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Sample records for single-strand annealing ssa

  1. BCR-ABL promotes the frequency of mutagenic single-strand annealing DNA repair

    Science.gov (United States)

    Fernandes, Margret S.; Reddy, Mamatha M.; Gonneville, Jeffrey R.; DeRoo, Scott C.; Podar, Klaus; Griffin, James D.; Weinstock, David M.

    2009-01-01

    Intracellular oxidative stress in cells transformed by the BCR-ABL oncogene is associated with increased DNA double-strand breaks. Imprecise repair of these breaks can result in the accumulation of mutations, leading to therapy-related drug resistance and disease progression. Using several BCR-ABL model systems, we found that BCR-ABL specifically promotes the repair of double-strand breaks through single-strand annealing (SSA), a mutagenic pathway that involves sequence repeats. Moreover, our results suggest that mutagenic SSA repair can be regulated through the interplay between BCR-ABL and extrinsic growth factors. Increased SSA activity required Y177 in BCR-ABL, as well as a functional PI3K and Ras pathway downstream of this site. Furthermore, our data hint at a common pathway for DSB repair whereby BCR-ABL, Tel-ABL, Tel-PDGFR, FLT3-ITD, and Jak2V617F all increase mutagenic repair. This increase in SSA may not be sufficiently suppressed by tyrosine kinase inhibitors in the stromal microenvironment. Therefore, drugs that target growth factor receptor signaling represent potential therapeutic agents to combat tyrosine kinase-induced genomic instability. PMID:19571320

  2. Functional characterization of an alkaline exonuclease and single strand annealing protein from the SXT genetic element of Vibrio cholerae

    Directory of Open Access Journals (Sweden)

    Huang Jian-dong

    2011-04-01

    Full Text Available Abstract Background SXT is an integrating conjugative element (ICE originally isolated from Vibrio cholerae, the bacterial pathogen that causes cholera. It houses multiple antibiotic and heavy metal resistance genes on its ca. 100 kb circular double stranded DNA (dsDNA genome, and functions as an effective vehicle for the horizontal transfer of resistance genes within susceptible bacterial populations. Here, we characterize the activities of an alkaline exonuclease (S066, SXT-Exo and single strand annealing protein (S065, SXT-Bet encoded on the SXT genetic element, which share significant sequence homology with Exo and Bet from bacteriophage lambda, respectively. Results SXT-Exo has the ability to degrade both linear dsDNA and single stranded DNA (ssDNA molecules, but has no detectable endonuclease or nicking activities. Adopting a stable trimeric arrangement in solution, the exonuclease activities of SXT-Exo are optimal at pH 8.2 and essentially require Mn2+ or Mg2+ ions. Similar to lambda-Exo, SXT-Exo hydrolyzes dsDNA with 5'- to 3'-polarity in a highly processive manner, and digests DNA substrates with 5'-phosphorylated termini significantly more effectively than those lacking 5'-phosphate groups. Notably, the dsDNA exonuclease activities of both SXT-Exo and lambda-Exo are stimulated by the addition of lambda-Bet, SXT-Bet or a single strand DNA binding protein encoded on the SXT genetic element (S064, SXT-Ssb. When co-expressed in E. coli cells, SXT-Bet and SXT-Exo mediate homologous recombination between a PCR-generated dsDNA fragment and the chromosome, analogous to RecET and lambda-Bet/Exo. Conclusions The activities of the SXT-Exo protein are consistent with it having the ability to resect the ends of linearized dsDNA molecules, forming partially ssDNA substrates for the partnering SXT-Bet single strand annealing protein. As such, SXT-Exo and SXT-Bet may function together to repair or process SXT genetic elements within infected V

  3. Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities

    DEFF Research Database (Denmark)

    Guo, Yang; Kragelund, Birthe Brandt; White, Malcolm F.

    2015-01-01

    encoding proteins of unknown function and forming an operon with ORF207 (gp19). SIRV2 gp17 was found to be a single-stranded DNA (ssDNA) binding protein different in structure from all previously characterized ssDNA binding proteins. Mutagenesis of a few conserved basic residues suggested a U......-shaped binding path for ssDNA. The recombinant gp18 showed an ssDNA annealing activity often associated with helicases and recombinases. To gain insight into the biological role of the entire operon, we characterized SIRV2 gp19 and showed it to possess a 5'→3' ssDNA exonuclease activity, in addition...... for rudiviruses and the close interaction among the ssDNA binding, annealing and nuclease proteins strongly point to a role of the gene operon in genome maturation and/or DNA recombination that may function in viral DNA replication/repair....

  4. Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus radiodurans Bacterium.

    Directory of Open Access Journals (Sweden)

    Solenne Ithurbide

    2015-10-01

    Full Text Available The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known. It is able to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Our work aims to highlight the genes involved in recombination between 438 bp direct repeats separated by intervening sequences of various lengths ranging from 1,479 bp to 10,500 bp to restore a functional tetA gene in the presence or absence of radiation-induced DNA double strand breaks. The frequency of spontaneous deletion events between the chromosomal direct repeats were the same in recA+ and in ΔrecA, ΔrecF, and ΔrecO bacteria, whereas recombination between chromosomal and plasmid DNA was shown to be strictly dependent on the RecA and RecF proteins. The presence of mutations in one of the repeated sequence reduced, in a MutS-dependent manner, the frequency of the deletion events. The distance between the repeats did not influence the frequencies of deletion events in recA+ as well in ΔrecA bacteria. The absence of the UvrD protein stimulated the recombination between the direct repeats whereas the absence of the DdrB protein, previously shown to be involved in DNA double strand break repair through a single strand annealing (SSA pathway, strongly reduces the frequency of RecA- (and RecO- independent deletions events. The absence of the DdrB protein also increased the lethal sectoring of cells devoid of RecA or RecO protein. γ-irradiation of recA+ cells increased about 10-fold the frequencies of the deletion events, but at a lesser extend in cells devoid of the DdrB protein. Altogether, our results suggest a major role of single strand annealing in DNA repeat deletion events in bacteria devoid of the RecA protein, and also in recA+ bacteria exposed to ionizing radiation.

  5. Escaping the cut by restriction enzymes through single-strand self-annealing of host-edited 12-bp and longer synthetic palindromes.

    Science.gov (United States)

    Castro-Chavez, Fernando

    2012-02-01

    Palindromati, the massive host-edited synthetic palindromic contamination found in GenBank, is illustrated and exemplified. Millions of contaminated sequences with portions or tandems of such portions derived from the ZAP adaptor or related linkers are shown (1) by the 12-bp sequence reported elsewhere, exon Xb, 5' CCCGAATTCGGG 3', (2) by a 22-bp related sequence 5' CTCGTGCCGAATTCGGCACGAG 3', and (3) by a longer 44-bp related sequence: 5' CTCGTGCCGAATTCGGCACGAGCTCGTGCCGAATTCGGCACGAG 3'. Possible reasons for why those long contaminating sequences continue in the databases are presented here: (1) the recognition site for the plus strand (+) is single-strand self-annealed; (2) the recognition site for the minus strand (-) is not only single-strand self-annealed but also located far away from the single-strand self-annealed plus strand, rendering impossible the formation of the active EcoRI enzyme dimer to cut on 5' G/AATTC 3', its target sequence. As a possible solution, it is suggested to rely on at least two or three independent results, such as sequences obtained by independent laboratories with the use, preferably, of independent sequencing methodologies. This information may help to develop tools for bioinformatics capable to detect/remove these contaminants and to infer why some damaged sequences which cause genetic diseases escape detection by the molecular quality control mechanism of cells and organisms, being undesirably transferred unchecked through the generations.

  6. Single--stranded DNA mycoplasmaviruses

    Energy Technology Data Exchange (ETDEWEB)

    Maniloff, J.; Das, J.; Nowak, J.A.

    1978-01-01

    Two general types of single--stranded DNA bacteriophases have been described, icosahedral virions (e.g., 0X174) and filamentous virions (e.g., M13). Mycoplasmavirus MVL51 appears to represent another type of single--stranded DNA phage, with a genome size close to that of 0X174 and a nonlytic mode of infection like that of filamentous phages. The bullet shaped MVL51 morphology is unlike that of other known phages.

  7. Hole hopping rates in single strand oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Borrelli, Raffaele [Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, TO (Italy); Capobianco, Amedeo [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy); Peluso, Andrea, E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy)

    2014-08-31

    Highlights: • DNA hole transfer rates have been computed. • Delocalized adenine domains significantly affect hole transfer rates in DNA. • Franck–Condon weighted density of state from DFT normal modes. • DNA application in molecular electronics. - Abstract: The rates of hole transfer between guanine and adenine in single strand DNA have been evaluated by using Fermi’s golden rule and Kubo’s generating function approach for the Franck–Condon weighted density of states. The whole sets of the normal modes and vibrational frequencies of the two nucleobases, obtained at DFT/B3LYP level of calculation, have been considered in computations. The results show that in single strand the pyramidalization/planarization mode of the amino groups of both nucleobases plays the major role. At room temperature, the Franck–Condon density of states extends over a wide range of hole site energy difference, 0–1 eV, giving some hints about the design of oligonucleotides of potential technological interest.

  8. DNA replication of single-stranded Escherichia coli DNA phages

    NARCIS (Netherlands)

    Baas, P.D.

    1985-01-01

    Research on single-stranded DNA phages has contributed tremendously to our knowledge of several fundamental life-processes. The small size of their genomes and the fast rate at which they multiply in their host, Escherichia coil, made them attractive candidates for various studies. There

  9. Detection of polymorphisms in leptin gene using single strand ...

    African Journals Online (AJOL)

    student

    Sachs B1 variant. Nucleic Acids Res. 19, 405-406. Barroso, A., Dunner, S. & Cañon, J., 1998. Technical note: detection of bovine kappa-casein variants A, B,. C and E by means of Polymerase Chain Reaction-Single Strand Conformation ...

  10. Self-assembly of complex two-dimensional shapes from single-stranded DNA tiles.

    Science.gov (United States)

    Wei, Bryan; Vhudzijena, Michelle K; Robaszewski, Joanna; Yin, Peng

    2015-05-08

    Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this article, we describe detailed protocols on how to fabricate sophisticated 2D shapes through the self-assembly of uniquely addressable single-stranded DNA tiles which act as molecular pixels on a molecular canvas. Each single-stranded tile (SST) is a 42-nucleotide DNA strand composed of four concatenated modular domains which bind to four neighbors during self-assembly. The molecular canvas is a rectangle structure self-assembled from SSTs. A prescribed complex 2D shape is formed by selecting the constituent molecular pixels (SSTs) from a 310-pixel molecular canvas and then subjecting the corresponding strands to one-pot annealing. Due to the modular nature of the SST approach we demonstrate the scalability, versatility and robustness of this method. Compared with alternative methods, the SST method enables a wider selection of information polymers and sequences through the use of de novo designed and synthesized short DNA strands.

  11. Improved single-strand DNA sizing accuracy in capillary electrophoresis.

    OpenAIRE

    Rosenblum, B B; Oaks, F; Menchen, S; Johnson, B

    1997-01-01

    Interpolation algorithms can be developed to size unknown single-stranded (ss) DNA fragments based on their electrophoretic mobilities, when they are compared with the mobilities of standard fragments of known sizes; however, sequence-specific anomalous electrophoretic migration can affect the accuracy and precision of the called sizes of the fragments. We used the anomalous migration of ssDNA fragments to optimize denaturation conditions for capillary electrophoresis. The capillary electroph...

  12. Single-strand DNA molecule translocation through nanoelectrode gaps

    International Nuclear Information System (INIS)

    Zhao Xiongce; Payne, Christina M; Cummings, Peter T; Lee, James W

    2007-01-01

    Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is ∼1.5 nm. The minimum force required to initiate the translocation within nanoseconds is ∼0.3 nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation

  13. Programmable autonomous synthesis of single-stranded DNA

    Science.gov (United States)

    Kishi, Jocelyn Y.; Schaus, Thomas E.; Gopalkrishnan, Nikhil; Xuan, Feng; Yin, Peng

    2018-02-01

    DNA performs diverse functional roles in biology, nanotechnology and biotechnology, but current methods for autonomously synthesizing arbitrary single-stranded DNA are limited. Here, we introduce the concept of primer exchange reaction (PER) cascades, which grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways. PER synthesis happens in a programmable, autonomous, in situ and environmentally responsive fashion, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal-processing and actuation capabilities. We experimentally demonstrate a nanodevice that transduces the detection of a trigger RNA into the production of a DNAzyme that degrades an independent RNA substrate, a signal amplifier that conditionally synthesizes long fluorescent strands only in the presence of a particular RNA signal, molecular computing circuits that evaluate logic (AND, OR, NOT) combinations of RNA inputs, and a temporal molecular event recorder that records in the PER transcript the order in which distinct RNA inputs are sequentially detected.

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

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

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

  15. Elastic properties of alternative versus single-stranded leveling archwires.

    Science.gov (United States)

    Rucker, Brian K; Kusy, Robert P

    2002-11-01

    The strength, stiffness, and range of single-stranded stainless steel (SS) and superelastic nickel-titanium (NiTi) archwires were compared with those of alternative leveling products, including nylon-coated and multistranded wires. Wire cross-sections were photographed after being potted in polymer, ground, and polished. Because the rectangular wires had rounded or beveled corners, gravimetric measurements and specific gravity calculations quantified the actual polygonal cross-sectional areas versus the ideal rectangular cross-sectional areas. Beveling reduced the cross-sectional areas by 7% to 8%; this decreased the wire stiffnesses by 15% to 19%. Using a testing machine, we measured the yield strengths, the elastic limits, and the ultimate tensile strengths in tension, and wire stiffnesses in 3-point bending. From cyclic loading tests, the elastic limits of the superelastic NiTi wires were approximately 90% and 45% of their ultimate tensile strengths for the round and rectangular wires, respectively. Using the measurements of the mechanical properties and geometric parameters of each wire, we computed the elastic property ratios (EPRs) versus a 16-mil (0.41 mm) NiTi wire. The single-stranded NiTi wires outperformed the alternative wires, whose EPRs varied from 0.05 to 0.32 for strength, from 0.11 to 1.55 for stiffness, and from 0.10 to 0.80 for range. Based on the current study and a review of the orthodontic literature, few superelastic wires are activated sufficiently in vivo to exhibit superelastic behavior. Therefore, the EPR data reported here for superelastic wires truly represent their performance in most clinical situations.

  16. Single-stranded regions in transforming deoxyribonucleic acid after uptake by competent Haemophilus influenzae

    Energy Technology Data Exchange (ETDEWEB)

    Sedgwick, B.; Setlow, J.K.

    1976-02-01

    About 15% of donor deoxyribonucleic acid (DNA) is single stranded immediately after uptake into competent Haemophilus influenzae wild-type cells, as judged by its sensitivity to S1 endonuclease. This amount decreases to 4 to 5% by 30 min after uptake. Mutants which are defective in the covalent association of recipient and donor DNA form little or no S1 endonuclease-sensitive donor. At 17 C donor DNA taken up by the wild type contains single-stranded regions although there is no observable association, either covalent or noncovalent. The single-stranded regions are at the ends of donor DNA molecules, as judged by the unchanged sedimentation velocity after S1 endonuclease digestion. The amount of single-stranded donor remains constant at 17 C for more than 60 min after uptake, suggesting that the decrease observed at 37 C is the result of association of single-stranded ends with single-stranded regions of recipient cell DNA. Three sequential steps necessary for the integration of donor DNA into recipient DNA are proposed: the synthesis of single-stranded regions in recipient DNA, the interaction of donor DNA with recipient DNA resulting in the production of single-stranded ends on donor DNA, and the stable pairing of homologous single-stranded regions. (auth)

  17. Regions of incompatibility in single-stranded DNA bacteriophages phi X174 and G4

    NARCIS (Netherlands)

    van der Avoort, H. G.; van der Ende, A.; van Arkel, G. A.; Weisbeek, P. J.

    1984-01-01

    The intracellular presence of a recombinant plasmid containing the intercistronic region between the genes H and A of bacteriophage phi X174 strongly inhibits the conversion of infecting single-stranded phi X DNA to parental replicative-form DNA. Also, transfection with single-stranded or

  18. Sulforaphane induces DNA single strand breaks in cultured human cells

    Energy Technology Data Exchange (ETDEWEB)

    Sestili, Piero, E-mail: piero.sestili@uniurb.it [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Paolillo, Marco [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Lenzi, Monia [Dipartimento di Farmacologia, Universita degli Studi di Bologna, Via Irnerio 48, 40126 Bologna (Italy); Colombo, Evelin; Vallorani, Luciana; Casadei, Lucia; Martinelli, Chiara [Dipartimento di Scienze Biomolecolari, Via Maggetti, 21, Universita degli Studi di Urbino ' Carlo Bo' , 61029 Urbino, PU (Italy); Fimognari, Carmela [Dipartimento di Farmacologia, Universita degli Studi di Bologna, Via Irnerio 48, 40126 Bologna (Italy)

    2010-07-07

    Sulforaphane (SFR), an isothiocyanate from cruciferous vegetables, possesses growth-inhibiting and apoptosis-inducing activities in cancer cell lines. Recently, SFR has been shown to promote the mitochondrial formation of reactive oxygen species (ROS) in human cancer cell lines. The present study was undertaken to see whether SFR-derived ROS might cause DNA damage in cultured human cells, namely T limphoblastoid Jurkat and human umbilical vein endothelial cells (HUVEC). 1-3 h treatments with 10-30 {mu}M SFR elicited intracellular ROS formation (as assayed with dihydrorhodamine, DHR, oxidation) as well as DNA breakage (as assessed with fast halo assay, FHA). These effects lacked cell-type specificity, since could be observed in both Jurkat and HUVEC. Differential-pH FHA analysis of damaged DNA showed that SFR causes frank DNA single strand breaks (SSBs); no DNA double strand breaks (DSBs) were found within the considered treatment times (up to 3 h). SFR-derived ROS were formed at the mitochondrial respiratory chain (MRC) level: indeed rotenone or myxothiazol (MRC Complex I and III inhibitors, respectively) abrogated ROS formation. Furthermore ROS were not formed in Jurkat cells pharmacologically depleted of respiring mitochondria (MRC-/Jurkat). Formation of ROS was causally linked to the induction of SSBs: indeed all the experimental conditions capable of preventing ROS formation also prevented the damage of nuclear DNA from SFR-intoxicated cells. As to the toxicological relevance of SSBs, we found that their prevention slightly but significantly attenuated SFR cytotoxicity, suggesting that high-dose SFR toxicity is the result of a complex series of events among which GSH depletion seems to play a pivotal role. In conclusion, the present study identifies a novel mechanism contributing to SFR toxicity which - since DNA damage is a prominent mechanism underlying the cytotoxic activity of established antineoplastic agents - might help to exploit the therapeutic value

  19. Sulforaphane induces DNA single strand breaks in cultured human cells

    International Nuclear Information System (INIS)

    Sestili, Piero; Paolillo, Marco; Lenzi, Monia; Colombo, Evelin; Vallorani, Luciana; Casadei, Lucia; Martinelli, Chiara; Fimognari, Carmela

    2010-01-01

    Sulforaphane (SFR), an isothiocyanate from cruciferous vegetables, possesses growth-inhibiting and apoptosis-inducing activities in cancer cell lines. Recently, SFR has been shown to promote the mitochondrial formation of reactive oxygen species (ROS) in human cancer cell lines. The present study was undertaken to see whether SFR-derived ROS might cause DNA damage in cultured human cells, namely T limphoblastoid Jurkat and human umbilical vein endothelial cells (HUVEC). 1-3 h treatments with 10-30 μM SFR elicited intracellular ROS formation (as assayed with dihydrorhodamine, DHR, oxidation) as well as DNA breakage (as assessed with fast halo assay, FHA). These effects lacked cell-type specificity, since could be observed in both Jurkat and HUVEC. Differential-pH FHA analysis of damaged DNA showed that SFR causes frank DNA single strand breaks (SSBs); no DNA double strand breaks (DSBs) were found within the considered treatment times (up to 3 h). SFR-derived ROS were formed at the mitochondrial respiratory chain (MRC) level: indeed rotenone or myxothiazol (MRC Complex I and III inhibitors, respectively) abrogated ROS formation. Furthermore ROS were not formed in Jurkat cells pharmacologically depleted of respiring mitochondria (MRC-/Jurkat). Formation of ROS was causally linked to the induction of SSBs: indeed all the experimental conditions capable of preventing ROS formation also prevented the damage of nuclear DNA from SFR-intoxicated cells. As to the toxicological relevance of SSBs, we found that their prevention slightly but significantly attenuated SFR cytotoxicity, suggesting that high-dose SFR toxicity is the result of a complex series of events among which GSH depletion seems to play a pivotal role. In conclusion, the present study identifies a novel mechanism contributing to SFR toxicity which - since DNA damage is a prominent mechanism underlying the cytotoxic activity of established antineoplastic agents - might help to exploit the therapeutic value of

  20. Screening for Breast Cancer Using Near-Field Infrared Spectroscopy of a Single Strand of Hair

    National Research Council Canada - National Science Library

    Erramilli, Shyamsunder

    2003-01-01

    .... In this study, we have successfully developed a new infrared method for the detection in a single strand of hair the presence of lipid deposits that were the putative cause of the observed x-ray patterns...

  1. Complex shapes self-assembled from single-stranded DNA tiles.

    Science.gov (United States)

    Wei, Bryan; Dai, Mingjie; Yin, Peng

    2012-05-30

    Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a 'single-stranded tile' (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly. Although ribbons and tubes with controlled circumferences have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands--folded into a 3 nm-by-7 nm tile and attached to four neighbouring tiles--acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.

  2. Genetic transformation of Streptococcus pneumoniae by DNA cloned into the single-stranded bacteriophage f1.

    OpenAIRE

    Barany, F; Boeke, J D

    1983-01-01

    A Staphylococcus aureus plasmid derivative, pFB9, coding for erythromycin and chloramphenicol resistance was cloned into the filamentous Escherichia coli phage f1. Recombinant phage-plasmid hybrids, designated plasmids, were isolated from E. coli and purified by transformation into Streptococcus pneumoniae. Single-stranded DNA was prepared from E. coli cells infected with two different plasmids, fBB101 and fBB103. Introduction of fully or partially single-stranded DNA into Streptococcus pneum...

  3. Saccharomyces cerevisiae Hrq1 helicase activity is affected by the sequence but not the length of single-stranded DNA.

    Science.gov (United States)

    Rogers, Cody M; Bochman, Matthew L

    2017-05-13

    Mutations in the human RecQ4 DNA helicase are associated with three different diseases characterized by genomic instability. To gain insight into how RecQ4 dysfunction leads to these pathologies, several groups have used the Saccharomyces cerevisiae RecQ4 homolog Hrq1 as an experimental model. Hrq1 displays many of the same functions as RecQ4 in vivo and in vitro. However, there is some disagreement in the literature about the effects of single-stranded DNA (ssDNA) length on Hrq1 helicase activity and the ability of Hrq1 to anneal complementary ssDNA oligonucleotides into duplex DNA. Here, we present a side-by-side comparison of Hrq1 and RecQ4 helicase activity, demonstrating that in both cases, long random-sequence 3' ssDNA tails inhibit DNA unwinding in vitro in a length-dependent manner. This appears to be due to the formation of secondary structures in the random-sequence ssDNA because Hrq1 preferentially unwound poly(dT)-tailed forks independent of ssDNA length. Further, RecQ4 is capable of ssDNA strand annealing and annealing-dependent strand exchange, but Hrq1 lacks these activities. These results establish the importance of DNA sequence in Hrq1 helicase activity, and the absence of Hrq1 strand annealing activity explains the previously identified discrepancies between S. cerevisiae Hrq1 and human RecQ4. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. POT1-independent single-strand telomeric DNA binding activities in Brassicaceae.

    Science.gov (United States)

    Shakirov, Eugene V; McKnight, Thomas D; Shippen, Dorothy E

    2009-06-01

    Telomeres define the ends of linear eukaryotic chromosomes and are required for genome maintenance and continued cell proliferation. The extreme ends of telomeres terminate in a single-strand protrusion, termed the G-overhang, which, in vertebrates and fission yeast, is bound by evolutionarily conserved members of the POT1 (protection of telomeres) protein family. Unlike most other model organisms, the flowering plant Arabidopsis thaliana encodes two divergent POT1-like proteins. Here we show that the single-strand telomeric DNA binding activity present in A. thaliana nuclear extracts is not dependent on POT1a or POT1b proteins. Furthermore, in contrast to POT1 proteins from yeast and vertebrates, recombinant POT1a and POT1b proteins from A. thaliana, and from two additional Brassicaceae species, Arabidopsis lyrata and Brassica oleracea (cauliflower), fail to bind single-strand telomeric DNA in vitro under the conditions tested. Finally, although we detected four single-strand telomeric DNA binding activities in nuclear extracts from B. oleracea, partial purification and DNA cross-linking analysis of these complexes identified proteins that are smaller than the predicted sizes of BoPOT1a or BoPOT1b. Taken together, these data suggest that POT1 proteins are not the major single-strand telomeric DNA binding activities in A. thaliana and its close relatives, underscoring the remarkable functional divergence of POT1 proteins from plants and other eukaryotes.

  5. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase.

    Science.gov (United States)

    Gansauge, Marie-Theres; Gerber, Tobias; Glocke, Isabelle; Korlevic, Petra; Lippik, Laurin; Nagel, Sarah; Riehl, Lara Maria; Schmidt, Anna; Meyer, Matthias

    2017-06-02

    DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3΄ biotinylated donor oligonucleotide. A thorough evaluation of this ligation scheme shows that single-stranded DNA can be ligated to adapter oligonucleotides in higher concentration than with CircLigase (an RNA ligase that was previously chosen for end-to-end ligation in single-stranded library preparation) and that biases in ligation can be minimized when choosing splinters with 7 or 8 random nucleotides. We show that ssDNA2.0 tolerates higher quantities of input DNA than CircLigase-based library preparation, is less costly and better compatible with automation. We also provide an in-depth comparison of library preparation methods on degraded DNA from various sources. Most strikingly, we find that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Repair of X-ray-induced single-strand breaks by a cell-free system

    International Nuclear Information System (INIS)

    Seki, Shuji; Ikeda, Shogo; Tsutui, Ken; Teraoka, Hirobumi

    1990-01-01

    Repair of X-ray-induced single-strand breaks of DNA was studied in vitro using an exonuclease purified from mouse ascites sarcoma (SR-C3H/He) cells. X-ray-dose-dependent unscheduled DNA synthesis was primed by the exonuclease. Repair of X-ray-induced single-strand breaks in pUC19 plasmid DNA was demonstrated by agarose gel electrophoresis after incubating the damaged DNA with the exonuclease, DNA polymerase (Klenow fragment of DNA polymerase I or DNA polymerase β purified from SR-C3H/He cells), four deoxynucleoside triphosphates, ATP and DNA ligase (T4 DNA ligase or DNA ligase I purified from calf thymus). The present results suggested that the exonuclease is involved in the initiation of repair of X-ray-induced single-strand breaks in removing 3' ends of X-ray-damaged DNA. (author)

  7. 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

  8. Rapid Synthesis of a Long Double-Stranded Oligonucleotide from a Single-Stranded Nucleotide Using Magnetic Beads and an Oligo Library.

    Directory of Open Access Journals (Sweden)

    Sumate Pengpumkiat

    Full Text Available Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry. Several methods for gene synthesis have been introduced in the growing area of genomics. In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer oligo fragments from a library were assembled through successive annealing and ligation processes, followed by PCR. First, two oligo fragments annealed to form a dsDNA molecule. The double-stranded oligo was immobilized onto magnetic beads (solid support via streptavidin-biotin binding. Next, single-stranded oligo fragments were added successively through ligation to form the complete DNA molecule. The synthesized DNA was amplified through PCR and gel electrophoresis was used to characterize the product. Sanger sequencing showed that more than 97% of the nucleotides matched the expected sequence. Extending the length of the DNA molecule by adding single-stranded oligonucleotides from a basis set (library via ligation enables a more convenient and rapid mechanism for the design and synthesis of oligonucleotides on the go. Coupled with an automated dispensing system and libraries of short oligo fragments, this novel DNA synthesis method would offer an efficient and cost-effective method for producing dsDNA.

  9. Adenovirus DNA replication in vitro: Duplication of single-stranded DNA containing a panhandle structure

    NARCIS (Netherlands)

    Leegwater, P.A.J.; Rombouts, R.F.A.; Vliet, P.C. van der

    1988-01-01

    Adenovirus DNA replicates by displacement of one of the parental strands followed by duplication of the displaced parental single strand (complementary strand synthesis). Displacement synthesis has been performed in a reconstituted system composed of viral and cellular proteins, employing either the

  10. Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein

    DEFF Research Database (Denmark)

    Bendtsen, Jannick Dyrløv; Nilsson, A.S.; Lehnherr, H.

    2002-01-01

    Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit...

  11. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Soumadwip; Dixit, Himanshu; Chakrabarti, Rajarshi, E-mail: rajarshi@chem.iitb.ac.in

    2015-09-28

    Highlights: • The dynamics of a single-stranded DNA in presence of different concentrations of Mg{sup 2+} is investigated. • The initial DNA chain collapse is characterized by the formation of non-sequentially stacked base pairs. • The DNA chain re-swells at high concentrations of Mg{sup 2+} as a consequence of overcharging. - Abstract: The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counterions. It is well known that the structural collapse of DNA is favoured in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl{sub 2}) single stranded DNA with base sequence 5′-CGCGAATTCGCG-3′ (Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics unlike a monovalent salt.

  12. Dynamics of RecA filaments on single-stranded DNA

    NARCIS (Netherlands)

    Van Loenhout, M.T.J.; Van der Heijden, T.; Kanaar, R.; Wyman, C.; Dekker, C.

    2009-01-01

    RecA, the key protein in homologous recombination, performs its actions as a helical filament on single-stranded DNA (ssDNA). ATP hydrolysis makes the RecA–ssDNA filament dynamic and is essential for successful recombination. RecA has been studied extensively by single-molecule techniques on

  13. Screening for Breast Cancer Using Near Field Infrared Spectroscopy of a Single Strand of Hair

    National Research Council Canada - National Science Library

    Erramilli, Shyamsunder

    2001-01-01

    ... predisposition to breast cancer because of the breast of a mutation of the BRCA1 gene. We would like to develop a new method for the screening of breast cancer based on infrared spectroscopy of a single strand of human hair...

  14. Phenylketonuria in The Netherlands : 93% of the mutations are detected by single-strand conformation analysis

    NARCIS (Netherlands)

    vanderSijsBos, CJM; Diepstraten, CM; Juyn, JA; Plaisier, M; Giltay, JC; vanSpronsen, FJ; Smit, GPA; Berger, R; Smeitink, JAM; PollThe, BT; vanAmstel, JKP

    1996-01-01

    Single-strand conformational analysis was used to screen for genetic defects in all thirteen exons of the phenylalanine hydroxylase gene (PAH) in phenylketonuria and hyperphenylalaninemia patients in the Netherlands. Exons that showed a bandshift were sequenced directly, In this way, we were able to

  15. Effects of single-stranded DNA binding proteins on primer extension by telomerase.

    Science.gov (United States)

    Cohen, Shlomit; Jacob, Eyal; Manor, Haim

    2004-08-12

    We present a biochemical analysis of the effects of three single-stranded DNA binding proteins on extension of oligonucleotide primers by the Tetrahymena telomerase. One of them, a human protein designated translin, which was shown to specifically bind the G-rich Tetrahymena and human telomeric repeats, slightly stimulated the primer extension reactions at molar ratios of translin/primer of primers, rather than by a direct interaction of this protein with telomerase. A second protein, the general human single-stranded DNA binding protein Replication Protein A (RPA), similarly affected the primer extension by telomerase, even though its mode of binding to DNA differs from that of translin. A third protein, the E. coli single-stranded DNA binding protein (SSB), whose binding to DNA is highly cooperative, caused more substantial stimulation and inhibition at the lower and the higher molar ratios of SSB/primer, respectively. Both telomere-specific and general single-stranded DNA binding proteins are found in living cells in telomeric complexes. Based on our data, we propose that these proteins may exert either stimulatory or inhibitory effects on intracellular telomerases, depending on their local concentrations. Copyright 2004 Elsevier B.V.

  16. Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket.

    Science.gov (United States)

    Pham, Hanh T; Bergoin, Max; Tijssen, Peter

    2013-03-14

    The genome of a novel virus of the house cricket consists of a 2,517-nucleotide (nt) circular single-stranded DNA (ssDNA) molecule with 4 open reading frames (ORFs). One ORF had a low identity to circovirus nucleotide sequences (NS). The unique properties of this volvovirus suggested that it belongs to a new virus family or genus.

  17. Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket

    OpenAIRE

    Pham, Hanh T.; Bergoin, Max; Tijssen, Peter

    2013-01-01

    International audience; The genome of a novel virus of the house cricket consists of a 2,517-nucleotide (nt) circular single-stranded DNA (ssDNA) molecule with 4 open reading frames (ORFs). One ORF had a low identity to circovirus nucleotide sequences (NS). The unique properties of this volvovirus suggested that it belongs to a new virus family or genus.

  18. Initiation signals for complementary strand DNA synthesis on single-stranded plasmid DNA

    NARCIS (Netherlands)

    van der Ende, A.; Teertstra, R.; van der Avoort, H. G.; Weisbeek, P. J.

    1983-01-01

    The bacteriophage 0X174 origin for (+) strand DNA synthesis, when inserted in a plasmid, is in vivo a substrate for the initiator A protein, that is produced by infecting phages. The result of this interaction is the packaging of single-stranded plasmid DNA into preformed phage coats. These plasmid

  19. Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Macek, B

    2006-01-01

    by kinase YwqD and phosphatase YwqE. Phosphorylation of B.subtilis SSB increased binding almost 200-fold to single-stranded DNA in vitro. Tyrosine phosphorylation of B.subtilis, S.coelicolor and Escherichia coli SSBs occured while they were expressed in E.coli, indicating that tyrosine phosphorylation...

  20. SSA Disability Claim Data

    Data.gov (United States)

    Social Security Administration — The dataset includes fiscal year data for initial claims for SSA disability benefits that were referred to a state agency for a disability determination. Specific...

  1. Genetic and biochemical identification of a novel single-stranded DNA binding complex in Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Amy eStroud

    2012-06-01

    Full Text Available Single-stranded DNA binding proteins play an essential role in DNA replication and repair. They use oligosaccharide-binding folds, a five-stranded ß-sheet coiled into a closed barrel, to bind to single-stranded DNA thereby protecting and stabilizing the DNA. In eukaryotes the single-stranded DNA binding protein is known as replication protein A (RPA and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed single-stranded DNA-binding protein (SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3 exist in operons with a novel gene specific to Euryarchaeota, this gene encodes a protein that we have termed rpa-associated protein (RPAP. The rpap genes encode proteins belonging to COG3390 group and feature oligosaccharide-binding folds, suggesting that they might cooperate with RPA in binding to single-stranded DNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only ∆rpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins. We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA binding complex that is unique to Euryarchaeota.

  2. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2015-07-28

    Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

  3. Sites of termination of in vitro DNA synthesis on psoralen phototreated single-stranded templates

    International Nuclear Information System (INIS)

    Piette, J.; Hearst, J.

    1985-01-01

    Single-stranded DNA has been photochemically induced to react with 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and used as substrate for DNA replication with E. coli DNA polymerase I large fragment. By using the dideoxy sequencing procedure, it is possible to map the termination sites on the template photoreacted with HMT. These sites occur at the nucleotides preceding each thymine residue (and a few cytosine residues), emphasizing the fact that in a single-stranded stretch of DNA, HMT reacts with each thymine residue without any specificity regarding the flanking base sequence of the thymine residues. In addition, termination of DNA synthesis due to psoralen-adducted thymine is not influenced by the efficiency of the 3'-5' exonuclease proof-reading activity of the DNA polymerase. (author)

  4. Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

    Science.gov (United States)

    Gray, J.W.; Pinkel, D.

    1991-07-02

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. The probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations. No Drawings

  5. Repair of single-strand breaks in normal and trisomic lymphocytes

    International Nuclear Information System (INIS)

    Leonard, J.C.; Merz, T.

    1982-01-01

    Recently, Athanasiou and colleagues (1981) reported a deficiency in the capacity of lymphocytes from persons with Down's syndrome to repair single-strand DNA breaks. They found that 1 h after exposure to 160 Gray, repair processes had restored the sedimentation profile of DNA from normal lymphocytes to control values, whereas the relative average molecular weight of DNA from irradiated lymphocytes from persons with Down's syndrome showed no increase during the repair interval. They have suggested that their data, in conjunction with the earlier data concerning the frequencies of induced chromosomal aberrations in lymphocytes from persons with Down's syndrome, reflect a decreased efficiency in some aspect of DNA repair in trisomic cells. However, for further studies of this hypothesis, it is more appropriate to study the rejoining of DNA single-strand breaks after doses comparable to those used in tests for chromosomal aberrations. (orig.)

  6. Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications

    Science.gov (United States)

    Hong, Ka Lok

    2015-01-01

    Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed. PMID:26199940

  7. Tailoring Thermal Conductivity of Single-stranded Carbon-chain Polymers through Atomic Mass Modification

    OpenAIRE

    Liao, Quanwen; Zeng, Lingping; Liu, Zhichun; Liu, Wei

    2016-01-01

    Tailoring the thermal conductivity of polymers is central to enlarge their applications in the thermal management of flexible integrated circuits. Progress has been made over the past decade by fabricating materials with various nanostructures, but a clear relationship between various functional groups and thermal properties of polymers remains to be established. Here, we numerically study the thermal conductivity of single-stranded carbon-chain polymers with multiple substituents of hydrogen...

  8. In vivo recombineering of bacteriophage λ by PCR fragments and single-strand oligonucleotides

    International Nuclear Information System (INIS)

    Oppenheim, Amos B.; Rattray, Alison J.; Bubunenko, Mikhail; Thomason, Lynn C.; Court, Donald L.

    2004-01-01

    We demonstrate that the bacteriophage λ Red functions efficiently recombine linear DNA or single-strand oligonucleotides (ss-oligos) into bacteriophage λ to create specific changes in the viral genome. Point mutations, deletions, and gene replacements have been created. While recombineering with oligonucleotides, we encountered other mutations accompanying the desired point mutational change. DNA sequence analysis suggests that these unwanted mutations are mainly frameshift deletions introduced during oligonucleotide synthesis

  9. Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis.

    Science.gov (United States)

    Olszewski, Marcin; Mickiewicz, Małgorzata; Kur, Józef

    2008-07-01

    The thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular mass of 17.29 and 16.96 kDa, respectively. They are the smallest known bacterial SSB proteins. The homology between amino acid sequences of these proteins is 40% identity and 53% similarity. They are functional as homotetramers, with each monomer encoding one single-stranded DNA binding domain (OB-fold). In fluorescence titrations with poly(dT), both proteins bind single-stranded DNA with a binding site size of about 40 nt per homotetramer. Thermostability with half-life of about 30 s at 95 degrees C makes TteSSB3 similar to the known SSB of Thermus aquaticus (TaqSSB). The TteSSB2 was fully active even after 6 h incubation at 100 degrees C. Here, we show for the first time paralogous thermostable homotetrameric SSBs, which could be an attractive alternative for known homodimeric thermostable SSB proteins in their applications for molecular biology methods and analytical purposes.

  10. Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana.

    Science.gov (United States)

    Edmondson, Andrew C; Song, Daqing; Alvarez, Luis A; Wall, Melisa K; Almond, David; McClellan, David A; Maxwell, Anthony; Nielsen, Brent L

    2005-04-01

    A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.

  11. Intercalation of single-strand oligonucleotides between nucleolipid anionic membranes: a neutron diffraction study.

    Science.gov (United States)

    Milani, Silvia; Berti, Debora; Dante, Silvia; Hauss, Thomas; Baglioni, Piero

    2009-04-07

    This contribution presents a neutron diffraction investigation of anionic lamellar phases composed of mixtures of 1-palmitoyl, 2-oleoyl phosphatidyl-nucleosides (POPN, where N is either adenosine or uridine), and POPC (1-palmitoyl,2-oleoyl-phosphatidyl-choline). Their behavior is studied for two different mole ratios and in the presence of nucleic acids. The samples are formed by the evaporation of liposomal dispersions prepared in water or in solutions containing single-strand oligonucleotides. Previous small angle X-ray scattering (SAXS) experiments on the system POPA/polyU (polyuridylic acid, high degree of polymerization, synthetic ribonucleic acid) proved that the insertion and ordering of the biopolymer in the phospholipid lamellae were driven by molecular recognition. In the present study, we extend the previous investigation to single-strand monodisperse oligonucleotides (50-mers). Structural details of the membranes were obtained from the analysis of the neutron diffraction scattering length density profiles. The evidence of direct and specific interactions, driven by molecular recognition between the nucleic polar heads of the nucleolipid and the single-strand nucleic acid, is strengthened by the comparison with identically charged bilayers formed by POPG/POPC. These results contribute to the understanding of the parameters governing the interactions between nucleolipid membranes and oligonucleotides, providing a novel strategy for the design of lipid-based vehicles for nucleic acids.

  12. Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores.

    Science.gov (United States)

    Belkin, Maxim; Maffeo, Christopher; Wells, David B; Aksimentiev, Aleksei

    2013-08-27

    Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4-8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA.

  13. Repair of ultraviolet light damage in Saccharomyces cerevisiae as studied with double- and single-stranded incoming DNAs

    International Nuclear Information System (INIS)

    Keszenman-Pereyra, D.; Hieda, K.

    1992-01-01

    Purified double- and single-stranded DNAs of the autonomously replicating vector M13RK9-T were irradiated with ultraviolet light (UV) in vitro and introduced into competent whole cells of Saccharomyces cerevisiae. Incoming double-stranded DNA was more sensitive to UV in excision repair-deficient rad2-1 cells than in proficient repair RAD + cells, while single-stranded DNA exhibited high sensitivity in both host cells. The results indicate that in yeast there is no effective rescue of UV-incoming single-stranded DNA by excision repair or other constitutive dark repair processes

  14. A neutral glyoxal gel electrophoresis method for the detection and semi-quantitation of DNA single-strand breaks.

    Science.gov (United States)

    Pachkowski, Brian; Nakamura, Jun

    2013-01-01

    Single-strand breaks are among the most prevalent lesions found in DNA. Traditional electrophoretic methods (e.g., the Comet assay) used for investigating these lesions rely on alkaline conditions to denature DNA prior to electrophoresis. However, the presence of alkali-labile sites in DNA can result in the introduction of additional single-strand breaks upon alkali treatment during DNA sample processing. Herein, we describe a neutral glyoxal gel electrophoresis assay which is based on alkali-free DNA denaturation and is suitable for qualitative and semi-quantitative analyses of single-strand breaks in DNA isolated from different organisms.

  15. Induction and repair of double- and single-strand DNA breaks in bacteriophage lambda superinfecting Escherichia coli

    International Nuclear Information System (INIS)

    Boye, E.; Krisch, R.E.

    1980-01-01

    Induction and repair of double-and single-strand DNA breaks have been measured after decays of 125 I and 3 H incorporated into the DNA and after external irradiation with 4 MeV electrons. For the decay experiments, cells of wild type Escherichia coli K-12 were superinfected with bacteriophage lambda DNA labelled with 5'-( 125 I)iodo-2'-deoxyuridine or with (methyl- 3 H)thymidine and frozen in liquid nitrogen. Aliquots were thawed at intervals and lysed at neutral pH, and the phage DNA was assayed for double- and single-strand breakage by neutral sucrose gradient centrifugation. The gradients used allowed measurements of both kinds of breaks in the same gradient. Decays of 125 I induced 0.39 single-strand breaks per double-strand break. No repair of either break type could be detected. Each 3 H disintegration caused 0.20 single-strand breaks and very few double-strand breaks. The single-strand breaks were rapidly rejoined after the cells were thawed. For irradiation with 4 MeV electrons, cells of wild type E. coli K-12 were superinfected with phage lambda and suspended in growth medium. Irradiation induced 42 single-strand breaks per double-strand break. The rates of break induction were 6.75 x 10 -14 (double-strand breaks) and 2.82 x 10 -12 (single-strand breaks) per rad and per dalton. The single-strand breaks were rapidly repaired upon incubation whereas the double-strand breaks seemed to remain unrepaired. It is concluded that double-strand breaks in superinfecting bacteriophage lambda DNA are repaired to a very small extent, if at all. (Author)

  16. A single-stranded architecture for cotranscriptional folding of RNA nanostructures

    DEFF Research Database (Denmark)

    Geary, Cody; Rothemund, Paul; Andersen, Ebbe Sloth

    2014-01-01

    . We introduce an architecture for designing artificial RNA structures that fold from a single strand, in which arrays of antiparallel RNA helices are precisely organized by RNA tertiary motifs and a new type of crossover pattern. We constructed RNA tiles that assemble into hexagonal lattices......Artificial DNA and RNA structures have been used as scaffolds for a variety of nanoscale devices. In comparison to DNA structures, RNA structures have been limited in size, but they also have advantages: RNA can fold during transcription and thus can be genetically encoded and expressed in cells...

  17. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

    DEFF Research Database (Denmark)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela

    2015-01-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA...... and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained...

  18. On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

    DEFF Research Database (Denmark)

    Baggesen, Lisbeth Munksgård; Hoffmann, S.V.; Nielsen, Steen Brøndsted

    2014-01-01

    a principal component analysis of the CD spectra, we extract fingerprint spectra of both the cyclobutane pyrimidine dimer (CPD) and the pyrimidine (6-4) pyrimidone photoadduct (64PP). Extending the CD measurements to the vacuum ultraviolet region in combination with systematic examinations of size effects...... of terminal thymines, i.e., the reaction does not occur preferentially at the extremities of the single strands as previously stated. It is even possible to form two dimers with only two bridging thymines. Finally, experiments conducted on calf thymus DNA provided a similar signature of the photodimer...

  19. In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil

    Directory of Open Access Journals (Sweden)

    Ryan M. Williams

    2014-01-01

    Full Text Available Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE specific for bromacil. We have identified one MRE with high affinity (Kd=9.6 nM and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device.

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

    Science.gov (United States)

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

    2017-04-20

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

  1. Single-strand-conformation polymorphism of ribosomal DNA for rapid species differentiation in genus Phytophthora.

    Science.gov (United States)

    Kong, Ping; Hong, Chuanxue; Richardson, Patricia A; Gallegly, Mannon E

    2003-08-01

    Single-strand-conformation polymorphism (SSCP) of ribosomal DNA of 29 species (282 isolates) of Phytophthora was characterized in this study. Phytophthora boehmeriae, Phytophthora botryosa, Phytophthora cactorum, Phytophthora cambivora, Phytophthora capsici, Phytophthora cinnamomi, Phytophthora colocasiae, Phytophthora fragariae, Phytophthora heveae, Phytophthora hibernalis, Phytophthora ilicis, Phytophthora infestans, Phytophthora katsurae, Phytophthora lateralis, Phytophthora meadii, Phytophthora medicaginis, Phytophthora megakarya, Phytophthora nicotianae, Phytophthora palmivora, Phytophthora phaseoli, Phytophthora pseudotsugae, Phytophthora sojae, Phytophthora syringae, and Phytophthora tropicalis each showed a unique SSCP pattern. Phytophthora citricola, Phytophthora citrophthora, Phytophthora cryptogea, Phytophthora drechsleri, and Phytophthora megasperma each had more than one distinct pattern. A single-stranded DNA ladder also was developed, which facilitates comparison of SSCP patterns within and between gels. With a single DNA fingerprint, 277 isolates of Phytophthora recovered from irrigation water and plant tissues in Virginia were all correctly identified into eight species at substantially reduced time, labor, and cost. The SSCP analysis presented in this work will aid in studies on taxonomy, genetics, and ecology of the genus Phytophthora.

  2. Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries.

    Science.gov (United States)

    Murgha, Yusuf E; Rouillard, Jean-Marie; Gulari, Erdogan

    2014-01-01

    Custom-defined oligonucleotide collections have a broad range of applications in fields of synthetic biology, targeted sequencing, and cytogenetics. Also, they are used to encode information for technologies like RNA interference, protein engineering and DNA-encoded libraries. High-throughput parallel DNA synthesis technologies developed for the manufacture of DNA microarrays can produce libraries of large numbers of different oligonucleotides, but in very limited amounts. Here, we compare three approaches to prepare large quantities of single-stranded oligonucleotide libraries derived from microarray synthesized collections. The first approach, alkaline melting of double-stranded PCR amplified libraries with a biotinylated strand captured on streptavidin coated magnetic beads results in little or no non-biotinylated ssDNA. The second method wherein the phosphorylated strand of PCR amplified libraries is nucleolyticaly hydrolyzed is recommended when small amounts of libraries are needed. The third method combining in vitro transcription of PCR amplified libraries to reverse transcription of the RNA product into single-stranded cDNA is our recommended method to produce large amounts of oligonucleotide libraries. Finally, we propose a method to remove any primer binding sequences introduced during library amplification.

  3. Tailoring Thermal Conductivity of Single-stranded Carbon-chain Polymers through Atomic Mass Modification.

    Science.gov (United States)

    Liao, Quanwen; Zeng, Lingping; Liu, Zhichun; Liu, Wei

    2016-10-07

    Tailoring the thermal conductivity of polymers is central to enlarge their applications in the thermal management of flexible integrated circuits. Progress has been made over the past decade by fabricating materials with various nanostructures, but a clear relationship between various functional groups and thermal properties of polymers remains to be established. Here, we numerically study the thermal conductivity of single-stranded carbon-chain polymers with multiple substituents of hydrogen atoms through atomic mass modification. We find that their thermal conductivity can be tuned by atomic mass modifications as revealed through molecular dynamics simulations. The simulation results suggest that heavy homogeneous substituents do not assist heat transport and trace amounts of heavy substituents can in fact hinder heat transport substantially. Our analysis indicates that carbon chain has the biggest contribution (over 80%) to the thermal conduction in single-stranded carbon-chain polymers. We further demonstrate that atomic mass modifications influence the phonon bands of bonding carbon atoms, and the discrepancies of phonon bands between carbon atoms are responsible for the remarkable drops in thermal conductivity and large thermal resistances in carbon chains. Our study provides fundamental insight into how to tailor the thermal conductivity of polymers through variable substituents.

  4. Empirical model for matching spectrophotometric reflectance of yarn windings and multispectral imaging reflectance of single strands of yarns.

    Science.gov (United States)

    Luo, Lin; Shen, Hui-Liang; Shao, Si-Jie; Xin, John

    2015-08-01

    The state-of-the-art multispectral imaging system can directly acquire the reflectance of a single strand of yarn that is impossible for traditional spectrophotometers. Instead, the spectrophotometric reflectance of a yarn winding, which is constituted by yarns wound on a background card, is regarded as the yarn reflectance in textile. While multispectral imaging systems and spectrophotometers can be separately used to acquire the reflectance of a single strand of yarn and corresponding yarn winding, the quantitative relationship between them is not yet known. In this paper, the relationship is established based on models that describe the spectral response of a spectrophotometer to a yarn winding and that of a multispectral imaging system to a single strand of yarn. The reflectance matching function from a single strand of yarn to corresponding yarn winding is derived to be a second degree polynomial function, which coefficients are the solutions of a constrained nonlinear optimization problem. Experiments on 100 pairs of samples show that the proposed approach can reduce the color difference between yarn windings and single strands of yarns from 2.449 to 1.082 CIEDE2000 units. The coefficients of the optimal reflection matching function imply that the reflectance of a yarn winding measured by a spectrophotometer consists of not only the intrinsic reflectance of yarn but also the nonignorable interreflection component between yarns.

  5. CdS nanowires formed by chemical synthesis using conjugated single-stranded DNA molecules

    Science.gov (United States)

    Sarangi, S. N.; Sahu, S. N.; Nozaki, S.

    2018-03-01

    CdS nanowires were successfully grown by chemical synthesis using two conjugated single-stranded (ss) DNA molecules, poly G (30) and poly C (30), as templates. During the early stage of the synthesis with the DNA molecules, the Cd 2+ interacts with Poly G and Poly C and produces the (Cd 2+)-Poly GC complex. As the growth proceeds, it results in nanowires. The structural analysis by grazing angle x-ray diffraction and transmission electron microscopy confirmed the zinc-blende CdS nanowires with the growth direction of . Although the nanowires are well surface-passivated with the DNA molecules, the photoluminescence quenching was caused by the electron transfer from the nanowires to the DNA molecules. The quenching can be used to detect and label the DNAs.

  6. Capillary Electrophoresis Single-Strand Conformational Polymorphisms as a Method to Differentiate Algal Species

    Directory of Open Access Journals (Sweden)

    Alice Jernigan

    2015-01-01

    Full Text Available Capillary electrophoresis single-strand conformational polymorphism (CE-SSCP was explored as a fast and inexpensive method to differentiate both prokaryotic (blue-green and eukaryotic (green and brown algae. A selection of two blue-green algae (Nostoc muscorum and Anabaena inaequalis, five green algae (Chlorella vulgaris, Oedogonium foveolatum, Mougeotia sp., Scenedesmus quadricauda, and Ulothrix fimbriata, and one brown algae (Ectocarpus sp. were examined and CE-SSCP electropherogram “fingerprints” were compared to each other for two variable regions of either the 16S or 18S rDNA gene. The electropherogram patterns were remarkably stable and consistent for each particular species. The patterns were unique to each species, although some common features were observed between the different types of algae. CE-SSCP could be a useful method for monitoring changes in an algae species over time as potential shifts in species occurred.

  7. The effects of radioprotective agents on the radiation-induced DNA single strand breaks

    International Nuclear Information System (INIS)

    Rhiu, Sung Ryul; Ko, Kyung Hwan; Jung, In Yong; Cho, Chul Ku; Kim, Tae Hwan; Park, Woo Wiun; Kim, Sung Ho; Ji, Young Hoon; Kim, Kyung Jung; Bang, Hio Chang; Jung, Young Suk; Choi, Moon Sik

    1992-04-01

    With the increased use of atomic energy in science, industry, medicine and public power production, the probability of nuclear accidents certainly appears to be on the increase. Therefore, early medical diagnosis and first-aid are needed urgently to establish an efficient treatment. We carried out the studies of radiation protector such as DDC, MEA, WR-2721 and variety of decontaminator with a view to establishing the protective measure and diagnostic standards for safety of worker and neighbors living around the radiation area in case of occurring the accidental contamination. In this experiment, we examined radiation-induced DNA single strand breaks as one of the study on molecular biology of the response of cells to radiation because an understanding of the radiation-induced damage in molecular level would add to our knowledge of radiation protection and treatment. (Author)

  8. Zinc(II) and the single-stranded DNA binding protein of bacteriophage T4

    International Nuclear Information System (INIS)

    Gauss, P.; Krassa, K.B.; McPheeters, D.S.; Nelson, M.A.; Gold, L.

    1987-01-01

    The DNA binding domain of the gene 32 protein of the bacteriophage T4 contains a single zinc-finger sequence. The gene 32 protein is an extensively studied member of a class of proteins that bind relatively nonspecifically to single-stranded DNA. The authors have sequenced and characterized mutations in gene 32 whose defective proteins are activated by increasing the Zn(II) concentration in the growth medium. The results identify a role for the gene 32 protein in activation of T4 late transcription. Several eukaryotic proteins with zinc fingers participate in activation of transcription, and the gene 32 protein of T4 should provide a simple, well-characterized system in which genetics can be utilized to study the role of a zinc finger in nucleic acid binding and gene expression

  9. Detection of antibodies to single-stranded DNA in naturally acquired and experimentally induced viral hepatitis

    Energy Technology Data Exchange (ETDEWEB)

    Gust, I.D.; Feinstone, S.M.; Purcell, R.H.; Alter, H.J.

    1980-01-01

    A sensitive ''Farr'' assay, utilizing /sup 125/I-labelled DNA was developed for detecting antibody to single-stranded DNA (anti-ssDNA). The test was shown to be specific and as sensitive as assays using /sup 14/C-labelled DNA, for the detection of antibody in patients with connective tissue diseases. Groups of sera from patients with naturally acquired viral hepatitis and experimentally infected chimpanzees were tested for anti-ssDNA by the /sup 125/I assay and by counterimmunoelectrophoresis (CIEP). No consistent pattern was observed with either technique, indicating the elevated levels of this antibody are not as reliable markers of parenchymal liver damage as had been previously suggested.

  10. Novel Circular Single-Stranded DNA Viruses among an Asteroid, Echinoid and Holothurian (Phylum: Echinodermata).

    Science.gov (United States)

    Jackson, Elliot W; Bistolas, Kalia S I; Button, Jason B; Hewson, Ian

    2016-01-01

    Echinoderms are prone to large population fluctuations that can be mediated by pervasive disease events. For the majority of echinoderm disease events the causative pathogen is unknown. Viruses have only recently been explored as potential pathogens using culture-independent techniques though little information currently exists on echinoderm viruses. In this study, ten circular ssDNA viruses were discovered in tissues among an asteroid (Asterias forbesi), an echinoid (Strongylocentrotus droebachiensis) and a holothurian (Parastichopus californicus) using viral metagenomics. Genome architecture and sequence similarity place these viruses among the rapidly expanding circular rep-encoding single stranded (CRESS) DNA viral group. Multiple genomes from the same tissue were no more similar in sequence identity to each other than when compared to other known CRESS DNA viruses. The results from this study are the first to describe a virus from a holothurian and continue to show the ubiquity of these viruses among aquatic invertebrates.

  11. Radioimmunoassay of single-stranded DNA antibodies for control of diagnosis and therapy

    International Nuclear Information System (INIS)

    Meffert, H.; Boehm, F.; Soennichsen, N.; Gens, J.

    1980-01-01

    Several years experience in quantitative determination of single-stranded DNA antibodies is reported and the normal range as well as the diagnostic hit rate of the method is outlined. In the controls the mean DNA attachment rate was 1.5% and the upper normal range limit was 12.8%, the risk of erroneous rejection being 1%. The DNA binding rate was greater than 12.8% in 74.7% of untreated patients suffering from lupus erythematodes visceralis, in 47.6% of patients with circumscribed sclerodermia, in 14.4% of patients with progressive sclerodermia, and in 10.3% of those suffering from lupus erythematodes chronicus. The findings emphasize the importance of regulatory mechanisms of the immune system to the process of autosensitization

  12. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

    Directory of Open Access Journals (Sweden)

    Simon Roux

    2016-12-01

    Full Text Available Background Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA viral genomes captured in quantitative viral metagenomes (viromes. This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation. Methods Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5% of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

  13. Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

    Directory of Open Access Journals (Sweden)

    Jie Zhu

    Full Text Available DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.

  14. Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif

    Science.gov (United States)

    Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

    2013-01-01

    DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889

  15. Human topoisomerase IIIalpha is a single-stranded DNA decatenase that is stimulated by BLM and RMI1

    DEFF Research Database (Denmark)

    Yang, Jay; Bachrati, Csanad Z; Ou, Jiongwen

    2010-01-01

    -passage mechanism. We generated single-stranded catenanes that resemble the proposed dissolution intermediate recognized by human topoisomerase IIIalpha. We demonstrate that human topoisomerase IIIalpha is a single-stranded DNA decatenase that is specifically stimulated by the BLM-RMI1 pair. In addition, RMI1......Human topoisomerase IIIalpha is a type IA DNA topoisomerase that functions with BLM and RMI1 to resolve DNA replication and recombination intermediates. BLM, human topoisomerase IIIalpha, and RMI1 catalyze the dissolution of double Holliday junctions into noncrossover products via a strand...

  16. The binding of in vitro synthesized adenovirus DNA binding protein to single-stranded DNA is stimulated by zinc ions

    NARCIS (Netherlands)

    Vos, H.L.; Lee, F.M. van der; Sussenbach, J.S.

    1988-01-01

    We have synthesized wild type DNA binding protein (DBP) of adenovirus type 5 (Ad5) and several truncated forms of this protein by a combination of in vitro transcription and translation. The proteins obtained were tested for binding to a single-stranded DNA-cellulose column. It could be shown that

  17. Cultivated single stranded DNA phages that infect marine Bacteroidetes prove difficult to detect with DNA binding stains

    DEFF Research Database (Denmark)

    Holmfeldt, Karin; Odic, Dusko; Sullivan, Matthew B.

    2012-01-01

    This is the first description of cultivated icosahedral single stranded DNA (ssDNA) phages isolated on heterotrophic marine bacterioplankton and with Bacteroidetes hosts. None of the 8 phages stained well with DNA binding stains, suggesting that in situ abundances of ssDNA phages are drastically...

  18. Single-strand conformation polymorphism analysis of ribosomal DNA for detection of Phytophthora ramorum directly from plant tissues

    Science.gov (United States)

    Ping Kong; Patricia A. Richardson; Chuanxue Hong; Thomas L. Kubisiak

    2006-01-01

    At the first Sudden Oak Death Science Symposium, we reported on the use of a single strand conformation polymorphism (SSCP) analysis for rapid identification of Phytophthora ramorum in culture. We have since assessed and improved the fingerprinting technique for detecting this pathogen directly from plant tissues. The improved SSCP protocol uses a...

  19. Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes

    Science.gov (United States)

    Ma, Enbo; Harrington, Lucas B.; O’Connell, Mitchell R.; Zhou, Kaihong; Doudna, Jennifer A.

    2015-01-01

    Summary Double-stranded DNA (dsDNA) cleavage by Cas9 is a hallmark of type II CRISPR-Cas immune systems. Cas9–guide RNA complexes recognize 20-base-pair sequences in DNA and generate a site-specific double-strand break, a robust activity harnessed for genome editing. DNA recognition by all studied Cas9 enzymes requires a protospacer adjacent motif (PAM) next to the target site. We show that Cas9 enzymes from evolutionarily divergent bacteria can recognize and cleave single-stranded DNA (ssDNA) by an RNA-guided, PAM-independent recognition mechanism. Comparative analysis shows that in contrast to the type II-A S. pyogenes Cas9 that is widely used for genome engineering, the smaller type II-C Cas9 proteins have limited dsDNA binding and unwinding activity and promiscuous guide-RNA specificity. These results indicate that inefficiency of type II-C Cas9 enzymes for genome editing results from a limited ability to cleave dsDNA, and suggest that ssDNA cleavage was an ancestral function of the Cas9 enzyme family. PMID:26545076

  20. Managing Single-Stranded DNA during Replication Stress in Fission Yeast

    Directory of Open Access Journals (Sweden)

    Sarah A. Sabatinos

    2015-09-01

    Full Text Available Replication fork stalling generates a variety of responses, most of which cause an increase in single-stranded DNA. ssDNA is a primary signal of replication distress that activates cellular checkpoints. It is also a potential source of genome instability and a substrate for mutation and recombination. Therefore, managing ssDNA levels is crucial to chromosome integrity. Limited ssDNA accumulation occurs in wild-type cells under stress. In contrast, cells lacking the replication checkpoint cannot arrest forks properly and accumulate large amounts of ssDNA. This likely occurs when the replication fork polymerase and helicase units are uncoupled. Some cells with mutations in the replication helicase (mcm-ts mimic checkpoint-deficient cells, and accumulate extensive areas of ssDNA to trigger the G2-checkpoint. Another category of helicase mutant (mcm4-degron causes fork stalling in early S-phase due to immediate loss of helicase function. Intriguingly, cells realize that ssDNA is present, but fail to detect that they accumulate ssDNA, and continue to divide. Thus, the cellular response to replication stalling depends on checkpoint activity and the time that replication stress occurs in S-phase. In this review we describe the signs, signals, and symptoms of replication arrest from an ssDNA perspective. We explore the possible mechanisms for these effects. We also advise the need for caution when detecting and interpreting data related to the accumulation of ssDNA.

  1. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity.

    Science.gov (United States)

    Petzold, Christine; Marceau, Aimee H; Miller, Katherine H; Marqusee, Susan; Keck, James L

    2015-06-05

    Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity*

    Science.gov (United States)

    Petzold, Christine; Marceau, Aimee H.; Miller, Katherine H.; Marqusee, Susan; Keck, James L.

    2015-01-01

    Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome. PMID:25903123

  3. Substrate-assisted 2D DNA lattices and algorithmic lattices from single-stranded tiles.

    Science.gov (United States)

    Kim, Junghoon; Ha, Tai Hwan; Park, Sung Ha

    2015-08-07

    We present a simple route to circumvent kinetic traps which affect many types of DNA nanostructures in their self-assembly process. Using this method, a new 2D DNA lattice made up of short, single-stranded tile (SST) motifs was created. Previously, the growth of SST DNA assemblies was restricted to 1D (tubes and ribbons) or finite-sized 2D (molecular canvases). By utilizing the substrate-assisted growth method, sets of SSTs were designed as unit cells to self-assemble into periodic and aperiodic 2D lattices which continuously grow both along and orthogonal to the helical axis. Notably, large-scale (∼1 μm(2)) fully periodic 2D lattices were fabricated using a minimum of just 2 strand species. Furthermore, the ability to create 2D lattices from a few motifs enables certain rules to be encoded into these SSTs to carry out algorithmic self-assembly. A set of these motifs was designed to execute simple 1-input 1-output COPY and NOT algorithms, the space-time manifestations which were aperiodic 2D algorithmic SST lattices. The methodology presented here can be straightforwardly applied to other motifs which fall into this type of kinetic trap to create novel DNA crystals.

  4. Sensitive multiplex RNA quantification using capillary electrophoresis-based single-strand conformation polymorphism.

    Science.gov (United States)

    Shin, Gi Won; Hwang, Hee Sung; Nam, Hong Gil; Oh, Mi-Hwa; Jung, Gyoo Yeol

    2010-05-01

    Quantification of RNA provides information crucial for various biological studies, including analysis of mRNA expression and that of microRNAs. Reverse transcription (RT) coupled with real-time polymerase chain reaction (PCR) is known to be the most accurate method for quantifying nucleic acids, and thus represents the state-of-the-art for RNA quantification. However, the use of real-time PCR for RNA quantification is limited to a single target per analytical run because of reductions in quantification power and limitations of fluorescence dyes associated with multiplex applications. Here, we report a novel multiplex RNA quantification method that uses capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) coupled with modified RT and asymmetric PCR. The reverse transcripts of seven in vitro transcribed RNAs were modified with common sequence tags and amplified by asymmetric PCR using primers specific to the common tags. The resulting amplicons were separated and quantified by CE-SSCP. A series of experiments using different amounts of RNA demonstrated that the assay had a limit of detection of 2 amol and a dynamic range of approximately 10(5). These results clearly indicate the potential of this method to provide robust and precise multiplex RNA quantification.

  5. Leishmania replication protein A-1 binds in vivo single-stranded telomeric DNA

    International Nuclear Information System (INIS)

    Neto, J.L. Siqueira; Lira, C.B.B.; Giardini, M.A.; Khater, L.; Perez, A.M.; Peroni, L.A.; Reis, J.R.R. dos; Freitas-Junior, L.H.; Ramos, C.H.I.; Cano, M.I.N.

    2007-01-01

    Replication protein A (RPA) is a highly conserved heterotrimeric single-stranded DNA-binding protein involved in different events of DNA metabolism. In yeast, subunits 1 (RPA-1) and 2 (RPA-2) work also as telomerase recruiters and, in humans, the complex unfolds G-quartet structures formed by the 3' G-rich telomeric strand. In most eukaryotes, RPA-1 and RPA-2 bind DNA using multiple OB fold domains. In trypanosomatids, including Leishmania, RPA-1 has a canonical OB fold and a truncated RFA-1 structural domain. In Leishmania amazonensis, RPA-1 alone can form a complex in vitro with the telomeric G-rich strand. In this work, we show that LaRPA-1 is a nuclear protein that associates in vivo with Leishmania telomeres. We mapped the boundaries of the OB fold DNA-binding domain using deletion mutants. Since Leishmania and other trypanosomatids lack homologues of known telomere end binding proteins, our results raise questions about the function of RPA-1 in parasite telomeres

  6. 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.

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

    Science.gov (United States)

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

    2009-05-01

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

  8. Biophysical characterization of the association of histones with single-stranded DNA.

    Science.gov (United States)

    Wang, Ying; van Merwyk, Luis; Tönsing, Katja; Walhorn, Volker; Anselmetti, Dario; Fernàndez-Busquets, Xavier

    2017-11-01

    Despite the profound current knowledge of the architecture and dynamics of nucleosomes, little is known about the structures generated by the interaction of histones with single-stranded DNA (ssDNA), which is widely present during replication and transcription. Non-denaturing gel electrophoresis, transmission electron microscopy, atomic force microscopy, magnetic tweezers. Histones have a high affinity for ssDNA in 0.15M NaCl ionic strength, with an apparent binding constant similar to that calculated for their association with double-stranded DNA (dsDNA). The length of DNA (number of nucleotides in ssDNA or base pairs in dsDNA) associated with a fixed core histone mass is the same for both ssDNA and dsDNA. Although histone-ssDNA complexes show a high tendency to aggregate, nucleosome-like structures are formed at physiological salt concentrations. Core histones are able to protect ssDNA from digestion by micrococcal nuclease, and a shortening of ssDNA occurs upon its interaction with histones. The purified (+) strand of a cloned DNA fragment of nucleosomal origin has a higher affinity for histones than the purified complementary (-) strand. At physiological ionic strength histones have high affinity for ssDNA, possibly associating with it into nucleosome-like structures. In the cell nucleus histones may spontaneously interact with ssDNA to facilitate their participation in the replication and transcription of chromatin. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Quantitation of ultraviolet-induced single-strand breaks using oligonucleotide chip

    International Nuclear Information System (INIS)

    Pal, Sukdeb; Kim, Min Jung; Choo, Jaebum; Kang, Seong Ho; Lee, Kyeong-Hee; Song, Joon Myong

    2008-01-01

    A simple, accurate and robust methodology was established for the direct quantification of ultraviolet (UV)-induced single-strand break (SSB) using oligonucleotide chip. Oligonucleotide chips were fabricated by covalently anchoring the fluorescent-labeled ssDNAs onto silicon dioxide chip surfaces. Assuming that the possibility of more than one UV-induced SSB to be generated in a small oligonucleotide is extremely low, SSB formation was investigated quantifying the endpoint probe density by fluorescence measurement upon UV irradiation. The SSB yields obtained based on the highly sensitive laser-induced fluorometric determination of fluorophore-labeled oligonucleotides were found to coincide well with that predicted from a theoretical extrapolation of the results obtained for plasmid DNAs using conventional agarose gel electrophoresis. The developed method has the potential to serve as a high throughput, sample-thrifty, and time saving tool to realize more realistic, and direct quantification of radiation and chemical-induced strand breaks. It will be especially useful for determining the frequency of SSBs or lesions convertible to SSBs by specific cleaving reagents or enzymes

  10. Effect of Conformational Entropy on the Nanomechanics of Microcantilever-Based Single-Stranded DNA Sensors

    Directory of Open Access Journals (Sweden)

    Zou-Qing Tan

    2014-09-01

    Full Text Available An entropy-controlled bending mechanism is presented to study the nanomechanics of microcantilever-based single-stranded DNA (ssDNA sensors. First; the conformational free energy of the ssDNA layer is given with an improved scaling theory of thermal blobs considering the curvature effect; and the mechanical energy of the non-biological layer is described by Zhang’s two-variable method for laminated beams. Then; an analytical model for static deflections of ssDNA microcantilevers is formulated by the principle of minimum energy. The comparisons of deflections predicted by the proposed model; Utz–Begley’s model and Hagan’s model are also examined. Numerical results show that the conformational entropy effect on microcantilever deflections cannot be ignored; especially at the conditions of high packing density or long chain systems; and the variation of deflection predicted by the proposed analytical model not only accords with that observed in the related experiments qualitatively; but also appears quantitatively closer to the experimental values than that by the preexisting models. In order to improve the sensitivity of static-mode biosensors; it should be as small as possible to reduce the substrate stiffness.

  11. In vitro selection and characterization of single stranded DNA aptamers for luteolin: A possible recognition tool.

    Science.gov (United States)

    Tuma Sabah, Jinan; Zulkifli, Razauden Mohamed; Shahir, Shafinaz; Ahmed, Farediah; Abdul Kadir, Mohammed Rafiq; Zakaria, Zarita

    2018-03-06

    Distinctive bioactivities possessed by luteolin (3', 4', 5, 7-tetrahydroxy-flavone) are advantageous for sundry practical applications. This paper reports the in vitro selection and characterization of single stranded-DNA (ssDNA) aptamers, specific for luteolin (LUT). 76-mer library containing 1015 randomized ssDNA were screened via systematic evolution of ligands by exponential enrichment (SELEX). The recovered ssDNA pool from the 8th round was amplified with unlabeled primers and cloned into PSTBlue-1 vector prior to sequencing. 22 of LUT-binding aptamer variants were further classified into one of the seven groups based on their N40 random sequence regions, wherein one representative from each group was characterized. The dissociation constant of aptamers designated as LUT#28, LUT#20 and LUT#3 was discerned to be 107, 214 and 109 nM, respectively with high binding affinity towards LUT. Prediction analysis of the secondary structure suggested discrete features with typical loop and stem motifs. Furthermore, LUT#3 displayed higher specificity with insignificant binding toward kaempferol and quercetin despite its structural and functional similarity compared to LUT#28 and LUT#20. Further LUT#3 can detect free luteolin within 0.2-1 mM in solution. It was suggested that LUT#3 aptamer were the most suitable for LUT recognition tool at laboratory scale based on the condition tested. Copyright © 2018. Published by Elsevier Inc.

  12. New Method for Differentiation of Granuloviruses (Betabaculoviruses Based on Multitemperature Single Stranded Conformational Polymorphism

    Directory of Open Access Journals (Sweden)

    Martyna Krejmer-Rabalska

    2017-12-01

    Full Text Available Baculoviruses have been used as biopesticides for decades. Recently, due to the excessive use of chemical pesticides there is a need for finding new agents that may be useful in biological protection. Sometimes few isolates or species are discovered in one host. In the past few years, many new baculovirus species have been isolated from environmental samples, thoroughly characterized and thanks to next generation sequencing methods their genomes are being deposited in the GenBank database. Next generation sequencing (NGS methodology is the most certain way of detection, but it has many disadvantages. During our studies, we have developed a method based on Polymerase chain reaction (PCR followed by Multitemperature Single Stranded Conformational Polymorphism (MSSCP which allows for distinguishing new granulovirus isolates in only a few hours and at low-cost. On the basis of phylogenetic analysis of betabaculoviruses, representative species have been chosen. The alignment of highly conserved genes—granulin and late expression factor-9, was performed and the degenerate primers were designed to amplify the most variable, short DNA fragments flanked with the most conserved sequences. Afterwards, products of PCR reaction were analysed by MSSCP technique. In our opinion, the proposed method may be used for screening of new isolates derived from environmental samples.

  13. Comparative studies on the minus origin mutants of Escherichia coli spherical single-stranded DNA phages.

    Science.gov (United States)

    Kodaira, K; Godson, N G; Taketo, A

    1995-01-25

    The minus origins for complementary strand DNA synthesis (-ori) of Escherichia coli spherical single-stranded DNA (microvirid) phages G4, phi K, alpha 3, and St-1 closely resemble each other in DNA structure and contain two potential secondary hairpin loops (I and II) that have been implicated as direct recognition sites for host E. coli dnaG protein (primase). We introduced mutations (deletion or insertion) within the -ori regions of phi K and G4 by the nuclease digestion method. Mutants thus constructed produced minute plaques, showed thermosensitivity, and they remarkably reduced the phage yield and rate of viral DNA synthesis. Deletions in the phi K mutants (dTa) were ranging from 1 nucleotide (nt) to 102 nt centered at the hairpin II; a dTa8 mutant was entirely lacking in the two hairpins besides the starting point for primer RNA synthesis. On the other hand, the G4 mutants (dSa) had deletions centered at hairpin I; two mutants dSa35 and dXN completely lost the hairpin I and the primer RNA starting point. In addition, progeny phage populations of several phi K and G4 mutants contained revertant-like phages. DNA sequencing analysis revealed that these secondary phages had been generated by spontaneous DNA rearrangement with additional insertion or deletion near the parental mutation sites, via an unknown recA-independent pathway.

  14. Delayed repair of DNA single-strand breaks does not increase cytogenetic damage

    International Nuclear Information System (INIS)

    Morgan, W.F.; Djordjevic, M.C.; Jostes, R.F.; Pantelias, G.E.

    1985-01-01

    DNA damage and cytogenetic effects of ionizing radiation were investigated in Chinese hamster ovary (CHO) cells and unstimulated human peripheral blood lymphocytes. DNA damage and repair were analysed by alkaline elution under conditions that predominantly measured DNA single-strand breaks (ssb). X-radiation (2.5 Gy) induced ssb in both CHO cells and unstimulated lymphocytes, and the breaks were repaired within 30 and 90 min, respectively. This rapid repair was delayed by the poly(ADP-ribose) polymerase inhibitor, 3-aminobenzamide (3AB). The cytogenetic effects of the 3AB-induced delay in DNA repair were examined by analysing sister chromatid exchange (SCE) frequency in CHO cells and fragmentation of prematurely condensed chromosomes (PCC) in unstimulated human lymphocytes after 2.5 Gy of X-rays. Although 3AB delayed the rejoining of DNA ssb, this delay did not result in increased cytogenetic damage manifested as either SCE or fragmentation of PCC. These results indicate that the rapidly rejoining DNA ssb are not important in the production of chromosome damage. (author)

  15. Viral single-strand DNA induces p53-dependent apoptosis in human embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Matthew L Hirsch

    Full Text Available Human embryonic stem cells (hESCs are primed for rapid apoptosis following mild forms of genotoxic stress. A natural form of such cellular stress occurs in response to recombinant adeno-associated virus (rAAV single-strand DNA genomes, which exploit the host DNA damage response for replication and genome persistence. Herein, we discovered a unique DNA damage response induced by rAAV transduction specific to pluripotent hESCs. Within hours following rAAV transduction, host DNA damage signaling was elicited as measured by increased gamma-H2AX, ser15-p53 phosphorylation, and subsequent p53-dependent transcriptional activation. Nucleotide incorporation assays demonstrated that rAAV transduced cells accumulated in early S-phase followed by the induction of apoptosis. This lethal signaling sequalae required p53 in a manner independent of transcriptional induction of Puma, Bax and Bcl-2 and was not evident in cells differentiated towards a neural lineage. Consistent with a lethal DNA damage response induced upon rAAV transduction of hESCs, empty AAV protein capsids demonstrated no toxicity. In contrast, DNA microinjections demonstrated that the minimal AAV origin of replication and, in particular, a 40 nucleotide G-rich tetrad repeat sequence, was sufficient for hESC apoptosis. Our data support a model in which rAAV transduction of hESCs induces a p53-dependent lethal response that is elicited by a telomeric sequence within the AAV origin of replication.

  16. Detection of hepatitis A virus by hybridization with single-stranded RNA probes

    International Nuclear Information System (INIS)

    Xi, J.; Estes, M.K.; Metcalf, T.G.

    1987-01-01

    An improved method of dot-blot hybridization to detect hepatitis A virus (HAV) was developed with single-stranded RNA (ssRNA) probes. Radioactive and nonradioactive ssRNA probes were generated by in vitro transcription of HAV templates inserted into the plasmid pGEM-1. 32 P-labeled ssRNA probes were at least eightfold more sensitive than the 32 P-labeled double-stranded cDNA counterparts, whereas biotin-labeled ssRNA probes showed a sensitivity comparable with that of the 32 P-labeled double-stranded cDNA counterparts. Hybridization of HAV with the ssRNA probes at high stringency revealed specific reactions with a high signal-to-noise ratio. The differential hybridization reactions seen with probes of positive and negative sense (compared with HAV genomic RNA) were used to detect HAV in clinical and field samples. A positive/negative ratio was introduced as an indicator that permitted an semiquantitative expression of a positive HAV reaction. Good agreement of this indicator was observed with normal stool samples and with HAV-seeded samples. By using this system, HAV was detected in estuarine and freshwater samples collected from a sewage-polluted bayou in Houston and a saltwater tributary of Galveston Bay

  17. Capillary electrophoresis single-strand conformation polymorphism for the monitoring of gastrointestinal microbiota of chicken flocks.

    Science.gov (United States)

    Pissavin, C; Burel, C; Gabriel, I; Beven, V; Mallet, S; Maurice, R; Queguiner, M; Lessire, M; Fravalo, P

    2012-09-01

    The objective of the present study was to evaluate the capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) to characterize poultry gut microbiota and the ability of this molecular method to detect modifications related to rearing conditions to be used as an epidemiological tool. The V3 region of the 16S rRNA gene was selected as the PCR target. Our results showed that this method provides reproducible data. The microbiota analysis of individuals showed that variability between individual fingerprints was higher for ileum and cloaca than for ceca. However, pooling the samples decreased this variability. To estimate the variability within and between farms, we compared molecular gut patterns of animals from the same hatchery reared under similar conditions and fed the same diet in 2 separate farms. Total aerobic bacteria, coliforms, and lactic acid bacteria were enumerated using conventional bacteriological methods. A significant difference was observed for coliforms present in the ceca and the cloaca depending on the farm. Ileal contents fingerprints were more closely related to those of cloacal contents than to those of ceca contents. When comparing samples from the 2 farms, a specific microbiota was highlighted for each farm. For each gut compartment, the microbiota fingerprints were joined in clusters according to the farm. Thus, this rapid and potentially high-throughput method to obtain gut flora fingerprints is sensitive enough to detect a "farm effect" on the balance of poultry gut microbiota despite the birds being fed the same regimens and reared under similar conditions.

  18. SSA State Agency Workload Data

    Data.gov (United States)

    Social Security Administration — The dataset is revised and expanded from 4 to 71 data fields. It includes monthly data from October 2000 onwards for SSA disability cases that were referred to the...

  19. Simultaneous identification of seven foodborne pathogens and Escherichia coli (pathogenic and nonpathogenic) using capillary electrophoresis-based single-strand conformation polymorphism coupled with multiplex PCR.

    Science.gov (United States)

    Oh, Mi-Hwa; Paek, Se-Hee; Shin, Gi Won; Kim, Hae-Yeong; Jung, Gyoo Yeol; Oh, Sangsuk

    2009-06-01

    The objective of this study was to develop a novel technique for parallel analysis of eight important foodborne microbes using capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) coupled with multiplex PCR. Specific primers for multiplex PCR amplification of the 16S rRNA gene were designed, corresponding to eight species of bacteria, including Escherichia coli, Clostridium perfringens, Campylobacter jejuni, Salmonella enterica, Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, and Bacillus cereus, for the species-specific identification and optimal separation of their PCR products in subsequent analysis by CE-SSCP. Multiplex PCR conditions including annealing temperature, extension time, the number of PCR cycles, and primer concentrations were then optimized for simultaneous detection of all target foodborne bacteria. The diagnostic system using CE-SSCP combined with multiplex PCR developed here can be used for rapid investigation of causative agents of foodborne illness. The simplicity and high sensitivity of the method may lead to improved management of safety and illness related to food.

  20. Mutability dynamics of an emergent single stranded DNA virus in a naïve host.

    Directory of Open Access Journals (Sweden)

    Subir Sarker

    Full Text Available Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of beak and feather disease virus (BFDV infection in the orange-bellied parrot (Neophema chrysogaster. Detailed health monitoring and the small population size (<300 individuals of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16 and Rep gene sequences (n = 35 revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved Rep gene and immunogenic capsid (Cap gene with a high evolutionary rate (3.41×10(-3 subs/site/year approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another.

  1. Carboplatin enhances the production and persistence of radiation-induced DNA single-strand breaks

    International Nuclear Information System (INIS)

    Yang, L.; Douple, E.B.; O'Hara, J.A.; Wang, H.J.

    1995-01-01

    Fluorometric analysis of DNA unwinding and alkaline elution were used to investigate the production and persistence of DNA single-strand breaks (SSBs) in Chinese hamster V79 and xrs-5 cells treated with the chemotherapeutic agent carboplatin in combination with radiation. Carboplatin was administered to cells before irradiation in hypoxic conditions, or the drug was added immediately after irradiation during the postirradiation recovery period in air. The results of DNA unwinding studies suggest that carboplatin enhances the production of radiation-induced SSBs in hypoxic V79 cells and xrs-5 cells by a factor of 1.86 and 1.83, respectively, when combined with radiation compared to the SSBs produced by irradiation alone. Carboplatin alone did not produce a measureable number of SSBs. Alkaline elution profiles also indicated that the rate of elution of SSBs was higher in cells treated with the carboplatin is present after irradiation and during the postirradiation recovery period, the rejoining of radiation-induced SSBs by a factor of 1.46 in V79 cells with 20 Gy irradiation and by a factor of 2.02 in xrs-5 cells with 20 Gy irradiation. When carboplatin is present after irradiation and during the postirradiation recovery period, the rejoining of radiation-induced SSBs is inhibited during this postirradiation incubation period (radiopotentiation) with a relative inhibition factor at 1 h postirradiation of 1.25 in V79 cells and 1.15 in xrs-5 cells. An increased production and persistence of SSBs resulting from the interaction of carboplatin with radiation may be an important step in the mechanism responsible for the potentiated cell killing previously from studies in animal tumors and in cultured cells. 31 refs., 7 figs

  2. Distinct circular single-stranded DNA viruses exist in different soil types.

    Science.gov (United States)

    Reavy, Brian; Swanson, Maud M; Cock, Peter J A; Dawson, Lorna; Freitag, Thomas E; Singh, Brajesh K; Torrance, Lesley; Mushegian, Arcady R; Taliansky, Michael

    2015-06-15

    The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  3. A high throughput system for the preparation of single stranded templates grown in microculture.

    Science.gov (United States)

    Kolner, D E; Guilfoyle, R A; Smith, L M

    1994-01-01

    A high throughput system for the preparation of single stranded M13 sequencing templates is described. Supernatants from clones grown in 48-well plates are treated with a chaotropic agent to dissociate the phage coat protein. Using a semi-automated cell harvester, the free nucleic acid is bound to a glass fiber filter in the presence of chaotrope and then washed with ethanol by aspiration. Individual glass fiber discs are punched out on the cell harvester and dried briefly. The DNA samples are then eluted in water by centrifugation. The processing time from 96 microcultures to sequence quality templates is approximately 1 hr. Assuming the ability to sequence 400 bases per clone, a 0.5 megabase per day genome sequencing facility will require 6250 purified templates a week. Toward accomplishing this goal we have developed a procedure which is a modification of a method that uses a chaotropic agent and glass fiber filter (Kristensen et al., 1987). By exploiting the ability of a cell harvester to uniformly aspirate and wash 96 samples, a rapid system for high quality template preparation has been developed. Other semi-automated systems for template preparation have been developed using commercially available robotic workstations like the Biomek (Mardis and Roe, 1989). Although minimal human intervention is required, processing time is at least twice as long. Custom systems based on paramagnetic beads (Hawkins et al., 1992) produce DNA in insufficient quantity for direct sequencing and therefore require cycle sequencing. These systems require custom programing, have a fairly high initial cost and have not proven to be as fast as the method reported here.

  4. Identification of five novel FBN1 mutations by non-radioactive single-strand conformation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Liu, W.; Qian, C.; Comeau, K.; Francke, U. [Stanford Univ. Medical Center, Stanford, CA (United States)

    1994-09-01

    Marfan syndrome (MFS), one of the most common genetic disorders of connective tissue, is characterized by variable manifestations in skeletal, cardiovascular and ocular systems. Mutations in the fibrillin gene on chromosome 15 (FBN1) have been shown to cause MFS. To examine the relationship between FBN1 gene mutations, fibrillin protein function and MFS phenotypes, we screened for alternations in the fibrillin coding sequence in fibroblast derived cDNA from MFS patients. To date, abnormally migrating bands in more than 20 unrelated MFS patients have been identified by using non-radioactive single-strand conformation analysis and silver staining. Five altered bands have been directly sequenced. Two missense mutations and three splice site mutations have been identified. Both missense mutations substitute another amino acid for a cysteine residue (C1402W and C1672R) in EGF-like motifs of the fibrillin polypeptide chain. The two splice site mutations are at nucleotide positions 6994+1 (G{yields}A), and 7205-2 (A{yields}G) and result in in-frame skipping of exon 56 and 58, respectively. Skipping of exon 56 occurs in 50% of mutant transcripts. Use of a cryptic splice site 51 bp upstream of the normal donor site results in half of the mutant transcripts containing part of exon 56. Both products contain in-frame deletions. Another splice site mutation, identified by exon screening from patient genomic DNA using intron primers, is at nucleotide position 2293+2 (T{yields}A), but the predicted exon skipping has not been detected at the RT-PCR level. This may be due to instability of the mutant transcript. Including the mutations reported here, a total of 8 out of 36 published FBN1 gene mutations involve exon skipping. It may be inferred that FBN1 exon skipping plays an important pathogenic role in MFS.

  5. Screening for mutations in human alpha-globin genes by nonradioactive single-strand conformation polymorphism

    Directory of Open Access Journals (Sweden)

    Jorge S.B.

    2003-01-01

    Full Text Available Point mutations and small insertions or deletions in the human alpha-globin genes may produce alpha-chain structural variants and alpha-thalassemia. Mutations can be detected either by direct DNA sequencing or by screening methods, which select the mutated exon for sequencing. Although small (about 1 kb, 3 exons and 2 introns, the alpha-globin genes are duplicate (alpha2 and alpha1 and highy G-C rich, which makes them difficult to denature, reducing sequencing efficiency and causing frequent artifacts. We modified some conditions for PCR and electrophoresis in order to detect mutations in these genes employing nonradioactive single-strand conformation polymorphism (SSCP. Primers previously described by other authors for radioactive SSCP and phast-SSCP plus denaturing gradient gel electrophoresis were here combined and the resultant fragments (6 new besides 6 original per alpha-gene submitted to silver staining SSCP. Nine structural and one thalassemic mutations were tested, under different conditions including two electrophoretic apparatus (PhastSystem(TM and GenePhor(TM, Amersham Biosciences, different polyacrylamide gel concentrations, run temperatures and denaturing agents, and entire and restriction enzyme cut fragments. One hundred percent of sensitivity was achieved with four of the new fragments formed, using the PhastSystem(TM and 20% gels at 15ºC, without the need of restriction enzymes. This nonradioactive PCR-SSCP approach showed to be simple, rapid and sensitive, reducing the costs involved in frequent sequencing repetitions and increasing the reliability of the results. It can be especially useful for laboratories which do not have an automated sequencer.

  6. 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.

  7. Ammonia disinfection of hatchery waste for elimination of single-stranded RNA viruses.

    Science.gov (United States)

    Emmoth, Eva; Ottoson, Jakob; Albihn, Ann; Belák, Sándor; Vinnerås, Björn

    2011-06-01

    Hatchery waste, an animal by-product of the poultry industry, needs sanitation treatment before further use as fertilizer or as a substrate in biogas or composting plants, owing to the potential presence of opportunistic pathogens, including zoonotic viruses. Effective sanitation is also important in viral epizootic outbreaks and as a routine, ensuring high hygiene standards on farms. This study examined the use of ammonia at different concentrations and temperatures to disinfect hatchery waste. Inactivation kinetics of high-pathogenic avian influenza virus H7N1 and low-pathogenic avian influenza virus H5N3, as representatives of notifiable avian viral diseases, were determined in spiked hatchery waste. Bovine parainfluenza virus type 3, feline coronavirus, and feline calicivirus were used as models for other important avian pathogens, such as Newcastle disease virus, infectious bronchitis virus, and avian hepatitis E virus. Bacteriophage MS2 was also monitored as a stable indicator. Coronavirus was the most sensitive virus, with decimal reduction (D) values of 1.2 and 0.63 h after addition of 0.5% (wt/wt) ammonia at 14 and 25°C, respectively. Under similar conditions, high-pathogenic avian influenza H7N1 was the most resistant, with D values of 3.0 and 1.4 h. MS2 was more resistant than the viruses to all treatments and proved to be a suitable indicator of viral inactivation. The results indicate that ammonia treatment of hatchery waste is efficient in inactivating enveloped and naked single-stranded RNA viruses. Based on the D values and confidence intervals obtained, guidelines for treatment were proposed, and one was successfully validated at full scale at a hatchery, with MS2 added to hatchery waste.

  8. Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.; Ansong, Charles; Brewer, Heather M.; Bogomolnaya, Lydia; Adams, L. Garry; McClelland, Michael; Adkins, Joshua N.; Andrews-Polymenis, Helene L.; Fang, Ferric C.

    2015-09-14

    Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.

  9. Electrical conduction and photoresponses of gamma-ray-irradiated single-stranded DNA/single-walled carbon nanotube composite systems

    Energy Technology Data Exchange (ETDEWEB)

    Hong, W.; Lee, E.M.; Kim, D.W.; Lee, Cheol Eui, E-mail: rscel@korea.ac.kr

    2015-04-15

    Highlights: •Effects of gamma-ray irradiation on single-stranded DNA (ssDNA)/single-walled carbon nanotube (SWNT) composite films. •Barrier for thermally activated conduction in the composite systems modified by the gamma-ray irradiation. •Photoresponses reveal photoexcitation and oxygen photodesorption modified by gamma-ray irradiation. -- Abstract: Effects of gamma-ray irradiation on the electrical conductivity and photoresponse have been studied for single-stranded DNA (ssDNA)/single-walled carbon nanotube (SWNT) composite films. The temperature-dependent electrical conductivity of the ssDNA/SWNT composite films, well described by a fluctuation-induced tunneling model, indicated modification of the barrier for thermally activated conduction by the gamma-ray irradiation. Besides, the photoresponse measurements indicated modified photoexcited charge carrier generation and oxygen photodesorption in the composite systems due to the gamma-ray irradiation.

  10. Stabilization of Pt nanoparticles by single stranded DNA and the binary assembly of Au and Pt nanoparticles without hybridization

    International Nuclear Information System (INIS)

    Yang, J.; Lee, Jim Yang; Too, Heng-Phon; Chow, Gan-Moog; Gan, Leong M.

    2006-01-01

    The non-specific interaction between single stranded DNA (ssDNA) and 12 nm Pt nanoparticles is investigated in this work. The data show a strong and non-specific interaction between the two which can be exploited for the stabilization of Pt nanoparticles in aqueous solutions. Based on the experimental findings, a non-hybridization based protocol to assemble 17 nm Au and Pt nanoparticles (12 nm cubic and 3.6 nm spherical) by single-stranded DNA was developed. Transmission electron microscopy (TEM) and UV-visible spectroscopy confirmed that Au and Pt nanoparticles could be assembled by the non-specific interaction in an orderly manner. The experimental results also caution against the potential pitfalls in using DNA melting point analysis to infer metal nanoparticle assembly by DNA hybridization

  11. Markers of Decompression Stress of Mass Stranded/Live Caught and Released vs. Single Stranded Marine Mammals

    Science.gov (United States)

    2014-09-30

    Caught and Released vs. Single Stranded Marine Mammals Michael Moore Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543...Society for Marine Mammalogy 2013 Biennial Conference on the Biology of Marine Mammals in New Zealand. Dr. Fahlman’s graduate student Lauren Gonzalez...Harabin, Metabolism and thermoregulation in guinea pigs in hyperbaric hydrogen: Effects of pressure. Journal of Thermal Biology , 1997. 22(1): p. 31-41

  12. Selective binding and reverse transcription inhibition of single-strand poly(A) RNA by metal TMPyP complexes.

    Science.gov (United States)

    Zhou, Zhu-Xin; Gao, Feng; Chen, Xing; Tian, Xiang-Jing; Ji, Liang-Nian

    2014-10-06

    Ni-, Cu-, and Zn-TMPyP are capable of binding to single-strand poly(A) RNA with high preference and affinity and inhibiting the reverse transcription of RNA by both M-MuLV and HIV-1 reverse transcriptase. With 10 nM azidothymidine, the IC50 value of M-TMPyP could be lowered to 10(-1) μM order.

  13. Stretching and Controlled Motion of Single-Stranded DNA in Locally-Heated Solid-State Nanopores

    Science.gov (United States)

    Belkin, Maxim; Maffeo, Christopher; Wells, David B.

    2013-01-01

    Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA. PMID:23876013

  14. Radiation-induced DNA single-strand scission and its rejoining in spermatogonia and spermatozoa of mouse

    International Nuclear Information System (INIS)

    Ono, T.; Okada, S.

    1977-01-01

    Gamma-ray-induced DNA single-strand scissions and the ability to repair the scissions in spermatogonia from young mice and in spermatozoa from adult mice were studied quantitatively by an alkaline sucrose density-gradient centrifugation method. The average size of DNAs in non-irradiated spermatogonia was 2.6-3.0xx10 8 daltons, similar to those of a spermatid-rich population, and the size of DNA in non-irradiated spermatozoa was 1.2x10 8 daltons. In spermatogonia, the radiosensitivity of DNA was 0.42 single-strand breaks/10 12 daltons of DNA/rad in oxic conditions and only 0.24 under anoxic conditions. In spermatozoa the break efficiency of DNA was 0.22 single-strand breaks/10 12 daltons of DNA/rad under oxic conditions and altered little under anoxic irradiation. The DNA scissions were efficiently repaired in spermatogonia within 10 min, whereas the breaks in spermatozoa were not rejoined at all even after two days of post-irradiation time. The radiosensitivities of DNA, repair capability and non- and/or slowreparable DNA scissions were compared in spermatogonium-rich, spermatid-rich and spermatozoanrich populations

  15. The Adsorption of Short Single-Stranded DNA Oligomers on Mineral Surfaces

    Science.gov (United States)

    Kopstein, M.; Sverjensky, D. A.; Hazen, R. M.; Cleaves, H. J.

    2009-12-01

    Previous studies have described feasible pathways for the synthesis of simple organic building blocks such as formaldehyde and hydrogen cyanide, and their reaction to form more complex biomolecules such as nucleotide bases, amino acids and sugars (Miller and Orgel 1974, Miller and Cleaves 2006). However, the polymerization of monomers into a useful genetic material remains problematic (Orgel 2004). Organic building blocks were unlikely to polymerize from very dilute aqueous solution in the primitive oceans. Mineral surface adsorption has been suggested as a possible mechanism for concentrating the necessary building blocks (Bernal 1951). This study focused on the adsorption behavior of single-stranded DNA homo-oligomers of adenine and thymine (including the monomers, dimers, tetramers, hexamers, octomers, and decamers) with five different mineral surfaces (pyrite, rutile, hematite, olivine and calcite). Adsorption was studied in 0.1 M pH 8.1 KHCO3 with0.05 M NaCl as background electrolyte. Solutions were mixed for 24 hours at room temperature, centrifuged and the supernatants analyzed by UV/visible spectrophotometry. Equilibrium solution concentrations were measured and used to determine the number of moles adsorbed per square meter. Langmuir isotherms were constructed using the experimental data. It was found that adenine-containing molecules tend to bind much more strongly than thymine-containing molecules. It was also found that the number of moles adsorbed at saturation tends to fall with increasing chain length, while adsorption affinity tends to rise. Oligomer length appears to affect adsorption more than the mineral type. These results may have implications for the primordial organization of the first nucleic acid molecules as the persistence of extra-cellular nucleic acids in the environment. References Bernal, J. D. (1951) The Physical Basis of Life (Routledge, London). Miller S.L. and Cleaves, H.J. (2006) Prebiotic chemistry on the primitive Earth. In

  16. Role of electrostatics in the assembly pathway of a single-stranded RNA virus.

    Science.gov (United States)

    Garmann, Rees F; Comas-Garcia, Mauricio; Koay, Melissa S T; Cornelissen, Jeroen J L M; Knobler, Charles M; Gelbart, William M

    2014-09-01

    We have recently discovered (R. D. Cadena-Nava et al., J. Virol. 86:3318-3326, 2012, doi:10.1128/JVI.06566-11) that the in vitro packaging of RNA by the capsid protein (CP) of cowpea chlorotic mottle virus is optimal when there is a significant excess of CP, specifically that complete packaging of all of the RNA in solution requires sufficient CP to provide charge matching of the N-terminal positively charged arginine-rich motifs (ARMS) of the CPs with the negatively charged phosphate backbone of the RNA. We show here that packaging results from the initial formation of a charge-matched protocapsid consisting of RNA decorated by a disordered arrangement of CPs. This protocapsid reorganizes into the final, icosahedrally symmetric nucleocapsid by displacing the excess CPs from the RNA to the exterior surface of the emerging capsid through electrostatic attraction between the ARMs of the excess CP and the negative charge density of the capsid exterior. As a test of this scenario, we prepare CP mutants with extra and missing (relative to the wild type) cationic residues and show that a correspondingly smaller and larger excess, respectively, of CP is needed for complete packaging of RNA. Cowpea chlorotic mottle virus (CCMV) has long been studied as a model system for the assembly of single-stranded RNA viruses. While much is known about the electrostatic interactions within the CCMV virion, relatively little is known about these interactions during assembly, i.e., within intermediate states preceding the final nucleocapsid structure. Theoretical models and coarse-grained molecular dynamics simulations suggest that viruses like CCMV assemble by the bulk adsorption of CPs onto the RNA driven by electrostatic attraction, followed by structural reorganization into the final capsid. Such a mechanism facilitates assembly by condensing the RNA for packaging while simultaneously concentrating the local density of CP for capsid nucleation. We provide experimental evidence of

  17. Oxidized Base Damage and Single-Strand Break Repair in Mammalian Genomes: Role of Disordered Regions and Posttranslational Modifications in Early Enzymes

    OpenAIRE

    Hegde, Muralidhar L.; Izumi, Tadahide; Mitra, Sankar

    2012-01-01

    Oxidative genome damage induced by reactive oxygen species includes oxidized bases, abasic (AP) sites, and single-strand breaks, all of which are repaired via the evolutionarily conserved base excision repair/single-strand break repair (BER/SSBR) pathway. BER/SSBR in mammalian cells is complex, with preferred and backup sub-pathways, and is linked to genome replication and transcription. The early BER/SSBR enzymes, namely, DNA glycosylases (DGs) and the end-processing proteins such as abasic ...

  18. Cisplatin GG-crosslinks within single-stranded DNA: origin of the preference for left-handed helicity.

    Science.gov (United States)

    Monnet, Jordan; Kozelka, Jiří

    2012-10-01

    Molecular dynamics (MD) simulations of the single-stranded DNA trinucleotide TG*G*, with the G* guanines crosslinked by the antitumor drug cisplatin, were performed with explicit representation of the water as solvent. The purpose of the simulations was to explain previous NMR observations indicating that in single-stranded cisplatin-DNA adducts, the crosslinked guanines adopt a left-handed helical orientation, whereas in duplexes, the orientation is right-handed. The analysis of the MD trajectory of TG*G* has ascribed a crucial role to hydrogen-bonding (direct or through-water) interactions of the 5'-oriented NH(3) ligand of platinum with acceptor groups at the 5'-side of the crosslink, namely the TpG* phosphate and the terminal 5'-OH group. These interactions bring about some strain into the trinucleotide which is slightly but significantly (1-1.5 kcal.mol(-1)) higher for the right-handed orientation than for the left-handed one. During the unconstrained, 3 ns long MD simulation, left-handed conformations were ~15 times more abundant than the right-handed ones. This sampling difference agrees roughly with the calculated energy difference in strain energy. Overall, these results show that the Pt-GG crosslink within single-stranded DNA is malleable and can access different conformations at a moderate energy cost. This malleability could be of importance in interactions between the platinated DNA and cellular proteins, in which the DNA is locally unwound. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Bacillus subtilis single-stranded DNA-binding protein SsbA is phosphorylated at threonine 38 by the serine/threonine kinase YabT

    DEFF Research Database (Denmark)

    Derouiche, Abderahmane; Petranovic, Dina; Macek, Boris

    2016-01-01

    Background and purpose: Single-stranded DNA-binding proteins participate in all stages of DNA metabolism that involve single-stranded DNA, from replication, recombination, repair of DNA damage, to natural competence in species such as Bacillus subtilis. B. subtilis single-stranded DNA-binding pro......Background and purpose: Single-stranded DNA-binding proteins participate in all stages of DNA metabolism that involve single-stranded DNA, from replication, recombination, repair of DNA damage, to natural competence in species such as Bacillus subtilis. B. subtilis single-stranded DNA...... assays.Results: In addition to the known tyrosine phosphorylation of SsbA on tyrosine 82, we identified a new phosphorylation site: threonine 38. The in vitro assays demonstrated that SsbA is preferentially phosphorylated by the B. subtilis Hanks-type kinase YabT, and phosphorylation of threonine 38...... leads to enhanced cooperative binding to DNA.Conclusions: Our findings contribute to the emerging picture that bacterial proteins, exemplified here by SsbA, undergo phosphorylation at multiple residues. This results in a complex regulation of cellular functions, and suggests that the complexity...

  20. Assembly of presynaptic filaments. Factors affecting the assembly of RecA protein onto single-stranded DNA

    DEFF Research Database (Denmark)

    Thresher, RJ; Christiansen, Gunna; Griffith, JD

    1988-01-01

    We have previously shown that the assembly of RecA protein onto single-stranded DNA (ssDNA) facilitated by SSB protein occurs in three steps: (1) rapid binding of SSB protein to the ssDNA; (2) nucleation of RecA protein onto this template; and (3) co-operative polymerization of additional Rec...... assembled onto ssDNA at net rates that varied from 250 to 900 RecA protein monomers per minute, with the rate inversely related to the concentration of SSB protein. Combined sucrose sedimentation and electron microscope analysis established that SSB protein was displaced from the ssDNA during RecA protein...

  1. Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds

    Directory of Open Access Journals (Sweden)

    R. Maeda

    2012-09-01

    Full Text Available Biopolymers are easily denatured by heating, a change in pH or chemical substances when they are immobilized on a substrate. To prevent denaturation of biopolymers, we developed a method to trap a polynucleotide on a substrate by hydrogen bonding using silica particles with surfaces modified by aminoalkyl chains ([A-AM silane]/SiO2. [A-AM silane]/SiO2 was synthesized by silane coupling reaction of N-2-(aminoethyl-3-aminopropyltrimethoxysilane (A-AM silane with SiO2 particles with a diameter of 5 μm at 100 °C for 20 min. The surface chemical structure of [A-AM silane]/SiO2 was characterized by Fourier transform infrared spectroscopy and molecular orbital calculations. The surface of the silica particles was modified with A-AM silane and primary amine groups were formed. [A-AM silane]/SiO2 was trapped with single-stranded nucleic acids [(Poly-X; X = A (adenine, G (guanine and C (cytosine] in PBS solution at 37 °C for 1 h. The single-stranded nucleic acids were trapped on the surface of the [A-AM silane]/SiO2 by hydrogen bonding to form conjugated materials. The resulting complexes were further conjugated by derivatives of acridine orange (AO as fluorescent labels under the same conditions to form [AO:Poly-X:A-AM silane]/SiO2 complexes. Changes in the fluorescence intensity of these complexes originating from interactions between the single-stranded nucleic acid and aromatic compounds were also evaluated. The change in intensity displayed the order [AO: Poly-G: A-AM silane]/SiO2 > [AO:Poly-A:A-AM silane]/SiO2 >> [AO:Poly-C:A-AM silane]/SiO2. This suggests that the single-stranded nucleic acids conjugated with aminoalkyl chains on the surfaces of SiO2 particles and the change in fluorescence intensity reflected the molecular interaction between AO and the nucleic-acid base in a polynucleotide.

  2. Opposite effects of nitric oxide donors on DNA single strand breakage and cytotoxicity caused by tert-butylhydroperoxide

    Science.gov (United States)

    Guidarelli, Andrea; Sestili, Piero; Cantoni, Orazio

    1998-01-01

    The effects of three different NO donors on tert-butylhydroperoxide (tB-OOH)-induced DNA cleavage and toxicity were investigated in U937 cells.Treatment with S-nitroso-N-acetyl-penicillamine (SNAP, 1–30 μM), while not in itself DNA-damaging, potentiated the DNA strand scission induced by 200 μM tB-OOH in a concentration-dependent fashion. The enhancing effects of SNAP were observed with two different techniques for the assessment of DNA damage. Decomposed SNAP was inactive. S-nitrosoglutathione (GSNO, 300 μM) and (Z)-1-[(2-aminoethyl)-N-(2-ammonioethyl) amino]diazen-1-ium-1,2-diolate (DETA-NO, 1 mM) also increased DNA cleavage generated by tB-OOH and these responses, as well as that mediated by SNAP, were prevented by the NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazolin-1-oxyl-3-oxide (PTIO).SNAP neither inhibited catalase activity nor increased the formation of DNA lesions in cells exposed to H2O2. Furthermore, SNAP did not affect the rate of rejoining of the DNA single strand breaks generated by tB-OOH.Under the conditions utilized in the DNA damage experiments, treatment with tB-OOH alone or associated with SNAP did not cause cell death. However, SNAP as well as GSNO markedly reduced the lethal response promoted by millimolar concentrations of tB-OOH and these effects were abolished by PTIO. Decomposed SNAP was inactive.It is concluded that low levels of NO donors, which probably release physiological concentrations of NO, enhance the accumulation of DNA single strand breaks in U937 cells exposed to tB-OOH. This NO-mediated effect appears to (a) not depend on inhibition of either DNA repair (which would increase the net accumulation of DNA lesions by preventing DNA single strand break removal) or catalase activity (which would also enhance the net accumulation of DNA lesions since H2O2 is one of the species mediating the tB-OOH-induced DNA cleavage) and (b) be caused by enforced formation of tB-OOH-derived DNA-damaging species. In contrast to

  3. Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism.

    Science.gov (United States)

    Zheng, Xuelian; Yang, Shixin; Zhang, Dengwei; Zhong, Zhaohui; Tang, Xu; Deng, Kejun; Zhou, Jianping; Qi, Yiping; Zhang, Yong

    2016-07-01

    A method based on DNA single-strand conformation polymorphism is demonstrated for effective genotyping of CRISPR/Cas9-induced mutants in rice. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) has been widely adopted for genome editing in many organisms. A large proportion of mutations generated by CRISPR/Cas9 are very small insertions and deletions (indels), presumably because Cas9 generates blunt-ended double-strand breaks which are subsequently repaired without extensive end-processing. CRISPR/Cas9 is highly effective for targeted mutagenesis in the important crop, rice. For example, homozygous mutant seedlings are commonly recovered from CRISPR/Cas9-treated calli. However, many current mutation detection methods are not very suitable for screening homozygous mutants that typically carry small indels. In this study, we tested a mutation detection method based on single-strand conformational polymorphism (SSCP). We found it can effectively detect small indels in pilot experiments. By applying the SSCP method for CRISRP-Cas9-mediated targeted mutagenesis in rice, we successfully identified multiple mutants of OsROC5 and OsDEP1. In conclusion, the SSCP analysis will be a useful genotyping method for rapid identification of CRISPR/Cas9-induced mutants, including the most desirable homozygous mutants. The method also has high potential for similar applications in other plant species.

  4. Characterization of the single-stranded DNA binding protein pV(VGJΦ) of VGJΦ phage from Vibrio cholerae.

    Science.gov (United States)

    Falero, Alina; Caballero, Andy; Trigueros, Sonia; Pérez, Celso; Campos, Javier; Marrero, Karen; Fando, Rafael

    2011-09-01

    pV(VGJΦ), a single-stranded DNA binding protein of the vibriophage VGJΦ was subject to biochemical analysis. Here, we show that this protein has a general affinity for single-stranded DNA (ssDNA) as documented by Electrophoretic Mobility Shift Assay (EMSA). The apparent molecular weight of the monomer is about 12.7kDa as measured by HPLC-SEC. Moreover, isoelectrofocusing showed an isoelectric point for pV(VGJΦ) of 6.82 pH units. Size exclusion chromatography in 150mM NaCl, 50mM sodium phosphate buffer, pH 7.0 revealed a major protein species of 27.0kDa, suggesting homodimeric protein architecture. Furthermore, pV(VGJΦ) binds ssDNA at extreme temperatures and the complex was stable after extended incubation times. Upon frozen storage at -20°C for a year the protein retained its integrity, biological activity and oligomericity. On the other hand, bioinformatics analysis predicted that pV(VGJΦ) protein has a disordered C-terminal, which might be involved in its functional activity. All the aforementioned features make pV(VGJΦ) interesting for biotechnological applications. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Size-controllable DNA nanoribbons assembled from three types of reusable brick single-strand DNA tiles.

    Science.gov (United States)

    Shi, Xiaolong; Chen, Congzhou; Li, Xin; Song, Tao; Chen, Zhihua; Zhang, Zheng; Wang, Yanfeng

    2015-11-21

    Precise control of nanostructure is a significant goal shared by supramolecular chemistry, nanotechnology and materials science. In DNA nanotechnology, methods of constructing desired DNA nanostructures using programmable DNA strands have been studied extensively and have become a promising branch of research, but developing universal and low-cost (in the sense of using fewer types of DNA strands) methods remains a challenge. In this work, we propose a novel approach to assemble size-controllable DNA nanoribbons with three types of reusable brick SSTs (single-stranded DNA tiles), where the control of ribbon size is achieved by regulating the concentration ratio between manipulative strands and packed single-stranded DNA tiles. In our method, three types of brick SSTs are sufficient in assembling DNA nanoribbons of different sizes, which is much less than the number of types of unique tile-programmable assembling strategy, thus achieving a universal and low-cost method. The assembled DNA nanoribbons are observed and analyzed by atomic force microscopy (AFM). Experimental observations strongly suggest the feasibility and reliability of our method.

  6. TrmBL2 from Pyrococcus furiosus Interacts Both with Double-Stranded and Single-Stranded DNA.

    Directory of Open Access Journals (Sweden)

    Sebastian Wierer

    Full Text Available In many hyperthermophilic archaea the DNA binding protein TrmBL2 or one of its homologues is abundantly expressed. TrmBL2 is thought to play a significant role in modulating the chromatin architecture in combination with the archaeal histone proteins and Alba. However, its precise physiological role is poorly understood. It has been previously shown that upon binding TrmBL2 covers double-stranded DNA, which leads to the formation of a thick and fibrous filament. Here we investigated the filament formation process as well as the stabilization of DNA by TrmBL2 from Pyroccocus furiosus in detail. We used magnetic tweezers that allow to monitor changes of the DNA mechanical properties upon TrmBL2 binding on the single-molecule level. Extended filaments formed in a cooperative manner and were considerably stiffer than bare double-stranded DNA. Unlike Alba, TrmBL2 did not form DNA cross-bridges. The protein was found to bind double- and single-stranded DNA with similar affinities. In mechanical disruption experiments of DNA hairpins this led to stabilization of both, the double- (before disruption and the single-stranded (after disruption DNA forms. Combined, these findings suggest that the biological function of TrmBL2 is not limited to modulating genome architecture and acting as a global repressor but that the protein acts additionally as a stabilizer of DNA secondary structure.

  7. Alkali-labile sites and post-irradiation effects in single-stranded DNA induced by H radicals

    International Nuclear Information System (INIS)

    Lafleur, M.V.M.; Heuvel, N. van; Woldhuis, J.; Loman, H.

    1978-01-01

    Single-stranded phiX174 DNA in aqueous solutions has been irradiated in the absence of oxygen, under conditions in which H radicals react with the DNA. It was shown that H radical reactions result in breaks, which contribute approximately 10 per cent inactivation. Further, two types of alkali-labile sites were formed. One was lethal and gave rise to single-strand breaks by alkali and was most probably identical with post-irradiation heat damage and contributed about 33 per cent to the inactivation mentioned above. The other consisted of non-lethal damage, partly dihydropyrimidine derivatives, and was converted to lethal damage by alkali. This followed from experiments in which the DNA was treated with osmium-tetroxide, which oxidized thymine to 5,6-dihydroxydihydrothymine. Treatment with alkali of this DNA gave the same temperature dependence as found for the non-lethal alkali-labile sites in irradiated DNA. A similar temperature dependence was found for dihydrothymine and irradiated pyrimidines with alkali. (author)

  8. Non-uniform binding of single-stranded DNA binding proteins to hybrids of single-stranded DNA and single-walled carbon nanotubes observed by atomic force microscopy in air and in liquid

    Energy Technology Data Exchange (ETDEWEB)

    Umemura, Kazuo, E-mail: meicun2006@163.com; Ishizaka, Kei; Nii, Daisuke; Izumi, Katsuki

    2016-12-01

    Highlights: • Conjugates of protein, DNA, and SWNTs were observed by AFM in liquid. • Non-uniform binding of proteins was visualized in liquid. • Thickness of DNA molecules on SWNT surfaces was well characterized in liquid. - Abstract: Using atomic force spectroscopy (AFM), we observed hybrids of single-stranded DNA (ssDNA) and single-walled carbon nanotubes (SWNTs) with or without protein molecules in air and in an aqueous solution. This is the first report of ssDNA–SWNT hybrids with proteins in solution analyzed by AFM. In the absence of protein, the height of the ssDNA–SWNT hybrids was 1.1 ± 0.3 nm and 2.4 ± 0.6 nm in air and liquid, respectively, suggesting that the ssDNA molecules adopted a flexible structure on the SWNT surface. In the presence of single-stranded DNA binding (SSB) proteins, the heights of the hybrids in air and liquid increased to 6.4 ± 3.1 nm and 10.0 ± 4.5 nm, respectively. The AFM images clearly showed binding of the SSB proteins to the ssDNA–SWNT hybrids. The morphology of the SSB–ssDNA–SWNT hybrids was non-uniform, particularly in aqueous solution. The variance of hybrid height was quantitatively estimated by cross-section analysis along the long-axis of each hybrid. The SSB–ssDNA–SWNT hybrids showed much larger variance than the ssDNA–SWNT hybrids.

  9. Base damage within single-strand DNA underlies in vivo hypermutability induced by a ubiquitous environmental agent.

    Directory of Open Access Journals (Sweden)

    Kin Chan

    Full Text Available Chromosomal DNA must be in single-strand form for important transactions such as replication, transcription, and recombination to occur. The single-strand DNA (ssDNA is more prone to damage than double-strand DNA (dsDNA, due to greater exposure of chemically reactive moieties in the nitrogenous bases. Thus, there can be agents that damage regions of ssDNA in vivo while being inert toward dsDNA. To assess the potential hazard posed by such agents, we devised an ssDNA-specific mutagenesis reporter system in budding yeast. The reporter strains bear the cdc13-1 temperature-sensitive mutation, such that shifting to 37°C results in telomere uncapping and ensuing 5' to 3' enzymatic resection. This exposes the reporter region, containing three closely-spaced reporter genes, as a long 3' ssDNA overhang. We validated the ability of the system to detect mutagenic damage within ssDNA by expressing a modified human single-strand specific cytosine deaminase, APOBEC3G. APOBEC3G induced a high density of substitutions at cytosines in the ssDNA overhang strand, resulting in frequent, simultaneous inactivation of two reporter genes. We then examined the mutagenicity of sulfites, a class of reactive sulfur oxides to which humans are exposed frequently via respiration and food intake. Sulfites, at a concentration similar to that found in some foods, induced a high density of mutations, almost always as substitutions at cytosines in the ssDNA overhang strand, resulting in simultaneous inactivation of at least two reporter genes. Furthermore, sulfites formed a long-lived adducted 2'-deoxyuracil intermediate in DNA that was resistant to excision by uracil-DNA N-glycosylase. This intermediate was bypassed by error-prone translesion DNA synthesis, frequently involving Pol ζ, during repair synthesis. Our results suggest that sulfite-induced lesions in DNA can be particularly deleterious, since cells might not possess the means to repair or bypass such lesions

  10. Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA

    DEFF Research Database (Denmark)

    Kumar, Vipin; Kesavan, Venkitasamy; Gothelf, Kurt Vesterager

    2015-01-01

    Acyclic (l)-threoninol nucleic acid (aTNA) containing thymine, cytosine and adenine nucleobases were synthesized and shown to form surprisingly stable triplexes with complementary single stranded homopurine DNA or RNA targets. The triplex structures consist of two (l)-aTNA strands and one DNA...... or RNA, and these triplexes are significantly stronger than the corresponding DNA or RNA duplexes as shown in competition experiments. As a unique property the (l)-aTNAs exclusively form triplex structures with DNA and RNA and no duplex structures are observed by gel electrophoresis. The results were...... compared to the known enantiomer (d)-aTNA, which forms much weaker triplexes depending upon temperature and time. It was demonstrated that (l)-aTNA triplexes are able to stop primer extension on a DNA template, showing the potential of (l)-aTNA for antisense applications....

  11. Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample.

    Science.gov (United States)

    Cui, Lunbiao; Wu, Binyao; Zhu, Xiaojuan; Guo, Xiling; Ge, Yiyue; Zhao, Kangchen; Qi, Xian; Shi, Zhiyang; Zhu, Fengcai; Sun, Lixin; Zhou, Minghao

    2017-11-01

    Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR). The predicted amino acid sequences of the Cap and Rep proteins of HRAPLV showed highest identity to those of porcine stool-associated circular virus 5 isolate CP3 (PoSCV 5) (53.0% and 48.9%, respectively). The host tropism of the virus is unknown, and further study is warranted to determine whether this novel virus is associated with human disease.

  12. Fabrication, characterization and electrochemical performance of single strand carbon fiber prepared by catalytic chemical vapor decomposition method

    Energy Technology Data Exchange (ETDEWEB)

    Joshi, Vrushali S. [Department of Chemistry, University of Pune, Ganeshkhind, Pune 411007, Maharashtra (India); Gokhale, Suresh P.; Patil, Kashinath R. [Physical and Material Chemistry Division, National Chemical Laboratory, Pune (India); Haram, Santosh K., E-mail: haram@chem.unipune.ernet.i [Department of Chemistry, University of Pune, Ganeshkhind, Pune 411007, Maharashtra (India)

    2010-02-15

    Preparation, fabrication and voltammetric characterizations of a single strand of carbon fiber (SSCF) electrode and their potential applications for biosensor are presented. SSCFs of diameter ca. 10 +- 2 mum and few millimeters in length are prepared by catalytic chemical vapor decomposition (CCVD) method. Voltammetry with potassium ferricyanide, alpha-methylferrocene methanol and hexaammineruthenium(III) chloride on SSCF electrode are used as bench marks to validate the electrode properties. Quasi-steady state voltammograms obtained were fitted into a cylindrical diffusion model. From which, the standard rate constant (k{sup 0}) and electron transfer coefficient (alpha) are obtained. The use of SSCF electrode is demonstrated for the voltammetric detection of the micromolar quantity of dopamine in the presence of large excess (ca. 200 times) of ascorbic acid, without any fouling of electrode surface. The kinetics of electron transfer are investigated.

  13. Fabrication, characterization and electrochemical performance of single strand carbon fiber prepared by catalytic chemical vapor decomposition method

    International Nuclear Information System (INIS)

    Joshi, Vrushali S.; Gokhale, Suresh P.; Patil, Kashinath R.; Haram, Santosh K.

    2010-01-01

    Preparation, fabrication and voltammetric characterizations of a single strand of carbon fiber (SSCF) electrode and their potential applications for biosensor are presented. SSCFs of diameter ca. 10 ± 2 μm and few millimeters in length are prepared by catalytic chemical vapor decomposition (CCVD) method. Voltammetry with potassium ferricyanide, α-methylferrocene methanol and hexaammineruthenium(III) chloride on SSCF electrode are used as bench marks to validate the electrode properties. Quasi-steady state voltammograms obtained were fitted into a cylindrical diffusion model. From which, the standard rate constant (k 0 ) and electron transfer coefficient (α) are obtained. The use of SSCF electrode is demonstrated for the voltammetric detection of the micromolar quantity of dopamine in the presence of large excess (ca. 200 times) of ascorbic acid, without any fouling of electrode surface. The kinetics of electron transfer are investigated.

  14. Quenching of Single-Walled Carbon Nanotube Fluorescence by Dissolved Oxygen Reveals Selective Single-Stranded DNA Affinities.

    Science.gov (United States)

    Zheng, Yu; Bachilo, Sergei M; Weisman, R Bruce

    2017-05-04

    The selective interactions between short oligomers of single-stranded DNA (ssDNA) and specific structures of single-walled carbon nanotubes have been exploited in powerful methods for nanotube sorting. We report here that nanotubes coated with ssDNA also display selective interactions through the selective quenching of nanotube fluorescence by dissolved oxygen. In aqueous solutions equilibrated under 1 atm of O 2 , emission intensity from semiconducting nanotubes is reduced by between 9 and 40%, varying with the combination of ssDNA sequence and nanotube structure. This quenching reverses promptly and completely on the removal of dissolved O 2 and may be due to physisorption on nanotube surfaces. Fluorescence quenching offers a simple, nondestructive approach for studying the structure-selective interactions of ssDNA with single-walled carbon nanotubes and identifying recognition sequences.

  15. Surface treatment on amorphous InGaZnO4 thin film for single-stranded DNA biosensing

    Science.gov (United States)

    Sun, Dali; Matsui, Hiroaki; Wu, Chun-Nan; Tabata, Hitoshi

    2015-01-01

    Amorphous InGaZnO4 (aIGZO) has been widely used as a transparent semiconductor. However, no research has been found yet applying aIGZO to biosensing. This paper examined the single strand DNA (ssDNA) immobilization on aIGZO by absorption with a comparison to ITO, which is the first step for many biosensing schemas. The DNA quantification by florescence intensity shows that the absorption capacity of aIGZO film to ssDNA is 6.7 times greater than that of ITO. XPS and contact angle analysis proved the high DNA absorption affinity on aIGZO film is related to its high effectiveness to OH- attachment. A feasible method to immobilized ssDNA on aIGZO thin film is evaluated in this paper, and consequently, enables a possible approach to apply aIGZO in biosensing.

  16. Multiplex and quantitative pathogen detection with high-resolution capillary electrophoresis-based single-strand conformation polymorphism.

    Science.gov (United States)

    Hwang, Hee Sung; Shin, Gi Won; Chung, Boram; Na, Jeongkyeong; Jung, Gyoo Yeol

    2013-01-01

    Among the molecular diagnostic methods for bacteria-induced diseases, capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) combined with 16S rRNA gene-specific PCR has enormous potential because it can separate sequence variants using a simple procedure. However, conventional CE-SSCP systems have limited resolution and cannot separate most 16S rRNA gene-specific markers into separate peaks. A high-resolution CE-SSCP system that uses a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer matrix was recently developed and shown to effectively separate highly similar PCR products. In this report, a protocol for the detection of 12 pathogenic bacteria is provided. Pathogen markers were amplified by PCR using universal primers and separated by CE-SSCP; each marker peak was well separated at baseline and showed a characteristic mobility, allowing the easy identification of the pathogens.

  17. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana.

    Science.gov (United States)

    Olszewski, Marcin; Grot, Anna; Wojciechowski, Marek; Nowak, Marta; Mickiewicz, Małgorzata; Kur, Józef

    2010-10-15

    In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively). They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold) in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC) the melting temperature (Tm) was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR).

  18. Charge enhancement of single-stranded DNA in negative electrospray ionization using the supercharging reagent meta-nitrobenzyl alcohol.

    Science.gov (United States)

    Brahim, Bessem; Alves, Sandra; Cole, Richard B; Tabet, Jean-Claude

    2013-12-01

    Charge enhancement of single-stranded oligonucleotide ions in negative ESI mode is investigated. The employed reagent, meta-nitrobenzyl alcohol (m-NBA), was found to improve total signal intensity (Itot), increase the highest observed charge states (zhigh), and raise the average charge states (zavg) of all tested oligonucleotides analyzed in negative ESI. To quantify these increases, signal enhancement ratios (SER1%) and charge enhancement coefficients (CEC1%) were introduced. The SER1%, (defined as the quotient of total oligonucleotide ion abundances with 1% m-NBA divided by total oligonucleotide abundance without m-NBA) was found to be greater than unity for every oligonucleotide tested. The CEC1% values (defined as the average charge state in the presence of 1% m-NBA minus the average charge state in the absence of m-NBA) were found to be uniformly positive. Upon close inspection, the degree of charge enhancement for longer oligonucleotides was found to be dependent upon thymine density (i.e., the number and the location of phospho-thymidine units). A correlation between the charge enhancement induced by the presence of m-NBA and the apparent gas-phase acidity (largely determined by the sequence of thymine units but also by the presence of protons on other nucleobases) of multiply deprotonated oligonucleotide species, was thus established. Ammonium cations appeared to be directly involved in the m-NBA supercharging mechanism, and their role seems to be consistent with previously postulated ESI mechanisms describing desorption/ionization of single-stranded DNA into the gas phase.

  19. Charge Enhancement of Single-Stranded DNA in Negative Electrospray Ionization Using the Supercharging Reagent Meta-nitrobenzyl Alcohol

    Science.gov (United States)

    Brahim, Bessem; Alves, Sandra; Cole, Richard B.; Tabet, Jean-Claude

    2013-12-01

    Charge enhancement of single-stranded oligonucleotide ions in negative ESI mode is investigated. The employed reagent, meta-nitrobenzyl alcohol (m-NBA), was found to improve total signal intensity (Itot), increase the highest observed charge states (zhigh), and raise the average charge states (zavg) of all tested oligonucleotides analyzed in negative ESI. To quantify these increases, signal enhancement ratios (SER1%) and charge enhancement coefficients (CEC1%) were introduced. The SER1%, (defined as the quotient of total oligonucleotide ion abundances with 1 % m-NBA divided by total oligonucleotide abundance without m-NBA) was found to be greater than unity for every oligonucleotide tested. The CEC1% values (defined as the average charge state in the presence of 1 % m-NBA minus the average charge state in the absence of m-NBA) were found to be uniformly positive. Upon close inspection, the degree of charge enhancement for longer oligonucleotides was found to be dependent upon thymine density (i.e., the number and the location of phospho-thymidine units). A correlation between the charge enhancement induced by the presence of m-NBA and the apparent gas-phase acidity (largely determined by the sequence of thymine units but also by the presence of protons on other nucleobases) of multiply deprotonated oligonucleotide species, was thus established. Ammonium cations appeared to be directly involved in the m-NBA supercharging mechanism, and their role seems to be consistent with previously postulated ESI mechanisms describing desorption/ionization of single-stranded DNA into the gas phase.

  20. Alkyladenine DNA glycosylase (AAG) localizes to mitochondria and interacts with mitochondrial single-stranded binding protein (mtSSB).

    Science.gov (United States)

    van Loon, Barbara; Samson, Leona D

    2013-03-01

    Due to a harsh environment mitochondrial genomes accumulate high levels of DNA damage, in particular oxidation, hydrolytic deamination, and alkylation adducts. While repair of alkylated bases in nuclear DNA has been explored in detail, much less is known about the repair of DNA alkylation damage in mitochondria. Alkyladenine DNA glycosylase (AAG) recognizes and removes numerous alkylated bases, but to date AAG has only been detected in the nucleus, even though mammalian mitochondria are known to repair DNA lesions that are specific substrates of AAG. Here we use immunofluorescence to show that AAG localizes to mitochondria, and we find that native AAG is present in purified human mitochondrial extracts, as well as that exposure to alkylating agent promotes AAG accumulation in the mitochondria. We identify mitochondrial single-stranded binding protein (mtSSB) as a novel interacting partner of AAG; interaction between mtSSB and AAG is direct and increases upon methyl methanesulfonate (MMS) treatment. The consequence of this interaction is specific inhibition of AAG glycosylase activity in the context of a single-stranded DNA (ssDNA), but not a double-stranded DNA (dsDNA) substrate. By inhibiting AAG-initiated processing of damaged bases, mtSSB potentially prevents formation of DNA breaks in ssDNA, ensuring that base removal primarily occurs in dsDNA. In summary, our findings suggest the existence of AAG-initiated BER in mitochondria and further support a role for mtSSB in DNA repair. Copyright © 2012. Published by Elsevier B.V.

  1. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana

    Directory of Open Access Journals (Sweden)

    Mickiewicz Małgorzata

    2010-10-01

    Full Text Available Abstract Background In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. Results We report the characterization of single-stranded DNA binding proteins (SSBs from the thermophilic bacteria Thermotoga maritima (TmaSSB and Thermotoga neapolitana (TneSSB. They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively. They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC the melting temperature (Tm was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. Conclusion The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR.

  2. Aptamer based voltammetric determination of ampicillin using a single-stranded DNA binding protein and DNA functionalized gold nanoparticles.

    Science.gov (United States)

    Wang, Jun; Ma, Kui; Yin, Huanshun; Zhou, Yunlei; Ai, Shiyun

    2017-12-20

    An aptamer based method is described for the electrochemical determination of ampicillin. It is based on the use of DNA aptamer, DNA functionalized gold nanoparticles (DNA-AuNPs), and single-stranded DNA binding protein (ssDNA-BP). When the aptamer hybridizes with the target DNA on the AuNPs, the ssDNA-BP is captured on the electrode surface via its specific interaction with ss-DNA. This results in a decreased electrochemical signal of the redox probe Fe(CN) 6 3- which is measured best at a voltage of 0.188 mV (vs. reference electrode). In the presence of ampicillin, the formation of aptamer-ampicillin conjugate blocks the further immobilization of DNA-AuNPs and ssDNA-BP, and this leads to an increased response. The method has a linear reposne that convers the 1 pM to 5 nM ampicillin concentration range, with a 0.38 pM detection limit (at an S/N ratio of 3). The assay is selective, stable and reproducible. It was applied to the determination of ampicillin in spiked milk samples where it gave recoveries ranging from 95.5 to 105.5%. Graphical abstract Schematic of a simple and sensitive electrochemical apta-biosensor for ampicillin detection. It is based on the use of gold nanoparticles (AuNPs), DNA aptamer, DNA functionalized AuNPs (DNA-AuNPs), and single-strand DNA binding protein (SSBP).

  3. Epidermal growth factor stimulating reparation of γ-ray-induced single-strand breaks predominantly in untranscribed DNA of HeLa cells

    International Nuclear Information System (INIS)

    Igusheva, O.A.; Bil'din, V.N.; Zhestyanikov, V.D.

    1994-01-01

    Considerable evidence suggest that genomic DNA undergoes reparation unevenly because of different transcription activities of its particular sequence. It is highly probably that transcriptional factors are necessary for postion stages of excision reparation and for reparation of single-strand DNA breaks caused by ionizing radiation. There is evidence suggesting that DNA lesions inflicted by γ-radiation is preferentially initiated in transcribed rather than in untranscribed DNA species. This paper looks at the relationship between stimulatory effect of epidermal growth factor (EGF) on reparation of single-strand DNA breaks and reparation of the damage done to active and inert fragments of chromatin. The results show that EGF stimulates reparation of single-strand DNA breaks induced by γ-radiation more effectively in untranscribed than in transcribed DNA. 13 refs., 1 fig., 1 tab

  4. Genetic evidence for single-strand lesions initiating Nbs1-dependent homologous recombination in diversification of Ig v in chicken B lymphocytes.

    Directory of Open Access Journals (Sweden)

    Makoto Nakahara

    2009-01-01

    Full Text Available Homologous recombination (HR is initiated by DNA double-strand breaks (DSB. However, it remains unclear whether single-strand lesions also initiate HR in genomic DNA. Chicken B lymphocytes diversify their Immunoglobulin (Ig V genes through HR (Ig gene conversion and non-templated hypermutation. Both types of Ig V diversification are initiated by AID-dependent abasic-site formation. Abasic sites stall replication, resulting in the formation of single-stranded gaps. These gaps can be filled by error-prone DNA polymerases, resulting in hypermutation. However, it is unclear whether these single-strand gaps can also initiate Ig gene conversion without being first converted to DSBs. The Mre11-Rad50-Nbs1 (MRN complex, which produces 3' single-strand overhangs, promotes the initiation of DSB-induced HR in yeast. We show that a DT40 line expressing only a truncated form of Nbs1 (Nbs1(p70 exhibits defective HR-dependent DSB repair, and a significant reduction in the rate--though not the fidelity--of Ig gene conversion. Interestingly, this defective gene conversion was restored to wild type levels by overproduction of Escherichia coli SbcB, a 3' to 5' single-strand-specific exonuclease, without affecting DSB repair. Conversely, overexpression of chicken Exo1 increased the efficiency of DSB-induced gene-targeting more than 10-fold, with no effect on Ig gene conversion. These results suggest that Ig gene conversion may be initiated by single-strand gaps rather than by DSBs, and, like SbcB, the MRN complex in DT40 may convert AID-induced lesions into single-strand gaps suitable for triggering HR. In summary, Ig gene conversion and hypermutation may share a common substrate-single-stranded gaps. Genetic analysis of the two types of Ig V diversification in DT40 provides a unique opportunity to gain insight into the molecular mechanisms underlying the filling of gaps that arise as a consequence of replication blocks at abasic sites, by HR and error

  5. Salt Dependence of the Radius of Gyration and Flexibility of Single-stranded DNA in Solution probed by Small-angle X-ray Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Sim, Adelene Y.L.; Lipfert, Jan; Herschlag, Daniel; Doniach, Sebastian

    2012-07-06

    Short single-stranded nucleic acids are ubiquitous in biological processes and understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small angle x-ray scattering to study 8-100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flexibility. For any number of residues, poly-A is consistently more elongated than poly-T, likely due to the tendency of A residues to form stronger base-stacking interactions than T residues.

  6. Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis.

    Science.gov (United States)

    Olszewski, Marcin; Nowak, Marta; Cyranka-Czaja, Anna; Kur, Józef

    2014-01-01

    Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNA replication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-like gene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoalteromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism. PhaSSB possesses a high sequence similarity to Escherichia coli SSB (48% identity and 57% similarity) and has the longest amino acid sequence (244 amino acid residues) of all the known bacterial SSBs with one OB-fold per monomer. An analysis of purified PhaSSB by means of chemical cross-linking experiments, sedimentation analysis and size exclusion chromatography revealed a stable tetramer in solution. Using EMSA, we characterized the stoichiometry of PhaSSB complexed with a series of ssDNA homopolymers, and the size of the binding site was determined as being approximately 35 nucleotides long. In fluorescence titrations, the occluded site size of PhaSSB on poly(dT) is 34 nucleotides per tetramer under low-salt conditions (2mM NaCl), but increases to 54-64 nucleotides at higher-salt conditions (100-300mM NaCl). This suggests that PhaSSB undergoes a transition between ssDNA binding modes, which is observed for EcoSSB. The binding properties of PhaSSB investigated using SPR technology revealed that the affinity of PhaSSB to ssDNA is typical of SSB proteins. The only difference in the binding mode of PhaSSB to ssDNA is a faster association phase, when compared to EcoSSB, though compensated by faster dissociation rate. When analyzed by differential scanning calorimetry (DSC), the melting temperature (Tm) was determined as 63 °C, which is only a few degrees lower than for EcoSSB. Copyright © 2013 Elsevier GmbH. All rights reserved.

  7. Changes in the infrared microspectroscopic characteristics of DNA caused by cationic elements, different base richness and single-stranded form.

    Directory of Open Access Journals (Sweden)

    Maria Luiza S Mello

    Full Text Available BACKGROUND: The infrared (IR analysis of dried samples of DNA and DNA-polypeptide complexes is still scarce. Here we have studied the FT-IR profiles of these components to further the understanding of the FT-IR signatures of chromatin and cell nuclei. METHODOLOGY/PRINCIPAL FINDINGS: Calf thymus and salmon testis DNA, and complexes of histone H1, protamine, poly-L-lysine and poly-L-arginine (histone-mimic macromolecules with DNA were analyzed in an IR microspectroscope equipped with an attenuated total reflection diamond objective and Grams software. Conditions including polypeptides bound to the DNA, DNA base composition, and single-stranded form were found to differently affect the vibrational characteristics of the chemical groups (especially, PO(2(- in the nucleic acid. The antisymmetric stretching (ν(as of the DNA PO(2(- was greater than the symmetric stretching (ν(s of these groups and increased in the polypeptide-DNA complexes. A shift of the ν(as of the DNA PO(2(- to a lower frequency and an increased intensity of this vibration were induced especially by lysine-rich histones. Lysine richness additionally contributed to an increase in the vibrational stretching of the amide I group. Even in simple molecules such as inorganic phosphates, the vibrational characteristics of the phosphate anions were differently affected by different cations. As a result of the optimization of the DNA conformation by binding to arginine-rich polypeptides, enhancements of the vibrational characteristics in the FT-IR fingerprint could be detected. Although different profiles were obtained for the DNA with different base compositions, this situation was no longer verified in the polypeptide-DNA complexes and most likely in isolated chromatin or cell nuclei. However, the ν(as PO(2(-/ν(s PO(2(- ratio could discriminate DNA with different base compositions and DNA in a single-stranded form. CONCLUSIONS/SIGNIFICANCE: FT-IR spectral profiles are a valuable tool

  8. Genetic and Biochemical Identification of a Novel Single-Stranded DNA-Binding Complex in Haloferax volcanii.

    Science.gov (United States)

    Stroud, Amy; Liddell, Susan; Allers, Thorsten

    2012-01-01

    Single-stranded DNA (ssDNA)-binding proteins play an essential role in DNA replication and repair. They use oligonucleotide/oligosaccharide-binding (OB)-folds, a five-stranded β-sheet coiled into a closed barrel, to bind to ssDNA thereby protecting and stabilizing the DNA. In eukaryotes the ssDNA-binding protein (SSB) is known as replication protein A (RPA) and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3) exist in operons with a novel gene specific to Euryarchaeota; this gene encodes a protein that we have termed RPA-associated protein (rpap). The rpap genes encode proteins belonging to COG3390 group and feature OB-folds, suggesting that they might cooperate with RPA in binding to ssDNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only Δrpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins (RPAPs). We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA-binding complex that is unique to Euryarchaeota.

  9. Gamma-ray induced double-strand breaks in DNA resulting from randomly-inflicted single-strand breaks: temporal local denaturation, a new radiation phenomenon?

    NARCIS (Netherlands)

    Schans, G.P. van der

    1978-01-01

    The induction of single- and double-strand breaks in DNA by γ-rays has been measured. The maximum number of nucleotide paris (a) between two independently induced single-strand breaks in opposite strands of the DNA which cannot prevent the occurrence of a double-strand break was found to amount to

  10. Molecular dosimetry of DNA damage caused by alkylation. I. Single-strand breaks induced by ethylating agents in cultured mammalian cells in relation to survival

    NARCIS (Netherlands)

    Abbondandolo, A.; Dogliotti, E.; Lohman, P.H.M.; Berends, F.

    1982-01-01

    Cultured Chinese hamster ovary cells were treated with ethylating agents. DNA lesions giving rise to single-strand breaks (ssb) or alkali-labile sites were measured by centrifugation in alkaline sucrose gradients after lysis in alkali. 4 agents with different tendencies to ethylate preferentially

  11. Initiation and termination of the bacteriophage phi X174 rolling circle DNA replication in vivo: packaging of plasmid single-stranded DNA into bacteriophage phi X174 coats

    NARCIS (Netherlands)

    van der Ende, A.; Teertstra, R.; Weisbeek, P. J.

    1982-01-01

    The bacteriophage phi X174 viral (+) origin when inserted in a plasmid can interact in vivo with the A protein produced by infecting phi X174 phages. A consequence of this interaction is packaging of single-stranded plasmid DNA into preformed phage coats resulting in infective particles (1). This

  12. Micronuclei, DNA single-strand breaks and DNA-repair activity in mice exposed to 1,3-butadiene by inhalation

    Czech Academy of Sciences Publication Activity Database

    Vodička, Pavel; Štětina, R.; Šmerák, P.; Vodičková, Ludmila; Naccarati, Alessio; Bárta, I.; Hemminki, K.

    2006-01-01

    Roč. 608, - (2006), s. 49-57 ISSN 1383-5718 R&D Projects: GA ČR(CZ) GA310/01/0802 Institutional research plan: CEZ:AV0Z50390512 Keywords : Single-strand DNA breaks * Micronucleus formation * DNA-repair activity Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.122, year: 2006

  13. Functional analysis of multiple single-stranded DNA-binding proteins from Methanosarcina acetivorans and their effects on DNA synthesis by DNA polymerase BI.

    Science.gov (United States)

    Robbins, Justin B; Murphy, Mary C; White, Bryan A; Mackie, Roderick I; Ha, Taekjip; Cann, Isaac K O

    2004-02-20

    Single-stranded DNA-binding proteins and their functional homologs, replication protein A, are essential components of cellular DNA replication, repair and recombination. We describe here the isolation and characterization of multiple replication protein A homologs, RPA1, RPA2, and RPA3, from the archaeon Methanosarcina acetivorans. RPA1 comprises four single-stranded DNA-binding domains, while RPA2 and RPA3 are each composed of two such domains and a zinc finger domain. Gel filtration analysis suggested that RPA1 exists as homotetramers and homodimers in solution, while RPA2 and RPA3 form only homodimers. Unlike the multiple RPA proteins found in other Archaea and eukaryotes, each of the M. acetivorans RPAs can act as a distinct single-stranded DNA-binding protein. Fluorescence resonance energy transfer and fluorescence polarization anisotropy studies revealed that the M. acetivorans RPAs bind to as few as 10 single-stranded DNA bases. However, more stable binding is achieved with single-stranded DNA of 18-23 bases, and for such substrates the estimated Kd was 3.82 +/- 0.28 nM, 173.6 +/- 105.17 nM, and 5.92 +/- 0.23 nM, for RPA1, RPA2, and RPA3, respectively. The architectures of the M. acetivorans RPAs are different from those of hitherto reported homologs. Thus, these proteins may represent novel forms of replication protein A. Most importantly, our results show that the three RPAs and their combinations highly stimulate the primer extension capacity of M. acetivorans DNA polymerase BI. Although bacterial SSB and eukaryotic RPA have been shown to stimulate DNA synthesis by their cognate DNA polymerases, our findings provide the first in vitro biochemical evidence for the conservation of this property in an archaeon.

  14. Characterization of the single stranded DNA binding protein SsbB encoded in the Gonoccocal Genetic Island.

    Directory of Open Access Journals (Sweden)

    Samta Jain

    Full Text Available Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in genetic islands of different proteobacteria. This cluster encodes DNA-processing enzymes such as the ParA and ParB partitioning proteins, the TopB topoisomerase, and four conserved hypothetical proteins. The SsbB homologs found in these clusters form a family separated from other ssDNA binding proteins.In contrast to most other SSBs, SsbB did not complement the Escherichia coli ssb deletion mutant. Purified SsbB forms a stable tetramer. Electrophoretic mobility shift assays and fluorescence titration assays, as well as atomic force microscopy demonstrate that SsbB binds ssDNA specifically with high affinity. SsbB binds single-stranded DNA with minimal binding frames for one or two SsbB tetramers of 15 and 70 nucleotides. The binding mode was independent of increasing Mg(2+ or NaCl concentrations. No role of SsbB in ssDNA secretion or DNA uptake could be identified, but SsbB strongly stimulated Topoisomerase I activity.We propose that these novel SsbBs play an unknown role in the maintenance of genetic islands.

  15. EFFECTOR OF TRANSCRIPTION2 is involved in xylem differentiation and includes a functional DNA single strand cutting domain.

    Science.gov (United States)

    Ivanov, Rumen; Tiedemann, Jens; Czihal, Andreas; Schallau, Anna; Diep, Le Hong; Mock, Hans-Peter; Claus, Bernhard; Tewes, Annegret; Bäumlein, Helmut

    2008-01-01

    EFFECTORS OF TRANSCRIPTION2 (ET) are plant-specific regulatory proteins characterized by the presence of two to five C-terminal DNA- and Zn-binding repeats, and a highly conserved cysteine pattern. We describe the structural characterization of the three member Arabidopsis thaliana ET gene family and reveal some allelic sequence polymorphisms. A mutation analysis showed that AtET2 affects the expression of various KNAT genes involved in the maintenance of the undifferentiated state of cambial meristem cells. It also plays a role in the regulation of GA5 (gibberellin 3-beta-dioxygenase) and the cell-cycle-related GASA4. A correlation was established between AtET2 expression and the cellular differentiation state. AtET-GFP fusion proteins shuttle between the cytoplasm and nucleus, with the AtET2 product prevented from entering the nucleus in non-differentiating cells. Within the nucleus, AtET2 probably acts via a single strand cutting domain. A more general regulatory role for ET factors is proposed, governing cell differentiation in cambial meristems, a crucial process for the development of plant vascular tissues.

  16. First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ming; Shandilya, Shivender M.D.; Carpenter, Michael A.; Rathore, Anurag; Brown, William L.; Perkins, Angela L.; Harki, Daniel A.; Solberg, Jonathan; Hook, Derek J.; Pandey, Krishan K.; Parniak, Michael A.; Johnson, Jeffrey R.; Krogan, Nevan J.; Somasundaran, Mohan; Ali, Akbar; Schiffer, Celia A.; Harris, Reuben S. (Pitt); (UMASS, MED); (SLUHSC); (UCSF); (UMM)

    2012-04-04

    APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.

  17. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity

    Energy Technology Data Exchange (ETDEWEB)

    Petzold, Christine; Marceau, Aimee H.; Miller, Katherine H.; Marqusee, Susan; Keck, James L. (UW-MED); (UCB)

    2015-04-22

    Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome.

  18. Change of conformation and internal dynamics of supercoiled DNA upon binding of Escherichia coli single-strand binding protein

    International Nuclear Information System (INIS)

    Langowski, J.; Benight, A.S.; Fujimoto, B.S.; Schurr, J.M.; Schomburg, U.

    1985-01-01

    The influence of Escherichia coli single-strand binding (SSB) protein on the conformation and internal dynamics of pBR322 and pUC8 supercoiled DNAs has been investigated by using dynamic light scattering at 632.8 and 351.1 nm and time-resolved fluorescence polarization anisotropy of intercalated ethidium. SSB protein binds to both DNAs up to a stoichiometry that is sufficient to almost completely relax the superhelical turns. Upon saturation binding, the translational diffusion coefficients (D 0 ) of both DNAs decrease by approximately 20%. Apparent diffusion coefficients (D/sub app/) obtained from dynamic light scattering display the well-known increase with K 2 (K = scattering vector), leveling off toward a plateau value (D/sub plat/) at high K 2 . For both DNAs, the difference D/sub plat/ - D 0 increases upon relaxation of supercoils by SSB protein, which indicates a corresponding enhancement of the subunit mobilities in internal motions. Fluorescence polarization anisotropy measurements on free and complexed pBR322 DNA indicate a (predominantly) uniform torsional rigidity for the saturated DNA/SSB protein complex that is significantly reduced compared to the free DNA. These observations are all consistent with the notion that binding of SSB protein is accompanied by a gradual loss of supercoils and saturates when the superhelical twist is largely removed

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

    Science.gov (United States)

    Piantanida, Ivo; Mašić, Lozika; Rusak, Gordana

    2009-04-01

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

  20. Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA

    International Nuclear Information System (INIS)

    Shokri, Leila; Williams, Mark C; Rouzina, Ioulia

    2009-01-01

    Bacteriophages T4 and T7 are well-studied model replication systems, which have allowed researchers to determine the roles of many proteins central to DNA replication, recombination and repair. Here we summarize and discuss the results from two recently developed single-molecule methods to determine the salt-dependent DNA-binding kinetics and thermodynamics of the single-stranded DNA (ssDNA)-binding proteins (SSBs) from these systems. We use these methods to characterize both the equilibrium double-stranded DNA (dsDNA) and ssDNA binding of the SSBs T4 gene 32 protein (gp32) and T7 gene 2.5 protein (gp2.5). Despite the overall two-orders-of-magnitude weaker binding of gp2.5 to both forms of DNA, we find that both proteins exhibit four-orders-of-magnitude preferential binding to ssDNA relative to dsDNA. This strong preferential ssDNA binding as well as the weak dsDNA binding is essential for the ability of both proteins to search dsDNA in one dimension to find available ssDNA-binding sites at the replication fork

  1. Capillary electrophoresis ribosomal RNA single-stranded conformation polymorphism: a new approach for characterization of low-diversity microbial communities.

    Science.gov (United States)

    Nai, Yi H; Zemb, Oliver; Gutierrez-Zamora, Maria-Luisa; Manefield, Mike; Powell, Shane M; Breadmore, Michael C

    2012-10-01

    Capillary electrophoresis (CE) has been the principle system for nucleic acid analysis since the early 1990s due to its inherent advantages such as fast analysis time, high resolution and efficiency, minimal sample requirement, high detection sensitivity, and automation. In the past few decades, microbial community fingerprinting methods such as terminal restriction fragment length polymorphism and single-stranded conformation polymorphism (SSCP) have migrated to CE to utilize its advantages over conventional slab gel electrophoresis. Recently, a gel-based direct rRNA fingerprint method was demonstrated. Different from other existing microbial community characterization approaches, this novel approach is polymerase chain reaction free and capable of providing information on the relative abundance of rRNA from individual phylotypes in low-diversity samples. As a gel-based method, it has a long analysis time and relatively large reagent and sample requirements. Here, we addressed these limitations by transferring the RNA fingerprint approach to the CE platform. Analysis time significantly improved from 24 h to 60 min, and the use of a fluorescently labeled hybridization probe as the detection strategy decreased the sample requirement by ten-fold. The combination of fast analysis time, low sample requirement, and sensitive fluorescence detection makes CE-RNA-SSCP an appealing new approach for characterizing low-diversity microbial communities.

  2. Genetic heterogeneity of glucose-6-phosphate dehydrogenase deficiency revealed by single-strand conformation and sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Calabro, V.; Mason, P.J.; Luzzatto, L. (Hammersmith Hospital, London (United Kingdom)); Filosa, S.; Martini, G. (CNR, Naples (Italy)); Civitelli, D.; Cittadella, R.; Brancati, C. (CNR, Cosenza (Italy))

    1993-03-01

    The authors have carried out a systematic study of the molecular basis of glucose-6-phosphate dehydrogenase (G6PD) deficiency on a sample of 53 male subjects from Calabria, in southern Italy. Their sequential approach consisted of the following steps: (1) Partial biochemical characterization was used to pinpoint candidate known variants. The identity of these was then varified by restriction-enzyme or allele-specific oligonucleotide hybridization analysis of the appropriate PCR-amplified fragment. (2) On samples for which there was no obvious candidate mutation, they proceeded to amplify the entire coding region in eight fragments, followed by single-strand conformation polymorphism (SSCP) analysis of each fragment. (3) The next step was M13 phage cloning and sequencing of those individual fragments that were found to be abnormal by SSCP. Through this approach they have identified the molecular lesion in 51 of the 53 samples. In these they found a total of nine different G6PD-deficient variants, five of which (G6PD Mediterranean, G6PD A[sup [minus

  3. Single-stranded DNA-binding protein recruits DNA polymerase V to primer termini on RecA-coated DNA.

    Science.gov (United States)

    Arad, Gali; Hendel, Ayal; Urbanke, Claus; Curth, Ute; Livneh, Zvi

    2008-03-28

    Translesion DNA synthesis (TLS) by DNA polymerase V (polV) in Escherichia coli involves accessory proteins, including RecA and single-stranded DNA-binding protein (SSB). To elucidate the role of SSB in TLS we used an in vitro exonuclease protection assay and found that SSB increases the accessibility of 3' primer termini located at abasic sites in RecA-coated gapped DNA. The mutant SSB-113 protein, which is defective in protein-protein interactions, but not in DNA binding, was as effective as wild-type SSB in increasing primer termini accessibility, but deficient in supporting polV-catalyzed TLS. Consistently, the heterologous SSB proteins gp32, encoded by phage T4, and ICP8, encoded by herpes simplex virus 1, could replace E. coli SSB in the TLS reaction, albeit with lower efficiency. Immunoprecipitation experiments indicated that polV directly interacts with SSB and that this interaction is disrupted by the SSB-113 mutation. Taken together our results suggest that SSB functions to recruit polV to primer termini on RecA-coated DNA, operating by two mechanisms: 1) increasing the accessibility of 3' primer termini caused by binding of SSB to DNA and 2) a direct SSB-polV interaction mediated by the C terminus of SSB.

  4. The single-strand DNA binding activity of human PC4 preventsmutagenesis and killing by oxidative DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jen-Yeu; Sarker, Altaf Hossain; Cooper, Priscilla K.; Volkert, Michael R.

    2004-02-01

    Human positive cofactor 4 (PC4) is a transcriptional coactivator with a highly conserved single-strand DNA (ssDNA) binding domain of unknown function. We identified PC4 as a suppressor of the oxidative mutator phenotype of the Escherichia coli fpg mutY mutant and demonstrate that this suppression requires its ssDNA binding activity. Yeast mutants lacking their PC4 ortholog Sub1 are sensitive to hydrogen peroxide and exhibit spontaneous and peroxide induced hypermutability. PC4 expression suppresses the peroxide sensitivity of the yeast sub l{Delta} mutant, suggesting that the human protein has a similar function. A role for yeast and human proteins in DNA repair is suggested by the demonstration that Sub1 acts in a peroxide-resistance pathway involving Rad2 and by the physical interaction of PC4 with the human Rad2 homolog XPG. We show XPG recruits PC4 to a bubble-containing DNA substrate with resulting displacement of XPG and formation of a PC4-DNA complex. We discuss the possible requirement for PC4 in either global or transcription-coupled repair of oxidative DNA damage to mediate the release of XPG bound to its substrate.

  5. Assembly of presynaptic filaments. Factors affecting the assembly of RecA protein onto single-stranded DNA

    DEFF Research Database (Denmark)

    Thresher, RJ; Christiansen, Gunna; Griffith, JD

    1988-01-01

    We have previously shown that the assembly of RecA protein onto single-stranded DNA (ssDNA) facilitated by SSB protein occurs in three steps: (1) rapid binding of SSB protein to the ssDNA; (2) nucleation of RecA protein onto this template; and (3) co-operative polymerization of additional Rec......M in the presence of 12 mM-Mg2+), and relatively low concentrations of SSB protein (1 monomer per 18 nucleotides). Assembly was depressed threefold when SSB protein was added to one monomer per nine nucleotides. These effects appeared to be exerted at the nucleation step. Following nucleation, RecA protein...... assembled onto ssDNA at net rates that varied from 250 to 900 RecA protein monomers per minute, with the rate inversely related to the concentration of SSB protein. Combined sucrose sedimentation and electron microscope analysis established that SSB protein was displaced from the ssDNA during RecA protein...

  6. Semiconductor annealing

    International Nuclear Information System (INIS)

    Young, J.M.; Scovell, P.D.

    1982-01-01

    A process for annealing crystal damage in ion implanted semiconductor devices in which the device is rapidly heated to a temperature between 450 and 900 0 C and allowed to cool. It has been found that such heating of the device to these relatively low temperatures results in rapid annealing. In one application the device may be heated on a graphite element mounted between electrodes in an inert atmosphere in a chamber. (author)

  7. BOREAS TE-01 SSA Soil Lab Data

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set provides a set of soil properties for the SSA. The soil samples were collected at sets of soil pits. Major soil properties include soil...

  8. BOREAS TE-01 SSA Soil Lab Data

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides a set of soil properties for the SSA. The soil samples were collected at sets of soil pits. Major soil properties include soil horizon; dry...

  9. Assessing single-stranded oligonucleotide drug-induced effects in vitro reveals key risk factors for thrombocytopenia.

    Directory of Open Access Journals (Sweden)

    Sabine Sewing

    Full Text Available Single-stranded oligonucleotides (ON comprise a promising therapeutic platform that enables selective modulation of currently undruggable targets. The development of novel ON drug candidates has demonstrated excellent efficacy, but in certain cases also some safety liabilities were reported. Among them are events of thrombocytopenia, which have recently been evident in late stage trials with ON drugs. The underlying mechanisms are poorly understood and the risk for ON candidates causing such events cannot be sufficiently assessed pre-clinically. We investigated potential thrombocytopenia risk factors of ONs and implemented a set of in vitro assays to assess these risks. Our findings support previous observations that phosphorothioate (PS-ONs can bind to platelet proteins such as platelet collagen receptor glycoprotein VI (GPVI and activate human platelets in vitro to various extents. We also show that these PS-ONs can bind to platelet factor 4 (PF4. Binding to platelet proteins and subsequent activation correlates with ON length and connected to this, the number of PS in the backbone of the molecule. Moreover, we demonstrate that locked nucleic acid (LNA ribosyl modifications in the wings of the PS-ONs strongly suppress binding to GPVI and PF4, paralleled by markedly reduced platelet activation. In addition, we provide evidence that PS-ONs do not directly affect hematopoietic cell differentiation in culture but at higher concentrations show a pro-inflammatory potential, which might contribute to platelet activation. Overall, our data confirm that certain molecular attributes of ONs are associated with a higher risk for thrombocytopenia. We propose that applying the in vitro assays discussed here during the lead optimization phase may aid in deprioritizing ONs with a potential to induce thrombocytopenia.

  10. Evidence of impurities in thiolated single-stranded DNA oligomers and their effect on DNA self-assembly on gold.

    Science.gov (United States)

    Lee, Chi-Ying; Canavan, Heather E; Gamble, Lara J; Castner, David G

    2005-05-24

    The diversity of techniques used in the synthesis, treatment, and purification of the single-stranded DNA oligomers containing a thiol anchor group (SH-ssDNA) has led to a significant variation in the purity of commercially available SH-ssDNA. In this work, we use X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study how the impurities present in commercially synthesized SH-ssDNA oligomers affected the structure of the resulting DNA films on Au. XPS results indicate that two of the purchased SH-ssDNA oligomers contain excess carbon and sulfur. The molecular fragmentation patterns obtained with ToF-SIMS were used to determine the identity of several contaminants in the DNA films, including poly(dimethylsiloxane) (PDMS), lipid molecules, and sulfur-containing molecules. In particular, the ToF-SIMS results determined that the excess sulfur detected by XPS was due to the presence of dithiothreitol, a reductant often used to cleave disulfide precursors. Furthermore, we found that the SH-ssDNA self-assembly process is affected by the presence of these contaminants. When relatively pure SH-ssDNA is used to prepare the DNA films, the P, N, O, and C atomic percentages were observed by XPS to increase over a 24-h time period. In contrast, surfaces prepared using SH-ssDNA containing higher levels of contaminants did not follow this trend. XPS result indicates that, after the initial SH-ssDNA adsorption, the remaining material incorporated into these films was due to contamination.

  11. The mechanism of the nitric oxide-mediated enhancement of tert-butylhydroperoxide-induced DNA single strand breakage

    Science.gov (United States)

    Guidarelli, Andrea; Clementi, Emilio; Sciorati, Clara; Cantoni, Orazio

    1998-01-01

    Caffeine (Cf) enhances the DNA cleavage induced by tert-butylhydroperoxide (tB-OOH) in U937 cells via a mechanism involving Ca2+-dependent mitochondrial formation of DNA-damaging species (Guidarelli et al., 1997b). Nitric oxide (NO) is not involved in this process since U937 cells do not express the constitutive nitric oxide synthase (cNOS).Treatment with the NO donors S-nitroso-N-acetyl-penicillamine (SNAP, 10 μM), or S-nitrosoglutathione (GSNO, 300 μM), however, potentiated the DNA strand scission induced by 200 μM tB-OOH. The DNA lesions generated by tB-OOH alone, or combined with SNAP, were repaired with superimposable kinetics and were insensitive to anti-oxidants and peroxynitrite scavengers but suppressed by iron chelators.SNAP or GSNO did not cause mitochondrial Ca2+ accumulation but their enhancing effects on the tB-OOH-induced DNA strand scission were prevented by ruthenium red, an inhibitor of the calcium uniporter of mitochondria. Furthermore, the enhancing effects of both SNAP and GSNO were identical to and not additive with those promoted by the Ca2+-mobilizing agents Cf or ATP.The SNAP- or GSNO-mediated enhancement of the tB-OOH-induced DNA cleavage was abolished by the respiratory chain inhibitors rotenone and myxothiazol and was not apparent in respiration-deficient cells.It is concluded that, in cells which do not express the enzyme cNOS, exogenous NO enhances the accumulation of DNA single strand breaks induced by tB-OOH via a mechanism involving inhibition of complex III. PMID:9846647

  12. Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter.

    Science.gov (United States)

    Akahori, Rena; Haga, Takanobu; Hatano, Toshiyuki; Yanagi, Itaru; Ohura, Takeshi; Hamamura, Hirotaka; Iwasaki, Tomio; Yokoi, Takahide; Anazawa, Takashi

    2014-07-11

    To slow the translocation of single-stranded DNA (ssDNA) through a solid-state nanopore, a nanopore was narrowed, and the effect of the narrowing on the DNA translocation speed was investigated. In order to accurately measure the speed, long (5.3 kb) ssDNA (namely, ss-poly(dA)) with uniform length (±0.4 kb) was synthesized. The diameters of nanopores fabricated by a transmission electron microscope were controlled by atomic-layer deposition. Reducing the nanopore diameter from 4.5 to 2.3 nm slowed down the translocation of ssDNA by more than 16 times (to 0.18 μs base(-1)) when 300 mV was applied across the nanopore. It is speculated that the interaction between the nanopore and the ssDNA dominates the translocation speed. Unexpectedly, the translocation speed of ssDNA through the 4.5 nm nanopore is more than two orders of magnitude higher than that of double-stranded DNA (dsDNA) through a nanopore of almost the same size. The cause of such a faster translocation of ssDNA can be explained by the weaker drag force inside the nanopore. Moreover, the measured translocation speeds of ssDNA and dsDNA agree well with those calculated by molecular-dynamics (MD) simulation. The MD simulation predicted that reducing the nanopore diameter to almost the same as that of ssDNA (i.e. 1.4 nm) decreases the translocation speed (to 1.4 μs base(-1)). Narrowing the nanopore is thus an effective approach for accomplishing nanopore DNA sequencing.

  13. Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

    Science.gov (United States)

    Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Gadura, N.; Schneider, P.; Sullivan, R.; Flamholz, A.; Lieberman, D.; Cheung, T. D.

    2009-08-01

    The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and 2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the observed fractal dimensions (R2~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression analysis decreases the R2 slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77 bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R2 ~ 0.997 for N =3. The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to sequences VNG7114 and VNG2184.

  14. Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Cyril Buhler

    2007-12-01

    Full Text Available DNA double-strand breaks (DSBs, which are formed by the Spo11 protein, initiate meiotic recombination. Previous DSB-mapping studies have used rad50S or sae2Delta mutants, which are defective in break processing, to accumulate Spo11-linked DSBs, and report large (> or = 50 kb "DSB-hot" regions that are separated by "DSB-cold" domains of similar size. Substantial recombination occurs in some DSB-cold regions, suggesting that DSB patterns are not normal in rad50S or sae2Delta mutants. We therefore developed a novel method to map genome-wide, single-strand DNA (ssDNA-associated DSBs that accumulate in processing-capable, repair-defective dmc1Delta and dmc1Delta rad51Delta mutants. DSBs were observed at known hot spots, but also in most previously identified "DSB-cold" regions, including near centromeres and telomeres. Although approximately 40% of the genome is DSB-cold in rad50S mutants, analysis of meiotic ssDNA from dmc1Delta shows that most of these regions have substantial DSB activity. Southern blot assays of DSBs in selected regions in dmc1Delta, rad50S, and wild-type cells confirm these findings. Thus, DSBs are distributed much more uniformly than was previously believed. Comparisons of DSB signals in dmc1, dmc1 rad51, and dmc1 spo11 mutant strains identify Dmc1 as a critical strand-exchange activity genome-wide, and confirm previous conclusions that Spo11-induced lesions initiate all meiotic recombination.

  15. UPregulated single-stranded DNA-binding protein 1 induces cell chemoresistance to cisplatin in lung cancer cell lines.

    Science.gov (United States)

    Zhao, Xiang; He, Rong; Liu, Yu; Wu, Yongkai; Kang, Leitao

    2017-07-01

    Cisplatin and its analogues are widely used as anti-tumor drugs in lung cancer but many cisplatin-resistant lung cancer cases have been identified in recent years. Single-stranded DNA-binding protein 1 (SSDBP1) can effectively induce H69 cell resistance to cisplatin in our previous identification; thus, it is necessary to explore the mechanism underlying the effects of SSDBP1-induced resistance to cisplatin. First, SSDBP1-overexpressed or silent cell line was constructed and used to analyze the effects of SSDBP1 on chemoresistance of lung cancer cells to cisplatin. SSDBP1 expression was assayed by real-time PCR and Western blot. Next, the effects of SSDBP1 on cisplatin sensitivity, proliferation, and apoptosis of lung cancer cell lines were assayed by MTT and flow cytometry, respectively; ABC transporters, apoptosis-related genes, and cell cycle-related genes by real-time PCR, and DNA wound repair by comet assay. Low expression of SSDBP1 was observed in H69 cells, while increased expression in cisplatin-resistant H69 cells. Upregulated expression of SSDBP1 in H69AR cells was identified to promote proliferation and cisplatin resistance and inhibit apoptosis, while downregulation of SSDBP1 to inhibit cisplatin resistance and proliferation and promoted apoptosis. Moreover, SSDBP1 promoted the expression of P2gp, MRP1, Cyclin D1, and CDK4 and inhibited the expression of caspase 3 and caspase 9. Furthermore, SSDBP1 promoted the DNA wound repair. These results indicated that SSDBP1 may induce cell chemoresistance of cisplatin through promoting DNA repair, resistance-related gene expression, cell proliferation, and inhibiting apoptosis.

  16. TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA.

    Science.gov (United States)

    Flynn, Rachel Litman; Centore, Richard C; O'Sullivan, Roderick J; Rai, Rekha; Tse, Alice; Songyang, Zhou; Chang, Sandy; Karlseder, Jan; Zou, Lee

    2011-03-24

    Maintenance of telomeres requires both DNA replication and telomere 'capping' by shelterin. These two processes use two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomeres 1 (POT1). Although RPA and POT1 each have a critical role at telomeres, how they function in concert is not clear. POT1 ablation leads to activation of the ataxia telangiectasia and Rad3-related (ATR) checkpoint kinase at telomeres, suggesting that POT1 antagonizes RPA binding to telomeric ssDNA. Unexpectedly, we found that purified POT1 and its functional partner TPP1 are unable to prevent RPA binding to telomeric ssDNA efficiently. In cell extracts, we identified a novel activity that specifically displaces RPA, but not POT1, from telomeric ssDNA. Using purified protein, here we show that the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) recapitulates the RPA displacing activity. The RPA displacing activity is inhibited by the telomeric repeat-containing RNA (TERRA) in early S phase, but is then unleashed in late S phase when TERRA levels decline at telomeres. Interestingly, TERRA also promotes POT1 binding to telomeric ssDNA by removing hnRNPA1, suggesting that the re-accumulation of TERRA after S phase helps to complete the RPA-to-POT1 switch on telomeric ssDNA. Together, our data suggest that hnRNPA1, TERRA and POT1 act in concert to displace RPA from telomeric ssDNA after DNA replication, and promote telomere capping to preserve genomic integrity.

  17. Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.

    Science.gov (United States)

    Zhang, Xueru; McGown, Linda B

    2013-06-01

    DNA analysis has widespread applicability in biology, medicine, biotechnology, and forensics. DNA separation by length is readily achieved using sieving gels in electrophoresis. Separation by sequence is less simple, generally requiring adequate differences in native or induced conformation or differences in thermal or chemical stability of the strands that are hybridized prior to measurement. We previously demonstrated separation of four single-stranded DNA 76-mers that differ by only a few A-G substitutions based solely on sequence using guanosine-5'-monophosphate (GMP) in the running buffer. We attributed separation to the unique self-assembly of GMP to form higher order structures. Here, we examine an expanded set of 76-mers designed to probe the mechanism of the separation and effects of experimental conditions. We were surprised to find that other ribonucleotides achieved the similar separation to GMP, and that some separation was achieved using sodium phosphate instead of GMP. Potassium phosphate achieved almost as good separations as the ribonucleotides. This suggests that the separation medium provides a physicochemical environment for the DNA that effects strand migration in a sequence-selective manner. Further investigation is needed to determine whether the mechanism involves specific interactions between the phosphates and the DNA strands or is a result of other properties of the separation medium. Phosphate generally has been avoided in DNA separations by capillary gel electrophoresis because its high ionic strength exacerbates Joule heating. Our results suggest that phosphate compounds should be examined for separation of DNA based on sequence. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Semiconductor annealing

    International Nuclear Information System (INIS)

    Young, J.M.; Scovell, P.D.

    1981-01-01

    A process for annealing crystal damage in ion implanted semiconductor devices is described in which the device is rapidly heated to a temperature between 450 and 600 0 C and allowed to cool. It has been found that such heating of the device to these relatively low temperatures results in rapid annealing. In one application the device may be heated on a graphite element mounted between electrodes in an inert atmosphere in a chamber. The process may be enhanced by the application of optical radiation from a Xenon lamp. (author)

  19. Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells

    Directory of Open Access Journals (Sweden)

    Muyrers Joep PP

    2003-01-01

    Full Text Available Abstract Background The phage protein pairs, RecE/RecT from Rac or Redα/Redβ from λ, initiate efficient double strand break repair (DSBR in Escherichia coli that has proven very useful for DNA engineering. These phage pairs initiate DSBR either by annealing or by another mechanism that is not defined. Results Here we report that these proteins also mediate single strand oligonucleotide repair (ssOR at high efficiencies. The ssOR activity, unlike DSBR, does not require a phage exonuclease (RecE or Redα but only requires a phage annealing protein (RecT or Redβ. Notably, the P22 phage annealing protein Erf, which does not mediate the same DSBR reactions, also delivers ssOR activity. By altering aspects of the oligonucleotides, we document length and design parameters that affect ssOR efficiency to show a simple relationship to homologies either side of the repair site. Notably, ssOR shows strand bias. Oligonucleotides that can prime lagging strand replication deliver more ssOR than their leading complements. This suggests a model in which the annealing proteins hybridize the oligonucleotides to single stranded regions near the replication fork. We also show that ssOR is a highly efficient way to engineer BACs and can be detected in a eukaryotic cell upon expression of a phage annealing protein. Conclusion Phage annealing proteins can initiate the recombination of single stranded oligonucleotides into endogenous targets in Escherichia coli at very high efficiencies. This expands the repertoire of useful DNA engineering strategies, shows promise for applications in eukaryotic cells, and has implications for the unanswered questions regarding DSBR mediated by RecE/RecT and Redα/Redβ.

  20. Hot topic: Bovine milk samples yielding negative or nonspecific results in bacterial culturing--the possible role of PCR-single strand conformation polymorphism in mastitis diagnosis.

    Science.gov (United States)

    Schwaiger, K; Wimmer, M; Huber-Schlenstedt, R; Fehlings, K; Hölzel, C S; Bauer, J

    2012-01-01

    A large proportion of mastitis milk samples yield negative or nonspecific results (i.e., no mastitis pathogen can be identified) in bacterial culturing. Therefore, the culture-independent PCR-single strand conformation polymorphism method was applied to the investigation of bovine mastitis milk samples. In addition to the known mastitis pathogens, the method was suitable for the detection of fastidious bacteria such as Mycoplasma spp., which are often missed by conventional culturing methods. The detection of Helcococcus ovis in 4 samples might indicate an involvement of this species in pathogenesis of bovine mastitis. In conclusion, PCR-single-strand conformation polymorphism is a promising tool for gaining new insights into the bacteriological etiology of mastitis. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  1. Genetic effects and reparation of single-stranded DNA breaks in Arabidopsis thaliana populations growing in the vicinity of the Chernobyl Nuclear Power Station

    International Nuclear Information System (INIS)

    Abramov, V.I.; Sergeeva, S.A.; Ptitsyna, S.N.; Semov, A.B.; Shevchenko, V.A.

    1992-01-01

    The genetic effects and efficiency of repair of single-stranded DNA breaks in natural populations of Arabidopsis growing within a thirty-kilometer zone of the Chernobyl Nuclear Power Station were studied. A direct relationship was found between the level of radioactive contamination and the frequency of embryonal lethal mutations in the Arabidopsis populations studied. A decrease in the efficiency of reparation of single-stranded DNA breaks was found in Arabidopsis plants growing in the contaminated sites. The level of efficiency of DNA reparation was dependent on the duration for which the Arabidopsis population had been growing in the contaminated sites and on the degree of radioactive contamination of the sites. 9 refs., 4 tabs

  2. Genotyping of human parvovirus B19 in clinical samples from Brazil and Paraguay using heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing

    Directory of Open Access Journals (Sweden)

    Marcos César Lima de Mendonça

    2011-06-01

    Full Text Available Heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing were utilised to genotype human parvovirus B19 samples from Brazil and Paraguay. Ninety-seven serum samples were collected from individuals presenting with abortion or erythema infectiosum, arthropathies, severe anaemia and transient aplastic crisis; two additional skin samples were collected by biopsy. After the procedure, all clinical samples were classified as genotype 1.

  3. Synthesis of a gene for the HIV transactivator protein TAT by a novel single stranded approach involving in vivo gap repair.

    OpenAIRE

    Adams, S E; Johnson, I D; Braddock, M; Kingsman, A J; Kingsman, S M; Edwards, R M

    1988-01-01

    The synthesis of a gene for the HIV TAT protein is described using a novel approach that capitalises on the ability to synthesise oligonucleotides of greater than 100 bp in length. It involves the synthesis of large oligomers covering one strand of the desired gene in its entirety and the use of small complementary bridging and adapter oligonucleotides to direct the assembly and cloning of the large oligomers. After ligation to the cloning vector the partially single stranded intermediate is ...

  4. Intensive Linkage Mapping in a Wasp (Bracon Hebetor) and a Mosquito (Aedes Aegypti) with Single-Strand Conformation Polymorphism Analysis of Random Amplified Polymorphic DNA Markers

    OpenAIRE

    Antolin, M. F.; Bosio, C. F.; Cotton, J.; Sweeney, W.; Strand, M. R.; Black-IV, W. C.

    1996-01-01

    The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a d...

  5. Coupled aggregation of mitochondrial single-strand DNA-binding protein tagged with Eos fluorescent protein visualizes synchronized activity of mitochondrial nucleoids

    Czech Academy of Sciences Publication Activity Database

    Olejár, Tomáš; Pajuelo-Reguera, David; Alán, Lukáš; Dlasková, Andrea; Ježek, Petr

    2015-01-01

    Roč. 12, č. 4 (2015), s. 5185-5190 ISSN 1791-2997 R&D Projects: GA ČR(CZ) GAP302/10/0346; GA MŠk(CZ) EE2.3.30.0025 Institutional support: RVO:67985823 Keywords : mitochondrial nucleoid * single- strand ed DNA -binding protein * photoconvertible fluorescent protein Eos Subject RIV: EA - Cell Biology Impact factor: 1.559, year: 2015

  6. The validity of sedimentation data from high molecular weight DNA and the effects of additives on radiation-induced single-strand breakage

    International Nuclear Information System (INIS)

    Dugle, D.L.

    1979-10-01

    The optimization of many of the factors governing reproducible sedimentation behaviour of high molecular weight single-strand DNA in a particular alkaline sucrose density gradient system is described. A range of angular momenta is defined for which a constant strand breakage efficiency is required, despite a rotor speed effect which increases the measured molecular weights at decreasing rotor speeds for larger DNA molecules. The possibility is discussed that the bimodal control DNA profiles obtained after sedimentation at 11 500 rev/min (12 400 g) or less represent structural subunits of the chromatid. The random induction of single-strand DNA breaks by ionizing radiation is demonstrated by the computer-derived fits to the experimental profiles. The enhancement of single-strand break (SSB) yields in hypoxic cells by oxygen, para-nitroacetophenone (PNAP), or any of the three nitrofuran derivatives used was well correlated with increased cell killing. Furthermore, reductions in SSB yields for known hydroxyl radical (OH.) scavengers correlates with the reactivities of these compounds toward OH.. This supports the contention that some type of OH.-induced initial lesion, which may ultimately be expressed as an unrepaired or misrepaired double-strand break, constitutes a lethal event. (author)

  7. Escherichia coli Single-Stranded DNA-Binding Protein: NanoESI-MS Studies of Salt-Modulated Subunit Exchange and DNA Binding Transactions

    Science.gov (United States)

    Mason, Claire E.; Jergic, Slobodan; Lo, Allen T. Y.; Wang, Yao; Dixon, Nicholas E.; Beck, Jennifer L.

    2013-02-01

    Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)70, one molecule of (dT)35, or two molecules of (dT)35] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.

  8. Formation of double-strand breaks in DNA of γ-irradiated bacteria depending on the function of fast repair processes of DNA single-strand breaks

    International Nuclear Information System (INIS)

    Petrov, S.I.; Gaziev, A.I.

    1980-01-01

    The formation of double-strand breaks in DNA of γ-irradiated ( 60 Co)Ex coli bacteria depending on the function of fast repair processes of DNA single-strand breaks, is investigated. The profiles of sedimentation of DNA Ex coli cells, irradiated at 0-2 deg C in the salt medium and in EDTA-borate buffer, are presented. It is shown that when irradiating cells in EDTA-borate buffer, the output of single- and double strand breaks in DNA is much higher than in the case of their irradiation in the minimum salt medium. The dependence of output of single-strand and double-strand breaks depending on the radiatier doze of E coli cells in the salt medium and EDTA-borate buffer, is studied. The supposition is made on the presence of a regulative interaction between the accumulation of DNA single-breaks and their repair with the formation of double-strand breaks. The functionating of fast and superfast repair processes considerably affects the formation of double-strand breaks in DNA of a bacterium cell. A considerable amount of double-breaks registered immediately after irradiation forms due to a close position of single-strand breaks on the opposite DNA strands

  9. The survival and repair of DNA single-strand breaks in gamma-irradiated Escherichia coli adapted to methyl methane sulfonate

    International Nuclear Information System (INIS)

    Zhestyanikov, V.D.; Savel'eva, G.E.

    1992-01-01

    The survival and repair of single-strand breaks of DNA in gamma-irradiated E.coli adapted to methyl methane sulfonate (MMS) (20 mkg/ml during 3 hours) have been investigated. It is shown that the survival of adapted bacteria of radioresistant strains B/r, H/r30, AB1157 and W3110 pol + increases with DMF (dose modification factor) ranging within 1.4-1.8 and in radiosensitive strains B s-1 , AB1157 recA13 and AB1157 lexA3 with DMF ranging within 1.3-1.4, and does not change in strains with mutation in poLA gene P3478 poLA1 and 016 res-3. The increase in radioresistance during the adaptation to MMS correlates with the acceleration of repair of gamma-ray-induced single-strand breaks in the radioresistant strains B/r and W3110 pol + and with the appearance of the ability to repair some part of DNA single-strand breaks in the mutant B s-1

  10. The colour potentials of SSA-containing mortar

    OpenAIRE

    Kappel, Annemette; Ottosen, Lisbeth M.; Kirkelund, Gunvor Marie; Bache, Anja Margrethe; Goltermann, Per

    2015-01-01

    This paper reports an experimental study of aesthetical qualities of mortar containing sewage sludgeash (SSA). SSA is the residue produced at water treatment plants where incineration of the sludge is applied in order to decrease volume and to prevent pathogens from spreading. Today SSA is with a few exceptions landfilled and thus, wasted.The purpose of the experiments was to examine the influence of SSA and how it affected the colour of mortar samples. SSA was ground in 6 different intervals...

  11. Dicty_cDB: SSA423 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available SS (Link to library) SSA423 (Link to dictyBase) - - - - SSA423F (Link to Original s...ite) SSA423F 443 - - - - - - Show SSA423 Library SS (Link to library) Clone ID SSA423 (Link to dictyBase) Atlas ID - NBRP ID - dict...yBase ID - Link to Contig - Original site URL http://dictycdb.biol.tsukuba.ac.jp/CSM/...FIIGFFLCLTVFLTFVNSSEIDHQYSLTSSINGSSSGVSNSTDNTGCGEYTSCGDCREDK GCVWCGSEGICTEGTFYGTKPLNINGACKDFMWMQCKIQGRWAILIA...VSNSTDNTGCGEYTSCGDCREDK GCVWCGSEGICTEGTFYGTKPLNINGACKDFMWMQCKIQGRWAILIAAGGAFLIIVFFFI CLCCCCCRRKKDKHYHNIQDDET

  12. Dicty_cDB: SSA581 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available SS (Link to library) SSA581 (Link to dictyBase) - - - Contig-U12576-1 SSA581Z (Link... to Original site) - - SSA581Z 504 - - - - Show SSA581 Library SS (Link to library) Clone ID SSA581 (Link to dict...yBase) Atlas ID - NBRP ID - dictyBase ID - Link to Contig Contig-U12576-1 Original site URL http://dict...SARPLGVAMILIGIDDELGPQLFKVDPAGVFTGYKATAAGEK EQESTNFLEKKFKSNPQLSKDETIQMAISTLQSVLGADLKSSDLEIGICTMDNRKFVIMT DEDI...QHASARPLGVAMILIGIDDELGPQLFKVDPAGVFTGYKATAAGEK EQESTNFLEKKFKSNPQLSKDETIQMAISTLQSVLGADLKSSDLEIGICTMDNRKFVIMT D

  13. Transient oxidative stress and inflammation after intraperitoneal administration of multiwalled carbon nanotubes functionalized with single strand DNA in rats

    Energy Technology Data Exchange (ETDEWEB)

    Clichici, Simona, E-mail: simonaclichici@yahoo.com [Department of Physiology, University of Medicine and Pharmacy, Cluj-Napoca (Romania); Biris, Alexandru Radu [National R and D Institute of Isotopic and Molecular Technologies, Cluj-Napoca (Romania); Tabaran, Flaviu [University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca (Romania); Filip, Adriana [Department of Physiology, University of Medicine and Pharmacy, Cluj-Napoca (Romania)

    2012-03-15

    Multi-walled carbon nanotubes (MWCNTs) are widely used for nanotechnology. Their impact on living organisms is, however, not entirely clarified. Oxidative stress and inflammation seem to be the key mechanisms involved in MWCNTs' cytotoxicity. Until present, pulmonary and skin models were the main tested experimental designs to assess carbon nanotubes' toxicity. The systemic administration of MWCNTs is essential, with respect for future medical applications. Our research is performed on Wistar rats and is focused on the dynamics of oxidative stress parameters in blood and liver and pro-inflammatory cytokines in liver, after single dose (270 mg l{sup −1}) ip administration of MWCNTs (exterior diameter 15–25 nm, interior diameter 10–15 nm, surface 88 m{sup 2} g{sup −1}) functionalized with single strand DNA (ss-DNA). The presence of MWCNTs in blood was assessed by Raman spectroscopy, while in liver histological examination and confocal microscopy were used. It was found that ss-DNA-MWCNTs induce oxidative stress in plasma and liver, with the return of the tested parameters to normal values, 6 h after ip injection of nanotubes, with the exception of reduced glutathione in plasma. The inflammatory cytokines (TNF-α, IL-1β) had a similar pattern of evolution. We also assessed the level of ERK1/2 and the phosphorylation of p65 subunit of NF-kB in liver that had a transient increase and returned to normal at the end of the tested period. Our results demonstrate that ss-DNA-MWCNTs produce oxidative stress and inflammation, but with a transient pattern. Given the fact that antioxidants modify the profile not only for oxidative stress, but also of inflammation, the dynamics of these alterations may be of practical importance for future protective strategies. -- Highlights: ► ss-DNA-MWCNTs ip administration induce oxidative stress in plasma and liver. ► ss-DNA-MWCNTs ip administration determine liver inflammation. ► ERK1/2 and p65 phosphorylated NF

  14. Reuse of sewage sludge ashes (SSA) in cement mixtures: the effect of SSA on the workability of cement mortars.

    Science.gov (United States)

    Monzó, J; Payá, J; Borrachero, M V; Girbés, I

    2003-01-01

    The influence of sewage sludge ash (SSA) on workability of cement mortars has been studied. The irregular morphology of SSA particles produced a decrease of mortar workability. A nonlinear reduction of workability in mortars containing SSA was observed, but when SSA content in mortars was increased the workability reduction was less significant. A superplasticizer is used in order to compensate the decrease of workability produced by SSA. When SSA sized fractions were used, only significant differences in workability for mortars prepared with high water volumes or with the presence of superplasticizer were observed.

  15. Data for increase of Lymantria dispar male survival after topical application of single-stranded RING domain fragment of IAP-3 gene of its nuclear polyhedrosis virus

    Science.gov (United States)

    Oberemok, Volodymyr V.; Laikova, Kateryna V.; Zaitsev, Aleksei S.; Gushchin, Vladimir A.; Skorokhod, Oleksii A.

    2016-01-01

    This data article is related to the research article entitled “The RING for gypsy moth control: topical application of fragment of its nuclear polyhedrosis virus anti-apoptosis gene as insecticide” [1]. This article reports on significantly higher survival of gypsy moth Lymantria dispar male individuals in response to topical application of single-stranded DNA, based on RING (really interesting new gene) domain fragment of LdMNPV (L. dispar multicapsid nuclear polyhedrosis virus) IAP-3 (inhibitor of apoptosis) gene and acted as DNA insecticide. PMID:27054151

  16. Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy

    OpenAIRE

    Shishmarev, Dmitry; Wang, Yao; Mason, Claire E.; Su, Xun-Cheng; Oakley, Aaron J.; Graham, Bim; Huber, Thomas; Dixon, Nicholas E.; Otting, Gottfried

    2013-01-01

    Single-stranded DNA (ssDNA) binding protein (SSB) is an essential protein to protect ssDNA and recruit specific ssDNA-processing proteins. Escherichia coli SSB forms a tetramer at neutral pH, comprising a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain) of ∼64 amino acid residues. The C-terminal eight-residue segment of SSB (C-peptide) has been shown to interact with the OB-domain, but crystal structures failed to reveal any electron den...

  17. Complementarily addressed modification and cleavage of a single-stranded fragment of DNA with the aid of alkylating derivatives of oligonucleotides

    International Nuclear Information System (INIS)

    Brosalina, E.B.; Vlasov, V.V.; Kutyavin, I.V.; Mamaev, S.V.; Pletnev, A.G.; Podyminogin, M.A.

    1986-01-01

    The chemical modification of a 303-nucleotide single-stranded fragment of DNA by alkylating oligonucleotide derivatives bearing 4-[N-methyl-N-(2-chloroethyl)amino]benzyl groups in the 5'-terminal phosphate of the 3'-terminal ribose residue has been investigated. It has been shown that under the conditions of the formation of a complex with the DNA fragment both types of derivatives specifically alkylate nucleotides of the DNA fragments that are located directly adjacent to the sections complementary to the oligonucleotides bearing the reactive groups. Alkylation takes place with a high efficiency, and the DNA fragment can be cleaved specifically at the position of the alkylated nucleotides

  18. Role of DNA repair in repair of cytogenetic damages. Contribution of repair of single-strand DNA breaks to cytogenetic damages repair

    International Nuclear Information System (INIS)

    Rozanova, O.M.; Zaichkina, S.I.; Aptikaev, G.F.; Ganassi, E.Eh.

    1989-01-01

    The comparison was made between the results of the effect of poly(ADP-ribosylation) ingibitors (e.g. nicotinamide and 3-aminobenzamide) and a chromatin proteinase ingibitor, phenylmethylsulfonylfluoride, on the cytogenetic damages repair, by a micronuclear test, and DNA repair in Chinese hamster fibroblasts. The values of the repair half-periods (5-7 min for the cytogenetic damages and 5 min for the rapidly repaired DNA damages) and a similar modyfying effect with regard to radiation cytogenetic damages and kynetics of DNA damages repair were found to be close. This confirms the contribution of repair of DNA single-strand breaks in the initiation of structural damages to chromosomes

  19. A single-stranded RNA copy of the Giardia lamblia virus double-stranded RNA genome is present in the infected Giardia lamblia.

    OpenAIRE

    Furfine, E S; White, T C; Wang, A L; Wang, C C

    1989-01-01

    An isolate of Giardia lamblia infected with the double-stranded RNA virus (GLV) has two major species of RNA that are not present in an uninfected isolate. One of these species is the previously characterized double-stranded RNA genome of GLV (1). The second species of RNA appears to be a full length copy of one strand of the double-stranded RNA genome. This full length single-stranded RNA is not present in viral particles isolated from the growth medium. The cellular concentration of the sin...

  20. Oxidized base damage and single-strand break repair in mammalian genomes: role of disordered regions and posttranslational modifications in early enzymes.

    Science.gov (United States)

    Hegde, Muralidhar L; Izumi, Tadahide; Mitra, Sankar

    2012-01-01

    Oxidative genome damage induced by reactive oxygen species includes oxidized bases, abasic (AP) sites, and single-strand breaks, all of which are repaired via the evolutionarily conserved base excision repair/single-strand break repair (BER/SSBR) pathway. BER/SSBR in mammalian cells is complex, with preferred and backup sub-pathways, and is linked to genome replication and transcription. The early BER/SSBR enzymes, namely, DNA glycosylases (DGs) and the end-processing proteins such as abasic endonuclease 1 (APE1), form complexes with downstream repair (and other noncanonical) proteins via pairwise interactions. Furthermore, a unique feature of mammalian early BER/SSBR enzymes is the presence of a disordered terminal extension that is absent in their Escherichia coli prototypes. These nonconserved segments usually contain organelle-targeting signals, common interaction interfaces, and sites of posttranslational modifications that may be involved in regulating their repair function including lesion scanning. Finally, the linkage of BER/SSBR deficiency to cancer, aging, and human neurodegenerative diseases, and therapeutic targeting of BER/SSBR are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Two-dimensional strandness-dependent electrophoresis: a method to characterize single-stranded DNA, double-stranded DNA, and RNA-DNA hybrids in complex samples.

    Science.gov (United States)

    Gunnarsson, Gudmundur H; Gudmundsson, Bjarki; Thormar, Hans G; Alfredsson, Arni; Jonsson, Jon J

    2006-03-01

    We describe two-dimensional strandness-dependent electrophoresis (2D-SDE) for quantification and length distribution analysis of single-stranded (ss) DNA fragments, double-stranded (ds) DNA fragments, RNA-DNA hybrids, and nicked DNA fragments in complex samples. In the first dimension nucleic acid molecules are separated based on strandness and length in the presence of 7 M urea. After the first-dimension electrophoresis all nucleic acid fragments are heat denatured in the gel. During the second-dimension electrophoresis all nucleic acid fragments are single-stranded and migrate according to length. 2D-SDE takes about 90 min and requires only basic skills and equipment. We show that 2D-SDE has many applications in analyzing complex nucleic acid samples including (1) estimation of renaturation efficiency and kinetics, (2) monitoring cDNA synthesis, (3) detection of nicked DNA fragments, and (4) estimation of quality and in vitro damage of nucleic acid samples. Results from 2D-SDE should be useful to validate techniques such as complex polymerase chain reaction, subtractive hybridization, cDNA synthesis, cDNA normalization, and microarray analysis. 2D-SDE could also be used, e.g., to characterize biological nucleic acid samples. Information obtained with 2D-SDE cannot be readily obtained with other methods. 2D-SDE can be used for preparative isolation of ssDNA fragments, dsDNA fragments, and RNA-DNA hybrids.

  2. A single-strand specific lesion drives MMS-induced hyper-mutability at a double-strand break in yeast.

    Science.gov (United States)

    Yang, Yong; Gordenin, Dmitry A; Resnick, Michael A

    2010-08-05

    Localized hyper-mutability (LHM) can be important in evolution, immunity, and genetic diseases. We previously reported that single-strand DNA (ssDNA) can be an important source of damage-induced LHM in yeast. Here, we establish that the generation of LHM by methyl methanesulfonate (MMS) during repair of a chromosomal double-strand break (DSB) can result in over 0.2 mutations/kb, which is approximately 20,000-fold higher than the MMS-induced mutation density without a DSB. The MMS-induced mutations associated with DSB repair were primarily due to substitutions via translesion DNA synthesis at damaged cytosines, even though there are nearly 10 times more MMS-induced lesions at other bases. Based on this mutation bias, the promutagenic lesion dominating LHM is likely 3-methylcytosine, which is single-strand specific. Thus, the dramatic increase in mutagenesis at a DSB is concluded to result primarily from the generation of non-repairable lesions in ssDNA associated with DSB repair along with efficient induction of highly mutagenic ssDNA-specific lesions. These findings with MMS-induced LHM have broad biological implications for unrepaired damage generated in ssDNA and possibly ssRNA. Published by Elsevier B.V.

  3. Isolation and characterization of a single-stranded DNA virus infecting the marine diatom Chaetoceros sp. strain SS628-11 isolated from western Japan.

    Directory of Open Access Journals (Sweden)

    Kei Kimura

    Full Text Available Diatoms are significant organisms for primary production in the earth's aquatic environment. Hence, their dynamics are an important focus area in current studies. Viruses are a great concern as potential factors of diatom mortality, along with other physical, chemical, and biological factors. We isolated and characterized a new diatom virus (Csp07DNAV that lyses the marine planktonic diatom Chaetoceros sp. strain SS628-11. This paper examines the physiological, morphological, and genomic characteristics of Csp07DNAV. The virus was isolated from a surface water sample that was collected at Hiroshima Bay, Japan. It was icosahedral, had a diameter of 34 nm, and accumulated in the nuclei of host cells. Rod-shaped virus particles also coexisted in the host nuclei. The latent period and burst size were estimated to be <12 h and 29 infectious units per host cell, respectively. Csp07DNAV had a closed circular single-stranded DNA genome (5,552 nucleotides, which included a double-stranded region and 3 open reading frames. The monophyly of Csp07DNAV and other Bacilladnavirus group single-stranded DNA viruses was supported by phylogenetic analysis that was based on the amino acid sequence of each virus protein. On the basis of these results, we considered Csp07DNAV to be a new member of the genus Bacilladnavirus.

  4. Monitoring the Retention of Human Proliferating Cell Nuclear Antigen at Primer/Template Junctions by Proteins That Bind Single-Stranded DNA.

    Science.gov (United States)

    Hedglin, Mark; Aitha, Mahesh; Benkovic, Stephen J

    2017-07-11

    In humans, proliferating cell nuclear antigen (PCNA) sliding clamps encircling DNA coordinate various aspects of DNA metabolism throughout the cell cycle. A critical aspect of this is restricting PCNA to the vicinity of its DNA target site. For example, PCNA must be maintained at or near primer/template (P/T) junctions during DNA synthesis. With a diverse array of cellular factors implicated, many of which interact with PCNA, DNA, or both, it is unknown how this critical feat is achieved. Furthermore, current biochemical assays that examine the retention of PCNA near P/T junctions are inefficient, discontinuous, and qualitative and significantly deviate from physiologically relevant conditions. To overcome these challenges and limitations, we recently developed a novel and convenient Förster resonance energy transfer (FRET) assay that directly and continuously monitors the retention of human PCNA at a P/T junction. Here we describe in detail the design, methodology, interpretation, and limitations of this quantitative FRET assay using the single-stranded DNA-binding protein, SSB, from Escherichia coli as an example. This powerful tool is broadly applicable to any single-stranded DNA-binding protein and may be utilized and/or expanded upon to dissect DNA metabolic pathways that are dependent upon PCNA.

  5. Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination.

    KAUST Repository

    Fornander, Louise H

    2012-02-22

    Human RAD51 protein (HsRad51) catalyses the DNA strand exchange reaction for homologous recombination. To clarify the molecular mechanism of the reaction in vitro being more effective in the presence of Ca(2+) than of Mg(2+), we have investigated the effect of these ions on the structure of HsRad51 filament complexes with single- and double-stranded DNA, the reaction intermediates. Flow linear dichroism spectroscopy shows that the two ionic conditions induce significantly different structures in the HsRad51/single-stranded DNA complex, while the HsRad51/double-stranded DNA complex does not demonstrate this ionic dependence. In the HsRad51/single-stranded DNA filament, the primary intermediate of the strand exchange reaction, ATP/Ca(2+) induces an ordered conformation of DNA, with preferentially perpendicular orientation of nucleobases relative to the filament axis, while the presence of ATP/Mg(2+), ADP/Mg(2+) or ADP/Ca(2+) does not. A high strand exchange activity is observed for the filament formed with ATP/Ca(2+), whereas the other filaments exhibit lower activity. Molecular modelling suggests that the structural variation is caused by the divalent cation interfering with the L2 loop close to the DNA-binding site. It is proposed that the larger Ca(2+) stabilizes the loop conformation and thereby the protein-DNA interaction. A tight binding of DNA, with bases perpendicularly oriented, could facilitate strand exchange.

  6. On-site detection of Phytophthora spp.—single-stranded target DNA as the limiting factor to improve on-chip hybridization

    International Nuclear Information System (INIS)

    Schwenkbier, Lydia; Pollok, Sibyll; Popp, Jürgen; Weber, Karina; König, Stephan; Wagner, Stefan; Werres, Sabine; Weber, Jörg; Hentschel, Martin

    2014-01-01

    We report on a lab-on-a-chip approach for on-site detection of Phytophthora species that allows visual signal readout. The results demonstrate the significance of single-stranded DNA (ssDNA) generation in terms of improving the intensity of the hybridization signal and to improve the reliability of the method. Conventional PCR with subsequent heat denaturation, sodium hydroxide-based denaturation, lambda exonuclease digestion and two asymmetric PCR methods were investigated for the species P. fragariae, P. kernoviae, and P. ramorum. The positioning of the capture probe within the amplified yeast GTP-binding protein (YPT1) target DNA was also of interest because it significantly influences the intensity of the signal. Statistical tests were used to validate the impact of the ssDNA generation methods and the capture-target probe position. The single-stranded target DNA generated by Linear-After-The-Exponential PCR (LATE-PCR) was found to produce signal intensities comparable to post-PCR exonuclease treatment. The LATE-PCR is the best method for the on-site detection of Phytophthora because the enzymatic digestion after PCR is more laborious and time-consuming. (author)

  7. Cascade annealing: an overview

    International Nuclear Information System (INIS)

    Doran, D.G.; Schiffgens, J.O.

    1976-04-01

    Concepts and an overview of radiation displacement damage modeling and annealing kinetics are presented. Short-term annealing methodology is described and results of annealing simulations performed on damage cascades generated using the Marlowe and Cascade programs are included. Observations concerning the inconsistencies and inadequacies of current methods are presented along with simulation of high energy cascades and simulation of longer-term annealing

  8. Synthesis of a wild-type and three mutant Cucurbita maxima trypsin inhibitor-encoding genes by a single-strand approach.

    Science.gov (United States)

    Botes, D P; Qobose, M D; Corfield, V A

    1991-09-15

    A single-strand approach to gene assembly, based on a modification of an in vitro complementary oligodeoxyribonucleotide template-directed ligation of the desired sequence to a linearized vector [Chen et al., Nucleic Acids Res. 18 (1990) 871-878], is described. The gene coding for the wild-type Cucurbita maxima trypsin inhibitor of 29 amino acid residues [Bode et al., FEBS Lett. 242 (1989) 285-292], as well as three mutant forms of the gene, in which two of the three disulfide bonds have been replaced singly or as a pair, have been synthesized in a single synthesis run with minimal manual intervention. Subsequent to ligation to pUC9 and in vivo gapped duplex repair by Escherichia coli, their sequences have been verified.

  9. The casein genes in goat breeds from different Continents: analysis by Polymerase Chain Reaction – Single Strand Conformation Polymorphism (PCR-SSCP

    Directory of Open Access Journals (Sweden)

    A. Caroli

    2010-04-01

    Full Text Available A screening of casein gene variability was carried out by Polymerase Chain Reaction – Single Strand Conformation Polymorphism in 8 goat breeds from Sudan (Nubian goat, Turkey (Angora Goat Lalahan Tiftic, Angora Goat Yerkoy, Hair goat and India (Jammu, Maharashtra, Rajasthan, South Goat. A total of 16 different alleles or groups of alleles were found, showing conspicuous differences among breeds. The allele frequencies were submitted to cluster analysis in order to highlight differences between breeds, also including data from Red Sokoto, West African Dwarf Nigeria, West African Dwarf Cameroon, and Borno Goat. The tree obtained from the cluster analysis showed two main lineages. The West African goat clustered together, the Indian and Turkish breeds were in the other group. Nubian goat was found in an intermediate position.

  10. Investigation of single-strand conformational polymorphism of the TP53 gene in women with a family history of breast cancer

    Directory of Open Access Journals (Sweden)

    R.R. Burbano

    2000-11-01

    Full Text Available Breast cancer in families with germ line mutations in the TP53 gene has been described in the medical literature. Mutation screening for susceptibility genes should allow effective prophylactic and preventive measures. Using single-strand conformational polymorphism, we screened for mutations in exons 5, 6, 7 and 8 of gene TP53 in the peripheral blood of 8 young non-affected members (17 to 36 years old of families with a history of breast cancer. Studies of this type on young patients (mean age, 25 years are very rare in the literature. The identification of these mutations would contribute to genetic counseling of members of families with predisposition to breast cancer. The results obtained did not show any polymorphism indicating mutation. In our sample, the familial tumorigenesis is probably related to other gene etiologies.

  11. UV light-induced DNA synthesis arrest in HeLa cells is associated with changes in phosphorylation of human single-stranded DNA-binding protein

    International Nuclear Information System (INIS)

    Carty, M.P.; Zernik-Kobak, M.; McGrath, S.; Dixon, K.

    1994-01-01

    We show that DNA replication activity in extracts of human HeLa cells decreases following UV irradiation. Alterations in replication activity in vitro parallel the UV-induced block in cell cycle progression of these cells in culture. UV irradiation also induces specific changes in the pattern of phosphorylation of the 34 kDa subunit of a DNA replication protein, human single-stranded DNA-binding protein (hSSB). The appearance of a hyperphosphorylated form of hSSB correlates with reduced in vitro DNA replication activity in extracts of UV-irradiated cells. Replication activity can be restored to these extracts in vitro by addition of purified hSSB. These results suggest that UV-induced DNA synthesis arrest may be mediated in part through phosphorylation-related alterations in the activity of hSSB, an essential component of the DNA replication apparatus. (Author)

  12. Influence of the single-strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano-cage family.

    Science.gov (United States)

    Iacovelli, Federico; Alves, Cassio; Falconi, Mattia; Oteri, Francesco; de Oliveira, Cristiano L P; Desideri, Alessandro

    2014-10-01

    The structural/dynamical properties of three truncated octahedral DNA nano-cages composed by identical double helices but single strand linkers with different composition, namely 7 thymidines, 7 adenines, and 7 alternated thymidines and adenines, have been investigated through classical molecular dynamics simulations. Trajectories have been analyzed to investigate the role of the linkers in defining nano-cages stability and flexibility, including possible influence on the internal cages motions. The data indicate that the cages behavior is almost identical and that the structural/dynamical parameters measured along the trajectories are not particularly affected by the presence of different bases. These results demonstrate that the constraints imposed by the nano-structure geometry are the main factor in modulating these properties

  13. Localization of specific sequences and DNA single-strand breaks in individual UV-A-irradiated human lymphocytes by COMET FISH

    Science.gov (United States)

    Bock, Claudia; Rapp, Alexander; Dittmar, Heike; Monajembashi, Shamci; Greulich, Karl-Otto

    1999-01-01

    The COMET assay, a single cell electrophoresis technique which allows to separate electrophoretically fractionated DNA according to size has been combined with fluorescence in situ hybridization (FISH) which allows to localize specific genes or gene regions. This combination (COMET FISH) allows the detection of DNA single strand breaks in specific regions of the genome of human lymphocytes at the single cell level. Various types of DNA probes, e.g. centromere-, (alpha) - satellite-, telomere-, whole chromosome-, single copy- and region specific DNA probes have been used to investigate whether the UV-A induced DNA single strand breaks are distributed randomly all over the human genome or induced at specific sites ('hot spots'). In the investigated human peripheral blood lymphocytes all but one centromere reveal low sensitivity for UV-A irradiation (500 kJ/m2), while telomeres are randomly distributed over COMET heads and tails. The human chromosome 1 is fractionated by irradiation, but remains in the COMET head, indicating an only moderate degree of fractionation. Among three tested single copy probes, c- myc, p53 and p58, the p53 gene located on chromosome 17p13.1 and the p58 gene (1p36) appear to be located in UV-A stable regions of the human genome in 95% of 65 investigated lymphocytes. In contrast, the c-myc proto-oncogene (8q24) is found in the COMET tail in 90% of the 27 investigated lymphocytes and thus appears to be more sensitive to UV-A irradiation.

  14. Evidence that single-stranded DNA breaks are a normal feature of koala sperm chromatin, while double-stranded DNA breaks are indicative of DNA damage.

    Science.gov (United States)

    Zee, Yeng Peng; López-Fernández, Carmen; Arroyo, F; Johnston, Stephen D; Holt, William V; Gosalvez, Jaime

    2009-08-01

    In this study, we have used single and double comet assays to differentiate between single- and double-stranded DNA damage in an effort to refine the interpretation of DNA damage in mature koala spermatozoa. We have also investigated the likelihood that single-stranded DNA breakage is part of the natural spermiogenic process in koalas, where its function would be the generation of structural bends in the DNA molecule so that appropriate packaging and compaction can occur. Koala spermatozoa were examined using the sperm chromatin dispersion test (SCDt) and comet assays to investigate non-orthodox double-stranded DNA. Comet assays were conducted under 1) neutral conditions; and 2) neutral followed by alkaline conditions (double comet assay); the latter technique enabled simultaneous visualisation of both single-stranded and double-stranded DNA breaks. Following the SCDt, there was a continuum of nuclear morphotypes, ranging from no apparent DNA fragmentation to those with highly dispersed and degraded chromatin. Dispersion morphotypes were mirrored by a similar diversity of comet morphologies that could be further differentiated using the double comet assay. The majority of koala spermatozoa had nuclei with DNA abasic-like residues that produced single-tailed comets following the double comet assay. The ubiquity of these residues suggests that constitutive alkali-labile sites are part of the structural configuration of the koala sperm nucleus. Spermatozoa with 'true' DNA fragmentation exhibited a continuum of comet morphologies, ranging from a more severe form of alkaline-susceptible DNA with a diffuse single tail to nuclei that exhibited both single- and double-stranded breaks with two comet tails.

  15. Functional roles of the N- and C-terminal regions of the human mitochondrial single-stranded DNA-binding protein.

    Directory of Open Access Journals (Sweden)

    Marcos T Oliveira

    2010-10-01

    Full Text Available Biochemical studies of the mitochondrial DNA (mtDNA replisome demonstrate that the mtDNA polymerase and the mtDNA helicase are stimulated by the mitochondrial single-stranded DNA-binding protein (mtSSB. Unlike Escherichia coli SSB, bacteriophage T7 gp2.5 and bacteriophage T4 gp32, mtSSBs lack a long, negatively charged C-terminal tail. Furthermore, additional residues at the N-terminus (notwithstanding the mitochondrial presequence are present in the sequence of species across the animal kingdom. We sought to analyze the functional importance of the N- and C-terminal regions of the human mtSSB in the context of mtDNA replication. We produced the mature wild-type human mtSSB and three terminal deletion variants, and examined their physical and biochemical properties. We demonstrate that the recombinant proteins adopt a tetrameric form, and bind single-stranded DNA with similar affinities. They also stimulate similarly the DNA unwinding activity of the human mtDNA helicase (up to 8-fold. Notably, we find that unlike the high level of stimulation that we observed previously in the Drosophila system, stimulation of DNA synthesis catalyzed by human mtDNA polymerase is only moderate, and occurs over a narrow range of salt concentrations. Interestingly, each of the deletion variants of human mtSSB stimulates DNA synthesis at a higher level than the wild-type protein, indicating that the termini modulate negatively functional interactions with the mitochondrial replicase. We discuss our findings in the context of species-specific components of the mtDNA replisome, and in comparison with various prokaryotic DNA replication machineries.

  16. BOREAS TE-1 SSA Soil Lab Data

    Science.gov (United States)

    Hall, Forrest G. (Editor); Knapp, David E. (Editor); Nerbas, Tim; Anderson, Darwin

    2000-01-01

    This data set was collected by TE-1 to provide a set of soil properties for BOREAS investigators in the SSA. The soil samples were collected at sets of soil pits in 1993 and 1994. Each set of soil pits was in the vicinity of one of the five flux towers in the BOREAS SSA. The collected soil samples were sent to a lab, where the major soil properties were determined. These properties include, but are not limited to, soil horizon; dry soil color; pH; bulk density; total, organic, and inorganic carbon; electric conductivity; cation exchange capacity; exchangeable sodium, potassium, calcium, magnesium, and hydrogen; water content at 0.01, 0.033, and 1.5 MPascals; nitrogen; phosphorus; particle size distribution; texture; pH of the mineral soil and of the organic soil; extractable acid; and sulfur. The data are stored in tabular ASCII text files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  17. The colour potentials of SSA-containing mortar

    DEFF Research Database (Denmark)

    Kappel, Annemette; Ottosen, Lisbeth M.; Kirkelund, Gunvor Marie

    2015-01-01

    is with a few exceptions landfilled and thus, wasted.The purpose of the experiments was to examine the influence of SSA and how it affected the colour of mortar samples. SSA was ground in 6 different intervals and added to mortar mixes by replacing 20% of the cement. An additional focus was to examine...

  18. The Aesthetical quality of SSA-containing mortar and concrete

    DEFF Research Database (Denmark)

    Kappel, Annemette; Kirkelund, Gunvor Marie; Ottosen, Lisbeth M.

    2014-01-01

    SSA (sewage sludge ash) is resulting ash from the combustion of sewage sludge, and is a method employed at some water treatment plants in order to decrease volume and hygenize the sludge. Today, SSA is with a few exceptions landfilled. As cement production is responsible for app. 5 % of the total...

  19. Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Kaushik; Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2016-05-28

    The noncovalent interaction between protein and DNA is responsible for regulating the genetic activities in living organisms. The most critical issue in this problem is to understand the underlying driving force for the formation and stability of the complex. To address this issue, we have performed atomistic molecular dynamics simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein (FBP) complexed with two single-stranded DNA (ss-DNA) oligomers in aqueous media. Attempts have been made to calculate the individual components of the net entropy change for the complexation process by adopting suitable statistical mechanical approaches. Our calculations reveal that translational, rotational, and configurational entropy changes of the protein and the DNA components have unfavourable contributions for this protein-DNA association process and such entropy lost is compensated by the entropy gained due to the release of hydration layer water molecules. The free energy change corresponding to the association process has also been calculated using the Free Energy Perturbation (FEP) method. The free energy gain associated with the KH4–DNA complex formation has been found to be noticeably higher than that involving the formation of the KH3–DNA complex.

  20. Hematopoietic Lineage Transcriptome Stability and Representation in PAXgeneTM Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray

    Directory of Open Access Journals (Sweden)

    Laura Kennedy

    2008-01-01

    Full Text Available Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgeneTM RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2TM enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgeneTM blood samples also advocate a short, fixed room temperature storage time for all PAXgeneTM blood samples collected for the purposes of global transcriptional profiling in clinical studies.

  1. Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray.

    Science.gov (United States)

    Kennedy, Laura; Vass, J Keith; Haggart, D Ross; Moore, Steve; Burczynski, Michael E; Crowther, Dan; Miele, Gino

    2008-08-25

    Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgene() RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2() enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgene() blood samples also advocate a short, fixed room temperature storage time for all PAXgene() blood samples collected for the purposes of global transcriptional profiling in clinical studies.

  2. Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene™ Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray

    Science.gov (United States)

    Kennedy, Laura; Vass, J. Keith; Haggart, D. Ross; Moore, Steve; Burczynski, Michael E.; Crowther, Dan; Miele, Gino

    2008-01-01

    Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgene™ RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2™ enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgene™ blood samples also advocate a short, fixed room temperature storage time for all PAXgene™ blood samples collected for the purposes of global transcriptional profiling in clinical studies. PMID:19578521

  3. A biomarker model of sublethal genotoxicity (DNA single-strand breaks and adducts) using the sentinel organism Aporrectodea longa in spiked soil

    International Nuclear Information System (INIS)

    Martin, Francis L.; Piearce, Trevor G.; Hewer, Alan; Phillips, David H.; Semple, Kirk T.

    2005-01-01

    There is a need to develop risk biomarkers during the remediation of contaminated land. We employed the earthworm, Aporrectodea longa (Ude), to determine whether genotoxicity measures could be applied to this organism's intestinal tissues. Earthworms were added, for 24 h or 7 days, to soil samples spiked with benzo[a]pyrene (B[a]P) and/or lindane. After exposure, intestinal tissues (crop/gizzard or intestine) were removed prior to the measurement in disaggregated cells of DNA single-strand breaks (SSBs) by the alkaline comet assay. Damage was quantified by comet tail length (CTL, μm). B[a]P 24-h exposure induced dose-related increases (P 32 P-postlabelling, showed a two-adduct-spot pattern. This preliminary investigation suggests that earthworm tissues may be incorporated into genotoxicity assays to facilitate hazard identification within terrestrial ecosystems. - Sublethal genotoxicity in the sentinel organism A. longa can be used to monitor the effects of contaminants in soil

  4. Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.

    Directory of Open Access Journals (Sweden)

    Malik Mumtaz Taqi

    Full Text Available Single-stranded DNA (ssDNA is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations. Here we used native polyacrylamide gel electrophoresis (PAGE, circular dichroism (CD spectroscopy and nuclear magnetic resonance (NMR spectroscopy to show that cytosine methylation at CpG sites affects the conformational flexibility of short ssDNA molecules. The CpG containing 37-nucleotide PDYN (prodynorphin fragments were used as model molecules. The presence of secondary DNA structures was evident from differences in oligonucleotide mobilities on PAGE, from CD spectra, and from formation of A-T, G-C, and non-canonical G-T base pairs observed by NMR spectroscopy. The oligonucleotides displayed secondary structures at 4°C, and some also at 37°C. Methylation at CpG sites prompted sequence-dependent formation of novel conformations, or shifted the equilibrium between different existing ssDNA conformations. The effects of methylation on gel mobility and base pairing were comparable in strength to the effects induced by point mutations in the DNA sequences. The conformational effects of methylation may be relevant for epigenetic regulatory events in a chromatin context, including DNA-protein or DNA-DNA recognition in the course of gene transcription, and DNA replication and recombination when double-stranded DNA is unwinded to ssDNA.

  5. Analysis of Coinfections with A/H1N1 Strain Variants among Pigs in Poland by Multitemperature Single-Strand Conformational Polymorphism

    Directory of Open Access Journals (Sweden)

    Krzysztof Lepek

    2015-01-01

    Full Text Available Monitoring and control of infections are key parts of surveillance systems and epidemiological risk prevention. In the case of influenza A viruses (IAVs, which show high variability, a wide range of hosts, and a potential of reassortment between different strains, it is essential to study not only people, but also animals living in the immediate surroundings. If understated, the animals might become a source of newly formed infectious strains with a pandemic potential. Special attention should be focused on pigs, because of the receptors specific for virus strains originating from different species, localized in their respiratory tract. Pigs are prone to mixed infections and may constitute a reservoir of potentially dangerous IAV strains resulting from genetic reassortment. It has been reported that a quadruple reassortant, A(H1N1pdm09, can be easily transmitted from humans to pigs and serve as a donor of genetic segments for new strains capable of infecting humans. Therefore, it is highly desirable to develop a simple, cost-effective, and rapid method for evaluation of IAV genetic variability. We describe a method based on multitemperature single-strand conformational polymorphism (MSSCP, using a fragment of the hemagglutinin (HA gene, for detection of coinfections and differentiation of genetic variants of the virus, difficult to identify by conventional diagnostic.

  6. Cells deficient in PARP-1 show an accelerated accumulation of DNA single strand breaks, but not AP sites, over the PARP-1-proficient cells exposed to MMS.

    Science.gov (United States)

    Pachkowski, Brian F; Tano, Keizo; Afonin, Valeriy; Elder, Rhoderick H; Takeda, Shunichi; Watanabe, Masami; Swenberg, James A; Nakamura, Jun

    2009-12-01

    Poly(ADP-ribose) polymerase-1 (PARP-1) is a base excision repair (BER) protein that binds to DNA single strand breaks (SSBs) and subsequently synthesizes and transfers poly(ADP-ribose) polymers to various nuclear proteins. Numerous biochemical studies have implicated PARP-1 as a modulator of BER; however, the role of PARP-1 in BER in living cells remains unclear partly due to lack of accurate quantitation of BER intermediates existing in cells. Since DT40 cells, chicken B lymphocytes, naturally lack PARP-2, DT40 cells allow for the investigation of the PARP-1 null phenotype without confounding by PARP-2. To test the hypothesis that PARP-1 is necessary for efficient BER during methylmethane sulfonate (MMS) exposure in vertebrate cells, intact DT40 cells and their isogenic PARP-1 null counterparts were challenged with different exposure scenarios for phenotypic characterization. With chronic exposure, PARP-1 null cells exhibited sensitivity to MMS but with an acute exposure did not accumulate base lesions or AP sites to a greater extent than wild-type cells. However, an increase in SSB content in PARP-1 null cell DNA, as indicated by glyoxal gel electrophoresis under neutral conditions, suggested the presence of BER intermediates. These data suggest that during exposure, PARP-1 impacts the stage of BER after excision of the deoxyribosephosphate moiety from the 5' end of DNA strand breaks by polymerase beta.

  7. In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against the Pesticide Fipronil and Sensitive Detection in River Water

    Directory of Open Access Journals (Sweden)

    Ka L. Hong

    2017-12-01

    Full Text Available Fipronil is a commonly used insecticide that has been shown to have environmental and human health risks. The current standard methods of detection for fipronil and its metabolites, such as GC-MS, are time consuming and labor intensive. In this study, a variant of systematic evolution of ligands by exponential enrichment (SELEX, was utilized to identify the first single-stranded DNA (ssDNA molecular recognition element (MRE that binds to fipronil with high affinity (Kd = 48 ± 8 nM. The selected MRE displayed low cross binding activity on various environmentally relevant, structurally unrelated herbicides and pesticides, in addition to broad-spectrum binding activity on major metabolites of fipronil and a structurally similar pesticide in prepared river samples. Additionally, a proof-of-principle fluorescent detection assay was developed by using the selected ssDNA MRE as a signal-reporting element, with a limit of detection of 105 nM in a prepared river water sample.

  8. Yield of radiation-induced DNA single-strand breaks in Escherichia coli and superinfecting phage lambda at different dose rates. Repair of strand breaks in different buffers

    International Nuclear Information System (INIS)

    Boye, E.; Johansen, I.; Brustad, T.

    1976-01-01

    Cells of E. coli K-12 strain AB 1886 were irradiated in oxygenated phosphate buffered saline at 2 0 C with electrons from a 4-MeV linear accelerator. The yield of DNA single-strand breaks was determined as a function of the dose rate between 2.5 and 21,000 krad/min. For dose rates over 100 krad/min the yield was found to be constant. Below 10 krad/min the yield of breaks decreases drastically. This is explained by rejoining of breaks during irradiation. Twenty percent of the breaks induced by acute exposure are repaired within 3 min at 2 0 C. Superinfecting phage lambda DNA is repaired at the same rate as chromosomal DNA. In contrast to the results obtained with phosphate-buffered saline, an increase in the number of breaks after irradiation is observed when the bacteria are suspended in tris buffer. It is suggested that buffers of low ionic strength facilitate the leakage through the membrane of a small-molecular-weight component(s) necessary for DNA strand rejoining

  9. Clonal origin of multiple lung cancers: K-ras and p53 mutations determined by nonradioisotopic single-strand conformation polymorphism analysis.

    Science.gov (United States)

    Lau, D H; Yang, B; Hu, R; Benfield, J R

    1997-08-01

    Disease stage is the most important factor in determining prognosis and treatment of lung cancer. Staging of lung cancer is complicated by presentation of multiple pulmonary malignant lesions with a similar histology. It is a dilemma to decide if these lesions are synchronous primaries arising from different malignant clones or metastases from a single clone. Lung cancer is associated with multiple genetic abnormalities including mutations of K-ras and p53, which are believed to occur prior to onset of metastasis. To determine the clonal origin of multiple pulmonary malginant nodules, we analyzed point-mutations of K-ras and p53 by microdissection, polymerase chain reactions (PCR), nonradioisotopic single-strand conformation polymorphism (SSCP) analysis, and DNA sequencing. Each pulmonary lesion was microdissected from paraffin slides. Genomic DNA was amplified by two sequential PCRs followed by electrophoresis in a minigel and silver staining. Deoxyribonucleic acid sequencing was performed if necessary to confirm a mutation found upon SSCP analysis. Applying this molecular approach, we were able to differentiate the clonal origins of multiple malignant nodules of the lung as exemplified by the two cases presented.

  10. Selection and Characterization of Single-Stranded DNA Aptamers Binding Human B-Cell Surface Protein CD20 by Cell-SELEX

    Directory of Open Access Journals (Sweden)

    Mansoureh Haghighi

    2018-03-01

    Full Text Available The B-lymphocyte antigen (CD20 is a suitable target for single-stranded (ss nucleic acid oligomer (aptamers. The aim of study was selection and characterization of a ssDNA aptamer against CD20 using Cell-Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX. The cDNA clone of CD20 (pcDNA-CD20 was transfected to human embryonic kidney (HEK293T cells. Ten rounds of Cell-SELEX was performed on recombinant HEK-CD20 cells. The final eluted ssDNA pool was amplified and ligated in T/A vector for cloning. The plasmids of positive clones were extracted, sequenced and the secondary structures of the aptamers predicted using DNAMAN® software. The sequencing results revealed 10 different types; three of them had the highest thermodynamic stability, named AP-1, AP-2 and AP-3. The AP-1 aptamer was the most thermodynamically stable one (ΔGAP-1 = −10.87 kcal/mol with the highest binding affinity to CD20 (96.91 ± 4.5 nM. Since, the CD20 is a suitable target for recognition of B-Cell. The selected aptamers could be comparable to antibodies with many advantages. The AP-1, AP-2 and AP-3 could be candidate instead of antibodies for diagnostic and therapeutic applications in immune deficiency, autoimmune diseases, leukemia and lymphoma.

  11. The interplay of primer-template DNA phosphorylation status and single-stranded DNA binding proteins in directing clamp loaders to the appropriate polarity of DNA.

    Science.gov (United States)

    Hayner, Jaclyn N; Douma, Lauren G; Bloom, Linda B

    2014-01-01

    Sliding clamps are loaded onto DNA by clamp loaders to serve the critical role of coordinating various enzymes on DNA. Clamp loaders must quickly and efficiently load clamps at primer/template (p/t) junctions containing a duplex region with a free 3'OH (3'DNA), but it is unclear how clamp loaders target these sites. To measure the Escherichia coli and Saccharomyces cerevisiae clamp loader specificity toward 3'DNA, fluorescent β and PCNA clamps were used to measure clamp closing triggered by DNA substrates of differing polarity, testing the role of both the 5'phosphate (5'P) and the presence of single-stranded binding proteins (SSBs). SSBs inhibit clamp loading by both clamp loaders on the incorrect polarity of DNA (5'DNA). The 5'P groups contribute selectivity to differing degrees for the two clamp loaders, suggesting variations in the mechanism by which clamp loaders target 3'DNA. Interestingly, the χ subunit of the E. coli clamp loader is not required for SSB to inhibit clamp loading on phosphorylated 5'DNA, showing that χ·SSB interactions are dispensable. These studies highlight a common role for SSBs in directing clamp loaders to 3'DNA, as well as uncover nuances in the mechanisms by which SSBs perform this vital role. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein.

    Science.gov (United States)

    Politis, Argyris; Park, Ah Young; Hall, Zoe; Ruotolo, Brandon T; Robinson, Carol V

    2013-11-29

    DNA polymerase III, a decameric 420-kDa assembly, simultaneously replicates both strands of the chromosome in Escherichia coli. A subassembly of this holoenzyme, the seven-subunit clamp loader complex, is responsible for loading the sliding clamp (β2) onto DNA. Here, we use structural information derived from ion mobility mass spectrometry (IM-MS) to build three-dimensional models of one form of the full clamp loader complex, γ3δδ'ψχ (254 kDa). By probing the interaction between the clamp loader and a single-stranded DNA (ssDNA) binding protein (SSB4) and by identifying two distinct conformational states, with and without ssDNA, we assemble models of ψχ-SSB4 (108 kDa) and the clamp loader-SSB4 (340 kDa) consistent with IM data. A significant increase in measured collision cross-section (~10%) of the clamp loader-SSB4 complex upon DNA binding suggests large conformational rearrangements. This DNA bound conformation represents the active state and, along with the presence of ψχ, stabilises the clamp loader-SSB4 complex. Overall, this study of a large heteromeric complex analysed by IM-MS, coupled with integrative modelling, highlights the potential of such an approach to reveal structural features of previously unknown complexes of high biological importance. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system.

    Science.gov (United States)

    Sinkunas, Tomas; Gasiunas, Giedrius; Fremaux, Christophe; Barrangou, Rodolphe; Horvath, Philippe; Siksnys, Virginijus

    2011-04-06

    Clustered regularly interspaced short palindromic repeat (CRISPR) is a recently discovered adaptive prokaryotic immune system that provides acquired immunity against foreign nucleic acids by utilizing small guide crRNAs (CRISPR RNAs) to interfere with invading viruses and plasmids. In Escherichia coli, Cas3 is essential for crRNA-guided interference with virus proliferation. Cas3 contains N-terminal HD phosphohydrolase and C-terminal Superfamily 2 (SF2) helicase domains. Here, we provide the first report of the cloning, expression, purification and in vitro functional analysis of the Cas3 protein of the Streptococcus thermophilus CRISPR4 (Ecoli subtype) system. Cas3 possesses a single-stranded DNA (ssDNA)-stimulated ATPase activity, which is coupled to unwinding of DNA/DNA and RNA/DNA duplexes. Cas3 also shows ATP-independent nuclease activity located in the HD domain with a preference for ssDNA substrates. To dissect the contribution of individual domains, Cas3 separation-of-function mutants (ATPase(+)/nuclease(-) and ATPase(-)/nuclease(+)) were obtained by site-directed mutagenesis. We propose that the Cas3 ATPase/helicase domain acts as a motor protein, which assists delivery of the nuclease activity to Cascade-crRNA complex targeting foreign DNA.

  14. ESA-SSA Review of Space Weather Measurement Requirements

    Science.gov (United States)

    Luntama, Juha-Pekka; Glover, Alexi; Hilgers, Alain

    2012-07-01

    The ESA Space Situational Awareness (SSA) Preparatory Programme was started in 2009. The objective of the programme is to support the European independent utilisation of and access to space. The first phase of the ESA SSA system development will be finished in 2012 and the next phase is foreseen to be started after the ESA Ministerial Council meeting in November 2012. The definition of measurement requirements for the Space Weather Segment (SWE) of the ESA SSA system has been based on the space weather service requirements defined the by expected users of the system. This document, SSA SWE Customer Requirements Document (CRD), has been defined in a iterative process together with the members of the SSA User Representative Group (URG) and the delegates representing the European states participating the programme. Based on the SWE CRD, ESA with the support of the European industry has produced two documents: SSA SWE System Requirements Document (SRD) and SSA SWE Product Specification (PS). SWE PS contains the requirements for the measurements data required by the SSA SWE system. The SWE PS document has been recently rigorously reviewed by the SSA URG in the framework of the SSA System Requirements Review (SRR). The support provided by the Steering Board of the ESA Space Weather Working Team (SWWT) in this review was extremely useful. The members of the SWWT SB representing the scientific community and the provisional service providers were able to give very detailed comments regarding the measurement requirements for accuracy, cadence, timeliness, etc. As these parameters will be provisional design and cost drivers for the ESA SSA system, definition of the appropriate values at this point in the programme is crucial. This paper provides an overview of the measurement requirements for the SWE Segment of the ESA SSA Programme. The paper discusses the requirement definition process, the customer and service provider inputs, and the critical requirements as they have

  15. porphyrin with single strand DNAs

    Indian Academy of Sciences (India)

    for organization of porphyrin molecules into extended assemblies, providing opportunities for construction of supramolecular structures.6–8 Among the porphyrin .... and consequently the mono- and bi-exponential nature of the decays were judged by the reduced chi-square. (χ2) values and distribution of the weighted ...

  16. Remote Control Southern Hemisphere SSA Observatory

    Science.gov (United States)

    Ritchie, I.; Pearson, M.; Sang, J.

    2013-09-01

    EOS Space Systems (EOSSS) is a research and development company which has developed custom observatories, camera and telescope systems for space surveillance since 1996, as well as creating several evolutions of systems control software for control of observatories and laser tracking systems. Our primary reserach observatory is the Space Reserach Centre (SRC) at Mount Stromlo Asutralia. The current SRC control systems are designed such that remote control can be offered for real time data collection, noise filtering and flexible session management. Several imaging fields of view are available simultaneously for tracking orbiting objects, with real time imaging to Mag 18. Orbiting objects can have the centroids post processed into orbital determination/ orbital projection (OD/OP) elements. With or without laser tracking of orbiting objects, they can be tracked in terminator conditions and their OD/OP data created, then enhanced by proprietary methods involving ballistic coefficient estimation and OD convergence pinning, using a priori radar elements. Sensors in development include a thermal imager for satellite thermal signature detection. Extending laser tracking range by use of adaptive optics beam control is also in development now. This Southern Hemisphere observatory is in a unique position to facilitate the study of space debris, either stand-alone or as part of a network such as Falcon. Current national and international contracts will enhance the remote control capabilities further, creating a resource ready to go for a wide variety of SSA missions.

  17. The colour potentials of SSA-containing mortar

    DEFF Research Database (Denmark)

    Kappel, Annemette; Ottosen, Lisbeth M.; Kirkelund, Gunvor Marie

    2015-01-01

    is with a few exceptions landfilled and thus, wasted.The purpose of the experiments was to examine the influence of SSA and how it affected the colour of mortar samples. SSA was ground in 6 different intervals and added to mortar mixes by replacing 20% of the cement. An additional focus was to examine...... the possibilities to accentuate the colours of the hardened mortar by using paper cuttings in the production of the samples. The result of the experiments showed that a colour scale can be developed from ground SSA, and that paper may have the potential of providing divers textural qualities when it is used...

  18. Effect of vanillin on methylene blue plus light-induced single-strand breaks in plasmid pBR322 DNA.

    Science.gov (United States)

    Kumar, S S; Ghosh, A; Devasagayam, T P; Chauhan, P S

    2000-09-20

    The ability of vanillin (4-hydroxy-3-methoxybenzaldehyde), a naturally occurring food flavouring agent, in inhibiting photosensitization-induced single-strand breaks (ssbs) in plasmid pBR322 DNA has been examined in an in vitro system, independent of DNA repair/replication processes. Photosensitization of DNA with methylene blue, visible light and oxygen, induced ssbs resulting in the production of open circular form (OC form) in a concentration-dependent manner. The yield of OC form induced by photosensitization was increased several-fold by deuteration of the buffer and was found to be inhibited by sodium azide, a scavenger of singlet oxygen (1O(2)). Vanillin, per se, did not induce but inhibited photosensitization-induced ssbs in plasmid DNA, at millimolar concentrations. The inhibitory effect of vanillin was both concentration- and time-dependent. On a molar basis, vanillin was, however, less effective than trolox, a water-soluble analogue of alpha-tocopherol. Photosensitization by methylene blue system generates singlet oxygen, as one of the major components of ROS. Therefore, interaction of singlet oxygen with vanillin was investigated. The rate constant of vanillin with 1O(2) was estimated to be 5.93x10(7)M(-1)s(-1) and that of sodium azide as 2. 7x10(8)M(-1)s(-1). The present investigations show that vanillin can protect against photosensitization-induced ssbs in the plasmid pBR322 DNA, and this effect may partly be due to its ability to scavenge 1O(2).

  19. Flow cytometry analysis of single-strand DNA damage in neuroblastoma cell lines using the F7-26 monoclonal antibody.

    Science.gov (United States)

    Grigoryan, Rita S; Yang, Bo; Keshelava, Nino; Barnhart, Jerry R; Reynolds, C Patrick

    2007-11-01

    The F7-26 monoclonal antibody (Mab) has been reported to be specific for single-strand DNA damage (ssDNA) and to also identify cells in apoptosis. We carriedout studies to determine if F7-26 binding measured by flow cytometry was able to specifically identify exogenous ssDNA as opposed to DNA damage from apoptosis. Neuroblastoma cells were treated with melphalan (L-PAM), fenretinide, 4-hydroperoxycyclophosphamide (4-HC)+/-pan-caspase inhibitor BOC-d-fmk, topotecan or with 10Gy gamma radiation+/-hydrogen peroxide (H2O2) and fixed immediately postradiation. Cytotoxicity was measured by DIMSCAN digital imaging fluorescence assay. The degree of ssDNA damage was analyzed by flow cytometry using Mab F7-26, with DNA visualized by propidium iodide counterstaining. Flow cytometry was used to measure apoptosis detected by terminal deoxynucleotidyltransferase (TUNEL) assay and reactive oxygen species (ROS) by carboxy-dichlorofluorescein diacetate. Irradiated and immediately fixed neuroblastoma cells showed increased ssDNA, but not apoptosis by TUNEL (TUNEL-negative). 4-HC or L-PAM+/-BOC-d-fmk increased ssDNA (F7-26-positive), but BOC-d-fmk prevented TUNEL staining. Fenretinide increased apoptosis by TUNEL but not ssDNA damage detected with F7-26. Enhanced ssDNA in neuroblastoma cells treated with radiation+H2O2 was associated with increased ROS. Topotecan increased both ssDNA and cytotoxicity in 4-HC-treated cells. These data demonstrate that Mab F7-26 recognized ssDNA due to exogenous DNA damage, rather than apoptosis. This assay should be useful to characterize the mechanism of action of antineoplastic drugs. Copyright (c) 2007 International Society for Analytical Cytology.

  20. Detection of rifampin resistance patterns in Mycobacterium tuberculosis strains isolated in Iran by polymerase chain reaction-single-strand conformation polymorphism and direct sequencing methods

    Directory of Open Access Journals (Sweden)

    Bahram Nasr Isfahani

    2006-09-01

    Full Text Available Mutations in the rpoB locus confer conformational changes leading to defective binding of rifampin (RIF to rpoB and consequently resistance in Mycobacterium tuberculosis. Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP was established as a rapid screening test for the detection of mutations in the rpoB gene, and direct sequencing has been unambiguously applied to characterize mutations. A total of 37 of Iranian isolates of M. tuberculosis, 16 sensitive and 21 resistant to RIF, were used in this study. A 193-bp region of the rpoB gene was amplified and PCR-SSCP patterns were determined by electrophoresis in 10% acrylamide gel and silver staining. Also, 21 samples of 193-bp rpoB amplicons with different PCR-SSCP patterns from RIFr and 10 from RIFs were sequenced. Seven distinguishable PCR-SSCP patterns were recognized in the 21 Iranian RIFr strains, while 15 out of 16 RIFs isolates demonstrated PCR-SSCP banding patterns similar to that of sensitive standard strain H37Rv. However one of the sensitive isolates demonstrated a different pattern. There were seen six different mutations in the amplified region of rpoB gene: codon 516(GAC/GTC, 523(GGG/GGT, 526(CAC/TAC, 531(TCG/TTG, 511(CTG/TTG, and 512(AGC/TCG. This study demonstrated the high specificity (93.8% and sensitivity (95.2% of PCR-SSCP method for detection of mutation in rpoB gene; 85.7% of RIFr strains showed a single mutation and 14.3% had no mutations. Three strains showed mutations caused polymorphism. Our data support the common notion that rifampin resistance genotypes are generally present mutations in codons 531 and 526, most frequently found in M. tuberculosis populations regardless of geographic origin.

  1. Detection of p53 mutations by single-strand conformation polymorphisms (SSCP) gel electrophoresis. A comparative study of radioactive and nonradioactive silver-stained SSCP analysis.

    Science.gov (United States)

    Bosari, S; Marchetti, A; Buttitta, F; Graziani, D; Borsani, G; Loda, M; Bevilacqua, G; Coggi, G

    1995-12-01

    p53 mutations are the most common genetic abnormality in humans tumors, but their clinical significance remains to be precisely elucidated. Conventional single-strand conformation polymorphism (SSCP) analysis, a well-established technique for detecting p53 mutations, uses radioactively labeled polymerase chain reaction (PCR) products, which migrate abnormally in the presence of mutations. We performed radioactive PCR-SSCP analysis in a series of 30 formalin-fixed, paraffin-embedded ovarian carcinomas and two cell lines (SW480 and Caov4) harboring known homozygous p53 mutations and compared the results with nonradioactive silver-stained SSCP. The purpose was to assess whether nonradioactive SSCP is suitable for detecting p53 mutations in a rapid, sensitive, cost-effective fashion, without the need of radioactive isotopes. We accomplished PCR amplification of p53 exons 5 through 8 in 26 carcinomas, and radioactive SSCP detected p53 mutations in 13 tumors; three mutations were localized in exon 5, six in exon 6, two in exon 7, and two in exon 8. All mutations were correctly identified with nonradioactive SSCP, except for one exon 8 mutation. To establish the sensitivity of nonradioactive SSCP, DNA samples of SW480 and Caov4 were mixed with increasing amounts (0-90%) of normal DNA and subjected to PCR-SSCP analysis. Mutations were detected until the concentration of SW480 and Caov4 was 15% and 10%, respectively, of the total sample. The results of our investigation demonstrate that nonradioactive silver-stained SSCP is a sensitive, rapid, and simple technique to detect p53 mutations, even in formalin-fixed tissues, and could be easily used to investigate large series of patients to assess the clinical significance of p53 mutations in human tumors.

  2. Ampelomyces mycoparasites from apple powdery mildew identified as a distinct group based on single-stranded conformation polymorphism analysis of the rDNA ITS region.

    Science.gov (United States)

    Szentiványi, Orsolya; Kiss, Levente; Russell, John C; Kovács, Gábor M; Varga, Krisztina; Jankovics, Tünde; Lesemann, Silke; Xu, Xiang-Ming; Jeffries, Peter

    2005-04-01

    Pycnidial fungi belonging to the genus Ampelomyces are the most common natural antagonists of powdery mildews worldwide. During a study of the interactions between apple powdery mildew (Podosphaera leucotricha) and Ampelomyces mycoparasites, 52 new Ampelomyces isolates were obtained from P. leucotricha and, in addition, 13 new isolates from other species of the Erysiphaceae in four European countries. Their genetic diversity was screened using single-stranded conformation polymorphism (SSCP) analysis of the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA). For comparison, 24 isolates obtained from genetic resource collections or other sources were included in this study. Based on the ITS-SSCP patterns, the isolates were placed in eight groups. The isolates belonged to two types based on their growth in culture. The faster-growing and the slower-growing isolates were included in different SSCP groups. A phylogenetic analysis of the ITS sequences of representatives of these groups confirmed the results obtained with the SSCP method, and showed that the faster-growing isolates do not belong to Ampelomyces as suggested by earlier studies. All the isolates from P. leucotricha fell into a distinct SSCP group of genetically homogeneous isolates. This suggests that Ampelomyces mycoparasites which occur in apple powdery mildew are slightly different from the other Ampelomyces groups which contain mycoparasites from various powdery mildew species. This may be because the main growth period of Ampelomyces mycoparasites in apple powdery mildew is isolated in time from that of Ampelomyces isolates that occur in other species of the Erysiphaceae. P. leucotricha starts its life-cycle early in the season, usually in March-April, while most powdery mildews are active in the same environments only late in the year.

  3. Single-stranded DNA aptamer targeting and neutralization of anti-D alloantibody: a potential therapeutic strategy for haemolytic diseases caused by Rhesus alloantibody.

    Science.gov (United States)

    Zhang, Yinze; Wu, Fan; Wang, Manni; Zhuang, Naibao; Zhou, Huayou; Xu, Hua

    2018-02-01

    Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. When RhD-negative individuals are exposed to RhD-positive blood, they may produce anti-D alloantibody, potentially resulting in delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn, which are difficult to treat. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases. In this study, single-stranded (ss) DNA aptamers, specifically binding to anti-D antibodies, were selected via systematic evolution of ligands by exponential enrichment (SELEX) technology. After 14 rounds of selection, the purified ssDNA was sequenced using a Personal Genome Machine system. Haemagglutination inhibition assays were performed to screen aptamers for biological activity in terms of blocking antigen-antibody reactions: the affinity and specificity of the aptamers were also determined. In addition to high specificity, the aptamers which were selected showed high affinity for anti-D antibodies with dissociation constant (K d ) values ranging from 51.46±14.90 to 543.30±92.59 nM. By the combined use of specific ssDNA aptamer 7 and auxiliary ssDNA aptamer 2, anti-D could be effectively neutralised at low concentrations of the aptamers. Our results demonstrate that ssDNA aptamers may be a novel, promising strategy for the treatment of delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn.

  4. Variabilidad genética de Aedes aegypti en algunas áreas del Perú usando Single Stranded Conformational Polymorphism (SSCP

    Directory of Open Access Journals (Sweden)

    Nélida Leiva G

    2004-07-01

    Full Text Available Aedes aegypti es el vector responsable de la transmisión del virus del dengue, su distribución geográfica se ha ampliado rápidamente debido principalmente a la intervención de los seres humanos. Objetivo: Analizar la variabilidad genética de este mosquito mediante la comparación del Segundo Espaciador Transcrito Interno (ITS 2 perteneciente al ADN ribosomal (rADN. Materiales y Métodos: Se analizaron muestras de ocho localidades (Jaén, Tingo María, Iquitos, Lambayeque, el distrito de El Rimac, Sullana y Zarumilla y uno de la provincia de Huaquillas (Ecuador. El análisis de la variabilidad se determinó usando la técnica conocida como SSCP (Single Stranded Conformation Polymorphism. Resultados: El estudio muestra que existe variabilidad genética entre las poblaciones analizadas, principalmente entre las muestras localizadas en la costa del Perú (Zarumilla, El Rímac, Sullana y Huaquillas y las muestras del nororiente (Tingo María, Iquitos, Jaén y Lambayeque Conclusión: Se determinaron dos variantes genéticas entre las poblaciones de Aedes aegypti: Costeña y Nororiental, que probablemente provienen de dos ancestros diferentes y cuyo ancestro común sufrió de aislamiento por distancia. Se observó que no existe relación entre las distancias genéticas y las distancias geográficas indicando que la migración de estas poblaciones es el resultado de la intervención de los seres humanos que diseminan al vector y no por la migración activa del mosquito. Se plantea el papel de la Cordillera de los Andes en la migración y separación de las poblaciones de Aedes.

  5. Detection of hybridization of single-strand DNA PCR products in temperature change process by a novel metal-clamping piezoelectric sensor.

    Science.gov (United States)

    Chen, Qinghai; Bian, Zhiheng; Hua, Xing; Yao, Chunyan; Wu, Wei; Zhang, Xue; Zhang, Bo; Huang, Junfu; Tang, Wanli; Fu, Weiling

    2010-05-15

    Oligonucleotide probes on the sensor surface can be hybridized with single-strand DNA (ssDNA) that is formed from PCR products in ice bath after degeneration. Thus, detection of PCR products by piezoelectric sensors requires the participation of ssDNA PCR products in ice bath. When PCR products in ice bath are added into the buffer of the sensor well at room temperature, there will be a temperature change process during mixing. However, it still remains unclear whether the temperature change affects the frequency baseline stability of the sensor and the result judgment, which is the basic condition for detecting hybridization of nucleic acid. In this study, we detected the hybridization of HPV PCR products during temperature change process by a self-designed adjustable metal-clamping piezoelectric sensor. The study mainly involves sensor adjustment, probe immobilization and ice bath sample addition (at different concentrations and different volumes). The response curve of basic frequency in temperature change process showed three stages, i.e., increase, decrease to baseline, and continuous decrease to stability. The early increase of frequency and duration of the time can reach 55+/-7.4 Hz and 39 min when 40 microL sample (0-1 degrees C) was added into 110 microL buffer (25 degrees C). The frequency increase effect caused by temperature difference at early stage depends on the volume ratio of two liquids and on the temperature difference. The results indicate that we should pay more attention to possibly small volume of PCR products in ice bath and minor temperature difference of two liquids in operation. 2010 Elsevier B.V. All rights reserved.

  6. Gauging the Nanotoxicity of h2D-C2N toward Single-Stranded DNA: An in Silico Molecular Simulation Approach.

    Science.gov (United States)

    Mukhopadhyay, Titas Kumar; Bhattacharyya, Kalishankar; Datta, Ayan

    2018-04-12

    Recent toxicological assessments of graphene, graphene oxides, and some other two-dimensional (2D) materials have shown them to be substantially toxic at the nanoscale, where they inhibit and eventually disrupt biological processes. These shortfalls of graphene and analogs have resulted in a quest for novel biocompatible 2D materials with minimum cytotoxicity. In this article, we demonstrate C 2 N (h2D-C 2 N), a newly synthesized 2D porous graphene analog, to be non-nanotoxic toward genetic materials from an "in-silico" point of view through sequence-dependent binding of different polynucleotide single-stranded DNA (ssDNA) onto it. The calculated binding energy of nucleobases and the free energy of binding of polynucleotides follow the common trait, cytosine > guanine > adenine > thymine, and are well within the limits of physisorption. Ab-initio simulations completely exclude the possibility of any chemical reaction, demonstrating purely noncovalent binding of nucleobases with C 2 N through a crucial interplay between hydrogen bonding and π-stacking interactions with the surface. Further, we show that the extent of distortion inflicted upon ssDNA by C 2 N is negligible. Analysis of the density of states of the nucleobase-C 2 N hybrids confirms minimum electronic perturbation of the bases after adsorption. Most importantly, we demonstrate the potency of C 2 N in nucleic acid transportation via reversible binding of ssDNA. The plausible use of C 2 N as a template for DNA repair is illustrated through an example of C 2 N-assisted complementary ssDNA winding.

  7. Characterization of isolates of Citrus tristeza virus by sequential analyses of enzyme immunoassays and capillary electrophoresis-single-strand conformation polymorphisms.

    Science.gov (United States)

    Licciardello, G; Raspagliesi, D; Bar-Joseph, M; Catara, A

    2012-05-01

    Citrus tristeza virus (CTV) is the causal agent of tristeza disease, which is one of the most devastating diseases of citrus crops worldwide. This paper describes a method for the rapid detection and genotyping of naturally spreading CTV isolates. This method uses ELISA or dot-blot immunological tests to detect trees infected with CTV. The reaction wells or membrane spots for which there is a positive reaction are sequentially treated by (i) washing and elution of viral RNA from the trapped samples, (ii) one-step synthesis of cDNA and PCR and (iii) automated fluorescence-based capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis of amplification products. Comparative CE-SSCP results are presented for CTV RNA extracted directly from infected leaves and ELISA plates or from membranes. In the analyses of all of these RNA samples, the p18, p27 and p23 CTV genes were targeted for amplification. Specific profiles of forward and reverse strands were obtained from a group of eight CTV isolates collected in Sicily, each with distinct biological characteristics, which were analyzed using the conventional two-step procedure (immunological detection followed by CE-SSCP molecular characterization after RNA isolation) or in a continuous process of ELISA/CE-SSCP or dot-blot/CE-SSCP starting from infected plant material. The combined method is simple, highly sensitive and reproducible, thus allowing the processing of numerous field samples for a variety of epidemiological needs. The sequential processing of an ELISA or dot-blot/ELISA followed by CE-SSCP is expected to allow the rapid detection of recent CTV infections along with the simultaneous characterization of the genetic diversity and structure of the population of newly invading CTV. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Single-stranded DNA fragments of insect-specific nuclear polyhedrosis virus act as selective DNA insecticides for gypsy moth control.

    Science.gov (United States)

    Oberemok, Volodymyr V; Skorokhod, Oleksii A

    2014-07-01

    This paper focuses on the DNA insecticides as a novel preparation against gypsy moth (Lymantria dispar) based on DNA fragments of the anti-apoptotic gene of its nuclear polyhedrosis virus. It was found that the external application of a solution with two single-stranded DNA fragments from BIR and RING domains of LdMNPV (L.dispar multicapsid nuclear polyhedrosis virus) IAP-3 (inhibitor of apoptosis) gene induces a significantly higher mortality of gypsy moth caterpillars in comparison with the application of the control solutions. This effect does not depend on the infection of caterpillars with LdMNPV. The results also show that DNA insecticides based on LdMNPV IAP-3 gene fragments can be selective in action, and at least are not harmful to tobacco hornworm (Manduca sexta) and black cutworm (Agrotis ipsilon). Part of the gypsy moth genome cloned with the fragments of BIR and RING domains of LdMNPV IAP-3 gene as primers, has an overlap with the corresponding part of the LdMNPV IAP-3 gene and L.dispar IAP-1 mRNA for an inhibitor of apoptosis protein with the high cover by query, allows assuming that we cloned a part of gypsy moth anti-apoptosis gene. This finding gives the grounding that proposed here DNA insecticides might act through the blocking of the mechanisms involved in post transcriptional expression of insect anti-apoptosis genes. The results show the insecticidal potential of the viral genome fragments that can be used to create safe and relatively fast-acting DNA insecticides to control the quantity of gypsy moth populations, important task for forestry and agriculture. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha

    2010-04-06

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. BOREAS TF-01 SSA-OA Soil Characteristics Data

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: Data collected in support of the effort to characterize and interpret soil information at the SSA-OA tower site in 1994. Data collected include soil...

  11. BOREAS TF-01 SSA-OA Soil Characteristics Data

    Data.gov (United States)

    National Aeronautics and Space Administration — Data collected in support of the effort to characterize and interpret soil information at the SSA-OA tower site in 1994. Data collected include soil respiration,...

  12. TiSSA eelkonverents doktorantidele Tallinnas / Koidu Saame

    Index Scriptorium Estoniae

    Saame, Koidu

    2010-01-01

    Tallinna Ülikoolis toimunud TiSSA doktorantide eelkonverentsist 22.-24. aug. 2010.a. Doktorantide ettekannetest. Esinesid: Hans-Uwe Otto, Andriy Yuryev, Tiina Naarits, Ivar Tröner, Koidu Saame, Maija Jäppinen, Janissa Miettinen

  13. BOREAS TE-18 Biomass Density Image of the SSA

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This biomass density image covers almost the entire BOREAS SSA. The pixels for which biomass density is computed include areas that are in conifer land...

  14. BOREAS TE-18 Biomass Density Image of the SSA

    Data.gov (United States)

    National Aeronautics and Space Administration — This biomass density image covers almost the entire BOREAS SSA. The pixels for which biomass density is computed include areas that are in conifer land cover classes...

  15. Data over the SSA in Raster Format and AEAC Projection

    Data.gov (United States)

    National Aeronautics and Space Administration — GIS layers that describe the soils of the BOREAS SSA. Original data were submitted as vector layers that were then gridded by BOREAS staff to a 30-meter pixel size...

  16. Data over the SSA in Raster Format and AEAC Projection

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: GIS layers that describe the soils of the BOREAS SSA. Original data were submitted as vector layers that were then gridded by BOREAS staff to a 30-meter...

  17. The Critical Role of Experimentation to Further SSA Understanding

    Science.gov (United States)

    Donnelly, P.; Ash, A.

    2016-09-01

    Dstl has developed an approach to explore the challenges of understanding the fundamental principles of SSA through the design and execution of a series of national and international SSA experiments conducted since 2008. These have involved a number of nations within different multi-lateral constructs (such as Combined Space Operations [CSPO] and NATO), and have also served as test case scenarios in support of international SSA research collaboration. It has been found that this experimentally-driven approach has been successful in linking government R&D activities to actual operations with UK MOD; enabling enhanced cooperation with academia through the provision of access to sensors and data; as well as an understanding of the operational imperatives and constraints, not usually available or apparent to these institutions. The experiences of the Dstl team over the past 8 years have yielded a number of lessons learnt that we believe the wider international community would benefit from in relation to effective SSA operations, including how to generate closer relationships between communities across government, industry, academia and operators. This paper describes the overall Dstl approach to a series of SSA experiments designed to inform the UK MOD on the challenges and potential technical solutions related to SSA mission areas. It includes details of the participants, design and execution; and illustrates some major findings of each event to date. Lessons learnt pertinent to the AMOS and wider SSA community are presented that will inform the audience on how this approach may be adopted to meet other SSA scenarios. Finally, it presents the UK roadmap for future experiments identified as possible activities under the CSPO initiative and the EU Space Surveillance and Tracking programme.

  18. Nitrogen Adsorption on Graphene Sponges Synthesized by Annealing a Mixture of Nickel and Carbon Powders

    Directory of Open Access Journals (Sweden)

    Grehov V.

    2017-08-01

    Full Text Available Adsorption by graphene sponge (GS manufactured by annealing nickel-carbon powder mixture in inert atmosphere has been studied. By determining the specific surface area (SSA for the GS sample, it has been found that Brunauer, Emmett, Teller method (BET of approximation of experimental isotherms gives wrong results in the pressure range of 0.025–0.12 because adsorption in this pressure region is affected by walls of ampoule. Real SSA value has been found by subtracting pore effect method (SPE or by BET approximation in a low range of relative pressure of 0.0004–0.002.

  19. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Galeano, Carlos H; Fernández, Andrea C; Gómez, Marcela; Blair, Matthew W

    2009-12-23

    Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation

  20. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Gómez Marcela

    2009-12-01

    Full Text Available Abstract Background Expressed sequence tags (ESTs are an important source of gene-based markers such as those based on insertion-deletions (Indels or single-nucleotide polymorphisms (SNPs. Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs, to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction

  1. Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans-Expression and characterization.

    Directory of Open Access Journals (Sweden)

    Marcin Olszewski

    Full Text Available DNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the Taq DNA Stoffel domain and a single-stranded DNA binding-like protein of Nanoarchaeum equitans in order to significantly improve the properties of DNA polymerase. The DNA coding sequence of Taq Stoffel DNA polymerase and the nonspecific DNA-binding protein of Nanoarchaeum equitans (NeqSSB-like protein were fused. A novel recombinant gene was obtained which was cloned into the pET-30 Ek/LIC vector and introduced into E. coli for expression. The recombinant enzyme was purified and its enzymatic properties including DNA polymerase activity, PCR amplification rate, thermostability, processivity and resistance to inhibitors, were tested. The yield of the target protein reached approximately 18 mg/l after 24 h of the IPTG induction. The specific activity of the polymerase was 2200 U/mg. The recombinant NeqSSB-TaqS exhibited a much higher extension rate (1000 bp template in 20 s, processivity (19 nt, thermostability (half-life 35 min at 95°C and higher tolerance to PCR inhibitors (0.3-1.25% of whole blood, 0.84-13.5 μg of lactoferrin and 4.7-150 ng of heparin than Taq Stoffel DNA polymerase. Furthermore, our studies show that NeqSSB-TaqS DNA polymerase has a high level of flexibility in relation to Mg2+ ions (from 1 to 5 mM and KCl or (NH42SO4 salts (more than 60 mM and 40 mM, respectively. Using NeqSSB-TaqS DNA polymerase instead of the Taq DNA polymerase could be a better choice in many PCR applications.

  2. Contribution of single-strand breaks and alkali-labile bonds to the loss of infectivity of γ-irradiated phiX174 RF-DNA in E. coli cells mutant in various repair functions

    International Nuclear Information System (INIS)

    McKee, R.H.

    1975-01-01

    Twenty-one radiation sensitive mutants have been examined for their capacity to support gamma-irradiated phiX174 RF-DNA. The survival of phiX174 RF-DNA was reduced in essentially all of the sensitive mutants. The irradiated phiX174 RF-DNA was then separated into populations containing either single-strand breaks or alkali-labile bonds to examine the capacity of the mutants to repair each of the classes of lesions. It was found that all E. coli strains are unable to repair 22 percent of the single-strand breaks and all sensitive mutants are unable to repair an additional 10 percent of the breaks. All the repair functions examined are involved in single-strand break repair and none are more or less necessary than any of the others. PhiX174 RF-DNA is also inactivated by alkali-labile bonds. In the normal strains the inactivation efficiency is 0.16 lethal events per lesion with a threshold dose of 15 to 20 krads. The mutants are divided into two classes by their sensitivity to alkali-labile bonds. Both classes of mutants are also inactivated by alkali-labile bonds with efficiencies of about 0.17 and 0.29 lethal events per lesion, respectively. It is proposed that the differences seen in survival curves of phiX174 measured in the sensitive mutants is due to this difference. Although in normal cells the efficiency of inactivation of phiX174 by single-strand breaks is 50 percent greater than by alkali-labile bonds, alkali-labile bonds are produced at approximately twice the rate of single-strand breaks so alkali-labile bonds account for about 61 percent of the overall inactivation. In the mutants of least sensitivity alkali-labile bonds account for about 54 percent of the inactivating events and in the most sensitive about 67 percent

  3. The colour potentials of SSA-containing mortar:the long version

    OpenAIRE

    Kappel, Annemette; Ottosen, Lisbeth M.; Kirkelund, Gunvor Marie; Bache, Anja Margrethe; Goltermann, Per

    2015-01-01

    This paper reports an experimental study of aesthetical qualities of mortar containing sewage sludgeash (SSA). SSA is the residue produced at water treatment plants where incineration of the sludge is applied in order to decrease volume and to prevent pathogens from spreading. Today SSA is with a few exceptions landfilled and thus, wasted.The purpose of the experiments was to examine the influence of SSA and how it affected the colour of mortar samples. SSA was ground in 6 different intervals...

  4. Clinical and Pathological Roles of Ro/SSA Autoantibody System

    Directory of Open Access Journals (Sweden)

    Ryusuke Yoshimi

    2012-01-01

    Full Text Available Anti-Ro/SSA antibodies are among the most frequently detected autoantibodies against extractable nuclear antigens and have been associated with systemic lupus erythematosus (SLE and Sjögren's syndrome (SS. Although the presence of these autoantibodies is one of the criteria for the diagnosis and classification of SS, they are also sometimes seen in other systemic autoimmune diseases. In the last few decades, the knowledge of the prevalence of anti-Ro/SSA antibodies in various autoimmune diseases and symptoms has been expanded, and the clinical importance of these antibodies is increasing. Nonetheless, the pathological role of the antibodies is still poorly understood. In this paper, we summarize the milestones of the anti-Ro/SSA autoantibody system and provide new insights into the association between the autoantibodies and the pathogenesis of autoimmune diseases.

  5. Arctic Region Space Weather Customers and SSA Services

    DEFF Research Database (Denmark)

    Høeg, Per; Kauristi, Kirsti; Wintoft, Peter

    and communication can be established without errors resulting from Space Weather effects. An ESA project have identified and clarified, how the products of the four ESA Space Weather Expert Service Centres (SWE) in the ESA Space Situational Awareness Programme (SSA), can contribute to the requirements of SSA...... services in Arctic, and how new products and services need to be developed and implemented in the roadmap of SWE for Arctic region network services. An important element in the project is the end-user requirements and needs in the public and commercial sector. A detailed user-survey and interviews with key......-companies in the region have been performed. The outcome has been analysed in view of the present SWE system, and products and suggestions to a roadmap for the development of coming Arctic region SSA services, have been established....

  6. Characterization of a Novel Megabirnavirus from Sclerotinia sclerotiorum Reveals Horizontal Gene Transfer from Single-Stranded RNA Virus to Double-Stranded RNA Virus.

    Science.gov (United States)

    Wang, Minghong; Wang, Yong; Sun, Xiangzhong; Cheng, Jiasen; Fu, Yanping; Liu, Huiquan; Jiang, Daohong; Ghabrial, Said A; Xie, Jiatao

    2015-08-01

    Mycoviruses have been detected in all major groups of filamentous fungi, and their study represents an important branch of virology. Here, we characterized a novel double-stranded RNA (dsRNA) mycovirus, Sclerotinia sclerotiorum megabirnavirus 1 (SsMBV1), in an apparently hypovirulent strain (SX466) of Sclerotinia sclerotiorum. Two similarly sized dsRNA segments (L1- and L2-dsRNA), the genome of SsMBV1, are packaged in rigid spherical particles purified from strain SX466. The full-length cDNA sequence of L1-dsRNA/SsMBV1 comprises two large open reading frames (ORF1 and ORF2), which encode a putative coat protein and an RNA-dependent RNA polymerase (RdRp), respectively. Phylogenetic analysis of the RdRp domain clearly indicates that SsMBV1 is related to Rosellinia necatrix megabirnavirus 1 (RnMBV1). L2-dsRNA/SsMBV1 comprises two nonoverlapping ORFs (ORFA and ORFB) encoding two hypothetical proteins with unknown functions. The 5'-terminal regions of L1- and L2-dsRNA/SsMBV1 share strictly conserved sequences and form stable stem-loop structures. Although L2-dsRNA/SsMBV1 is dispensable for replication, genome packaging, and pathogenicity of SsMBV1, it enhances transcript accumulation of L1-dsRNA/SsMBV1 and stability of virus-like particles (VLPs). Interestingly, a conserved papain-like protease domain similar to a multifunctional protein (p29) of Cryphonectria hypovirus 1 was detected in the ORFA-encoded protein of L2-dsRNA/SsMBV1. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer may have occurred from a single-stranded RNA (ssRNA) virus (hypovirus) to a dsRNA virus, SsMBV1. Our results reveal that SsMBV1 has a slight impact on the fundamental biological characteristics of its host regardless of the presence or absence of L2-dsRNA/SsMBV1. Mycoviruses are widespread in all major fungal groups, and they possess diverse genomes of mostly ssRNA and dsRNA and, recently, circular ssDNA. Here, we have characterized a novel dsRNA virus

  7. RecO protein initiates DNA recombination and strand annealing through two alternative DNA binding mechanisms.

    Science.gov (United States)

    Ryzhikov, Mikhail; Gupta, Richa; Glickman, Michael; Korolev, Sergey

    2014-10-17

    Recombination mediator proteins (RMPs) are important for genome stability in all organisms. Several RMPs support two alternative reactions: initiation of homologous recombination and DNA annealing. We examined mechanisms of RMPs in both reactions with Mycobacterium smegmatis RecO (MsRecO) and demonstrated that MsRecO interacts with ssDNA by two distinct mechanisms. Zinc stimulates MsRecO binding to ssDNA during annealing, whereas the recombination function is zinc-independent and is regulated by interaction with MsRecR. Thus, different structural motifs or conformations of MsRecO are responsible for interaction with ssDNA during annealing and recombination. Neither annealing nor recombinase loading depends on MsRecO interaction with the conserved C-terminal tail of single-stranded (ss) DNA-binding protein (SSB), which is known to bind Escherichia coli RecO. However, similarly to E. coli proteins, MsRecO and MsRecOR do not dismiss SSB from ssDNA, suggesting that RMPs form a complex with SSB-ssDNA even in the absence of binding to the major protein interaction motif. We propose that alternative conformations of such complexes define the mechanism by which RMPs initiate the repair of stalled replication and support two different functions during recombinational repair of DNA breaks. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Preliminary approach of the MELiSSA loop energy balance

    Science.gov (United States)

    Poulet, Lucie; Lamaze, Brigitte; Lebrun, Jean

    Long duration missions, such as the establishment of permanent bases on the lunar surface or the travel to Mars, require a huge amount of life support consumables (e.g. food, water and oxygen). Current rockets are at the moment unable to launch such a mass from Earth. Consequently Regenerative Life Support Systems are necessary to sustain long-term manned space mission to increase recycling rates and so reduce the launched mass. Thus the European and Canadian research has been concentrating on the MELiSSA (Micro-Ecological Life Support System Alternative) project over the last 20 years. MELiSSA is an Environmental Controlled Life Support System (ECLSS), i.e. a closed regenerative loop inspired of a lake ecosystem. Using light as a source of energy, MELiSSA's goal is the recovery of food, water and oxygen from CO2 and organic wastes, using microorganisms and higher plants. The architecture of a ECLSS depends widely on the mission scenario. To compare several ECLSS architectures and in order to be able to evaluate them, ESA is developing a multi criteria evaluation tool: ALISSE (Advanced LIfe Support System Evaluator). One of these criteria is the energy needed to operate the ECLSS. Unlike other criteria like the physical mass, the energy criterion has not been investigated yet and needs hence a detailed analysis. It will consequently be the focus of this study. The main objective of the work presented here is to develop a dynamic tool able to estimate the energy balance for several configurations of the MELiSSA loop. The first step consists in establishing the energy balance using concrete figures from the MELiSSA Pilot Plant (MPP). This facility located at the Universitat Autonoma de Barcelona (UAB) is aimed at the ground demonstration of the MELiSSA loop. The MELiSSA loop is structured on several subsystems; each of them is characterized by supplies, exhausts and process reactions. For the purpose of this study (i.e. a generic tool) the solver EES (Engineering

  9. The application of strand invasion phenomenon, directed by peptide nucleic acid (PNA) and single-stranded DNA binding protein (SSB) for the recognition of specific sequences of human endogenous retroviral HERV-W family.

    Science.gov (United States)

    Machnik, Grzegorz; Bułdak, Łukasz; Ruczyński, Jarosław; Gąsior, Tomasz; Huzarska, Małgorzata; Belowski, Dariusz; Alenowicz, Magdalena; Mucha, Piotr; Rekowski, Piotr; Okopień, Bogusław

    2017-05-01

    The HERV-W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV-W-derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin-1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV-W members is highly desirable. A peptide nucleic acid (PNA)-mediated technique for the discrimination between multiple sclerosis-associated retrovirus and ERVWE1 sequence has been developed. The assay uses a PNA probe that, being fully complementary to the ERVWE1 but not to multiple sclerosis-associated retrovirus (MSRV) template, shows high selective potential. Single-stranded DNA binding protein facilitates the PNA-mediated, sequence-specific formation of strand invasion complex and, consequently, local DNA unwinding. The target DNA may be then excluded from further analysis in any downstream process such as single-stranded DNA-specific exonuclease action. Finally, the reaction conditions have been optimized, and several PNA probes that are targeted toward distinct loci along whole HERV-W env sequences have been evaluated. We believe that PNA/single-stranded DNA binding protein-based application has the potential to selectively discriminate particular HERV-W molecules as they are at least suspected to play pathogenic role in a broad range of medical conditions, from psycho-neurologic disorders (multiple sclerosis and schizophrenia) and cancers (breast cancer) to that of an auto-immunologic background (psoriasis and lupus erythematosus). Copyright © 2016 John Wiley & Sons, Ltd.

  10. Application of Single Strand Conformational Polymorphism (PCR-SSCP) in Identification of Some Beta-Globin Gene Mutations in A Group of Egyptian Beta-Thalassemia Patients and Carriers

    International Nuclear Information System (INIS)

    Somaya, E.T.; Soliman, M.D

    2010-01-01

    The present study investigated whether the single-strand conformational polymorphism (SSCP) method could be employed to identify (rather than simply detect) four of the most common beta-globin gene mutations in the Egyptian population: IVS-I-110, IVS-I-6, the IVS-I-1, and Codon 39. Using DNA from 90 beta-thalassemia patients and carriers, by PCR the appropriate 238-bp region of the human beta-globin gene was amplified, the reaction products (Single-stranded DNA) were analyzed by none denaturing polyacrylamide gel electrophoresis, and the bands visualized by silver staining. Single-stranded DNA (ssDNA) fragments showed reproducible pattern of bands that were characteristic of the mutations present. With the use of control samples containing six of the 10 possible combinations of the four beta-globin gene mutations under study, we were able to predict the mutations present in 23 out of 90 (26.4%) of the patients studied. These predictions were confirmed independently by the amplification refractory mutation system (ARMS) method. It is concluded that this non-radioactive PCR-SSCP method can be used to reliably identify mutations in beta-thalassemia patients, provided that suitable controls are available. However, usefulness of this method for determining the genotype of beta-thalassaemic individuals is obviously limited by the great number of controls required. Moreover, the ability to detect mutations by SSCP is in general lower compared to other methods, ARMS, DGGE or DHPLC, which are reported to detect 49.5% to 73% of the mutations present. The SSCP method is nevertheless much easier to employ than other methods and is especially successful for beta-thalassemia carriers. This method would thus be particularly useful for an initial screening of target groups (prenatal diagnosis)

  11. Increased type I collagen content and DNA binding activity of a single-stranded, cytosine-rich sequence in the high-salt buffer protein extract of the copper-deficient rat heart.

    Science.gov (United States)

    Zeng, Huawei; Saari, Jack T

    2004-11-01

    Dietary copper (Cu) deficiency not only causes a hypertrophic cardiomyopathy but also increases cancer risk in rodent models. However, a possible alteration in gene expression has not been fully examined. The present study was undertaken to determine the effect of Cu deficiency on protein profiles in rat heart tissue. Male Sprague-Dawley rats were fed diets that were either a Cu-adequate diet (6.0 microg Cu/g diet, n = 6) or a Cu-deficient diet (0.3 microg Cu/g diet, n = 6) for 5 weeks. The high-salt buffer (HSB) protein extract from heart tissue of Cu-deficient, but not Cu-adequate rats showed a 132 kDa protein band by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. This protein band stained pink with Coomassie Blue, suggesting the presence of collagens or other proline-rich proteins. Dot immunoblotting demonstrated that total type I collagen was increased by 110% in HSB protein extract from Cu-deficient, relative to Cu-adequate, rats. Liquid chromatography with mass spectrometry analysis indicated that the 132 kDa protein band contained a collagen alpha (I) chain precursor as well as a leucine-rich protein 130 (LRP130) in HSB protein extract from Cu-deficient but not Cu-adequate rats. A gel shift assay showed that HSB protein extract from Cu-deficient rats bound to a single-stranded cytosine-rich DNA with higher affinity than the extract of Cu-adequate rats, similar to reports of an increase in LRP130 single-stranded DNA binding activity in several types of tumor cells. Collectively, these results not only suggest an additional feature of altered collagen metabolism with Cu deficiency but also demonstrate for the first time an increase in single-stranded cytosine-rich DNA binding in Cu-deficient rat heart.

  12. Protective effects of pulmonary epithelial lining fluid on oxidative stress and DNA single-strand breaks caused by ultrafine carbon black, ferrous sulphate and organic extract of diesel exhaust particles

    Energy Technology Data Exchange (ETDEWEB)

    Chuang, Hsiao-Chi [School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan (China); Cheng, Yi-Ling; Lei, Yu-Chen [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Chang, Hui-Hsien [Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Cheng, Tsun-Jen, E-mail: tcheng@ntu.edu.tw [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China)

    2013-02-01

    Pulmonary epithelial lining fluid (ELF) is the first substance to make contact with inhaled particulate matter (PM) and interacts chemically with PM components. The objective of this study was to determine the role of ELF in oxidative stress, DNA damage and the production of proinflammatory cytokines following physicochemical exposure to PM. Ultrafine carbon black (ufCB, 15 nm; a model carbonaceous core), ferrous sulphate (FeSO{sub 4}; a model transition metal) and a diesel exhaust particle (DEP) extract (a model organic compound) were used to examine the acellular oxidative potential of synthetic ELF and non-ELF systems. We compared the effects of exposure to ufCB, FeSO{sub 4} and DEP extract on human alveolar epithelial Type II (A549) cells to determine the levels of oxidative stress, DNA single-strand breaks and interleukin-8 (IL-8) production in ELF and non-ELF systems. The effects of ufCB and FeSO{sub 4} on the acellular oxidative potential, cellular oxidative stress and DNA single-strand breakage were mitigated significantly by the addition of ELF, whereas there was no decrease following treatment with the DEP extract. There was no significant effect on IL-8 production following exposure to samples that were suspended in ELF/non-ELF systems. The results of the present study indicate that ELF plays an important role in the initial defence against PM in the pulmonary environment. Experimental components, such as ufCB and FeSO{sub 4}, induced the production of oxidative stress and led to DNA single-strand breaks, which were moderately prevented by the addition of ELF. These findings suggest that ELF plays a protective role against PM-driven oxidative stress and DNA damage. -- Highlights: ► To determine the role of ELF in ROS, DNA damage and IL-8 after exposure to PM. ► ufCB, FeSO{sub 4} and DEP extract were used to examine the protective effects of ELF. ► PM-driven oxidative stress and DNA single-strand breakage were mitigated by ELF. ► The findings

  13. Ro60-associated single-stranded RNA links inflammation with fetal cardiac fibrosis via ligation of TLRs: a novel pathway to autoimmune-associated heart block.

    Science.gov (United States)

    Clancy, Robert M; Alvarez, David; Komissarova, Elena; Barrat, Franck J; Swartz, Jordan; Buyon, Jill P

    2010-02-15

    Activation of TLR by ssRNA after FcgammaR-mediated phagocytosis of immune complexes (IC) may be relevant in autoimmune-associated congenital heart block (CHB) where the obligate factor is a maternal anti-SSA/Ro Ab and the fetal factors, protein/RNA on an apoptotic cardiocyte and infiltrating macrophages. This study addressed the hypothesis that Ro60-associated ssRNAs link macrophage activation to fibrosis via TLR engagement. Both macrophage transfection with noncoding ssRNA that bind Ro60 and an IC generated by incubation of Ro60-ssRNA with an IgG fraction from a CHB mother or affinity purified anti-Ro60 significantly increased TNF-alpha secretion, an effect not observed using control RNAs or normal IgG. Dependence on TLR was supported by the significant inhibition of TNF-alpha release by IRS661 and chloroquine. The requirement for FcgammaRIIIa-mediated delivery was provided by inhibition with an anti-CD16a Ab. Fibrosis markers were noticeably increased in fetal cardiac fibroblasts after incubation with supernatants generated from macrophages transfected with ssRNA or incubated with the IC. Supernatants generated from macrophages with ssRNA in the presence of IRS661 or chloroquine did not cause fibrosis. In a CHB heart, but not a healthy heart, TLR7 immunostaining was localized to a region near the atrioventricular groove at a site enriched in mononuclear cells and fibrosis. These data support a novel injury model in CHB, whereby endogenous ligand, Ro60-associated ssRNA, forges a nexus between TLR ligation and fibrosis instigated by binding of anti-Ro Abs to the target protein likely accessible via apoptosis.

  14. 20 CFR 411.630 - Is SSA's decision final?

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Is SSA's decision final? 411.630 Section 411.630 Employees' Benefits SOCIAL SECURITY ADMINISTRATION THE TICKET TO WORK AND SELF-SUFFICIENCY PROGRAM Ticket to Work Program Dispute Resolution Disputes Between Beneficiaries and Employment Networks § 411...

  15. 20 CFR 411.660 - Is SSA's decision final?

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Is SSA's decision final? 411.660 Section 411.660 Employees' Benefits SOCIAL SECURITY ADMINISTRATION THE TICKET TO WORK AND SELF-SUFFICIENCY PROGRAM Ticket to Work Program Dispute Resolution Disputes Between Employment Networks and Program Managers § 411...

  16. Evaluating Options for Civil Space Situational Awareness (SSA)

    Science.gov (United States)

    Lal, B.; Carioscia, S. A.

    In recent years, the number of active satellites and human-made orbital space debris has increased dramatically. An expansion of activities in space, as is currently being proposed by many commercial and international entities, is expected to further exacerbate this challenge. The 18th Space Control Squadron under the Department of Defense (DOD) United States Strategic Command provides space situational awareness (SSA) services to users outside the national security community at no cost. International and commercial users demand better SSA service than is currently feasible, and the demand comes at a time when DOD is under pressure to better prepare for and respond to growing space-based threats to national security. Concerned about the possibility of overextending across conflicting missions in a fiscally constrained environment, some DOD officials have publicly noted a desire to move SSA services not related to national security out of DOD purview. Responding to a request from the Federal Aviation Administration (FAA) Office of Commercial Space Transportation (AST), researchers at the Science and Technology Policy Institute (STPI) identified and evaluated potential approaches for providing SSA services for civil and commercial operations in space. In this paper, we summarize the report [1] and present the pros and cons of four approaches to the provision of civil SSA services in the United States: (1) maintaining status quo through continued provision by DOD; (2) provision by a civil government entity; (3) industry self-provision; and (4) provision by an international organization. Within the second approach, assuming the provision of SSA by a civil agency, STPI further identified and discussed four options: (1) civil agency service capability embedded within DOD; (2) independent civil service capability, using DOD software and systems; (3) independent civil service capability, using commercial software and systems; and (4) the government certifies non

  17. Non-traditional Sensor Tasking for SSA: A Case Study

    Science.gov (United States)

    Herz, A.; Herz, E.; Center, K.; Martinez, I.; Favero, N.; Clark, C.; Therien, W.; Jeffries, M.

    Industry has recognized that maintaining SSA of the orbital environment going forward is too challenging for the government alone. Consequently there are a significant number of commercial activities in various stages of development standing-up novel sensors and sensor networks to assist in SSA gathering and dissemination. Use of these systems will allow government and military operators to focus on the most sensitive space control issues while allocating routine or lower priority data gathering responsibility to the commercial side. The fact that there will be multiple (perhaps many) commercial sensor capabilities available in this new operational model begets a common access solution. Absent a central access point to assert data needs, optimized use of all commercial sensor resources is not possible and the opportunity for coordinated collections satisfying overarching SSA-elevating objectives is lost. Orbit Logic is maturing its Heimdall Web system - an architecture facilitating “data requestor” perspectives (allowing government operations centers to assert SSA data gathering objectives) and “sensor operator” perspectives (through which multiple sensors of varying phenomenology and capability are integrated via machine -machine interfaces). When requestors submit their needs, Heimdall’s planning engine determines tasking schedules across all sensors, optimizing their use via an SSA-specific figure-of-merit. ExoAnalytic was a key partner in refining the sensor operator interfaces, working with Orbit Logic through specific details of sensor tasking schedule delivery and the return of observation data. Scant preparation on both sides preceded several integration exercises (walk-then-run style), which culminated in successful demonstration of the ability to supply optimized schedules for routine public catalog data collection – then adapt sensor tasking schedules in real-time upon receipt of urgent data collection requests. This paper will provide a

  18. The early UL31 gene of equine herpesvirus 1 encodes a single-stranded DNA-binding protein that has a nuclear localization signal sequence at the C-terminus

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seongman; Chul Ahn, Byung; O' Callaghan, Dennis J. [Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Louisiana State University Health Sciences Center, Shreveport, LA 71130-3932 (United States); Kim, Seong Kee, E-mail: skim1@lsuhsc.edu [Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Louisiana State University Health Sciences Center, Shreveport, LA 71130-3932 (United States)

    2012-10-25

    The amino acid sequence of the UL31 protein (UL31P) of equine herpesvirus 1 (EHV-1) has homology to that of the ICP8 of herpes simplex virus type 1 (HSV-1). Here we show that the UL31 gene is synergistically trans-activated by the IEP and the UL5P (EICP27). Detection of the UL31 RNA transcript and the UL31P in EHV-1-infected cells at 6 h post-infection (hpi) as well as metabolic inhibition assays indicated that UL31 is an early gene. The UL31P preferentially bound to single-stranded DNA over double-stranded DNA in gel shift assays. Subcellular localization of the green fluorescent protein (GFP)-UL31 fusion proteins revealed that the C-terminal 32 amino acid residues of the UL31P are responsible for the nuclear localization. These findings may contribute to defining the role of the UL31P single-stranded DNA-binding protein in EHV-1 DNA replication.

  19. A novel technique using DNA denaturation to detect multiply induced single-strand breaks in a hydrated plasmid DNA molecule by X-ray and 4He2+ ion irradiation

    International Nuclear Information System (INIS)

    Yokoya, A.; Shikazono, N.; Fujii, K.; Noguchi, M.; Urushibara, A.

    2011-01-01

    To detect multiple single-strand breaks (SSBs) produced in plasmid DNA molecules by direct energy deposition from radiation tracks, we have developed a novel technique using DNA denaturation by which irradiated DNA is analysed as single-strand DNA (SS-DNA). The multiple SSBs that arise in both strands of DNA, but do not induce a double-strand break, are quantified as loss of SS-DNA using agarose gel electrophoresis. We have applied this method to X-ray and 4 He 2+ ion-irradiated samples of fully hydrated pUC18 plasmid DNA. The fractions of both SS-DNA and closed circular DNA (CC-DNA) exponentially decrease with the increasing dose of X rays and 4 He 2+ ions. The efficiency of the loss of SS-DNA was half that of CC-DNA for both types of irradiation, indicating that one of two strands in DNA is not broken when one SSB is produced in CC-DNA by irradiation. Contrary to our initial expectation, these results indicate that SSBs are not multiply induced even by high linear energy transfer radiation distributed in both strands. (authors)

  20. The early UL31 gene of equine herpesvirus 1 encodes a single-stranded DNA-binding protein that has a nuclear localization signal sequence at the C-terminus

    International Nuclear Information System (INIS)

    Kim, Seongman; Chul Ahn, Byung; O’Callaghan, Dennis J.; Kim, Seong Kee

    2012-01-01

    The amino acid sequence of the UL31 protein (UL31P) of equine herpesvirus 1 (EHV-1) has homology to that of the ICP8 of herpes simplex virus type 1 (HSV-1). Here we show that the UL31 gene is synergistically trans-activated by the IEP and the UL5P (EICP27). Detection of the UL31 RNA transcript and the UL31P in EHV-1-infected cells at 6 h post-infection (hpi) as well as metabolic inhibition assays indicated that UL31 is an early gene. The UL31P preferentially bound to single-stranded DNA over double-stranded DNA in gel shift assays. Subcellular localization of the green fluorescent protein (GFP)–UL31 fusion proteins revealed that the C-terminal 32 amino acid residues of the UL31P are responsible for the nuclear localization. These findings may contribute to defining the role of the UL31P single-stranded DNA-binding protein in EHV-1 DNA replication.

  1. The Ro/SSA Complex in Systemic Lupus Erythematosus Patients

    OpenAIRE

    Do Nascimento, Noelle Mariane

    2017-01-01

    In this work the involved mechanisms between Ro/SSA complex, composed also by the tripartite motif 21 (TRIM21alpha) and trove domain 2 (TROVE2) proteins, with respect to systemic lupus erythematosus (SLE) autoantibodies is studied. The work is divided in three chapters: I- In vitro and in silico analysis of the molecular recognition between lupus autoantibodies and TRIM21alpha Fc Receptor ; II- In vitro evidence of bipolar-bridged immune TROVE2 complexes in the pathogenesis of systemic lupus ...

  2. Systematic Sustainability Assessment (SSA) Tool for Hydroelectric Project in Malaysia

    Science.gov (United States)

    Turan, Faiz Mohd; Johan, Kartina

    2017-08-01

    Sustainably developed and managed hydropower has enormous potential to contribute to global sustainability goals. It is known that hydroelectricity contributing small amounts to greenhouse gas emissions and other atmospheric pollutants. However, developing the remaining hydroelectric potential offers many challenges, and public pressure and expectations on the environmental and social performance of hydroelectric tend to increase over time. This paper aims to develop Systematic Sustainability Assessment (SSA) Tool that promotes and guides more sustainable hydroelectric projects in the context of Malaysia. The proposed SSA tool which not only provide a quality and quantitative report of sustainability performance but also act as Self-Assessment Report (SAR) to provide roadmap to achieve greater level of sustainability in project management for continuous improvement. It is expected to provide a common language that allow government, civil society, financial institutions and the hydroelectric sector to talk about and evaluate sustainability issues. The advantage of SSA tool is it can be used at any stage of hydroelectric development, from the earliest planning stages right through to operation.

  3. HIV-1 nucleocapsid protein switches the pathway of transactivation response element RNA/DNA annealing from loop-loop "kissing" to "zipper".

    Science.gov (United States)

    Vo, My-Nuong; Barany, George; Rouzina, Ioulia; Musier-Forsyth, Karin

    2009-02-27

    The chaperone activity of HIV-1 (human immunodeficiency virus type 1) nucleocapsid protein (NC) facilitates multiple nucleic acid rearrangements that are critical for reverse transcription of the single-stranded RNA genome into double-stranded DNA. Annealing of the transactivation response element (TAR) RNA hairpin to a complementary TAR DNA hairpin is an essential step in the minus-strand transfer step of reverse transcription. Previously, we used truncated 27-nt mini-TAR RNA and DNA constructs to investigate this annealing reaction pathway in the presence and in the absence of HIV-1 NC. In this work, full-length 59-nt TAR RNA and TAR DNA constructs were used to systematically study TAR hairpin annealing kinetics. In the absence of NC, full-length TAR hairpin annealing is approximately 10-fold slower than mini-TAR annealing. Similar to mini-TAR annealing, the reaction pathway for TAR in the absence of NC involves the fast formation of an unstable "kissing" loop intermediate, followed by a slower conversion to an extended duplex. NC facilitates the annealing of TAR by approximately 10(5)-fold by stabilizing the bimolecular intermediate ( approximately 10(4)-fold) and promoting the subsequent exchange reaction ( approximately 10-fold). In contrast to the mini-TAR annealing pathway, wherein NC-mediated annealing can initiate through both loop-loop kissing and a distinct "zipper" pathway involving nucleation at the 3'-/5'-terminal ends, full-length TAR hairpin annealing switches predominantly to the zipper pathway in the presence of saturated NC.

  4. BOREAS TE-12 SSA Leaf Water Potential Data

    Science.gov (United States)

    Hall, Forrest G. (Editor); Curd, Shelaine (Editor); Walter-Shea, Elizabeth A.; Mesarch, Mark A.; Chen, L.; Yang, Litao

    2000-01-01

    The Boreal Ecosystem-Atmospheric Study (BOREAS) TE-12 (Terrestrial Ecology) team collected water potential data in 1993 and 1994 from aspen, jack pine, and black spruce leaves/needles. Collections were made at the Southern Study Area Nipawin Fen Site (SSA FEN), Young Jack Pine (YJP), Young Aspen (YA), Old Aspen (OA), and Old Black Spruce (OBS) sites. Measurements were made using a pressure chamber on a platform in the field. The data are provided in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  5. ESA's SSA Programme: Activities in Space Surveillance and Tracking

    Science.gov (United States)

    Flohrer, T.; Krag, H.

    Today, satellites and space-based systems are indispensable for the provision of critical services. Understanding and forecasting the space environment, especially space weather, near-Earth objects, and the population of space debris is needed to protect our space-based infrastructure. The rapidly growing number of smaller satellites and maturing plans for deploying large constellations of satellites further increase the need for reliable and timely information on the space object population. Since 2009 the European Space Agency (ESA) has been undertaking an Space Situational Awareness (SSA) Program with three segments Space Weather (SWE), Near Earth Objects (NEO) and Space Surveillance and Tracking (SST). Period 3 of the program has been approved at the ESA Ministerial Council in December 2016 for a 3-year period starting 2017. A total of 19 member states of ESA participate in the SSA program, of which 11 subscribed to the SST segment. In SST, the development of the technologies for detection, cataloguing and follow-up of space objects, and of the derived applications for conjunction event prediction, re-entry predictions, and fragmentation event detection are considered as the first important steps towards an European SST capability. To achieve this goal, ESA is focusing on research and development, supporting national initiatives, and staying complementary with other European approaches in SST. It is expected that in Europe a demand for larger, cross-national SST components and technology developments arises to ensure interoperability of systems. Examples of planned activities are space-based SST sensors, processing software, facilitating data exchange mechanisms, and common data processing techniques and formats. With the activities of the SSA program ESA’s expertise will be further exploited in supporting the research, development, and coordination of space-related technologies in a multinational environment, and in assessing and maturing the relevant

  6. Radiation annealing in cuprous oxide

    DEFF Research Database (Denmark)

    Vajda, P.

    1966-01-01

    Experimental results from high-intensity gamma-irradiation of cuprous oxide are used to investigate the annealing of defects with increasing radiation dose. The results are analysed on the basis of the Balarin and Hauser (1965) statistical model of radiation annealing, giving a square-root relati......Experimental results from high-intensity gamma-irradiation of cuprous oxide are used to investigate the annealing of defects with increasing radiation dose. The results are analysed on the basis of the Balarin and Hauser (1965) statistical model of radiation annealing, giving a square...

  7. BOREAS TE-1 SSA-Fen Soil Profile Nutrient Data

    Science.gov (United States)

    Papagno, Andrea; Anderson, Darwin; Newcomer, Jeffrey A. (Editor); Hall, Forrest G. (Editor)

    2000-01-01

    The BOREAS TE-1 team collected various data to characterize the soil-plant systems in the BOREAS SSA. Particular emphasis was placed on nutrient biochemistry, the stores and transfers of organic carbon, and how the characteristics were related to measured methane fluxes. The overall traniect in the Prince Albert National Park (Saskatchewan, Canada) included the major plant communities and related soils that occurred in that section of the boreal forest. Soil physical, chemical, and biological measurements along the transect were used to characterize the static environment, which allowed them to be related to methane fluxes. Chamber techniques were used to provide a measure of methane production/uptake. Chamber measurements coupled with flask sampling were used to determine the seasonality of methane fluxes. This particular data set contains soil profile measurements of various nutrients at the SSA-Fen site. The data were collected from 23-May to 21-Oct- 1994. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  8. Influence of alloying and secondary annealing on anneal hardening ...

    Indian Academy of Sciences (India)

    Unknown

    Influence of alloying and secondary annealing on anneal hardening effect at sintered copper alloys. SVETLANA NESTOROVIC. Technical Faculty Bor, University of Belgrade, Bor, Yugoslavia. MS received 11 February 2004; revised 29 October 2004. Abstract. This paper reports results of investigation carried out on sintered ...

  9. DOE's annealing prototype demonstration projects

    International Nuclear Information System (INIS)

    Warren, J.; Nakos, J.; Rochau, G.

    1997-01-01

    One of the challenges U.S. utilities face in addressing technical issues associated with the aging of nuclear power plants is the long-term effect of plant operation on reactor pressure vessels (RPVs). As a nuclear plant operates, its RPV is exposed to neutrons. For certain plants, this neutron exposure can cause embrittlement of some of the RPV welds which can shorten the useful life of the RPV. This RPV embrittlement issue has the potential to affect the continued operation of a number of operating U.S. pressurized water reactor (PWR) plants. However, RPV material properties affected by long-term irradiation are recoverable through a thermal annealing treatment of the RPV. Although a dozen Russian-designed RPVs and several U.S. military vessels have been successfully annealed, U.S. utilities have stated that a successful annealing demonstration of a U.S. RPV is a prerequisite for annealing a licensed U.S. nuclear power plant. In May 1995, the Department of Energy's Sandia National Laboratories awarded two cost-shared contracts to evaluate the feasibility of annealing U.S. licensed plants by conducting an anneal of an installed RPV using two different heating technologies. The contracts were awarded to the American Society of Mechanical Engineers (ASME) Center for Research and Technology Development (CRTD) and MPR Associates (MPR). The ASME team completed its annealing prototype demonstration in July 1996, using an indirect gas furnace at the uncompleted Public Service of Indiana's Marble Hill nuclear power plant. The MPR team's annealing prototype demonstration was scheduled to be completed in early 1997, using a direct heat electrical furnace at the uncompleted Consumers Power Company's nuclear power plant at Midland, Michigan. This paper describes the Department's annealing prototype demonstration goals and objectives; the tasks, deliverables, and results to date for each annealing prototype demonstration; and the remaining annealing technology challenges

  10. Radiation annealing in cuprous oxide

    DEFF Research Database (Denmark)

    Vajda, P.

    1966-01-01

    Experimental results from high-intensity gamma-irradiation of cuprous oxide are used to investigate the annealing of defects with increasing radiation dose. The results are analysed on the basis of the Balarin and Hauser (1965) statistical model of radiation annealing, giving a square...

  11. MELiSSA Food Characterization general approach and current status

    Science.gov (United States)

    Weihreter, Martin; Chaerle, Laury; Secco, Benjamin; Molders, Katrien; van der Straeten, Dominique; Duliere, Eric; Pieters, Serge; Maclean, Heather; Dochain, Denis; Quinet, Muriel; Lutts, Stanley; Graham, Thomas; Stasiak, Michael; Rondeau Vuk, Theresa; Zheng, Youbin; Dixon, Mike; Laniau, Martine; Larreture, Alain; Timsit, Michel; Aronne, Giovanna; Barbieri, Giancarlo; Buonomo, Roberta; Veronica; Paradiso, Roberta; de Pascale, Stafania; Galbiati, Massimo; Troia, A. R.; Nobili, Matteo; Bucchieri, Lorenzo; Page, Valérie; Feller, Urs; Lasseur, Christophe

    Higher plants play an important role in closed ecological life support systems as oxygen pro-ducers, carbon dioxide and water recyclers, and as a food source. For an integration of higher plant chambers into the MELiSSA (Micro Ecological Life Support System Alternative) loop, a detailed characterization and optimization of the full food production and preparation chain is needed. This implies the prediction and control of the nutritional quality of the final products consumed by the crew, the prediction of the wastes quality and quantity produced along the chain for further waste treatment (MELiSSA waste treatment) and the optimization of overall efficiencies. To reach this goal several issues have to be studied in an integrated manner: the physiological responses of crops to a range of environmental parameters, crop yield efficiencies and respective ratio and composition of edible and inedible biomass, the processability and storability of the produced food and last but not least composition of wastes in view of further degradation (fiber content). Within the Food Characterization (FC) project several compar-ative plant growth bench tests were carried out to obtain preliminary data regarding these aspects. Four pre-selected cultivars of each of the four energy-rich crops with worldwide usage -wheat, durum wheat, potato and soybean -were grown under well-characterized environmental conditions. The different cultivars of each species are screened for their performance in view of a closed loop application by parameter ranking. This comprises the characterization of edi-ble/inedible biomass ratio, nutritional quality, processability and overall performance under the specific conditions of hydroponic cultivation and artificial illumination. A second closely linked goal of the FC project is to develop a mechanistic physiological plant model, which will ease the integration of higher plants compartments in the MELiSSA concept by virtue of its predictive abilities

  12. Human Decision Processes: Implications for SSA Support Tools

    Science.gov (United States)

    Picciano, P.

    2013-09-01

    Despite significant advances in computing power and artificial intelligence (AI), few critical decisions are made without a human decision maker in the loop. Space Situational Awareness (SSA) missions are both critical and complex, typically adhering to the human-in-the-loop (HITL) model. The collection of human operators injects a needed diversity of expert knowledge, experience, and authority required to successfully fulfill SSA tasking. A wealth of literature on human decision making exists citing myriad empirical studies and offering a varied set of prescriptive and descriptive models of judgment and decision making (Hastie & Dawes, 2001; Baron, 2000). Many findings have been proven sufficiently robust to allow information architects or system/interface designers to take action to improve decision processes. For the purpose of discussion, these concepts are bifurcated in two groups: 1) vulnerabilities to mitigate, and 2) capabilities to augment. These vulnerabilities and capabilities refer specifically to the decision process and should not be confused with a shortcoming or skill of a specific human operator. Thus the framing of questions and orders, the automated tools with which to collaborate, priming and contextual data, and the delivery of information all play a critical role in human judgment and choice. Evaluating the merits of any decision can be elusive; in order to constrain this discussion, ‘rational choice' will tend toward the economic model characteristics such as maximizing utility and selection consistency (e.g., if A preferred to B, and B preferred to C, than A should be preferred to C). Simple decision models often encourage one to list the pros and cons of a decision, perhaps use a weighting schema, but one way or another weigh the future benefit (or harm) of making a selection. The result (sought by the rationalist models) should drive toward higher utility. Despite notable differences in researchers' theses (to be discussed in the full

  13. The Rev1 interacting region (RIR) motif in the scaffold protein XRCC1 mediates a low-affinity interaction with polynucleotide kinase/phosphatase (PNKP) during DNA single-strand break repair.

    Science.gov (United States)

    Breslin, Claire; Mani, Rajam S; Fanta, Mesfin; Hoch, Nicolas; Weinfeld, Michael; Caldecott, Keith W

    2017-09-29

    The scaffold protein X-ray repair cross-complementing 1 (XRCC1) interacts with multiple enzymes involved in DNA base excision repair and single-strand break repair (SSBR) and is important for genetic integrity and normal neurological function. One of the most important interactions of XRCC1 is that with polynucleotide kinase/phosphatase (PNKP), a dual-function DNA kinase/phosphatase that processes damaged DNA termini and that, if mutated, results in ataxia with oculomotor apraxia 4 (AOA4) and microcephaly with early-onset seizures and developmental delay (MCSZ). XRCC1 and PNKP interact via a high-affinity phosphorylation-dependent interaction site in XRCC1 and a forkhead-associated domain in PNKP. Here, we identified using biochemical and biophysical approaches a second PNKP interaction site in XRCC1 that binds PNKP with lower affinity and independently of XRCC1 phosphorylation. However, this interaction nevertheless stimulated PNKP activity and promoted SSBR and cell survival. The low-affinity interaction site required the highly conserved Rev1-interacting region (RIR) motif in XRCC1 and included three critical and evolutionarily invariant phenylalanine residues. We propose a bipartite interaction model in which the previously identified high-affinity interaction acts as a molecular tether, holding XRCC1 and PNKP together and thereby promoting the low-affinity interaction identified here, which then stimulates PNKP directly. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

    Directory of Open Access Journals (Sweden)

    Pooja H. Gupta

    2015-05-01

    Full Text Available Aim: An attempt has been made to study the toll-like receptors 4 (TLR4 gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR, respectively from Kankrej (22 and Triple cross (24 cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p˂0.05. Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05. Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance.

  15. Accumulation of single-strand breaks doses not result in double-strand DNA breaks: peculiarity of transcribing fragment of human ribosomal operon that allows its detection in biological fluids at the death of various cells in organism

    International Nuclear Information System (INIS)

    Vejko, N.N.; Spitkovskij, D.M.

    2000-01-01

    The evidences of stability of the human ribosomal gene in the transcribing range (TR-rDNA) to fragmentation are presented in two groups of experiments: 1) in the case of availability of the fragments in the cells of sectional corpse material (necrosis and apoptosis) and by pathologies accompanied by the cells death through the apoptosis or necrosis mechanism; 2) in the model experiments, wherein the separated genomes DNA is subjected to the impact of nucleases initiating single-strand breaks (SB), or chemical introduction with a subsequent comparative analysis of stability to fragmentation of various DNA sequences including TR-rDNA. The DNA solutions were subjected to γ-radiation with the dose rate of 4.8 Gy/min. It is shown that in spite of the great number of the SBs the TR-rDNA is characterized by increased stability to fragmentation, which makes it possible to propose this DNA fragment for application as a cell death marker in biological fluids [ru

  16. OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

    Directory of Open Access Journals (Sweden)

    Kevin M. Bradley

    2014-08-01

    Full Text Available Synthetic biologists wishing to self-assemble large DNA (L-DNA constructs from small DNA fragments made by automated synthesis need fragments that hybridize predictably. Such predictability is difficult to obtain with nucleotides built from just the four standard nucleotides. Natural DNA's peculiar combination of strong and weak G:C and A:T pairs, the context-dependence of the strengths of those pairs, unimolecular strand folding that competes with desired interstrand hybridization, and non-Watson–Crick interactions available to standard DNA, all contribute to this unpredictability. In principle, adding extra nucleotides to the genetic alphabet can improve the predictability and reliability of autonomous DNA self-assembly, simply by increasing the information density of oligonucleotide sequences. These extra nucleotides are now available as parts of artificially expanded genetic information systems (AEGIS, and tools are now available to generate entirely standard DNA from AEGIS DNA during PCR amplification. Here, we describe the OligArch (for "oligonucleotide architecting" software, an application that permits synthetic biologists to engineer optimally self-assembling DNA constructs from both six- and eight-letter AEGIS alphabets. This software has been used to design oligonucleotides that self-assemble to form complete genes from 20 or more single-stranded synthetic oligonucleotides. OligArch is therefore a key element of a scalable and integrated infrastructure for the rapid and designed engineering of biology.

  17. The interaction of hyperthermophilic TATA-box binding protein with single-stranded DNA is entropically favorable and exhibits a large negative heat capacity change at high salt concentration.

    Science.gov (United States)

    Nagatoishi, Satoru; Tanaka, Yoshikazu; Kudou, Motonori; Tsumoto, Kouhei

    2009-09-01

    We have investigated the thermodynamics of the interaction between the TATA-box-binding protein from Pyrococcus horikoshii (PhoTBP) and its target DNA (TATA-1). The interaction between PhoTBP and double-stranded DNA (dsDNA) is entropically favorable and enthalpically unfavorable. The thermodynamic parameters for TATA-1 duplex formation in the presence of PhoTBP, that is, ternary PhoTBP-dsDNA complexation, are similar to those for TATA-1 duplex formation, which is enthalpically favorable. Surface plasmon resonance analysis indicates that the interaction between PhoTBP and single-stranded DNA (ssDNA) of TATA-1 is entropy driven and has a large negative heat capacity change (-1.19 kcal mol(-1) K(-1)) at high salt concentration (800 mM NaCl). These results suggest that the favorable entropic effect corresponding to the interaction between PhoTBP and dsDNA is due not to ternary complexation but to the interaction between PhoTBP and ssDNA. This report is the first to describe the thermodynamics of the interaction between TBP and ssDNA.

  18. 20 CFR 411.330 - How will SSA evaluate an EN's performance?

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false How will SSA evaluate an EN's performance? 411.330 Section 411.330 Employees' Benefits SOCIAL SECURITY ADMINISTRATION THE TICKET TO WORK AND SELF-SUFFICIENCY PROGRAM Employment Networks § 411.330 How will SSA evaluate an EN's performance? (a) We will...

  19. 77 FR 43639 - Privacy Act of 1974, as Amended; Computer Matching Program (Social Security Administration (SSA...

    Science.gov (United States)

    2012-07-25

    ...)/Department of Veterans Affairs (VA), Veterans Benefits Administration (VBA))--Match Number 1008 AGENCY: SSA... of an existing computer matching program that we are currently conducting with VA/VBA. DATES: We will... Benefits Administration (VBA) A. Participating Agencies SSA and VA/VBA. B. Purpose of the Matching Program...

  20. 77 FR 54943 - Privacy Act of 1974, as Amended; Computer Matching Program (Social Security Administration (SSA...

    Science.gov (United States)

    2012-09-06

    ...)/Department of Veterans Affairs (VA), Veterans Benefits Administration (VBA))--Match Number 1309 AGENCY: SSA... of an existing computer matching program that we are currently conducting with VA/VBA. DATES: We will... Benefits Administration (VBA). A. Participating Agencies SSA and VA/VBA. B. Purpose of the Matching Program...

  1. Isolated anti-Ro/SSA thrombocytopenia: a rare feature of neonatal ...

    African Journals Online (AJOL)

    We report a rare case of isolated thrombocytopenia related to anti-Ro/SSA antibodies. The mother was followed for unlabeled familial thrombocytopenia. The mother had positive anti-Ro/SSA antibodies. She was asymptomatic without skin lesions or other criteria neither of systemic lupus erythematosus nor other connective ...

  2. Arrhythmogenicity of Anti-Ro/SSA Antibodies in Patients With Torsades de Pointes.

    Science.gov (United States)

    Lazzerini, Pietro Enea; Yue, Yuankun; Srivastava, Ujala; Fabris, Frank; Capecchi, Pier Leopoldo; Bertolozzi, Iacopo; Bacarelli, Maria Romana; Morozzi, Gabriella; Acampa, Maurizio; Natale, Mariarita; El-Sherif, Nabil; Galeazzi, Mauro; Laghi-Pasini, Franco; Boutjdir, Mohamed

    2016-04-01

    In patients with autoimmune disease, anti-Ro/SSA antibodies (anti-Ro/SSA) are responsible for a novel autoimmune-associated long-QT syndrome by targeting the hERG potassium channel and inhibiting the related current (IKr). Because anti-Ro/SSA are also present in a significant proportion of healthy subjects and may be associated with torsades de pointes (TdP) arrhythmia, we tested the hypothesis that anti-Ro/SSA may represent a silent risk factor in patients developing TdP. Twenty-five consecutive patients who experienced TdP were prospectively collected independent of ongoing therapies and concomitant diseases. Anti-Ro/SSA were detected by fluoroenzyme immunoassay, immuno-Western blotting, and line-blot immunoassay. Purified IgGs from anti-Ro/SSA-positive and anti-Ro/SSA-negative patients were tested on IKr using HEK293 cells stably expressing the hERG channel. As expected, in TdP patients, many known corrected QT interval-prolonging risk factors were simultaneously present, including hypokalemia that was the most common (52%). Anti-Ro/SSA were present in 60% of the subjects, mostly the anti-Ro/SSA-52-kD subtype detected by immuno-Western blotting only. A history of autoimmune disease was found in only 2 of anti-Ro/SSA-positive patients. Experimental data demonstrated that purified anti-Ro/SSA-positive IgGs significantly inhibited IKr and cross reacted with hERG-channel proteins. Moreover, anti-Ro/SSA-positive sera exhibited high reactivity with a peptide corresponding to the hERG-channel pore-forming region. Anti-Ro/SSA may represent a clinically silent novel risk factor for TdP development via an autoimmune-mediated electrophysiological interference with the hERG channel. We propose that TdP patients may benefit from specific anti-Ro/SSA testing even in the absence of autoimmune diseases as immunomodulating therapies may be effective in shortening corrected QT interval and reducing TdP recurrence risk. © 2016 American Heart Association, Inc.

  3. 78 FR 16564 - Privacy Act of 1974, as Amended; Computer Matching Program (SSA/Office of Personnel Management...

    Science.gov (United States)

    2013-03-15

    ... (SSN) verification to our Master Files of SSN Holders and SSN Applications. The Federal Register designation for the SSA file is Master Files of SSN Holders and SSN Applications, SSA/OSR, 60-0058. Those...

  4. Evaluation of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis for the detection of the rpoB mutations associated with resistance to rifampicin in Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Lee, H.; Cho, S.-N.; Bang, H.-E.; Kim, S.-C.; Victor, T.C.; Jordaan, A.; Suffys, P.N.; Gomes, H.M.; Singh, U.; Suresh, V.N.; Khan, B.K.

    2003-01-01

    Resistance of Mycobacterium tuberculosis to rifampicin (RIF) has been associated with mutations of the rpoB gene, which encodes for the RNA polymerase B subunit. Based on this information, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) has been suggested as a sensitive and rapid screening test for the detection of RIF-resistant M. tuberculosis from clinical isolates. PCR-SSCP analyses with radioisotopes and without radioisotopes were employed to detect mutations of the rpoB gene associated with resistance to RIF in four laboratories, and results were compared with those of sequence analysis and the conventional proportion method of drug susceptibility test between laboratories. Radioisotopic PCR-SSCP showed an excellent correlation with sequence analysis of the 157 bp region of the rpoB gene by identifying correctly all 32 isolates analyzed in this study, with a high resolution of the banding patterns obtained. In a separate study, non-radioisotopic PCR-SSCP also gave a good correlation with sequence analysis in 22 isolates, but two (9.1%) isolates were classified as resistant by PCR-SSCP despite wild type sequences. When PCR-SSCP was compared with the results obtained using the proportion method, sensitivity of 44% to 85% were obtained in the 4 laboratories that participated in this study. Possible reasons for discordant results are discussed. It has been concluded that despite discordant results, which were sometimes observed, depending on the experimental conditions, PCR-SSCP appears to be an effective and promising method for the rapid detection of RIF-resistant M. tuberculosis, a marker of multidrug resistant tuberculosis. (author)

  5. One-dimensional TRFLP-SSCP is an effective DNA fingerprinting strategy for soil Archaea that is able to simultaneously differentiate broad taxonomic clades based on terminal fragment length polymorphisms and closely related sequences based on single stranded conformation polymorphisms.

    Science.gov (United States)

    Swanson, Colby A; Sliwinski, Marek K

    2013-09-01

    DNA fingerprinting methods provide a means to rapidly compare microbial assemblages from environmental samples without the need to first cultivate species in the laboratory. The profiles generated by these techniques are able to identify statistically significant temporal and spatial patterns, correlations to environmental gradients, and biological variability to estimate the number of replicates for clone libraries or next generation sequencing (NGS) surveys. Here we describe an improved DNA fingerprinting technique that combines terminal restriction fragment length polymorphisms (TRFLP) and single stranded conformation polymorphisms (SSCP) so that both can be used to profile a sample simultaneously rather than requiring two sequential steps as in traditional two-dimensional (2-D) gel electrophoresis. For the purpose of profiling Archaeal 16S rRNA genes from soil, the dynamic range of this combined 1-D TRFLP-SSCP approach was superior to TRFLP and SSCP. 1-D TRFLP-SSCP was able to distinguish broad taxonomic clades with genetic distances greater than 10%, such as Euryarchaeota and the Thaumarchaeal clades g_Ca. Nitrososphaera (formerly 1.1b) and o_NRP-J (formerly 1.1c) better than SSCP. In addition, 1-D TRFLP-SSCP was able to simultaneously distinguish closely related clades within a genus such as s_SCA1145 and s_SCA1170 better than TRFLP. We also tested the utility of 1-D TRFLP-SSCP fingerprinting of environmental assemblages by comparing this method to the generation of a 16S rRNA clone library of soil Archaea from a restored Tallgrass prairie. This study shows 1-D TRFLP-SSCP fingerprinting provides a rapid and phylogenetically informative screen of Archaeal 16S rRNA genes in soil samples. © 2013.

  6. A G-C-rich palindromic structural motif and a stretch of single-stranded purines are required for optimal packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA.

    Science.gov (United States)

    Jaballah, Soumeya Ali; Aktar, Suriya J; Ali, Jahabar; Phillip, Pretty Susan; Al Dhaheri, Noura Salem; Jabeen, Aayesha; Rizvi, Tahir A

    2010-09-03

    During retroviral RNA packaging, two copies of genomic RNA are preferentially packaged into the budding virus particles whereas the spliced viral RNAs and the cellular RNAs are excluded during this process. Specificity towards retroviral RNA packaging is dependent upon sequences at the 5' end of the viral genome, which at times extend into Gag sequences. It has earlier been suggested that the Mason-Pfizer monkey virus (MPMV) contains packaging sequences within the 5' untranslated region (UTR) and Gag. These studies have also suggested that the packaging determinants of MPMV that lie in the UTR are bipartite and are divided into two regions both upstream and downstream of the major splice donor. However, the precise boundaries of these discontinuous regions within the UTR and the role of the intervening sequences between these dipartite sequences towards MPMV packaging have not been investigated. Employing a combination of genetic and structural prediction analyses, we have shown that region "A", immediately downstream of the primer binding site, is composed of 50 nt, whereas region "B" is composed of the last 23 nt of UTR, and the intervening 55 nt between these two discontinuous regions do not contribute towards MPMV RNA packaging. In addition, we have identified a 14-nt G-C-rich palindromic sequence (with 100% autocomplementarity) within region A that has been predicted to fold into a structural motif and is essential for optimal MPMV RNA packaging. Furthermore, we have also identified a stretch of single-stranded purines (ssPurines) within the UTR and 8 nt of these ssPurines are duplicated in region B. The native ssPurines or its repeat in region B when predicted to refold as ssPurines has been shown to be essential for RNA packaging, possibly functioning as a potential nucleocapsid binding site. Findings from this study should enhance our understanding of the steps involved in MPMV replication including RNA encapsidation process. Copyright (c) 2010 Elsevier Ltd

  7. A single-stranded conformational polymorphism (SSCP)-derived quantitative variable to monitor the virulence of a Barley yellow dwarf virus-PAV (BYDV-PAV) isolate during adaptation to the TC14 resistant wheat line.

    Science.gov (United States)

    Delaunay, Agnes; Lacroix, Christelle; Morliere, Stephanie; Riault, Gerard; Chain, Florian; Trottet, Maxime; Jacquot, Emmanuel

    2010-09-01

    A standardized single-stranded conformational polymorphism (SSCP) procedure is proposed as an alternative to the time-consuming biological characterization of Barley yellow dwarf virus-PAV (BYDV-PAV) isolates. Using this procedure, six of 21 overlapping regions used to scan the viral genome gave patterns specific to '4E' (avirulent) or '4T' ('4E'-derived virulent) isolates. The calibration of samples and integration of SSCP patterns corresponding to the nucleotide region 1482-2023 allowed the estimation of P(T) values that reflect the proportions of a '4T'-specific band. Analysis of the biological (area under the pathogen progress curve) and molecular (P(T)) data suggested a positive linear relation between these variables. Moreover, sequence analysis of the nucleotide region 1482-2023 highlighted the presence of a nucleotide polymorphism (C/A(1835)) which can be considered as a candidate for virus-host interactions linked to the monitored virulence. According to these parameters, P(T) values associated with '4E'- and '4T'-derived populations show that: (i) long-term infection of a BYDV-PAV isolate on the 'TC14' resistant host leads to the fixation of virulent individuals in viral populations; and (ii) the introduction of susceptible hosts in successive 'TC14' infections results in the maintenance of low virulence of the populations. Thus, the presented study demonstrates that SSCP is a useful tool for monitoring viral populations during the host adaptation process. The described impact of host alternation provides new opportunities for the use of the 'TC14' resistance source in BYDV-resistant breeding programmes. This study is part of the global effort made by the scientific community to propose sustainable alternatives to the chemical control of this viral disease.

  8. Ex vivo gene editing of the dystrophin gene in muscle stem cells mediated by peptide nucleic acid single stranded oligodeoxynucleotides induces stable expression of dystrophin in a mouse model for Duchenne muscular dystrophy.

    Science.gov (United States)

    Nik-Ahd, Farnoosh; Bertoni, Carmen

    2014-07-01

    Duchenne muscular dystrophy (DMD) is a fatal disease caused by mutations in the dystrophin gene, which result in the complete absence of dystrophin protein throughout the body. Gene correction strategies hold promise to treating DMD. Our laboratory has previously demonstrated the ability of peptide nucleic acid single-stranded oligodeoxynucleotides (PNA-ssODNs) to permanently correct single-point mutations at the genomic level. In this study, we show that PNA-ssODNs can target and correct muscle satellite cells (SCs), a population of stem cells capable of self-renewing and differentiating into muscle fibers. When transplanted into skeletal muscles, SCs transfected with correcting PNA-ssODNs were able to engraft and to restore dystrophin expression. The number of dystrophin-positive fibers was shown to significantly increase over time. Expression was confirmed to be the result of the activation of a subpopulation of SCs that had undergone repair as demonstrated by immunofluorescence analyses of engrafted muscles using antibodies specific to full-length dystrophin transcripts and by genomic DNA analysis of dystrophin-positive fibers. Furthermore, the increase in dystrophin expression detected over time resulted in a significant improvement in muscle morphology. The ability of transplanted cells to return into quiescence and to activate upon demand was confirmed in all engrafted muscles following injury. These results demonstrate the feasibility of using gene editing strategies to target and correct SCs and further establish the therapeutic potential of this approach to permanently restore dystrophin expression into muscle of DMD patients. © 2014 AlphaMed Press.

  9. VBA SSA Acc To Fed Rec Online (SAFRO) - Also known as Veterans Benefit Administration Query (VBAQ).

    Data.gov (United States)

    Social Security Administration — The purpose of this query is to provide SSA field office personnel with real-time access to military discharge data from the VA BIRLS database. This information is...

  10. Shock Hazard Prevention through Self-Healing Insulative Coating on SSA Metallic Bearings, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The space suit assembly (SSA) contains metallic bearings at the wrist, neck, and waist, which are exposed to space environment, and pose a potential shock hazard....

  11. Resonance assignments for the substrate binding domain of Hsp70 chaperone Ssa1 from Saccharomyces cerevisiae.

    Science.gov (United States)

    Hu, Wanhui; Wu, Huiwen; Zhang, Hong; Gong, Weibin; Perrett, Sarah

    2015-10-01

    Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and the cell cycle. However, no structural data has been obtained for Ssa1 up to now. Here we report the almost complete (96 %) (1)H, (13)C, (15)N backbone and side chain NMR assignment of the 18.8 kDa Ssa1 substrate binding domain. The construct includes residues 382-554, which corresponds to the entire substrate binding domain and two following α-helices in homologous structures. The secondary structure predicted from the assigned chemical shifts is consistent with that of homologous Hsp70 substrate binding domains.

  12. BOREAS RSS-08 SSA IFC-3 Digitized Stereo Imagery at the OBS, OA, and OJP Sites

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: The RSS08 team acquired stereo photography from the double-scaffold towers at the Southern Study Area (SSA), Old Black Spruce (OBS), Old Aspen (OA), and...

  13. BOREAS RSS-08 SSA IFC-3 Digitized Stereo Imagery at the OBS, OA, and OJP Sites

    Data.gov (United States)

    National Aeronautics and Space Administration — The RSS08 team acquired stereo photography from the double-scaffold towers at the Southern Study Area (SSA), Old Black Spruce (OBS), Old Aspen (OA), and Old Jack...

  14. BOREAS TE-18 Landsat TM Physical Classification Image of the SSA

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: The objective of this classification is to provide BOREAS investigators with a data product that characterizes the land cover of the SSA. A Landsat-5 TM...

  15. Possible role of anti-SSA/Ro antibodies in the pathogenesis of pulmonary hypertension

    Directory of Open Access Journals (Sweden)

    Kelsey Guerreso

    2016-01-01

    Conclusion: It is known that pulmonary hypertension has association with autoimmune diseases, however no clear markers yet exist. Anti-SSA/Ro antibodies have been rarely described in cases of pulmonary disease, and less so in pulmonary hypertension. This case describes a unique association between isolated pulmonary hypertension and anti-SSA/Ro antibody, thereby illustrating the need to investigate this autoantibody and others in the pathogenesis of autoimmune pulmonary hypertension.

  16. Newborn infant with maternal anti-SSA antibody-induced complete heart block accompanying cardiomyopathy.

    Science.gov (United States)

    Iida, Midori; Inamura, Noboru; Takeuchi, Makoto

    2006-01-01

    Newborn case of maternal anti-SSA antibody-induced congenital complete heart block (CCHB) accompanying cardiomyopathy is presented. Unexpectedly, she died of ventricular tachycardia, not bradycardia, 6 days after birth. Autopsy revealed left ventricular cardiomyopathy with endocardial fibroelastosis. Thus, when evaluating fetal cardiac performance in cases of maternal anti-SSA antibody-induced CCHB, it is necessary to pay attention to myocardial attributes such as endocardial hyperplasia.

  17. GillespieSSA: Implementing the Gillespie Stochastic Simulation Algorithm in R

    Directory of Open Access Journals (Sweden)

    Mario Pineda-Krch

    2008-02-01

    Full Text Available The deterministic dynamics of populations in continuous time are traditionally described using coupled, first-order ordinary differential equations. While this approach is accurate for large systems, it is often inadequate for small systems where key species may be present in small numbers or where key reactions occur at a low rate. The Gillespie stochastic simulation algorithm (SSA is a procedure for generating time-evolution trajectories of finite populations in continuous time and has become the standard algorithm for these types of stochastic models. This article presents a simple-to-use and flexible framework for implementing the SSA using the high-level statistical computing language R and the package GillespieSSA. Using three ecological models as examples (logistic growth, Rosenzweig-MacArthur predator-prey model, and Kermack-McKendrick SIRS metapopulation model, this paper shows how a deterministic model can be formulated as a finite-population stochastic model within the framework of SSA theory and how it can be implemented in R. Simulations of the stochastic models are performed using four different SSA Monte Carlo methods: one exact method (Gillespie's direct method; and three approximate methods (explicit, binomial, and optimized tau-leap methods. Comparison of simulation results confirms that while the time-evolution trajectories obtained from the different SSA methods are indistinguishable, the approximate methods are up to four orders of magnitude faster than the exact methods.

  18. Hydraulic and mechanical behavior of landfill clay liner containing SSA in contact with leachate.

    Science.gov (United States)

    Zhang, Qian; Lu, Haijun; Liu, Junzhu; Wang, Weiwei; Zhang, Xiong

    2018-05-01

    Sewage sludge ash (SSA) produced by municipal sludge can be used as a modified additive for clay liner, and improves the working performance of landfill clay liner in contact with leachate. Under the action of landfill leachate, the permeability, shear strength, phase composition, and pore structure of the modified clay are investigated through the flexible wall permeability test, triaxial shear test, thermal gravimetric and differential thermal analysis, and low-temperature nitrogen adsorption test, respectively. The hydraulic conductivity of the modified clay containing 0-5% SSA is in the range of 3.94 × 10 -8 -1.16 × 10 -7  cm/s, and the pollutant concentration of the sample without SSA was higher than others. The shear strength of the modified clay is more than that of the traditional clay liner, the cohesion rate of modified clay increases from 32.5 to 199.91 kPa, and the internal friction angle decreases from 32.5° to 15.6°. Furthermore, the weight loss rates of the samples are 15.69%, 17.92%, 18.06%, and 20.68%, respectively, when the SSA content increases from 0% to 5%. The total pore volume and average pore diameter of the modified clay decrease with the increase in the SSA content, respectively. However, the specific area of the modified clay increases with the increase in the SSA content.

  19. Influence of alloying and secondary annealing on anneal hardening ...

    Indian Academy of Sciences (India)

    Unknown

    Abstract. This paper reports results of investigation carried out on sintered copper alloys (Cu, 8 at%; Zn,. Ni, Al and Cu–Au with 4 at%Au). The alloys were subjected to cold rolling (30, 50 and 70%) and annealed isochronally up to recrystallization temperature. Changes in hardness and electrical conductivity were fol-.

  20. Management of the Bohunice RPVs annealing procedures

    International Nuclear Information System (INIS)

    Repka, M.

    1994-01-01

    The program of annealing regeneration procedure of RPVs units 1 and 2 of NPP V-1 (EBO) realization in the year 1993, is the topic of this paper. In the paper the following steps are described in detail: the preparation works, the annealing procedure realization schedule and safety management: starting with zero conditions, assembling of annealing apparatus, annealing procedure, cooling down and disassembling procedure of annealing apparatus. At the end the programs of annealing of both RPVs including the dosimetry measurements are discussed and evaluated. (author). 3 figs

  1. Mutagenesis of the Agrobacterium VirE2 single-stranded DNA-binding protein identifies regions required for self-association and interaction with VirE1 and a permissive site for hybrid protein construction.

    Science.gov (United States)

    Zhou, X R; Christie, P J

    1999-07-01

    The VirE2 single-stranded DNA-binding protein (SSB) of Agrobacterium tumefaciens is required for delivery of T-DNA to the nuclei of susceptible plant cells. By yeast two-hybrid and immunoprecipitation analyses, VirE2 was shown to self-associate and to interact with VirE1. VirE2 mutants with small deletions or insertions of a 31-residue oligopeptide (i31) at the N or C terminus or with an i31 peptide insertion at Leu236 retained the capacity to form homomultimers. By contrast, VirE2 mutants with modifications outside a central region located between residues 320 and 390 retained the capacity to interact with VirE1. These findings suggest the tertiary structure of VirE2 is important for homomultimer formation whereas a central domain mediates formation of a complex with VirE1. The capacity of VirE2 mutants to interact with full-length VirE2 in the yeast Saccharomyces cerevisiae correlated with the abundance of the mutant proteins in A. tumefaciens, suggesting that VirE2 is stabilized by homomultimerization in the bacterium. We further characterized the promoter and N- and C-terminal sequence requirements for synthesis of functional VirE2. A PvirB::virE2 construct yielded functional VirE2 protein as defined by complementation of a virE2 null mutation. By contrast, PvirE or Plac promoter constructs yielded functional VirE2 only if virE1 was coexpressed with virE2. Deletion of 10 or 9 residues from the N or C terminus of VirE2, respectively, or addition of heterologous peptides or proteins to either terminus resulted in a loss of protein function. However, an i31 peptide insertion at Tyr39 had no effect on protein function as defined by the capacity of the mutant protein to (i) interact with native VirE2, (ii) interact with VirE1, (iii) accumulate at abundant levels in A. tumefaciens, and (iv) restore wild-type virulence to a virE2 null mutant. We propose that Tyr39 of VirE2 corresponds to a permissive site for insertion of heterologous peptides or proteins of interest

  2. Pulsed Laser Annealing of Carbon

    Science.gov (United States)

    Abrahamson, Joseph P.

    This dissertation investigates laser heating of carbon materials. The carbon industry has been annealing carbon via traditional furnace heating since at least 1800, when Sir Humphry Davy produced an electric arc with carbon electrodes made from carbonized wood. Much knowledge has been accumulated about carbon since then and carbon materials have become instrumental both scientifically and technologically. However, to this day the kinetics of annealing are not known due to the slow heating and cooling rates of furnaces. Additionally, consensus has yet to be reached on the cause of nongraphitizability. Annealing trajectories with respect to time at temperature are observed from a commercial carbon black (R250), model graphitizable carbon (anthracene coke) and a model nongraphitizable carbon (sucrose char) via rapid laser heating. Materials were heated with 1064 nm and 10.6 im laser radiation from a Q-switched Nd:YAG laser and a continuous wave CO2 laser, respectively. A pulse generator was used reduce the CO2 laser pulse width and provide high temporal control. Time-temperature-histories with nanosecond temporal resolution and temperature reproducibility within tens of degrees Celsius were determined by spectrally resolving the laser induced incandescence signal and applying multiwavelength pyrometry. The Nd:YAG laser fluences include: 25, 50, 100, 200, 300, and 550 mJ/cm2. The maximum observed temperature ranged from 2,400 °C to the C2 sublimation temperature of 4,180 °C. The CO2 laser was used to collect a series of isothermal (1,200 and 2,600 °C) heat treatments versus time (100 milliseconds to 30 seconds). Laser heated samples are compared to furnace annealing at 1,200 and 2,600 °C for 1 hour. The material transformation trajectory of Nd:YAG laser heated carbon is different than traditional furnace heating. The traditional furnace annealing pathway is followed for CO2 laser heating as based upon equivalent end structures. The nanostructure of sucrose char

  3. Automatic Satellite Telemetry Analysis for SSA using Artificial Intelligence Techniques

    Science.gov (United States)

    Stottler, R.; Mao, J.

    In April 2016, General Hyten, commander of Air Force Space Command, announced the Space Enterprise Vision (SEV) (http://www.af.mil/News/Article-Display/Article/719941/hyten-announces-space-enterprise-vision/). The SEV addresses increasing threats to space-related systems. The vision includes an integrated approach across all mission areas (communications, positioning, navigation and timing, missile warning, and weather data) and emphasizes improved access to data across the entire enterprise and the ability to protect space-related assets and capabilities. "The future space enterprise will maintain our nation's ability to deliver critical space effects throughout all phases of conflict," Hyten said. Satellite telemetry is going to become available to a new audience. While that telemetry information should be valuable for achieving Space Situational Awareness (SSA), these new satellite telemetry data consumers will not know how to utilize it. We were tasked with applying AI techniques to build an infrastructure to process satellite telemetry into higher abstraction level symbolic space situational awareness and to initially populate that infrastructure with useful data analysis methods. We are working with two organizations, Montana State University (MSU) and the Air Force Academy, both of whom control satellites and therefore currently analyze satellite telemetry to assess the health and circumstances of their satellites. The design which has resulted from our knowledge elicitation and cognitive task analysis is a hybrid approach which combines symbolic processing techniques of Case-Based Reasoning (CBR) and Behavior Transition Networks (BTNs) with current Machine Learning approaches. BTNs are used to represent the process and associated formulas to check telemetry values against anticipated problems and issues. CBR is used to represent and retrieve BTNs that represent an investigative process that should be applied to the telemetry in certain circumstances

  4. Morphological, thermal and annealed microhardness ...

    Indian Academy of Sciences (India)

    Unknown

    blended with sugarcane bagasse which showed good me- chanical properties when investigated by SEM, thermal gravimetric analysis (TGA), DSC and tensile testing (Chiel- lini et al 2001). An increase in the engineering yield stress was observed, with a decline in tensile impact strength. With DSC on annealing, a small ...

  5. Morphological, thermal and annealed microhardness ...

    Indian Academy of Sciences (India)

    The present paper reports the preparation of full IPNs of gelatin and polyacrylonitrile. Various compositions of gluteraldehyde crosslinked gelatin and N,N′-methylene-bis-acrylamide crosslinked PAN were characterized by SEM and DSC techniques. The IPNs were also thermally pretreated by the annealing process.

  6. Anti-Ro/SSA antibodies and cardiac arrhythmias in the adult: facts and hypotheses.

    Science.gov (United States)

    Lazzerini, P E; Capecchi, P L; Laghi-Pasini, F

    2010-09-01

    It is well established that the passive trans-placental passage of anti-Ro/SSA antibodies from mother to foetus is associated with the risk to develop an uncommon syndrome named neonatal lupus (NLE), where the congenital heart block represents the most severe clinical feature. Recent evidence demonstrated that also adult heart, classically considered invulnerable to the anti-Ro/SSA antibodies, may represent a target of the arrhythmogenicity of these autoantibodies. In particular, the prolongation of the QTc interval appears the most frequent abnormality observed in adults with circulating anti-Ro/SSA antibodies, with some data suggesting an association with an increased risk of ventricular arrhythmias, also life threatening. Moreover, even though the association between anti-Ro/SSA antibodies and conduction disturbances is undoubtedly less evident in adults than in infants, from the accurate dissection of the literature data the possibility arises that sometimes also the adult cardiac conduction tissue may be affected by such antibodies. The exact arrhythmogenic mechanisms involved in foetus/newborns and adults, respectively, have not been completely clarified as yet. However, increasing evidence suggests that anti-Ro/SSA antibodies may trigger rhythm disturbances through an inhibiting cross-reaction with several cardiac ionic channels, particularly the calcium channels (L-type and T-type), but also the potassium channel hERG, whose different expression and involvement in the cardiac electrophysiology during lifespan might account for the occurrence of age-related differences.

  7. Synthesis and crystal structures of a novel layered silicate SSA-1 and its microporous derivatives by topotactic transformation.

    Science.gov (United States)

    Takahashi, S; Kurita, Y; Ikeda, T; Miyamoto, M; Uemiya, S; Oumi, Y

    2016-10-18

    The synthesis of a novel layered silicate SSA-1 (SSA: silicate synthesized with a quaternary amine) was achieved in the SiO 2 -H 2 O-TEAOH (TEAOH: tetraethylammonium hydroxide - as an organic structural directing agent) system. The crystal structure of SSA-1 involved two silicate layers composed of bre [10T]-type CBU (Composite Building Unit) and TEAOH in interlayers. The topotactic transformation of SSA-1 by calcination was examined, resulting in a porous material (PML-1: porous material transformed from a layered silicate) with a 108 m 2 g -1 BET surface area and 0.035 cm 3 g -1 pore volume. PML-1 is a siliceous microporous material with silanols in the framework and possesses unique properties, such as hydrophilicity, in spite of all its silica composition. The most reasonable crystal structure of PML-1 was successfully determined on the basis of the crystal structure of SSA-1 by a combination of manual modelling, PXRD pattern simulation, DFT optimization and Rietveld analysis. Additionally, an interlayer expanded siliceous zeolite SSA-1 (IEZ-SSA-1) was also successfully prepared by silylation using trichloro(methyl)silane under acidic conditions. IEZ-SSA-1 showed hydrophilicity or hydrophobicity properties by changing the functional group of the pillar part in the interlayer. Additionally, IEZ-SSA-1 showed a large gas adsorption property (537 m 2 g -1 and 0.21 cm 3 g -1 ).

  8. Simulated annealing model of acupuncture

    Science.gov (United States)

    Shang, Charles; Szu, Harold

    2015-05-01

    The growth control singularity model suggests that acupuncture points (acupoints) originate from organizers in embryogenesis. Organizers are singular points in growth control. Acupuncture can cause perturbation of a system with effects similar to simulated annealing. In clinical trial, the goal of a treatment is to relieve certain disorder which corresponds to reaching certain local optimum in simulated annealing. The self-organizing effect of the system is limited and related to the person's general health and age. Perturbation at acupoints can lead a stronger local excitation (analogous to higher annealing temperature) compared to perturbation at non-singular points (placebo control points). Such difference diminishes as the number of perturbed points increases due to the wider distribution of the limited self-organizing activity. This model explains the following facts from systematic reviews of acupuncture trials: 1. Properly chosen single acupoint treatment for certain disorder can lead to highly repeatable efficacy above placebo 2. When multiple acupoints are used, the result can be highly repeatable if the patients are relatively healthy and young but are usually mixed if the patients are old, frail and have multiple disorders at the same time as the number of local optima or comorbidities increases. 3. As number of acupoints used increases, the efficacy difference between sham and real acupuncture often diminishes. It predicted that the efficacy of acupuncture is negatively correlated to the disease chronicity, severity and patient's age. This is the first biological - physical model of acupuncture which can predict and guide clinical acupuncture research.

  9. MELiSSA celebrates 25 years of research into life support

    International Nuclear Information System (INIS)

    2015-01-01

    MELiSSA (Micro-Ecological Life Support System Alternative) is a collaborative project with the European Space Agency ESA and various other scientific partners. The objective of MELiSSA is to develop a system that is able to provide manned space missions with food, drinking water and oxygen autonomously in space. Drinkable water and oxygen are currently being made in the international space station ISS by filtering waste water and by electrolysing water. However, such physiochemical technologies do not offer a solution for food. The MELiSSA project intends to reuse waste products, which include CO2, water, stools and urine from the astronauts, and even the perspiration moisture in the cabin and to transfer these into food through the use of micro-organisms.

  10. BOREAS TE-1 Soils Data Over The SSA Tower Sites in Raster Format

    Science.gov (United States)

    Hall, Forrest G. (Editor); Anderson, Darwin; Knapp, David E.

    2000-01-01

    The BOREAS TE-1 team collected various data to characterize the soil-plant systems in the BOREAS SSA. This data set was gridded from vector layers of soil maps that were received from Dr. Darwin Anderson (TE-1), who did the original soil mapping in the field during 1994. The vector layers were gridded into raster files that cover approximately 1 square kilometer over each of the tower sites in the SSA. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  11. Quantum annealing for combinatorial clustering

    Science.gov (United States)

    Kumar, Vaibhaw; Bass, Gideon; Tomlin, Casey; Dulny, Joseph

    2018-02-01

    Clustering is a powerful machine learning technique that groups "similar" data points based on their characteristics. Many clustering algorithms work by approximating the minimization of an objective function, namely the sum of within-the-cluster distances between points. The straightforward approach involves examining all the possible assignments of points to each of the clusters. This approach guarantees the solution will be a global minimum; however, the number of possible assignments scales quickly with the number of data points and becomes computationally intractable even for very small datasets. In order to circumvent this issue, cost function minima are found using popular local search-based heuristic approaches such as k-means and hierarchical clustering. Due to their greedy nature, such techniques do not guarantee that a global minimum will be found and can lead to sub-optimal clustering assignments. Other classes of global search-based techniques, such as simulated annealing, tabu search, and genetic algorithms, may offer better quality results but can be too time-consuming to implement. In this work, we describe how quantum annealing can be used to carry out clustering. We map the clustering objective to a quadratic binary optimization problem and discuss two clustering algorithms which are then implemented on commercially available quantum annealing hardware, as well as on a purely classical solver "qbsolv." The first algorithm assigns N data points to K clusters, and the second one can be used to perform binary clustering in a hierarchical manner. We present our results in the form of benchmarks against well-known k-means clustering and discuss the advantages and disadvantages of the proposed techniques.

  12. Loviisa Unit One: Annealing - healing

    Energy Technology Data Exchange (ETDEWEB)

    Kohopaeae, J.; Virsu, R. [ed.; Henriksson, A. [ed.

    1997-11-01

    Unit 1 of the Loviisa nuclear powerplant was annealed in connection with the refuelling outage in the summer of 1996. This type of heat treatment restored the toughness properties of the pressure vessel weld, which had been embrittled be neutron radiation, so that it is almost equivalent to a new weld. The treatment itself was an ordinary metallurgical procedure that took only a few days. But the material studies that preceded it began over fifteen years ago and have put IVO at the forefront of world-wide expertise in the area of radiation embrittlement

  13. 75 FR 7648 - Privacy Act of 1974, as Amended; Computer Matching Program (SSA/Department of Veterans Affairs...

    Science.gov (United States)

    2010-02-22

    .../Veterans Benefits Administration (VA/ VBA))--Match Number 1309 AGENCY: Social Security Administration (SSA... announces a renewal of an existing computer matching program that we are currently conducting with VA/VBA... Matching Program, SSA With the Department of Veterans Affairs/Veterans Benefits Administration (VA/VBA) A...

  14. 20 CFR 408.1235 - How does the State transfer funds to SSA to administer its recognition payment program?

    Science.gov (United States)

    2010-04-01

    ... administer its recognition payment program? 408.1235 Section 408.1235 Employees' Benefits SOCIAL SECURITY... fifth business day following such date. (b) Accounting of State funds. (1) As soon as feasible after the... balance of the State's cash on deposit with SSA. (2) SSA will provide the State with an accounting of...

  15. 20 CFR 411.597 - Will SSA periodically review the outcome payment system and the outcome-milestone payment system...

    Science.gov (United States)

    2010-04-01

    ... Employment Network Payment Systems § 411.597 Will SSA periodically review the outcome payment system and the outcome-milestone payment system for possible modifications? (a) Yes. We will periodically review the... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Will SSA periodically review the outcome...

  16. 76 FR 55690 - Submission for OMB Review; Comment Request; The SSA-NIH Collaboration To Improve the Disability...

    Science.gov (United States)

    2011-09-08

    ...; Comment Request; The SSA-NIH Collaboration To Improve the Disability Determination Process: Validation of... Collection: Title: The SSA-NIH Collaboration to Improve the Disability Determination Process: Validation of IRT-CAT tools. Type of Information Collection Request: NEW. Need and Use of Information Collection...

  17. Lupus systémique et atteinte rénale: Apport des anticorps anti-SSA ...

    African Journals Online (AJOL)

    -SSA dans 12 cas (40%).Cinq patients (62.5%) ayant une atteinte rénale avaient des anticorps anti DNA négatifs. Parmi ces patients avec atteinte rénale, 37.5% avaient des anticorps anti SSA sans anticorps anti DNA. La moitié des patients ...

  18. Simulated annealing with constant thermodynamic speed

    International Nuclear Information System (INIS)

    Salamon, P.; Ruppeiner, G.; Liao, L.; Pedersen, J.

    1987-01-01

    Arguments are presented to the effect that the optimal annealing schedule for simulated annealing proceeds with constant thermodynamic speed, i.e., with dT/dt = -(v T)/(ε-√C), where T is the temperature, ε- is the relaxation time, C ist the heat capacity, t is the time, and v is the thermodynamic speed. Experimental results consistent with this conjecture are presented from simulated annealing on graph partitioning problems. (orig.)

  19. Keystream Generator Based On Simulated Annealing

    Directory of Open Access Journals (Sweden)

    Ayad A. Abdulsalam

    2011-01-01

    Full Text Available Advances in the design of keystream generator using heuristic techniques are reported. A simulated annealing algorithm for generating random keystream with large complexity is presented. Simulated annealing technique is adapted to locate these requirements. The definitions for some cryptographic properties are generalized, providing a measure suitable for use as an objective function in a simulated annealing algorithm, seeking randomness that satisfy both correlation immunity and the large linear complexity. Results are presented demonstrating the effectiveness of the method.

  20. An application of the Krylov-FSP-SSA method to parameter fitting with maximum likelihood

    Science.gov (United States)

    Dinh, Khanh N.; Sidje, Roger B.

    2017-12-01

    Monte Carlo methods such as the stochastic simulation algorithm (SSA) have traditionally been employed in gene regulation problems. However, there has been increasing interest to directly obtain the probability distribution of the molecules involved by solving the chemical master equation (CME). This requires addressing the curse of dimensionality that is inherent in most gene regulation problems. The finite state projection (FSP) seeks to address the challenge and there have been variants that further reduce the size of the projection or that accelerate the resulting matrix exponential. The Krylov-FSP-SSA variant has proved numerically efficient by combining, on one hand, the SSA to adaptively drive the FSP, and on the other hand, adaptive Krylov techniques to evaluate the matrix exponential. Here we apply this Krylov-FSP-SSA to a mutual inhibitory gene network synthetically engineered in Saccharomyces cerevisiae, in which bimodality arises. We show numerically that the approach can efficiently approximate the transient probability distribution, and this has important implications for parameter fitting, where the CME has to be solved for many different parameter sets. The fitting scheme amounts to an optimization problem of finding the parameter set so that the transient probability distributions fit the observations with maximum likelihood. We compare five optimization schemes for this difficult problem, thereby providing further insights into this approach of parameter estimation that is often applied to models in systems biology where there is a need to calibrate free parameters. Work supported by NSF grant DMS-1320849.

  1. Ro/SSA autoantibody-positive pregnancy: reactions to serial fetal Doppler echocardiographic surveillance.

    Science.gov (United States)

    Tingström, J; Hjelmstedt, A; Welin Henriksson, E; Sonesson, S-E; Wahren-Herlenius, M

    2015-12-01

    The risk for congenital heart block (CHB) associated with maternal Ro/SSA autoantibodies is low, but the possibility of treating early stages of disease has seen the introduction of Doppler echocardiographic surveillance programs with serial examinations during the CHB susceptibility weeks of pregnancy. The aim of the present study was to understand how Ro/SSA autoantibody-positive women having undergone Doppler echocardiographic surveillance programs and giving birth to children without CHB experienced their pregnancy and frequent ultrasound examinations. A validated questionnaire based on data from an interview-study was distributed to Ro/SSA-positive women supervised with Doppler examinations during their pregnancy (n = 100). The response rate was 79%. The majority of the women (61%) reported that the increased number of ultrasound examinations influenced their pregnancy, but in a positive way, with qualified information and additional support from health care personnel in conjunction with the examinations. Further, the visits to the clinic provided opportunities to see the ultrasound picture of the expected infant. However, one-third of the women also reported stress in relation to the examinations. Fetal echocardiographic surveillance holds many and predominantly positive effects for Ro/SSA-positive women during pregnancy in addition to the medical advantages. © The Author(s) 2015.

  2. Possible role of anti-SSA/Ro antibodies in the pathogenesis of pulmonary hypertension.

    Science.gov (United States)

    Guerreso, Kelsey; Conner, Edward Alexander

    2016-01-01

    There are many different causes of pulmonary hypertension and the pathogenesis of the disease is still being elucidated. Although they are not the most common, autoimmunity and inflammation have been identified as possible causes. No one autoantibody has been identified as the definite cause of pulmonary hypertension. We present a rare association of anti-SSA/Ro antibodies and isolated pulmonary hypertension. A 53 year old African American female presented with abdominal pain, nausea, weight loss, dyspnea and fatigue. Upon further exam she was found to have high titers of antinuclear antibodies and anti-SSA/Ro antibodies. This antibody profile would typically be suggestive of Sjögren's Syndrome, which is characterized by dry eyes and poor salivary gland function. However, since this patient did not have any symptoms consistent with the disease a diagnosis of Sjögren's Syndrome could not be made. A combination of laboratory, imaging and diagnostic studies were done that revealed a final diagnosis of pulmonary hypertension. It is known that pulmonary hypertension has association with autoimmune diseases, however no clear markers yet exist. Anti-SSA/Ro antibodies have been rarely described in cases of pulmonary disease, and less so in pulmonary hypertension. This case describes a unique association between isolated pulmonary hypertension and anti-SSA/Ro antibody, thereby illustrating the need to investigate this autoantibody and others in the pathogenesis of autoimmune pulmonary hypertension.

  3. ESA SSA Space Radiation Expert Service Centre: the Importance of Community Feedback

    Science.gov (United States)

    Crosby, Norma; Dierckxsens, Mark; Kruglanski, Michel; De Donder, Erwin; Calders, Stijn; Messios, Neophytos; Glover, Alexi

    2017-04-01

    End-users in a wide range of sectors both in space and on the ground are affected by space weather. In the frame of its Space Situational Awareness (SSA) programme (http://swe.ssa.esa.int/) the European Space Agency (ESA) is establishing a Space Weather (SWE) Service Network to support end-users in three ways: mitigate the effects of space weather on their systems, reduce costs, and improve reliability. Almost 40 expert groups from institutes and organisations across Europe contribute to this Network organised in five Expert Service Centres (ESCs) - Solar Weather, Heliospheric Weather, Space Radiation, Ionospheric Weather, Geomagnetic Conditions. To understand the end-user needs, the ESCs are supported by the SSCC (SSA Space Weather Coordination Centre) that offers first line support to the end-users. Here we present the mission of the Space Radiation ESC (R-ESC) (http://swe.ssa.esa.int/space-radiation) and the space domain services it supports. Furthermore, we describe how the R-ESC project complements past and ongoing projects both on national level as well as international (e.g. EU projects), emphasizing the importance of inter-disciplinary communication between different communities ranging from scientists, engineers to end-users. Such collaboration is needed if basic science is to be used most efficiently for the development of products and tools that provide end-users with what they actually need. Additionally, feedback from the various communities (projects) is also essential when defining future projects.

  4. BOREAS TF-1 SSA-OA Understory Flux, Meteorological, and Soil Temperature Data

    Science.gov (United States)

    Hall, Forrest G. (Editor); Huemmrich, Karl (Editor); Black, T. Andrew; Chen, Z.; Nesic, Zoran

    2000-01-01

    The BOREAS TF-1 team collected energy, carbon dioxide, and momentum flux data under the canopy along with meteorological and soils data at the BOREAS SSA-OA site from mid-October to mid-November of 1993 and throughout all of 1994. The data are available in tabular ASCII files.

  5. BOREAS TF-9 SSA-OBS Tower Flux, Meteorological, and Soil Temperature Data

    Science.gov (United States)

    Hall, Forrest G. (Editor); Huemmrich, Karl (Editor); Massheder, Jonathan M.; Moncrieff, John B.; Rayment, Mark B.; Jarvis, Paul G.

    2000-01-01

    The BOREAS TF-9 team collected energy, carbon dioxide, and water vapor flux data at the BOREAS SSA-OBS site during the growing season of 1994 and most of the year for 1996. From the winter of 1995 to 1996, soil temperature data were also collected and provided. The data are available in tabular ASCII files.

  6. BOREAS TF-1 SSA-OA Tower Flux, Meteorological, and Soil Temperature Data

    Science.gov (United States)

    Hall, Forrest G. (Editor); Huemmrich, Karl (Editor); Black, T. Andrew; Chen, Z.; Nesic, Zoran

    2000-01-01

    The BOREAS TF-1 team collected energy, carbon dioxide, and momentum flux data above the canopy along with meteorological and soils data at the BOREAS SSA-OA site from mid-April to the end of the year for 1996. The data are available in tabular ASCII files.

  7. Semantic search via concept annealing

    Science.gov (United States)

    Dunkelberger, Kirk A.

    2007-04-01

    Annealing, in metallurgy and materials science, is a heat treatment wherein the microstructure of a material is altered, causing changes in its properties such as strength and hardness. We define concept annealing as a lexical, syntactic, and semantic expansion capability (the removal of defects and the internal stresses that cause term- and phrase-based search failure) coupled with a directed contraction capability (semantically-related terms, queries, and concepts nucleate and grow to replace those originally deformed by internal stresses). These two capabilities are tied together in a control loop mediated by the information retrieval precision and recall metrics coupled with intuition provided by the operator. The specific representations developed have been targeted at facilitating highly efficient and effective semantic indexing and searching. This new generation of Find capability enables additional processing (i.e. all-source tracking, relationship extraction, and total system resource management) at rates, precisions, and accuracies previously considered infeasible. In a recent experiment, an order magnitude reduction in time to actionable intelligence and nearly three orderss magnitude reduction in false alarm rate was achieved.

  8. Anti-TNFa treatment in patients with rheumatoid arthritis and anti-Ro/SSA antibodies

    Directory of Open Access Journals (Sweden)

    P. Airò

    2011-09-01

    Full Text Available Objective: To analyse clinical efficacy, onset of new autoantibodies or symptoms of autoimmune disease in patients affected by rheumatoid arthritis with anti-Ro/SSA treated with anti-TNFa agents. Methods: Six anti-Ro/SSA positive subjects with RA were studied every six months until 24th month of treatment in order to detect ANA titer (IFI, anti-dsDNA (Farr, anti-cardiolipin and anti-beta2glycoprotein I (ELISA, anti-ENA (CIE. The titre of anti-Ro/SSA were analysed by ELISA. Four patients were diagnosed as overlap RA/SS. Results: Six female patients (mean age 58ys, SD 9.8ys, with long-standing RA (mean 7ys, range 5-22 ys were treated with anti-TNFa agents for a mean of 31 months (SD: 20.4 m: 4 with Infliximab and 2 with Etanercept. All the patients showed a significant reduction of DAS until 24th month (p<0.006 with stability of sicca symptoms. The titer of ANA and anti-Ro/SSA was stable, while 4 subjects developed anti-dsDNA at low titer within 6-12 months. One patient withdrawn the treatment, because of lupus-like features; another one, with HCV hepatitis, interrupted Etanercept because of elevation of liver enzymes. No anticardiolipin or antibeta2GPI antibodies were detected. One subject with RA-SS also presented a primary biliary cirrhosis: clinical and histological features of cholangitis remained stable during Etanercept treatment. Conclusions: Anti-TNFa treatment showed good efficacy and safety in anti-Ro/SSA positive patients with RA. Anti-ds- DNA antibodies at low titer appeared in most patients while the onset of lupus-like disease could be considered a rare event also in RA patients with a rich autoimmune repertoire.

  9. Elevated IL-1β levels in anti-Ro/SSA connective tissue diseases patients with prolonged corrected QTc interval.

    Science.gov (United States)

    Pisoni, Cecilia N; Reina, Silvia; Arakaki, Diego; Eimon, Alicia; Carrizo, Carolina; Borda, Enri

    2015-01-01

    Patients with systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) have increased IL-1β levels. IL-1β and other pro-inflammatory cytokines have a modulating activity on cardiac ion channels and have been associated with increased arrhythmic risk in rheumatoid arthritis patients. Likewise, adult patients with connective tissue diseases (CTDs) may have prolonged QTc intervals associated with the presence of anti-Ro/SSA antibodies. Our objective was to evaluate the presence of serum IL-1β in subjects with CTDs, in relation to the presence of anti-Ro/SSA antibodies and QTc interval duration. 12-lead electrocardiograms (ECG) were performed and blood was withdrawn, measuring electrolytes, IL-1β anti-Ro/SSA antibodies by ELISA in 73 patients with CTDs. 55 patients were anti-Ro/SSA positive and 18 were anti-Ro/SSA negative. Patients with anti-Ro/SSA positive antibodies had a significantly greater median IL-1β serum level: 7.29 (range: 0.17-17.3 pg/ml) compared to patients with anti-Ro/SSA negative antibodies whose median was: 1.67 (range 0.55-4.12 pg/ml) pRo/SSA positive versus 0 (0 %) in anti-Ro/SSA negative patients p=0.05. Median IL-1β levels were: 8.7 (range: 2.69-15.1 pg/ml) in patients with prolonged QTc interval versus median: 5.0 (range: 0.17-17.3 pg/ml) in those with normal QTc interval values (Ro/SSA antibodies and prolonged QTc intervals.

  10. Anti-Ro/SSA antibodies are associated with severe mitral valve regurgitation in patients with systemic lupus erythematosus.

    Science.gov (United States)

    Higuera-Ortiz, Violeta; Mora-Arias, Tania; Castillo-Martinez, Diana; Amezcua-Guerra, Luis M

    2017-05-01

    To assess whether anti-Ro/SSA antibodies are associated with cardiac valve disease in lupus. A single-center, medical chart review was performed. Lupus patients were divided according to its anti-Ro/SSA status and subgroups were compared for valvular abnormalities and other characteristics. Dependence of anti-Ro/SSA reactivity to anti-Ro52/TRIM21 antibodies was also evaluated. Eighty-nine lupus patients were analyzed. The most common valvular abnormalities were tricuspid (60%), mitral (41%) and pulmonary (14%) regurgitation. Thirty-six patients were positive and 53 negative for anti-Ro/SSA antibodies. In patients positive to anti-Ro/SSA, a difference was noted for anti-dsDNA (67 versus 45%; p = 0.04) and anti-La/SSB (19 versus 2%; p = 0.004) antibodies. An association between anti-Ro/SSA antibodies and severe mitral regurgitation was observed; indeed, 4/15 patients with anti-Ro/SSA and mitral regurgitation had severe forms of valvulopathy as compared to only 1/22 patients with mitral regurgitation but negative to such antibody (27 versus 5%; p = 0.02). Anti-Ro/SSA antibodies significantly elevated the risk of severe mitral regurgitation (OR = 5). Anti-Ro52/TRIM21 levels (103 ± 29 versus 42 ± 43 U/mL; p = 0.03) and anti-Ro52/TRIM21: anti-Ro/SSA ratios (0.88 ± 0.02 versus 0.35 ± 0.37; p = 0.03) were higher in patients with mitral valve regurgitation than in those with no valvulopathy. Anti-Ro/SSA antibodies, mainly against Ro52/TRIM21 antigens, may be pathologically involved in lupus-associated mitral valve regurgitation.

  11. The Bipolar Filaments Formed by Herpes Simplex Virus Type 1 SSB/Recombination Protein (ICP8) Suggest a Mechanism for DNA Annealing

    Energy Technology Data Exchange (ETDEWEB)

    Makhov, A.M.; Simon, M.; Sen, A.; Yu, X.; Griffith, J. D.; Egelman, E. H.

    2009-02-20

    Herpes simplex virus type 1 encodes a multifunctional protein, ICP8, which serves both as a single-strand binding protein and as a recombinase, catalyzing reactions involved in replication and recombination of the viral genome. In the presence of divalent ions and at low temperature, previous electron microscopic studies showed that ICP8 will form long left-handed helical filaments. Here, electron microscopic image reconstruction reveals that the filaments are bipolar, with an asymmetric unit containing two subunits of ICP8 that constitute a symmetrical dimer. This organization of the filament has been confirmed using scanning transmission electron microscopy. The pitch of the filaments is {approx} 250 {angstrom}, with {approx} 6.2 dimers per turn. Docking of a crystal structure of ICP8 into the reconstructed filament shows that the C-terminal domain of ICP8, attached to the body of the subunit by a flexible linker containing {approx} 10 residues, is packed into a pocket in the body of a neighboring subunit in the crystal in a similar manner as in the filament. However, the interactions between the large N-terminal domains are quite different in the filament from that observed in the crystal. A previously proposed model for ICP8 binding single-stranded DNA (ssDNA), based upon the crystal structure, leads to a model for a continuous strand of ssDNA near the filament axis. The bipolar nature of the ICP8 filaments means that a second strand of ssDNA would be running through this filament in the opposite orientation, and this provides a potential mechanism for how ICP8 anneals complementary ssDNA into double-stranded DNA, where each strand runs in opposite directions.

  12. GPU accelerated population annealing algorithm

    Science.gov (United States)

    Barash, Lev Yu.; Weigel, Martin; Borovský, Michal; Janke, Wolfhard; Shchur, Lev N.

    2017-11-01

    Population annealing is a promising recent approach for Monte Carlo simulations in statistical physics, in particular for the simulation of systems with complex free-energy landscapes. It is a hybrid method, combining importance sampling through Markov chains with elements of sequential Monte Carlo in the form of population control. While it appears to provide algorithmic capabilities for the simulation of such systems that are roughly comparable to those of more established approaches such as parallel tempering, it is intrinsically much more suitable for massively parallel computing. Here, we tap into this structural advantage and present a highly optimized implementation of the population annealing algorithm on GPUs that promises speed-ups of several orders of magnitude as compared to a serial implementation on CPUs. While the sample code is for simulations of the 2D ferromagnetic Ising model, it should be easily adapted for simulations of other spin models, including disordered systems. Our code includes implementations of some advanced algorithmic features that have only recently been suggested, namely the automatic adaptation of temperature steps and a multi-histogram analysis of the data at different temperatures. Program Files doi:http://dx.doi.org/10.17632/sgzt4b7b3m.1 Licensing provisions: Creative Commons Attribution license (CC BY 4.0) Programming language: C, CUDA External routines/libraries: NVIDIA CUDA Toolkit 6.5 or newer Nature of problem: The program calculates the internal energy, specific heat, several magnetization moments, entropy and free energy of the 2D Ising model on square lattices of edge length L with periodic boundary conditions as a function of inverse temperature β. Solution method: The code uses population annealing, a hybrid method combining Markov chain updates with population control. The code is implemented for NVIDIA GPUs using the CUDA language and employs advanced techniques such as multi-spin coding, adaptive temperature

  13. Understanding the microwave annealing of silicon

    Directory of Open Access Journals (Sweden)

    Chaochao Fu

    2017-03-01

    Full Text Available Though microwave annealing appears to be very appealing due to its unique features, lacking an in-depth understanding and accurate model hinder its application in semiconductor processing. In this paper, the physics-based model and accurate calculation for the microwave annealing of silicon are presented. Both thermal effects, including ohmic conduction loss and dielectric polarization loss, and non-thermal effects are thoroughly analyzed. We designed unique experiments to verify the mechanism and extract relevant parameters. We also explicitly illustrate the dynamic interaction processes of the microwave annealing of silicon. This work provides an in-depth understanding that can expedite the application of microwave annealing in semiconductor processing and open the door to implementing microwave annealing for future research and applications.

  14. Understanding Large-scale Structure in the SSA22 Protocluster Region Using Cosmological Simulations

    Science.gov (United States)

    Topping, Michael W.; Shapley, Alice E.; Steidel, Charles C.; Naoz, Smadar; Primack, Joel R.

    2018-01-01

    We investigate the nature and evolution of large-scale structure within the SSA22 protocluster region at z = 3.09 using cosmological simulations. A redshift histogram constructed from current spectroscopic observations of the SSA22 protocluster reveals two separate peaks at z = 3.065 (blue) and z = 3.095 (red). Based on these data, we report updated overdensity and mass calculations for the SSA22 protocluster. We find {δ }b,{gal}=4.8+/- 1.8 and {δ }r,{gal}=9.5+/- 2.0 for the blue and red peaks, respectively, and {δ }t,{gal}=7.6+/- 1.4 for the entire region. These overdensities correspond to masses of {M}b=(0.76+/- 0.17)× {10}15{h}-1 {M}ȯ , {M}r=(2.15+/- 0.32)× {10}15{h}-1 {M}ȯ , and {M}t=(3.19+/- 0.40)× {10}15{h}-1 {M}ȯ for the red, blue, and total peaks, respectively. We use the Small MultiDark Planck (SMDPL) simulation to identify comparably massive z∼ 3 protoclusters, and uncover the underlying structure and ultimate fate of the SSA22 protocluster. For this analysis, we construct mock redshift histograms for each simulated z∼ 3 protocluster, quantitatively comparing them with the observed SSA22 data. We find that the observed double-peaked structure in the SSA22 redshift histogram corresponds not to a single coalescing cluster, but rather the proximity of a ∼ {10}15{h}-1 {M}ȯ protocluster and at least one > {10}14{h}-1 {M}ȯ cluster progenitor. Such associations in the SMDPL simulation are easily understood within the framework of hierarchical clustering of dark matter halos. We finally find that the opportunity to observe such a phenomenon is incredibly rare, with an occurrence rate of 7.4{h}3 {{{Gpc}}}-3. Based on data obtained at the W.M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration, and was made possible by the generous financial support of the W.M. Keck Foundation.

  15. SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.

    Science.gov (United States)

    Tsang, Herbert H; Wiese, Kay C

    2010-01-01

    Ribonucleic acid (RNA), a single-stranded linear molecule, is essential to all biological systems. Different regions of the same RNA strand will fold together via base pair interactions to make intricate secondary and tertiary structures that guide crucial homeostatic processes in living organisms. Since the structure of RNA molecules is the key to their function, algorithms for the prediction of RNA structure are of great value. In this article, we demonstrate the usefulness of SARNA-Predict, an RNA secondary structure prediction algorithm based on Simulated Annealing (SA). A performance evaluation of SARNA-Predict in terms of prediction accuracy is made via comparison with eight state-of-the-art RNA prediction algorithms: mfold, Pseudoknot (pknotsRE), NUPACK, pknotsRG-mfe, Sfold, HotKnots, ILM, and STAR. These algorithms are from three different classes: heuristic, dynamic programming, and statistical sampling techniques. An evaluation for the performance of SARNA-Predict in terms of prediction accuracy was verified with native structures. Experiments on 33 individual known structures from eleven RNA classes (tRNA, viral RNA, antigenomic HDV, telomerase RNA, tmRNA, rRNA, RNaseP, 5S rRNA, Group I intron 23S rRNA, Group I intron 16S rRNA, and 16S rRNA) were performed. The results presented in this paper demonstrate that SARNA-Predict can out-perform other state-of-the-art algorithms in terms of prediction accuracy. Furthermore, there is substantial improvement of prediction accuracy by incorporating a more sophisticated thermodynamic model (efn2).

  16. Joint AGU/SSA Statement on the Comprehensive Test Ban Treaty

    Science.gov (United States)

    Lanzerotti, Louis J.

    Recognizing that the debate in the U.S. Senate on whether to ratify the Comprehensive Test Ban Treaty (CTBT) could benefit from a clear analysis of the technical limits to monitoring nuclear explosions, AGU joined with the Seismological Society of America (SSA) to carry out such an analysis. In the following policy statement, approved by both societies, seismologists speak with essentially one voice about this crucial aspect of the CTBT. This is the first time that AGU has prepared a policy statement jointly with another society, and this is the first policy statement SSA has adopted.The policy regarding AGU's procedures for developing position statements on public issues, the Union's role in advocacy of the statements, and all current AGU position statements are available online at http://www.agu. org/sci_soc/policy/sci_ pol.html.

  17. Factors influencing fetal cardiac conduction in anti-Ro/SSA-positive pregnancies.

    Science.gov (United States)

    Sonesson, Sven-Erik; Hedlund, Malin; Ambrosi, Aurélie; Wahren-Herlenius, Marie

    2017-10-01

    Congenital heart block (CHB) develops in 1-2% of anti-Ro/SSA-positive pregnancies and has a recurrence rate of 12-20%, which indicates that factors other than maternal autoantibodies are crucial for CHB to occur. Here, we aimed to evaluate the influence of factors previously associated with CHB on the occurrence of milder forms of fetal cardiac conduction disturbances, shown to occur in up to 30% of anti-Ro/SSA-positive pregnancies, and on neonatal outcome in a large cohort of prospectively followed pregnancies. The association of maternal age, season of the year and history of atrioventricular block (AVB) with the development of fetal Doppler and neonatal ECG conduction disturbances was evaluated in 212 anti-Ro52/SSA-positive singleton pregnancies. Maternal age was significantly higher in AVB II-III pregnancies but was not correlated with fetal AV time intervals in fetuses without signs of AVB II-III. AV time intervals of fetuses surveilled during the winter were significantly longer than those of fetuses surveilled during the summer. Fetal AV time intervals in consecutive pregnancies from the same women were significantly correlated. A history of AVB II-III was associated with significantly longer AV time intervals, and AVB I-III was observed at birth in 38% of babies born after a sibling with abnormal fetal AV conduction. Our study shows that AV time intervals in anti-Ro/SSA antibody-exposed fetuses during the CHB risk period are influenced by the season of the year, and reveals that the recurrence of conduction disturbances in antibody-exposed fetuses is higher than previously reported when milder forms are taken into account. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  18. Precision Laser Annealing of Focal Plane Arrays

    Energy Technology Data Exchange (ETDEWEB)

    Bender, Daniel A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); DeRose, Christopher [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Starbuck, Andrew Lea [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jenkins, Mark W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    We present results from laser annealing experiments in Si using a passively Q-switched Nd:YAG microlaser. Exposure with laser at fluence values above the damage threshold of commercially available photodiodes results in electrical damage (as measured by an increase in photodiode dark current). We show that increasing the laser fluence to values in excess of the damage threshold can result in annealing of a damage site and a reduction in detector dark current by as much as 100x in some cases. A still further increase in fluence results in irreparable damage. Thus we demonstrate the presence of a laser annealing window over which performance of damaged detectors can be at least partially reconstituted. Moreover dark current reduction is observed over the entire operating range of the diode indicating that device performance has been improved for all values of reverse bias voltage. Additionally, we will present results of laser annealing in Si waveguides. By exposing a small (<10 um) length of a Si waveguide to an annealing laser pulse, the longitudinal phase of light acquired in propagating through the waveguide can be modified with high precision, <15 milliradian per laser pulse. Phase tuning by 180 degrees is exhibited with multiple exposures to one arm of a Mach-Zehnder interferometer at fluence values below the morphological damage threshold of an etched Si waveguide. No reduction in optical transmission at 1550 nm was found after 220 annealing laser shots. Modeling results for laser annealing in Si are also presented.

  19. Rapid assessment of populations trends of invasive species: Singular Spectrum Analysis (SSA

    Directory of Open Access Journals (Sweden)

    DANA, ED

    2010-01-01

    Full Text Available Singular Spectrum Analysis (SSA is a powerful analytical approach for biodi-versity management. Its main advan-tages are due to its intuitive processing and visualization, since mathematical workflow is conceptually similar to the widely accepted Principal Components Analysis. Detailed analyses of popula-tion trends with mathematical tools are often difficult to achieve for managers by a number of reasons (large numbers or areas monitored, large number of species, insufficient statistics skills, strong knowledge level in demographic analyses, etc.. SSA has been used since the 1970’s in signal processing to clarify signal vs. noisy information, but it has also been used in climate change analy-sis and other developmental areas. Be-sides, SSA is a rapid-learning method for technicians and managers with medium level of mathematical knowledge. Free software in Unix environment is avail-able. Unfortunately, no free and friendly software is available for Win-dows SO. Although R package may offer solutions for really advanced users, it does not fit real work situations for managers of biological invasions. Cater-pillar (Gistat Group, Ltd is by now, the best option found by the author in terms of price, facility for results inter-pretation and time consumed in learn-ing. The main disadvantage is the poor content of tutorial files

  20. Sewage sludge ash (SSA in high performance concrete: characterization and application

    Directory of Open Access Journals (Sweden)

    C. M. A. Fontes

    Full Text Available ABSTRACT Sewage sludge originated from the process of treatment of wastewater has become an environmental issue for three main reasons: contains pathogens, heavy metals and organic compounds that are harmful to the environmental and human health; high volumes are daily generated; and shortage of landfill sites for proper disposal. This research deals with the viability study of sewage sludge utilization, after calcination process, as mineral admixture in the production of concrete. High-performance concretes were produced with replacement content of 5% and 10% by weight of Portland cement with sewage sludge ash (SSA. The influence of this ash was analyzed through physical and mechanical tests. Analysis showed that the mixtures containing SSA have lower values of compressive strength than the reference. The results of absorptivity, porosity and accelerated penetration of chloride ions, presents that mixtures containing ash showed reductions compared to the reference. This indicates that SSA provided refinement of the pore structure, which was confirmed by mercury intrusion porosimetry test.

  1. Cylinder packing by simulated annealing

    Directory of Open Access Journals (Sweden)

    M. Helena Correia

    2000-12-01

    Full Text Available This paper is motivated by the problem of loading identical items of circular base (tubes, rolls, ... into a rectangular base (the pallet. For practical reasons, all the loaded items are considered to have the same height. The resolution of this problem consists in determining the positioning pattern of the circular bases of the items on the rectangular pallet, while maximizing the number of items. This pattern will be repeated for each layer stacked on the pallet. Two algorithms based on the meta-heuristic Simulated Annealing have been developed and implemented. The tuning of these algorithms parameters implied running intensive tests in order to improve its efficiency. The algorithms developed were easily extended to the case of non-identical circles.Este artigo aborda o problema de posicionamento de objetos de base circular (tubos, rolos, ... sobre uma base retangular de maiores dimensões. Por razões práticas, considera-se que todos os objetos a carregar apresentam a mesma altura. A resolução do problema consiste na determinação do padrão de posicionamento das bases circulares dos referidos objetos sobre a base de forma retangular, tendo como objetivo a maximização do número de objetos estritamente posicionados no interior dessa base. Este padrão de posicionamento será repetido em cada uma das camadas a carregar sobre a base retangular. Apresentam-se dois algoritmos para a resolução do problema. Estes algoritmos baseiam-se numa meta-heurística, Simulated Annealling, cuja afinação de parâmetros requereu a execução de testes intensivos com o objetivo de atingir um elevado grau de eficiência no seu desempenho. As características dos algoritmos implementados permitiram que a sua extensão à consideração de círculos com raios diferentes fosse facilmente conseguida.

  2. SSA DISABILITY. SGA Levels Appear to Affect the Work Behavior of Relatively Few Beneficiaries, but More Data Needed

    National Research Council Canada - National Science Library

    Baucus, Max

    2002-01-01

    ... physical or mental impairment has earnings that exceed the Substantial Gainful Activity (SGA) level, which represents SSA's principal standard for determining whether a disabled individual is able to work...

  3. The East Asian Development Experience: Policy Lessons, Implications, and Recommendations for Sub-Saharan Africa (SSA) Global Competitiveness

    OpenAIRE

    Ashford C. Chea

    2012-01-01

    The paper looks at the development experience of East Asia and draws lessons for Sub-Saharan Africa in building global competitiveness. It starts with a historical perspective of both regions’ developmental trajectories. This is followed by an analysis of the causes of East Asia’s superior economic performance and development and SSA underdevelopment. The article also draws policy lessons from East Asia development strategies for SSA global competitiveness. The paper ends with a presentation ...

  4. Enthalpy relaxation and annealing effect in polystyrene.

    Science.gov (United States)

    Sakatsuji, Waki; Konishi, Takashi; Miyamoto, Yoshihisa

    2013-07-01

    The effects of thermal history on the enthalpy relaxation in polystyrene are studied by differential scanning calorimetry. The temperature dependence of the specific heat in the liquid and the glassy states, that of relaxation time, and the exponent of the Kohlrausch-Williams-Watts function are determined by measurements of the thermal response against sinusoidal temperature variation. A phenomenological model equation previously proposed to interpret the memory effect in the frozen state is applied to the enthalpy relaxation and the evolution of entropy under a given thermal history is calculated. The annealing below the glass transition temperature produces two effects on enthalpy relaxation: the decay of excess entropy with annealing time in the early stage of annealing and the increase in relaxation time due to physical aging in the later stage. The crossover of these effects is reflected in the variation of temperature of the maximum specific heat observed in the heating process after annealing and cooling.

  5. Annealing behavior of high permeability amorphous alloys

    International Nuclear Information System (INIS)

    Rabenberg, L.

    1980-06-01

    Effects of low temperature annealing on the magnetic properties of the amorphous alloy Co 71 4 Fe 4 6 Si 9 6 B 14 4 were investigated. Annealing this alloy below 400 0 C results in magnetic hardening; annealing above 400 0 C but below the crystallization temperature results in magnetic softening. Above the crystallization temperature the alloy hardens drastically and irreversibly. Conventional and high resolution transmission electron microscopy were used to show that the magnetic property changes at low temperatures occur while the alloy is truly amorphous. By imaging the magnetic microstructures, Lorentz electron microscopy has been able to detect the presence of microscopic inhomogeneities in this alloy. The low temperature annealing behavior of this alloy has been explained in terms of atomic pair ordering in the presence of the internal molecular field. Lorentz electron microscopy has been used to confirm this explanation

  6. Global warming: Temperature estimation in annealers

    Directory of Open Access Journals (Sweden)

    Jack Raymond

    2016-11-01

    Full Text Available Sampling from a Boltzmann distribution is NP-hard and so requires heuristic approaches. Quantum annealing is one promising candidate. The failure of annealing dynamics to equilibrate on practical time scales is a well understood limitation, but does not always prevent a heuristically useful distribution from being generated. In this paper we evaluate several methods for determining a useful operational temperature range for annealers. We show that, even where distributions deviate from the Boltzmann distribution due to ergodicity breaking, these estimates can be useful. We introduce the concepts of local and global temperatures that are captured by different estimation methods. We argue that for practical application it often makes sense to analyze annealers that are subject to post-processing in order to isolate the macroscopic distribution deviations that are a practical barrier to their application.

  7. SSa ameliorates the Glu uptaking capacity of astrocytes in epilepsy via AP-1/miR-155/GLAST.

    Science.gov (United States)

    Gao, Wei; Bi, Yongfeng; Ding, Li; Zhu, Weiwei; Ye, Ming

    2017-11-25

    Neuronal glutamate (Glu) release has been reported to mediate the neuronal injury of epilepsy, while Saikosaponin a (Ssa) was shown to ameliorate the epilepsy that induced by pentylenetetrazol (PTZ). However, potential interactions between glutamate release and Ssa has not been fully identified. Herein, PTZ-induced rat model were established to evaluate the neuron injury, while Ssa was used to treat the model rat. Rat astrocytes were isolated and induced by PTZ to construct cell models of epilepsy, real-time PCR and western blot were used to determine genes' expression. Luciferase reporter assay were performed to validate the relationship between miR-155-5p and glutamate aspartate transporter (GLAST). The level of Glu was sampled for HPLC measurement. Ssa treatment could decrease the level of Glu in hippocampus of rat. PTZ-induced astrocytes pretreated with Ssa significantly decreased the expression of AP-1 and miR-155, but increased the expression of GLAST, furthermore, PTZ stimulation enables astrocytes to uptake large amount of extracellular Glu. AP-1 could bind with the promoter of miR-155 to promote its transcription. MiR-155 tragets GLAST to govern its expression. Ssa treatment played pivotal roles in PTZ-induced epilepsy by promoting the expression of GLAT1 and uptaking of Glu, which was mediated by the expression of AP-1 and miR-155. Copyright © 2017. Published by Elsevier Inc.

  8. Structural relaxation in annealed hyperquenched basaltic glasses

    DEFF Research Database (Denmark)

    Guo, Xiaoju; Mauro, John C.; Potuzak, M.

    2012-01-01

    The enthalpy relaxation behavior of hyperquenched (HQ) and annealed hyperquenched (AHQ) basaltic glass is investigated through calorimetric measurements. The results reveal a common onset temperature of the glass transition for all the HQ and AHQ glasses under study, indicating that the primary...... relaxation is activated at the same temperature regardless of the initial departure from equilibrium. The analysis of secondary relaxation at different annealing temperatures provides insights into the enthalpy recovery of HQ glasses....

  9. Irradiation embrittlement and optimisation of annealing

    International Nuclear Information System (INIS)

    1993-01-01

    This conference is composed of 30 papers grouped in 6 sessions related to the following themes: neutron irradiation effects in pressure vessel steels and weldments used in PWR, WWER and BWR nuclear plants; results from surveillance programmes (irradiation induced damage and annealing processes); studies on the influence of variations in irradiation conditions and mechanisms, and modelling; mitigation of irradiation effects, especially through thermal annealing; mechanical test procedures and specimen size effects

  10. Boosting quantum annealer performance via sample persistence

    Science.gov (United States)

    Karimi, Hamed; Rosenberg, Gili

    2017-07-01

    We propose a novel method for reducing the number of variables in quadratic unconstrained binary optimization problems, using a quantum annealer (or any sampler) to fix the value of a large portion of the variables to values that have a high probability of being optimal. The resulting problems are usually much easier for the quantum annealer to solve, due to their being smaller and consisting of disconnected components. This approach significantly increases the success rate and number of observations of the best known energy value in samples obtained from the quantum annealer, when compared with calling the quantum annealer without using it, even when using fewer annealing cycles. Use of the method results in a considerable improvement in success metrics even for problems with high-precision couplers and biases, which are more challenging for the quantum annealer to solve. The results are further enhanced by applying the method iteratively and combining it with classical pre-processing. We present results for both Chimera graph-structured problems and embedded problems from a real-world application.

  11. Nanocrystalline magnetic materials obtained by flash annealing

    Directory of Open Access Journals (Sweden)

    Murakami R.K.

    1999-01-01

    Full Text Available The aim of the present work was to produce enhanced-remanence nanocrystalline magnetic material by crystallizing amorphous or partially amorphous Pr4.5Fe77B18.5 alloys by the flash annealing process, also known as the dc-Joule heating process, and to determine the optimal conditions for obtaining good magnetic coupling between the magnetic phases present in this material. Ribbons of Pr4.5Fe77B18.5 were produced by melt spinning and then annealed for 10-30 s at temperatures 500 - 640 °C by passing current through the sample to develop the enhanced-remanence nanocrystalline magnetic material. These materials were studied by X-ray diffraction, differential thermal analysis and magnetic measurements. Coercivity increases of up to 15% were systematically observed in relation to furnace-annealed material. Two different samples were carefully examined: (i a sample annealed at 600 °C which showed the highest coercive field Hc and remanence ratio Mr/Ms and (ii a sample annealed at 520 °C which showed phase separation in the second quadrant demagnetization curve. Our results are in agreement with other studies which show that flash annealing improves the magnetic properties of some amorphous ferromagnetic ribbons.

  12. Energy Saving in Industrial Annealing Furnaces

    Directory of Open Access Journals (Sweden)

    Fatma ÇANKA KILIÇ

    2018-03-01

    Full Text Available In this study, an energy efficiency studies have been carried out in a natural gas-fired rolling mill annealing furnace of an industrial establishment. In this context, exhaust gas from the furnace has been examined in terms of waste heat potential. In the examinations that have been made in detail; waste heat potential was found as 3.630,31 kW. Technical and feasibility studies have been carried out to realize electricity production through an Organic Rankine Cycle (ORC system for evaluating the waste heat potential of the annealing furnace. It has been calculated that 1.626.378,88 kWh/year of electricity can be generated by using the exhaust gas waste heat of the annealing furnace through an ORC system to produce electric energy with a net efficiency of 16%. The financial value of this energy was determined as 436.032,18 TL/year and the simple repayment period of the investment was 8,12 years. Since the annealing period of the annealing furnace is 2800 hours/year, the investment has not been found to be feasible in terms of the feasibility studies. However, the investment suitability can be assured when the annealing furnace is operating at full capacity for 8,000 hours or more annually.

  13. Origin of reverse annealing effect in hydrogen-implanted silicon

    Energy Technology Data Exchange (ETDEWEB)

    Di, Zengfeng [Los Alamos National Laboratory; Nastasi, Michael A [Los Alamos National Laboratory; Wang, Yongqiang [Los Alamos National Laboratory

    2009-01-01

    In contradiction to conventional damage annealing, thermally annealed H-implanted Si exhibits an increase in damage or reverse annealing behavior, whose mechanism has remained elusive. On the basis of quantitative high resolution transmission electron microscopy combined with channeling Rutherford backscattering analysis, we conclusively elucidate that the reverse annealing effect is due to the nucleation and growth of hydrogen-induce platelets. Platelets are responsible for an increase in the height and width the channeling damage peak following increased isochronal anneals.

  14. Swarm Utilisation Analysis: LEO satellite observations for the ESA's SSA Space Weather network

    Science.gov (United States)

    Kervalishvili, Guram; Stolle, Claudia; Rauberg, Jan; Olsen, Nils; Vennerstrøm, Susanne; Gullikstad Johnsen, Magnar; Hall, Chris

    2017-04-01

    ESA's (European Space Agency) constellation mission Swarm was successfully launched on 22 November 2013. The three satellites achieved their final constellation on 17 April 2014 and since then Swarm-A and Swarm-C orbiting the Earth at about 470 km (flying side-by-side) and Swarm-B at about 520 km altitude. Each of Swarm satellite carries instruments with high precision to measure magnetic and electric fields, neutral and plasma densities, and TEC (Total Electron Content) for which a dual frequency GPS receiver is used. SUA (Swarm Utilisation Analysis) is a project of the ESA's SSA (Space Situational Awareness) SWE (Space Weather) program. Within this framework GFZ (German Research Centre for Geosciences, Potsdam, Germany) and DTU (National Space Institute, Kongens Lyngby, Denmark) have developed two new Swarm products ROT (Rate Of change of TEC) and PEJ (Location and intensity level of Polar Electrojets), respectively. ROT is derived as the first time derivative from the Swarm measurements of TEC at 1 Hz sampling. ROT is highly relevant for users in navigation and communications: strong plasma gradients cause GPS signal degradation or even loss of GPS signal. Also, ROT is a relevant space weather asset irrespective of geomagnetic activity, e.g., high amplitude values of ROT occur during all geomagnetic conditions. PEJ is derived from the Swarm measurements of the magnetic field strength at 1 Hz sampling. PEJ has a high-level importance for power grid companies since the polar electrojet is a major cause for ground-induced currents. ROT and PEJ together with five existing Swarm products TEC, electron density, IBI (Ionospheric Bubble Index), FAC (Field-Aligned Current), and vector magnetic field build the SUA service prototype. This prototype will be integrated into ESA's SSA Space Weather network as a federated service and will be available soon from ESA's SSA SWE Ionospheric Weather and Geomagnetic Conditions Expert Service Centres (ESCs).

  15. Overview of Human-Centric Space Situational Awareness (SSA) Science and Technology (S&T)

    Science.gov (United States)

    Ianni, J.; Aleva, D.; Ellis, S.

    2012-09-01

    A number of organizations, within the government, industry, and academia, are researching ways to help humans understand and react to events in space. The problem is both helped and complicated by the fact that there are numerous data sources that need to be planned (i.e., tasked), collected, processed, analyzed, and disseminated. A large part of the research is in support of the Joint Space Operational Center (JSpOC), National Air and Space Intelligence Center (NASIC), and similar organizations. Much recent research has been specifically targeting the JSpOC Mission System (JMS) which has provided a unifying software architecture. This paper will first outline areas of science and technology (S&T) related to human-centric space situational awareness (SSA) and space command and control (C2) including: 1. Object visualization - especially data fused from disparate sources. Also satellite catalog visualizations that convey the physical relationships between space objects. 2. Data visualization - improve data trend analysis as in visual analytics and interactive visualization; e.g., satellite anomaly trends over time, space weather visualization, dynamic visualizations 3. Workflow support - human-computer interfaces that encapsulate multiple computer services (i.e., algorithms, programs, applications) into a 4. Command and control - e.g., tools that support course of action (COA) development and selection, tasking for satellites and sensors, etc. 5. Collaboration - improve individuals or teams ability to work with others; e.g., video teleconferencing, shared virtual spaces, file sharing, virtual white-boards, chat, and knowledge search. 6. Hardware/facilities - e.g., optimal layouts for operations centers, ergonomic workstations, immersive displays, interaction technologies, and mobile computing. Secondly we will provide a survey of organizations working these areas and suggest where more attention may be needed. Although no detailed master plan exists for human

  16. Potential use of sewage sludge ash (SSA as a cement replacement in precast concrete blocks

    Directory of Open Access Journals (Sweden)

    Pérez-Carrión, M.

    2014-03-01

    Full Text Available The present study explored the technological feasibility of re-using sewage sludge ash (SSA as a Portland cement replacement in commercially manufactured pre cast concrete blocks. The blocks analysed were made to the guidelines laid down in Spain’s National Plan for Waste Water Treatment Plant Sludge, 2001–2006, and European Union specifications (CE marking for such products. Performance was compared in three families of blocks, with 0, 10 and 20% SSA. The findings proved that SSA is apt for pre cast concrete block manufacture and that, in addition to the economic and environmental benefits afforded, its use would improve certain of the properties of conventional block.El objetivo de esta investigación es estudiar el uso potencial de las cenizas de lodos de depuradora (CLD, como sustitución del cemento Portland en bloques de hormigón prefabricados, de forma que se pueda lograr una revalorización de este material de desecho mediante este procedimiento. La metodología utilizada en este trabajo se rige por las directrices del Plan Nacional Español de Lodos de Aguas Residuales de 2001–2006, y por las exigencias del Consejo Europeo (marcado CE, que es obligatorio para este tipo de productos. Se han utilizado dos niveles de sustitución de cemento (10% y 20%, y todos los resultados han sido referidos a las muestras control. Los resultados obtenidos muestran que es posible utilizar una sustitución parcial del cemento por CLD, en la fabricación de bloques de hormigón prefabricados, y por lo tanto, se pueden conseguir beneficios económicos y ambientales, así como la mejora de una serie de propiedades.

  17. MELiSSA third compartment: Nitrosomonas europaea and Nitrobacter winogradskyi axenic cultures in bioreactors

    Science.gov (United States)

    Cruvellier, Nelly; Lasseur, Christophe; Poughon, Laurent; Creuly, Catherine; Dussap, Gilles

    Nitrogen is a key element for the life and its balance on Earth is regulated by the nitrogen cycle. This loop includes several steps among which nitrification that permits the transformation of the ammonium into nitrate. The MELiSSA loop is an artificial ecosystem designed for life support systems (LSS). It is based on the carbon and nitrogen cycles and the recycling of the non-edible part of the higher plants and the waste produced by the crew. In this order, all the wastes are collected in the first compartment to degrade them into organic acids and CO2. These compounds are joining the second compartment which is a photoheterotrophic compartment where at the outlet an organic-free medium containing ammonium is produced. This solution will be the substrate of the third compartment where nitrification is done. This compartment has to oxidize the ammonium into nitrate, and this biological reaction needs two steps. In the MELiSSA loop, the nitrification is carried out by two bacteria: Nitrosomonas europaea ATCC® 19718™ which is oxidizing ammonia into nitrite and Nitrobacter winogradskyi ATCC® 25391™ which is producing nitrate from nitrite in the third compartment. These two bacteria are growing in axenic conditions on a fixed bed bioreactor filled with Biostyr® beads. The nitrogen compounds are controlled by Ionic Chromatography and colorimetric titration for each sample. The work presented here deals with the culture of both bacteria in pure cultures and mixed cultures in stirred and aerated bioreactors of different volumes. The first aim of our work is the characterization of the bacteria growth in bioreactors and in the nitrifying fixed-bed column. The experimental results confirm that the growth is slow; the maximal growth rate in suspended cultures is 0.054h-1 for Nitrosomonas europaea and 0.022h-1 for Nitrobacter winogradskyi. Mixed cultures are difficult to control and operate but one could be done for more than 500 hours. The characterization of the

  18. Spatial correlation between submillimetre and Lyman-alpha galaxies in the SSA 22 protocluster.

    Science.gov (United States)

    Tamura, Yoichi; Kohno, Kotaro; Nakanishi, Kouichiro; Hatsukade, Bunyo; Iono, Daisuke; Wilson, Grant W; Yun, Min S; Takata, Tadafumi; Matsuda, Yuichi; Tosaki, Tomoka; Ezawa, Hajime; Perera, Thushara A; Scott, Kimberly S; Austermann, Jason E; Hughes, David H; Aretxaga, Itziar; Chung, Aeree; Oshima, Tai; Yamaguchi, Nobuyuki; Tanaka, Kunihiko; Kawabe, Ryohei

    2009-05-07

    Lyman-alpha emitters are thought to be young, low-mass galaxies with ages of approximately 10(8) yr (refs 1, 2). An overdensity of them in one region of the sky (the SSA 22 field) traces out a filamentary structure in the early Universe at a redshift of z approximately 3.1 (equivalent to 15 per cent of the age of the Universe) and is believed to mark a forming protocluster. Galaxies that are bright at (sub)millimetre wavelengths are undergoing violent episodes of star formation, and there is evidence that they are preferentially associated with high-redshift radio galaxies, so the question of whether they are also associated with the most significant large-scale structure growing at high redshift (as outlined by Lyman-alpha emitters) naturally arises. Here we report an imaging survey of 1,100-microm emission in the SSA 22 region. We find an enhancement of submillimetre galaxies near the core of the protocluster, and a large-scale correlation between the submillimetre galaxies and the low-mass Lyman-alpha emitters, suggesting synchronous formation of the two very different types of star-forming galaxy within the same structure at high redshift. These results are in general agreement with our understanding of the formation of cosmic structure.

  19. BOREAS TE-1 CO2 and CH4 Flux Data Over the SSA-OBS Site

    Science.gov (United States)

    Anderson, Darwin; Papagno, Andrea; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor)

    2000-01-01

    The BOREAS TE-1 team collected various data to characterize the soil-plant systems in the BOREAS SSA. Particular emphasis was placed on nutrient biochemistry, the stores and transfers of organic carbon, and how the characteristics were related to measured methane fluxes. The overall transect in the Prince Albert National Park (Saskatchewan, Canada) included the major plant communities and related soils that occurred in that section of the boreal forest. Soil physical, chemical, and biological measurements along the transect were used to characterize the static environment, which allowed them to be related to methane fluxes. Chamber techniques were used to provide a measure of methane production/uptake. Chamber measurements coupled with flask sampling were used to determine the seasonality of methane fluxes. This particular data set contains carbon dioxide and methane flux values from the SSA-OBS site. The data were collected from 09-Jun to 04-Sep-1994. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  20. BOREAS TE-1 CH4 Flux Data Over The SSA-OA

    Science.gov (United States)

    Anderson, Darwin; Papagno, Andrea; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor)

    2000-01-01

    The BOREAS TE-1 team collected various data to characterize the soil-plant systems in the BOREAS SSA. Particular emphasis was placed on nutrient biochemistry, the stores and transfers of organic carbon, and how the characteristics were related to measured methane fluxes. The overall transect in the Prince Albert National Park (Saskatchewan, Canada) included the major plant communities and related soils that occurred in that section of the boreal forest. Soil physical, chemical, and biological measurements along the transect were used to characterize the static environment, which allowed them to be related to methane fluxes. Chamber techniques were used to provide a measure of methane production/uptake. Chamber measurements coupled with flask sampling were used to determine the seasonality of methane fluxes. This particular data set contains methane flux and soil profile methane concentration values from the SSA-OA site. The data were collected from 29-May to 17-Sep-1994. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  1. Deterministic quantum annealing expectation-maximization algorithm

    Science.gov (United States)

    Miyahara, Hideyuki; Tsumura, Koji; Sughiyama, Yuki

    2017-11-01

    Maximum likelihood estimation (MLE) is one of the most important methods in machine learning, and the expectation-maximization (EM) algorithm is often used to obtain maximum likelihood estimates. However, EM heavily depends on initial configurations and fails to find the global optimum. On the other hand, in the field of physics, quantum annealing (QA) was proposed as a novel optimization approach. Motivated by QA, we propose a quantum annealing extension of EM, which we call the deterministic quantum annealing expectation-maximization (DQAEM) algorithm. We also discuss its advantage in terms of the path integral formulation. Furthermore, by employing numerical simulations, we illustrate how DQAEM works in MLE and show that DQAEM moderate the problem of local optima in EM.

  2. Traffic Flow Optimization Using a Quantum Annealer

    Directory of Open Access Journals (Sweden)

    Florian Neukart

    2017-12-01

    Full Text Available Quantum annealing algorithms belong to the class of metaheuristic tools, applicable for solving binary optimization problems. Hardware implementations of quantum annealing, such as the quantum processing units (QPUs produced by D-Wave Systems, have been subject to multiple analyses in research, with the aim of characterizing the technology’s usefulness for optimization and sampling tasks. In this paper, we present a real-world application that uses quantum technologies. Specifically, we show how to map certain parts of a real-world traffic flow optimization problem to be suitable for quantum annealing. We show that time-critical optimization tasks, such as continuous redistribution of position data for cars in dense road networks, are suitable candidates for quantum computing. Due to the limited size and connectivity of current-generation D-Wave QPUs, we use a hybrid quantum and classical approach to solve the traffic flow problem.

  3. Thermal annealing of tilted fiber Bragg gratings

    Science.gov (United States)

    González-Vila, Á.; Rodríguez-Cobo, L.; Mégret, P.; Caucheteur, C.; López-Higuera, J. M.

    2016-05-01

    We report a practical study of the thermal decay of cladding mode resonances in tilted fiber Bragg gratings, establishing an analogy with the "power law" evolution previously observed on uniform gratings. We examine how this process contributes to a great thermal stability, even improving it by means of a second cycle slightly increasing the annealing temperature. In addition, we show an improvement of the grating spectrum after annealing, with respect to the one just after inscription, which suggests the application of this method to be employed to improve saturation issues during the photo-inscription process.

  4. Hardening by annealing: insights from different alloys

    International Nuclear Information System (INIS)

    Renk, O; Pippan, R; Hohenwarter, A; Schuh, B; Li, J H

    2015-01-01

    In contrast to the general notion about the annealing behavior of coarse grained materials, hardening phenomena in nanocrystalline materials can occur. Although the phenomena have already been recognized several years ago, the mechanisms behind are still controversially discussed. For example, the influence of solutes segregated to grain boundaries on the strengthening mechanism is unclear. We present a combination of atom probe tomography and mechanical data to reveal the role of segregations to the strengthening. The results show that despite large modifications of the boundary chemistry the mechanical behavior remains widely unaffected. Additionally, it will be shown that hardening upon annealing can only occur below a material-specific grain size threshold value. (paper)

  5. Modular annealing apparatus for in situ reactor vessel annealing and related method of assembly

    International Nuclear Information System (INIS)

    Bau, F.I.; Mavretish, R.S.

    1992-01-01

    This patent describes a method for annealing a nuclear reactor vessel in a containment building. It comprises pre-fabricating a plurality of heater segments at a location outside the containment building; transporting the plurality of heater segments to the containment building; removing the core and internals and storing same; installing temporary shielding for the stored internals; introducing each of the plurality of heater segments through an equipment hatch in the containment building; assembling the plurality of heater segments to form an annealing apparatus; and annealing the reactor vessel

  6. Rad51 ATP binding but not hydrolysis is required to recruit Rad10 in synthesis-dependent strand annealing sites inS. cerevisiae.

    Science.gov (United States)

    Karlin, Justin; Fischhaber, Paula L

    2013-06-01

    Several modes of eukaryotic of DNA double strand break repair (DSBR) depend on synapsis of complementary DNA. The Rad51 ATPase, the S. cerevisiae homolog of E. coli RecA, plays a key role in this process by catalyzing homology searching and strand exchange between an invading DNA strand and a repair template (e.g. sister chromatid or homologous chromosome). Synthesis dependent strand annealing (SDSA), a mode of DSBR, requires Rad51. Another repair enzyme, the Rad1-Rad10 endonuclease, acts in the final stages of SDSA, hydrolyzing 3' overhanging single-stranded DNA. Here we show in vivo by fluorescence microscopy that the ATP binding function of yeast Rad51 is required to recruit Rad10 SDSA sites indicating that Rad51 pre-synaptic filament formation must occur prior to the recruitment of Rad1-Rad10. Our data also show that Rad51 ATPase activity, an important step in Rad51 filament disassembly, is not absolutely required in order to recruit Rad1-Rad10 to DSB sites.

  7. A Cloud-based, Open-Source, Command-and-Control Software Paradigm for Space Situational Awareness (SSA)

    Science.gov (United States)

    Melton, R.; Thomas, J.

    With the rapid growth in the number of space actors, there has been a marked increase in the complexity and diversity of software systems utilized to support SSA target tracking, indication, warning, and collision avoidance. Historically, most SSA software has been constructed with "closed" proprietary code, which limits interoperability, inhibits the code transparency that some SSA customers need to develop domain expertise, and prevents the rapid injection of innovative concepts into these systems. Open-source aerospace software, a rapidly emerging, alternative trend in code development, is based on open collaboration, which has the potential to bring greater transparency, interoperability, flexibility, and reduced development costs. Open-source software is easily adaptable, geared to rapidly changing mission needs, and can generally be delivered at lower costs to meet mission requirements. This paper outlines Ball's COSMOS C2 system, a fully open-source, web-enabled, command-and-control software architecture which provides several unique capabilities to move the current legacy SSA software paradigm to an open source model that effectively enables pre- and post-launch asset command and control. Among the unique characteristics of COSMOS is the ease with which it can integrate with diverse hardware. This characteristic enables COSMOS to serve as the command-and-control platform for the full life-cycle development of SSA assets, from board test, to box test, to system integration and test, to on-orbit operations. The use of a modern scripting language, Ruby, also permits automated procedures to provide highly complex decision making for the tasking of SSA assets based on both telemetry data and data received from outside sources. Detailed logging enables quick anomaly detection and resolution. Integrated real-time and offline data graphing renders the visualization of the both ground and on-orbit assets simple and straightforward.

  8. Intelligent medical image processing by simulated annealing

    International Nuclear Information System (INIS)

    Ohyama, Nagaaki

    1992-01-01

    Image processing is being widely used in the medical field and already has become very important, especially when used for image reconstruction purposes. In this paper, it is shown that image processing can be classified into 4 categories; passive, active, intelligent and visual image processing. These 4 classes are explained at first through the use of several examples. The results show that the passive image processing does not give better results than the others. Intelligent image processing, then, is addressed, and the simulated annealing method is introduced. Due to the flexibility of the simulated annealing, formulated intelligence is shown to be easily introduced in an image reconstruction problem. As a practical example, 3D blood vessel reconstruction from a small number of projections, which is insufficient for conventional method to give good reconstruction, is proposed, and computer simulation clearly shows the effectiveness of simulated annealing method. Prior to the conclusion, medical file systems such as IS and C (Image Save and Carry) is pointed out to have potential for formulating knowledge, which is indispensable for intelligent image processing. This paper concludes by summarizing the advantages of simulated annealing. (author)

  9. Influence of Intercritical Annealing Temperature on Mechanical ...

    African Journals Online (AJOL)

    The fracture surfaces of the impact test samples were examined using the scanning electron microscope (SEM). Micros structural evolution of the samples was also examined with an optical microscope. The results showed that all the evaluated mechanical properties were improved by intercritical annealing, with the ...

  10. Finite-time thermodynamics and simulated annealing

    International Nuclear Information System (INIS)

    Andresen, B.

    1989-01-01

    When the general, global optimization technique simulated annealing was introduced by Kirkpatrick et al. (1983), this mathematical algorithm was based on an analogy to the statistical mechanical behavior of real physical systems like spin glasses, hence the name. In the intervening span of years the method has proven exceptionally useful for a great variety of extremely complicated problems, notably NP-problems like the travelling salesman, DNA sequencing, and graph partitioning. Only a few highly optimized heuristic algorithms (e.g. Lin, Kernighan 1973) have outperformed simulated annealing on their respective problems (Johnson et al. 1989). Simulated annealing in its current form relies only on the static quantity 'energy' to describe the system, whereas questions of rate, as in the temperature path (annealing schedule, see below), are left to intuition. We extent the connection to physical systems and take over further components from thermodynamics like ensemble, heat capacity, and relaxation time. Finally we refer to finite-time thermodynamics (Andresen, Salomon, Berry 1984) for a dynamical estimate of the optimal temperature path. (orig.)

  11. influence of intercritical annealing temperature on mechanical

    African Journals Online (AJOL)

    User

    Keywords: intercritical annealing, dual phase steel, mechanical properties, microstructure. 1. INTRODUCTION. Steel, is world's most “advanced” material. It is the most widely used engineering material, essentially due to the fact that it can be manufactured at very competitive cost in large quantities to very precise.

  12. Thermal annealing in neutron-irradiated tribromobenzenes

    DEFF Research Database (Denmark)

    Siekierska, K.E.; Halpern, A.; Maddock, A. G.

    1968-01-01

    The distribution of 82Br among various products in neutron-irradiated isomers of tribromobenzene has been investigated, and the effect of thermal annealing examined. Reversed-phase partition chromatography was employed for the determination of radioactive organic products, and atomic bromine...

  13. The UL8 subunit of the helicase-primase complex of herpes simplex virus promotes DNA annealing and has a high affinity for replication forks.

    Science.gov (United States)

    Bermek, Oya; Weller, Sandra K; Griffith, Jack D

    2017-09-22

    During lytic infection, herpes simplex virus (HSV) DNA is replicated by a mechanism involving DNA recombination. For instance, replication of the HSV-1 genome produces X- and Y-branched structures, reminiscent of recombination intermediates. HSV-1's replication machinery includes a trimeric helicase-primase composed of helicase (UL5) and primase (UL52) subunits and a third subunit, UL8. UL8 has been reported to stimulate the helicase and primase activities of the complex in the presence of ICP8, an HSV-1 protein that functions as an annealase, a protein that binds complementary single-stranded DNA (ssDNA) and facilitates its annealing to duplex DNA. UL8 also influences the intracellular localization of the UL5/UL52 subunits, but UL8's catalytic activities are not known. In this study we used a combination of biochemical techniques and transmission electron microscopy. First, we report that UL8 alone forms protein filaments in solution. Moreover, we also found that UL8 binds to ssDNAs >50-nucletides long and promotes the annealing of complementary ssDNA to generate highly branched duplex DNA structures. Finally, UL8 has a very high affinity for replication fork structures containing a gap in the lagging strand as short as 15 nucleotides, suggesting that UL8 may aid in directing or loading the trimeric complex onto a replication fork. The properties of UL8 uncovered here suggest that UL8 may be involved in the generation of the X- and Y-branched structures that are the hallmarks of HSV replication. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. On application of the SSA method in the pulsating combustion studies

    Science.gov (United States)

    Berg, I. A.; Porshnev, S. V.; Oshchepkova, V. Y.

    2017-11-01

    Pulsating combustion is among combustion control methods used to suppress formation of NOx. An upgraded automatic setup with a direct gas injection burner was used for pulsating torch studies. Experiments resulted in obtaining time series of torch area changing in longitudinal section. Singular Spectral Analysis method (SSA) upgraded to allow for choosing the size of the window was used. Spectra of the extracted components of the time series demonstrate that they contain periodic components that match the fuel supply valve on/off cycle frequency. When increasing the control frequency the spectrum of the extracted component of the time series gets broader. With further frequency increase, the spectrum approaches that of no control action and the system operates in quasi-continuous mode. The results correspond to the results obtained earlier through the spectrum analysis that confirms the phenomenon of periodic change of the torch core area in the longitudinal section under pulsating supply of fuel.

  15. Analysis on the spatial structure of Shanghai tourism industry using the SSA method

    Directory of Open Access Journals (Sweden)

    LIU Jinwei

    2013-10-01

    Full Text Available This paper utilizes SSA method to calculate the comparative advantage of tourism industry over the other main departments in the tertiary industry in Shanghai from 2000 to 2010.The research results indicate that the structural advantage and competitive of Shanghai tourism industry are obvious,being stronger than the financial,real estate.While the developing levels among different districts are in great difference.The central metropolitan area has a higher gross value and more commercial patterns,and makes more contribution to the whole city tourism than those in suburb area;while its developing speed is slowing down.In the suburb area the gross value in tourism industry is lower,but it is increasing faster than those in urban area.The tourism industry in this area is facing with some problems as the changes in the development pattern,the cooperation of different tourism enterprises.

  16. Scalable effective-temperature reduction for quantum annealers via nested quantum annealing correction

    Science.gov (United States)

    Vinci, Walter; Lidar, Daniel A.

    2018-02-01

    Nested quantum annealing correction (NQAC) is an error-correcting scheme for quantum annealing that allows for the encoding of a logical qubit into an arbitrarily large number of physical qubits. The encoding replaces each logical qubit by a complete graph of degree C . The nesting level C represents the distance of the error-correcting code and controls the amount of protection against thermal and control errors. Theoretical mean-field analyses and empirical data obtained with a D-Wave Two quantum annealer (supporting up to 512 qubits) showed that NQAC has the potential to achieve a scalable effective-temperature reduction, Teff˜C-η , with 0 learning applications. Since we demonstrate that NQAC achieves error correction via a reduction of the effective-temperature of the quantum annealing device, our results address the problem of the "temperature scaling law for quantum annealers," which requires the temperature of quantum annealers to be reduced as problems of larger sizes are attempted to be solved.

  17. Leptin gene polymorphism in Indian Sahiwal cattle by single strand ...

    African Journals Online (AJOL)

    These leptin gene variants can be sequenced and screened in the entire population to develop single nucleotide polymorphisms (SNPs) for association studies with different productive and reproductive performances and marker assisted selection. Keywords: Leptin gene, PCR-SSCP, genetic variability, dairy cattle

  18. Low titer, isolated anti Ro/SSA 60 kd antibodies is correlated with positive pregnancy outcomes in women at risk of congenital heart block.

    Science.gov (United States)

    Tonello, Marta; Hoxha, Ariela; Mattia, Elena; Zambon, Alessandra; Visentin, Silvia; Cerutti, Alessia; Ghirardello, Anna; Milanesi, Ornella; Ruffatti, Amelia

    2017-05-01

    Congenital heart block (CHB) is an autoantibody mediated disorder presumably caused by placental transmission of maternal autoantibodies to Ro/SSA 52 kd, p200, Ro/SSA 60 kd, La/SSB ribonucleoproteins. This study investigated the clinical significance of isolated anti-Ro/SSA 52 kd, anti-p200, anti-Ro/SSA 60 kd, and anti-La/SSB antibodies in positive pregnant patients. One hundred sixty-three pregnant women positive to anti-Ro/SSA 52 kd and/or anti-Ro/SSA 60 kd and/or anti-La/SSB antibodies were prospectively enrolled in the study. Anti-Ro52, anti-Ro60, anti-p200, and anti-La antibodies were assayed using home-made ELISA assays. Isolated antibody positivity was found in 25 women (15.3%), while multiple antibody positivity in 138 (84.7%). Twenty-four developed CHB, and the 139 had a favorable pregnancy outcome. The prevalence of isolated anti-Ro/SSA 60 kd antibodies was significantly higher (p Ro/SSA 60 kd antibodies.

  19. 75 FR 30839 - Privacy Act of 1974; CMS Computer Match No. 2010-03, HHS Computer Match No. 1003, SSA Computer...

    Science.gov (United States)

    2010-06-02

    ... Match No. 1003 SSA Computer Match No. 1048 IRS Project No. 241 NAME: ``Medicare Secondary Payer (MSP... 1974; CMS Computer Match No. 2010-03, HHS Computer Match No. 1003, SSA Computer Match No. 1048, IRS Project No. 241 AGENCY: Department of Health and Human Services (HHS), Centers for Medicare & Medicaid...

  20. Validation study - on-road evaluation of the Cooperative Intersection Collision Avoidance System - Stop Sign Assist sign : (CICAS-SSA Report #5).

    Science.gov (United States)

    2009-11-01

    The CICAS-SSA sign is a roadside driver support system that is intended to improve gap rejection at rural stop-controlled intersections. The CICAS-SSA system tracks vehicle locations on a major roadway and then displays a message to a driver on the m...

  1. 20 CFR 411.321 - Under what conditions will SSA terminate an agreement with an EN due to inadequate performance?

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Under what conditions will SSA terminate an agreement with an EN due to inadequate performance? 411.321 Section 411.321 Employees' Benefits SOCIAL SECURITY ADMINISTRATION THE TICKET TO WORK AND SELF-SUFFICIENCY PROGRAM Employment Networks § 411.321 Under...

  2. Outcome in 212 anti-Ro/SSA-positive pregnancies and population-based incidence of congenital heart block.

    Science.gov (United States)

    Skog, Amanda; Lagnefeldt, Linda; Conner, Peter; Wahren-Herlenius, Marie; Sonesson, Sven-Erik

    2016-01-01

    We investigated the effects of maternal autoimmune disease and fetal congenital heart block (CHB) on pregnancy outcomes in anti-Ro/SSA-positive women and assessed the population-based incidence of isolated CHB. One hundred and ninety nine anti-Ro/SSA-positive pregnancies were prospectively followed at our center (2000-2013). Seven fetuses developed atrioventricular block (AVB) II-III. In this period, another 13 anti-Ro/SSA-positive pregnancies were referred for fetal bradycardia, subsequently diagnosed with AVB II-III. Cesarean section rates, gestational age, body measurements at birth, and the incidence of CHB in these 212 pregnancies were analyzed in relation to fetal atrioventricular conduction and maternal diagnosis and compared with data from the Medical Birth Registry on 352,104 pregnancies in the Stockholm County. The prevalence of maternal systemic lupus erythematosus (SLE) and primary Sjögren's syndrome and the outcomes at birth were similar in normal conduction and AVB I cases. Only 1/20 AVB II-III cases (0/7 in the surveillance group) had a mother diagnosed with SLE, compared with 73/192 in cases with normal conduction or AVB I. Excluding cases with AVB II-III, SLE mothers more frequently delivered by cesarean section (31% vs. 20%, p Ro/SSA-positive women, which has clinical relevance when counseling rheumatic patients considering pregnancy. © 2015 Nordic Federation of Societies of Obstetrics and Gynecology.

  3. Persistent fetal sinus bradycardia associated with maternal anti-SSA/Ro and anti-SSB/La antibodies

    NARCIS (Netherlands)

    Chockalingam, Priya; Jaeggi, Edgar T.; Rammeloo, Lukas A.; Haak, Monique C.; Adama van Scheltema, Phebe N.; Breur, Johannes M. P. J.; Bartelings, Margot M.; Clur, Sally-Ann B.; Blom, Nico A.

    2011-01-01

    To study the clinical course and outcome of fetal sinus bradycardia (SB) due to maternal antibody-induced sinus node dysfunction. We reviewed the maternal, prenatal, and postnatal findings of fetuses with SB associated with elevated maternal anti-SSA/Ro and anti-SSB/La antibodies. Of the 6 cases

  4. 76 FR 77238 - Submission for OMB Review; Comment Request; The SSA-NIH Collaboration to Improve the Disability...

    Science.gov (United States)

    2011-12-12

    ... Collaboration to Improve the Disability Determination Process: Validation of IRT-CAT tools. Type of Information...; Comment Request; The SSA-NIH Collaboration to Improve the Disability Determination Process: Validation of... in RMD will be collecting information through a contractor (Boston University- Health and Disability...

  5. 76 FR 12397 - Privacy Act of 1974, as Amended; Computer Matching Program (SSA/Bureau of the Public Debt (BPD...

    Science.gov (United States)

    2011-03-07

    ...; Computer Matching Program (SSA/ Bureau of the Public Debt (BPD))--Match Number 1038 AGENCY: Social Security... 1795. The relevant BPD SORs are Treasury/ BPD.002, United States Savings Type Securities, and Treasury... containing SSNs extracted from the Supplemental Security Record database. Exchanges for this computer...

  6. 78 FR 69925 - Privacy Act of 1974, as Amended; Computer Matching Program (SSA/Bureau of the Fiscal Service...

    Science.gov (United States)

    2013-11-21

    ... savings securities. C. Authority for Conducting the Matching Program This computer matching agreement sets..., United States Savings Type Securities, and Treasury/BPD.008, Retail Treasury Securities Access... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA 2013-0058] Privacy Act of 1974, as Amended...

  7. Computational Bottlenecks of Quantum Adiabatic Annealing

    Science.gov (United States)

    Knysh, Sergey

    2015-03-01

    Quantum annealing in a transverse field with rate dΓ / dt inversely proportional to the system size N suppresses non-adiabatic transitions for fully connected spin glass such as the Sherrington-Kirpatrick (SK) model at the quantum critical point. This alone is not sufficient to ensure that the problem is solvable in polynomial time. I conjecture the appearance of small gaps associated with macroscopic tunneling events deep in the spin glass phase. This effect is demonstrated rigorously for the annealing of a toy model that shares a set of crtical exponents with SK model: Hopfield network with two Gaussian patterns. It presents with 0 . 15 lnN additional bottlenecks with gaps that scale as a stretched exponential exp[-c (NΓ) 3 / 4]. Further, I extend the analysis to the ρ-landscapes model (random energy model with correlations) which more faithfully represents real spin glasses.

  8. Dynamical Frustration in ANNNI Model and Annealing

    Science.gov (United States)

    Sen, Parongama; Das, Pratap K.

    Simulated annealing is usually applied to systems with frustration, like spin glasses and optimisation problems, where the energy landscape is complex with many spurious minima. There are certain other systems, however, which have very simple energy landscape picture and ground states, but still the system fails to reach its ground state during a energy-lowering dynamical process. This situation corresponds to "dynamical frustration ". We have specifically considered the case of the axial next nearest neighbour (ANNNI) chain, where such a situation is encountered. In Sect. II, we elaborate the notion of dynamic frustration with examples and in Sect. III, the dynamics in ANNNI model is discussed in detail. The results of application of the classical and quantum annealing are discussed in Sects. IV and V. Summary and some concluding comments are given in the last section.

  9. Simulated annealing algorithm for optimal capital growth

    Science.gov (United States)

    Luo, Yong; Zhu, Bo; Tang, Yong

    2014-08-01

    We investigate the problem of dynamic optimal capital growth of a portfolio. A general framework that one strives to maximize the expected logarithm utility of long term growth rate was developed. Exact optimization algorithms run into difficulties in this framework and this motivates the investigation of applying simulated annealing optimized algorithm to optimize the capital growth of a given portfolio. Empirical results with real financial data indicate that the approach is inspiring for capital growth portfolio.

  10. Optimization Via Open System Quantum Annealing

    Science.gov (United States)

    2016-01-07

    be solved by a quantum evolution from a strong transverse field to a spin glass Hamiltonian (also known as quantum annealing or QA). We have...reduced to Quadratic Unconstrained Binary Optimization (QUBO), which can be solved by a quantum evolution from a strong transverse field to a spin...Excellence grant for Education , Research and Engineering: The number of undergraduates funded by your agreement who graduated during this period and

  11. The influence of quorum sensing in compartment II of the MELiSSA loop

    Science.gov (United States)

    Condori, Sandra; Mastroleo, Felice; Wattiez, Ruddy; Leys, Natalie

    MELiSSA (Micro-Ecological Life Support System Alternative) has been conceived as a 5 compartments microorganisms and higher plants recycling system for long haul space flights. Rhodospirillum rubrum S1H colonizes compartment II. Previous work reported that continuous culture of the bacterium in a photobioreactor could lead to thick biofilm formation, leading to bioreactor arrest. Our aim is to investigate the unknown quorum sensing (QS) system of R. rubrum S1H, specifically under MELiSSA relevant culture conditions meaning light anaerobic (LAN) and using acetate as carbon source. In that purpose an autoinducer synthase gene (Rru_A3396) knockout mutant was constructed by allelic exchange generating strain M68. In addition phenotypic comparison between wild type (WT) and M68 was performed. Results of thin layer chromatography assay where Agrobacterium tumefaciens NT1 have been used as reporter strain showed that WT produces acyl-homoserine lactones (AHLs) from C4 to C12 acyl carbon chain length; however, in M68 no AHLs were detected confirming that gene Rru_A3396 (named rruI) encodes an autoinducer synthase. Interestingly under a low shear or static environment M68 showed cell aggregation similar as reported in a closely related bacterium Rhodobacter sphaeroides (cerI mutant). In contrast to WT, M68 did not form biofilm and exhibited a decreased motility and pigment content. M68 vs wild type transcriptomics results showed that 326 genes were statistically significant differentially expressed. Downregulation of genes related to photosynthesis e.g., reaction center subunits, light harvesting complex and photosynthetic assembly proteins was observed. Similar results were obtained for preliminary proteomic analysis. Results obtained showed that in R. rubrum S1H the AHL-based QS system regulates almost 8% of the genome which is linked to biofilm formation among other biological processes described above. Since strain M68 could not be used in compartment II due to its less

  12. Thermal properties of poly(ethylene oxide)/lauric acid blends. A SSA-DSC study

    Energy Technology Data Exchange (ETDEWEB)

    Pielichowski, Krzysztof; Flejtuch, Kinga [Department of Chemistry and Technology of Polymers, Cracow University of Technology, ul. Warszawska 24, 31-155 Krakow (Poland)

    2006-03-15

    A series of poly(ethylene oxide) (PEO)/lauric acid blends with different compositions has been prepared and characterised by differential scanning calorimetry (DSC) in dynamic mode. It has been found that the enthalpy of melting and crystallisation reaches its highest value for PEO/lauric acid blend (1:1, w/w) which makes this system a promising candidate for thermal energy storage applications. Further studies by step-scan alternating (SSA)-DSC revealed that an increase of the temperature step causes that the average total heating rate is also increasing and the heat flow is characterised by higher values. Reversing component of the heat flow during melting reaches lowest values at highest step (step=1{sup o}) when the re-crystallisation of PEO is hindered. An increase of step generally leads to an increase of the number of non-equilibrium effects and facilitates the activation of kinetic non-reversing processes, hindering the overall crystallisation of PEO. For lauric acid, due to facile crystallisation and self-association, formation of ordered regular structures takes place faster and is influenced by non-reversing processes in higher proportion. (author)

  13. SPITZER OBSERVATIONS OF EXTENDED LYMAN-α CLOUDS IN THE SSA22 FIELD

    International Nuclear Information System (INIS)

    Webb, T. M. A.; Gonzalez, M.; Yamada, T.; Huang, J.-S.; Ashby, M. L. N; Matsuda, Y.; Egami, E.; Hayashimo, T.

    2009-01-01

    We present the results of a Spitzer IRAC and MIPS 24 μm study of extended Lyman-α clouds (or Lyman-α Blobs, LABs) within the SSA22 filamentary structure at z = 3.09. We detect 6/26 LABs in all IRAC filters, four of which are also detected at 24 μm, and find good correspondence with the 850 μm measurements of Geach et al. An analysis of the rest-frame ultraviolet, optical, near- and mid-infrared colors reveals that these six systems exhibit signs of nuclear activity (active galactic nucleus (AGN)) and/or extreme star formation. Notably, they have properties that bridge galaxies dominated by star formation (Lyman-break galaxies (LBGs)) and those with AGNs (LBGs classified as QSOs). The LAB systems not detected in all four IRAC bands, on the other hand, are, as a group, consistent with pure star-forming systems, similar to the majority of the LBGs within the filament. These results indicate that the galaxies within LABs do not comprise a homogeneous population, though they are also consistent with scenarios in which the gas halos are ionized through a common mechanism such as galaxy-scale winds driven by the galaxies within them, or gravitational heating of the collapsing cloud itself.

  14. Benefits of Applying Predictive Intelligence to the Space Situational Awareness (SSA) Mission

    Science.gov (United States)

    Lane, B.; Mann, B.; Millard, C.

    Recent events have heightened the interest in providing improved Space Situational Awareness (SSA) to the warfighter using novel techniques that are affordable and effective. The current Space Surveillance Network (SSN) detects, tracks, catalogs and identifies artificial objects orbiting earth and provides information on Resident Space Objects (RSO) as well as new foreign launch (NFL) satellites. The reactive nature of the SSN provides little to no warning on changes to the expected states of these RSOs or NFLs. This paper will detail the use of the historical data collected on RSOs to characterize what their steady state is, proactively help identify when changes or anomalies have occurred using a pattern-of-like activity based intelligence approach, and apply dynamic, adaptive mission planning to the observables that lead up to a NFL. Multiple hypotheses will be carried along with the intent or the changes to the steady state to assist the SSN in tasking the various sensors in the network to collect the relevant data needed to help prune the number of hypotheses by assigning likelihood to each of those activities. Depending on the hypothesis and thresholds set, these likelihoods will then be used in turn to alert the SSN operator with changes to the steady state, prioritize additional data collections, and provide a watch list of likely next activities.

  15. Ro/SSA autoantibodies directly bind cardiomyocytes, disturb calcium homeostasis, and mediate congenital heart block.

    Science.gov (United States)

    Salomonsson, Stina; Sonesson, Sven-Erik; Ottosson, Lars; Muhallab, Saad; Olsson, Tomas; Sunnerhagen, Maria; Kuchroo, Vijay K; Thorén, Peter; Herlenius, Eric; Wahren-Herlenius, Marie

    2005-01-03

    Congenital heart block develops in fetuses after placental transfer of Ro/SSA autoantibodies from rheumatic mothers. The condition is often fatal and the majority of live-born children require a pacemaker at an early age. The specific antibody that induces the heart block and the mechanism by which it mediates the pathogenic effect have not been elucidated. In this study, we define the cellular mechanism leading to the disease and show that maternal autoantibodies directed to a specific epitope within the leucine zipper amino acid sequence 200-239 (p200) of the Ro52 protein correlate with prolongation of fetal atrioventricular (AV) time and heart block. This finding was further confirmed experimentally in that pups born to rats immunized with p200 peptide developed AV block. p200-specific autoantibodies cloned from patients bound cultured cardiomyocytes and severely affected Ca2+ oscillations, leading to accumulating levels and overload of intracellular Ca2+ levels with subsequent loss of contractility and ultimately apoptosis. These findings suggest that passive transfer of maternal p200 autoantibodies causes congenital heart block by dysregulating Ca2+ homeostasis and inducing death in affected cells.

  16. Are crude oil markets multifractal? Evidence from MF-DFA and MF-SSA perspectives

    Science.gov (United States)

    He, Ling-Yun; Chen, Shu-Peng

    2010-08-01

    In this article, we investigated the multifractality and its underlying formation mechanisms in international crude oil markets, namely, Brent and WTI, which are the most important oil pricing benchmarks globally. We attempt to find the answers to the following questions: (1) Are those different markets multifractal? (2) What are the dynamical causes for multifractality in those markets (if any)? To answer these questions, we applied both multifractal detrended fluctuation analysis (MF-DFA) and multifractal singular spectrum analysis (MF-SSA) based on the partition function, two widely used multifractality detecting methods. We found that both markets exhibit multifractal properties by means of these methods. Furthermore, in order to identify the underlying formation mechanisms of multifractal features, we destroyed the underlying nonlinear temporal correlation by shuffling the original time series; thus, we identified that the causes of the multifractality are influenced mainly by a nonlinear temporal correlation mechanism instead of a non-Gaussian distribution. At last, by tracking the evolution of left- and right-half multifractal spectra, we found that the dynamics of the large price fluctuations is significantly different from that of the small ones. Our main contribution is that we not only provided empirical evidence of the existence of multifractality in the markets, but also the sources of multifractality and plausible explanations to current literature; furthermore, we investigated the different dynamical price behaviors influenced by large and small price fluctuations.

  17. Anti-Ro52 antibody level is an important marker of fetal congenital heart block risk in anti-Ro/SSA antibody positive pregnancy.

    Science.gov (United States)

    Miyasato-Isoda, Mai; Waguri, Masako; Yamada, Yuko; Miyano, Akira; Wada, Yoshinao

    2017-09-21

    The aims of this study are to determine the incidence of congenital heart block (CHB) in the Japanese population and identify maternal factors predicting fetal CHB in anti-Ro/SSA antibody positive pregnancy. A retrospective study was performed using 52,147 clinical records of pregnancies followed in a single center. For 183 anti-Ro/SSA antibody-positive women, anti-Ro52 and Ro60 antibodies were measured, and the odds of CHB in relation to maternal clinical features were calculated by multivariate analysis. The receiver-operating characteristic (ROC) curves for predicting CHB were constructed for the titers of anti-Ro/SSA, anti-Ro52 and anti-Ro60 antibodies. Fetal CHB occurred in two pregnancies among those without known risks such as positive anti-Ro/SSA antibody or previous CHB-affected pregnancy, suggesting an incidence similar to that in Caucasian populations. As for the anti-Ro/SSA antibody positive pregnancies, the titers of anti-Ro/SSA, anti-Ro52 and anti-Ro60 antibodies were independent risk factors for fetal CHB and the use of corticosteroids before 18 gestational weeks was an independent protective factor. The area under the ROC was 0.84, 0.73 and 0.74 for anti-Ro52, anti-Ro60 and anti-Ro/SSA antibodies, respectively. CHB occurred in two among approximately 50,000 pregnancies without known risks such as positive anti-Ro/SSA antibody or previous delivery of CHB-affected babies. Measurement of anti-Ro52 antibody levels may be helpful in extracting a risk group of delivering CHB infants in the anti-Ro/SSA antibody positive pregnancy.

  18. Parameterization of single-scattering albedo (SSA) and absorption Ångström exponent (AAE) with EC / OC for aerosol emissions from biomass burning

    Science.gov (United States)

    Pokhrel, Rudra P.; Wagner, Nick L.; Langridge, Justin M.; Lack, Daniel A.; Jayarathne, Thilina; Stone, Elizabeth A.; Stockwell, Chelsea E.; Yokelson, Robert J.; Murphy, Shane M.

    2016-08-01

    Single-scattering albedo (SSA) and absorption Ångström exponent (AAE) are two critical parameters in determining the impact of absorbing aerosol on the Earth's radiative balance. Aerosol emitted by biomass burning represent a significant fraction of absorbing aerosol globally, but it remains difficult to accurately predict SSA and AAE for biomass burning aerosol. Black carbon (BC), brown carbon (BrC), and non-absorbing coatings all make substantial contributions to the absorption coefficient of biomass burning aerosol. SSA and AAE cannot be directly predicted based on fuel type because they depend strongly on burn conditions. It has been suggested that SSA can be effectively parameterized via the modified combustion efficiency (MCE) of a biomass burning event and that this would be useful because emission factors for CO and CO2, from which MCE can be calculated, are available for a large number of fuels. Here we demonstrate, with data from the FLAME-4 experiment, that for a wide variety of globally relevant biomass fuels, over a range of combustion conditions, parameterizations of SSA and AAE based on the elemental carbon (EC) to organic carbon (OC) mass ratio are quantitatively superior to parameterizations based on MCE. We show that the EC / OC ratio and the ratio of EC / (EC + OC) both have significantly better correlations with SSA than MCE. Furthermore, the relationship of EC / (EC + OC) with SSA is linear. These improved parameterizations are significant because, similar to MCE, emission factors for EC (or black carbon) and OC are available for a wide range of biomass fuels. Fitting SSA with MCE yields correlation coefficients (Pearson's r) of ˜ 0.65 at the visible wavelengths of 405, 532, and 660 nm while fitting SSA with EC / OC or EC / (EC + OC) yields a Pearson's r of 0.94-0.97 at these same wavelengths. The strong correlation coefficient at 405 nm (r = 0.97) suggests that parameterizations based on EC / OC or EC / (EC + OC) have good predictive

  19. Interference Alignment Using Variational Mean Field Annealing

    DEFF Research Database (Denmark)

    Badiu, Mihai Alin; Guillaud, Maxime; Fleury, Bernard Henri

    2014-01-01

    We study the problem of interference alignment in the multiple-input multiple- output interference channel. Aiming at minimizing the interference leakage power relative to the receiver noise level, we use the deterministic annealing approach to solve the optimization problem. In the corresponding...... for interference alignment. We also show that the iterative leakage minimization algorithm by Gomadam et al. and the alternating minimization algorithm by Peters and Heath, Jr. are instances of our method. Finally, we assess the performance of the proposed algorithm through computer simulations....

  20. Simulated annealing for tensor network states

    International Nuclear Information System (INIS)

    Iblisdir, S

    2014-01-01

    Markov chains for probability distributions related to matrix product states and one-dimensional Hamiltonians are introduced. With appropriate ‘inverse temperature’ schedules, these chains can be combined into a simulated annealing scheme for ground states of such Hamiltonians. Numerical experiments suggest that a linear, i.e., fast, schedule is possible in non-trivial cases. A natural extension of these chains to two-dimensional settings is next presented and tested. The obtained results compare well with Euclidean evolution. The proposed Markov chains are easy to implement and are inherently sign problem free (even for fermionic degrees of freedom). (paper)

  1. Binary Sparse Phase Retrieval via Simulated Annealing

    Directory of Open Access Journals (Sweden)

    Wei Peng

    2016-01-01

    Full Text Available This paper presents the Simulated Annealing Sparse PhAse Recovery (SASPAR algorithm for reconstructing sparse binary signals from their phaseless magnitudes of the Fourier transform. The greedy strategy version is also proposed for a comparison, which is a parameter-free algorithm. Sufficient numeric simulations indicate that our method is quite effective and suggest the binary model is robust. The SASPAR algorithm seems competitive to the existing methods for its efficiency and high recovery rate even with fewer Fourier measurements.

  2. Implantation annealing in GaAs by incoherent light

    International Nuclear Information System (INIS)

    Davies, D.E.; Ryan, T.G.; Soda, K.J.; Comer, J.J.

    1983-01-01

    Implanted GaAs has been successfully activated through concentrating the output of quartz halogen lamps to anneal in times of the order of 1 sec. The resulting layers are not restricted by the reduced mobilities and thermal instabilities of laser annealed GaAs. Better activation can be obtained than with furnace annealing but this generally requires maximum temperatures >= 1050degC. (author)

  3. Benefits of Intercritical Annealing in Quenching and Partitioning Steel

    Science.gov (United States)

    Wang, X.; Liu, L.; Liu, R. D.; Huang, M. X.

    2018-03-01

    Compared to the quenching and partitioning (Q&P) steel produced by full austenization annealing, the Q&P steel produced by the intercritical annealing shows a similar ultimate tensile stress but a larger tensile ductility. This property is attributable to the higher volume fraction and the better mechanical stability of the retained austenite after the intercritical annealing. Moreover, intercritical annealing produces more ferrite and fewer martensite phases in the microstructure, making an additional contribution to a higher work hardening rate and therefore a better tensile ductility.

  4. Magnetic field annealing for improved creep resistance

    Science.gov (United States)

    Brady, Michael P.; Ludtka, Gail M.; Ludtka, Gerard M.; Muralidharan, Govindarajan; Nicholson, Don M.; Rios, Orlando; Yamamoto, Yukinori

    2015-12-22

    The method provides heat-resistant chromia- or alumina-forming Fe-, Fe(Ni), Ni(Fe), or Ni-based alloys having improved creep resistance. A precursor is provided containing preselected constituents of a chromia- or alumina-forming Fe-, Fe(Ni), Ni(Fe), or Ni-based alloy, at least one of the constituents for forming a nanoscale precipitate MaXb where M is Cr, Nb, Ti, V, Zr, or Hf, individually and in combination, and X is C, N, O, B, individually and in combination, a=1 to 23 and b=1 to 6. The precursor is annealed at a temperature of 1000-1500.degree. C. for 1-48 h in the presence of a magnetic field of at least 5 Tesla to enhance supersaturation of the M.sub.aX.sub.b constituents in the annealed precursor. This forms nanoscale M.sub.aX.sub.b precipitates for improved creep resistance when the alloy is used at service temperatures of 500-1000.degree. C. Alloys having improved creep resistance are also disclosed.

  5. Superplasticity of Annealed H13 Steel

    Directory of Open Access Journals (Sweden)

    Zhenxin Duan

    2017-07-01

    Full Text Available H13 steel is a widely used hot work die material. A new type of hot working method is imperative to develop complex and precise dies. In this paper, the heat treatment of H13 steel (AISI was carried out by annealing, the final structure is a point or spherical pearlite, and the grain size is about 30–40 μm. The tensile properties of the annealed microstructure were investigated at 650, 750, and 850 °C with the strain rates of 1 × 10−3 s−1, 5 × 10−4 s−1, and 1 × 10−4 s−1. The tensile fracture and microstructure were analyzed by SEM and HREM. The results show that the tensile samples reach superplasticity at the strain rate of 1 × 10−4 s−1 in the temperature range of 750–850 °C. When the temperature is 850 °C, the maximum elongation rate reaches 112.5%. This demonstrates the possibility of making superplastic forming molds. During the tensile process, the refined M23C6 and other high hardness carbides which are dispersed uniformly in the matrix, effectively inhibits grain growth and hinders dislocation movement, leading to the improvement of plasticity.

  6. Mean Field Analysis of Quantum Annealing Correction.

    Science.gov (United States)

    Matsuura, Shunji; Nishimori, Hidetoshi; Albash, Tameem; Lidar, Daniel A

    2016-06-03

    Quantum annealing correction (QAC) is a method that combines encoding with energy penalties and decoding to suppress and correct errors that degrade the performance of quantum annealers in solving optimization problems. While QAC has been experimentally demonstrated to successfully error correct a range of optimization problems, a clear understanding of its operating mechanism has been lacking. Here we bridge this gap using tools from quantum statistical mechanics. We study analytically tractable models using a mean-field analysis, specifically the p-body ferromagnetic infinite-range transverse-field Ising model as well as the quantum Hopfield model. We demonstrate that for p=2, where the phase transition is of second order, QAC pushes the transition to increasingly larger transverse field strengths. For p≥3, where the phase transition is of first order, QAC softens the closing of the gap for small energy penalty values and prevents its closure for sufficiently large energy penalty values. Thus QAC provides protection from excitations that occur near the quantum critical point. We find similar results for the Hopfield model, thus demonstrating that our conclusions hold in the presence of disorder.

  7. Superplasticity of Annealed H13 Steel.

    Science.gov (United States)

    Duan, Zhenxin; Pei, Wen; Gong, Xuebo; Chen, Hua

    2017-07-28

    H13 steel is a widely used hot work die material. A new type of hot working method is imperative to develop complex and precise dies. In this paper, the heat treatment of H13 steel (AISI) was carried out by annealing, the final structure is a point or spherical pearlite, and the grain size is about 30-40 μm. The tensile properties of the annealed microstructure were investigated at 650, 750, and 850 °C with the strain rates of 1 × 10 -3 s -1 , 5 × 10 -4 s -1 , and 1 × 10 -4 s -1 . The tensile fracture and microstructure were analyzed by SEM and HREM. The results show that the tensile samples reach superplasticity at the strain rate of 1 × 10 -4 s -1 in the temperature range of 750-850 °C. When the temperature is 850 °C, the maximum elongation rate reaches 112.5%. This demonstrates the possibility of making superplastic forming molds. During the tensile process, the refined M 23 C₆ and other high hardness carbides which are dispersed uniformly in the matrix, effectively inhibits grain growth and hinders dislocation movement, leading to the improvement of plasticity.

  8. A coherent quantum annealer with Rydberg atoms

    Science.gov (United States)

    Glaetzle, A. W.; van Bijnen, R. M. W.; Zoller, P.; Lechner, W.

    2017-06-01

    There is a significant ongoing effort in realizing quantum annealing with different physical platforms. The challenge is to achieve a fully programmable quantum device featuring coherent adiabatic quantum dynamics. Here we show that combining the well-developed quantum simulation toolbox for Rydberg atoms with the recently proposed Lechner-Hauke-Zoller (LHZ) architecture allows one to build a prototype for a coherent adiabatic quantum computer with all-to-all Ising interactions and, therefore, a platform for quantum annealing. In LHZ an infinite-range spin-glass is mapped onto the low energy subspace of a spin-1/2 lattice gauge model with quasi-local four-body parity constraints. This spin model can be emulated in a natural way with Rubidium and Caesium atoms in a bipartite optical lattice involving laser-dressed Rydberg-Rydberg interactions, which are several orders of magnitude larger than the relevant decoherence rates. This makes the exploration of coherent quantum enhanced optimization protocols accessible with state-of-the-art atomic physics experiments.

  9. MEDICAL STAFF SCHEDULING USING SIMULATED ANNEALING

    Directory of Open Access Journals (Sweden)

    Ladislav Rosocha

    2015-07-01

    Full Text Available Purpose: The efficiency of medical staff is a fundamental feature of healthcare facilities quality. Therefore the better implementation of their preferences into the scheduling problem might not only rise the work-life balance of doctors and nurses, but also may result into better patient care. This paper focuses on optimization of medical staff preferences considering the scheduling problem.Methodology/Approach: We propose a medical staff scheduling algorithm based on simulated annealing, a well-known method from statistical thermodynamics. We define hard constraints, which are linked to legal and working regulations, and minimize the violations of soft constraints, which are related to the quality of work, psychic, and work-life balance of staff.Findings: On a sample of 60 physicians and nurses from gynecology department we generated monthly schedules and optimized their preferences in terms of soft constraints. Our results indicate that the final value of objective function optimized by proposed algorithm is more than 18-times better in violations of soft constraints than initially generated random schedule that satisfied hard constraints.Research Limitation/implication: Even though the global optimality of final outcome is not guaranteed, desirable solutionwas obtained in reasonable time. Originality/Value of paper: We show that designed algorithm is able to successfully generate schedules regarding hard and soft constraints. Moreover, presented method is significantly faster than standard schedule generation and is able to effectively reschedule due to the local neighborhood search characteristics of simulated annealing.

  10. Automatic, Rapid Replanning of Satellite Operations for Space Situational Awareness (SSA)

    Science.gov (United States)

    Stottler, D.; Mahan, K.

    An important component of Space Situational Awareness (SSA) is knowledge of the status and tasking of blue forces (e.g. satellites and ground stations) and the rapid determination of the impacts of real or hypothetical changes and the ability to quickly replan based on those changes. For example, if an antenna goes down (either for benign reasons or from purposeful interference) determining which missions will be impacted is important. It is not simply the set of missions that were scheduled to utilize that antenna, because highly expert human schedulers will respond to the outage by intelligently replanning the real-time schedule. We have developed an automatic scheduling and deconfliction engine, called MIDAS (for Managed Intelligent Deconfliction And Scheduling) that interfaces to the current legacy system (ESD 2.7) which can perform this replanning function automatically. In addition to determining the impact of failed resources, MIDAS can also replan in response to a satellite under attack. In this situation, additional supports must be quickly scheduled and executed (while minimizing impacts to other missions). Because MIDAS is a fully automatic system, replacing a current human labor-intensive process, and provides very rapid turnaround (seconds) it can also be used by commanders to consider what-if questions and focus limited protection resources on the most critical resources. For example, the commander can determine the impact of a successful attack on one of two ground stations and place heavier emphasis on protecting the station whose loss would create the most severe impacts. The system is currently transitioning to operational use. The MIDAS system and its interface to the legacy ESD 2.7 system will be described along with the ConOps for different types of detailed operational scenarios.

  11. SsaA, a Member of a Novel Class of Transcriptional Regulators, Controls Sansanmycin Production in Streptomyces sp. Strain SS through a Feedback Mechanism

    Science.gov (United States)

    Li, Qinglian; Wang, Lifei; Xie, Yunying; Wang, Songmei; Chen, Ruxian

    2013-01-01

    Sansanmycins, produced by Streptomyces sp. strain SS, are uridyl peptide antibiotics with activities against Pseudomonas aeruginosa and multidrug-resistant Mycobacterium tuberculosis. In this work, the biosynthetic gene cluster of sansanmycins, comprised of 25 open reading frames (ORFs) showing considerable amino acid sequence identity to those of the pacidamycin and napsamycin gene cluster, was identified. SsaA, the archetype of a novel class of transcriptional regulators, was characterized in the sansanmycin gene cluster, with an N-terminal fork head-associated (FHA) domain and a C-terminal LuxR-type helix-turn-helix (HTH) motif. The disruption of ssaA abolished sansanmycin production, as well as the expression of the structural genes for sansanmycin biosynthesis, indicating that SsaA is a pivotal activator for sansanmycin biosynthesis. SsaA was proved to directly bind several putative promoter regions of biosynthetic genes, and comparison of sequences of the binding sites allowed the identification of a consensus SsaA binding sequence, GTMCTGACAN2TGTCAGKAC. The DNA binding activity of SsaA was inhibited by sansanmycins A and H in a concentration-dependent manner. Furthermore, sansanmycins A and H were found to directly interact with SsaA. These results indicated that SsaA strictly controls the production of sansanmycins at the transcriptional level in a feedback regulatory mechanism by sensing the accumulation of the end products. As the first characterized regulator of uridyl peptide antibiotic biosynthesis, the understanding of this autoregulatory process involved in sansanmycin biosynthesis will likely provide an effective strategy for rational improvements in the yields of these uridyl peptide antibiotics. PMID:23475969

  12. The SSB-positive/SSA-negative antibody profile is not associated with key phenotypic features of Sjögren's syndrome

    DEFF Research Database (Denmark)

    Baer, Alan N; McAdams DeMarco, Mara; Shiboski, Stephen C

    2015-01-01

    phenotypic features. Among SICCA participants classified with SS on the basis of the American-European Consensus Group or American College of Rheumatology criteria, only 2% required the anti-SSB-alone test result to meet these criteria. CONCLUSIONS: The presence of anti-SSB, without anti-SSA antibodies, had...... participants, 2061 (63%) had negative anti-SSA/anti-SSB, 1162 (35%) had anti-SSA with or without anti-SSB, and 74 (2%) anti-SSB alone. Key SS phenotypic features were more prevalent and had measures indicative of greater disease activity in those participants with anti-SSA, either alone or with anti-SSB, than...... in those with anti-SSB alone or negative SSA/SSB serology. These between-group differences were highly significant and not explained by confounding by age, race/ethnicity or gender. Participants with anti-SSB alone were comparable to those with negative SSA/SSB serology in their association with these key...

  13. Investigation of annealing-treatment on structural and optical ...

    Indian Academy of Sciences (India)

    Administrator

    This conforms to the results already reported by Moustaghfir et al (2003). A higher annealing tempera- ture enhances the formation of larger and more closely packed crystals. The increase of the refractive index with increasing annealing temperature can be partly attributed to improvement in film quality with the reduction in.

  14. Effect of annealing temperature on the structural–microstructural and ...

    Indian Academy of Sciences (India)

    In order to get good quality reproducible films of Tl : HTSC system, we have studied the different annealing conditions to finally achieve the optimized annealing condition. In the present investigation, Tl–Ca–Ba–Cu–O superconducting films have been prepared on YSZ (100) and MgO (100) single crystal substrates via ...

  15. Effect of isochronal annealing on phase transformation studies of ...

    Indian Academy of Sciences (India)

    Abstract. The effect of isochronal annealing on the phase transformation in iron oxide nanoparticles is reported in this work. Iron oxide nanoparticles were successfully synthesized using an ash supported technique followed by annealing for 2 h at various temperatures between 300 and 700◦C. It was observed using X-ray ...

  16. Effect of annealing treatment on optical properties and ...

    Indian Academy of Sciences (India)

    2018-03-28

    Mar 28, 2018 ... C. UV–visible spectrophotometer showed that the annealing treatment of the first WO3 layer enhanced the transparency of films in the visible region. The innovations of the present study have been based on the annealing of the films and finding an optimum thickness for the Ag film at 12–14 nm.

  17. Effect of heat moisture treatment and annealing on physicochemical ...

    African Journals Online (AJOL)

    Red sorghum starch was physically modified by annealing and heat moisture treatment. The swelling power and solubility increased with increasing temperature range (60-90°), while annealing and heatmoisture treatment decreased swelling power and solubility of starch. Solubility and swelling were pH dependent with ...

  18. Simulated annealing approach for solving economic load dispatch ...

    African Journals Online (AJOL)

    user

    Abstract. This paper presents Simulated Annealing (SA) algorithm for optimization inspired by the process of annealing in ... Various classical optimization techniques were used to solve the ELD problem, for example: lambda iteration approach, ...... Research of fuzzy self-adaptive immune algorithm and its application.

  19. Effect of isochronal annealing on phase transformation studies of ...

    Indian Academy of Sciences (India)

    The effect of isochronal annealing on the phase transformation in iron oxide nanoparticles is reported in this work. Iron oxide nanoparticles were successfully synthesized using an ash supported technique followed by annealing for 2 h at various temperatures between 300 and 700° C. It was observed using X-ray diffraction ...

  20. Effect of annealing process of iron powder on magnetic properties ...

    Indian Academy of Sciences (India)

    Administrator

    The amplitude permeability and magnetic loss of the cores reached the maximum and minimum values, respectively. The magnetic loss of the cores was separated into hysteresis loss and eddy current loss by Stoppels Method which were decreased by the annealing process. Keywords. Reduced iron powders; annealing ...

  1. A note on simulated annealing to computer laboratory scheduling ...

    African Journals Online (AJOL)

    Simulated Annealing algorithm is used in solving real life problem of Computer Laboratory scheduling in order to maximize the use of scarce and insufficient resources. KEY WORDS: Simulated Annealing (SA), Computer Laboratory Scheduling, Statistical Thermodynamics, Energy Function, and Heuristic etc. Global Jnl of ...

  2. Response of neutron-irradiated RPV steels to thermal annealing

    Energy Technology Data Exchange (ETDEWEB)

    Iskander, S.K.; Sokolov, M.A.; Nanstad, R.K.

    1997-03-01

    One of the options to mitigate the effects of irradiation on reactor pressure vessels (RPVs) is to thermally anneal them to restore the fracture toughness properties that have been degraded by neutron irradiation. This paper summarizes experimental results of work performed at the Oak Ridge National Laboratory (ORNL) to study the annealing response of several irradiated RPV steels.

  3. Improvements in or relating to laser annealed electronic devices

    International Nuclear Information System (INIS)

    Barraclough, K.G.; Cullis, A.G.; Webber, H.C.

    1981-01-01

    A method of producing laser annealed electronic devices is described. The technique involves irradiating semiconductor material such as silicon or germanium to produce a neutron transmuted semiconductor material and laser annealing a selected region or regions in a slice of the transmuted material to a sub-micron depth. (U.K.)

  4. Effect of annealing on magnetic properties and silicide formation at ...

    Indian Academy of Sciences (India)

    coercivity decreases and remanence increases. The values of remanence of pristine Co/Si and annealed at 300°C are. 0⋅80 and 0⋅98, respectively. 3.3 AFM measurement. Morphological changes of silicide surface during high temperature annealing have been investigated by AFM in terms of the RMS surface roughness.

  5. Stored energy and annealing behavior of heavily deformed aluminium

    DEFF Research Database (Denmark)

    Kamikawa, Naoya; Huang, Xiaoxu; Kondo, Yuka

    2012-01-01

    are quantified such as boundary spacing, misorientation angle and dislocation density for 99.99% aluminium deformed by accumulative roll-bonding to a strain of 4.8. Two different annealing processes have been applied; (i) one-step annealing for 0.5 h at 100-400°C and (ii) two-step annealing for 6 h at 175°C......It has been demonstrated in previous work that a two-step annealing treatment, including a low-temperature, long-time annealing and a subsequent high-temperature annealing, is a promising route to control the microstructure of a heavily deformed metal. In the present study, structural parameters...... followed by 0.5 h annealing at 200-600°C, where the former treatment leads to discontinuous recrystallization and the latter to uniform structural coarsening. This behavior has been analyzed in terms of the relative change during annealing of energy stored as elastic energy in the dislocation structure...

  6. Angular filter refractometry analysis using simulated annealing.

    Science.gov (United States)

    Angland, P; Haberberger, D; Ivancic, S T; Froula, D H

    2017-10-01

    Angular filter refractometry (AFR) is a novel technique used to characterize the density profiles of laser-produced, long-scale-length plasmas [Haberberger et al., Phys. Plasmas 21, 056304 (2014)]. A new method of analysis for AFR images was developed using an annealing algorithm to iteratively converge upon a solution. A synthetic AFR image is constructed by a user-defined density profile described by eight parameters, and the algorithm systematically alters the parameters until the comparison is optimized. The optimization and statistical uncertainty calculation is based on the minimization of the χ 2 test statistic. The algorithm was successfully applied to experimental data of plasma expanding from a flat, laser-irradiated target, resulting in an average uncertainty in the density profile of 5%-20% in the region of interest.

  7. Coupled Quantum Fluctuations and Quantum Annealing

    Science.gov (United States)

    Hormozi, Layla; Kerman, Jamie

    We study the relative effectiveness of coupled quantum fluctuations, compared to single spin fluctuations, in the performance of quantum annealing. We focus on problem Hamiltonians resembling the the Sherrington-Kirkpatrick model of Ising spin glass and compare the effectiveness of different types of fluctuations by numerically calculating the relative success probabilities and residual energies in fully-connected spin systems. We find that for a small class of instances coupled fluctuations can provide improvement over single spin fluctuations and analyze the properties of the corresponding class. Disclaimer: This research was funded by ODNI, IARPA via MIT Lincoln Laboratory under Air Force Contract No. FA8721-05-C-0002. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of ODNI, IARPA, or the US Government.

  8. Inferring hierarchical clustering structures by deterministic annealing

    International Nuclear Information System (INIS)

    Hofmann, T.; Buhmann, J.M.

    1996-01-01

    The unsupervised detection of hierarchical structures is a major topic in unsupervised learning and one of the key questions in data analysis and representation. We propose a novel algorithm for the problem of learning decision trees for data clustering and related problems. In contrast to many other methods based on successive tree growing and pruning, we propose an objective function for tree evaluation and we derive a non-greedy technique for tree growing. Applying the principles of maximum entropy and minimum cross entropy, a deterministic annealing algorithm is derived in a meanfield approximation. This technique allows us to canonically superimpose tree structures and to fit parameters to averaged or open-quote fuzzified close-quote trees

  9. Annealing effects on cathodoluminescence of zircon

    Science.gov (United States)

    Tsuchiya, Y.; Nishido, H.; Noumi, Y.

    2011-12-01

    U-Pb zircon dating (e. g., SHRIMP) is an important tool to interpret a history of the minerals at a micrometer-scale, where cathodoluminescence (CL) imaging allows us to recognize internal zones and domains with different chemical compositions and structural disorder at high spatial resolution. The CL of zircon is attributed by various types of emission centers, which are extrinsic ones such as REE impurities and intrinsic ones such as structural defects. Metamictization resulted from radiation damage to the lattice by alpha particles from the decay of U and Th mostly causes an effect on the CL features of zircon as a defect center. However, slightly radiation-damaged zircon, which is almost nondetectable by XRD, has not been characterized using CL method. In this study, annealing effects on CL of zircon has been investigated to clarify a recovery process of the damaged lattice at low radiation dose. A single crystal of zircon from Malawi was selected for CL measurements. It contains HfO2: 2.30 w.t %, U: 241 ppm and Th: 177 ppm. Two plate samples perpendicular to c and a axes were prepared for annealing experiments during 12 hours from room temperature to 1400 degree C. Color CL images were captured using a cold-cathode microscope (Luminoscope: Nuclide ELM-3R). CL spectral measurements were conducted using an SEM (JEOL: JSM-5410) combined with a grating monochromator (Oxford: Mono CL2) to measure CL spectra ranging from 300 to 800 nm in 1 nm steps with a temperature controlled stage. The dispersed CL was collected by a photoncounting method using a photomultiplier tube (Hamamatsu: R2228) and converted to digital data. All CL spectra were corrected for the total instrumental response. Spectral analysis reveals an anisotropy of the CL emission bands related to intrinsic defect center in blue region, radiation-induced defect center from 500 to 700 nm, and trivalent Dy impurity center at 480 and 580 nm, but their relative intensities are almost constant. CL on the

  10. Efficiency of quantum vs. classical annealing in nonconvex learning problems.

    Science.gov (United States)

    Baldassi, Carlo; Zecchina, Riccardo

    2018-02-13

    Quantum annealers aim at solving nonconvex optimization problems by exploiting cooperative tunneling effects to escape local minima. The underlying idea consists of designing a classical energy function whose ground states are the sought optimal solutions of the original optimization problem and add a controllable quantum transverse field to generate tunneling processes. A key challenge is to identify classes of nonconvex optimization problems for which quantum annealing remains efficient while thermal annealing fails. We show that this happens for a wide class of problems which are central to machine learning. Their energy landscapes are dominated by local minima that cause exponential slowdown of classical thermal annealers while simulated quantum annealing converges efficiently to rare dense regions of optimal solutions. Copyright © 2018 the Author(s). Published by PNAS.

  11. Heart sounds at home: feasibility of an ambulatory fetal heart rhythm surveillance program for anti-SSA-positive pregnancies.

    Science.gov (United States)

    Cuneo, B F; Moon-Grady, A J; Sonesson, S-E; Levasseur, S; Hornberger, L; Donofrio, M T; Krishnan, A; Szwast, A; Howley, L; Benson, D W; Jaeggi, E

    2017-03-01

    Fetuses exposed to anti-SSA (Sjögren's) antibodies are at risk of developing irreversible complete atrioventricular block (CAVB), resulting in death or permanent cardiac pacing. Anti-inflammatory treatment during the transition period from normal heart rhythm (fetal heart rhythm (FHR)) to CAVB (emergent CAVB) can restore sinus rhythm, but detection of emergent CAVB is challenging, because it can develop in ⩽24 h. We tested the feasibility of a new technique that relies on home FHR monitoring by the mother, to surveil for emergent CAVB. We recruited anti-SSA-positive mothers at 16 to 18 weeks gestation (baseline) from 8 centers and instructed them to monitor FHR two times a day until 26 weeks, using a Doppler device at home. FHR was also surveilled by weekly or every other week fetal echo. If FHR was irregular, the mother underwent additional fetal echo. We compared maternal stress/anxiety before and after monitoring. Postnatally, infants underwent a 12-lead electrocardiogram. Among 133 recruited, 125 (94%) enrolled. Among those enrolled, 96% completed the study. Reasons for withdrawal (n=5) were as follows: termination of pregnancy, monitoring too time consuming or moved away. During home monitoring, 9 (7.5%) mothers detected irregular FHR diagnosed by fetal echo as normal (false positive, n=2) or benign atrial arrhythmia (n=7). No CAVB was undetected or developed after monitoring. Questionnaire analysis indicated mothers felt comforted by the experience and would monitor again in future pregnancies. These data suggest ambulatory FHR surveillance of anti-SSA-positive pregnancies is feasible, has a low false positive rate and is empowering to mothers.

  12. Pregnancy outcome of 126 anti-SSA/Ro-positive patients during the past 24 years--a retrospective cohort study.

    Science.gov (United States)

    Luo, Yan; Zhang, Lili; Fei, Yunyun; Li, Yiqun; Hao, Donglin; Liu, Yi; Zhao, Yan

    2015-10-01

    The aims of our study are to observe the pregnancy outcome of anti-Sjögren's syndrome-related antigen A (SSA)/Ro-positive women and to predict the risk factors for adverse pregnancy outcome and neonatal lupus erythematosus (NLE). Clinical data of 126 anti-SSA/Ro-positive patients with 140 pregnancies were evaluated retrospectively, and the newborns were followed up as a cohort in 3 months. χ (2) test or logistic regression was used to predict the risk factors of lupus flares during pregnancy, fetal loss, and NLE. Twenty-six out of 93 pregnancies with systemic lupus erythematosus (SLE) experienced flares during pregnancy. Active disease prior to conception was the independent risk factor for flares [P = 0.002, odds ratio (OR) = 10.41 (95 % confidence interval (CI) = 2.34∼46.26)]. Continuous use of steroids and hydroxychloroquine (HCQ) might help decrease the risk (P = 0.041 and 0.015, respectively). Eleven out of 140 pregnancies ended with fetal loss, and 9 out of 113 live births were diagnosed with NLE. The presence of anti-phospholipid syndrome (APS) was associated with fetal loss (P = 0.018, OR = 6.41 (95 % CI = 1.57-26.14)). The presence of anti-Sjögren's syndrome-related antigen B (SSB)/La antibodies tended to increase the risk of giving birth to an infant with NLE (P = 0.140); on the other hand, duration of disease, history of renal involvement, and active SLE during pregnancy did not contribute to the incidence of NLE (P = 0.649, 0.685, and 1.000, respectively). Active disease without regular follow-up before conception significantly increased the risk of lupus flares during pregnancy. The continuous use of low-dose steroids and hydroxychloroquine might help maintain lower SLE activity. Concurrent APS instead of high titer of anti-SSA/Ro might raise the risk of fetal loss in anti-SSA/Ro-positive patients.

  13. The changes of ADI structure during high temperature annealing

    Directory of Open Access Journals (Sweden)

    A. Krzyńska

    2010-01-01

    Full Text Available The results of structure investigations of ADI during it was annealing at elevated temperature are presented. Ductile iron austempered at temperature 325oC was then isothermally annealed 360 minutes at temperature 400, 450, 500 and 550oC. The structure investigations showed that annealing at these temperatures caused substantial structure changes and thus essential hardness decrease, which is most useful property of ADI from point of view its practical application. Degradation advance of the structure depends mainly on annealing temperature, less on the time of the heat treatment. It was concluded that high temperature annealing caused precipitation of Fe3C type carbides, which morphology and distribution depend on temperature. In case of 400oC annealing the carbides precipitates inside bainitic ferrite lath in specific crystallographic planes and partly at the grain boundaries. The annealing at the temperature 550oC caused disappearing of characteristic for ADI needle or lath – like morphology, which is replaced with equiaxed grains. In this case Fe3C carbides take the form very fine precipitates with spheroidal geometry.

  14. Grain coarsening mechanism of Cu thin films by rapid annealing

    International Nuclear Information System (INIS)

    Sasajima, Yasushi; Kageyama, Junpei; Khoo, Khyoupin; Onuki, Jin

    2010-01-01

    Cu thin films have been produced by an electroplating method using nominal 9N anode and nominal 6N CuSO 4 .5H 2 O electrolyte. Film samples were heat-treated by two procedures: conventional isothermal annealing in hydrogen atmosphere (abbreviated as H 2 annealing) and rapid thermal annealing with an infrared lamp (abbreviated as RTA). After heat treatment, the average grain diameters and the grain orientation distributions were examined by electron backscattering pattern analysis. The RTA samples (400 o C for 5 min) have a larger average grain diameter, more uniform grain distribution and higher ratio of (111) orientation than H 2 annealed samples (400 o C for 30 min). This means that RTA can produce films with coarser and more uniformly distributed grains than H 2 annealing within a short time, i.e. only a few minutes. To clarify the grain coarsening mechanism, grain growth by RTA was simulated using the phase field method. The simulated grain diameter reaches its maximum at a heating rate which is the same order as that in the actual RTA experiment. The maximum grain diameter is larger than that obtained by H 2 annealing with the same annealing time at the isothermal stage as in RTA. The distribution of the misorientation was analyzed which led to a proposed grain growth model for the RTA method.

  15. Annealed Scaling for a Charged Polymer

    International Nuclear Information System (INIS)

    Caravenna, F.; Hollander, F. den; Pétrélis, N.; Poisat, J.

    2016-01-01

    This paper studies an undirected polymer chain living on the one-dimensional integer lattice and carrying i.i.d. random charges. Each self-intersection of the polymer chain contributes to the interaction Hamiltonian an energy that is equal to the product of the charges of the two monomers that meet. The joint probability distribution for the polymer chain and the charges is given by the Gibbs distribution associated with the interaction Hamiltonian. The focus is on the annealed free energy per monomer in the limit as the length of the polymer chain tends to infinity. We derive a spectral representation for the free energy and use this to prove that there is a critical curve in the parameter plane of charge bias versus inverse temperature separating a ballistic phase from a subballistic phase. We show that the phase transition is first order. We prove large deviation principles for the laws of the empirical speed and the empirical charge, and derive a spectral representation for the associated rate functions. Interestingly, in both phases both rate functions exhibit flat pieces, which correspond to an inhomogeneous strategy for the polymer to realise a large deviation. The large deviation principles in turn lead to laws of large numbers and central limit theorems. We identify the scaling behaviour of the critical curve for small and for large charge bias. In addition, we identify the scaling behaviour of the free energy for small charge bias and small inverse temperature. Both are linked to an associated Sturm-Liouville eigenvalue problem. A key tool in our analysis is the Ray-Knight formula for the local times of the one-dimensional simple random walk. This formula is exploited to derive a closed form expression for the generating function of the annealed partition function, and for several related quantities. This expression in turn serves as the starting point for the derivation of the spectral representation for the free energy, and for the scaling theorems

  16. The phase diagram of annealed Ge(111)/Ga

    DEFF Research Database (Denmark)

    Molinàs-Mata, P.; Böhringer, M.; Artacho, E.

    1995-01-01

    A study of the annealed phases of Ge(111)/Ga for coverages above 0.05 ML is presented. The surfaces are investigated by low-energy electron diffraction, scanning tunneling microscopy, and partly by photoemission and surface X-ray diffraction using synchrotron radiation. For Ga coverages beyond 0.......05 ML and up to about 2 ML and annealing temperatures higher than 500 degrees C four different phases appear. They all can be characterized as being discommensurate. Surprisingly, no commensurate superstructure appears on annealed Ge(111)/Ga....

  17. Structural study of conventional and bulk metallic glasses during annealing

    International Nuclear Information System (INIS)

    Pineda, E.; Hidalgo, I.; Bruna, P.; Pradell, T.; Labrador, A.; Crespo, D.

    2009-01-01

    Metallic glasses with conventional glass-forming ability (Al-Fe-Nd, Fe-Zr-B, Fe-B-Nb compositions) and bulk metallic glasses (Ca-Mg-Cu compositions) were studied by synchrotron X-ray diffraction during annealing throughout glass transition and crystallization temperatures. The analysis of the first diffraction peak position during the annealing process allowed us to follow the free volume change during relaxation and glass transition. The structure factor and the radial distribution function of the glasses were obtained from the X-ray measurements. The structural changes occurred during annealing are analyzed and discussed.

  18. Anisotropic annealing of fission fragments in synthetic quartz

    CERN Document Server

    Sawamura, T; Narita, M

    1999-01-01

    A study on the thermal annealing behavior of fission fragments in synthetic quartz crystals was performed for application of synthetic quartz to track detectors under high temperature circumstances: x-, y-, and z-cut quartz plates were exposed to fission fragments from sup 2 sup 5 sup 2 Cf and were annealed up to 750 deg. C. It was found that track retention depended on the crystallographic structure: the annealing temperature, where the number of etched tracks was sharply reduced, was 550 deg. C for the x- and y-cut plates and 750 deg. C for z-cut plates. Track sizes decrease and disperse with reductions in the track retention.

  19. Radiation damage and annealing in plutonium tetrafluoride

    Energy Technology Data Exchange (ETDEWEB)

    McCoy, Kaylyn; Casella, Amanda; Sinkov, Sergey; Sweet, Lucas; McNamara, Bruce; Delegard, Calvin; Jevremovic, Tatjana

    2017-12-01

    Plutonium tetrafluoride that was separated prior to 1966 at the Hanford Site in Washington State was analyzed at the Pacific Northwest National Laboratory (PNNL) in 2015 and 2016. The plutonium tetrafluoride, as received, was an off-normal color and considering the age of the plutonium, there were questions about the condition of the material. These questions had to be answered in order to determine the suitability of the material for future use or long-term storage. Therefore, Thermogravimetric/Differential Thermal Analysis and X-ray Diffraction evaluations were conducted to determine the plutonium’s crystal structure, oxide content, and moisture content; these analyses reported that the plutonium was predominately amorphous and tetrafluoride, with an oxide content near ten percent. Freshly fluorinated plutonium tetrafluoride is known to be monoclinic. During the initial Thermogravimetric/Differential Thermal analyses, it was discovered that an exothermic event occurred within the material near 414°C. X-ray Diffraction analyses were conducted on the annealed tetrafluoride. The X-ray Diffraction analyses indicated that some degree of recrystallization occurred in conjunction with the 414°C event. The following commentary describes the series of Thermogravimetric/Differential Thermal and X-ray Diffraction analyses that were conducted as part of this investigation at PNNL, in collaboration with the University of Utah Nuclear Engineering Program.

  20. Production characteristics of lettuce Lactuca sativa L. in the frame of the first crop tests in the Higher Plant Chamber integrated into the MELiSSA Pilot Plant

    Science.gov (United States)

    Tikhomirova, Natalia; Lawson, Jamie; Stasiak, Michael; Dixon, Mike; Paille, Christel; Peiro, Enrique; Fossen, Arnaud; Godia, Francesc

    Micro-Ecological Life Support System Alternative (MELiSSA) is an artificial closed ecosystem that is considered a tool for the development of a bioregenerative life support system for manned space missions. One of the five compartments of MELiSSA loop -Higher Plant Chamber was recently integrated into the MELiSSA Pilot Plant facility at Universitat Aut`noma deo Barcelona. The main contributions expected by integration of this photosynthetic compartment are oxygen, water, vegetable food production and CO2 consumption. Production characteristics of Lactuca sativa L., as a MELiSSA candidate crop, were investigated in this work in the first crop experiments in the MELiSSA Pilot Plant facility. The plants were grown in batch culture and totaled 100 plants with a growing area 5 m long and 1 m wide in a sealed controlled environment. Several replicates of the experiments were carried out with varying duration. It was shown that after 46 days of lettuce cultivation dry edible biomass averaged 27, 2 g per plant. However accumulation of oxygen in the chamber, which required purging of the chamber, and decrease in the food value of the plants was observed. Reducing the duration of the tests allowed uninterrupted test without opening the system and also allowed estimation of the crop's carbon balance. Results of productivity, tissue composition, nutrient uptake and canopy photosynthesis of lettuce regardless of test duration are discussed in the paper.

  1. BOREAS HYP-8 DEM Data Over The NSA-MSA and SSA-MSA in The AEAC Projection

    Science.gov (United States)

    Knapp, David E.; Hall, Forrest G. (Editor); Wang, Xue-Wen; Band, L. E.; Smith, David E. (Technical Monitor)

    2000-01-01

    These data were derived from the original Digital Elevation Models (DEMs) produced by the Boreal Ecosystem-Atmosphere Study (BOREAS) Hydrology (HYD)-8 team. The original DEMs were in the Universal Transverse Mercator (UTM) projection, while this product is projected in the Albers Equal-Area Conic (AEAC) projection. The pixel size of the data is 100 meters, which is appropriate for the 1:50,000-scale contours from which the DEMs were made. The original data were compiled from information available in the 1970s and 1980s. This data set covers the two Modeling Sub-Areas (MSAs) that are contained within the Southern Study Area (SSA) and the Northern Study Area (NSA). The data are stored in binary, image format files. The DEM data over the NSA-MSA and SSA-MSA in the AEAC projection are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  2. Induction of Osmoadaptive Mechanisms and Modulation of Cellular Physiology Help Bacillus licheniformis Strain SSA 61 Adapt to Salt Stress

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Sangeeta; Aggarwal, Chetana; Thakur, Jyoti Kumar; Bandeppa, G. S.; Khan, Md. Aslam; Pearson, Lauren M.; Babnigg, Gyorgy; Giometti, Carol S.; Joachimiak, Andrzej

    2015-01-06

    Bacillus licheniformis strain SSA 61, originally isolated from Sambhar salt lake, was observed to grow even in the presence of 25 % salt stress. Osmoadaptive mechanisms of this halotolerant B. licheniformis strain SSA 61, for long-term survival and growth under salt stress, were determined. Proline was the preferentially accumulated compatible osmolyte. There was also increased accumulation of antioxidants ascorbic acid and glutathione. Among the different antioxidative enzymes assayed, superoxide dismutase played the most crucial role in defense against salt-induced stress in the organism. Adaptation to stress by the organism involved modulation of cellular physiology at various levels. There was enhanced expression of known proteins playing essential roles in stress adaptation, such as chaperones DnaK and GroEL, and general stress protein YfkM and polynucleotide phosphorylase/polyadenylase. Proteins involved in amino acid biosynthetic pathway, ribosome structure, and peptide elongation were also overexpressed. Salt stress-induced modulation of expression of enzymes involved in carbon metabolism was observed. There was up-regulation of a number of enzymes involved in generation of NADH and NADPH, indicating increased cellular demand for both energy and reducing power.

  3. Solvent vapor annealing of an insoluble molecular semiconductor

    KAUST Repository

    Amassian, Aram

    2010-01-01

    Solvent vapor annealing has been proposed as a low-cost, highly versatile, and room-temperature alternative to thermal annealing of organic semiconductors and devices. In this article, we investigate the solvent vapor annealing process of a model insoluble molecular semiconductor thin film - pentacene on SiO 2 exposed to acetone vapor - using a combination of optical reflectance and two-dimensional grazing incidence X-ray diffraction measurements performed in situ, during processing. These measurements provide valuable and new insight into the solvent vapor annealing process; they demonstrate that solvent molecules interact mainly with the surface of the film to induce a solid-solid transition without noticeable swelling, dissolving or melting of the molecular material. © 2010 The Royal Society of Chemistry.

  4. Structural changes during annealing of GaInAsN

    International Nuclear Information System (INIS)

    Kurtz, Sarah; Webb, J.; Gedvilas, L.; Friedman, D.; Geisz, J.; Olson, J.; King, R.; Joslin, D.; Karam, N.

    2001-01-01

    The alloy GaInAsN has great potential as a lower-band-gap material lattice matched to GaAs, but there is little understanding of what causes its poor optoelectronic properties and why these improve with annealing. This study provides information about the structural changes that occur when GaInAsN is annealed. The Fourier transform infrared spectra exhibit two primary features: a triplet at ∼470 cm-1 (Ga--N stretch) and two or three bands at ∼3100 cm-1 (N--H stretch). The change in the Ga--N stretch absorption can be explained if the nitrogen environment is converted from NGa 4 to NInGa 3 after annealing. The N--H stretch is also changed after annealing, implying a second, and unrelated, structural change

  5. Performance of two different quantum annealing correction codes

    Science.gov (United States)

    Mishra, Anurag; Albash, Tameem; Lidar, Daniel A.

    2016-02-01

    Quantum annealing is a promising approach for solving optimization problems, but like all other quantum information processing methods, it requires error correction to ensure scalability. In this work, we experimentally compare two quantum annealing correction (QAC) codes in the setting of antiferromagnetic chains, using two different quantum annealing processors. The lower-temperature processor gives rise to higher success probabilities. The two codes differ in a number of interesting and important ways, but both require four physical qubits per encoded qubit. We find significant performance differences, which we explain in terms of the effective energy boost provided by the respective redundantly encoded logical operators of the two codes. The code with the higher energy boost results in improved performance, at the expense of a lower-degree encoded graph. Therefore, we find that there exists an important trade-off between encoded connectivity and performance for quantum annealing correction codes.

  6. Stochastic search in structural optimization - Genetic algorithms and simulated annealing

    Science.gov (United States)

    Hajela, Prabhat

    1993-01-01

    An account is given of illustrative applications of genetic algorithms and simulated annealing methods in structural optimization. The advantages of such stochastic search methods over traditional mathematical programming strategies are emphasized; it is noted that these methods offer a significantly higher probability of locating the global optimum in a multimodal design space. Both genetic-search and simulated annealing can be effectively used in problems with a mix of continuous, discrete, and integer design variables.

  7. Simulated annealing image reconstruction for positron emission tomography

    International Nuclear Information System (INIS)

    Sundermann, E.; Lemahieu, I.; Desmedt, P.

    1994-01-01

    In Positron Emission Tomography (PET) images have to be reconstructed from moisy projection data. The noise on the PET data can be modeled by a Poison distribution. In this paper, we present the results of using the simulated annealing technique to reconstruct PET images. Various parameter settings of the simulated annealing algorithm are discussed and optimized. The reconstructed images are of good quality and high contrast, in comparison to other reconstruction techniques. (authors)

  8. Far-infrared spectroscopy of thermally annealed tungsten silicide films

    International Nuclear Information System (INIS)

    Amiotti, M.; Borghesi, A.; Guizzetti, G.; Nava, F.; Santoro, G.

    1991-01-01

    The far-infrared transmittance spectrum of tungsten silicide has been observed for the first time. WSi 2 polycrystalline films were prepared by coevaporation and chemical-vapour deposition on silicon wafers, and subsequently thermally annealed at different temperatures. The observed structures are interpreted, on the basis of the symmetry properties of the crystal, such as infrared-active vibrational modes. Moreover, the marked lineshape dependence on annealing temperature enables this technique to analyse the formation of the solid silicide phases

  9. Population annealing: Theory and application in spin glasses

    OpenAIRE

    Wang, Wenlong; Machta, Jonathan; Katzgraber, Helmut G.

    2015-01-01

    Population annealing is an efficient sequential Monte Carlo algorithm for simulating equilibrium states of systems with rough free energy landscapes. The theory of population annealing is presented, and systematic and statistical errors are discussed. The behavior of the algorithm is studied in the context of large-scale simulations of the three-dimensional Ising spin glass and the performance of the algorithm is compared to parallel tempering. It is found that the two algorithms are similar ...

  10. Conventional treatment planning optimization using simulated annealing

    International Nuclear Information System (INIS)

    Morrill, S.M.; Langer, M.; Lane, R.G.

    1995-01-01

    Purpose: Simulated annealing (SA) allows for the implementation of realistic biological and clinical cost functions into treatment plan optimization. However, a drawback to the clinical implementation of SA optimization is that large numbers of beams appear in the final solution, some with insignificant weights, preventing the delivery of these optimized plans using conventional (limited to a few coplanar beams) radiation therapy. A preliminary study suggested two promising algorithms for restricting the number of beam weights. The purpose of this investigation was to compare these two algorithms using our current SA algorithm with the aim of producing a algorithm to allow clinically useful radiation therapy treatment planning optimization. Method: Our current SA algorithm, Variable Stepsize Generalized Simulated Annealing (VSGSA) was modified with two algorithms to restrict the number of beam weights in the final solution. The first algorithm selected combinations of a fixed number of beams from the complete solution space at each iterative step of the optimization process. The second reduced the allowed number of beams by a factor of two at periodic steps during the optimization process until only the specified number of beams remained. Results of optimization of beam weights and angles using these algorithms were compared using a standard cadre of abdominal cases. The solution space was defined as a set of 36 custom-shaped open and wedged-filtered fields at 10 deg. increments with a target constant target volume margin of 1.2 cm. For each case a clinically-accepted cost function, minimum tumor dose was maximized subject to a set of normal tissue binary dose-volume constraints. For this study, the optimized plan was restricted to four (4) fields suitable for delivery with conventional therapy equipment. Results: The table gives the mean value of the minimum target dose obtained for each algorithm averaged over 5 different runs and the comparable manual treatment

  11. Thermalization, Freeze-out, and Noise: Deciphering Experimental Quantum Annealers

    Science.gov (United States)

    Marshall, Jeffrey; Rieffel, Eleanor G.; Hen, Itay

    2017-12-01

    By contrasting the performance of two quantum annealers operating at different temperatures, we address recent questions related to the role of temperature in these devices and their function as "Boltzmann samplers." Using a method to reliably calculate the degeneracies of the energy levels of large-scale spin-glass instances, we are able to estimate the instance-dependent effective temperature from the output of annealing runs. Our results corroborate the "freeze-out" picture which posits two regimes, one in which the final state corresponds to a Boltzmann distribution of the final Hamiltonian with a well-defined "effective temperature" determined at a freeze-out point late in the annealing schedule, and another regime in which such a distribution is not necessarily expected. We find that the output distributions of the annealers do not, in general, correspond to a classical Boltzmann distribution for the final Hamiltonian. We also find that the effective temperatures at different programing cycles fluctuate greatly, with the effect worsening with problem size. We discuss the implications of our results for the design of future quantum annealers to act as more-effective Boltzmann samplers and for the programing of such annealers.

  12. Optimization using quantum mechanics: quantum annealing through adiabatic evolution

    International Nuclear Information System (INIS)

    Santoro, Giuseppe E; Tosatti, Erio

    2006-01-01

    We review here some recent work in the field of quantum annealing, alias adiabatic quantum computation. The idea of quantum annealing is to perform optimization by a quantum adiabatic evolution which tracks the ground state of a suitable time-dependent Hamiltonian, where 'ℎ' is slowly switched off. We illustrate several applications of quantum annealing strategies, starting from textbook toy-models-double-well potentials and other one-dimensional examples, with and without disorder. These examples display in a clear way the crucial differences between classical and quantum annealing. We then discuss applications of quantum annealing to challenging hard optimization problems, such as the random Ising model, the travelling salesman problem and Boolean satisfiability problems. The techniques used to implement quantum annealing are either deterministic Schroedinger's evolutions, for the toy models, or path-integral Monte Carlo and Green's function Monte Carlo approaches, for the hard optimization problems. The crucial role played by disorder and the associated non-trivial Landau-Zener tunnelling phenomena is discussed and emphasized. (topical review)

  13. Formation of oxygen related donors in step-annealed CZ–silicon

    Indian Academy of Sciences (India)

    The effect of step-annealing necessitated by the difficulties being faced in the long duration annealing treatments to be given to CZ–silicon has been studied. One pre-anneal of 10 h followed by annealing of 10 h causes a decrease in the absorption coefficient for carbon (c). Oxygen and carbon both accelerate thermal ...

  14. Rapid hardening induced by electric pulse annealing in nanostructured pure aluminum

    DEFF Research Database (Denmark)

    Zeng, Wei; Shen, Yao; Zhang, Ning

    2012-01-01

    Nanostructured pure aluminum was fabricated by heavy cold-rolling and then subjected to recovery annealing either by applying electric pulse annealing or by traditional air furnace annealing. Both annealing treatments resulted in an increase in yield strength due to the occurrence of a “dislocation...

  15. Ultraviolet radiation (UVR) induces cell-surface Ro/SSA antigen expression by human keratinocytes in vitro: a possible mechanism for the UVR induction of cutaneous lupus lesions

    International Nuclear Information System (INIS)

    Jones, S.K.

    1992-01-01

    Antinuclear antibodies are useful markers of connective tissue disease. In this study, UVB but not UVA induced the expression of Ro/SSA antigen on keratinocyte surfaces in vitro. This expression was also found with the extractable nuclear antigens RnP and Sm, but not with single or double-stranded DNA. The expression was prevented by blocking protein synthesis, suggesting that it was an active process. The results suggest that UVB exposure may result in the expression of Ro/SSA antigen on the surfaces of basal keratinocytes in vivo. This antigen could then bind circulating antibody leading to the cutaneous lesions in neonatal and subacute cutaneous lupus erythematosus. (Author)

  16. An analysis of the potential for achieving the fourth millennium development goal in SSA with domestic resources.

    Science.gov (United States)

    O'Hare, Bernadette; Makuta, Innocent

    2015-02-25

    The importance of good health is reflected in the fact that more than half of the eight Millennium Development Goals (MDGs) are aimed at improving health status. Goal 4 (MDG4) aims to reduce child mortality. The progress indicator for goal 4 is the under-five mortality rate (U5M), with a targeted reduction of two thirds by 2015 from 1990 levels. This paper seeks to compare the time (in years) Sub Saharan African (SSA) countries will take to reach their MDG4 target at the current rate of decline, and the time it could have taken to reach their target if domestic resources had not been lost through illicit financial flows, corruption and servicing of debt since 2000. We estimate the amount by which the Gross Domestic Product (GDP) per capita would increase (in percentage terms) if losses of resource through illicit financial flows, corruption and debt servicing, were reduced. Using the income elasticity of U5M, a metric which reports the percentage change in U5M for a one percent change in GDP per capita, we estimate the potential gains in the annual reduction of the under-five mortality if these resource losses were reduced. At the current rate of reduction in U5M, nine countries out of this sample of 36 SSA countries (25%) will achieve their MDG4 target by 2015. In the absence of the leakages (IFF, corruption and debt service) 30 out of 36 (83%) would reach their MDG4 target by 2015 and all except one country, Zimbabwe would have achieved their MDG4 by 2017 (97%). In view of the uncertainty of the legitimacy of African debts we have also provided results where we excluded debt repayment from our analysis. Most countries would have met MDG4 target by curtailing these outflows. In order to release latent resources in SSA for development, action will be needed both by African countries and internationally. We consider that stemming these outflows, and thereby reducing the need for aid, can be achieved with a more transparent global financial system.

  17. Note: Improving long-term stability of hot-wire anemometer sensors by means of annealing.

    Science.gov (United States)

    Lundström, H

    2015-08-01

    Annealing procedures for hot-wire sensors of platinum and platinum-plated tungsten have been investigated experimentally. It was discovered that the two investigated sensor metals behave quite differently during the annealing process, but for both types annealing may improve long-term stability considerably. Measured drift of sensors both without and with prior annealing is presented. Suggestions for suitable annealing temperatures and times are given.

  18. Liquid nitrogen enhancement of partially annealed fission tracks in glass

    International Nuclear Information System (INIS)

    Pilione, L.J.; Gold, D.P.

    1976-01-01

    It is known that the number density of fission tracks in solids is reduced if the sample is heated before chemical etching, and the effect of annealing must be allowed for before an age can be assigned to the sample. The extent of annealing can be determined by measuring the reduction of track parameters (diameter and/or length) and comparison with unannealed tracks. Correct ages can be obtained by careful calibration studies of track density reduction against track diameter or length reduction at different annealing temperatures and times. For crystallised minerals, however, the resulting correction techniques are not generally valid. In the experimental work described glass samples were partially annealed and then immersed in liquid N 2 for various periods, and it was shown that the properties of the glass and the track parameters could be altered so as to observe tracks that would normally be erased by annealing. The results of track density measurements against liquid N 2 immersion times are shown graphically. A gain of about 40% was achieved after 760 hours immersion time. The size of the tracks was not noticeably affected by the immersion. It was thought that thermal shock might be the cause of the track enhancement, but it was found that repeated immersion for about 2 hours did not lead to an increase in track density. Other studies suggest that the mechanism that erases the tracks through annealing may be partially reversed when the temperature of the sample is significantly lowered for a sufficient length of time. Further work is under way to find whether or not the process of enhancement is a reversal of the annealing process. Similar enhancement effects using liquid N 2 have been observed for d-particle tracks in polycarbonate detectors. (U.K.)

  19. BOREAS HYD-8 DEM Data Over the NSA-MSA and SSA-MSA in the UTM Projection

    Science.gov (United States)

    Wang, Xue-Wen; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Band, L. E.; Smith, David E. (Technical Monitor)

    2000-01-01

    The BOREAS HYD-8 team focused on describing the scaling behavior of water and carbon flux processes at local and regional scales. These DEMs were produced from digitized contours at a cell resolution of 100 meters. Vector contours of the area were used as input to a software package that interpolates between contours to create a DEM representing the terrain surface. The vector contours had a contour interval of 25 feet. The data cover the BOREAS MSAs of the SSA and NSA and are given in a UTM map projection. Most of the elevation data from which the DEM was produced were collected in the 1970s or 1980s. The data are stored in binary, image format files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  20. Prognostic implications of antibodies to Ro/SSA and soluble liver antigen in type 1 autoimmune hepatitis.

    Science.gov (United States)

    Montano-Loza, Aldo J; Shums, Zakera; Norman, Gary L; Czaja, Albert J

    2012-01-01

    Antibodies to soluble liver antigen are frequently co-expressed with antibodies to ribonucleoprotein/Sjögren's syndrome A (Ro/SSA) in autoimmune hepatitis. Our goals were to evaluate the prognostic implications of antibodies to Ro/SSA in type 1 autoimmune hepatitis and to determine their independence from antibodies to soluble liver antigen. Three hundred and seventy-six serum samples from 170 patients were tested by enzyme immunoassays. Sixty-five patients (38%) had antibodies to Ro52; 11 patients (6%) had antibodies to Ro60; and 27 patients had antibodies to soluble liver antigen (16%). Twenty-six patients with antibodies to Ro52 had antibodies to soluble liver antigen (40%), and 26 patients with antibodies to soluble liver antigen had antibodies to Ro52 (96%). Patients with antibodies to Ro52 and antibodies to soluble liver antigen had a higher frequency of human leucocyte antigen (HLA) DRB1(*) 03 (78 vs 50%, P=0.05) and lower occurrence of HLA DRB1(*) 04 (22 vs 57%, P=0.01) than patients with antibodies to Ro52 alone. Antibodies to Ro52 alone [hazard ratio (HR), 2.90; 95% confidence interval (CI), 1.18-7.14, P=0.02] and antibodies to Ro52 in conjunction with antibodies to soluble liver antigen (HR, 2.98; 95% CI, 1.07-8.43, P=0.04) were independently associated with the development of cirrhosis and hepatic death or liver transplantation. Antibodies to Ro52 alone and antibodies to Ro52 in conjunction with antibodies to soluble liver antigen are independently associated with a poor prognosis in type 1 autoimmune hepatitis. The prognostic implications ascribed to antibodies to soluble liver antigen may reflect their almost invariable concurrence with antibodies to Ro52. © 2011 John Wiley & Sons A/S.

  1. High pressure annealing of Europium implanted GaN

    KAUST Repository

    Lorenz, K.

    2012-02-09

    GaN epilayers were implanted with Eu to fluences of 1×10^13 Eu/cm2 and 1×10^15 Eu/cm2. Post-implant thermal annealing was performed in ultra-high nitrogen pressures at temperatures up to 1450 ºC. For the lower fluence effective structural recovery of the crystal was observed for annealing at 1000 ºC while optical activation could be further improved at higher annealing temperatures. The higher fluence samples also reveal good optical activation; however, some residual implantation damage remains even for annealing at 1450 ºC which leads to a reduced incorporation of Eu on substitutional sites, a broadening of the Eu luminescence lines and to a strongly reduced fraction of optically active Eu ions. Possibilities for further optimization of implantation and annealing conditions are discussed.© (2012) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  2. Experimental quantum annealing: case study involving the graph isomorphism problem

    Science.gov (United States)

    Zick, Kenneth M.; Shehab, Omar; French, Matthew

    2015-01-01

    Quantum annealing is a proposed combinatorial optimization technique meant to exploit quantum mechanical effects such as tunneling and entanglement. Real-world quantum annealing-based solvers require a combination of annealing and classical pre- and post-processing; at this early stage, little is known about how to partition and optimize the processing. This article presents an experimental case study of quantum annealing and some of the factors involved in real-world solvers, using a 504-qubit D-Wave Two machine and the graph isomorphism problem. To illustrate the role of classical pre-processing, a compact Hamiltonian is presented that enables a reduced Ising model for each problem instance. On random N-vertex graphs, the median number of variables is reduced from N2 to fewer than N log2 N and solvable graph sizes increase from N = 5 to N = 13. Additionally, error correction via classical post-processing majority voting is evaluated. While the solution times are not competitive with classical approaches to graph isomorphism, the enhanced solver ultimately classified correctly every problem that was mapped to the processor and demonstrated clear advantages over the baseline approach. The results shed some light on the nature of real-world quantum annealing and the associated hybrid classical-quantum solvers. PMID:26053973

  3. Laser annealing heals radiation damage in avalanche photodiodes

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Jin Gyu [University of Waterloo, Institute for Quantum Computing, Waterloo, ON (Canada); University of Waterloo, Department of Electrical and Computer Engineering, Waterloo, ON (Canada); Anisimova, Elena; Higgins, Brendon L.; Bourgoin, Jean-Philippe [University of Waterloo, Institute for Quantum Computing, Waterloo, ON (Canada); University of Waterloo, Department of Physics and Astronomy, Waterloo, ON (Canada); Jennewein, Thomas [University of Waterloo, Institute for Quantum Computing, Waterloo, ON (Canada); University of Waterloo, Department of Physics and Astronomy, Waterloo, ON (Canada); Canadian Institute for Advanced Research, Quantum Information Science Program, Toronto, ON (Canada); Makarov, Vadim [University of Waterloo, Institute for Quantum Computing, Waterloo, ON (Canada); University of Waterloo, Department of Electrical and Computer Engineering, Waterloo, ON (Canada); University of Waterloo, Department of Physics and Astronomy, Waterloo, ON (Canada)

    2017-12-15

    Avalanche photodiodes (APDs) are a practical option for space-based quantum communications requiring single-photon detection. However, radiation damage to APDs significantly increases their dark count rates and thus reduces their useful lifetimes in orbit. We show that high-power laser annealing of irradiated APDs of three different models (Excelitas C30902SH, Excelitas SLiK, and Laser Components SAP500S2) heals the radiation damage and several APDs are restored to typical pre-radiation dark count rates. Of nine samples we test, six APDs were thermally annealed in a previous experiment as another solution to mitigate the radiation damage. Laser annealing reduces the dark count rates further in all samples with the maximum dark count rate reduction factor varying between 5.3 and 758 when operating at -80 C. This indicates that laser annealing is a more effective method than thermal annealing. The illumination power to reach these reduction factors ranges from 0.8 to 1.6 W. Other photon detection characteristics, such as photon detection efficiency, timing jitter, and afterpulsing probability, fluctuate but the overall performance of quantum communications should be largely unaffected by these variations. These results herald a promising method to extend the lifetime of a quantum satellite equipped with APDs. (orig.)

  4. Partially Annealed Disorder and Collapse of Like-Charged Macroions

    Science.gov (United States)

    Mamasakhlisov, Yevgeni S.; Naji, Ali; Podgornik, Rudolf

    2008-11-01

    Charged systems with partially annealed charge disorder are investigated using field-theoretic and replica methods. Charge disorder is assumed to be confined to macroion surfaces surrounded by a cloud of mobile neutralizing counterions in an aqueous solvent. A general formalism is developed by assuming that the disorder is partially annealed (with purely annealed and purely quenched disorder included as special cases), i.e., we assume in general that the disorder undergoes a slow dynamics relative to fast-relaxing counterions making it possible thus to study the stationary-state properties of the system using methods similar to those available in equilibrium statistical mechanics. By focusing on the specific case of two planar surfaces of equal mean surface charge and disorder variance, it is shown that partial annealing of the quenched disorder leads to renormalization of the mean surface charge density and thus a reduction of the inter-plate repulsion on the mean-field or weak-coupling level. In the strong-coupling limit, charge disorder induces a long-range attraction resulting in a continuous disorder-driven collapse transition for the two surfaces as the disorder variance exceeds a threshold value. Disorder annealing further enhances the attraction and, in the limit of low screening, leads to a global attractive instability in the system.

  5. On simulated annealing phase transitions in phylogeny reconstruction.

    Science.gov (United States)

    Strobl, Maximilian A R; Barker, Daniel

    2016-08-01

    Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Enhancing quantum annealing performance for the molecular similarity problem

    Science.gov (United States)

    Hernandez, Maritza; Aramon, Maliheh

    2017-05-01

    Quantum annealing is a promising technique which leverages quantum mechanics to solve hard optimization problems. Considerable progress has been made in the development of a physical quantum annealer, motivating the study of methods to enhance the efficiency of such a solver. In this work, we present a quantum annealing approach to measure similarity among molecular structures. Implementing real-world problems on a quantum annealer is challenging due to hardware limitations such as sparse connectivity, intrinsic control error, and limited precision. In order to overcome the limited connectivity, a problem must be reformulated using minor-embedding techniques. Using a real data set, we investigate the performance of a quantum annealer in solving the molecular similarity problem. We provide experimental evidence that common practices for embedding can be replaced by new alternatives which mitigate some of the hardware limitations and enhance its performance. Common practices for embedding include minimizing either the number of qubits or the chain length and determining the strength of ferromagnetic couplers empirically. We show that current criteria for selecting an embedding do not improve the hardware's performance for the molecular similarity problem. Furthermore, we use a theoretical approach to determine the strength of ferromagnetic couplers. Such an approach removes the computational burden of the current empirical approaches and also results in hardware solutions that can benefit from simple local classical improvement. Although our results are limited to the problems considered here, they can be generalized to guide future benchmarking studies.

  7. Efficient Embedding of Integer Programming Problems on Quantum Annealers

    Science.gov (United States)

    Venturelli, Davide; Trummer, Immanuel

    Quantum Annealers are being considered as a possible platform to solve challenging Integer Optimization Problems (IOP). Hard-coding an IOP as an Ising model onto an annealer is however no easy task due to the severe restrictions imposed mostly by the connectivity of the graph implemented by the hardware architecture, as it has widely discussed for the D-Wave machines. The current approaches employ graph minor embedding algorithms that require a significant overhead of resources (number of qubits, computing power) with respect to the number of logical variables in the IOP. This overhead is arguably the primary problems for practitioners of quantum annealing. We present a new method to deterministically embed an arbitrary IOP in a generic class of annealing chip layouts such that the asymptotic scaling beats all the current methods. It is shown on the latest D-Wave chips to allow programming of problems, relevant for database and space sciences, with approximately 5-10x more variables with respect to the published approaches. The method is efficient in the sense that a valid embedding can be computed at run-time in polynomial time. The discussed methods can inform the design of next-generation of quantum annealers.

  8. 78 FR 48170 - Privacy Act of 1974; CMS Computer Match No. 2013-12; HHS Computer Match No. 1307; SSA Computer...

    Science.gov (United States)

    2013-08-07

    ... 1974; CMS Computer Match No. 2013-12; HHS Computer Match No. 1307; SSA Computer Match No. 1097-1899...). ACTION: Notice of Computer Matching Program (CMP). SUMMARY: In accordance with the requirements of the....hhs.gov . SUPPLEMENTARY INFORMATION: The Computer Matching and Privacy Protection Act of 1988 (Public...

  9. TiSSA pleenum "Sotsiaaltöö kriisi ajal" : mida on sotsiaaltööl pakkuda ja kes saab sellest kasu? / Regina Lind

    Index Scriptorium Estoniae

    Lind, Regina

    2010-01-01

    22.-27. aug. 2010 toimus Tallinna Ülikoolis TiSSA doktorantide eelkonverents ja pleenum. Pleenumil peetud sotsiaalteadlaste ettekannetest. Esinesid: Holger Ziegler, Karin Böllert, Catrin Heite, Hans van Ewijk, Walter Lorenz, Mikko Mäntysaari, Heinz Sünker, Synnöve Karvinen-Niinikoski, Olga Borodkina

  10. Impaired clearance of apoptotic cardiocytes is linked to anti-SSA/Ro and -SSB/La antibodies in the pathogenesis of congenital heart block.

    Science.gov (United States)

    Clancy, Robert M; Neufing, Petra J; Zheng, Ping; O'Mahony, Marguerita; Nimmerjahn, Falk; Gordon, Tom P; Buyon, Jill P

    2006-09-01

    The role of cardiocytes in physiologic removal of apoptotic cells and the subsequent effect of surface binding by anti-SSA/Ro and -SSB/La antibodies was addressed. Initial experiments evaluated induction of apoptosis by extrinsic and intrinsic pathways. Nuclear injury and the translocation of SSA/Ro and SSB/La antigens to the fetal cardiocyte plasma membrane were common downstream events of Fas and TNF receptor ligation, requiring caspase activation. As assessed by phase-contrast and confirmed by confocal microscopy, coculturing of healthy cardiocytes with cardiocytes rendered apoptotic via extrinsic pathways revealed a clearance mechanism that to our knowledge has not previously been described. Cultured fetal cardiocytes expressed phosphatidylserine receptors (PSRs), as did cardiac tissue from a fetus with congenital heart block (CHB) and an age-matched control. Phagocytic uptake was blocked by anti-PSR antibodies and was significantly inhibited following preincubation of apoptotic cardiocytes with chicken and murine anti-SSA/Ro and -SSB/La antibodies, with IgG from an anti-SSA/Ro- and -SSB/La-positive mother of a CHB child, but not with anti-HLA class I antibody. In a murine model, anti-Ro60 bound and inhibited uptake of apoptotic cardiocytes from wild-type but not Ro60-knockout mice. Our results suggest that resident cardiocytes participate in physiologic clearance of apoptotic cardiocytes but that clearance is inhibited by opsonization via maternal autoantibodies, resulting in accumulation of apoptotic cells, promoting inflammation and subsequent scarring.

  11. Formability of Annealed Ni-Ti Shape Memory Alloy Sheet

    Science.gov (United States)

    Fann, K. J.; Su, J. Y.; Chang, C. H.

    2018-03-01

    Ni-Ti shape memory alloy has two specific properties, superelasiticity and shape memory effect, and thus is widely applied in diverse industries. To extend its application, this study attempts to investigate the strength and cold formability of its sheet blank, which is annealed at various temperatures, by hardness test and by Erichsen-like cupping test. As a result, the higher the annealing temperature, the lower the hardness, the lower the maximum punch load as the sheet blank fractured, and the lower the Erichsen-like index or the lower the formability. In general, the Ni-Ti sheet after annealing has an Erichsen-like index between 8 mm and 9 mm. This study has also confirmed via DSC that the Ni-Ti shape memory alloy possesses the austenitic phase and shows the superelasticity at room temperature.

  12. Rapid Thermal annealing of silicon layers amorphized by ion implantation

    International Nuclear Information System (INIS)

    Hasenack, C.M.

    1986-01-01

    The recrystallization behavior and the supression mechanisms of the residual defects of silicon layers amorphized by ion implantation, were investigated. The samples were annealed with the aid of a rapid thermal annealing (RTA) system at temperature range from 850 to 1200 0 C, and annealing time up to 120 s. Random and aligned Rutherford backscattering spectroscopy were used to analyse the samples. Similarities in the recrystallization behavior for layers implanted with ions of the same chemical groups such as As or Sb; Ge, Sn or Pb, In or Ga, are observed. The results show that the effective supression of resisual defects of the recrystallired layers is vinculated to the redistribution of impurities via thermal diffusion. (author) [pt

  13. NRC assessment of the Department of Energy annealing demonstration project

    International Nuclear Information System (INIS)

    Jackson, D.A.; Malik, S.N.

    1997-01-01

    Thermal annealing is the only known method for mitigating the effects of neutron irradiation embrittlement in reactor pressure vessel (RPV) steels. In May 1996, the US Department of Energy (DOE) in conjunction with the American Society of Mechanical Engineers, Westinghouse, Cooperheat, Electric Power Research Institute (with participating utilities), Westinghouse Owner's Group, Consumers Power, Electricite' de France, Duquesne Light and the Central Research Institute of the Electric Power Industry (Japan) sponsored an annealing demonstration project (ADP) at Marble Hill. The Marble Hill Plant, located in Madison, Indiana, is a Westinghouse 4 loop design. The plant was nearly 70% completed when the project was canceled. Hence, the RPV was never irradiated. The paper will present highlights from the NRCs independent evaluation of the Marble Hill Annealing Demonstration Project

  14. Morphology and annealing kinetics of ion tracks in minerals

    Directory of Open Access Journals (Sweden)

    Ewing R. C.

    2012-10-01

    Full Text Available We have studied the morphology and annealing kinetics of ion tracks in Durango apatite using synchrotron small angle X-ray scattering. The non-destructive, artefact-free technique enables us to determine the track radii with a resolution of fractions of a nanometre. The tracks were generated using different heavy ions with energies between 185 MeV and 2.6 GeV. The track morphology is consistent with the formation of long cylindrical amorphous tracks. The annealing kinetics, measured by SAXS in combination with ex situ and in situ annealing experiments, suggests structural relaxation followed by recrystallisation of the damaged material. The measurement methodology shown here provides a new means for in-depth studies of ion-track formation in minerals under a wide variety of geological conditions.

  15. Molecular dynamics simulation of annealed ZnO surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Min, Tjun Kit; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

    2015-04-24

    The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.

  16. Mean field annealing approach to large residual-statics estimation

    Science.gov (United States)

    Cary, Peter W.; Upham, Warren

    1993-12-01

    We present a new method for solving the large residual-statics problem, called mean field annealing, which may be capable of overcoming some of the limitations of stochastic methods. Mean field annealing is a global-search method that is governed by a purely deterministic set of equations. The mean field annealing method approaches global optimization problems in a fundamentally different way from stochastic global-search methods. The mean field approach never samples individual trial solutions in model space. Instead, the mean field equations, which are solved at successively lower temperatures with a fixed-point method, involve solving for the probability distributions of each variable rather than solving for the variables themselves. The probability distribution of each variable is resolved separately by replacing all other variables that occur in the energy function by their expectation values.

  17. Doped ZnO nanowires obtained by thermal annealing.

    Science.gov (United States)

    Shan, C X; Liu, Z; Wong, C C; Hark, S K

    2007-02-01

    Doped ZnO nanowires were prepared in a very simple and inexpensive thermal annealing method using ZnSe nanowires as a precursor. As doped, P doped, and As/P codoped ZnO nanowires were obtained in this method. X-ray diffraction shows that the zincblende ZnSe nanowires were converted to doped wurtzite ZnO nanowires. The incorporation of the dopants was confirmed by energy dispersive X-ray spectroscopy. The doping concentration could be adjusted by changing the annealing temperature and duration. Scanning electron microscopy indicated that the morphology of the ZnSe nanowires was essentially retained after the annealing and doping process. Photoluminescence spectroscopy also verified the incorporation of the dopants into the nanowires.

  18. Phase annealing for the conditional simulation of spatial random fields

    Science.gov (United States)

    Hörning, S.; Bárdossy, A.

    2018-03-01

    Simulated annealing (SA) is a popular geostatistical simulation method as it provides great flexibility. In this paper possible problems of conditioning its realizations are discussed. A statistical test to recognize whether the observations are well embedded in their simulated neighborhood or not is developed. A new simulated annealing method, phase annealing (PA), is presented which makes it possible to avoid poor embedding of observations. PA is based on the Fourier representation of the spatial field. Instead of the individual pixel values, phases corresponding to different Fourier components are modified (i.e. shifted) in order to match prescribed statistics. The method treats neighborhoods together and thus avoids singularities at observation locations. It is faster than SA and can be used for the simulation of high resolution fields. Examples demonstrate the applicability of the method.

  19. Toward understanding dynamic annealing processes in irradiated ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Myers, Michael Thomas [Texas A & M Univ., College Station, TX (United States)

    2013-05-01

    High energy particle irradiation inevitably generates defects in solids. The ballistic formation and thermalization of the defect creation process occur rapidly, and are believed to be reasonably well understood. However, knowledge of the evolution of defects after damage cascade thermalization, referred to as dynamic annealing, is quite limited. Unraveling the mechanisms associated with dynamic annealing is crucial since such processes play an important role in the formation of stable postirradiation disorder in ion-beam-processing of semiconductors, and determines the “radiation tolerance” of many nuclear materials. The purpose of this dissertation is to further our understanding of the processes involved in dynamic annealing. In order to achieve this, two main tasks are undertaken.

  20. Chaotic Multiquenching Annealing Applied to the Protein Folding Problem

    Directory of Open Access Journals (Sweden)

    Juan Frausto-Solis

    2014-01-01

    Full Text Available The Chaotic Multiquenching Annealing algorithm (CMQA is proposed. CMQA is a new algorithm, which is applied to protein folding problem (PFP. This algorithm is divided into three phases: (i multiquenching phase (MQP, (ii annealing phase (AP, and (iii dynamical equilibrium phase (DEP. MQP enforces several stages of quick quenching processes that include chaotic functions. The chaotic functions can increase the exploration potential of solutions space of PFP. AP phase implements a simulated annealing algorithm (SA with an exponential cooling function. MQP and AP are delimited by different ranges of temperatures; MQP is applied for a range of temperatures which goes from extremely high values to very high values; AP searches for solutions in a range of temperatures from high values to extremely low values. DEP phase finds the equilibrium in a dynamic way by applying least squares method. CMQA is tested with several instances of PFP.