duplex could also be perceived, but less pronounced. © 2012 Acoustical Society of America.

  19. Small-incision lenticule extraction (SMILE)

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... 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...

  20. Incision Coordination in Nucleotide Excision Repair

    NARCIS (Netherlands)

    W.L. de Laat (Wouter)

    1998-01-01

    textabstractThis thesis aims to contribute to the understanding of the molecular mechanism that underlies one of the main DNA repair pathways in mammals, nucleotide excision rcpair. In chapter 1 the relevance of DNA repair in general is outlined. An overview of mammalian strategies to counteract DNA

  1. 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.

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

    Science.gov (United States)

    Jeon, Seung Bae; Ahn, Hee Chang; Ahn, Yong Su; Choi, Matthew Seung Suk

    2015-11-01

    Surgical 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. A 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. The 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). Compared 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.

  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 ex...... to be published to confirm its value. An ideal training route for surgeons who are adopting the technique was agreed upon, as was the need for a single, large clinical registry of data....

  4. 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.

  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. 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)

  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. Development of a novel quantitative real-time assay using duplex mutation primers for rapid detection of Candida species.

    Science.gov (United States)

    Xia, Qian-Feng; Liu, Jin-Bo; Liu, Ping; Qin, Xi; Qian, Shi-Yun; Tu, Zhi-Guang

    2012-01-01

    We developed a novel quantitative real-time PCR for quantitating Candida DNA based on the duplex mutation primer principle, in which a signal is generated by melting a duplex mutation primer during renaturation. The duplex mutation primers are much more specific than double-stranded DNA dyes such as SYBR-Green I and, unlike other probes, do not require the double-labeled synthesis of fluorophore and a quencher on the same molecule. A total of 176 clinical blood specimens were obtained from patients hospitalized in our hospital with clinically proven or suspected systemic Candida infection. The presence of DNA from pathogens in the Candida species was detected using real-time PCR targeting of an internal transcribed spacer region of a fungal gene. The assay exhibited a low limit of detection (10 CFU/ml of blood), an excellent reproducibility and specificity. Twenty-eight positive samples exhibited a wide range of Candida species loads, extending from 13 to 90,528 CFU/ml of blood. The sensitivity and specificity of the present assay were 100 and 97.4%, respectively, compared with the results of blood culture. Our data suggest that this assay may be appropriate for use in clinical laboratories as a simple, low-cost and rapid screening test for the most frequently encountered Candida species.

  9. Hypospadias and concomitant undescended testis: Comparison of no skin incision with inguinal and scrotal skin incision orchiopexy.

    Science.gov (United States)

    Sabetkish, Shabnam; Kajbafzadeh, Abdol-Mohammad; Sabetkish, Nastaran

    2015-10-01

    To present the feasibility of no skin incision orchiopexy in children with concomitant hypospadias and undescended testis (UDT) by a single subcoronal incision technique. To introduce the creation of subdartos muscle scrotal pouch with no scrotal skin incision. From one thousand and twenty-one children with hypospadias, 61 patients presented with concomitant palpable UDT and hypospadias. In group I (N = 34) single subcoronal incision with no scrotal skin incision was applied. In group II (N = 27), multi-incision technique was applied for classical orchiopexy and hypospadias surgery. For hypospadias reconstruction, all patients had classical subcoronal and para urethral plate incision with penile skin degloving according to the location of urethral meatus. Early and late complications, surgical time, hospital stay, and cosmetic results were recorded. Children with unilateral UDT and hypospadias had one incision in group I and three skin incisions in group II. Patients with bilateral UDT had one incision in group I and five skin incisions in group II. The operation time was significantly shorter in group I (93 ± 11 min) compared with group II (138 ± 17 min) (P = 0.03). Both groups were operated as day care basis; however, the hospital stay was slightly longer in group II (group I = 12 ± 2 h, vs group II = 16 ± 3 h) (P = 0.07). All testes were satisfactorily positioned into the bottom of the scrotum without development of any testicular atrophy. Single subcoronal penile skin incision is a feasible, safe, and cosmetically satisfactory technique in patients with hypospadias and concomitant UDT. Reduced postoperative pain, better objective cosmetic results, shorter operative time and comfortable post-operative period are the most significant advantages of this approach. Copyright © 2015 IJS Publishing Group Limited. Published by Elsevier Ltd. All rights reserved.

  10. 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......-stenotic pressure gradient measurement (PGM) as reference. Material and Methods The renal arteries of 58 consecutive patients evaluated for renovascular hypertension were examined by RADUS and PGM. Conclusive measurements with both methods were obtained in 76 arteries. Hemodynamically significant RAS was defined...... as PGM ≥15 mmHg and was found in 43 of the 76 arteries. RADUS parameters included renal artery peak systolic velocity (PSV) and the renal-aortic ratio (RAR) of flow velocities. Receiver operating characteristic curves (ROCs) and Youden's index were used to calculate optimal RADUS criteria for RAS...

  11. 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

  12. The ABCs of molecular dynamics simulations on B-DNA, circa 2012

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... This article provides a retrospective on the ABC initiative in the area of all-atom molecular dynamics (MD) simulations including explicit solvent on all tetranucleotide steps of duplex B-form DNA duplex, ca. 2012. The ABC consortium has completed two phases of simulations, the most current being a set of ...

  13. Single-Incision Laparoscopic Surgery (SILS Assisted Sigma Resection Via Pfannenstiel Incision for Complicated Diverticulitis

    Directory of Open Access Journals (Sweden)

    Arne Dietrich

    2014-02-01

    Results: The operation time ranged from 89 to 280 min. There were no conversions, and no additional trocars were used. The postoperative hospital stay ranged from 5 to 14 days. All patients were discharged without any intraoperative or postoperative complications. Conclusions: SILS sigma or anterior rectum resection for complicated diverticulitis can be performed via a Pfannenstiel incision. This approach provides direct visualization and access into the pelvis as well as the option to benefit from open surgery devices. The Pfannenstiel incision may generally be recommended for the favorable cosmetic effect and the very low rate of incisional hernias, as reported in the literature. [Arch Clin Exp Surg 2014; 3(1.000: 10-15

  14. Diathermy versus Scalpel incision in elective midline laparotomy: A ...

    African Journals Online (AJOL)

    ... two groups with respect to the mean length of hospital stay (p = 0.834). Conclusion: We conclude that diathermy incision in elective midline laparotomy has significant advantages compared with the scalpel because of reduced incision time, less blood loss, reduced early postoperative pain and analgesic requirements.

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

    African Journals Online (AJOL)

    Dr. C. Pedro-Egbe

    Department of Ophthalmology, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria. ABSTRACT. Aim: To compare the visual outcome of a superiorly placed limbal incision ..... Roman SJ, Auclin FX, Chong-Sit DA, Ullern MM. Surgically induced astigmatism with superior and temporal incisions in cases of ...

  16. 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)

  17. 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....

  18. 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 ...

  19. 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.

  20. 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.

  1. Atomistic Simulations of Complex DNA DSBs and the Interactions with Ku70/80 Heterodimer

    Science.gov (United States)

    Hu, Shaowen; Cucinotta, Francis A.

    2011-01-01

    Compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex. Binding of Ku drastically reduces the structural disruption and flexibility caused by the complex lesions. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. Binding of Ku promotes the rigidity of DNA duplexes, due to the clamp structure of the inner surface of the rings of Ku70/80.

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  3. 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.

  4. First Canadian experience with robotic single-incision pyeloplasty: Comparison with multi-incision technique.

    Science.gov (United States)

    Law, Jeffrey; Rowe, Neal; Archambault, Jason; Nastis, Sofia; Sener, Alp; Luke, Patrick P

    2016-01-01

    We compared the outcomes of single-incision, robot-assisted laparoscopic pyeloplasty vs. multiple-incision pyeloplasty using the da Vinci robotic system. We reviewed all consecutive robotic pyeloplasties by a single surgeon from January 2011 to August 2015. A total of 30 procedures were performed (16 single:14 multi-port). Two different single-port devices were compared: the GelPort (Applied Medical, Rancho Santa Margarita, CA) and the Intuitive single-site access port (Intuitive Surgical, Sunnyvale, CA). Patient demographics were similar between the two groups. Mean operating time was similar among the single and multi-port groups (225.2 min vs. 198.9 minutes [p=0.33]). There was no significant difference in length of hospital stay in either group (86.2 hr vs. 93.2 hr [p=0.76]). There was no difference in success rates or postoperative complications among groups. Single-port robotic pyeloplasty is non-inferior to multiple-incision robotic surgery in terms of operative times, hospitalization time, success rates, and complications. Verifying these results with larger cohorts is required prior to the wide adoption of this technique. Ongoing objective measurements of cosmesis and patient satisfaction are being evaluated.

  5. Vertical compared with transverse incisions in abdominal surgery

    DEFF Research Database (Denmark)

    Grantcharov, T P; Rosenberg, J

    2001-01-01

    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...... postoperative pain and fewer pulmonary complications. Vertical laparotomy, however, is associated with shorter operating time and better possibilities for extension of the incision. The pooled odds ratio for burst abdomen in the vertical incision group was 2.86 (95% confidence interval 1.72 to 4.73, p = 0.......0001), and regarding late incisional hernia the pooled odds ratio was 1.68 (95% confidence interval 1.10 to 2.57. p = 0.02). CONCLUSIONS: Transverse incisions in abdominal surgery are based on better anatomical and physiological principles. They should be recommended, as the early postoperative period is associated...

  6. 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.

  7. Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double-Crossover Tiles.

    Science.gov (United States)

    De Stefano, Mattia; Vesterager Gothelf, Kurt

    2016-06-16

    Designed nanostructures formed by self-assembly of multiple DNA strands suffer from low stability at elevated temperature and under other denaturing conditions. Here, we propose a method for covalent coupling of DNA strands in such structures by the formation of disulfide bonds; this allows disassembly of the structure under reducing conditions. The dynamic chemistry of disulfides and thiols was applied to crosslink DNA strands with terminal disulfide modifications. The formation of disulfide-linked DNA duplexes consisting of three strands is demonstrated, as well as a more-complex DNA double-crossover tile. All the strands in the fully disulfide-linked structures are covalently and geometrically interlocked, and it is demonstrated that the structures are stable under heating and in the presence of denaturants. Such a reversible system can be exploited in applications where higher DNA stability is needed only temporarily, such as delivery of cargoes to cells by DNA nanostructures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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.

  9. 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

  10. Duplex colour Doppler sonography — role in neck metastasis

    OpenAIRE

    Puri, R.; Srinath, V. S.; Chakravarti, A. L.

    2002-01-01

    The present study was done to evaluate the rote of Duplex colour Doppler Sonography in neck metastasis. 30 patients with primary head and neck cancer were evaluated by Duplex colour Doppier sonography and results analysed. In more than 95% of cases, the vascular status could be established before any form of therapy was instituted. Compression and infiltration of carotids and internal jugular vein (IJV) could be demonstrated and a structured and dynamic relationship of metastatic nodes to the...

  11. A NEW APPROACH AT SURFACE ENGINEERING; DUPLEX SURFACE TREATMENT

    Directory of Open Access Journals (Sweden)

    Akgün ALSARAN

    2003-01-01

    Full Text Available Duplex surface process was developed to deposite thin ceramic film coating on commonly manufacturing used low alloy steels. Low alloy steel having low strength by this process was first plasma nitrided with purpose enhancing load bearing capacity and then deposited with such ceramic coating. In this study, the duplex surface treatment was deal with main lines and informed about advantage and disadvantage.

  12. Bypass of a protein barrier by a replicative DNA helicase

    NARCIS (Netherlands)

    Yardimci, Hasan; Wang, Xindan; Loveland, Anna B.; Tappin, Inger; Rudner, David Z.; Hurwitz, Jerard; van Oijen, Antoine M.; Walter, Johannes C.

    2012-01-01

    Replicative DNA helicases generally unwind DNA as a single hexamer that encircles and translocates along one strand of the duplex while excluding the complementary strand (known as steric exclusion). By contrast, large T antigen, the replicative DNA helicase of the simian virus 40 (SV40), is

  13. 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

  14. Simplex and duplex event-specific analytical methods for functional biotech maize.

    Science.gov (United States)

    Lee, Seong-Hun; Kim, Su-Jeong; Yi, Bu-Young

    2009-08-26

    Analytical methods are very important in the control of genetically modified organism (GMO) labeling systems or living modified organism (LMO) management for biotech crops. Event-specific primers and probes were developed for qualitative and quantitative analysis for biotech maize event 3272 and LY 038 on the basis of the 3' flanking regions, respectively. The qualitative primers confirmed the specificity by a single PCR product and sensitivity to 0.05% as a limit of detection (LOD). Simplex and duplex quantitative methods were also developed using TaqMan real-time PCR. One synthetic plasmid was constructed from two taxon-specific DNA sequences of maize and two event-specific 3' flanking DNA sequences of event 3272 and LY 038 as reference molecules. In-house validation of the quantitative methods was performed using six levels of mixing samples, from 0.1 to 10.0%. As a result, the biases from the true value and the relative deviations were all within the range of +/-30%. Limits of quantitation (LOQs) of the quantitative methods were all 0.1% for simplex real-time PCRs of event 3272 and LY 038 and 0.5% for duplex real-time PCR of LY 038. This study reports that event-specific analytical methods were applicable for qualitative and quantitative analysis for biotech maize event 3272 and LY 038.

  15. 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.

  16. Bacillus subtilis 168 RecR protein-DNA complexes visualized as looped structures.

    Science.gov (United States)

    Ayora, S; Stiege, A C; Lurz, R; Alonso, J C

    1997-03-18

    The Bacillus subtilis 168 RecR protein bound to duplex DNA in the presence of ATP and divalent cations (Mg2+ and Zn2+) was visualized by electron microscopy as a nearly spherical particle. A RecR homomultimer is frequently located at the intersection of two duplex DNA strands in an interwound DNA molecule, generating DNA loops of variable length. Two individual DNA molecules bound to the same protein are seen at a very low frequency, if at all. The association of RecR with the intersection of two duplex DNA strands is more often seen in supercoiled than with relaxed or linear DNA. The RecR protein displays a slight but significant preference for negatively supercoiled over linear DNA. The minimum substrate size for RecR protein is about 150 bp in length. A possible mechanism for RecR function in DNA repair is discussed.

  17. 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

  18. Phase transformations in cast duplex stainless steels

    Science.gov (United States)

    Kim, Yoon-Jun

    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 sigma (sigma) and chi (chi) 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 (sigma + chi) formation were analyzed using the Johnson-Mehl-Avrami (JMA) 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, a was stabilized with increasing Cr addition and chi by increasing Mo addition. However, a delicate balance among Ni and other minor elements such as N and Si also exists. Phase equilibria in

  19. 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...

  20. 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

  1. Duplex and Triplex Formation of Mixed Pyrimidine Oligonucleotides with Stacking of Phenyl-triazole Moieties in the Major Groove

    DEFF Research Database (Denmark)

    Andersen, Nicolai Krog; Døssing, Holger; Jensen, Frank

    2011-01-01

    5-(1-Phenyl-1,2,3-triazol-4-yl)-2'-deoxycytidine was synthesized from a modified CuAAC protocol and incorporated into mixed pyrimidine oligonucleotide sequences together with the corresponding 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine. With consecutive incorporations of the two modified...... nucleosides, improved duplex formation with a complementary RNA and improved triplex formation with a complementary DNA duplex were observed. The improvement is due to π-π stacking of the phenyl-triazole moieties in the major groove. The strongest stacking and most pronounced positive influence on thermal...... stability was found in between the uridine analogues or with the cytidine analogue placed in the 3' direction to the uridine analogue. Modeling indicated a different orientation of the phenyl-triazole moieties in the major groove to account for the difference between the two nucleotides. The modified...

  2. New Economical 19Cr Duplex Stainless Steels

    Science.gov (United States)

    Li, Jun; Zhang, Zixing; Chen, Hong; Xiao, Xueshan; Zhao, Junliang; Jiang, Laizhu

    2012-02-01

    New economical duplex stainless steels (DSSs) containing 19Cr-6Mn- xNi-1.0Mo-0.5W-0.5Cu-0.2N ( x = 0.5 to 2.0) were developed, and the microstructure, impact property, and corrosion resistance of the alloys were studied. The ferrite content increases with the solution treatment temperature, but decreases with an increase in nickel. The sigma phase is not found precipitating in the alloys treated with solution from 1023 K to 1523 K (750 °C to 1250 °C). The low-temperature impact energy of the experimental alloys increases first and then decreases rapidly with an increase in nickel, which is mainly due to the martensite transformation with an increase in austenite. The alloys have a better mechanical property and pitting corrosion resistance than AISI 304. Among the designed DSS alloys, 19Cr-6Mn-1.3Ni-1.0Mo-0.5W-0.5Cu-0.2N is found to be an optimum alloy with proper phase proportion, a better combination of mechanical strength and elongation, and higher pitting corrosion resistance compared with those of the other alloys.

  3. 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)

  4. 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......) and sequence specificity of binding (singly mismatched duplexes) using mainly absorption hypochromicity melting curves and isothermal titration calorimetry. For perfectly sequence-matched duplexes of varying lengths (6-20 bp), the average free energy of binding (DeltaG degrees ) was determined to be -6...... relative to that of the perfectly matched sequence with a corresponding free energy penalty of about 15 kJ mol(-1) bp(-1). The average cost of a single mismatch is therefore estimated to be on the order of or larger than the gain of two matched base pairs, resulting in an apparent binding constant of only...

  5. 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...

  6. Normalizing cDNA libraries.

    Science.gov (United States)

    Bogdanov, Ekaterina A; Shagina, Irina; Barsova, Ekaterina V; Kelmanson, Ilya; Shagin, Dmitry A; Lukyanov, Sergey A

    2010-04-01

    The characterization of rare messages in cDNA libraries is complicated by the substantial variations that exist in the abundance levels of different transcripts in cells and tissues. The equalization (normalization) of cDNA is a helpful approach for decreasing the prevalence of abundant transcripts, thereby facilitating the assessment of rare transcripts. This unit provides a method for duplex-specific nuclease (DSN)-based normalization, which allows for the fast and reliable equalization of cDNA, thereby facilitating the generation of normalized, full-length-enriched cDNA libraries, and enabling efficient RNA analyses. (c) 2010 by John Wiley & Sons, Inc.

  7. 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.

  8. Cyclic steps incised on experimental bedrock

    Science.gov (United States)

    Yokokawa, M.; Kyogoku, A.; Kotera, A.; Izumi, N.

    2013-12-01

    the step shape has been predicted by the mathematical model (Izumi et al., 2012). Among three cases of sediment supply: 1 g/sec, 3 g/sec, and 6 g/sec with fixed water discharge (52 g/sec), the erosion rate was maximized in the cases of the sediment supply of 3 g/sec both in the cement-sand-water ratios of 2:150:50 and 3:150:50. The erosion rate is higher in the case of the moderate amount of sediment supply rather than in the case of the largest amount of sediment supply in which the alluvial cover effect inhibited erosion. This result is consistent with that observed in previous studies (Sklar & Dietrich, 2004; Johnson & Whipple, 2010). References Izumi, N., Yokokawa, M. & Parker G. 2012. Cyclic step morphology formed on bedrock. Annual Journal of Hydraulic Engineering 68(4) : I_955-I_960. Johnson, J.P.L. & Whipple, K.X. 2010. Evaluating the controls of shear stress, sediment supply, alluvial cover, and channel morphology on experimental bedrock incision rate. Journal of Geophysical Research 115, F02018, doi:10.1029/2009JF001335. Sklar, L.S. & Dietrich, W.E. 2004. A mechanistic model for river incision into bedrock by sultating bedload. Water Resources Re-search 40, W06301, doi:10.1029/2003WR002496.

  9. 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.

  10. A novel duplex real-time PCR permits simultaneous detection and differentiation of Borrelia miyamotoi and Borrelia burgdorferi sensu lato.

    Science.gov (United States)

    Venczel, R; Knoke, L; Pavlovic, M; Dzaferovic, E; Vaculova, T; Silaghi, C; Overzier, E; Konrad, R; Kolenčík, S; Derdakova, M; Sing, A; Schaub, G A; Margos, G; Fingerle, V

    2016-02-01

    For simultaneous detection of Borrelia miyamotoi (relapsing fever spirochete) and Borrelia burgdorferi sensu lato, we have developed a duplex real-time PCR targeting the flagellin gene (flaB; p41), a locus frequently used in routine diagnostic PCR for B. burgdorferi s.l. detection. Primers and probes were designed using multiple alignments of flaB sequences of B. miyamotoi and B. burgdorferi s.l. species. The sensitivity and specificity of primers and probes were determined using serial dilutions (ranging from 10(4) to 10(-1)) of B. miyamotoi and B. burgdorferi s.l. DNA and of several species of relapsing fever spirochetes. Conventional PCR on recG and glpQ and sequencing of p41 PCR products were used to confirm the species assignment. The detection limit of both singleplex and duplex PCR was 10 genome equivalents except for B. spielmanii and two B. garinii genotypes which showed a detection limit of 10(2) genome equivalents. There was no cross reactivity of the B. miyamotoi primers/probes with B. burgdorferi s.l. DNA, while the B. burgdorferi s.l. primer/probe generated a signal with B. hermsii DNA. Out of 2341 Ixodes ricinus ticks from Germany and Slovakia that were screened simultaneously for the presence of B. miyamotoi and B. burgdorferi s.l., 52 were positive for B. miyamotoi and 276 for B. burgdorferi s.l., denoting an average prevalence of 2.2% for B. miyamotoi and 11.8% for B. burgdorferi s.l., and B. miyamotoi DNA was also detectable by PCR using artificial clinical samples. The duplex real-time PCR developed here represents a method that permits simultaneous detection and differentiation of B. burgdorferi s.l. and B. miyamotoi in environmental and potentially clinical samples.

  11. 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.

  12. Vertical compared with transverse incisions in abdominal surgery

    DEFF Research Database (Denmark)

    Grantcharov, T P; Rosenberg, J

    2001-01-01

    . 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...... with fewer complications (pain, burst abdomen, and pulmonary morbidity) and there is lower incidence of late incisional hernia after transverse compared with vertical laparotomy. A midline incision is still the incision of choice in conditions that require rapid intra-abdominal entry (such as trauma...

  13. 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)

  14. Rectus abdominis atrophy after ventral abdominal incisions: midline versus chevron.

    Science.gov (United States)

    Vigneswaran, Y; Poli, E; Talamonti, M S; Haggerty, S P; Linn, J G; Ujiki, M B

    2017-08-01

    Although many outcomes have been compared between a midline and chevron incision, this is the first study to examine rectus abdominis atrophy after these two types of incisions. Patients undergoing open pancreaticobiliary surgery between 2007 and 2011 at our single institution were included in this study. Rectus abdominis muscle thickness was measured on both preoperative and follow-up computed tomography (CT) scans to calculate percent atrophy of the muscle after surgery. At average follow-up of 24.5 and 19.0 months, respectively, rectus abdominis atrophy was 18.9% greater in the chevron (n = 30) than in the midline (n = 180) group (21.8 vs. 2.9%, p 20% atrophy at follow-up compared with 10% with a midline incision [odds ratio (OR) 9.0, p atrophy of the rectus abdominis compared with midline incisions. The long-term effects of transecting the rectus abdominis and disrupting its innervation creates challenging abdominal wall pathology. Atrophy of the abdominal wall can not be readily fixed with an operation, and this significant side effect of a transverse incision should be factored into the surgeon's decision-making process when choosing a transverse over a midline incision.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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)

  20. 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.

  1. Cytotoxicity of new duplex drugs linking 3'-C-ethynylcytidine and 5-fluor-2'-deoxyuridine against human melanoma cells.

    Science.gov (United States)

    Schott, Sarah; Niessner, Heike; Sinnberg, Tobias; Venturelli, Sascha; Berger, Alexander; Ikenberg, Kristian; Villanueva, Jessie; Meier, Friedegund; Garbe, Claus; Busch, Christian

    2012-11-01

    Melanoma is an increasingly common and potentially fatal malignancy of the skin and some mucous membranes. As no cure exists for metastatic disease, there is an urgent need for novel drugs. 2'-Deoxy-5-fluorouridylyl-(3'-5')-3'-C-ethynylcytidine [5-FdU(3'-5')ECyd] and 3'-C-ethynylcytidinylyl-(5' → 1-O)-2-O-octadecyl-sn-glycerylyl-(3-O → 5')-2'-deoxy-5-fluorouridine [ECyd-lipid-5-FdU] represent cytostatic active duplex drugs, which can be metabolized into various active antimetabolites. We evaluated the cytotoxicity of these heterodinucleoside phosphate analogs, their corresponding monomers ECyd and 5-FdU and combinations thereof on six metastatic melanoma cell lines and six ex vivo patient-derived melanoma cells in comparison to current standard cytostatic agents and the BRAF V600E inhibitor Vemurafenib. In vitro (real-time)-proliferation assays demonstrated that 5-FdU(3'-5')ECyd and ECyd-lipid-5-FdU had a high cytotoxic efficacy causing 75% melanoma cell death at concentrations in the nanomolar and micromolar range. Cytotoxicity was conducted by induction of DNA cleavage indicating apoptotic cells. Chicken embryotoxicity demonstrated that the duplex drugs were less toxic than 5-FdU at 0.01 μM. In vivo the duplex drug 5-FdU(3'-5')ECyd was efficacious in the murine LOX IMVI melanoma xenograph model on administration of 11.2 mg/kg/injection every fourth day. Both duplex drugs are promising novel cytostatic agents for the treatment of malignant melanoma meriting clinical evaluation. Copyright © 2012 UICC.

  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. Calculation of nucleation free energy for duplex oligomers in the context of nearest neighbor models.

    Science.gov (United States)

    Guerra, João Carlos de Oliveira

    2013-08-01

    Additive physical properties of DNA double strand polymers have been expanded in terms of 8 irreducible parameters. This provided consistency relations among the corresponding 10 duplex dimer contributions. To allow for oligomer analysis, end parameters were often added, and this would add extra degrees of freedom to the fore mentioned parameters. Statistical mechanics approaches were then connected to the nearest neighbor (NN) approach in the framework of the two-states model. Ad hoc end effects were thus (wrongly) correlated to nucleation phenomena and this lead to a critique for its role in NN modeling. With this motivation, a new NN model is proposed that accommodates the nucleation free energies. The model relates the nucleation free energy to the mean composition of the chain and permits to obtain a good estimate for the free energy associated only to the Watson-Crick base pairings. Copyright © 2013 Wiley Periodicals, Inc.

  4. DNA nanostructures: Through, rather than across

    Science.gov (United States)

    Bruchez, Marcel P.

    2018-02-01

    Dye molecules are shown to assemble into J-aggregate arrays by sequence-specific organization in the minor groove of DNA duplex sequences. Energy transfer through these structures displays the hallmarks of coherent coupling over distances that exceed those of conventional dipole-coupling processes.

  5. 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.

  6. Small incision removal of nylon foil orbital implants.

    Science.gov (United States)

    Liu, Catherine Y; Vemuri, Swapna; Tao, Jeremiah P

    2015-01-01

    To describe a small incision technique for the removal of a nylon foil orbital wall implant. The authors retrospectively reviewed the charts of 9 patients who underwent a minimally invasive anterior orbitotomy for nylon foil explantation. Indications for removal and surgical technique, including size of orbitotomy incision and extent of orbital dissection, were recorded. Motility, globe position, strabismus pre- and post procedure, and complications were also assessed. Photographs, videos, and postoperative imaging were included, when available. The indications for removal were adjacent sinusitis (4 cases), undesirable implant position (3), orbital abscess (1), and adjacent orbital emphysema (1). The removal technique was associated with no changes in motility, globe position, or strabismus postprocedure. The average incision size was 1.1 cm, and the procedure was rapid, usually seconds once the anterior aspect of the implant was exposed and grasped with a hemostat. The dissection in all cases was to the anterior aspect of the implant without a need for deep orbital manipulation. The authors demonstrate through video that the implant folds to exit through a small incision. No adverse events were noted. Nasal endoscopy and radiography demonstrated a fibrous capsule that maintained orbital structure and support. Thin nylon foil implant can be explanted safely and efficiently through a very small incision. The orbit maintains structure and configuration postexplantation in this series.

  7. External defibrillation failure due to antimicrobial incise drape.

    Science.gov (United States)

    Barbara, David W; Dietz, Niki M; White, Roger D; Pochettino, Alberto; Nuttall, Gregory A

    2013-09-01

    Antimicrobial incise drapes adhere to a patient's skin during surgery in an attempt to reduce surgical infections. We describe a patient undergoing repeated aortic valve replacement who experienced sudden ventricular fibrillation before median sternotomy. External defibrillation was unsuccessful on multiple attempts using several defibrillators. On removal of the incise drape from the patient's chest, external defibrillation was immediately successful. Increased transthoracic impedance can be caused by multiple factors and may prevent defibrillation. To our knowledge, this is the first reported case of an antimicrobial incise drape preventing defibrillation. If external defibrillation, cardioversion, or pacing is indicated intraoperatively, we recommend prompt removal of the antimicrobial incise drapes before electrode placement if the drapes overlay the intended pad position. Since this case, our institutional practice has now changed to placement of 2 external adhesive defibrillator electrodes onto the patient's skin lateral to the surgical field before incise drape application to allow for defibrillation. Copyright © 2013 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

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

    African Journals Online (AJOL)

    2015-09-21

    Sep 21, 2015 ... Background: Peripheral limb vascular diseases form one of the most common diseases that affect the middle-aged and the ... author is credited and the new creations are licensed under the identical terms. .... Table 4: Relationship of major duplex ultrasound findings with age, gender and clinical information.

  9. 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.

  10. 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 ...

  11. Risk Factors of Deep Venous Thrombosis in Duplex and Colour ...

    African Journals Online (AJOL)

    Risk Factors of Deep Venous Thrombosis in Duplex and Colour Doppler Ultrasound at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia. ... Thus early, correct and definitive diagnosis is crucial in assessing thromboembolic risk and initiating therapy. In this regard Patients at risk must be identified and given ...

  12. 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.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    S. C. Dutta

    2013-06-01

    Full Text Available 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.

  15. 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.

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

    Science.gov (United States)

    Palle-Reisch, Monika; Cichna-Markl, Margit; Hochegger, Rupert

    2014-06-15

    The paper presents a duplex real-time PCR assay for the simultaneous detection of three potentially allergenic mustard species commonly used in food: white mustard (Sinapis alba), black mustard (Brassica nigra) and brown mustard (Brassica juncea). White mustard is detected in the "green" and black/brown mustard in the "yellow" channel. The duplex real-time PCR assay does not show cross-reactivity with other Brassicaceae species including broccoli, cauliflower, radish and rapeseed. Low cross-reactivities (difference in the Ct value ⩾ 11.91 compared with the positive control) were obtained with cumin, fenugreek, ginger, rye and turmeric. When applying 500 ng DNA per PCR tube, the duplex real-time PCR assay allowed the detection of white, black and brown mustard in brewed model sausages down to a concentration of 5mg/kg in 10 out of 10 replicates. The duplex real-time PCR assay was applied to verify correct labelling of commercial foodstuffs. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    DEFF Research Database (Denmark)

    Mahmood, Nurul Huda; Mogensen, Preben Elgaard

    2017-01-01

    Full duplex communication enables simultaneous transmission from both ends of a communication link, thereby promising gains in terms of the throughput and the delay. Such compelling gains are conditioned on a number of design constraints. Generally, it has been shown that the throughput gain and ...... 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....... 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...

  18. Sharp compared with blunt fascial incision at cesarean delivery

    DEFF Research Database (Denmark)

    Aabakke, Anna J M; Hare, Kristine J; Krebs, Lone

    2014-01-01

    OBJECTIVE: To compare patient preference for either sharp incision with scissors or blunt manual cleavage of the fascia at cesarean delivery in a randomized controlled trial in which each woman was her own control. STUDY DESIGN: Women undergoing primary cesarean delivery (n=34) were randomized...... to side distribution of sharp or blunt incision of the fascia (sharp right and blunt left or blunt right and sharp left) and followed three months postoperatively. The primary outcome was patient preference for the right or left side of the scar 3 months postoperatively and modeled by polytomous logistic...... difference was found in patient preference with regard to sharp or blunt incision of the fascia, nor was there a significant difference in postoperative pain scores. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov: www.clinicaltrials.org;NCT01297725....

  19. The problem of insufficient incisal display: a case presentation.

    Science.gov (United States)

    Castillo, Rodrigo

    2010-01-01

    Enhancement of facial beauty is one of the primary elective goals of patients seeking dental care. Frequently, improvements in natural beauty can be expected to follow restoration of ideal relationships between the denture and the facial soft tissues. A very important feature in a youthful appearance is the incisal tooth display; the amount of maxillary incisal exposure gradually decreases with age, accompanied by a gradual increase in mandibular incisal exposure. However, this problem could be present in young people where the effects of age should not be apparent yet. There are some other factors that could accelerate this process. The present case illustrates the improvement and rejuvenation of an unesthetic young smile through restorative treatment.

  20. Giant Nasolabial Cyst Treated Using Neumann Incision: Case Report

    Directory of Open Access Journals (Sweden)

    Ordones, Alexandre Beraldo

    2013-09-01

    Full Text Available Introduction: A nasolabial cyst is an ectodermal development cyst. It presents as a fullness of canine fossa, nasal ala, or vestibule of the nose. It is rare and usually small. Treatment consists of complete surgical excision or transnasal endoscopic marsupialization. Objective: To describe a giant nasolabial cyst case treated using Neumann incision. Case Report: A 37-year-old man was referred to the otolaryngology department with nasal obstruction and nasal deformity. Computed tomography showed a nasal cystic lesion 4 × 4.5 × 5 cm wide. Surgical excision using Neumann incision was performed. Discussion: Neumann incision provides wide access to the nasal cavity and may be useful in nasolabial cyst treatment.

  1. Force modeling for incision surgery into tissue with haptic application

    Science.gov (United States)

    Kim, Pyunghwa; Kim, Soomin; Choi, Seung-Hyun; Oh, Jong-Seok; Choi, Seung-Bok

    2015-04-01

    This paper presents a novel force modeling for an incision surgery into tissue and its haptic application for a surgeon. During the robot-assisted incision surgery, it is highly urgent to develop the haptic system for realizing sense of touch in the surgical area because surgeons cannot sense sensations. To achieve this goal, the force modeling related to reaction force of biological tissue is proposed in the perspective on energy. The force model describes reaction force focused on the elastic feature of tissue during the incision surgery. Furthermore, the force is realized using calculated information from the model by haptic device using magnetorheological fluid (MRF). The performance of realized force that is controlled by PID controller with open loop control is evaluated.

  2. 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 .

  3. Single-incision sling operations for urinary incontinence in women.

    Science.gov (United States)

    Nambiar, Arjun; Cody, June D; Jeffery, Stephen T

    2014-06-01

    Urinary incontinence has been shown to affect up to 50% of women. Studies in the United States have shown that up to 80% of these women have an element of stress urinary incontinence. Colposuspension and now mid-urethral slings have been shown to be effective in treating patients with stress incontinence. However, associated adverse events include bladder and bowel injury, groin pain and haematoma formation. This has led to the development of third-generation single-incision slings, also referred to as mini-slings.It should be noted that TVT-Secur (Gynecare, Bridgewater, NJ, USA) is one type of single-incision sling; it has been withdrawn from the market because of poor results. However, it is one of the most widely studied single-incision slings and was used in several of the trials included in this review. Despite its withdrawal from clinical use, it was decided that data pertaining to this sling should be included in the first iteration of this review, so that level 1a data are available in the literature to confirm its lack of efficacy. To assess the effectiveness of mini-sling procedures in women with urodynamic clinical stress or mixed urinary incontinence in terms of improved continence status, quality of life or adverse events. We searched the Cochrane Incontinence Group Specialised Trials Register, which contains trials identified from the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE and MEDLINE in process; we handsearched journals and conference proceedings (searched 6 February 2013) and searched ClinicalTrials.gov (searched 20 September 2012), the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (searched 20 September 2012) and the reference lists of relevant articles. Randomised or quasi-randomised controlled trials in women with urodynamic stress incontinence, symptoms of stress incontinence or stress-predominant mixed urinary incontinence, in which at least one trial arm involves one of the

  4. Small incision transcutaneous levator aponeurotic repair for blepharoptosis.

    Science.gov (United States)

    Baroody, Michael; Holds, John B; Sakamoto, Douglas K; Vick, Valerie L; Hartstein, Morris E

    2004-06-01

    Patients presenting with blepharoptosis due to disinsertion or thinning of the levator aponeurosis require surgical repair. A minimally invasive approach directed specifically at the levator aponeurotic anatomic defect may provide benefits to the patient. Proposed advantages of a small eyelid incision (8-13 mm) include less local anesthetic and tissue distortion, less ecchymosis and edema, decreased operative times, a shortened recovery period, and improved surgical results. We describe our results with the use of a small incision ptosis repair in select patients. A retrospective chart review between January 2000 and September 2001 included 91 patients and 118 eyelids with blepharoptosis due to aponeurotic disinsertion, corrected by a minimally invasive approach. The small incision technique comprised levator aponeurotic resection and advancement. Pre- and postoperative upper eyelid marginal reflex distances (MRD1), eyelid contour, need for reoperation, and complications (overcorrection, undercorrection, hematoma, and infection) were recorded. The average preoperative MRD1 measured 0.5 +/- 1.1 mm, with a range of -2.0 to 2.5 mm. The average postoperative MRD1 measured 2.6 +/- 0.8 mm, with a range of 1 to 5.5 mm (P < 0.0001). Of the 118 eyelids corrected by a small incision technique, there were 4 overcorrections, 3 undercorrections, 1 failure, 1 postoperative ptosis procedure of the contralateral upper eyelid secondary to Hering's law ptosis, and 4 patients requesting surgical treatment of dermatochalasis. No symptomatic dry eye, exposure keratopathy, or other complication resulted in association with the overcorrections. No contour abnormalities, infections, hematomas, or other complications were noted. Our experience suggests that utilization of a small skin incision is safe, precise, and efficient and allows for more rapid recovery from surgery. The authors note a decreased incidence of reoperation and postoperative complaints compared with historical larger-incision

  5. 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....

  6. 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......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...

  7. 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.

  8. 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 stabilization...... to a maximum of 9°C per incorporation. Using fluorescence, ultraviolet and nuclear magnetic resonance (NMR) spectroscopy, we show that the stabilization is achieved by pyrene intercalation in the dsDNA duplex. The pyrene moiety is not restricted to one intercalation site but rather switches between multiple...... sites in intermediate exchange on the NMR timescale, resulting in broad lines in NMR spectra. We identified two intercalation sites with NOE data showing that the pyrene prefers to intercalate one base pair away from the modified nucleotide with its linker curled up in the minor groove. Both...

  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. Enzyme-catalyzed DNA unwinding: studies on Escherichia coli rep protein.

    Science.gov (United States)

    Yarranton, G T; Gefter, M L

    1979-04-01

    Replication in vitro of the replicative form (RF) I DNA of bacteriophage varphiX174 requires the phage-induced cistron A (cisA) protein, the host rep protein, DNA-binding protein, ATP, and DNA polymerase III plus replication factors. The rep protein is a single-stranded DNA-dependent ATPase. In this paper we show that varphiX174 RF I DNA cut by the cisA protein acts as a duplex DNA cofactor for the rep protein ATPase activity, provided that DNA-binding protein is present. In this latter reaction the duplex DNA is unwound by the rep protein with concomitant hydrolysis of ATP. The extents of ATP hydrolysis, DNA unwinding, and, where appropriate, DNA synthesis are proportional to the amounts of DNA-binding protein present. Two ATP molecules are hydrolyzed per base pair unwound. We propose that the obligatory requirement for the cisA protein in the unwinding of varphiX174 RF I DNA is not simply due to its endonuclease activity but rather is due to its provision of a site for the binding of the rep protein. The rep protein in the presence of DNA-binding protein, but in the absence of cisA protein, unwinds duplex DNA when one strand extends to generate a single-stranded leader region preceding the duplex. We show that rep protein translocates along the leader single strand in a 5'-to-3' direction only and then invades the duplex DNA. The rep protein shows a directional specificity for translocation and unwinding. A model is presented to explain the mechanism of DNA unwinding catalyzed by the rep protein.

  11. Sensitive detection of microRNAs based on the conversion of colorimetric assay into electrochemical analysis with duplex-specific nuclease-assisted signal amplification.

    Science.gov (United States)

    Xia, Ning; Liu, Ke; Zhou, Yingying; Li, Yuanyuan; Yi, Xinyao

    2017-01-01

    miRNAs have emerged as new biomarkers for the detection of a wide variety of cancers. By employing duplex-specific nuclease for signal amplification and gold nanoparticles (AuNPs) as the carriers of detection probes, a novel electrochemical assay of miRNAs was performed. The method is based on conversion of the well-known colorimetric assay into electrochemical analysis with enhanced sensitivity. DNA capture probes immobilized on the electrode surface and ferrocene (Fc)-labeled DNA detection probes (denoted "Fc-DNA-Fc") presented in the solution induced the assembly of positively charged AuNPs on the electrode surface through the electrostatic interaction. As a result, a large number of Fc-DNA-Fc molecules were attached on the electrode surface, thus amplifying the electrochemical signal. When duplex-specific nuclease was added to recycle the process of miRNA-initiated digestion of the immobilized DNA probes, Fc-DNA-Fc-induced assembly of AuNPs on the electrode surface could not occur. This resulted in a significant fall in the oxidation current of Fc. The current was found to be inversely proportional to the concentration of miRNAs in the range of 0-25 fM, and a detection limit of 0.1 fM was achieved. Moreover, this work presents a new method for converting colorimetric assays into sensitive electrochemical analyses, and thus would be valuable for design of novel chemical/biosensors.

  12. Incised plate urethroplasty in perineal and perineo-scrotal ...

    African Journals Online (AJOL)

    Objective: The ideal replacement of the urethra is the urethra itself. However, when the urethra is not available, flaps or tubes are used as substitutes in hypospadias repair. The urethral plate, when preserved, is an excellent tool for tubularization and urethral reconstruction. Tubularized incise plate (TIP) repair has become ...

  13. Versatility of tubularized incised plate urethroplasty in the ...

    African Journals Online (AJOL)

    Background: The outcomes of urethroplasty in the management of different types of hypospadias have continued to improve since the introduction of the tubularized incised plate (TIP) urethroplasty (Snodgrass method). The aim of this study was to evaluate the feasibility and applicability of TIP urethroplasty in the ...

  14. Feasibility of a tubularised incised-plate urethroplasty with double ...

    African Journals Online (AJOL)

    Background: Reoperation for failed hypospadias has been considered to be seriously problematic. The dense fibrotic tissue causes difficulties in wound healing and increases the rate of complications. The tubularised incised-plate urethroplasty (TIPU) method has become a preferred method for all varieties of hypospadias ...

  15. Tubularized Incised Plate (TIP) Urethroplasty: Extended Use in ...

    African Journals Online (AJOL)

    Objective: Recently, tubularized incised plate (TIP) urethroplasty (Snodgrass repair) has gained popularity for the primary repair of distal and proximal hypospadias. This study was carried out to evaluate TIP urethroplasty in the repair of failed and complicated hypospadias cases. Patients and Methods: This study was ...

  16. Combined use of Mathieu and incised plate technique (Snodgrass ...

    African Journals Online (AJOL)

    Objectives: To evaluate the results and complications after combined use of Mathieu and incised plate technique for management of distal hypospadias in older children. Patients and methods: A total of 33 patients with primary distal penile hypospadias were operated upon using the Mathieu technique combined with deep ...

  17. Tubularized incised plate urethroplasty repair in adult hypospadias ...

    African Journals Online (AJOL)

    Objective: Most studies published in the literature report on the results of tubularized incised plate urethroplasty (TIPU) for hypospadias repair in children. Hence, the objective of this study was to evaluate the results of TIPU repair in adults. Patients and methods: The records of 60 adult patients with primary hypospadias ...

  18. Incised plate urethroplasty in perineal and perineo-scrotal ...

    African Journals Online (AJOL)

    A. Bhat

    Abstract. Objective: The ideal replacement of the urethra is the urethra itself. However, when the urethra is not available, flaps or tubes are used as substitutes in hypospadias repair. The urethral plate, when preserved, is an excellent tool for tubularization and urethral reconstruction. Tubularized incise plate (TIP) repair.

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

    African Journals Online (AJOL)

    Annals of Pediatric Surgery 2012, 8:80–85. Keywords: recurrent hypospadias, salvage hypospadias, tubularized incised plate. aDepartment of Surgery, Division of Pediatric and Plastic Surgery, Faculty of. Medicine, Suez Canal University, Ismailia and bDepartment of Surgery, Faculty of. Medicine, Menoufia University ...

  20. a comparative study between manual small incision cataract surgery ...

    African Journals Online (AJOL)

    ... October 2012 to October 2014 for cataract surgery were followed up for 6 weeks after surgery. They were divided into two groups based on the type of surgical procedure opted by the patients. Group A consisted of 50 patients who underwent Manual Small Incision Cataract. Surgery with rigid Polymethyl Methacrylate IOL ...

  1. Anastomosis Procedure through an Inguinal Hernia Incision in ...

    African Journals Online (AJOL)

    was laparoscopically transected by a stapler. A 4 cm skin incision was then made in the left inguinal region and carried down to the peritoneum through the hernia sac [Figure 1]. Bowel resection was performed extracorporeally, and an anvil was placed at the proximal end of the colon, over a purse-string suture. [Figure 2].

  2. rubularised Incised Plate Hypospadias Urethroplasty In A Regional ...

    African Journals Online (AJOL)

    1t the Coast Province General Hospital in Mombasa. Xenya and in some private hospitals, nearby. junction. Artificial erection test is done to check for residual chordee20. Residual penile curvature is corrected by dorsal tunica albuginea plication8. - The glans wings are mobilized laterally. A midline relaxing incision is made ...

  3. Treatment of pharyngocutaneous fistula acquired from incisions and ...

    African Journals Online (AJOL)

    Treatment of pharyngocutaneous fistula acquired from incisions and drainage of deep neck space abscess in a patient with occult third branchial anomaly. ... We did surgical exploration to excise and close the fistula but only succeeded at the second attempt. Conclusion: We conclude that branchial apparatus anomaly ...

  4. 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.

  5. 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

    OBJECTIVE: Compare arthroscopic partial meniscectomy to a true sham intervention. METHODS: Sham-controlled superiority trial performed in three county hospitals in Denmark comparing arthroscopic partial meniscectomy to skin incisions only in patients aged 35-55 years with persistent knee pain and...

  6. Feasibility of reduced port surgery applying Higuchi's transverse incision

    Directory of Open Access Journals (Sweden)

    Kazu Ueda

    2017-02-01

    Conclusion: We reported novel forms of reduced port surgery applying Higuchi's transverse incision. It was suggested that these procedures are relatively simple, but ensure the same safety and efficacy as conventional methods. We intend to increase the number of cases and examine safety, efficacy, and patient satisfaction for these procedures.

  7. Short communication Combined use of Mathieu and incised plate ...

    African Journals Online (AJOL)

    Objectives: To evaluate the results and complications after combined use of Mathieu and incised plate technique for management of distal hypospadias in older children. Patients and methods: A total of 33 patients with primary distal penile hypospadias were operated upon using the Mathieu technique combined with deep ...

  8. Topical‑intracameral anesthesia in manual small incision cataract ...

    African Journals Online (AJOL)

    Background: Cataract remains a leading cause of blindness worldwide. Manual small incision cataract surgery (MSICS) is currently practiced as the technique of choice in Sub‑Saharan Africa to reduce the backlog of cataract blindness. Optimal pain control during surgery remains a challenge to cataract surgeons. Aim: To ...

  9. Visual Outcome after Small Incision Cataract Surgery in ...

    African Journals Online (AJOL)

    Objective: The aim of this study was to determine the visual outcome of patients who had manual small incision cataract surgery in a high volume secondary eye hospital in southwestern Nigeria, and to identify reasons for poor outcome. Methodology: This is an observational descriptive, longitudinal study of consecutive ...

  10. Ankle fusion using a 2-incision, 3-screw technique

    NARCIS (Netherlands)

    Hendrickx, R. P. M.; Kerkhoffs, G. M. M. J.; Stufkens, S. A. S.; van Dijk, C. N.; Marti, R. K.

    2011-01-01

    Reliable fusion and optimal correction of the alignment of the ankle joint using a 2-incision, 3-screw technique. Symptomatic osteoarthritis of the ankle joint after insufficient other treatment, severe deformity of the osteoarthritic ankle joint, or salvation procedure after failed arthroplasty.

  11. DOES CONJUNCTIVAL INCISION INFLUENCE MEDIAL RECTUS MUSCLE RECESSIONS?

    Directory of Open Access Journals (Sweden)

    Galina G. Dimitrova

    2015-09-01

    Full Text Available Purpose: To evaluate the role of conjunctival incision in medial rectus muscle recessions as surgical treatment of choice in esotropia. Methods: The study included 200 patients (370 eyes, operated on for esotropia in the period of 2000-2014. 170 of them (340 eyes underwent bilateral medial rectus muscle recessions and 30- unilateral medial rectus muscle recession for various forms of alternating/alternated esotropia. We compared the effect (Δ/mm recession of fornix and limbal approach. Diagnostic, surgical and statistical methods were used. Results: Limbal incision was performed on 110 patients (55,3% and fornix approach was done in 89 cases (44,7%. The mean effect corrected prism diopters for each mm of recession (Δ/mm differed significantly in the two groups, being bigger in cases with fornix incision (p<0,001 . Conclusion: The type of conjunctival incision in medial rectus muscle recessions have an influence not only on the cosmetic appearance, but also on the functional result. This is especially true for large recessions.

  12. 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.

  13. Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA.

    Science.gov (United States)

    Sun, Yan; Borbat, Peter P; Grigoryants, Vladimir M; Myers, William K; Freed, Jack H; Scholes, Charles P

    2015-02-17

    Pulse dipolar electron-spin resonance in the form of double electron electron resonance was applied to strategically placed, site-specifically attached pairs of nitroxide spin labels to monitor changes in the mini TAR DNA stem-loop structure brought on by the HIV-1 nucleocapsid protein NCp7. The biophysical structural evidence was at Ångstrom-level resolution under solution conditions not amenable to crystallography or NMR. In the absence of complementary TAR RNA, double labels located in both the upper and the lower stem of mini TAR DNA showed in the presence of NCp7 a broadened distance distribution between the points of attachment, and there was evidence for several conformers. Next, when equimolar amounts of mini TAR DNA and complementary mini TAR RNA were present, NCp7 enhanced the annealing of their stem-loop structures to form duplex DNA-RNA. When duplex TAR DNA-TAR RNA formed, double labels initially located 27.5 Å apart at the 3'- and 5'-termini of the 27-base mini TAR DNA relocated to opposite ends of a 27 bp RNA-DNA duplex with 76.5 Å between labels, a distance which was consistent with the distance between the two labels in a thermally annealed 27-bp TAR DNA-TAR RNA duplex. Different sets of double labels initially located 26-27 Å apart in the mini TAR DNA upper stem, appropriately altered their interlabel distance to ~35 Å when a 27 bp TAR DNA-TAR RNA duplex formed, where the formation was caused either through NCp7-induced annealing or by thermal annealing. In summary, clear structural evidence was obtained for the fraying and destabilization brought on by NCp7 in its biochemical function as an annealing agent and for the detailed structural change from stem-loop to duplex RNA-DNA when complementary RNA was present. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Quantitative detection method for Roundup Ready soybean in food using duplex real-time PCR MGB chemistry.

    Science.gov (United States)

    Samson, Maria Cristina; Gullì, Mariolina; Marmiroli, Nelson

    2010-07-01

    Methodologies that enable the detection of genetically modified organisms (GMOs) (authorized and non-authorized) in food and feed strongly influence the potential for adequate updating and implementation of legislation together with labeling requirements. Quantitative polymerase chain reaction (qPCR) systems were designed to boost the sensitivity and specificity on the identification of GMOs in highly degraded DNA samples; however, such testing will become economically difficult to cope with due to increasing numbers of approved genetically modified (GM) lines. Multiplexing approaches are therefore in development to provide cost-efficient solution. Construct-specific primers and probe were developed for quantitative analysis of Roundup Ready soybean (RRS) event glyphosate-tolerant soybean (GTS) 40-3-2. The lectin gene (Le1) was used as a reference gene, and its specificity was verified. RRS- and Le1-specific quantitative real-time PCR (qRTPCR) were optimized in a duplex platform that has been validated with respect to limit of detection (LOD) and limit of quantification (LOQ), as well as accuracy. The analysis of model processed food samples showed that the degradation of DNA has no adverse or little effects on the performance of quantification assay. In this study, a duplex qRTPCR using TaqMan minor groove binder-non-fluorescent quencher (MGB-NFQ) chemistry was developed for specific detection and quantification of RRS event GTS 40-3-2 that can be used for practical monitoring in processed food products.

  15. 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.

  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. 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.)

  18. Differentiation of midbrain cystic lesions by duplex Doppler US

    International Nuclear Information System (INIS)

    Horgan, J.G.; Taylor, K.J.W.; Sarwar, M.; Weltin, G.; Klier, L.

    1986-01-01

    The addition of Doppler technology to an ultrasound imaging system allows easy differentiation of vascular from nonvascular masses. In addition, the characteristic flow in different arteries, veins, and arteriovenous communications allows accurate diagnosis of vascular structures. Cystic lesions in the region of the midbrain are uncommon but not rare in neonates, and it is important to differentiate between quadrigeminal plate cysts and vein of Galen aneurysms. Six neonates with cystic midbrain structures lying above the tectum were studied over a 2-year period. All were examined with duplex Doppler imaging and followed up by CT and angiography, when indicated. In two of the six infants a highly vascular signal was demonstrated with high flow rates and low impedance. Subsequent CT and angiography revealed typical vein of Galen aneurysms. The remaining four infants had cystic lesions that were avascular on Doppler imaging and demonstrated no enhancement on CT. Duplex Doppler imaging is helpful in the initial investigation of patients with midbrain cystic lesions

  19. Herpes Zoster Duplex Unilateralis: Two Cases and Brief Literature Review.

    Science.gov (United States)

    Son, Jee Hee; Chung, Bo Young; Kim, Hye One; Cho, Hee Jin; Park, Chun Wook

    2016-12-01

    Cases involving dermatomal herpes zoster in two or more locations are rare, especially in immunocompetent patients. When two noncontiguous dermatomes are involved, if affected unilaterally, it is called herpes zoster duplex unilateralis; if bilaterally, bilateralis. Here, we report two cases of herpes zoster duplex unilateralis. A 66-year-old man presented with painful erythematous grouped vesicles on his left scalp, forehead, trunk, and back (left [Lt.] V1, Lt. T8). Histologic findings were consistent with herpetic infection. A 33-year-old woman presented with painful erythematous grouped vesicles and crust on her left forehead and neck (Lt. V1, Lt. C5). Both patients were treated with oral administration of famcyclovir 750 mg/day for seven days.

  20. 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...

  1. A 2-order MIMO Full-Duplex Antenna System

    DEFF Research Database (Denmark)

    Tsakalaki, Elpiniki; Foroozanfard, Ehsan; De Carvalho, Elisabeth

    2014-01-01

    The paper presents an antenna system with combined full-duplex and 2-order multiple-input-multiple-output (MIMO) functionalities, i.e., a system capable of spatially multiplexing and spatially demultiplexing 2 datastreams in the same frequency and in the same time. By exploiting symmetries....... On the other hand, the 2 MIMO ports (either at the Tx or at the Rx) are sufficiently decoupled thanks to polarization diversity. The proposed antenna system exhibits a remarkable level of fullduplex isolation over a wide bandwidth while maintaining low coupling between its MIMO ports and can serve...... as a concrete implementation of an antenna system equipped with both MIMO as well as full-duplex capabilities....

  2. DNA-DNA interaction beyond the ground state.

    Science.gov (United States)

    Lee, D J; Wynveen, A; Kornyshev, A A

    2004-11-01

    The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic "snap-shot" recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a "torsional alignment transition," which is first order for nonhomologous DNA and weaker order for homologous sequences.

  3. 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.

  4. 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....

  5. Effect of heat treatment on corrosion behavior of duplex coatings

    Directory of Open Access Journals (Sweden)

    K. Raghu Ram Mohan Reddy

    2017-01-01

    Full Text Available In the present paper, duplex WC-Co/NiCrAlY coating is coated onto Ti6Al4V substrate and vacuum heat treatment is employed to investigate the corrosion behavior of heat treated samples as well as Ti6Al4V substrate for comparison. In this duplex coating system, High Velocity Oxy Fuel (HVOF process is used to deposit NiCrAlY interlayer with a constant thickness of 200 μm and WC-Co ceramic top layer with varying thickness of 250 μm, 350 μm and 450 μm deposited by Detonation Spray (DS process. Different heat treatment temperatures (600–1150 °C were employed for the coated samples to study the microstructure and the effect on corrosion resistance of the duplex coatings. Potentiodynamic polarization tests were carried to investigate the corrosion performance of duplex coated heat treated samples and the substrate in Ringer’s solution at 37 °C and prepared the pH to 5.7. The microstructure upon corrosion after heat treatment was characterized by SEM analysis to understand the corrosion behavior. The results disclosed that at all heat treatment temperatures, all the coated samples exhibited better corrosion resistance than the base substrate. However, during 950 °C and 1150 °C heat treatment temperatures, it was observed highest corrosion potential than 600 °C and 800 °C. The 350 μm thickness, coated sample exhibited highest corrosion resistance compared to other two coated samples and the substrate at all heat treatment temperatures.

  6. Herpes zoster duplex bilateralis in an immunocompetent host

    Directory of Open Access Journals (Sweden)

    Pratik Gahalaut

    2012-01-01

    Full Text Available Varicella zoster virus causes both chicken pox and herpes zoster. The phenomenon of herpes zoster occurring concurrently in two non-contiguous dermatomes involving different halves of the body is termed herpes zoster duplex bilateralis (HZDB. Few cases, reported in the literature, were seen in either an immunosuppressed host or in the older age group. Here we present a case of HZDB in an immunocompetent host, probably the first in India.

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

    Science.gov (United States)

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

    1994-01-01

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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  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. 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

  17. 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

  18. Functional and aesthetic results of various lip-splitting incisions: A clinical analysis of 60 cases.

    Science.gov (United States)

    Rapidis, A D; Valsamis, S; Anterriotis, D A; Skouteris, C A

    2001-11-01

    This study retrospectively evaluated the functional and aesthetic results of various types of lip-splitting incisions in a group of patients in whom this approach was used to treat intraoral tumors. Between 1992 and 1998, 87 consecutive patients were subjected to either mandibulotomy or mandibulectomy using a lip-splitting incision. During this period, 4 types of incisions were sequentially used: straight midline incision, lateral lip-splitting incision, midline splitting with extension around the contour of the chin, and the chevron chin-contour incision. Sixty patients with a follow-up of at least 6 months were included in the study. The patients were asked to answer a questionnaire regarding the degree of satisfaction with the cosmetic result of the procedure and were clinically assessed for sensory and functional impairment resulting from the incision. The remaining 27 patients were lost to follow-up or had died of their disease. The lateral lip-splitting incision caused the fewest postoperative problems in patients subjected to either mandibulotomy or mandibulectomy. The best overall results were achieved by the chevron-chin contour incision. The incision that followed the contour of the chin and the straight midline incision showed less satisfactory results. The chevron chin-contour incision, along with meticulous soft tissue closure, produces the best aesthetic and functional results. Copyright 2001 American Association of Oral and Maxillofacial Surgeons

  19. Effect of intercalator substituent and nucleotide sequence on the stability of DNA- and RNA-naphthalimide complexes.

    Science.gov (United States)

    Johnson, Charles A; Hudson, Graham A; Hardebeck, Laura K E; Jolley, Elizabeth A; Ren, Yi; Lewis, Michael; Znosko, Brent M

    2015-07-01

    DNA intercalators are commonly used as anti-cancer and anti-tumor agents. As a result, it is imperative to understand how changes in intercalator structure affect binding affinity to DNA. Amonafide and mitonafide, two naphthalimide derivatives that are active against HeLa and KB cells in vitro, were previously shown to intercalate into DNA. Here, a systematic study was undertaken to change the 3-substituent on the aromatic intercalator 1,8-naphthalimide to determine how 11 different functional groups with a variety of physical and electronic properties affect binding of the naphthalimide to DNA and RNA duplexes of different sequence compositions and lengths. Wavelength scans, NMR titrations, and circular dichroism were used to investigate the binding mode of 1,8-naphthalimide derivatives to short synthetic DNA. Optical melting experiments were used to measure the change in melting temperature of the DNA and RNA duplexes due to intercalation, which ranged from 0 to 19.4°C. Thermal stabilities were affected by changing the substituent, and several patterns and idiosyncrasies were identified. By systematically varying the 3-substituent, the binding strength of the same derivative to various DNA and RNA duplexes was compared. The binding strength of different derivatives to the same DNA and RNA sequences was also compared. The results of these comparisons shed light on the complexities of site specificity and binding strength in DNA-intercalator complexes. For example, the consequences of adding a 5'-TpG-3' or 5'-GpT-3' step to a duplex is dependent on the sequence composition of the duplex. When added to a poly-AT duplex, naphthalimide binding was enhanced by 5.6-11.5°C, but when added to a poly-GC duplex, naphthalimide binding was diminished by 3.2-6.9°C. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. 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

  1. 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.

  2. Duplex ultrasound scanning of peripheral arterial disease of the lower limb

    DEFF Research Database (Denmark)

    Eiberg, Jonas Peter; Rasmussen, John Bøje Grønvall; Hansen, Marc Allan

    2010-01-01

    To assess the reliability and applicability of duplex ultrasound scanning (DUS) of lower limb arteries, compared with digital subtraction angiography (DSA), in patients with peripheral arterial disease (PAD)....

  3. Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide.

    Science.gov (United States)

    Srikannathasan, Velupillai; Wohlkonig, Alexandre; Shillings, Anthony; Singh, Onkar; Chan, Pan F; Huang, Jianzhong; Gwynn, Michael N; Fosberry, Andrew P; Homes, Paul; Hibbs, Martin; Theobald, Andrew J; Spitzfaden, Claus; Bax, Benjamin D

    2015-10-01

    Fluoroquinolone drugs such as moxifloxacin kill bacteria by stabilizing the normally transient double-stranded DNA breaks created by bacterial type IIA topoisomerases. Previous crystal structures of Staphylococcus aureus DNA gyrase with asymmetric DNAs have had static disorder (with the DNA duplex observed in two orientations related by the pseudo-twofold axis of the complex). Here, 20-base-pair DNA homoduplexes were used to obtain crystals of covalent DNA-cleavage complexes of S. aureus DNA gyrase. Crystals with QPT-1, moxifloxacin or etoposide diffracted to between 2.45 and 3.15 Å resolution. A G/T mismatch introduced at the ends of the DNA duplexes facilitated the crystallization of slightly asymmetric complexes of the inherently flexible DNA-cleavage complexes.

  4. Incision of Licus Vallis, Mars, From Multiple Lake Overflow Floods

    Science.gov (United States)

    Goudge, Timothy A.; Fassett, Caleb I.

    2018-02-01

    Licus Vallis is a large valley (>350 km long, >2 km wide, and >150 m deep) that heads at the outlet breach of an 30 km diameter impact crater. We present observations of the geomorphology and topography of this paleolake outlet valley and associated tributary valleys to constrain the history of incision of the Licus Vallis system. Licus Vallis has an abrupt increase in gradient by a factor of approximately 4 along its longitudinal profile, and a knickpoint that drops 200 m over a reach of 2 km approximately 12 km downstream from the valley head. We also describe a set of paired terraces within Licus Vallis, which are continuous for tens of kilometers and define an interior valley >2 km in width. We interpret the geomorphology of Licus Vallis as recording at least two discrete, major episodes of valley incision, both driven by lake overflow floods. The main portion of Licus Vallis formed by overflow flooding from a large ( 103-104 km2) lake contained in an intercrater basin. Subsequently, overflow flooding from a lake within the 30 km diameter impact crater reactivated Licus Vallis, forming a major knickpoint at the valley head and establishing the upstream section of the valley at a lower slope. Farther down the valley, this flood event incised an interior valley bounded by paired terraces. Regional tributary valleys that feed Licus Vallis also have prominent knickpoints, which have retreated farthest for downstream valleys. We conclude that these knickpoints record successive waves of incision that swept up Licus Vallis during lake overflow flooding, with erosion in the main trunk of the valley (from overflow floods) significantly outpacing erosion in the tributary valleys (from regional surface runoff). These observations of Licus Vallis illustrate how lake overflow floods may have provided an important control on the pace of landscape evolution on Mars.

  5. Robot-assisted submandibular gland excision via modified facelift incision

    OpenAIRE

    Jung, Seung Wook; Kim, Young Kwan; Cha, Yong Hoon; Koh, Yoon Woo; Nam, Woong

    2017-01-01

    Background The conventional transcervical resection for submandibular gland disease has some risks and an unsatisfactory cosmetic result. Recently, robot-assisted surgery has been developed as a plausible substitute for conventional surgery which provides an excellent cosmetic outcome. Case presentation The authors performed robot-assisted sialadenectomy via modified facelift incision using the da Vinci Xi surgical system (Intuitive Surgical Inc., CA, USA) with two endowrist arms (monopolar c...

  6. Rehabilitation of anterior teeth with customised incisal guide table.

    Science.gov (United States)

    Mall, Priyanka; Singh, Kamleshwar; Rao, Jitendra; Kumar, Lakshya

    2013-05-24

    Restoration of anterior guidance is a major challenge to the clinician in planning of all restorative treatments. An accurate anterior guidance is important for proper function, aesthetics, comfort and phonetics. This article describes anterior rehabilitation of a patient who met with a road traffic accident and lost his anterior teeth. Anterior guidance developed in the provisional restorations was accurately recorded in the customised incisal guide table and permanent restorations were fabricated accordingly.

  7. Rehabilitation of anterior teeth with customised incisal guide table

    OpenAIRE

    Mall, Priyanka; Singh, Kamleshwar; Rao, Jitendra; Kumar, Lakshya

    2013-01-01

    Restoration of anterior guidance is a major challenge to the clinician in planning of all restorative treatments. An accurate anterior guidance is important for proper function, aesthetics, comfort and phonetics. This article describes anterior rehabilitation of a patient who met with a road traffic accident and lost his anterior teeth. Anterior guidance developed in the provisional restorations was accurately recorded in the customised incisal guide table and permanent restorations were fabr...

  8. Rehabilitation of anterior teeth with customised incisal guide table

    Science.gov (United States)

    Mall, Priyanka; Singh, Kamleshwar; Rao, Jitendra; Kumar, Lakshya

    2013-01-01

    Restoration of anterior guidance is a major challenge to the clinician in planning of all restorative treatments. An accurate anterior guidance is important for proper function, aesthetics, comfort and phonetics. This article describes anterior rehabilitation of a patient who met with a road traffic accident and lost his anterior teeth. Anterior guidance developed in the provisional restorations was accurately recorded in the customised incisal guide table and permanent restorations were fabricated accordingly. PMID:23709546

  9. Mini incision open pyeloplasty - Improvement in patient outcome

    Directory of Open Access Journals (Sweden)

    Vishwajeet Singh

    2015-10-01

    Full Text Available ABSTRACT Purpose: To assess the subjective and objective outcomes of mini-incision dismembered Anderson-Hynes pyeloplasty in the treatment of primary ureteropelvic junction obstruction (UPJO. Materials and Methods: Between January 2008 to January 2013, Anderson-Hynes pyeloplasty was performed in 71 patients diagnosed with primary UPJO. Small subcostal muscle splitting incision was used in all cases. Sixteen patients with renal calculi underwent concomitant pyelolithotomy. Subjective outcome was assessed using visual pain analogue score (VAS. For objective assessment, the improvement in differential renal function (DRF and radio-tracer wash out time (T1/2 on Tc-99m DTPA scan and decrease in hydronephrosis (HDN on renal ultrasound (USG and urography (IVU were assessed. Results: Mean incision length was 5.2 cm. The average operating time and postoperative hospital stay was 63 (52-124 minutes and 2.5 (2–6 days respectively. Concomitant renal calculi were successfully removed in all the patients. Overall complication rates were 8.4% and overall success rate was 98.6% at median follow-up of 16 months. There was significant improvement in pain score (p=0.0001 and significant decrease in HDN after the procedure. While preoperative mean T1/2 was 26.7±6.4 minutes, postoperative half-time decreased to 7.8±4.2 minutes at 6 months and to 6.7±3.3 minutes at 1 year. Mean pre-operative DRF was 26.45% and it was 31.38% and 33.19% at 6 months and 1 year respectively. Conclusions: Mini-incision pyeloplasty is a safe and effective technique with combined advantage of high success rates of standard open pyeloplasty with decreased morbidity of laparoscopic approach. Excellent functional and objective outcomes can be achieved without extra technical difficulty.

  10. Single incision laparoscopic hepatectomy: Advances in laparoscopic liver surgery.

    Science.gov (United States)

    Tayar, Claude; Claude, Tayar; Subar, Daren; Daren, Subar; Salloum, Chady; Chady, Salloum; Malek, Alexandre; Alexandre, Malek; Laurent, Alexis; Alexis, Laurent; Azoulay, Daniel; Daniel, Azoulay

    2014-01-01

    Laparoscopic liver surgery is now an established practice in many institutions. It is a safe and feasible approach in experienced hands. Single incision laparoscopic surgery (SILS) has been performed for cholecystectomies, nephrectomies, splenectomies and obesity surgery. However, the use of SILS in liver surgery has been rarely reported. We report our initial experience in seven patients on single incision laparoscopic hepatectomy (SILH). From October 2010 to September 2012, seven patients underwent single-incision laparoscopic liver surgery. The abdomen was approached through a 25 mm periumbilical incision. No supplemental ports were required. The liver was transected using a combination of LigaSure™ (Covidien-Valleylab. Boulder. USA), Harmonic Scalpel and Ligaclips (Ethicon Endo-Surgery, Inc.). Liver resection was successfully completed for the seven patients. The procedures consisted of two partial resections of segment three, two partial resections of segment five and three partial resections of segment six. The mean operative time was 98.3 min (range: 60-150 min) and the mean estimated blood loss was 57 ml (range: 25-150 ml). The postoperative courses were uneventful and the mean hospital stay was 5.1 days (range: 1-13 days). Pathology identified three benign and four malignant liver tumours with clear margins. SILH is a technically feasible and safe approach for wedge resections of the liver without oncological compromise and with favourable cosmetic results. This surgical technique requires relatively advanced laparoscopic skills. Further studies are needed to determine the potential advantages of this technique, apart from the better cosmetic result, compared to the conventional laparoscopic approach.

  11. 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 ...

  12. Single incision laparoscopic hepatectomy: Advances in laparoscopic liver surgery

    Directory of Open Access Journals (Sweden)

    Tayar Claude

    2014-01-01

    Full Text Available Background: Laparoscopic liver surgery is now an established practice in many institutions. It is a safe and feasible approach in experienced hands. Single incision laparoscopic surgery (SILS has been performed for cholecystectomies, nephrectomies, splenectomies and obesity surgery. However, the use of SILS in liver surgery has been rarely reported. We report our initial experience in seven patients on single incision laparoscopic hepatectomy (SILH. Patients and Methods: From October 2010 to September 2012, seven patients underwent single-incision laparoscopic liver surgery. The abdomen was approached through a 25 mm periumbilical incision. No supplemental ports were required. The liver was transected using a combination of LigaSure TM (Covidien-Valleylab. Boulder. USA, Harmonic Scalpel and Ligaclips (Ethicon Endo-Surgery, Inc.. Results: Liver resection was successfully completed for the seven patients. The procedures consisted of two partial resections of segment three, two partial resections of segment five and three partial resections of segment six. The mean operative time was 98.3 min (range: 60-150 min and the mean estimated blood loss was 57 ml (range: 25-150 ml. The postoperative courses were uneventful and the mean hospital stay was 5.1 days (range: 1-13 days. Pathology identified three benign and four malignant liver tumours with clear margins. Conclusion: SILH is a technically feasible and safe approach for wedge resections of the liver without oncological compromise and with favourable cosmetic results. This surgical technique requires relatively advanced laparoscopic skills. Further studies are needed to determine the potential advantages of this technique, apart from the better cosmetic result, compared to the conventional laparoscopic approach.

  13. Endoscope-assisted transoral thyroidectomy using a frenotomy incision.

    Science.gov (United States)

    Woo, Seung Hoon

    2014-05-01

    Natural orifice translumenal endoscopic surgery (NOTES(®); American Society for Gastrointestinal Endoscopy [Oak Brook, IL] and Society of American Gastrointestinal and Endoscopic Surgeons [Los Angeles, CA]) has generated excitement among surgeons as potentially scar-free surgery. We developed this technique while taking into consideration that it could also be applied to transoral thyroid surgery. We report the case of a 35-year-old woman with a 0.5×0.5-cm papillary thyroid microcarcinoma. We implemented a modified approach for the removal of the thyroid by using a frenotomy incision of the mouth, accompanied by an endoscope system. A modified approach for the removal of the thyroid was used on the patient. The total operating time was 120 minutes, and there were no specific complications. The patient continues to be free of any diseases 12 months after the excision. Thyroidectomy can be performed by a transoral endoscope-assisted approach through a frenotomy incision of the mouth. We describe the detailed procedures for an endoscope-assisted transoral thyroidectomy using a frenotomy incision.

  14. 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

  15. 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

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

    Science.gov (United States)

    Moore, Elaine Ann; Xu, Yao-Zhong

    2017-01-01

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

  17. 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.

  18. The bacterial DnaA-trio replication origin element specifies single-stranded DNA initiator binding.

    Science.gov (United States)

    Richardson, Tomas T; Harran, Omar; Murray, Heath

    2016-06-16

    DNA replication is tightly controlled to ensure accurate inheritance of genetic information. In all organisms, initiator proteins possessing AAA+ (ATPases associated with various cellular activities) domains bind replication origins to license new rounds of DNA synthesis. In bacteria the master initiator protein, DnaA, is highly conserved and has two crucial DNA binding activities. DnaA monomers recognize the replication origin (oriC) by binding double-stranded DNA sequences (DnaA-boxes); subsequently, DnaA filaments assemble and promote duplex unwinding by engaging and stretching a single DNA strand. While the specificity for duplex DnaA-boxes by DnaA has been appreciated for over 30 years, the sequence specificity for single-strand DNA binding has remained unknown. Here we identify a new indispensable bacterial replication origin element composed of a repeating trinucleotide motif that we term the DnaA-trio. We show that the function of the DnaA-trio is to stabilize DnaA filaments on a single DNA strand, thus providing essential precision to this binding mechanism. Bioinformatic analysis detects DnaA-trios in replication origins throughout the bacterial kingdom, indicating that this element is part of the core oriC structure. The discovery and characterization of the novel DnaA-trio extends our fundamental understanding of bacterial DNA replication initiation, and because of the conserved structure of AAA+ initiator proteins these findings raise the possibility of specific recognition motifs within replication origins of higher organisms.

  19. 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...

  20. 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)

  1. 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

  2. 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.

  3. A DNA 3′-phosphatase functions in active DNA demethylation in Arabidopsis

    OpenAIRE

    Martínez-Macías, María Isabel; Qian, Weiqiang; Miki, Daisuke; Pontes, Olga; Liu, Yunhua; Tang, Kai; Liu, Renyi; Morales-Ruiz, Teresa; Ariza, Rafael R.; Roldán-Arjona, Teresa; Zhu, Jian-Kang

    2012-01-01

    DNA methylation is an important epigenetic mark established by the combined actions of methylation and demethylation reactions. Plants use a base excision repair pathway for active DNA demethylation. After 5-methylcytosine removal, the Arabidopsis DNA glycosylase/lyase ROS1 incises the DNA backbone and part of the product has a single-nucleotide gap flanked by 3′- and 5′-phosphate termini. Here we show that the DNA phosphatase ZDP removes the blocking 3′-phosphate, allowing subsequent DNA pol...

  4. Weld failure analysis of 2205 duplex stainless steel nozzle

    Directory of Open Access Journals (Sweden)

    Jingqiang Yang

    2014-10-01

    Full Text Available Failure analyses of weld joint between the nozzle and the head of the reactor made of 2205 duplex stainless steel was performed by optical microscopy (OM and scanning electron microscopy (SEM. Cracks were found in HAZ of the weld. The depth of the cracks is equal to the thickness of the inner weld. Localized uneven distribution of ferrite/austenite with 80–90% ferrite in weld is found. Results show that the cracks occurred along columnar granular with cleavage fracture. Poor weld process probably results in these cracks.

  5. Weld failure analysis of 2205 duplex stainless steel nozzle

    OpenAIRE

    Jingqiang Yang; Qiongqi Wang; Zhongkun Wei; Kaishu Guan

    2014-01-01

    Failure analyses of weld joint between the nozzle and the head of the reactor made of 2205 duplex stainless steel was performed by optical microscopy (OM) and scanning electron microscopy (SEM). Cracks were found in HAZ of the weld. The depth of the cracks is equal to the thickness of the inner weld. Localized uneven distribution of ferrite/austenite with 80–90% ferrite in weld is found. Results show that the cracks occurred along columnar granular with cleavage fracture. Poor weld process pr...

  6. The Terahertz Controlled Duplex Isolator: Physical Grounds and Numerical Experiment

    Directory of Open Access Journals (Sweden)

    Konstantin Vytovtov

    2016-01-01

    Full Text Available Electromagnetic properties of an anisotropic stratified slab with an arbitrary orientation of the anisotropy axis under an oblique incidence of a plane harmonic wave are studied. The dependence of the eigenwave wavenumbers and the reflection coefficient on an anisotropy axis orientation and frequency is investigated. For the first time, the expression for the translation matrix is obtained in the compact analytical form. The controlled two-way dual-frequency (duplex isolator based on the above described slab is presented for the first time. It is based on the properties of the anisotropic structure described here but not on the Faraday effect.

  7. 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...

  8. 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.

  9. 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.)

  10. 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....

  11. Complexities due to single-stranded RNA during antibody detection of genomic rna:dna hybrids.

    Science.gov (United States)

    Zhang, Zheng Z; Pannunzio, Nicholas R; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R

    2015-04-08

    Long genomic R-loops in eukaryotes were first described at the immunoglobulin heavy chain locus switch regions using bisulfite sequencing and functional studies. A mouse monoclonal antibody called S9.6 has been used for immunoprecipitation (IP) to identify R-loops, based on the assumption that it is specific for RNA:DNA over other nucleic acid duplexes. However, recent work has demonstrated that a variable domain of S9.6 binds AU-rich RNA:RNA duplexes with a KD that is only 5.6-fold weaker than for RNA:DNA duplexes. Most IP protocols do not pre-clear the genomic nucleic acid with RNase A to remove free RNA. Fold back of ssRNA can readily generate RNA:RNA duplexes that may bind the S9.6 antibody, and adventitious binding of RNA may also create short RNA:DNA regions. Here we investigate whether RNase A is needed to obtain reliable IP with S9.6. As our test locus, we chose the most well-documented site for kilobase-long mammalian genomic R-loops, the immunoglobulin heavy chain locus (IgH) class switch regions. The R-loops at this locus can be induced by using cytokines to stimulate transcription from germline transcript promoters. We tested IP using S9.6 with and without various RNase treatments. The RNase treatments included RNase H to destroy the RNA in an RNA:DNA duplex and RNase A to destroy single-stranded (ss) RNA to prevent it from binding S9.6 directly (as duplex RNA) and to prevent the ssRNA from annealing to the genome, resulting in adventitious RNA:DNA hybrids. We find that optimal detection of RNA:DNA duplexes requires removal of ssRNA using RNase A. Without RNase A treatment, known regions of R-loop formation containing RNA:DNA duplexes can not be reliably detected. With RNase A treatment, a signal can be detected over background, but only within a limited 2 or 3-fold range, even with a stable kilobase-long genomic R-loop. Any use of the S9.6 antibody must be preceded by RNase A treatment to remove free ssRNA that may compete for the S9.6 binding by

  12. 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.

  13. One-incision versus two-incision techniques for arthroscopically assisted anterior cruciate ligament reconstruction in adults.

    Science.gov (United States)

    Rezende, Fernando C; Moraes, Vinícius Y; Franciozi, Carlos Es; Debieux, Pedro; Luzo, Marcus V; Belloti, João Carlos

    2017-12-15

    Anterior cruciate ligament (ACL) tears are serious knee injuries that are frequently treated surgically in the form of arthroscopically assisted reconstruction with grafts from the patella or hamstrings tendons. We reviewed the evidence for the choice of arthroscopically assisted ACL reconstruction technique in terms of whether it should involve one incision (femoral tunnel drilled from inside the knee joint under arthroscopic visualisation) or two incisions (femoral tunnel drilled from outside to inside the knee joint). To assess the effects (benefits and harms) of one-incision versus two-incision techniques for arthroscopically assisted ACL reconstruction in adults. We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, Latin American and Caribbean Health Sciences (LILACS), the World Health Organization International Clinical Trials Registry Platform, ClinicalTrials.gov, reference lists, and conference abstracts. The date of the search was 16 August 2017. Randomised and quasi-randomised controlled clinical trials evaluating one-incision versus two-incision techniques for arthroscopically assisted ACL reconstruction in adults. Two review authors independently searched and selected studies, and extracted data and assessed the risk of bias of the eligible studies. We undertook limited pooling of data using the fixed-effect model. We included five trials (four randomised and one quasi-randomised) evaluating a total of 320 participants who were mainly in their 20s. All participants underwent ACL reconstruction with patella tendon grafts. All five included trials were at a high risk of bias, particularly performance bias. Based on these limitations and the insufficiency of the available data resulting in imprecision of effect estimates, we judged the quality of the evidence as very low for all outcomes. This means that we are uncertain of the findings of the

  14. Detection of Ultra-Rare Mitochondrial Mutations in Breast Stem Cells by Duplex Sequencing

    Science.gov (United States)

    Ahn, Eun Hyun; Hirohata, Kensen; Kohrn, Brendan F.; Fox, Edward J.; Chang, Chia-Cheng; Loeb, Lawrence A.

    2015-01-01

    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. PMID:26305705

  15. 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.

  16. Throughput Analysis of Full Duplex Communication with Asymmetric Traffic in Small Cell Systems

    DEFF Research Database (Denmark)

    Mahmood, Nurul Huda; Berardinelli, Gilberto; Mogensen, Preben Elgaard

    2015-01-01

    Full duplex communication promises a 100% throughput gain by enabling simultaneous transmission and reception. However, such simultaneous communication leads to a corresponding increase in the network interference. In addition, full duplex communication can only be exploited when traffic...... is available in both uplink and downlink directions; while, cellular network traffic tend to be downlink heavy in practice. The potential throughput gains of full duplex communication over conventional half duplex transmission in a small cell network with asymmetric traffic conditions are investigated...... in this contribution using network analysis tools from stochastic geometry. The analytical findings are further confirmed through computer-based Monte-Carlo simulations. Asymmetric downlink/uplink traffic pattern and the increased network interference stemming from full duplex transmissions are found to limit its...

  17. 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.

  18. 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...

  19. A model of EcoRII restriction endonuclease action: the active complex is most likely formed by one protein subunit and one DNA recognition site

    Science.gov (United States)

    Karpova, E. A.; Kubareva, E. A.; Shabarova, Z. A.

    1999-01-01

    To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'. All binding substrate or substrate analogues tested could be divided into two major groups: (i) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type of complex, observed both in the presence and absence of Mg2+. Unlike the latter, duplexes under the first group can be hydrolyzed by endonuclease. Data obtained suggest that the active complex is most likely formed by one protein subunit and one DNA recognition sequence. A model of EcoRII endonuclease action is presented.

  20. Bio-recognitive photonics of a DNA-guided organic semiconductor

    OpenAIRE

    Back, Seung Hyuk; Park, Jin Hyuk; Cui, Chunzhi; Ahn, Dong June

    2016-01-01

    Incorporation of duplex DNA with higher molecular weights has attracted attention for a new opportunity towards a better organic light-emitting diode (OLED) capability. However, biological recognition by OLED materials is yet to be addressed. In this study, specific oligomeric DNA?DNA recognition is successfully achieved by tri (8-hydroxyquinoline) aluminium (Alq3), an organic semiconductor. Alq3 rods crystallized with guidance from single-strand DNA molecules show, strikingly, a unique distr...

  1. 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.

  2. Effect of dual torch technique on duplex stainless steel welds

    International Nuclear Information System (INIS)

    Sun, Z.; Kuo, M.; Annergren, I.; Pan, D.

    2003-01-01

    Duplex stainless steels are characterized by balanced ferrite/austenite microstructures and are well known for their superior corrosion resistance and higher strength compared with the common austenitic stainless steels. One major concern, however, is that welding might degrade the corrosion resistance by producing unbalanced phase content, detrimental precipitates, and possible embrittlement of the weldment. In this paper, a dual-torch arc welding technique (plasma torch followed by a gas tungsten arc (GTA) torch) was proposed. Effects of the dual-torch technique on the microstructural changes and corrosion properties were investigated. The preliminary study indicated that a correlation between the welding parameters and the microstructural changes and corrosion resistance existed. It was found that the corrosion rate increases with increasing torch pitch and/or decreasing GTA welding current. By adjusting the distance between the torches, modification of weld microstructure may be realized. Although further studies are required to fine-tune the technique, the present study demonstrated the potential of using dual torch technique to improve weldability of duplex stainless steels

  3. 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.

  4. 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.

  5. Pressure Irrigation of Surgical Incisions and Traumatic Wounds.

    Science.gov (United States)

    Fry, Donald E

    Pressure irrigation of surgical incisions and traumatic wounds is commonly used to prevent infections. Commercial pressure irrigation devices have proliferated rapidly, but scientific validation of clinical benefit or appropriate use remains uncertain. The published experimental and clinical investigations of pressure irrigation have been reviewed since the introduction of the Waterpik device in 1967 to identify the evidence for use to prevent soft tissue infections associated with injury wounds or surgical incisions. The published literature favors low pressure irrigation between 5-15 pounds/square inch (psi) for experimental removal of bacteria from contaminated tissues, with pressures higher being associated with soft tissue and bone injury. No experimental or clinical data have demonstrated improved benefit from pulsed over continuous lavage. Clinical studies have been very heterogeneous in patient populations and study design; meta-analysis was not feasible. High-risk abdominal operations may have lower surgical site infection rates with pressure irrigation. Pressure irrigation in fractures and joint replacement surgery has shown mixed results. The largest multi-center randomized trial showed no benefit of pulsed (8-10 psi) lavage over conventional continuous gravity irrigation of open fractures. Experimental studies have shown effective removal of bacteria and contamination, but with a potential risk of tissue injury or displacement of contamination deeper into the soft tissues. Rigorous clinical documentation has not validated the optimum flow or pressure characteristics of pressure lavage in clinical practice. There is need for randomized clinical trials to validate pressure lavage in the prevention of infections in soft tissue injuries or high-risk surgical incisions.

  6. Single transverse extended incision for radical neck dissection

    Directory of Open Access Journals (Sweden)

    José Francisco Sales Chagas

    Full Text Available ABSTRACT Objective: to assess the efficacy of the single transverse extended cervical incision in radical neck dissection. Method: we conducted a prospective study, from January 2008 to January 2009, with 18 patients undergoing surgical treatment of malignant tumors of the upper aero-digestive tract. The primary lesion was located in the oral cavity in eight cases, in the oropharynx in three, in the hypopharynx in three, in the larynx in two, in the maxillary sinus, and in one case, the primary injury was hidden. There were 29 neck dissections, eight bilateral and 10 unilateral (26 radical and three selective. Staging revealed nine patients with T4 tumor, one T3, six T2, one T1 and one Tx. Five patients were N0, nine N2b, one N2c and three N3. The average number of dissected lymph nodes was 34.25. We performed the neck dissection through a single incision located in the middle neck, coincident with the skinfold, with a length of about 2 to 3 cm behind the anterior edge of the trapezius muscle and 3 to 4 cm from the midline for the unilateral neck dissections. Results: as complications, there were myocutaneous flap necrosis in one patient with prior radiation therapy, one lymphatic fistula, one dehiscence of the tracheostomy, one cervical abscess, one salivary fistula and one suture dehiscence. Conclusions: the single extended incision provides adequate exposure of the neck structures, without compromising surgical time, even in bilateral dissections. It does not compromise the resection of all cervical lymph nodes; it has excellent aesthetic and functional results and is easily associated with other approaches to resection of the primary tumor.

  7. 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.

  8. 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

  9. 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.

  10. A case of endophthalmitis associated with limbal relaxing incision

    Directory of Open Access Journals (Sweden)

    Aravind Haripriya

    2012-01-01

    Full Text Available Limbal relaxing incisions (LRIs are considered a relatively safe procedure with rapid stabilization and absence of infectious complications. Do we need to readdress this last impression? We report a case of nocardia endophthalmitis associated with an exudate at the site of an LRI in a patient who underwent routine cataract surgery. This case, to the best of our knowledge, is the first report of its kind, stressing the need for a cautious approach to the adoption of this method of astigmatic correction.

  11. [Preliminary clinical experience of single incision laparoscopic colorectal surgery].

    Science.gov (United States)

    Wu, S D; Han, J Y

    2016-06-01

    Objective: To discuss the preliminary experience of single incision laparoscopic colorectal surgery. Methods: The clinical data and surgical outcomes of 104 selected patients who underwent single incision laparoscopic colorectal surgery in the 2 nd Department of General Surgery, Shengjing Hospital of China Medical University from January 2010 to September 2015 were retrospectively analyzed. There were 62 male and 42 female patients, aging from 21 to 87 years with a mean of (61±12) years. Eighty-five patients were diagnosed with malignancy while the rest 19 cases were benign diseases. All the procedures were performed by the same surgeon using the rigid laparoscopic instruments. Surgical and oncological outcomes were analyzed in 4 kinds of procedures which are over 5 cases respectively, including low anterior resection, abdominoperineal resection, radical right colon resection and radical sigmoidectomy. Results: Single incision laparoscopic colorectal surgery was performed in 104 selected patients and was successfully managed in 99 cases with a total conversion rate of 4.8%. Radical procedures for malignancy in cases with the number of patients more than 5 were performed for 74 cases. For low anterior resection, 35 cases with an average surgical time of (191±57) minutes, average estimated blood loss of (117±72) ml and average number of harvested lymph nodes of 14.6±1.1. For abdominoperineal resection, 9 cases with an average surgical time of (226±54) minutes, average estimated blood loss of (194±95) ml and average number of harvested lymph nodes of 14.1±1.5. For radical right colon resection, 16 cases with an average surgical time of (222±62) minutes, average estimated blood loss of (142±68) ml and average number of harvested lymph nodes of 15.4±2.4. For radical sigmoidectomy, 14 cases with an average surgical time of (159±32) minutes, average estimated blood loss of (94±33) ml and average number of harvested lymph nodes of 13.9±1.5. The overall

  12. 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

  13. 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.

  14. Characterization of Interstrand DNA-DNA Cross-Links Using the α-Hemolysin Protein Nanopore.

    Science.gov (United States)

    Zhang, Xinyue; Price, Nathan E; Fang, Xi; Yang, Zhiyu; Gu, Li-Qun; Gates, Kent S

    2015-12-22

    Nanopore-based sensors have been studied extensively as potential tools for DNA sequencing, characterization of epigenetic modifications such as 5-methylcytosine, and detection of microRNA biomarkers. In the studies described here, the α-hemolysin protein nanopore embedded in a lipid bilayer was used for the detection and characterization of interstrand cross-links in duplex DNA. Interstrand cross-links are important lesions in medicinal chemistry and toxicology because they prevent the strand separation that is required for read-out of genetic information from DNA in cells. In addition, interstrand cross-links are used for the stabilization of duplex DNA in structural biology and materials science. Cross-linked DNA fragments produced unmistakable current signatures in the nanopore experiment. Some cross-linked substrates gave irreversible current blocks of >10 min, while others produced long current blocks (10-100 s) before the double-stranded DNA cross-link translocated through the α-hemolysin channel in a voltage-driven manner. The duration of the current block for the different cross-linked substrates examined here may be dictated by the stability of the duplex region left in the vestibule of the nanopore following partial unzipping of the cross-linked DNA. Construction of calibration curves measuring the frequency of cross-link blocking events (1/τon) as a function of cross-link concentration enabled quantitative determination of the amounts of cross-linked DNA present in samples. The unique current signatures generated by cross-linked DNA in the α-HL nanopore may enable the detection and characterization of DNA cross-links that are important in toxicology, medicine, and materials science.

  15. Definitive differentiation between single and mixed mycobacterial infections in red deer (Cervus elaphus) by a combination of duplex amplification of p34 and f57 sequences and Hpy188I enzymatic restriction of duplex amplicons.

    Science.gov (United States)

    Godfroid, Jacques; Delcorps, Cathy; Irenge, Leonid M; Walravens, Karl; Marché, Sylvie; Gala, Jean-Luc

    2005-09-01

    Severe emaciation and mortalities suggestive of mycobacterial infections were recently reported for both adult and young wild red deer (Cervus elaphus) in the southeastern part of Belgium. In deer, tuberculous lesions are not pathognomonic of Mycobacterium bovis infection due to gross and microscopic similarities with lesions caused by Mycobacterium avium subsp. paratuberculosis or M. avium subsp. avium. The aim of this study was to improve molecular methods for the species-specific identification of M. bovis, M. avium subsp. avium, and M. avium subsp. paratuberculosis in mycobacterial infections of deer. DNA banding patterns were assessed prior to and after Hpy188I restriction of f57-upstream (us)-p34 duplex amplicons. The duplex f57-us-p34 PCR differentiated M. bovis from M. avium subsp. paratuberculosis and M. avium subsp. avium infections, whereas the restriction step differentiated single M. avium subsp. paratuberculosis or M. avium subsp. avium infections from mixed M. avium subsp. paratuberculosis/M. avium subsp. avium infections. The endonuclease Hpy188I cleaves DNA between nucleotides N and G in the unique TCNGA sequence. This restriction site was found at position 168 upstream of the us-p34 initiation codon in all M. avium subsp. avium strains tested, regardless of their origin and the results of IS901 PCR. In contrast, the restriction site was abrogated in all M. avium subsp. paratuberculosis strains tested, independent of their origin, Mycobactin J dependency, and IS900 PCR results. Consequently, a two-step strategy, i.e., duplex us-p34-f57 PCR and Hpy188I restriction, allowed us to exclude M. bovis infection and to identify single (M. avium subsp. paratuberculosis or M. avium subsp. avium) or mixed (M. avium subsp. paratuberculosis/M. avium subsp. avium) infections in wild red deer in Belgium. Accordingly, we propose to integrate, in a functional molecular definition of M. avium subsp. paratuberculosis, the absence of the Hpy188I restriction site from

  16. 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.

  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. 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.

  19. 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

  20. Thermal and electrochemical gate effects on DNA conductance

    International Nuclear Information System (INIS)

    Hihath, Joshua; Chen Fang; Zhang Peiming; Tao Nongjian

    2007-01-01

    In an attempt to understand the complexities of DNA charge transport we have used a scanning tunnelling microscope break junction to repeatedly form a large number of Au-DNA-Au junctions. The DNA is covalently bound to the Au electrodes via gold-thiol bonds, and all measurements are carried out in an aqueous buffer solution to maintain a biological conformation of the duplex. A statistical analysis is carried out to determine the conductance of a single DNA duplex. Previously, we have seen an algebraic dependence of the conductance on length, suggesting a hopping mechanism. To attempt to verify this as the conduction mechanism we have changed the solution temperature and applied an electrochemical gate to the molecular junction to help elucidate the charge transport properties. In an alternating GC sequence with a length of eight base pairs, neither the temperature nor the gate potential caused a significant change in the conductance within the available experimental window

  1. Thermal and electrochemical gate effects on DNA conductance

    Energy Technology Data Exchange (ETDEWEB)

    Hihath, Joshua [Department of Electrical Engineering and Center for Solid State Electronics Research, Arizona State University, Tempe, AZ 85287 (United States); Chen Fang [Department of Electrical Engineering and Center for Solid State Electronics Research, Arizona State University, Tempe, AZ 85287 (United States); Zhang Peiming [Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Tao Nongjian [Department of Electrical Engineering and Center for Solid State Electronics Research, Arizona State University, Tempe, AZ 85287 (United States)

    2007-05-30

    In an attempt to understand the complexities of DNA charge transport we have used a scanning tunnelling microscope break junction to repeatedly form a large number of Au-DNA-Au junctions. The DNA is covalently bound to the Au electrodes via gold-thiol bonds, and all measurements are carried out in an aqueous buffer solution to maintain a biological conformation of the duplex. A statistical analysis is carried out to determine the conductance of a single DNA duplex. Previously, we have seen an algebraic dependence of the conductance on length, suggesting a hopping mechanism. To attempt to verify this as the conduction mechanism we have changed the solution temperature and applied an electrochemical gate to the molecular junction to help elucidate the charge transport properties. In an alternating GC sequence with a length of eight base pairs, neither the temperature nor the gate potential caused a significant change in the conductance within the available experimental window.

  2. [Duplex real-time PCR assay for rapid detection of E. coli O157 and E. coli O104 in the legume plants and its products].

    Science.gov (United States)

    Zhao, Xiaomei; Zhao, Guiming; Wang, Ping; Chen, Ying; Jiao, Yanchao; Luo, Adong

    2016-03-01

    To establish a rapid assay to detect enterohemorrhagic Escherichia coli O157 (E. coli O157) and enterohemorrhagic Escherichia coli O104 (E. coli O104) in the legume plants and its products by using the duplex real-time PCR. Based on part fragments of E. coli O157 specific gene rfbE and E. coli O104 specific gene wzy, primers and Taq-Man probes were designed. Results DNA (Q157): DNA (O104) = 1 : 3, DNA 2 μL, Master Mix 12.5 μL, primers (10 μmol/L) 1 μL,Taq-Man probes( 10 μmol/L) 0.5 μL, ddH2O 25 μL. The two pathogens could be detected in one reaction system, the lowest limit of detection sensitivity was 10(2) CFU/mL(g). This method is rapid and convenient, with good specificity, high sensitivity. The duplex real-time PCR assay could provide a cost-effective and convenient method for detect foodborne pathogenic bacteria.

  3. Single Incision Laparoscopic Cholecystectomy vs Conventional Cholecystectomy in Developing Country

    Directory of Open Access Journals (Sweden)

    P B Thapa

    2010-09-01

    Full Text Available INTRODUCTION: Use of laparoscopic surgery has demanded principles of less trauma of access hence less scar and so probably less complications. Hence conventional laparoscopic surgeries were tried with natural orifice transluminal surgery (NOTES and then single incision laparoscopic surgery (SILS. With refinement in instruments and surgeons skills SILS have bridged up between conventional and NOTES in order to quench the desire of less or no scar at all. METHODS: Comparative case control study between conventional laparoscopic cholecystectomy and SILS in public teaching hospital. RESULTS: Total 20 patients underwent SILS cholecystectomy and 20 underwent conventional cholecystectomy and found that no difference between both in terms of post operative pain score, hospital stay and post operative wound infection except significant difference in mean operative time and patient's level of satisfaction was less in patient with SILC if were subjected to pay for instruments in order to maintain cosmesis. CONCLUSIONS: Though SILS have gained rapid acceptance in surgical fraternity, large number of randomized controlled trials are necessary to show its benefit over conventional laparoscopic cholecystectomy. Keywords: cholecystectomy, conventional, laparoscopy, single incision, surgery

  4. Single-incision laparoscopic surgery for diverticulitis in overweight patients.

    Science.gov (United States)

    Rink, Andreas D; Vestweber, Boris; Hahn, Jasmina; Alfes, Angelika; Paul, Claudia; Vestweber, Karl-Heinz

    2015-10-01

    Single-incision laparoscopic surgery (SILS) has been introduced as a new technique for the treatment of various colorectal diseases. Recurrent or complicated diverticulitis of the sigmoid colon is a frequent indication for minimally invasive sigmoid colectomy. The aim of this study was to investigate the impact of obesity on the outcome of SILS sigmoid colectomy. From September 2009 to October 2014, data from 377 patients who had intended SILS sigmoid colectomy for diverticulitis at our institution were collected in a prospective database. The patients were categorized in the following subgroups: group 1 (normal weight, body mass index (BMI)  35 kg/m(2)). The groups were equivalent for sex, age, status of diverticulitis, the presence of acute inflammation in the specimen, and the percentage of teaching operations, but the percentage of patients with accompanying diseases was significantly more frequent in groups 2, 3, and 4 (p = 0.04, 0.008, and 0.018, respectively). As compared to group 1, the conversion rate was significantly increased in groups 2 and 4 (2.3 vs. 9.3% (p = 0.013) and 2.3 vs. 12.5% (p = 0.017), respectively). The duration of surgery, hospitalization, and morbidity did not differ between the four groups. Up to a body mass index of 35 kg/m(2), increased body weight does not significantly reduce the feasibility and outcome of single-incision laparoscopic surgery for diverticulitis.

  5. 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.

  6. Unilateral corneal ectasia following small-incision lenticule extraction.

    Science.gov (United States)

    Sachdev, Gitansha; Sachdev, Mahipal S; Sachdev, Ritika; Gupta, Hemlata

    2015-09-01

    We describe a case of unilateral corneal ectasia in a 26-year-old man following small-incision lenticule extraction. The preoperative corneal topography was normal, with a minimum corneal thickness of 511 μm and 513 μm in the right eye and left eye, respectively. Lenticules of 85 μm and 82 μm were fashioned to offer a refractive correction of -3.75 -1.50 × 180 and -3.50 -1.50 × 165 in the right eye and left eye, respectively. Twelve months after small-incision lenticule extraction, the patient presented with early signs of ectasia in the left eye on corneal topography, which had worsened at the 18-month examination. Intrastromal corneal ring segment implantation with corneal collagen crosslinking was performed to arrest further progression and to improve uncorrected distance visual acuity. On the last examination, the corrected distance visual acuity was 20/20(-2). Dr. Mahipal S. Sachdev receives travel grants from Carl Zeiss Meditec AG. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2015 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  7. Endoscopy-assisted cerebral falx incision via unilateral

    Directory of Open Access Journals (Sweden)

    DONG Ji-rong

    2012-04-01

    Full Text Available 【Abstract】Objective: To investigate the clinical features and treatment strategy of dissymmetric bilateral frontal contusion, and to summarize our experience in treat-ing these patients by minimally invasive surgery. Methods: Over the past 3 years, we have treated a total of 31 patients with dissymmetric bilateral frontal contusion using endoscopy-assisted unilateral cerebral falx incision. Other 30 patients treated by routine bilateral approaches within the same period were taken as control. Results: Seventeen cases (54.8% in the unilateral operation group survived and were in good condition, 8 (25.8% had moderate disability, 4 (12.9% had severe disability, 1 (3.2% was in vegetative state, and 1 (3.2% died. Compared with the control group, the Glasgow Out-come Scale score was not significantly different in the uni-lateral operation group, but the operation time, blood trans-fusion volume, the length of hospital stay, the incidences of mental disorder and olfactory nerve injury were greatly reduced in the unilateral operation group. Conclusions: Endoscopy-assisted unilateral cerebral falx incision can shorten the operation time, reduce surgical trauma and complications in treatment of patients with dis-symmetric bilateral frontal contusion. It can obviously di-minish the chance of delayed intracerebral hematoma and subsequently minimize the incidences of subfalcial and centrencephalic herniation. Key words: Brain injuries; Intracranial hemorrage, traumatic; Endoscopy; Surgically procedures, minimally invasive

  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

    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

  10. 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.

  11. Influence of upper and temporal transconjunctival sclerocorneal incision on marginal reflex distance after cataract surgery

    OpenAIRE

    Tamaki, Rikiya; Gosho, Masahiko; Mizumoto, Kyoichi; Kato, Nahoko; Zako, Masahiro

    2016-01-01

    Background Ptosis incidence following cataract surgery is reduced with a recently developed phacoemulsification technique using a small incision. However, it remains uncertain whether an upper transconjunctival sclerocorneal incision can cause minor blepharoptosis. In the present prospective study, patients underwent cataract surgery with either an upper or temporal 2.4-mm transconjunctival sclerocorneal incision. We measured the marginal reflex distance 1 (MRD1) preoperatively and postoperat...

  12. 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

  13. Autogenic entrenchment patterns and terraces due to coupling with lateral erosion in incising alluvial channels

    Science.gov (United States)

    Malatesta, Luca C.; Prancevic, Jeffrey P.; Avouac, Jean-Philippe

    2017-01-01

    The abandonment of terraces in incising alluvial rivers can be used to infer tectonic and climatic histories. A river incising into alluvium erodes both vertically and laterally as it abandons fill-cut terraces. We argue that the input of sediment from the valley walls during entrenchment can alter the incision dynamics of a stream by promoting vertical incision over lateral erosion. Using a numerical model, we investigate how valley wall feedbacks may affect incision rates and terrace abandonment as the channel becomes progressively more entrenched in its valley. We postulate that erosion of taller valley walls delivers large pulses of sediment to the incising channel, potentially overwhelming the local sediment transport capacity. Based on field observations, we propose that these pulses of sediment can form talus piles that shield the valley wall from subsequent erosion and potentially force progressive channel narrowing. Our model shows that this positive feedback mechanism can enhance vertical incision relative to 1-D predictions that ignore lateral erosion. We find that incision is most significantly enhanced when sediment transport rates are low relative to the typical volume of material collapsed from the valley walls. The model also shows a systematic erosion of the youngest terraces when river incision slows down. The autogenic entrenchment due to lateral feedbacks with valley walls should be taken into account in the interpretation of complex-response terraces.

  14. Safety of cesarean delivery through placental incision in patients with anterior placenta previa.

    Science.gov (United States)

    Hong, Deok-Ho; Kim, Eugene; Kyeong, Kyu-Sang; Hong, Seung Hwa; Jeong, Eun-Hwan

    2016-03-01

    To demonstrate the safety of fetal delivery through placental incision in a placenta previa pregnancy. We examined the medical records of 80 women with singleton pregnancy diagnosed with placenta previa who underwent cesarean section between May 2010 and May 2015 at the Department of Obstetrics and Gynecology, Chungbuk National University Hospital. Among the women with placenta previa, those who did not have the placenta in the uterine incision site gave birth via conventional uterine incision, while those with anterior placenta previa or had placenta attached to the uterine incision site gave birth via uterine incision plus placental incision. We compared the postoperative hemoglobin level and duration of hospital stay for the mother and newborn of the two groups. There was no difference between the placental incision group and non-incision group in terms of preoperative and postoperative hemoglobin change, the amount of blood transfusions required by the mother, newborns with 1-min or 5-min Apgar scores below 7 points or showing signs of acidosis on umbilical cord blood gas analysis result of pH below 7.20. Moreover, neonatal hemoglobin levels did not differ between the two groups. Fetal delivery through placental incision during cesarean section for placenta previa pregnancy does not negatively influence the prognosis of the mother or the newborn, and therefore, is considered a safe surgical technique.

  15. A performance analysis in AF full duplex relay selection network

    Science.gov (United States)

    Ngoc, Long Nguyen; Hong, Nhu Nguyen; Loan, Nguyen Thi Phuong; Kieu, Tam Nguyen; Voznak, Miroslav; Zdralek, Jaroslav

    2018-04-01

    This paper studies on the relaying selective matter in amplify-and-forward (AF) cooperation communication with full-duplex (FD) activity. Various relay choice models supposing the present of different instant information are investigated. We examine a maximal relaying choice that optimizes the instant FD channel capacity and asks for global channel state information (CSI) as well as partial CSI learning. To make comparison easy, accurate outage probability clauses and asymptote form of these strategies that give a diversity rank are extracted. From that, we can see clearly that the number of relays, noise factor, the transmittance coefficient as well as the information transfer power had impacted on their performance. Besides, the optimal relay selection (ORS) model can promote than that of the partial relay selection (PRS) model.

  16. Cranial duplex sonography of the infant and neonate

    International Nuclear Information System (INIS)

    Grant, E.G.; White, E.M.; Schellinger, D.; Choyke, P.L.; Lane, P.E.; Sarcone, A.L.

    1986-01-01

    This study was implemented to assess the feasibility of using duplex sonography in imaging the infant brain and to evaluate flow patterns in healthy preterm infants, preterm infants with intracranial hemorrhage, healthy term infants, and hydrocephalics. In almost every subject the pericallosal, callosomarginal anterior cerebral, basilar, middle cerebral, and internal carotid arteries as well as the vein of Galen were evaluated. Ten patients from each of the four groups were evaluated. Evaluation of flow was undertaken using both absolute velocity values and pulsatility index. The most significant variable was gestational age; preterm infants tended to have much lower flow velocity than term infants. Term infants always exhibited diphasic flow patterns, whereas diastolic flow to zero was noted in a significant number of preterm infants. No preterm infants with and without intracranial hemorrhage were compared. Flow to zero during diastole was noted in both groups. Finally, no difference in flow was noted between hydrocephalic infants and healthy infants

  17. Technology of Welding Joints Mixed with Duplex Steel

    Directory of Open Access Journals (Sweden)

    Słania J.

    2016-03-01

    Full Text Available Results of the examinations of sample plates of mixed joints with the duplex steel were discussed. Examinations were taken on the sample plates of mixed joints of sheet plates type P355NL1 and X2CrNiMoN22-5-3 welded by the flux-cored wire DW-329A by the Kobelco company of the following category T 22 9 3 NL RC/M3 in the gas shroud M21 (Ar+18%CO2 (plate no.1, and nickel covered electrodes E Ni 6082 by the Böhler company (plate no. 2. Results of the side bend test of welded joint, transverse tensile test, stretching of the weld metal, impact strength, micro and macroscopic metallographic examinations, and measurements of the delta ferrite content were presented.

  18. Electromagnetic non-destructive technique for duplex stainless steel characterization

    Science.gov (United States)

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

    2016-02-01

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

  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. 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.

  1. Physical-Layer Security with Full-Duplex Transceivers and Multiuser Receiver at Eve

    DEFF Research Database (Denmark)

    Mahmood, Nurul Huda; Shafique Ansari, Imran; Popovski, Petar

    2017-01-01

    Full-duplex communication enables simultaneous transmission from both ends of a communication link, thereby promising significant performance gains. Generally, it has been shown that the throughput and delay gains of full-duplex communication are somewhat limited in realistic network settings......, leading researchers to study other possible applications that can accord higher gains. The potential of full-duplex communication in improving the physical-layer security of a communication link is investigated in this contribution. We specifically present a thorough analysis of the achievable ergodic...

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

    OpenAIRE

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

    2013-01-01

    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 d...

  3. Multicenter assessment of venous reflux by duplex ultrasound.

    Science.gov (United States)

    Lurie, Fedor; Comerota, Anthony; Eklof, Bo; Kistner, Robert L; Labropoulos, Nicos; Lohr, Joann; Marston, William; Meissner, Mark; Moneta, Gregory; Neglén, Peter; Neuhardt, Diana; Padberg, Frank; Welsh, Harold J

    2012-02-01

    This prospective multicenter investigation was conducted to define the repeatability of duplex-based identification of venous reflux and the relative effect of key parameters on the reproducibility of the test. Repeatability was studied by having the same technologist perform duplicate tests, at the same time of the day, using the same reflux-provoking maneuver and with the patient in the same position. Reproducibility was examined by having two different technologists perform the test at the same time of the day, using the same reflux-provoking maneuver and with the patient in the same position. Facilitated reproducibility was studied by having two different technologists examine the same patients immediately after an educational intervention. Limits of agreement between two duplex scans were studied by changing three elements of the test: time of the day (morning vs afternoon), patient's position (standing vs supine), and reflux initiation (manual vs automatic compression-decompression). The study enrolled 17 healthy volunteers and 57 patients with primary chronic venous disease. Repeatability of reflux time measurements in deep veins did not significantly differ with the time of day, the patient's position, or the reflux-provoking maneuver. Reflux measurements in the superficial veins were more repeatable (P ultrasound detection of venous reflux. Reports should include information on the time of the test, the patient's position, and the provoking maneuver used. Adopting a uniform cut point of 0.5 second for pathologic reflux can significantly improve the reliability of reflux detection. Implementation of a standard protocol should elevate the minimal standard for agreement between repeated tests from the current 70% to at least 80% and with more rigid standardization, to 90%. Copyright © 2012 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

  4. Assay for human Rad51-mediated DNA displacement loop formation.

    Science.gov (United States)

    Raynard, Steven; Sung, Patrick

    2009-01-01

    Homologous recombination is an important mechanism for the repair of damaged chromosomes, for preventing the demise of damaged replication forks, and for several other aspects of chromosome metabolism and maintenance. The homologous recombination reaction is mediated by the Rad51 recombinase. In the presence of ATP, Rad51 polymerizes on single-stranded DNA (ssDNA) to form a nucleoprotein filament that is commonly referred to as the "presynaptic filament." The presynaptic filament is capable of locating a homologous duplex DNA molecule and catalyzing invasion of the duplex to form a DNA displacement loop called the "D-loop." This protocol describes an in vitro D-loop assay that uses a radiolabeled ssDNA oligonucleotide and a nonlabeled homologous supercoiled duplex DNA as substrates, and agarose gel electrophoresis together with PhosphorImaging for product analysis. To enhance the efficiency of the D-loop reaction, an ancillary factor (the Hop2-Mnd1 complex or Rad54) is included in the reaction. This reconstituted system provides researchers a biochemical means to dissect the mechanisms of the homologous recombination machinery.

  5. 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

  6. 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).

  7. Single-incision laparoscopic splenectomy with innovative gastric traction suture

    Directory of Open Access Journals (Sweden)

    Srikanth G

    2011-01-01

    Full Text Available Laparoscopic splenectomy is now the gold standard for patients with idiopathic thrombocytopenic purpura (ITP undergoing splenectomy. There are a few reports in literature on single-incision laparoscopic (SIL splenectomy. Herein, we describe a patient undergoing SIL splenectomy for ITP without the use of a disposable port device. We report a 20-year-old female patient with steroid-refractory ITP having a platelet count of 14,000/cmm who underwent a SIL splenectomy. Dissection was facilitated by the use of a single articulating grasper and a gastric traction suture and splenic vessels were secured at the hilum with an endo-GIA stapler. She made an uneventful postoperative recovery and was discharged on the second postoperative day. She is doing well with no visible scar at 8-month follow-up.

  8. 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

  9. 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.

  10. Recognition of DNA/RNA bulges by antimicrobial and antitumor metallohelices.

    Science.gov (United States)

    Malina, Jaroslav; Scott, Peter; Brabec, Viktor

    2015-09-07

    Bulged structures have been identified in nucleic acids and have been shown to be linked to biomolecular processes involved in numerous diseases. Thus, chemical agents with affinity for bulged nucleic acids are of general biological significance. Herein, the mechanism of specific recognition and stabilization of bulged DNA and RNA by helical bimetallic species was established through detailed molecular biophysics and biochemistry assays. These agents, known as 'flexicates', are potential mimetics of α-helical peptides in cancer treatment, exhibiting antimicrobial and antitumor effects. The flexicates have positive impacts on the thermal stability of DNA duplexes containing bulges, which means that the flexicates interact with the duplexes containing bulges, and that these interactions stabilize the secondary structures of these duplexes. Notably, the stabilising effect of the flexicates increases with the size of the bulge, the maximal stabilization is observed for the duplexes containing a bulge composed of at least three bases. The flexicates bind most preferentially to the bulges composed of pyrimidines flanked on both sides also by pyrimidines. It is suggested that it is so because these bulges exhibit greatest conformational variability in comparison with other combinations of bases in the bulge loop and bases flanking the bulge. Finally, the results indicate that there is only one dominant binding site for the flexicates on the DNA and RNA bulges and that the flexicates bind directly to the bulge or in its close proximity. It is also shown that the flexicates effectively bind to RNA duplexes containing the bulged region of HIV-1 TAR RNA.

  11. A 1-D morphodynamic model of postglacial valley incision

    Science.gov (United States)

    Tunnicliffe, Jon F.; Church, Michael

    2015-11-01

    Chilliwack River is typical of many Cordilleran valley river systems that have undergone dramatic Holocene degradation of valley fills that built up over the course of Pleistocene glaciation. Downstream controls on base level, mainly blockage of valleys by glaciers, led to aggradation of significant glaciofluvial and glaciolacustrine valley fills and fan deposits, subsequently incised by fluvial action. Models of such large-scale, long-term degradation present a number of important challenges since the evolution of model parameters, such as the rate of bedload transport and grain size characteristics, are governed by the nature of the deposit. Sediment sampling in the Chilliwack Valley reveals a complex sequence of very coarse to fine textural modes. We present a 1-D numerical morphodynamic model for the river-floodplain system tailored to conditions in the valley. The model is adapted to dynamically adjust channel width to optimize sediment transporting capacity and to integrate relict valley fill material as the channel incises through valley deposits. Sensitivity to model parameters is studied using four principal criteria: profile concavity, rate of downstream grain size fining, bed surface sand content, and the timescale to equilibrium. Model results indicate that rates of abrasion and coarsening of the grain size distributions exert the strongest controls on all of the interrelated model performance criteria. While there are a number of difficulties in satisfying all model criteria simultaneously, results indicate that 1-D models of valley bottom sedimentary systems can provide a suitable framework for integrating results from sediment budget studies and chronologies of sediment evacuation established from dating.

  12. Enzymatic repair of uv-irradiated DNA in vitro

    International Nuclear Information System (INIS)

    Hamilton, L.D.; Mahler, I.; Grossman, L.

    1975-01-01

    Excision repair of uv-damaged Bacillus subtilis transforming DNA has been carried out by a sequential enzyme system in vitro. Incision adjacent to the pyrimidine dimer in the DNA strand by correndonuclease II-initiated excision of the damage by the 5' → 3'-directed exonuclease of the Micrococcus luteus DNA polymerase. Reinsertion of nucleotides into the gap in the strand by the DNA polymerase at 10 0 C terminated in a single-strand break which was sealed by a polynucleotide ligase, thereby repairing the DNA strand. This restored biological activity to damaged DNA up to doses resulting in 60 percent inactivation of transforming activity. At higher doses, less repair was achieved, due to the development of double-strand breaks during the in vitro incision and excision steps

  13. Cost-effectiveness of identifying aortoiliac and femoropopliteal arterial disease with angiography or duplex scanning

    NARCIS (Netherlands)

    Coffi, S. B.; Ubbink, D. Th; Dijkgraaf, M. G. W.; Reekers, J. A.; Legemate, D. A.

    2008-01-01

    OBJECTIVES: Cost-effectiveness analysis of three diagnostic imaging strategies for the assessment of aortoiliac and femoropopliteal arteries in patients with peripheral arterial occlusive disease. The strategies were: angiography as the reference strategy, duplex scanning (DS) plus supplementary

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

    Science.gov (United States)

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

    2016-05-01

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

  15. Phase transformations evaluation on a UNS S31803 duplex stainless steel based on nondestructive testing

    Energy Technology Data Exchange (ETDEWEB)

    Macedo Silva, Edgard de, E-mail: edgard@cefetpb.edu.br [Centro federal de Educacao Tecnologica da Paraiba (CEFET PB), Area da Industria, Avenida 1o de Maio, 720 - 58015-430 - Joao Pessoa/PB (Brazil); Costa de Albuquerque, Victor Hugo, E-mail: victor.albuquerque@fe.up.pt [Universidade Federal da Paraiba (UFPB), Departamento de Engenharia Mecanica (DEM), Cidade Universitaria, S/N - 58059-900 - Joao Pessoa/PB (Brazil); Pereira Leite, Josinaldo, E-mail: josinaldo@ct.ufpb.br [Universidade Federal da Paraiba (UFPB), Departamento de Engenharia Mecanica (DEM), Cidade Universitaria, S/N - 58059-900 - Joao Pessoa/PB (Brazil); Gomes Varela, Antonio Carlos, E-mail: varela@cefetpb.edu.br [Universidade Federal da Paraiba (UFPB), Departamento de Engenharia Mecanica (DEM), Cidade Universitaria, S/N - 58059-900 - Joao Pessoa/PB (Brazil); Pinho de Moura, Elineudo, E-mail: elineudo@pq.cnpq.br [Universidade Federal do Ceara (UFC), Departamento de Engenharia Metalurgica e de Materiais, Campus do Pici, Bloco 715, 60455-760 - Fortaleza/CE (Brazil); Tavares, Joao Manuel R.S., E-mail: tavares@fe.up.pt [Faculdade de Engenharia da Universidade do Porto (FEUP), Departamento de Engenharia Mecanica e Gestao Industrial (DEMEGI)/Instituto de Engenharia Mecanica e Gestao Industrial - INEGI, Rua Dr. Roberto Frias, s/n, 4200-465 Porto (Portugal)

    2009-08-15

    Duplex stainless steel presents special mechanical properties such as, for example, mechanical and corrosion strength, becoming competitive in relation to the other types of stainless steel. One of the great problems of duplex stainless steel microstructural changes study is related to embrittlement above 300 deg. C, with the precipitation of the {alpha}' phase occurring over the ferritic microstructure. Aiming to characterise embrittlement of duplex stainless steel, hardening kinetics, from 425 to 475 deg. C, was analysed through the speed of sound, Charpy impact energy, X-ray diffraction, hardness and microscopy parameters. The presence of two hardening stages, detected through the speed of sound, was observed, one being of brittle characteristic and the other ductile. Moreover, the speed of sound showed a direct correlation with the material's hardness. Thus, it is concluded that the speed of sound is a promising nondestructive parameter to follow-up embrittlement in duplex stainless steel.

  16. Phase transformations evaluation on a UNS S31803 duplex stainless steel based on nondestructive testing

    International Nuclear Information System (INIS)

    Macedo Silva, Edgard de; Costa de Albuquerque, Victor Hugo; Pereira Leite, Josinaldo; Gomes Varela, Antonio Carlos; Pinho de Moura, Elineudo; Tavares, Joao Manuel R.S.

    2009-01-01

    Duplex stainless steel presents special mechanical properties such as, for example, mechanical and corrosion strength, becoming competitive in relation to the other types of stainless steel. One of the great problems of duplex stainless steel microstructural changes study is related to embrittlement above 300 deg. C, with the precipitation of the α' phase occurring over the ferritic microstructure. Aiming to characterise embrittlement of duplex stainless steel, hardening kinetics, from 425 to 475 deg. C, was analysed through the speed of sound, Charpy impact energy, X-ray diffraction, hardness and microscopy parameters. The presence of two hardening stages, detected through the speed of sound, was observed, one being of brittle characteristic and the other ductile. Moreover, the speed of sound showed a direct correlation with the material's hardness. Thus, it is concluded that the speed of sound is a promising nondestructive parameter to follow-up embrittlement in duplex stainless steel.

  17. Corrosion Behavior of Austenitic and Duplex Stainless Steels in Lithium Bromide

    Directory of Open Access Journals (Sweden)

    Ayo Samuel AFOLABI

    2009-07-01

    Full Text Available The corrosion behavior of austenitic and duplex stainless steels in various concentrations of lithium, bromide solution was investigated by using the conventional weight loss measurement method. The results obtained show that corrosion of these steels occurred due to the aggressive bromide ion in the medium. Duplex stainless steel shows a greater resistance to corrosion than austenitic stainless steel in the medium. This was attributed to equal volume proportion of ferrite and austenite in the structure of duplex stainless steel coupled with higher content of chromium in its composition. Both steels produced electrochemical noise at increased concentrations of lithium bromide due to continuous film breakdown and repair caused by reduction in medium concentration by the alkaline corrosion product while surface passivity observed in duplex stainless steel is attributed to film stability on this steel.

  18. 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

  19. European Hernia Society guidelines on the closure of abdominal wall incisions

    DEFF Research Database (Denmark)

    Muysoms, F E; Antoniou, S A; Bury, K

    2015-01-01

    BACKGROUND: The material and the surgical technique used to close an abdominal wall incision are important determinants of the risk of developing an incisional hernia. Optimising closure of abdominal wall incisions holds a potential to prevent patients suffering from incisional hernias and for im...

  20. 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...

  1. 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 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.

  2. 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...

  3. On the kinetics of martensite formation in a duplex stainless steel ...

    African Journals Online (AJOL)

    Studies have been made of the kinetics of martensite transformation in a duplex stainless steel of composition 21Cr-6.6Ni, 2.5M0, 1.6Cu, <.0.03C (wt.%) Solution treatment at 1050οC for 1 hr was followed by deformation at the subzero temperatures of –70 and –196οC. The kinetics of the γ → α1 transformation in the duplex ...

  4. Influence of upper and temporal transconjunctival sclerocorneal incision on marginal reflex distance after cataract surgery.

    Science.gov (United States)

    Tamaki, Rikiya; Gosho, Masahiko; Mizumoto, Kyoichi; Kato, Nahoko; Zako, Masahiro

    2016-07-07

    Ptosis incidence following cataract surgery is reduced with a recently developed phacoemulsification technique using a small incision. However, it remains uncertain whether an upper transconjunctival sclerocorneal incision can cause minor blepharoptosis. In the present prospective study, patients underwent cataract surgery with either an upper or temporal 2.4-mm transconjunctival sclerocorneal incision. We measured the marginal reflex distance 1 (MRD1) preoperatively and postoperatively, and compared these measurements between the two different incision types. Further we explored the risk factors of the postoperative MRD1 reduction. The study population included patients who underwent cataract surgery on both eyes at Aichi Medical University between October 2013 and September 2015. In each patient, one eye was operated using an upper 2.4-mm transconjunctival sclerocorneal incision, and the other with a temporal incision. We prespecified that an MRD1 difference of ≥0.5 mm between the pre- and post-surgical measurements indicated postoperative ptosis, which was a strict criterion. MRD1 was measured using digital photography, and we calculated the difference between the preoperative and postoperative MRD1 values. This change in MRD1 was compared between the groups with different incision locations. The change in MRD1 was analyzed by using the multivariate regression model including incision position (temporal or upper), preoperative MRD1, and preoperative distance between medial and lateral canthi. We assessed data from a total of 34 patients. The mean change in MRD1 from pre-operation to post-operation measurements was -0.26 ± 0.93 with the temporal incision and -0.24 ± 0.86 with the upper incision. The mean difference in the change in MRD1 between the different two incision types was -0.02, with a 95 % CI of -0.24 to 0.20, establishing equivalence between these incision types. The multivariate regression analysis showed that the preoperative MRD1 was

  5. Molecular structure of r/GCG/d/TATACGC/ - A DNA-RNA hybrid helix joined to double helical DNA

    Science.gov (United States)

    Wang, A. H.-J.; Fujii, S.; Rich, A.; Van Boom, J. H.; Van Der Marel, G. A.; Van Boeckel, S. A. A.

    1982-01-01

    The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA-RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

  6. Transscleral tunnel incision related arterial hemorrhage in 23-gauge Vitrectomy: case report.

    Science.gov (United States)

    Liu, Bingqian; Li, Yonghao; Li, Tao; Lin, Ying; Ma, Wei; Lu, Lin

    2018-01-17

    Transscleral tunnel incisions are commonly made to avoid postoperative leakage in small gauge sutureless vitrectomy. We present an unreported intraoperative complication, tunnel incision related arterial hemorrhage from sclerotomy, in 23-gauge (23G) vitrectomy. Two cases of intraocular arterial hemorrhage from superonasal sclerotomy were observed at the beginning of vitrectomy. The bleeding filled the vitreous cavity quickly and gushed out from the incision port after the involved supronasal cannula was removed. The active bleeding seemed not to stop spontaneously. We controlled the active bleeding by relocating the involved cannula, elevating the intraocular pressure and compressing the sclera wound. Post-operative intraocular hemorrhage from the sclerotomy was not found in any of the two cases. We suggest that the bleeding was from injured ciliary artery when the incision crossed 3 or 9 o'clock accidently. Surgeons might avoid this complication by locating the superior incisions away from the horizontal axis, and should be aware the proper management.

  7. In-Band α-Duplex Scheme for Cellular Networks: A Stochastic Geometry Approach

    KAUST Repository

    Alammouri, Ahmad

    2016-07-13

    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 paper presents a tractable framework, based on stochastic geometry, to study FD communications in 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 FD rate gains harvested in the downlink (up to 97%) come 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 -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 -duplex scheme and show its superiority to both the FD and half-duplex (HD) schemes. In particular, we show that the -duplex scheme provides a simultaneous improvement of 28% for the downlink rate and 56% for the uplink rate. Finally, we show that the amount of the overlap can be optimized based on the network design objective.

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

    Science.gov (United States)

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

    2015-02-01

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

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

    Science.gov (United States)

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

    2018-01-30

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

  10. 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.

  11. 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.

  12. Single transverse extended incision for radical neck dissection.

    Science.gov (United States)

    Chagas, José Francisco Sales; Pascoal, Maria Beatriz Nogueira; Aquino, José Luís Braga; Brandi, Luís Antônio; Previtale, Evandro Von Zuben; Trillo, Ana Sofia Pontes; Curioni, Otávio Alberto; Rapoport, Abrão; Dedivitis, Rogério Aparecido

    2016-01-01

    to assess the efficacy of the single transverse extended cervical incision in radical neck dissection. we conducted a prospective study, from January 2008 to January 2009, with 18 patients undergoing surgical treatment of malignant tumors of the upper aero-digestive tract. The primary lesion was located in the oral cavity in eight cases, in the oropharynx in three, in the hypopharynx in three, in the larynx in two, in the maxillary sinus, and in one case, the primary injury was hidden. There were 29 neck dissections, eight bilateral and 10 unilateral (26 radical and three selective). Staging revealed nine patients with T4 tumor, one T3, six T2, one T1 and one Tx. Five patients were N0, nine N2b, one N2c and three N3. The average number of dissected lymph nodes was 34.25. We performed the neck dissection through a single incision located in the middle neck, coincident with the skinfold, with a length of about 2 to 3 cm behind the anterior edge of the trapezius muscle and 3 to 4 cm from the midline for the unilateral neck dissections. as complications, there were myocutaneous flap necrosis in one patient with prior radiation therapy, one lymphatic fistula, one dehiscence of the tracheostomy, one cervical abscess, one salivary fistula and one suture dehiscence. the single extended incision provides adequate exposure of the neck structures, without compromising surgical time, even in bilateral dissections. It does not compromise the resection of all cervical lymph nodes; it has excellent aesthetic and functional results and is easily associated with other approaches to resection of the primary tumor. verificar a eficácia da incisão cervical única, transversa e estendida, para o esvaziamento cervical radical. estudo prospectivo, de janeiro de 2008 a janeiro de 2009, de 18 pacientes submetidos a tratamento cirúrgico de tumores malignos da via aero-digestiva superior. A lesão primária se situava na cavidade oral em oito casos, na orofaringe em três, no seio

  13. Effect of incision design on interproximal bone loss of teeth adjacent to single implants. A randomized controlled clinical trial comparing intrasulcular vs paramarginal incision.

    Science.gov (United States)

    Girbés-Ballester, Paula; Viña-Almunia, Jose; Balaguer-Martí, Jose C; Peñarrocha-Diago, Miguel; Peñarrocha-Oltra, David

    2018-02-16

    To evaluate the effect of incision design in implant surgery on interproximal bone loss of posterior teeth adjacent to interdental single implants, comparing intrasulcular and paramarginal incision. A further aim was to assess the influence of the incision technique on peri-implant bone remodeling. A controlled randomized clinical trial was carried out in a University Clinic. All the patients received an interdental posterior single implant. The incision type was randomly divided into two groups: (a) intrasulcular or (b) paramarginal. Standardized periapical digital radiographs were made with the parallel technique and a silicone index individualized in each patient. Radiographs were made immediately after implant placement, at abutment connection, 6 and 12 months post-loading. Two radiographic reference points were detected at the interproximal aspect of the adjacent teeth: (A) the cementoenamel junction and (B) the most coronal aspect of the bone crest. The interproximal bone loss of the adjacent teeth was calculated as the difference from A to B between the different follow-up periods and baseline. Two different examiners evaluated the radiographic measurements twice. Sixty patients, each with one implant, were included, 30 in each group. A mean interproximal bone loss in teeth of 0.09 mm in the intrasulcular and 0.10 mm in the paramarginal group was found at 12 months post-loading. Mean peri-implant bone remodeling was 0.17 mm in the intrasulcular group and 0.15 mm in the paramarginal group. Differences between incision types were not statistically significant (p > .05). Both incision designs used to place interdental single implants resulted in minimum bone loss at the interproximal aspect of adjacent teeth. The incision design did not significantly influence the radiographically assessed interproximal bone loss nor peri-implant bone remodeling. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. cDNA library preparation.

    Science.gov (United States)

    Kooiker, Maarten; Xue, Gang-Ping

    2014-01-01

    The construction of full-length cDNA libraries allows researchers to study gene expression and protein interactions and undertake gene discovery. Recent improvements allow the construction of high-quality cDNA libraries, with small amounts of mRNA. In parallel, these improvements allow for the incorporation of adapters into the cDNA, both at the 5' and 3' end of the cDNA. The 3' adapter is attached to the oligo-dT primer that is used by the reverse transcriptase, whereas the 5' adapter is incorporated by the template switching properties of the MMLV reverse transcriptase. This allows directional cloning and eliminates inefficient steps like adapter ligation, phosphorylation, and methylation. Another important step in the construction of high-quality cDNA libraries is the normalization. The difference in the levels of expression between genes might be several orders of magnitude. Therefore, it is essential that the cDNA library is normalized. With a recently discovered enzyme, duplex-specific nuclease, it is possible to normalize the cDNA library, based on the fact that more abundant molecules are more likely to reanneal after denaturation compared to rare molecules.

  15. 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)

  16. Fatigue damage in coarse-grained lean duplex stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Strubbia, R., E-mail: strubbia@ifir-conicet.gov.ar; Hereñú, S.; Marinelli, M.C.; Alvarez-Armas, I.

    2016-04-06

    The present investigation is focused on assessing the effect of a thermal treatment for grain coarsening on the low cycle fatigue damage evolution in two types of Lean Duplex Stainless Steels (LDSSs). The dislocation structure developed during cycling is observed by transmission electron microscopy (TEM). Additionally, a detailed analysis of short crack initiated and grown during low cycle fatigue (LCF) is performed by means of optical and scanning electron (SEM) microscopy in combination with automated electron back-scattered diffraction (EBSD) technique. Though in both coarse-grained LDSSs the short cracks nucleate in the ferrite phase, in each steels its origin is different. The embrittlement caused by the Cr{sub 2}N precipitation and the plastic activity sustained by each phase can explain this difference. The propagation behavior of the short cracks present two alternative growing mechanisms: the crack grows along a favorable slip plane with high Schmid Factor (SF) or the crack alternates between two slip systems. In both cases, the crack follows the path with the smallest tilt angle (β) at a grain boundary.

  17. Detection of pseudorabies virus by duplex droplet digital PCR assay.

    Science.gov (United States)

    Ren, Meishen; Lin, Hua; Chen, Shijie; Yang, Miao; An, Wei; Wang, Yin; Xue, Changhua; Sun, Yinjie; Yan, Yubao; Hu, Juan

    2018-01-01

    Aujeszky's disease, caused by pseudorabies virus (PRV), has damaged the economy of the Chinese swine industry. A large number of PRV gene-deleted vaccines have been constructed based on deletion of the glycoprotein E ( gE) gene combined with other virulence-related gene deletions, such as thymidine kinase ( TK), whereas PRV wild-type strains contain an intact gE gene. We developed a sensitive duplex droplet digital PCR (ddPCR) assay to rapidly detect PRV wild-type isolates and gE gene-deleted viral vaccines. We compared this assay with a TaqMan real-time PCR (qPCR) using the same primers and probes. Both assays exhibited good linearity and repeatability; however, ddPCR maintained linearity at extremely low concentrations, whereas qPCR did not. Based on positive results for both gE and gB, the detection limit of ddPCR was found to be 4.75 copies/µL in contrast of 76 copies/µL for qPCR, showing that ddPCR provided a 16-fold improvement in sensitivity. In addition, no nonspecific amplification was shown in specificity testing, and the PRV wild-type was distinguished from a gE-deleted strain. The ddPCR was more sensitive when analyzing clinical serum samples. Thus, ddPCR may become an appropriate detection platform for PRV.

  18. Transperitoneal laparoscopic heminephrectomy in duplex kidneys: a one centre experience

    Directory of Open Access Journals (Sweden)

    Mehdi Abedinzadeh

    2012-02-01

    Full Text Available Purpose: The standard treatment for a duplex kidney with poorly functioning upper pole moiety is ipsilateral upper pole heminephrectomy. This procedure is usually performed by open surgery, but with recent developments in techniques of uro-laparoscopy, it can be done with it, safely. In this study we evaluated the results and safety of laparoscopic heminephrectomy in our consecutive cases.Materials and Methods: From February 2001 to May 2007 fourteen unilateral laparoscopic heminephrectomy were performed in our center. Patients' characteristics, presenting symptoms, operative time, and blood loss, early and late complications were all collected retrospectively. Using pre-operative ultrasonography, intravenous pyelography (IVP and CT scanning, unilateral upper pole hydronephrosis was detected in all cases. By DMSA isotope scan hypofunctioning of ipsilateral moieties was detected in all cases.Results: Mean operative time was 203±80 minutes. No major intra-operative or early complications were identified. Mean hospital stay was 4.1 days. On mean follow-up of 32 months no disturbing symptoms or episodes of urinary tract infections (UTIs were detected. Atrophic kidney was detected in one case in post-operative IVP.Conclusion: Laparoscopic heminephrectomy is a valuable minimal invasive procedure that can be performed safely in experienced hands without any important complication. Perfect renal pedicles vascular system manipulation is important for the preservation of renal function post-operatively.

  19. Eddy current techniques for super duplex stainless steel characterization

    International Nuclear Information System (INIS)

    Camerini, C.; Sacramento, R.; Areiza, M.C.; Rocha, A.; Santos, R.; Rebello, J.M.; Pereira, G.

    2015-01-01

    Super duplex stainless steel (SDSS) is a two-phase material where the microstructure consists of grains of ferrite (δ) and austenite (γ). SDSS exhibit an attractive combination of properties, such as: strength, toughness and stress corrosion cracking resistance. Nevertheless, SDSS attain these properties after a controlled solution heat treatment, leading to a similar volumetric fraction of δ and γ. Any further heat treatment, welding operation for example, can change the balance of the original phases, or may also lead to precipitation of a deleterious phase, such as sigma (σ). For these situations, the material corrosion resistance is severely impaired. In the present study, several SDSS samples with low σ phase content and non-balanced microstructure were intentionally obtained by thermally treating SDSS specimens. Electromagnetic techniques, conventional Eddy Current Testing (ECT) and Saturated Low Frequency Eddy Current (SLOFEC), were employed to characterize the SDSS samples. The results showed that ECT and SLOFEC are reliable techniques to evaluate σ phase presence in SDSS and can provide an estimation of the δ content. - Highlights: • Sigma phase precipitation, even for low amounts, dramatically affects SDSS properties. • SDSS samples were thermally treated and carefully characterized by X-Ray Diffraction. • NDT techniques detected low amounts of sigma phase in SDSS microstructure

  20. Fracture toughness of a welded super duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Pilhagen, Johan, E-mail: pilhagen@kth.se [Department of Materials Science and Engineering, KTH Royal Institute of Technology, Stockholm (Sweden); Sieurin, Henrik [Scania CV AB, Södertälje (Sweden); Sandström, Rolf [Department of Materials Science and Engineering, KTH Royal Institute of Technology, Stockholm (Sweden)

    2014-06-01

    Fracture toughness testing was conducted on standard single-edge notched bend bar specimens of base and weld metal. The material was the SAF 2906 super duplex stainless steel. The aim was to evaluate the susceptibility for brittle failure at sub-zero temperatures for the base and weld metal. The base metal was tested between −103 and −60 °C and was evaluated according to the crack-tip opening displacement method. The fracture event at and below −80 °C can be described as ductile until critical cleavage initiation occurs, which caused unstable failure of the specimen. The welding method used was submerged arc welding with a 7 wt% nickel filler metal. The welded specimens were post-weld heat treated (PWHT) at 1100 °C for 20 min and then quenched. Energy-dispersive X-ray spectroscopy analysis showed that during PWHT substitutional element partitioning occurred which resulted in decreased nickel content in the ferrite. The PWHT weld metal specimens were tested at −72 °C. The fracture sequence was critical cleavage fracture initiation after minor crack-tip blunting and ductile fracture.

  1. Eddy current techniques for super duplex stainless steel characterization

    Science.gov (United States)

    Camerini, C.; Sacramento, R.; Areiza, M. C.; Rocha, A.; Santos, R.; Rebello, J. M.; Pereira, G.

    2015-08-01

    Super duplex stainless steel (SDSS) is a two-phase material where the microstructure consists of grains of ferrite (δ) and austenite (γ). SDSS exhibit an attractive combination of properties, such as: strength, toughness and stress corrosion cracking resistance. Nevertheless, SDSS attain these properties after a controlled solution heat treatment, leading to a similar volumetric fraction of δ and γ. Any further heat treatment, welding operation for example, can change the balance of the original phases, or may also lead to precipitation of a deleterious phase, such as sigma (σ). For these situations, the material corrosion resistance is severely impaired. In the present study, several SDSS samples with low σ phase content and non-balanced microstructure were intentionally obtained by thermally treating SDSS specimens. Electromagnetic techniques, conventional Eddy Current Testing (ECT) and Saturated Low Frequency Eddy Current (SLOFEC), were employed to characterize the SDSS samples. The results showed that ECT and SLOFEC are reliable techniques to evaluate σ phase presence in SDSS and can provide an estimation of the δ content.

  2. Eddy current techniques for super duplex stainless steel characterization

    Energy Technology Data Exchange (ETDEWEB)

    Camerini, C., E-mail: cgcamerini@metalmat.ufrj.br [Laboratory of Non-Destructive Testing, Corrosion and Welding, Department of Metallurgical and Materials Engineering, Federal University of Rio de Janeiro (Brazil); Sacramento, R.; Areiza, M.C.; Rocha, A. [Laboratory of Non-Destructive Testing, Corrosion and Welding, Department of Metallurgical and Materials Engineering, Federal University of Rio de Janeiro (Brazil); Santos, R. [PETROBRAS R& D Center, Rio de Janeiro (Brazil); Rebello, J.M.; Pereira, G. [Laboratory of Non-Destructive Testing, Corrosion and Welding, Department of Metallurgical and Materials Engineering, Federal University of Rio de Janeiro (Brazil)

    2015-08-15

    Super duplex stainless steel (SDSS) is a two-phase material where the microstructure consists of grains of ferrite (δ) and austenite (γ). SDSS exhibit an attractive combination of properties, such as: strength, toughness and stress corrosion cracking resistance. Nevertheless, SDSS attain these properties after a controlled solution heat treatment, leading to a similar volumetric fraction of δ and γ. Any further heat treatment, welding operation for example, can change the balance of the original phases, or may also lead to precipitation of a deleterious phase, such as sigma (σ). For these situations, the material corrosion resistance is severely impaired. In the present study, several SDSS samples with low σ phase content and non-balanced microstructure were intentionally obtained by thermally treating SDSS specimens. Electromagnetic techniques, conventional Eddy Current Testing (ECT) and Saturated Low Frequency Eddy Current (SLOFEC), were employed to characterize the SDSS samples. The results showed that ECT and SLOFEC are reliable techniques to evaluate σ phase presence in SDSS and can provide an estimation of the δ content. - Highlights: • Sigma phase precipitation, even for low amounts, dramatically affects SDSS properties. • SDSS samples were thermally treated and carefully characterized by X-Ray Diffraction. • NDT techniques detected low amounts of sigma phase in SDSS microstructure.

  3. Precipitation Mechanism of Sigma Phase in Super Duplex Stainless Steels

    Science.gov (United States)

    Nakade, Katsuyuki; Kuroda, Toshio

    The influence of alloying elements on the precipitation behavior of sigma (σ) phase was investigated for conventional SAF2205 and SAF2507 super duplex stainless steel. Time-Temperature-Precipitation (T-T-P) diagram of sigma phase of SAF2507 were shifted toward to shorter times compared to SAF2205. The precipitation of sigma phase was accelerated with increasing Cr and Mo concentration. According to the microstructure observation, the sigma phase began to precipitate at ferrite (α) ⁄ austenite (γ) phase boundaries and grew into ferrite for SAF2507 and SAF2205 steel. In the as-received condition, Cr and Mo concentration in ferrite was clearly higher than that in austenite. Especially, it was found that Mo concentration in ferrite of SAF2507 was higher than that in ferrite of SAF2205. The result of EPMA-measurement showed that sigma phase was mainly Fe-Cr-Mo intermetallic compound and Mo was significantly enriched into sigma phase. The difference of Mo concentration in ferrite significantly affected to the sigma phase precipitation. The secondary austenite formation was also induced by sigma phase precipitation. Cr and Mo were ejected to the remained ferrite ⁄ austenite phase boundaries by secondary austenite formation. Consequently, sigma phase precipitation was more accelerated by the reheating.

  4. Quantification of cerebral blood flow via Duplex sonography

    International Nuclear Information System (INIS)

    Vogl, G.; Pohl, P.; Willeit, J.; Aichner, F.

    1987-01-01

    An attempt was made to measure quantitatively the total cerebral blood flow by means of Duplex sonography. In a group of healthy young subjects a median value for total cerebral blood flow was obtained amounting to 469 ml/min ± 30%, repeat measurements yielded a maximum deviation of ± 11%. In three patients the values obtained after severe apoplectic insult due to occlusion of the internal carotid artery were definitely below the value of the group of healthy subjects, whereas the value for the total blood flow was in the upper range of normal values in a patient with occlusion of the a. cerebri media. Comparative measurements of the regional cerebral blood flow with xenon 13 yielded in those patients with occlusion of the internal carotid artery a markedly reduced mean flow and in the patient with occlusion of the a. cerebri media a less markedly reduced mean flow. Regionally reduced perfusion was seen in all the four patients in the range of the clinically and computer tomographically well-known ischaemia zone. Thanks to the simplicity of this sonographic examination method it could be a useful decision parameter in determining the indication for a reconstruction of the carotid artery, especially in asymptotic patients. (orig.) [de

  5. Microstructural morphology and stability of rapidly solidified duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Cvijovic, Z.M.; Mihajlovic, D.V.; Knezevic, V.R. [Belgrade Univ. (Yugoslavia). Faculty of Technology and Metallurgy

    1998-10-01

    The microstructure susceptibility of duplex stainless steel alloy with high ratio of Cr{sub eq}/Ni{sub eq} to unequilibrium solidification conditions were studied after rapid solidification. Three methods of locally surface melting were used: stationary gas tungsten arc, plasma arc and electron beam arc melting. Applying relatively high cooling rates in the range from 10{sup 1} to 10{sup 3} Cs{sup -1} and undercooling of 1.5-13 C, the primary ferrite with second-phase austenite (FA) solidification mode was unchanged, but significant changes in microstructure morphology, such as intercellular austenite, very fine microstructural constituents and increase of volume fraction of retained ferrite were observed. At the critical cooling rate of the order of 10{sup 4} Cs{sup -1} and undercooling {Delta}T>75 C a transformation of solidification mode from FA to single-phase ferrite (F) and developing of ferrite grain structure with Widmanstaetten austenite was demonstrated. Based on these results the partitionless solidification of ferrite and undercooling below the ferrite T{sub 0} curve was suggested. The fact that ferritic solidification was favored, was explained by the chemical composition of the alloy. During the subsequent annealing the obtained microstructures were highly unequilibrium and hence unstable. (orig.) 19 refs.

  6. Hepatic venous pressure gradients measured by duplex ultrasound

    International Nuclear Information System (INIS)

    Tasu, J.-P.; Rocher, L.; Peletier, G.; Kuoch, V.; Kulh, E.; Miquel, A.; Buffet, C.; Biery, M.

    2002-01-01

    AIMS: The hepatic venous pressure gradient is a major prognostic factor in portal hypertension but its measurement is complex and requires invasive angiography. This study investigated the relationship between the hepatic venous pressure gradient and a number of Doppler measurements, including the arterial acceleration index. METHOD: We measured the hepatic venous pressure gradient in 50 fasting patients at hepatic venography. Immediately afterwards, a duplex sonographic examination of the liver was performed at which multiple measurements and indices of the venous and arterial hepatic vasculature were made. RESULTS: Hepatic arterial acceleration was correlated directly with the hepatic venous pressure gradient (r = 0.83, P -2 provided a positive predictive value of 95%, a sensitivity of 65% and a specificity of 95% for detecting patients with severe portal hypertension (hepatic venous pressure gradient > 12 mmHg). A correlation between the hepatic venous pressure gradient and the congestion index of the portal vein velocity (r = 0.45,P = 0.01) and portal vein velocity (r = 0.40,P = 0.044), was also noted. CONCLUSION: Measuring the hepatic arterial acceleration index may help in the non-invasive evaluation of portal hypertension. Tasu, J.-P. et al. (2002)

  7. Methods of DNA sequencing by hybridization based on optimizing concentration of matrix-bound oligonucleotide and device for carrying out same

    Science.gov (United States)

    Khrapko, Konstantin R.; Khorlin, Alexandr A.; Ivanov, Igor B.; Ershov, Gennady M.; Lysov, Jury P.; Florentiev, Vladimir L.; Mirzabekov, Andrei D.

    1996-09-03

    A method for sequencing DNA by hybridization that includes the following steps: forming an array of oligonucleotides at such concentrations that either ensure the same dissociation temperature for all fully complementary duplexes or allows hybridization and washing of such duplexes to be conducted at the same temperature; hybridizing said oligonucleotide array with labeled test DNA; washing in duplex dissociation conditions; identifying single-base substitutions in the test DNA by analyzing the distribution of the dissociation temperatures and reconstructing the DNA nucleotide sequence based on the above analysis. A device for carrying out the method comprises a solid substrate and a matrix rigidly bound to the substrate. The matrix contains the oligonucleotide array and consists of a multiplicity of gel portions. Each gel portion contains one oligonucleotide of desired length. The gel portions are separated from one another by interstices and have a thickness not exceeding 30 .mu.m.

  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. 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.

  10. THE EFFECT OF WOUND INCISION CARE USING HONEY AND POVIDONE IODINE 10%

    Directory of Open Access Journals (Sweden)

    M. Zakariya

    2017-07-01

    Full Text Available Introduction : Povidoe iodine often used in incision treatment. This study was aimed to explain the differences between honey and povidone iodine 10% on incision healing, were unknown. Method : This study used a true experiment design with 18 samples of 3 years old-male guinea pigs, divided into three groups. One-control group and 2 treatment groups. This classification was done randomize. The independent variable was used of honey and 10-% povidon iodin and the dependent variable was inflammation phase (squeezing, edema, plasma of incision and proliferation (granulation, incision edge unification, skin structure were assessed in the third and sixth days.  Data were collected by using observation of the signs both of inflammation and proliferation phase and analyzed using Chi Square with level of significance α ≤ 0.05. Result : Results showed that there was no significant difference in the third and sixth days inflammation. In contrast, a significant difference was obtained in the third and sixth days proliferation. Granulation (p< 0,05, incision edge unification (p< 0,05, establishment of skin structures (p< 0,05. Analysis : It can be concluded that the honey usage was proven to be more effective in accelerated incision healing, increasing proliferation and reduce any infection risks. Discussion : For future research there is neeed to conduct a microscopically observation of numerous changes in collagen, PMN-cell (neutrophile and MN-cell (lymphocyte and monocyte, inflammation and proliferation as well as incision healing process.

  11. 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.

  12. An investigation of the ionic and solvation patterns of dsDNG versus dsDNA by use of molecular dynamics simulations.

    Science.gov (United States)

    Toporowski, Joseph W; Reddy, Swarnalatha Y; Bruice, Thomas C

    2007-03-01

    Molecular dynamics has been employed to analyze the counterion and water atmospheres around the deoxynucleic guanidine (DNG) duplex G(12)-C(12). These features are compared to those of DNA G(12)-C(12). The chloride counterions of cationic DNG demonstrate fewer penetrations and only fleeting residence times in the minor groove, as opposed to the multi-nanosecond visits seen by sodium ions in DNA minor grooves. The 10 ns simulations also show the differences in hydration patterns between the DNG and DNA duplexes.

  13. Potential of duplex fuel in prebreeder, breeder, and power reactor designs: tests and analyses (AWBA Development Program)

    International Nuclear Information System (INIS)

    Chao, T.L.; Brennan, J.J.; Duncombe, E.; Schneider, M.J.; Johnson, R.G.R.

    1982-09-01

    Dual region fuel pellets, called duplex pellets, are comprised of an outer annular region of relatively high uranium fuel enrichment and a center pellet of fertile material with no enrichment. UO 2 and ThO 2 are the fissile and fertile materials of interest. Both prebreeders and breeders are discussed as are the performance advantages of duplex pellets over solid pellets in these two pressurized water reactor types. Advantages of duplex pellets for commercial reactor fuel rods are also discussed. Both irradiation test data and analytical results are used in comparisons. Manufacturing of duplex fuel is discussed

  14. Reproductive Outcome of Transcervical Uterine Incision in Unicornuate Uterus.

    Science.gov (United States)

    Xia, En-Lan; Li, Tin-Chiu; Choi, Sze-Ngar Sylvia; Zhou, Qiao-Yun

    2017-02-05

    The pregnancy outcome of the unicornuate uterus is associated with an increased risk of miscarriage, cervical incompetence, and a number of obstetric complications. However, at present, there is no accepted treatment method for women with unicornuate uterus, other than expectant measures. The aim of this study was to evaluate the reproductive outcome of transcervical uterine incision (TCUI) in patients with unicornuate uterus. Thirty-three patients with unicornuate uterus presented to our tertiary center for infertility or miscarriage. All 33 patients underwent TCUI and were followed up for 10-52 months. The pregnancy outcomes ( first-trimester miscarriage, second-trimester miscarriage, preterm, term, intrauterine death, ongoing pregnancy, and live birth) before and after TCUI were compared by t- test. Among 31 patients who attempted to conceive after TCUI, twenty conceived including one termination of pregnancy, one second-trimester miscarriage, one ectopic pregnancy, five preterm deliveries, 11 term delivery, and one ongoing pregnancy. There were 16 live births in total. There was significant reduction in the first-trimester miscarriage rate (t = 4.890; Puterus presenting with infertility or miscarriage.

  15. Small incision lenticule extraction (SMILE) monovision for presbyopia correction.

    Science.gov (United States)

    Luft, Nikolaus; Siedlecki, Jakob; Sekundo, Walter; Wertheimer, Christian; Kreutzer, Thomas C; Mayer, Wolfgang J; Priglinger, Siegfried G; Dirisamer, Martin

    2017-11-04

    To evaluate the outcomes of myopic small incision lenticule extraction (SMILE) monovision in presbyopic patients. This study included 49 presbyopic patients older than 45 years seeking surgical correction of myopia or myopic astigmatism who underwent bilateral SMILE with planned monovision in the SMILE Eyes Clinic Linz, Austria. Target refraction was plano for dominant (distance) eyes and ranged between -1.25 and -0.50 D for nondominant (near) eyes. Best-corrected distance visual acuity, uncorrected distance visual acuity (UDVA), uncorrected near visual acuity, as well as spectacle dependence were assessed after a mean postoperative period of 7.2 ± 4.8 months. Mean age was 49 ± 3 years and female to male ratio was 30:19. Distance eyes achieved a spherical equivalent correction of ±0.50 D from target refraction in 80% of patients and 96% were within ±1.0 D. Binocular UDVA of 20/20 or better was achieved by 90% of patients and all patients achieved 20/25 or better. The proportion of patients with a binocular UDVA of 20/20 or better who could read J2 or better amounted to 84%. Complete spectacle independence was achieved by 84% of patients and independence from reading glasses was achieved in 92% of cases. No patient requested refractive enhancement or monovision reversal. This first evaluation of SMILE monovision endorses the approach as a safe and effective option for the correction of presbyopia in myopic patients seeking refractive surgery.

  16. 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.

  17. Surgical incision can alter capsaicin-induced central sensitization in rat brainstem nociceptive neurons.

    Science.gov (United States)

    Lam, D K; Sessle, B J; Hu, J W

    2008-10-15

    Surgical trauma can affect spinal neuronal excitability, but there have been no studies of the effects of surgical cutaneous injury on central nociceptive processing of deep afferent inputs evoked by noxious stimuli such as capsaicin. Thus our aim was to test the effect of surgical cutaneous incision in influencing central sensitization induced by capsaicin injection into the temporomandibular joint (TMJ). The activity of single nociceptive neurons activated by noxious mechanical stimulation of the TMJ was recorded in the trigeminal subnucleus caudalis/upper cervical cord of halothane-anesthetized rats. The cutaneous mechanoreceptive field (RF), cutaneous mechanical activation threshold (MAT) and TMJ MAT of neurons before and after both surgical cutaneous incision alone and capsaicin injection were compared with results of incision and lidocaine pretreatment of the facial skin overlying the TMJ and capsaicin injection into the TMJ. Incision itself induced a barrage of neuronal spikes and excitability increases reflecting central sensitization (cutaneous RF expansion, cutaneous MAT reduction) in most neurons tested whereas lidocaine pretreatment significantly attenuated the barrage and central sensitization. Capsaicin injection into the TMJ induced cutaneous RF expansion, cutaneous MAT reduction and TMJ MAT reduction following lidocaine pretreatment of the cutaneous incision site whereas capsaicin injection following incision alone not only failed to induce further central sensitization but also decreased the existing incision-induced central sensitization (no cutaneous RF expansion, increased cutaneous MAT and TMJ MAT) in most neurons tested. These findings suggest that central sensitization induced by capsaicin alone or by cutaneous incision alone can readily occur in TMJ-responsive nociceptive neurons and that following incision-induced excitability increases, capsaicin may result in a temporary suppression of nociceptive neuronal changes reflecting central

  18. Incision rate changes in the upper Var River catchment, southern French Alps: from observations to models.

    Science.gov (United States)

    Petit, Carole; Rolland, Yann; Goren, Liran; Bourlès, Didier; Braucher, Régis; Saillard, Marianne; Cassol, Davide

    2017-04-01

    Cosmic Ray Exposure (CRE) dating on river polished surfaces from gorges located in the Var River catchment (Southern French Alps) reveals high incision rate pulses (>10 mm.yr-1) related with climate changes, and in particular with glacial-interglacial transitions. In addition, they show that the onset of the last deglaciation in this area occurred shortly after the Last Glacial Maximum (LGM), i.e. 16-19 ka ago. Extrapolating these results to longer time scales suggests that the post 140 ka history of this landscape was dominated by fluvial incision. Inverse models based on the stream power law are then used to determine uplift rate variations in several small tributaries of this catchment with respect to the main channel. These inverse models show that all tributaries have consistent incision rate histories with alternating high and low values, and a comparison with global temperature curves shows that these variations significantly correlate with quaternary climate changes. We suggest that during warm periods, a wave of regressive erosion propagates in the main channel, while its tributaries deeply incise their substratum to catch up with the falling base-level. We then perform forward models of river incision and simulate the incision of the main channel system over a time span of 600 ka. This model allows us to extract time and space incision rate variations along the Tinée River channel (the largest tributary of the Var River). With a background of a few mm.yr-1, incision rate can increase up to more than 10 mm.yr-1 during short episodes, in agreement with CRE dating. 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 kyr ago.

  19. DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA.

    Science.gov (United States)

    Zheng, Yuxuan; Lorenzo, Claire; Beal, Peter A

    2017-04-07

    Adenosine deaminases that act on RNA (ADARs) carry out adenosine (A) to inosine (I) editing reactions with a known requirement for duplex RNA. Here, we show that ADARs also react with DNA/RNA hybrid duplexes. Hybrid substrates are deaminated efficiently by ADAR deaminase domains at dA-C mismatches and with E to Q mutations in the base flipping loop of the enzyme. For a long, perfectly matched hybrid, deamination is more efficient with full length ADAR2 than its isolated deaminase domain. Guide RNA strands for directed DNA editing by ADAR were used to target six different 2΄-deoxyadenosines in the M13 bacteriophage ssDNA genome. DNA editing efficiencies varied depending on the sequence context of the editing site consistent with known sequence preferences for ADARs. These observations suggest the reaction within DNA/RNA hybrids may be a natural function of human ADARs. In addition, this work sets the stage for development of a new class of genome editing tools based on directed deamination of 2΄-deoxyadenosines in DNA/RNA hybrids. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. 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...

  1. Mycobacterium tuberculosis UvrB Is a Robust DNA-Stimulated ATPase That Also Possesses Structure-Specific ATP-Dependent DNA Helicase Activity.

    Science.gov (United States)

    Thakur, Manoj; Kumar, Mohan B J; Muniyappa, K

    2016-10-18

    Much is known about the Escherichia coli nucleotide excision repair (NER) pathway; however, very little is understood about the proteins involved and the molecular mechanism of NER in mycobacteria. In this study, we show that Mycobacterium tuberculosis UvrB (MtUvrB), which exists in solution as a monomer, binds to DNA in a structure-dependent manner. A systematic examination of MtUvrB substrate specificity reveals that it associates preferentially with single-stranded DNA, duplexes with 3' or 5' overhangs, and linear duplex DNA with splayed arms. Whereas E. coli UvrB (EcUvrB) binds weakly to undamaged DNA and has no ATPase activity, MtUvrB possesses intrinsic ATPase activity that is greatly stimulated by both single- and double-stranded DNA. Strikingly, we found that MtUvrB, but not EcUvrB, possesses the DNA unwinding activity characteristic of an ATP-dependent DNA helicase. The helicase activity of MtUvrB proceeds in the 3' to 5' direction and is strongly modulated by a nontranslocating 5' single-stranded tail, indicating that in addition to the translocating strand it also interacts with the 5' end of the substrate. The fraction of DNA unwound by MtUvrB decreases significantly as the length of the duplex increases: it fails to unwind duplexes longer than 70 bp. These results, on one hand, reveal significant mechanistic differences between MtUvrB and EcUvrB and, on the other, support an alternative role for UvrB in the processing of key DNA replication intermediates. Altogether, our findings provide insights into the catalytic functions of UvrB and lay the foundation for further understanding of the NER pathway in M. tuberculosis.

  2. 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.

  3. 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.

  4. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone

    DEFF Research Database (Denmark)

    Kumar, P.; Sharma, P. K.; Madsen, Charlotte S.

    2013-01-01

    Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.......Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand....

  5. Human DNA polymerase η accommodates RNA for strand extension.

    Science.gov (United States)

    Su, Yan; Egli, Martin; Guengerich, F Peter

    2017-11-03

    Ribonucleotides are the natural analogs of deoxyribonucleotides, which can be misinserted by DNA polymerases, leading to the most abundant DNA lesions in genomes. During replication, DNA polymerases tolerate patches of ribonucleotides on the parental strands to different extents. The majority of human DNA polymerases have been reported to misinsert ribonucleotides into genomes. However, only PrimPol, DNA polymerase α, telomerase, and the mitochondrial human DNA polymerase (hpol) γ have been shown to tolerate an entire RNA strand. Y-family hpol η is known for translesion synthesis opposite the UV-induced DNA lesion cyclobutane pyrimidine dimer and was recently found to incorporate ribonucleotides into DNA. Here, we report that hpol η is able to bind DNA/DNA, RNA/DNA, and DNA/RNA duplexes with similar affinities. In addition, hpol η, as well as another Y-family DNA polymerase, hpol κ, accommodates RNA as one of the two strands during primer extension, mainly by inserting dNMPs opposite unmodified templates or DNA lesions, such as 8-oxo-2'-deoxyguanosine or cyclobutane pyrimidine dimer, even in the presence of an equal amount of the DNA/DNA substrate. The discovery of this RNA-accommodating ability of hpol η redefines the traditional concept of human DNA polymerases and indicates potential new functions of hpol η in vivo . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Structure of DNA damaged by UV and psoralen

    International Nuclear Information System (INIS)

    Sung-hou Kim; Tomic, M.T.; Wemmer, D.E.; Pearlman, D.; Holbrook, S.

    1988-01-01

    The authors have used NMR methods to determine a three-dimensional model of an 8 base-pair DNA fragment cross-linked with psoralen. The duplex form of the self-complementary deoxyribonucleotide d-GGGTACCC, contains a psoralen cross-linkable site at the center of the duplex. The cross-link was formed by UV irradiation of a mixture of the purified DNA octamer and 4'-(aminomethyl)-4,5',8-trimethylpsoralen (AMT). Structural information was obtained using one and two-dimensional NMR techniques. Two-dimensional NOE experiments were used to assign the spectrum and estimate distances for many pairs of protons in the cross-linked DNA. Structural parameters obtained are qualitatively consistent with a previously proposed model for kinked and unwound cross-linked B-form DNA derived from crystallography and molecular modeling. The NMR derived model has a 53 degree bend into the major groove occuring primarily at the site of drug addition, and a 56 degree unwinding spanning the 8 base pair duplex. (author)

  7. Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme

    Czech Academy of Sciences Publication Activity Database

    Cséfalvay, Eva; Lapkouski, Mikalai; Guzanová, Alena; Cséfalvay, Ladislav; Baikova, T.; Shevelev, Igor; Bialevich, V.; Shamayeva, Katerina; Janščák, Pavel; Kutá-Smatanová, Ivana; Panjikar, S.; Carey, J.; Weiserová, Marie; Ettrich, Rüdiger

    2015-01-01

    Roč. 10, č. 6 (2015), e0128700 E-ISSN 1932-6203 R&D Projects: GA ČR GAP207/12/2323; GA ČR GAP305/10/0281 Institutional support: RVO:67179843 ; RVO:61388971 ; RVO:68378050 Keywords : Escherichia - Coli * Endonuclease ecor1241 * HSDR subunit * RECBCD enzyme * proteins * genes * helicase * sequence * family * domain Subject RIV: CE - Biochemistry Impact factor: 3.057, year: 2015

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

    Directory of Open Access Journals (Sweden)

    Koray Yurtisik

    2013-09-01

    Full Text Available 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 microstructure without compromising the welding efficiency. 11.1 mm-thick standard duplex stainless steel plates were joined in a single-pass using this novel technique. Same plates were also subjected to conventional gas metal arc and plasma arc welding processes, providing benchmarks for the investigation of the weldability of the material. In the first place, the hybrid welding process enabled us to achieve less heat input compared to gas metal arc welding. Consequently, the precipitation of secondary phases, which are known to be detrimental to the toughness and corrosion resistance of duplex stainless steels, was significantly suppressed in both fusion and heat affected zones. Secondly, contrary to other keyhole techniques, proper cooling time and weld metal chemistry were achieved during the process, facilitating sufficient reconstructive transformation of austenite in the ferrite phase.

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

    Science.gov (United States)

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

    2017-11-01

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

  10. A morphological evaluation of a duplex stainless steel processed by high energy Ball Mill

    International Nuclear Information System (INIS)

    Yonekubo, Ariane Emi; Cintho, Osvaldo Mitsuyuki; Aguiar, Denilson Jose Marcolino de; Capocchi, Jose Deodoro Trani

    2009-01-01

    The duplex stainless steels are formed by a ferrite and austenite mixture, giving them a combination of properties. Commercially, these steels are hot rolled, developing an anisotropic, alternated ferrite and austenite elongated lamellae microstructure. In this work, a duplex stainless steel was produced by the mixture of elementary powders with the composition Fe-19.5Cr-5Ni processed in an ATTRITOR ball mill during periods up to 15 hours. The powders obtained were compressed in specimens and were heat treated in the temperatures of 900, 1050 and 1200 °C during 1 hour and analysed by x ray diffraction, optic microscopy, scanning electron microscopy and energy dispersion spectroscopy. An optimized microstructure with ultrafine, equiaxial and regular duplex microstructure was obtained in the 15 hour milling and 1200 °C heat treatment. Afterwards, a commercially super duplex stainless steel UNS S32520 was aged at 800 °C aiming the precipitation of σ phase in order to reduce its toughness and then, milled in SPEX mill. The resulting microstructure was a very fine duplex type with irregular grain boundary morphology duo to the grain growth barrier promoted by the renascent σ phase particles during sintering process. (author)

  11. Heat treatment temperature influence on ASTM A890 GR 6A super duplex stainless steel microstructure

    International Nuclear Information System (INIS)

    Martins, Marcelo; Casteletti, Luiz Carlos

    2005-01-01

    Duplex and super duplex stainless steels are ferrous alloys with up to 26% chromium, 8% nickel, 5% molybdenum and 0.3% nitrogen, which are largely used in applications in media containing ions from the halogen family, mainly the chloride ion (Cl - ). The emergence of this material aimed at substituting Copper-Nickel alloys (Cupro-Nickel) that despite presenting good corrosion resistance, has mechanical properties quite inferior to steel properties. The metallurgy of duplex and super duplex stainless steel is complex due to high sensitiveness to sigma phase precipitation that becomes apparent, due to the temperatures they are exposed on cooling from solidification as well as from heat treatment processes. The objective of this study was to verify the influence of heat treating temperatures on the microstructure and hardness of ASTM A890/A890M Gr 6A super duplex stainless steel type. Microstructure control is of extreme importance for castings, as the chemical composition and cooling during solidification inevitably provide conditions for precipitation of sigma phase. Higher hardness in these materials is directly associated to high sigma phase concentration in the microstructure, precipitated in the ferrite/austenite interface. While heat treatment temperature during solution treatment increases, the sigma phase content in the microstructure decreases and consequently, the material hardness diminishes. When the sigma phase was completely dissolved by the heat treatment, the material hardness was influenced only due to ferrite and austenite contents in the microstructure

  12. Atomistic details of the molecular recognition of DNA-RNA hybrid ...

    Indian Academy of Sciences (India)

    127, No. 10, October 2015, pp. 1701–1713. c Indian Academy of Sciences. DOI 10.1007/s12039-015-0942-7. Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme. GORLE SURESH and U DEVA PRIYAKUMAR∗. Center for Computational Natural Sciences and Bioinformatics, ...

  13. Phacoemulsification versus small incision cataract surgery in patients with uveitis

    Directory of Open Access Journals (Sweden)

    Rahul Bhargava

    2015-10-01

    Full Text Available AIM: To compare the safety and efficacy of phacoemulsification and small incision cataract surgery (SICS in patients with uveitic cataract.METHODS:In aprospective, randomized multi-centric study, consecutive patients with uveitic cataract were randomized to receive phacoemulsification or manual SICS by either of two surgeons well versed with both the techniques. A minimum inflammation free period of 3mo (defined as less than 5 cells per high power field in anterior chamber was a pre-requisite for eligibility for surgery. Superior scleral tunnel incisions were used for both techniques. Improvement in visual acuity post-operatively was the primary outcome measure and the rate of post-operative complications and surgical time were secondary outcome measures, respectively. Means of groups were compared using t-tests. One way analysis of variance (ANOVA was used when there were more than two groups. Chi-square tests were used for proportions. Kaplan Meyer survival analysis was done and means for survival time was estimated at 95% confidence interval (CI. A P value of <0.05 was considered statistically significant.RESULTS:One hundred and twenty-six of 139 patients (90.6% completed the 6-month follow-up. Seven patients were lost in follow up and another six excluded due to either follow-up less than six months (n=1 or inability implant an intraocular lens (IOL because of insufficient capsular support following posterior capsule rupture (n=5. There was significant improvement in vision after both the procedures (paired t-test; P<0.001. On first postoperative day, uncorrected distance visual acuity (UDVA was 20/63 or better in 31 (47% patients in Phaco group and 26 (43.3% patients in SICS group (P=0.384. The mean surgically induced astigmatism (SIA was 0.86±0.34 dioptres (D in the phacoemulsification group and 1.16±0.28 D in SICS group. The difference between the groups was significant (t-test, P=0.002. At 6mo, corrected distance visual acuity (CDVA

  14. Early clinical outcomes after small incision lenticule extraction surgery (SMILE).

    Science.gov (United States)

    Recchioni, Alberto; Hartwig, Andreas; Dermott, Jay; Vaswani, Sundeep; Bhatt, Jay; Morris, Robert; O'Donnell, Clare

    2018-02-01

    Dry eye is known to impact on clinical outcomes after laser vision correction and the use of a newer 'all femtosecond laser' surgical approach may be associated with less impact on the ocular surface post-operatively. The purpose of this study was to evaluate the early clinical outcomes and tear instability after the first small incision lenticule extraction (SMILE) cases undertaken by three surgeons at a single site in the UK. Retrospective audit. Seventy-one eyes of 37 patients underwent SMILE surgery using the Zeiss VisuMax laser system (Carl Zeiss Meditec, Germany). Uncorrected and corrected distance visual acuity, spherical equivalent refraction, fluorescein enhanced tear break up time, simulated keratometry and complications were evaluated pre- and post-operatively where applicable. The study population consisted of 21 males and 16 females. The mean±standard deviation age was 33±8years. The results showed that 100% of eyes achieved 20/40 or better and 88% achieved 20/20 or better uncorrected distance visual acuity. The spherical equivalent refraction after surgery was within ±0.50D in 82% of eyes at three months. There was no significant difference in tear break up time from pre-operative levels at three months. Complications were infrequent. This early data from surgeons' first SMILE procedures suggest SMILE provides good outcomes in terms of refractive predictability and visual acuity with minimal impact on the tear film. Longitudinal research will further improve our understanding of the longer-term impact of SMILE on clinical outcomes, ocular surface metrics and patient reported outcomes. Copyright © 2017. Published by Elsevier Ltd.

  15. Polydioxanone versus polypropylene closure for midline abdominal incisions

    International Nuclear Information System (INIS)

    Naz, S.; Jamali, M.A.

    2017-01-01

    Background: Midline laparotomy is the most common technique of abdominal incisions because it is simple, provides adequate exposure to all four quadrants, and is rapid to open. A major problem after midline laparotomy remains the adequate technique of abdominal fascia closure. This study was conducted to see the role of Polydioxanone and Prolene for midline abdominal closure in terms of postoperative wound infection and wound pain. Methods: This study was carried out at surgical unit II, Federal Government Services Hospital Islamabad. Patients were equally divided in two groups, i.e., A and B. Groups A and B patients undergone midline abdominal closure with Polydioxanone number 1 and Polypropylene number 1 sutures respectively. Results: Total 620 patients were included in this study. Post-operative wound pain score according to Visual analogue scale (VAS) was compared in terms of no pain (0), mild pain (1-3), moderate pain (4-6), severe pain (7-9). In group A (Polydioxanone), the frequency and percentages of no, mild, moderate and severe pain were 101 (32.6%), 95 (30.6%), 81 (26.1%) and 33 (10.6%) respectively, where as in group B (polypropylene) it was 82 (26.5%), 43 (13.9%), 59 (19%) and 126 (40.6%) respectively. Similarly, the frequency and percentages of post-operative wound infection in group A (Polydioxanone) and group B (polypropylene) was 105 (33.9%) and 208 (67.1%) respectively. Conclusion: Polydioxanone results in less wound pain and wound infection when compared to Polypropylene. (author)

  16. Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

    Science.gov (United States)

    Kékedy-Nagy, László; Shipovskov, Stepan; Ferapontova, Elena E

    2016-08-16

    Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the "on-off" signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami , E. ; Clima , L. ; Gothelf , K. ; Ferapontova , E. E. Anal. Chem. 2011 , 83 , 1594 ) providing the robust "off-on" nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.

  17. Office-based relaxing incision procedure for correction of astigmatism after deep anterior lamellar keratoplasty

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Javadi

    2017-01-01

    Conclusion: Office-based relaxing incision is a safe and effective procedure for the treatment of corneal graft astigmatism after DALK. This approach effectively decreases the need for the more costly alternative in the operating room.

  18. Relaxation incisions of venomous snake "Japanese mamushi" bites to the hand

    Directory of Open Access Journals (Sweden)

    Sugamata A

    2011-12-01

    Full Text Available Akira Sugamata, Naoki Yoshizawa, Takahiro OkadaDepartment of Plastic and Reconstructive Surgery, Tokyo Medical University Hachioji Medical Center, Tokyo, JapanAbstract: Gloydius blomhoffii, commonly known as Japanese mamushi, is a venomous viper species found widely in Japan. The most frequently bitten regions are the fingers and toes, and severe swelling causes compression of peripheral arteries and/or compartment syndrome of the extremities. We experienced four cases of mamushi bites to the hand, and undertook relaxation incision in the hands of three of these patients. As a result, the patients who underwent relaxation incision did not show any skin necrosis or permanent sensory disturbance in the affected fingers. Relaxation incision can be useful to not only decompress subcutaneous and compartment pressure of the hand, but also to wash out the venom from the bitten region by improving venous and lymphatic drainage.Keywords: mamushi, snakebite, viper, relaxation incision

  19. Type of incision does not predict abdominal wall outcome after emergency surgery for colonic anastomotic leakage

    DEFF Research Database (Denmark)

    Jensen, Kristian Kiim; Oma, Erling; Harling, Henrik

    2017-01-01

    PURPOSE: Most literature on abdominal incision is based on patients undergoing elective surgery. In a cohort of patients with anastomotic leakage after colonic cancer resection, we analyzed the association between type of incision, fascial dehiscence, and incisional hernia. METHODS: Data were...... extracted from the Danish Colorectal Cancer Group database and merged with information from the Danish National Patient Register. All patients with anastomotic leakage after colonic resection in Denmark from 2001 until 2008 were included and surgical records on re-operations were retrieved. The primary...... for anastomotic leakage were included with a median follow-up of 5.4 years. Incisional hernia occurred in 41 of 227 (15.3%) patients undergoing midline incision compared with 14 of 81 (14.7%) following transverse incision, P = 1.00. After adjusting for confounders, there was no association between the type...

  20. Induced astigmatism in a 6.0 mm no-stitch frown incision.

    Science.gov (United States)

    Sinskey, R M; Stoppel, J O

    1994-07-01

    Fifty-five consecutive patients had cataract extraction with a 6 mm no-stitch frown incision and implantation of a 6 mm optic three-piece posterior chamber lens. Vector analysis calculations of diopters (D) of mean induced keratometric astigmatism for this incision were 0.70 D at one day, 0.76 D at one week, 0.50 D at one month, and 0.50 D at three months. The Naeser's polar value showed a mean with-the-rule astigmatism of +0.42 D at one day and -0.08 D against-the-rule astigmatism at three months. The results suggest that the 6.0 mm no-stitch frown incision induces a low postoperative astigmatism and provides a stable incision.