Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast.

Science.gov (United States)

Yu, Chuanhe; Gan, Haiyun; Zhang, Zhiguo

2018-01-01

DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.

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

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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

Mouse RAD54 affects DNA double-strand break repair and sister chromatid exchange

NARCIS (Netherlands)

H.B. Beverloo (Berna); R.D. Johnson (Roger); M. Jasin (Maria); R. Kanaar (Roland); J.H.J. Hoeijmakers (Jan); M.L.G. Dronkert (Mies)

2000-01-01

textabstractCells can achieve error-free repair of DNA double-strand breaks (DSBs) by homologous recombination through gene conversion with or without crossover. In contrast, an alternative homology-dependent DSB repair pathway, single-strand annealing (SSA), results in deletions. In this study, we

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.

Natural minus-strand RNAs of alfalfa mosaic virus as in vitro templates for viral RNA polymerase. 3'-Terminal non-coded guanosine and coat protein are insufficient factors for full-size plus-strand synthesis

NARCIS (Netherlands)

Houwing, C.J.; Huis in 't Veld, M.; Zuidema, D.; Graaff, de M.; Jaspars, E.M.J.

2001-01-01

Replication complexes of alfalfa mosaic virus produce in vivo large quantities of plus-strand RNAs, but this production is fully dependent on the presence of coat protein. In order to study this process of RNA-dependent and coat protein-regulated RNA synthesis we have isolated the three natural

Competition between the DNA unwinding and strand pairing activities of the Werner and Bloom syndrome proteins

Directory of Open Access Journals (Sweden)

Orren David K

2006-01-01

Full Text Available Abstract Background The premature aging and cancer-prone Werner and Bloom syndromes are caused by defects in the RecQ helicase enzymes WRN and BLM, respectively. Recently, both WRN and BLM (as well as several other RecQ members have been shown to possess a strand annealing activity in addition to the requisite DNA unwinding activity. Since an annealing function would appear to directly oppose the action of a helicase, we have examined in this study the dynamic equilibrium between unwinding and annealing mediated by either WRN or BLM. Results Our investigation into the competition between annealing and unwinding demonstrates that, under standard reaction conditions, WRN- or BLM-mediated annealing can partially or completely mask unwinding as measured in standard helicase assays. Several strategies were employed to suppress the annealing activity so that the actual strength of WRN- or BLM-dependent unwinding could be more accurately assessed. Interestingly, if a DNA oligomer complementary to one strand of the DNA substrate to be unwound is added during the helicase reaction, both WRN and BLM unwinding is enhanced, presumably by preventing protein-mediated re-annealing. This strategy allowed measurement of WRN-catalyzed unwinding of long (80 base pair duplex regions and fully complementary, blunt-ended duplexes, both of which were otherwise quite refractory to the helicase activity of WRN. Similarly, the addition of trap strand stimulated the ability of BLM to unwind long and blunt-ended duplexes. The stimulatory effect of the human replication protein A (hRPA, the eukaryotic single-stranded DNA binding protein on both WRN- and BLM-dependent unwinding was also re-examined in light of its possible role in preventing re-annealing. Our results show that hRPA influences the outcome of WRN and BLM helicase assays by both inhibiting re-annealing and directly promoting unwinding, with the larger contribution from the latter mechanism. Conclusion These

Rotavirus NSP2 interferes with the core lattice protein VP2 in initiation of minus-strand synthesis

International Nuclear Information System (INIS)

Vende, Patrice; Tortorici, M. Alejandra; Taraporewala, Zenobia F.; Patton, John T.

2003-01-01

The rotavirus nonstructural protein NSP2 self-assembles into stable octameric structures that possess nonspecific affinity for single-stranded (ss)RNA and RNA-RNA helix-destabilizing and NTPase activities. Furthermore, NSP2 is a component of replication intermediates with replicase activity and plays a critical role in the packaging and replication of the segmented dsRNA genome of rotavirus. To better understand the function of the protein in genome replication, we examined the effect that purified recombinant NSP2 had on the synthesis of dsRNA by the open core replication system. The results showed that NSP2 inhibited the synthesis of dsRNA from viral mRNA in vitro, in a concentration-dependent manner. The inhibition was overcome by adding increasing amounts of viral mRNA or nonviral ssRNA to the system, indicating that the inhibition was mediated by the nonspecific RNA-binding activity of NSP2. Further analysis revealed that NSP2 interfered with the ability of the open core proteins, GTP, and viral mRNA to form the initiation complex for (-) strand synthesis. Additional experiments indicated that NSP2 did not perturb recognition of viral mRNA by the viral RNA polymerase VP1, but rather interfered with the function of VP2, a protein that is essential for (-) strand initiation and dsRNA synthesis and that forms the T = 1 lattice of the virion core. In contrast to initiation, NSP2 did not inhibit (-) strand elongation. Collectively, the findings provide evidence that the temporal order of interaction of RNA-binding proteins with viral mRNA is a crucial factor impacting the formation of replication intermediates

Role of the Pepino mosaic virus 3'-untranslated region elements in negative-strand RNA synthesis in vitro.

Science.gov (United States)

Osman, Toba A M; Olsthoorn, René C L; Livieratos, Ioannis C

2014-09-22

Pepino mosaic virus (PepMV) is a mechanically-transmitted positive-strand RNA potexvirus, with a 6410 nt long single-stranded (ss) RNA genome flanked by a 5'-methylguanosine cap and a 3' poly-A tail. Computer-assisted folding of the 64 nt long PepMV 3'-untranslated region (UTR) resulted in the prediction of three stem-loop structures (hp1, hp2, and hp3 in the 3'-5' direction). The importance of these structures and/or sequences for promotion of negative-strand RNA synthesis and binding to the RNA dependent RNA polymerase (RdRp) was tested in vitro using a specific RdRp assay. Hp1, which is highly variable among different PepMV isolates, appeared dispensable for negative-strand synthesis. Hp2, which is characterized by a large U-rich loop, tolerated base-pair changes in its stem as long as they maintained the stem integrity but was very sensitive to changes in the U-rich loop. Hp3, which harbours the conserved potexvirus ACUUAA hexamer motif, was essential for template activity. Template-RNA polymerase binding competition experiments showed that the ACUUAA sequence represents a high-affinity RdRp binding element. Copyright © 2014 Elsevier B.V. All rights reserved.

Chlamydomonas chloroplasts can use short dispersed repeats and multiple pathways to repair a double-strand break in the genome.

Science.gov (United States)

Odom, Obed W; Baek, Kwang-Hyun; Dani, Radhika N; Herrin, David L

2008-03-01

Certain group I introns insert into intronless DNA via an endonuclease that creates a double-strand break (DSB). There are two models for intron homing in phage: synthesis-dependent strand annealing (SDSA) and double-strand break repair (DSBR). The Cr.psbA4 intron homes efficiently from a plasmid into the chloroplast psbA gene in Chlamydomonas, but little is known about the mechanism. Analysis of co-transformants selected using a spectinomycin-resistant 16S gene (16S(spec)) provided evidence for both pathways. We also examined the consequences of the donor DNA having only one-sided or no homology with the psbA gene. When there was no homology with the donor DNA, deletions of up to 5 kb involving direct repeats that flank the psbA gene were obtained. Remarkably, repeats as short as 15 bp were used for this repair, which is consistent with the single-strand annealing (SSA) pathway. When the donor had one-sided homology, the DSB in most co-transformants was repaired using two DNAs, the donor and the 16S(spec) plasmid, which, coincidentally, contained a region that is repeated upstream of psbA. DSB repair using two separate DNAs provides further evidence for the SDSA pathway. These data show that the chloroplast can repair a DSB using short dispersed repeats located proximally, distally, or even on separate molecules relative to the DSB. They also provide a rationale for the extensive repertoire of repeated sequences in this genome.

Pyrolytic citrate synthesis and ozone annealing

International Nuclear Information System (INIS)

Celani, F.; Saggese, A.; Giovannella, C.; Messi, R.; Merlo, V.

1988-01-01

A pyrolytic procedure is described that via a citrate synthesis allowed us to obtain very fine grained YBCO powders that, after a first furnace thermal treatment in ozone, results already to contain a large amount of superconducting microcrystals. A second identical thermal treatment gives a final product strongly textured, as shown by magnetic torque measurements. Complementary structural and diamagnetic measurement show the high quality of these sintered pellets. The role covered by both the pyrolytic preparation and the ozone annealing are discussed

The 3'-terminal 55 nucleotides of bovine coronavirus defective interfering RNA harbor cis-acting elements required for both negative- and positive-strand RNA synthesis.

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Wei-Yu Liao

Full Text Available The synthesis of the negative-strand [(--strand] complement of the ∼30 kilobase, positive-strand [(+-strand] coronaviral genome is a necessary early step for genome replication. The identification of cis-acting elements required for (--strand RNA synthesis in coronaviruses, however, has been hampered due to insufficiencies in the techniques used to detect the (--strand RNA species. Here, we employed a method of head-to-tail ligation and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR to detect and quantitate the synthesis of bovine coronavirus (BCoV defective interfering (DI RNA (- strands. Furthermore, using the aforementioned techniques along with Northern blot assay, we specifically defined the cis-acting RNA elements within the 3'-terminal 55 nucleotides (nts which function in the synthesis of (-- or (+-strand BCoV DI RNA. The major findings are as follows: (i nts from -5 to -39 within the 3'-terminal 55 nts are the cis-acting elements responsible for (--strand BCoV DI RNA synthesis, (ii nts from -3 to -34 within the 3'-terminal 55 nts are cis-acting elements required for (+-strand BCoV DI RNA synthesis, and (iii the nucleotide species at the 3'-most position (-1 is important, but not critical, for both (-- and (+-strand BCoV DI RNA synthesis. These results demonstrate that the 3'-terminal 55 nts in BCoV DI RNA harbor cis-acting RNA elements required for both (-- and (+-strand DI RNA synthesis and extend our knowledge on the mechanisms of coronavirus replication. The method of head-to-tail ligation and qRT-PCR employed in the study may also be applied to identify other cis-acting elements required for (--strand RNA synthesis in coronaviruses.

The RNA synthesis machinery of negative-stranded RNA viruses

International Nuclear Information System (INIS)

Ortín, Juan; Martín-Benito, Jaime

2015-01-01

The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes

The RNA synthesis machinery of negative-stranded RNA viruses

Energy Technology Data Exchange (ETDEWEB)

Ortín, Juan, E-mail: jortin@cnb.csic.es [Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC) and CIBER de Enfermedades Respiratorias (ISCIII), Madrid (Spain); Martín-Benito, Jaime, E-mail: jmartinb@cnb.csic.es [Department of Macromolecular Structures, Centro Nacional de Biotecnología (CSIC), Madrid (Spain)

2015-05-15

The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes.

Signals for the initiation and termination of synthesis of the viral strand of bacteriophage f1

International Nuclear Information System (INIS)

Dotto, G.P.; Horiuchi, K.; Jakes, K.S.; Zinder, N.D.

1983-01-01

In this paper the sequence around the plus origin that is required for efficient plus-strand synthesis as well as that necessary for gene-II-protein recognition is described. Results which demonstrate that the nucleotide sequence of the f1 plus origin contains two overlapping but distinct signals, one for initiation and the other for termination of plus-strand synthesis is presented. 29 references, 6 figures, 1 table

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....

Possible roles of HIV-1 nucleocapsid protein in the specificity of proviral DNA synthesis and in its variability.

Science.gov (United States)

Lapadat-Tapolsky, M; Gabus, C; Rau, M; Darlix, J L

1997-05-02

Retroviral nucleocapsid (NC) protein is an integral part of the virion nucleocapsid where it coats the dimeric RNA genome. Due to its nucleic acid binding and annealing activities, NC protein directs the annealing of the tRNA primer to the primer binding site and greatly facilitates minus strand DNA elongation and transfer while protecting the nucleic acids against nuclease degradation. To understand the role of NCp7 in viral DNA synthesis, we examined the influence of NCp7 on self-primed versus primer-specific reverse transcription. The results show that HIV-1 NCp7 can extensively inhibit self-primed reverse transcription of viral and cellular RNAs while promoting primer-specific synthesis of proviral DNA. The role of NCp7 vis-a-vis the presence of mutations in the viral DNA during minus strand elongation was examined. NCp7 maximized the annealing between a cDNA(-) primer containing one to five consecutive errors and an RNA representing the 3' end of the genome. The ability of reverse transcriptase (RT) in the presence of NCp7 to subsequently extend the mutated primers depended upon the position of the mismatch within the primer:template complex. When the mutations were at the polymerisation site, primer extension by RT in the presence of NCp7 was very high, about 40% for one mismatch and 3% for five consecutive mismatches. Mutations within the DNA primer or at its 5' end had little effect on the extension of viral DNA by RT. Taken together these results indicate that NCp7 plays major roles in proviral DNA synthesis within the virion core due to its ability to promote prime-specific proviral DNA synthesis while concurrently inhibiting non-specific reverse transcription of viral and cellular RNAs. Moreover, the observation that NCp7 enhances the incorporation of mutations during minus strand DNA elongation favours the notion that NCp7 is a factor contributing to the high mutation rate of HIV-1.

Importance of the efficiency of double-stranded DNA formation in cDNA synthesis for the imprecision of microarray expression analysis.

Science.gov (United States)

Thormar, Hans G; Gudmundsson, Bjarki; Eiriksdottir, Freyja; Kil, Siyoen; Gunnarsson, Gudmundur H; Magnusson, Magnus Karl; Hsu, Jason C; Jonsson, Jon J

2013-04-01

The causes of imprecision in microarray expression analysis are poorly understood, limiting the use of this technology in molecular diagnostics. Two-dimensional strandness-dependent electrophoresis (2D-SDE) separates nucleic acid molecules on the basis of length and strandness, i.e., double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA·DNA hybrids. We used 2D-SDE to measure the efficiency of cDNA synthesis and its importance for the imprecision of an in vitro transcription-based microarray expression analysis. The relative amount of double-stranded cDNA formed in replicate experiments that used the same RNA sample template was highly variable, ranging between 0% and 72% of the total DNA. Microarray experiments showed an inverse relationship between the difference between sample pairs in probe variance and the relative amount of dsDNA. Approximately 15% of probes showed between-sample variation (P cDNA synthesized can be an important component of the imprecision in T7 RNA polymerase-based microarray expression analysis. © 2013 American Association for Clinical Chemistry

Bacillus subtilis DNA polymerases, PolC and DnaE, are required for both leading and lagging strand synthesis in SPP1 origin-dependent DNA replication

Science.gov (United States)

Seco, Elena M.

2017-01-01

Abstract Firmicutes have two distinct replicative DNA polymerases, the PolC leading strand polymerase, and PolC and DnaE synthesizing the lagging strand. We have reconstituted in vitro Bacillus subtilis bacteriophage SPP1 θ-type DNA replication, which initiates unidirectionally at oriL. With this system we show that DnaE is not only restricted to lagging strand synthesis as previously suggested. DnaG primase and DnaE polymerase are required for initiation of DNA replication on both strands. DnaE and DnaG synthesize in concert a hybrid RNA/DNA ‘initiation primer’ on both leading and lagging strands at the SPP1 oriL region, as it does the eukaryotic Pol α complex. DnaE, as a RNA-primed DNA polymerase, extends this initial primer in a reaction modulated by DnaG and one single-strand binding protein (SSB, SsbA or G36P), and hands off the initiation primer to PolC, a DNA-primed DNA polymerase. Then, PolC, stimulated by DnaG and the SSBs, performs the bulk of DNA chain elongation at both leading and lagging strands. Overall, these modulations by the SSBs and DnaG may contribute to the mechanism of polymerase switch at Firmicutes replisomes. PMID:28575448

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

Luminescence lifetimes in quartz: dependence on annealing temperature prior to beta irradiation

International Nuclear Information System (INIS)

Galloway, R.B.

2002-01-01

It is well known that the thermal history of a quartz sample influences the optically stimulated luminescence sensitivity of the quartz. It is found that the optically stimulated luminescence lifetime, determined from time resolved spectra obtained with pulsed stimulation, also depends on past thermal treatment. For samples at 20 deg. C during stimulation, the lifetime depends on beta dose and on duration of preheating at 220 deg. C prior to stimulation for quartz annealed at 600 deg. C and above, but is independent of these factors for quartz annealed at 500 deg. C and below. For stimulation at higher temperatures, the lifetime becomes shorter if the sample is held at temperatures above 125 deg. C during stimulation, in a manner consistent with thermal quenching. A single exponential decay is all that is required to fit the time resolved spectra for un-annealed quartz regardless of the temperature during stimulation (20-175 deg. C), or to fit the time resolved spectra from all samples held at 20 deg. C during stimulation, regardless of annealing temperature (20-1000 deg. C). An additional shorter lifetime is found for some combinations of annealing temperature and temperature during stimulation. The results are discussed in terms of a model previously used to explain thermal sensitisation. The luminescence lifetime data are best explained by the presence of two principal luminescence centres, their relative importance depending on the annealing temperature, with a third centre involved for limited combinations of annealing temperature and temperature during stimulation

Dynamics of Leading-strand Lesion Skipping by the Replisome

Science.gov (United States)

Yeeles, Joseph T.P.; Marians, Kenneth J.

2013-01-01

SUMMARY The E. coli replisome stalls transiently when it encounters a lesion in the leading-strand template, skipping over the damage by reinitiating replication at a new primer synthesized downstream by the primase. We report here that template unwinding and lagging-strand synthesis continue downstream of the lesion at a reduced rate after replisome stalling, that one replisome is capable of skipping multiple lesions, and that the rate limiting steps of replication restart involve the synthesis and activation of the new primer downstream. We also find little support for the concept that polymerase uncoupling, where extensive lagging-strand synthesis proceeds downstream in the absence of leading-strand synthesis, involves physical separation of the leading-strand polymerase from the replisome. Instead, our data indicate that extensive uncoupled replication likely results from a failure of the leading-strand polymerase still associated with the DNA helicase and the lagging-strand polymerase that are proceeding downstream to reinitiate synthesis. PMID:24268579

Conserved helicase domain of human RecQ4 is required for strand annealing-independent DNA unwinding

DEFF Research Database (Denmark)

Rossi, Marie L; Ghosh, Avik K; Kulikowicz, Tomasz

2010-01-01

Humans have five members of the well conserved RecQ helicase family: RecQ1, Bloom syndrome protein (BLM), Werner syndrome protein (WRN), RecQ4, and RecQ5, which are all known for their roles in maintaining genome stability. BLM, WRN, and RecQ4 are associated with premature aging and cancer...... provide the first evidence that human RecQ4's unwinding is independent of strand annealing, and that it does not require the presence of excess ssDNA. Moreover, we demonstrate that a point mutation of the conserved lysine in the Walker A motif abolished helicase activity, implying that not the N...... activities and protein partners of RecQ4 are conserved with those of the other RecQ helicases....

A self-propagation high-temperature synthesis and annealing route to synthesis of wave-like boron nitride nanotubes

Energy Technology Data Exchange (ETDEWEB)

Wang, Jilin; Zhang, Laiping [School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, Hubei, 430073 (China); Gu, Yunle, E-mail: ncm@mail.wit.edu.cn [School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, Hubei, 430073 (China); Pan, Xinye; Zhao, Guowei; Zhang, Zhanhui [School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, Hubei, 430073 (China)

2013-03-15

Highlights: ► Large quantities of wave-like BN nanotubes were synthesized by SHS-annealing method. ► The catalytic boron-containing porous precursor was produced by self-propagation high-temperature synthesis method. ► Three growth models were proposed to explain the growth mechanism of the wave-like BN nanotubes. - Abstract: Large quantities of boron nitride (BN) nanotubes were synthesized by annealing a catalytic boron-containing porous precursor in flowing NH{sub 3} gas at 1180 °C. The porous precursor was prepared by self-propagation high-temperature synthesis (SHS) method at 800 °C using Mg, B{sub 2}O{sub 3} and amorphous boron powder (α-B) as the starting materials. The porous precursor played an important role in large quantities synthesis of BN nanotubes. The as-synthesized product was characterized by X-ray diffractometer (XRD), Fourier transform infrared spectrometer (FTIR), Raman, Scanning electron microscopy (SEM), X-ray energy dispersive spectroscopy (EDS), Transmission electron microscopy (TEM) and High-resolution transmission electron microscopy (HRTEM). Characterization results indicated that the BN nanotubes displayed wave-like inner structures with diameters in the range of 50–300 nm and average lengths of more than 10 μm. The possible growth mechanism of the BN nanotubes was also discussed.

Excess single-stranded DNA inhibits meiotic double-strand break repair.

Directory of Open Access Journals (Sweden)

Rebecca Johnson

2007-11-01

Full Text Available During meiosis, self-inflicted DNA double-strand breaks (DSBs are created by the protein Spo11 and repaired by homologous recombination leading to gene conversions and crossovers. Crossover formation is vital for the segregation of homologous chromosomes during the first meiotic division and requires the RecA orthologue, Dmc1. We analyzed repair during meiosis of site-specific DSBs created by another nuclease, VMA1-derived endonuclease (VDE, in cells lacking Dmc1 strand-exchange protein. Turnover and resection of the VDE-DSBs was assessed in two different reporter cassettes that can repair using flanking direct repeat sequences, thereby obviating the need for a Dmc1-dependent DNA strand invasion step. Access of the single-strand binding complex replication protein A, which is normally used in all modes of DSB repair, was checked in chromatin immunoprecipitation experiments, using antibody against Rfa1. Repair of the VDE-DSBs was severely inhibited in dmc1Delta cells, a defect that was associated with a reduction in the long tract resection required to initiate single-strand annealing between the flanking repeat sequences. Mutants that either reduce Spo11-DSB formation or abolish resection at Spo11-DSBs rescued the repair block. We also found that a replication protein A component, Rfa1, does not accumulate to expected levels at unrepaired single-stranded DNA (ssDNA in dmc1Delta cells. The requirement of Dmc1 for VDE-DSB repair using flanking repeats appears to be caused by the accumulation of large quantities of ssDNA that accumulate at Spo11-DSBs when Dmc1 is absent. We propose that these resected DSBs sequester both resection machinery and ssDNA binding proteins, which in wild-type cells would normally be recycled as Spo11-DSBs repair. The implication is that repair proteins are in limited supply, and this could reflect an underlying mechanism for regulating DSB repair in wild-type cells, providing protection from potentially harmful effects

Double-Strand DNA Break Repair in Mycobacteria.

Science.gov (United States)

Glickman, Michael S

2014-10-01

Discontinuity of both strands of the chromosome is a lethal event in all living organisms because it compromises chromosome replication. As such, a diversity of DNA repair systems has evolved to repair double-strand DNA breaks (DSBs). In part, this diversity of DSB repair systems has evolved to repair breaks that arise in diverse physiologic circumstances or sequence contexts, including cellular states of nonreplication or breaks that arise between repeats. Mycobacteria elaborate a set of three genetically distinct DNA repair pathways: homologous recombination, nonhomologous end joining, and single-strand annealing. As such, mycobacterial DSB repair diverges substantially from the standard model of prokaryotic DSB repair and represents an attractive new model system. In addition, the presence in mycobacteria of a DSB repair system that can repair DSBs in nonreplicating cells (nonhomologous end joining) or when DSBs arise between repeats (single-strand annealing) has clear potential relevance to Mycobacterium tuberculosis pathogenesis, although the exact role of these systems in M. tuberculosis pathogenesis is still being elucidated. In this article we will review the genetics of mycobacterial DSB repair systems, focusing on recent insights.

Synthesis of double-stranded RNA in a virus-enriched fraction from Agaricus bisporus

International Nuclear Information System (INIS)

Sriskantha, A.; Wach, P.; Schlagnhaufer, B.; Romaine, C.P.

1986-01-01

Partially purified virus preparations from sporophores of Agaricus bisporus affected with LaFrance disease had up to a 15-fold-higher RNA-dependent RNA polymerase activity than did comparable preparations from health sporophores. Enzyme activity was dependent upon the presence of Mg 2+ and the four nucleoside triphosphates and was insensitive to actinomycin D, α-amanitin, and rifampin. The 3 H-labeled enzyme reaction products were double-stranded RNA (dsRNA) as indicated by CF-11 cellulose column chromatography and by their ionic-strength-dependent sensitivity to hydrolysis by RNase A. The principal dsRNA products had estimated molecular weights of 4.3 /times/ 10 6 and 1.4 /times/ 10 6 . Cs 2 SO 4 equilibrium centrifugation of the virus preparation resolved a single peak of RNA polymerase activity that banded with a 35-nm spherical virus particle containing dsRNAs with molecular weights of 4.3 /times/ 10 6 and 1.4 /times/ 10 6 . The data suggest that the RNA-dependent RNA polymerase associated with the 35-nm spherical virus is a replicase which catalyzes the synthesis of the genomic dsRNAs

Stimulation of NADH-dependent microsomal DNA strand cleavage by rifamycin SV.

Science.gov (United States)

Kukiełka, E; Cederbaum, A I

1995-04-15

Rifamycin SV is an antibiotic anti-bacterial agent used in the treatment of tuberculosis. This drug can autoxidize, especially in the presence of metals, and generate reactive oxygen species. A previous study indicated that rifamycin SV can increase NADH-dependent microsomal production of reactive oxygen species. The current study evaluated the ability of rifamycin SV to interact with iron and increase microsomal production of hydroxyl radical, as detected by conversion of supercoiled plasmid DNA into the relaxed open circular state. The plasmid used was pBluescript II KS(-), and the forms of DNA were separated by agarose-gel electrophoresis. Incubation of rat liver microsomes with plasmid plus NADH plus ferric-ATP caused DNA strand cleavage. The addition of rifamycin SV produced a time- and concentration-dependent increase in DNA-strand cleavage. No stimulation by rifamycin SV occurred in the absence of microsomes, NADH or ferric-ATP. Stimulation occurred with other ferric complexes besides ferric-ATP, e.g. ferric-histidine, ferric-citrate, ferric-EDTA, and ferric-(NH4)2SO4. Rifamycin SV did not significantly increase the high rates of DNA strand cleavage found with NADPH as the microsomal reductant. The stimulation of NADH-dependent microsomal DNA strand cleavage was completely blocked by catalase, superoxide dismutase, GSH and a variety of hydroxyl-radical-scavenging agents, but not by anti-oxidants that prevent microsomal lipid peroxidation. Redox cycling agents, such as menadione and paraquat, in contrast with rifamycin SV, stimulated the NADPH-dependent reaction; menadione and rifamycin SV were superior to paraquat in stimulating the NADH-dependent reaction. These results indicate that rifamycin SV can, in the presence of an iron catalyst, increase microsomal production of reactive oxygen species which can cause DNA-strand cleavage. In contrast with other redox cycling agents, the stimulation by rifamycin SV is more pronounced with NADH than with NADPH as the

Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis

International Nuclear Information System (INIS)

Burkovics, Peter; Sebesta, Marek; Kolesar, Peter; Sisakova, Alexandra; Marini, Victoria; Plault, Nicolas; Szukacsov, Valeria; Pinter, Lajos; Haracska, Lajos; Robert, Thomas; Kolesar, Peter; Gangloff, Serge; Krejci, Lumir

2013-01-01

Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. (authors)

Xrcc1-dependent and Ku-dependent DNA double-strand break repair kinetics in Arabidopsis plants.

Science.gov (United States)

Charbonnel, Cyril; Gallego, Maria E; White, Charles I

2010-10-01

Double-strand breakage (DSB) of DNA involves loss of information on the two strands of the DNA fibre and thus cannot be repaired by simple copying of the complementary strand which is possible with single-strand DNA damage. Homologous recombination (HR) can precisely repair DSB using another copy of the genome as template and non-homologous recombination (NHR) permits repair of DSB with little or no dependence on DNA sequence homology. In addition to the well-characterised Ku-dependent non-homologous end-joining (NHEJ) pathway, much recent attention has been focused on Ku-independent NHR. The complex interrelationships and regulation of NHR pathways remain poorly understood, even more so in the case of plants, and we present here an analysis of Ku-dependent and Ku-independent repair of DSB in Arabidopsis thaliana. We have characterised an Arabidopsis xrcc1 mutant and developed quantitative analysis of the kinetics of appearance and loss of γ-H2AX foci as a tool to measure DSB repair in dividing root tip cells of γ-irradiated plants in vivo. This approach has permitted determination of DSB repair kinetics in planta following a short pulse of γ-irradiation, establishing the existence of a Ku-independent, Xrcc1-dependent DSB repair pathway. Furthermore, our data show a role for Ku80 during the first minutes post-irradiation and that Xrcc1 also plays such a role, but only in the absence of Ku. The importance of Xrcc1 is, however, clearly visible at later times in the presence of Ku, showing that alternative end-joining plays an important role in DSB repair even in the presence of active NHEJ. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

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.

Synthesis mechanism of heterovalent Sn2O3 nanosheets in oxidation annealing process

International Nuclear Information System (INIS)

Zhao Jun-Hua; Wu Guo-Qiang; Yang Xu-Feng; Tan Rui-Qin; Yang Ye; Xu Wei; Li Jia; Shen Wen-Feng; Song Wei-Jie

2015-01-01

Heterovalent Sn 2 O 3 nanosheets were fabricated via an oxidation annealing process and the formation mechanism was investigated. The temperature required to complete the phase transformation from Sn 3 O 4 to Sn 2 O 3 was considered. Two contrasting experiments showed that both oxygen and heating were not necessary conditions for the phase transition. Sn 2 O 3 was formed under an argon protective atmosphere by annealing and could also be obtained at room temperature by exposing Sn 3 O 4 in atmosphere or dispersing in ethanol. The synthesis mechanism was proposed and discussed. This fundamental research is important for the technological applications of intermediate tin oxide materials. (paper)

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

Science.gov (United States)

Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew D.; Brodbelt, Jennifer S.

2010-01-01

Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads. PMID:19746468

Radiation annealing mechanisms of low-alloy reactor pressure vessel steels dependent on irradiation temperature and neutron fluence

International Nuclear Information System (INIS)

Pachur, D.

1982-01-01

Heat treatment after irradiation of reactor pressure vessel steels showed annealing of irradiation embrittlement. Depending on the irradiation temperature, the embrittlement started to anneal at about 220 0 C and was completely annealed at 500 0 C with 4 h of annealing time. The annealing behavior was normally measured in terms of the Vickers hardness increase produced by irradiation relative to the initial hardness as a function of the annealing temperature. Annealing results of other mechanical properties correspond to hardness results. During annealing, various recovery mechanisms occur in different temperature ranges. These are characterized by activation energies from 1.5 to 2.1 eV. The individual mechanisms were determined by the different time dependencies at various temperatures. The relative contributions of the mechanisms showed a neutron fluence dependence, with the lower activation energy mechanisms being predominant at low fluence and vice versa. In the temperature range where partial annealing of a mechanism took place during irradiation, an increase in activation energy was observed. Trend curves for the increase in transition temperature with irradiation, for the relative increase of Vickers hardness and yield strength, and for the relative decrease of Charpy-V upper shelf energy are interpreted by the behavior of different mechanisms

Reactive-inspired ball-milling synthesis of an ODS steel: study of the influence of ball-milling and annealing

International Nuclear Information System (INIS)

Brocq, M.

2010-10-01

In the context of the development of new ODS (Oxide Dispersion Strengthened) steels as core materials in future nuclear reactors, we investigated a new process inspired by reactive ball-milling which consists in using YFe 3 andFe 2 O 3 as starting reactants instead of Y 2 O 3 to produce a dispersion of nano-oxides in a steel matrix and the influence of synthesis conditions on the nano-oxide characteristics were studied. For that aim, ODS steels were prepared by ball-milling and then annealed. Multi-scale characterizations were performed after each synthesis step, using notably atom probe tomography and small angle neutron scattering. The process inspired by reactive ball-milling was shown to be efficient for ODS steel synthesis, but it does not modify the nano-oxide characteristics as compared to those of oxides directly incorporated in the matrix by ball-milling. Broadly speaking, the nature of the starting oxygen bearing reactants has no influence on nano-oxide formation. Moreover, we showed that the nucleation of nano-oxides nucleation can start during milling and continues during annealing with a very fast kinetic. The final characteristics of nano-oxides formed in this way can be monitored through ball-milling parameters (intensity, temperature and atmosphere) and annealing parameters (duration and temperature). (author)

Temperature-dependent photoluminescence analysis of ZnO nanowire array annealed in air

Science.gov (United States)

Sun, Yanan; Gu, Xiuquan; Zhao, Yulong; Wang, Linmeng; Qiang, Yinghuai

2018-05-01

ZnO nanowire arrays (NWAs) were prepared on transparent conducting fluorine doped tin oxide (FTO) substrates through a facile hydrothermal method, followed by a 500 °C annealing to improve their crystalline qualities and photoelectrochemical (PEC) activities. It was found that the annealing didn't change the morphology, but resulted in a significant reduction of the donor concentration. Temperature-dependent photoluminescence (PL) was carried out for a comprehensive analysis of the effect from annealing. Noteworthy, four dominant peaks were identified from the 10 K spectrum of a 500 °C annealed sample, and they were assigned to FX, D0X, (e, D0) and (e, D0) -1LO, respectively. Of them, the FX emission was only existed below 130 K, while the room-temperature (RT) PL spectrum was dominated by the D0X emission.

Replisome-mediated Translesion Synthesis and Leading Strand Template Lesion Skipping Are Competing Bypass Mechanisms*

Science.gov (United States)

Gabbai, Carolina B.; Yeeles, Joseph T. P.; Marians, Kenneth J.

2014-01-01

A number of different enzymatic pathways have evolved to ensure that DNA replication can proceed past template base damage. These pathways include lesion skipping by the replisome, replication fork regression followed by either correction of the damage and origin-independent replication restart or homologous recombination-mediated restart of replication downstream of the lesion, and bypass of the damage by a translesion synthesis DNA polymerase. We report here that of two translesion synthesis polymerases tested, only DNA polymerase IV, not DNA polymerase II, could engage productively with the Escherichia coli replisome to bypass leading strand template damage, despite the fact that both enzymes are shown to be interacting with the replicase. Inactivation of the 3′ → 5′ proofreading exonuclease of DNA polymerase II did not enable bypass. Bypass by DNA polymerase IV required its ability to interact with the β clamp and act as a translesion polymerase but did not require its “little finger” domain, a secondary region of interaction with the β clamp. Bypass by DNA polymerase IV came at the expense of the inherent leading strand lesion skipping activity of the replisome, indicating that they are competing reactions. PMID:25301949

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)

Time-dependent evolution of strand transfer length in pretensioned prestressed concrete members

Science.gov (United States)

Caro, L. A.; Martí-Vargas, J. R.; Serna, P.

2013-11-01

For design purposes, it is generally considered that prestressing strand transfer length does not change with time. However, some experimental studies on the effect of time on transfer lengths show contradictory results. In this paper, an experimental research to study transfer length changes over time is presented. A test procedure based on the ECADA testing technique to measure prestressing strand force variation over time in pretensioned prestressed concrete specimens has been set up. With this test method, an experimental program that varies concrete strength, specimen cross section, age of release, prestress transfer method, and embedment length has been carried out. Both the initial and long-term transfer lengths of 13-mm prestressing steel strands have been measured. The test results show that transfer length variation exists for some prestressing load conditions, resulting in increased transfer length over time. The applied test method based on prestressing strand force measurements has shown more reliable results than procedures based on measuring free end slips and longitudinal strains of concrete. An additional factor for transfer length models is proposed in order to include the time-dependent evolution of strand transfer length in pretensioned prestressed concrete members.

Synthesis of copper nanoparticles in a fluoropolymer matrix by annealing in vacuum

Energy Technology Data Exchange (ETDEWEB)

Safonov, Alexey, E-mail: safonov@itp.nsc.ru [Kutateladze Institute of Thermophysics SB RAS, Lavrentyev Ave. 1, 630090, Novosibirsk (Russian Federation); Sulyaeva, Veronica [Nikolaev Institute of Inorganic Chemistry SB RAS, Lavrentyev Ave. 3, 630090, Novosibirsk (Russian Federation); Timoshenko, Nikolay; Starinskiy, Sergey [Kutateladze Institute of Thermophysics SB RAS, Lavrentyev Ave. 1, 630090, Novosibirsk (Russian Federation)

2017-07-12

In this paper, a method for synthesizing copper nanoparticles in a fluoropolymer matrix is proposed which prevents the reduction in the plasmonic properties due to the oxidation of the metal. The basic idea of the proposed method of nanoparticle synthesis is to anneal of thin metal film coated with a thin layer of fluoropolymer. The morphology and optical properties of the resulting composites were determined. The optical properties remained unchanged after several months of storage under standard conditions. - Highlights: • The copper-fluoropolymer composites are obtained by a combination of GJD and HWCVD. • The annealing of thin Cu film covered with fluoropolymer leads to formation of NPs. • The dilution of the localized surface plasmon resonance due to oxidation was analyzed. • The plasmonic properties of the Cu NPs are saved in the fluoropolymer matrix. • The fluoropolymer matrix prevents oxidation of metal NPs.

CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication.

Science.gov (United States)

Langston, Lance D; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E; Finkelstein, Jeff; Yao, Nina Y; Indiani, Chiara; O'Donnell, Mike E

2014-10-28

DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.

Postreplicational formation and repair of DNA double-strand breaks in UV-irradiated Escherichia coli uvrB cells

International Nuclear Information System (INIS)

Wang, Tzuchien V.; Smith, K.C.

1986-01-01

The number of DNA double-strand breaks formed in UV-irradiated uvrB recF recB cells correlates with the number of unrepaired DNA daughter-strand gaps, and is dependent on DNA synthesis after UV-irradiation. These results are consistent with the model that the DNA double-strand breaks that are produced in UV-irradiated excision-deficient cells occur as the result of breaks in the parental DNA opposite unrepaired DNA daughter-strand gaps. By employing a temperature-sensitive recA200 mutation, we have devised an improved assay for studying the formation and repair of these DNA double-strand breaks. Possible mechanisms for the postreplication repair of DNA double-strand breaks are discussed. (Auth.)

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.

In vitro Assays for Eukaryotic Leading/Lagging Strand DNA Replication.

Science.gov (United States)

Schauer, Grant; Finkelstein, Jeff; O'Donnell, Mike

2017-09-20

The eukaryotic replisome is a multiprotein complex that duplicates DNA. The replisome is sculpted to couple continuous leading strand synthesis with discontinuous lagging strand synthesis, primarily carried out by DNA polymerases ε and δ, respectively, along with helicases, polymerase α-primase, DNA sliding clamps, clamp loaders and many other proteins. We have previously established the mechanisms by which the polymerases ε and δ are targeted to their 'correct' strands, as well as quality control mechanisms that evict polymerases when they associate with an 'incorrect' strand. Here, we provide a practical guide to differentially assay leading and lagging strand replication in vitro using pure proteins.

Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae

Directory of Open Access Journals (Sweden)

Maia Segura-Wang

2017-10-01

Full Text Available To ensure genomic integrity, living organisms have evolved diverse molecular processes for sensing and repairing damaged DNA. If improperly repaired, DNA damage can give rise to different types of mutations, an important class of which are genomic structural variants (SVs. In spite of their importance for phenotypic variation and genome evolution, potential contributors to SV formation in Saccharomyces cerevisiae (budding yeast, a highly tractable model organism, are not fully recognized. Here, we developed and applied a genome-wide assay to identify yeast gene knockout mutants associated with de novo deletion formation, in particular single-strand annealing (SSA-mediated deletion formation, in a systematic manner. In addition to genes previously linked to genome instability, our approach implicates novel genes involved in chromatin remodeling and meiosis in affecting the rate of SSA-mediated deletion formation in the presence or absence of stress conditions induced by DNA-damaging agents. We closely examined two candidate genes, the chromatin remodeling gene IOC4 and the meiosis-related gene MSH4, which when knocked-out resulted in gene expression alterations affecting genes involved in cell division and chromosome organization, as well as DNA repair and recombination, respectively. Our high-throughput approach facilitates the systematic identification of processes linked to the formation of a major class of genetic variation.

a-Si:H crystallization from isothermal annealing and its dependence on the substrate used

Energy Technology Data Exchange (ETDEWEB)

Rojas-Lopez, M., E-mail: marlonrl@yahoo.com.mx [CIBA-Tlaxcala, Instituto Politecnico Nacional, Tepetitla, Tlax. 90700 (Mexico); Orduna-Diaz, A.; Delgado-Macuil, R.; Gayou, V.L.; Bibbins-Martinez, M. [CIBA-Tlaxcala, Instituto Politecnico Nacional, Tepetitla, Tlax. 90700 (Mexico); Torres-Jacome, A.; Trevino-Palacios, C.G. [INAOE, Tonantzintla, Puebla, Pue. 72000 (Mexico)

2010-10-25

We present hydrogenated amorphous silicon (a-Si:H) films which were deposited on two different substrates (glass and mono-crystalline silicon) after an isothermal annealing treatment at 250 deg. C for up to 14 h. The annealed amorphous films were analyzed using atomic force microscopy, Raman and FTIR spectroscopy. Films deposited on glass substrate experienced an amorphous-crystalline phase transition after annealing because of the metal-induced crystallization effect, reaching approximately 70% conversion after 14 h of annealing. An absorption frequency of the TO-phonon mode that varies systematically with the substoichiometry of the silicon oxide in the 1046-1170 cm{sup -1} region was observed, revealing the reactivity of the film with the annealing time. For similar annealing time, films deposited on mono-crystalline silicon substrate remained mainly amorphous with minimal Si-crystalline formation. Therefore, the crystalline formations and the shape of the films surfaces depends on the annealing time as well as on the substrate employed during the deposition process of the a-Si:H film.

Annealing cycles and the self-organization of functionalized colloids

Science.gov (United States)

Dias, Cristóvão S.; Araújo, Nuno A. M.; Telo da Gama, Margarida M.

2018-01-01

The self-assembly of functionalized (patchy) particles with directional interactions into target structures is still a challenge, despite the significant experimental advances in their synthesis. Self-assembly pathways are typically characterized by high energy barriers that hinder access to stable (equilibrium) structures. A possible strategy to tackle this challenge is to perform annealing cycles. By periodically switching on and off the inter-particle bonds, one expects to smooth-out the kinetic pathways and favor the assembly of targeted structures. Preliminary results have shown that the efficiency of annealing cycles depends strongly on their frequency. Here, we study numerically how this frequency-dependence scales with the strength of the directional interactions (size of the patch σ). We use analytical arguments to show that the scaling results from the statistics of a random walk in configurational space.

Double-stranded DNA-dependent ATPase Irc3p is directly involved in mitochondrial genome maintenance.

Science.gov (United States)

Sedman, Tiina; Gaidutšik, Ilja; Villemson, Karin; Hou, YingJian; Sedman, Juhan

2014-12-01

Nucleic acid-dependent ATPases are involved in nearly all aspects of DNA and RNA metabolism. Previous studies have described a number of mitochondrial helicases. However, double-stranded DNA-dependent ATPases, including translocases or enzymes remodeling DNA-protein complexes, have not been identified in mitochondria of the yeast Saccharomyces cerevisae. Here, we demonstrate that Irc3p is a mitochondrial double-stranded DNA-dependent ATPase of the Superfamily II. In contrast to the other mitochondrial Superfamily II enzymes Mss116p, Suv3p and Mrh4p, which are RNA helicases, Irc3p has a direct role in mitochondrial DNA (mtDNA) maintenance. Specific Irc3p-dependent mtDNA metabolic intermediates can be detected, including high levels of double-stranded DNA breaks that accumulate in irc3Δ mutants. irc3Δ-related topology changes in rho- mtDNA can be reversed by the deletion of mitochondrial RNA polymerase RPO41, suggesting that Irc3p counterbalances adverse effects of transcription on mitochondrial genome stability. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Role of teh Rad52 Amino-terminal DNA Binding Activity in DNA Strand Capture in Homologous Recombination

DEFF Research Database (Denmark)

Shi, Idina; Hallwyl, Swee Chuang Lim; Seong, Changhyun

2009-01-01

Saccharomyces cerevisiae Rad52 protein promotes homologous recombination by nucleating the Rad51 recombinase onto replication protein A-coated single-stranded DNA strands and also by directly annealing such strands. We show that the purified rad52-R70A mutant protein, with a compromised amino-ter...

Toehold-mediated strand displacement reaction-dependent fluorescent strategy for sensitive detection of uracil-DNA glycosylase activity.

Science.gov (United States)

Wu, Yushu; Wang, Lei; Jiang, Wei

2017-03-15

Sensitive detection of uracil-DNA glycosylase (UDG) activity is beneficial for evaluating the repairing process of DNA lesions. Here, toehold-mediated strand displacement reaction (TSDR)-dependent fluorescent strategy was constructed for sensitive detection of UDG activity. A single-stranded DNA (ssDNA) probe with two uracil bases and a trigger sequence were designed. A hairpin probe with toehold domain was designed, and a reporter probe was also designed. Under the action of UDG, two uracil bases were removed from ssDNA probe, generating apurinic/apyrimidinic (AP) sites. Then, the AP sites could inhibit the TSDR between ssDNA probe and hairpin probe, leaving the trigger sequence in ssDNA probe still free. Subsequently, the trigger sequence was annealed with the reporter probe, initiating the polymerization and nicking amplification reaction. As a result, numerous G-quadruplex (G4) structures were formed, which could bind with N-methyl-mesoporphyrin IX (NMM) to generate enhanced fluorescent signal. In the absence of UDG, the ssDNA probe could hybridize with the toehold domain of the hairpin probe to initiate TSDR, blocking the trigger sequence, and then the subsequent amplification reaction would not occur. The proposed strategy was successfully implemented for detecting UDG activity with a detection limit of 2.7×10 -5 U/mL. Moreover, the strategy could distinguish UDG well from other interference enzymes. Furthermore, the strategy was also applied for detecting UDG activity in HeLa cells lysate with low effect of cellular components. These results indicated that the proposed strategy offered a promising tool for sensitive quantification of UDG activity in UDG-related function study and disease prognosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Solvent annealing induced phase separation and dewetting in PMMA∕SAN blend film: film thickness and solvent dependence.

Science.gov (United States)

You, Jichun; Zhang, Shuangshuang; Huang, Gang; Shi, Tongfei; Li, Yongjin

2013-06-28

The competition between "dewetting" and "phase separation" behaviors in polymer blend films attracts significant attention in the last decade. The simultaneous phase separation and dewetting in PMMA∕SAN [poly(methyl methacrylate) and poly(styrene-ran-acrylonitrile)] blend ultrathin films upon solvent annealing have been observed for the first time in our previous work. In this work, film thickness and annealing solvent dependence of phase behaviors in this system has been investigated using atomic force microscopy and grazing incidence small-angle X-ray scattering (GISAXS). On one hand, both vertical phase separation and dewetting take place upon selective solvent vapor annealing, leading to the formation of droplet∕mimic-film structures with various sizes (depending on original film thickness). On the other hand, the whole blend film dewets the substrate and produces dispersed droplets on the silicon oxide upon common solvent annealing. GISAXS results demonstrate the phase separation in the big dewetted droplets resulted from the thicker film (39.8 nm). In contrast, no period structure is detected in small droplets from the thinner film (5.1 nm and 9.7 nm). This investigation indicates that dewetting and phase separation in PMMA∕SAN blend film upon solvent annealing depend crucially on the film thickness and the atmosphere during annealing.

Annealing dependence of magnetic properties in nanostructured Sm0.5Y0.5Co5

International Nuclear Information System (INIS)

Elizalde-Galindo, J.T.; Hidalgo, J.L.; Botez, C.E.; Matutes-Aquino, J.A.

2008-01-01

Nanocrystalline Sm 0.5 Y 0.5 Co 5 powders with high coercivity H C and enhanced remanence M r were prepared by mechanical milling and subsequent annealing. Annealing temperatures T ranging from 973 to 1173 K, and times t ranging from 1 to 5 min were used. X-ray diffraction (XRD) and DC-magnetization measurements were carried out to study the microstructure and magnetic properties of these samples. XRD patterns demonstrate that the average grain size of the nanocrystalline powders depends on the annealing temperature T and time t: ranges from 11 nm (for T=973 K and t=1 min) to 93 nm (for T=1173 K and t=5 min). Magnetic measurements performed at room temperature indicate high coercivity values (H C >955 kA/m), and enhanced remanence (M r /M max >0.5) for all samples. A strong annealing-induced grain size dependence of these magnetic properties was found

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination

OpenAIRE

Uringa, Evert-Jan; Youds, Jillian L.; Lisaingo, Kathleen; Lansdorp, Peter M.; Boulton, Simon J.

2010-01-01

Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron–sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homolo...

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.

Science.gov (United States)

Jamsen, Joonas A; Beard, William A; Pedersen, Lars C; Shock, David D; Moon, Andrea F; Krahn, Juno M; Bebenek, Katarzyna; Kunkel, Thomas A; Wilson, Samuel H

2017-08-15

DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PP i . The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol μ is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) μ functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol µ during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.

Detection of bacteriophage phi 6 minus-strand RNA and novel mRNA isoconformers synthesized in vivo and in vitro, by strand-separating agarose gels

International Nuclear Information System (INIS)

Pagratis, N.; Revel, H.R.

1990-01-01

Two urea-free agarose gel protocols that resolve the six individual strands of bacteriophage phi 6 dsRNA were developed and used to analyze phage RNA synthesis in vivo and in vitro. Citrate gels separate strands of the large and medium chromosomes while Tris-borate-EDTA (TBE) gels resolve the medium and small dsRNA segments. Minus strands migrate faster than plus strands on citrate gels but are retarded on TBE gels. A study of electrophoretic conditions showed that pH affects strand resolution on citrate gels, and that voltage gradient, agarose concentration, and ethidium bromide significantly alter strand migration on TBE gels. Analysis of native phi 6 RNA synthesized in vivo and in vitro showed that the large and medium message RNAs comigrate with the corresponding plus strands of denatured virion dsRNA. The small messenger RNA is exceptional. Native small mRNA was detected as three isoconformers in vivo and in vitro. The isoconformers were converted by heat denaturation to a single RNA species that comigrates with the virion s+ strand. Minus strands labeled in vivo were detected only after heat denaturation. Minus strand synthesis was detected also in heat-denatured samples from in vitro phi 6 nucleocapsid RNA polymerase reactions at pH values suboptimal for transcription

Synthesis of CuInSe2 thin films from electrodeposited Cu11In9 precursors by two-step annealing

Directory of Open Access Journals (Sweden)

TSUNG-WEI CHANG

2014-02-01

Full Text Available In this study, copper indium selenide (CIS films were synthesized from electrodeposited Cu-In-Se precursors by two-step annealing. The agglomeration phenomenon of the electrodeposited In layer usually occurred on the Cu surface. A thermal process was adopted to turn Cu-In precursors into uniform Cu11In9 binary compounds. After deposition of the Se layer, annealing was employed to form chalcopyrite CIS. However, synthesis of CIS from Cu11In9 requires sufficient thermal energy. Annealing temperature and time were investigated to grow high quality CIS film. Various electrodeposition conditions were investigated to achieve the proper atomic ratio of CIS. The properties of the CIS films were characterized by scanning electron microscopy (SEM, X-ray Diffraction (XRD, and Raman spectra.

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

Science.gov (United States)

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

2018-05-25

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

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

DEFF Research Database (Denmark)

Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie

2014-01-01

The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sec...

Poly(ADP-ribose polymerase (PARP-1 is not involved in DNA double-strand break recovery

Directory of Open Access Journals (Sweden)

Fernet Marie

2003-07-01

Full Text Available Abstract Background The cytotoxicity and the rejoining of DNA double-strand breaks induced by γ-rays, H2O2 and neocarzinostatin, were investigated in normal and PARP-1 knockout mouse 3T3 fibroblasts to determine the role of poly(ADP-ribose polymerase (PARP-1 in DNA double-strand break repair. Results PARP-1-/- were considerably more sensitive than PARP-1+/+ 3T3s to induced cell kill by γ-rays and H2O2. However, the two cell lines did not show any significant difference in the susceptibility to neocarzinostatin below 1.5 nM drug. Restoration of PARP-1 expression in PARP-1-/- 3T3s by retroviral transfection of the full PARP-1 cDNA did not induce any change in neocarzinostatin response. Moreover the incidence and the rejoining kinetics of neocarzinostatin-induced DNA double-strand breaks were identical in PARP-1+/+ and PARP-1-/- 3T3s. Poly(ADP-ribose synthesis following γ-rays and H2O2 was observed in PARP-1-proficient cells only. In contrast neocarzinostatin, even at supra-lethal concentration, was unable to initiate PARP-1 activation yet it induced H2AX histone phosphorylation in both PARP1+/+ and PARP-1-/- 3T3s as efficiently as γ-rays and H2O2. Conclusions The results show that PARP-1 is not a major determinant of DNA double-strand break recovery with either strand break rejoining or cell survival as an endpoint. Even though both PARP-1 and ATM activation are major determinants of the cell response to γ-rays and H2O2, data suggest that PARP-1-dependent poly(ADP-ribose synthesis and ATM-dependent H2AX phosphorylation, are not inter-related in the repair pathway of neocarzinostatin-induced DNA double-strand breaks.

Residual Resistivity Ratio (RRR) Measurements of LHC Superconducting NbTi Cable Strands

CERN Document Server

Charifoulline, Z

2006-01-01

The Rutherford-type superconducting NbTi cables of the LHC accelerator are currently manufactured by six industrial companies. As a part of the acceptance tests, the Residual Resistivity Ratio (RRR) of superconducting strands is systematically measured on virgin strands to qualify the strands before cabling and on extracted strands to qualify the cables and to check the final heat treatment (controlled oxidation to control interstrand resistance). More than 12000 samples of virgin and extracted strands have been measured during last five years. Results show good correlation with the measurements done by the companies and reflect well the technological process of cable production (strand annealing, cabling, cable heat treatment). This paper presents a description of the RRR-test station and the measurement procedure, the summary of the results over all suppliers and finally the correlation between RRR-values of the cables and the magnets.

CTC1-STN1 coordinates G- and C-strand synthesis to regulate telomere length.

Science.gov (United States)

Gu, Peili; Jia, Shuting; Takasugi, Taylor; Smith, Eric; Nandakumar, Jayakrishnan; Hendrickson, Eric; Chang, Sandy

2018-05-17

Coats plus (CP) is a rare autosomal recessive disorder caused by mutations in CTC1, a component of the CST (CTC1, STN1, and TEN1) complex important for telomere length maintenance. The molecular basis of how CP mutations impact upon telomere length remains unclear. The CP CTC1 L1142H mutation has been previously shown to disrupt telomere maintenance. In this study, we used CRISPR/Cas9 to engineer this mutation into both alleles of HCT116 and RPE cells to demonstrate that CTC1:STN1 interaction is required to repress telomerase activity. CTC1 L1142H interacts poorly with STN1, leading to telomerase-mediated telomere elongation. Impaired interaction between CTC1 L1142H :STN1 and DNA Pol-α results in increased telomerase recruitment to telomeres and further telomere elongation, revealing that C:S binding to DNA Pol-α is required to fully repress telomerase activity. CP CTC1 mutants that fail to interact with DNA Pol-α resulted in loss of C-strand maintenance and catastrophic telomere shortening. Our findings place the CST complex as an important regulator of both G-strand extensions by telomerase and C-strand synthesis by DNA Pol-α. © 2018 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.

Science.gov (United States)

Burnham, Daniel R; Nijholt, Bas; De Vlaminck, Iwijn; Quan, Jinhua; Yusufzai, Timur; Dekker, Cees

2017-05-05

We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis-Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dielectric response of capacitor structures based on PZT annealed at different temperatures

Energy Technology Data Exchange (ETDEWEB)

Kamenshchikov, Mikhail V., E-mail: Mikhailkamenshchikov@yandex.ru [Tver State University, 170002, Tver (Russian Federation); Solnyshkin, Alexander V. [Tver State University, 170002, Tver (Russian Federation); Pronin, Igor P. [Ioffe Institute, 194021, St. Petersburg (Russian Federation)

2016-12-09

Highlights: • Correlation of the microstructure of PZT films and dielectric response was found. • Difference of dielectric responses under low and high bias is caused by domains. • Internal fields is discussed on the basis of the space charges. • Dependences of PZT films characteristics on synthesis temperature are extremal. - Abstract: Dielectric response of thin-film capacitor structures of Pt/PZT/Pt deposited by the RF magnetron sputtering method and annealed at temperatures of 540–570 °C was investigated. It was found that dielectric properties of these structures depend on the synthesis temperature. Stability of a polarized state is considered on the basis of the analysis of hysteresis loops and capacitance–voltage (C–V) characteristics. The contribution of the domain mechanism in the dielectric response of the capacitor structure comprising a ferroelectric is discussed. Extreme dependences of electrophysical characteristics of PZT films on their synthesis temperature were observed. Correlation of dielectric properties with microstructure of these films is found out.

Annealing temperature dependence of the structures and properties of Co-implanted ZnO films

International Nuclear Information System (INIS)

Chen, Bin; Tang, Kun; Gu, Shulin; Ye, Jiandong; Huang, Shimin; Gu, Ran; Zhang, Yang; Yao, Zhengrong; Zhu, Shunming; Zheng, Youdou

2014-01-01

Highlights: • To avoid the forming of Co clusters and explore the origin of the magnetism, detailed investigation on the properties of the Co-implanted ZnO films with a rather low dose of 8 × 10 15 cm −2 and high implantation energy of 1 MeV were carried out. • The crystalline structure of the damaged region caused by ion-implantation has been recovered via the thermal annealing treatment at the temperature of 900 °C and above. • The low temperature magnetic hysteresis loops have indicated paramagnetism for the annealed films with weak ferromagnetic characteristics. • The zero-field cooling (ZFC) magnetization curves of the Co-implanted ZnO samples have varied from concave shape to convex one as the annealing temperature increased from 750 °C to 1000 °C. - Abstract: The effects of thermal annealing treatment on the structural, electrical, optical and magnetic properties of Co-implanted ZnO (0 0 0 1) films have been investigated in detail. The crystalline structure of the damaged region caused by ion implantation has been recovered via the thermal annealing at the temperature of 900 °C and above, and no Co clusters or its related oxide phases have been observed. The electrical and optical properties of the annealed films have shown strong dependence on the annealing temperature. The zero field cooling magnetization curves of the annealed films have varied from concave shape to convex one as the annealing temperature increased from 750 °C to 1000 °C, which are possibly tuned by the changes of the ratio of the itinerant carriers over the localized spin density. The low temperature magnetic hysteresis loops have indicated paramagnetic behavior for the annealed films with weak ferromagnetic characteristics. The ferromagnetism is attributed to the substituted Co 2+ ions and vacancy defects, while the paramagnetism could be induced by ionized interstitial Zn defects

DNA synthesis in vitro in human fibroblast preparations

Energy Technology Data Exchange (ETDEWEB)

Kaufmann, W.K.

1983-01-01

When confluent cultures of human fibroblasts were ultraviolet irradiated and either permeabilized or lysed, three types of DNA synthesis were subsequently observed during incubation in vitro: (A) a low level of DNA replication, which ceased after 15-30 min incubation at 37/sup 0/C; (B) radiation-dependent reparative gap-filling, which also ceased after 15 min at 37/sup 0/C; and (C) radiation-independent DNA synthesis, which was not semiconservative and proceeded at a linear rate for 1 hr at 37/sup 0/C. Normal and xeroderma pigmentosum fibroblasts displayed different rates of radiation-dependent reparative gap-filling after lysis but similar rates of radiation-independent DNA synthesis. The rates of DNA replication and radiation-independent DNA synthesis were less in the permeable cell system than in the lysed cell system, whereas radiation-dependent reparative gap-filling was the same in both. Preparations of permeable and lysed cells activated radiation-dependent reparative gap-filling at about 15% of the rate estimated for intact cells. No radiation-dependent DNA strand breaks, as assayed by alkaline elution, were observed in the lysed cell preparation. Some radiation-dependent breaks were observed in the permeable cell preparation, but radiation-dependent DNA breakage was less than that seen in intact cells. This inability to incise DNA at damaged sites could account for the low rate of activation of reparative gap-filling in vitro. DNA strand breaks were produced in fibroblast preparations nonspecifically during lysis or permeabilization and incubation in vitro, and this breakage of DNA probably was responsible for the radiation-independent DNA synthesis.

Strand Displacement by DNA Polymerase III Occurs through a τ-ψ-χ Link to Single-stranded DNA-binding Protein Coating the Lagging Strand Template*

OpenAIRE

Yuan, Quan; McHenry, Charles S.

2009-01-01

In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of γ-complex to support the reaction in the absence of τ. However, if γ-complex is p...

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)

Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome.

Science.gov (United States)

Lewis, Jacob S; Spenkelink, Lisanne M; Schauer, Grant D; Hill, Flynn R; Georgescu, Roxanna E; O'Donnell, Michael E; van Oijen, Antoine M

2017-10-03

The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ε DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1-Tof1-Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication.

Initiation of poliovirus plus-strand RNA synthesis in a membrane complex of infected HeLa cells

International Nuclear Information System (INIS)

Takeda, N.; Kuhn, R.J.; Yang, C.F.; Takegami, T.; Wimmer, E.

1986-01-01

An in vitro poliovirus RNA-synthesizing system derived from a crude membrance fraction of infected HeLa cells was used to analyze the mechanism of initiation of poliovirus plus-strand RNA synthesis. This system contains an activity that synthesizes the nucleotidyl proteins VPg-pU and VPg-pUpU. These molecules represent the 5'-terminal structure of nascent RNA molecules and of virion RNA. The membranous replication complex is also capable of synthesizing mucleotidyl proteins containing nine or more of the poliovirus 5'-proximal nucleotides as assayed by the formation of the RNase T 1 -resistant oligonucleotide VPg-pUUAAAACAGp or by fingerprint analysis of the in vitro-synthesized 32 P-RNA. Incubation of preformed VPg-pUpU with unlabeled nucleoside triphosphates resulted in the formation of VPg-pUUAAAACAGp. This reaction, which appeared to be an elongation of VPg-pUpU, was stimulated by the addition of a soluble fraction (S-10) obtained from uninfected HeLa cells. Preformed VPg-pU could be chased into VPg-pUpU in the presence of UTP. The data are consistent with a model that VPg-pU can function as a primer for poliovirus plus-strand RNA synthesis in the membranous replication complex and that the elongation reaction may be stimulated by a host cellular factor

TALE activators regulate gene expression in a position- and strand-dependent manner in mammalian cells.

Science.gov (United States)

Uhde-Stone, Claudia; Cheung, Edna; Lu, Biao

2014-01-24

Transcription activator-like effectors (TALEs) are a class of transcription factors that are readily programmable to regulate gene expression. Despite their growing popularity, little is known about binding site parameters that influence TALE-mediated gene activation in mammalian cells. We demonstrate that TALE activators modulate gene expression in mammalian cells in a position- and strand-dependent manner. To study the effects of binding site location, we engineered TALEs customized to recognize specific DNA sequences located in either the promoter or the transcribed region of reporter genes. We found that TALE activators robustly activated reporter genes when their binding sites were located within the promoter region. In contrast, TALE activators inhibited the expression of reporter genes when their binding sites were located on the sense strand of the transcribed region. Notably, this repression was independent of the effector domain utilized, suggesting a simple blockage mechanism. We conclude that TALE activators in mammalian cells regulate genes in a position- and strand-dependent manner that is substantially different from gene activation by native TALEs in plants. These findings have implications for optimizing the design of custom TALEs for genetic manipulation in mammalian cells. Copyright © 2013 Elsevier Inc. All rights reserved.

Chromatin Controls DNA Replication Origin Selection, Lagging-Strand Synthesis, and Replication Fork Rates.

Science.gov (United States)

Kurat, Christoph F; Yeeles, Joseph T P; Patel, Harshil; Early, Anne; Diffley, John F X

2017-01-05

The integrity of eukaryotic genomes requires rapid and regulated chromatin replication. How this is accomplished is still poorly understood. Using purified yeast replication proteins and fully chromatinized templates, we have reconstituted this process in vitro. We show that chromatin enforces DNA replication origin specificity by preventing non-specific MCM helicase loading. Helicase activation occurs efficiently in the context of chromatin, but subsequent replisome progression requires the histone chaperone FACT (facilitates chromatin transcription). The FACT-associated Nhp6 protein, the nucleosome remodelers INO80 or ISW1A, and the lysine acetyltransferases Gcn5 and Esa1 each contribute separately to maximum DNA synthesis rates. Chromatin promotes the regular priming of lagging-strand DNA synthesis by facilitating DNA polymerase α function at replication forks. Finally, nucleosomes disrupted during replication are efficiently re-assembled into regular arrays on nascent DNA. Our work defines the minimum requirements for chromatin replication in vitro and shows how multiple chromatin factors might modulate replication fork rates in vivo. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Synthesis of stoichiometric Ca{sub 2}Fe{sub 2}O{sub 5} nanoparticles by high-energy ball milling and thermal annealing

Energy Technology Data Exchange (ETDEWEB)

Amorim, B.F.; Morales, M.A.; Bohn, F.; Carriço, A.S. [Departamento de Física Teórica e Experimental, Universidade Federal do Rio Grande do Norte, 59078-900 Natal, RN (Brazil); Medeiros, S.N. de, E-mail: sndemedeiros@gmail.com [Departamento de Física Teórica e Experimental, Universidade Federal do Rio Grande do Norte, 59078-900 Natal, RN (Brazil); Dantas, A.L. [Departamento de Física, Universidade do Estado do Rio Grande do Norte, 59610-210 Mossoró, RN (Brazil)

2016-05-01

We report the synthesis of Ca{sub 2}Fe{sub 2}O{sub 5} nanoparticles by high-energy ball milling and thermal annealing from α-Fe{sub 2}O{sub 3} and CaCO{sub 3}. Magnetization measurements, Mössbauer and X-ray spectra reveal that annealing at high temperatures leads to better quality samples. Our results indicate nanoparticles produced by 10 h high-energy ball milling and thermal annealing for 2 h at 1100 °C achieve improved stoichiometry and the full weak ferromagnetic signal of Ca{sub 2}Fe{sub 2}O{sub 5}. Samples annealed at lower temperatures show departure from stoichiometry, with a higher occupancy of Fe{sup 3+} in octahedral sites, and a reduced magnetization. Thermal relaxation for temperatures in the 700–1100 °C range is well represented by a Néel model, assuming a random orientation of the weak ferromagnetic moment of the Ca{sub 2}Fe{sub 2}O{sub 5} nanoparticles.

TALEN-Induced Double-Strand Break Repair of CTG Trinucleotide Repeats

Directory of Open Access Journals (Sweden)

Valentine Mosbach

2018-02-01

Full Text Available Trinucleotide repeat expansions involving CTG/CAG triplets are responsible for several neurodegenerative disorders, including myotonic dystrophy and Huntington’s disease. Because expansions trigger the disease, contracting repeat length could be a possible approach to gene therapy for these disorders. Here, we show that a TALEN-induced double-strand break was very efficient at contracting expanded CTG repeats in yeast. We show that RAD51, POL32, and DNL4 are dispensable for double-strand break repair within CTG repeats, the only required genes being RAD50, SAE2, and RAD52. Resection was totally abolished in the absence of RAD50 on both sides of the break, whereas it was reduced in a sae2Δ mutant on the side of the break containing the longest repeat tract, suggesting that secondary structures at double-strand break ends must be removed by the Mre11-Rad50 complex and Sae2. Following the TALEN double-strand break, single-strand annealing occurred between both sides of the repeat tract, leading to repeat contraction.

Strand displacement activated peroxidase activity of hemin for fluorescent DNA sensing.

Science.gov (United States)

Wang, Quanbo; Xu, Nan; Gui, Zhen; Lei, Jianping; Ju, Huangxian; Yan, Feng

2015-10-07

To efficiently regulate the catalytic activity of the peroxidase mimic hemin, this work designs a double-stranded DNA probe containing an intermolecular dimer of hemin, whose peroxidase activity can be activated by a DNA strand displacement reaction. The double-stranded probe is prepared by annealing two strands of hemin labelled DNA oligonucleotides. Using the fluorescent oxidation product of tyramine by H2O2 as a tracing molecule, the low peroxidase activity of the hemin dimer ensures a low fluorescence background. The strand displacement reaction of the target DNA dissociates the hemin dimer and thus significantly increases the catalytic activity of hemin to produce a large amount of dityramine for fluorescence signal readout. Based on the strand displacement regulated peroxidase activity, a simple and sensitive homogeneous fluorescent DNA sensing method is proposed. The detection can conveniently be carried out in a 96-well plate within 20 min with a detection limit of 0.18 nM. This method shows high specificity, which can effectively distinguish single-base mismatched DNA from perfectly matched target DNA. The DNA strand displacement regulated catalytic activity of hemin has promising application in the determination of various DNA analytes.

Asymmetric strand segregation: epigenetic costs of genetic fidelity?

Directory of Open Access Journals (Sweden)

Diane P Genereux

2009-06-01

Full Text Available Asymmetric strand segregation has been proposed as a mechanism to minimize effective mutation rates in epithelial tissues. Under asymmetric strand segregation, the double-stranded molecule that contains the oldest DNA strand is preferentially targeted to the somatic stem cell after each round of DNA replication. This oldest DNA strand is expected to have fewer errors than younger strands because some of the errors that arise on daughter strands during their synthesis fail to be repaired. Empirical findings suggest the possibility of asymmetric strand segregation in a subset of mammalian cell lineages, indicating that it may indeed function to increase genetic fidelity. However, the implications of asymmetric strand segregation for the fidelity of epigenetic information remain unexplored. Here, I explore the impact of strand-segregation dynamics on epigenetic fidelity using a mathematical-modelling approach that draws on the known molecular mechanisms of DNA methylation and existing rate estimates from empirical methylation data. I find that, for a wide range of starting methylation densities, asymmetric -- but not symmetric -- strand segregation leads to systematic increases in methylation levels if parent strands are subject to de novo methylation events. I found that epigenetic fidelity can be compromised when enhanced genetic fidelity is achieved through asymmetric strand segregation. Strand segregation dynamics could thus explain the increased DNA methylation densities that are observed in structured cellular populations during aging and in disease.

Genetic ecotoxicology IV: survival and DNA strand breakage is dependent on genotype in radionuclide-exposed mosquitofish

Energy Technology Data Exchange (ETDEWEB)

Theodorakis, C.W. [Texas A and M University, Department of Wildlife and Fisheries Sciences, College Station, TX 77843-2258 (United States); Elbl, T. [University of Pennsylvania, Department of Cell and Molecular Biology, Philadelphia, PA 19102 (United States); Shugart, L.R. [L.R. Shugart and Associates, Oak Ridge, TN 37831 (United States)

1999-05-01

Western mosquitofish (Gambusia affinis) were caged in situ in a radioactively-contaminated pond in order to determine if survival and amount of DNA strand breakage were dependent on genotype. Genotypes of fish were determined using the randomly amplified polymorphic (RAPD) technique, and DNA strand breakage was determined using agarose gel electrophoresis. This study is a continuation of research undertaken at the Oak Ridge National Laboratory, which examined the effects of radionuclide contamination on the population genetic structure of mosquitofish. The previous research found 17 RAPD markers that were present at a higher frequency in contaminated than in reference populations ('contaminant-indicative bands'), and fish from contaminated sites which possessed these markers had higher fecundity and fewer strand breaks than fish which did not. One of the contaminated populations (Pond 3513) was colonized from one of the reference populations (Crystal Springs) in 1977. In the present study, fish were obtained from Crystal Springs and an additional reference site, and caged in Pond 3513. The percent survival and amount of DNA strand breakage were then determined for fish with and without the contaminant-indicative markers. When Crystal Springs fish were caged in Pond 3513, it was found that the genotypic distribution of the survivors was more similar to the native Pond 3513 population than to the Crystal Springs population. Furthermore, for nine of the contaminant-indicative markers, the percent survival was greater for fish which possessed these markers than for fish which did not. For five of these markers, fish which possessed them had higher DNA integrity (fewer strand breaks) than fish which did not. These data indicate that probability of survival and degree of DNA strand breakage in radionuclide-exposed mosquitofish are dependent on RAPD genotype, and are consistent with the hypothesis that the contaminant-indicative RAPD bands are markers of loci

Temperature dependence of radiation colloidal centers production and annealing in alkali halide crystals

International Nuclear Information System (INIS)

Kristapson, J.Z.; Ozerskii, V.J.

1981-01-01

The investigation results on temperature dependences of production and annealing of radiation colloidal color centers have been reviewed. In order to produce such centers in NaCl, KCl and KBr crystals the doses of 10 2 -10 4 Mrad as well as irradiation temperatures of 300-600 K and post-irradiation heating of up to 800 K were applied. It has been demonstrated that to produce X-centers, it is necessary to have optimal temperature and initial critical dose during both irradiation and post-irradiation heating of crystals. It has been also found that during annealing hole centers produced are different with regard to thermal stability. The possible recombination mechanisms of hole and electron products of radiolysis during post-irradiation heating has been analyzed [ru

Strand displacement by DNA polymerase III occurs through a tau-psi-chi link to single-stranded DNA-binding protein coating the lagging strand template.

Science.gov (United States)

Yuan, Quan; McHenry, Charles S

2009-11-13

In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of gamma-complex to support the reaction in the absence of tau. However, if gamma-complex is present to load beta(2), a truncated tau protein containing only domains III-V will suffice. This truncated protein is sufficient to bind both the alpha subunit of DNA polymerase (Pol) III and chipsi. This is reminiscent of the minimal requirements for Pol III to replicate short single-stranded DNA-binding protein (SSB)-coated templates where tau is only required to serve as a scaffold to hold Pol III and chi in the same complex (Glover, B., and McHenry, C. (1998) J. Biol. Chem. 273, 23476-23484). We propose a model in which strand displacement by DNA polymerase III holoenzyme depends upon a Pol III-tau-psi-chi-SSB binding network, where SSB is bound to the displaced strand, stabilizing the Pol III-template interaction. The same interaction network is probably important for stabilizing the leading strand polymerase interactions with authentic replication forks. The specificity constant (k(cat)/K(m)) for the strand displacement reaction is approximately 300-fold less favorable than reactions on single-stranded templates and proceeds with a slower rate (150 nucleotides/s) and only moderate processivity (approximately 300 nucleotides). PriA, the initiator of replication restart on collapsed or misassembled replication forks, blocks the strand displacement reaction, even if added to an ongoing reaction.

A cascade autocatalytic strand displacement amplification and hybridization chain reaction event for label-free and ultrasensitive electrochemical nucleic acid biosensing.

Science.gov (United States)

Chen, Zhiqiang; Liu, Ying; Xin, Chen; Zhao, Jikuan; Liu, Shufeng

2018-04-23

Herein, an autocatalytic strand displacement amplification (ASDA) strategy was proposed for the first time, which was further ingeniously coupled with hybridization chain reaction (HCR) event for the isothermal, label-free and multiple amplification toward nucleic acid detection. During the ASDA module, the target recognition opens the immobilized hairpin probe (IP) and initiates the annealing of the auxiliary DNA strand (AS) with the opened IP for the successive polymerization and nicking reaction in the presence of DNA polymerase and nicking endonuclease. This induces the target recycling and generation of a large amount of intermediate DNA sequences, which can be used as target analogy to execute the autocatalytic strand displacement amplification. Simultaneously, the introduced AS strand can propagate the HCR between two hairpins (H1 and H2) to form a linear DNA concatamer with cytosine (C)-rich loop region, which can facilitate the in-situ synthesis of silver nanoclusters (AgNCs) as electrochemical tags for further amplification toward target responses. With current cascade ASDA and HCR strategy, the detection of target DNA could be achieved with a low detection limit of about 0.16 fM and a good selectivity. The developed biosensor also exhibits the distinct advantages of flexibility and simplicity in probe design and biosensor fabrication, and label-free electrochemical detection, thus opens a promising avenue for the detection of nucleic acid with low abundance in bioanalysis and clinical biomedicine. Copyright © 2018 Elsevier B.V. All rights reserved.

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination.

Science.gov (United States)

Uringa, Evert-Jan; Youds, Jillian L; Lisaingo, Kathleen; Lansdorp, Peter M; Boulton, Simon J

2011-03-01

Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron-sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1's enzymatic activity to its function in telomere maintenance and DNA repair.

Radiation-induced DNA damage in tumors and normal tissues. III. Oxygen dependence of the formation of strand breaks and DNA-protein crosslinks

International Nuclear Information System (INIS)

Zhang, H.; Wallen, C.A.; Wheeler, K.T.; Joch, C.J.

1995-01-01

Results from several laboratories, including ours, have suggested that measurements of radiation-induced DNA strand breaks and DNA-protein crosslinks (DPCs) may be used to estimate the hypoxic fraction or fractional hypoxic volume of tumors and normal tissues. This suggestion has been predicated on both published and nonpublished information that (1) the oxygen dependence of the formation of strand breaks in irradiated mammalian cells is similar to the oxygen dependence of radiation-produced cell killing, and (2) the oxygen dependence of the formation of DPCs in irradiated mammalian cells is the mirror image of the oxygen dependence of radiation-induced cell killing. However, the published studies that attempted to determine the relationship between the oxygen dependence of the formation of strand breaks and the radiation sensitivity of mammalian cells were not performed at 37 degrees C, the exact oxygen concentrations were not always known, and the results were conflicting. In addition, most of the data on the oxygen dependence of the formation of DPCs are unpublished. Consequently, we have undertaken a comprehensive investigation of one cell line, 9L/Ro rat brain tumor cells, to determine if the shape of the oxygen dependence curve and the K m value for radiation-induced strand breaks and DPCs were similar when 9L cells were irradiated under both ideal gas-liquid equilibrium conditions at 4 degrees C and nonideal gas-liquid equilibrium conditions at 37 degrees C. At 4 degrees C under ideal gas-liquid equilibrium conditions, the K m for the formation of strand breaks was approximately 0.0045 mM, and Km for radiation sensitivity was approximately 0.005mM. A similar comparison for the formation of DPCs at 4 degrees C could not be made, because the efficiency of the formation of DPC was much lower at 4 degrees C than at 37 degrees C. 30 refs., 3 figs

Composition dependent thermal annealing behaviour of ion tracks in apatite

Energy Technology Data Exchange (ETDEWEB)

Nadzri, A., E-mail: allina.nadzri@anu.edu.au [Department of Electronic Materials Engineering, Research School of Physics and Engineering, Australian National University, Canberra, ACT 2601 (Australia); Schauries, D.; Mota-Santiago, P.; Muradoglu, S. [Department of Electronic Materials Engineering, Research School of Physics and Engineering, Australian National University, Canberra, ACT 2601 (Australia); Trautmann, C. [GSI Helmholtz Centre for Heavy Ion Research, Planckstrasse 1, 64291 Darmstadt (Germany); Technische Universität Darmstadt, 64287 Darmstadt (Germany); Gleadow, A.J.W. [School of Earth Science, University of Melbourne, Melbourne, VIC 3010 (Australia); Hawley, A. [Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168 (Australia); Kluth, P. [Department of Electronic Materials Engineering, Research School of Physics and Engineering, Australian National University, Canberra, ACT 2601 (Australia)

2016-07-15

Natural apatite samples with different F/Cl content from a variety of geological locations (Durango, Mexico; Mud Tank, Australia; and Snarum, Norway) were irradiated with swift heavy ions to simulate fission tracks. The annealing kinetics of the resulting ion tracks was investigated using synchrotron-based small-angle X-ray scattering (SAXS) combined with ex situ annealing. The activation energies for track recrystallization were extracted and consistent with previous studies using track-etching, tracks in the chlorine-rich Snarum apatite are more resistant to annealing than in the other compositions.

Two- and three-step annealing effects of metallic and semiconducting iron silicides formed by ion beam synthesis

Energy Technology Data Exchange (ETDEWEB)

Katsumata, Hiroshi [Meiji Univ., Tokyo (Japan); Makita, Yunosuke; Kobayashi, Naoto [and others

1997-03-01

Polycrystalline {beta}-FeSi{sub 2} was formed by ion beam synthesis (IBS). Annealing was made using two different procedures; 1) two-step annealing (2SA) ((T{sub 1} = 600degC, 1 hr) + (T{sub 2} = 900degC, 2 hrs)), 2) three-step annealing (3SA) ((T{sub 1} = 600degC, 1 hr) + (T{sub 2} = 1100degC, 1 min) + (T{sub 3} = 800 - 900degC, 18 hrs)). All the synthesized {beta}-FeSi{sub 2} layers presented an n-type conductivity with resistivities of 0.24 - 0.25 {Omega}{center_dot}cm, and they showed a direct band-gap of 0.801 - 0.824 eV with a moderate contribution of an indirect band-gap which is a few tens meV lower than the direct one. Although RBS and optical absorption measurements showed a superior crystalline quality of 3SA-samples to 2SA-samples, Raman scattering signals appeared only for 2SA-samples at 198 and 250 cm{sup -1}. This is explained by considering a decrease in the amount of {beta}-FeSi{sub 2} for 3SA-samples, which was deduced from the results of X-ray diffraction (XRD) analysis. The most adequate annealing temperature (T{sub 3}) for transforming {alpha}-Fe{sub 2}Si{sub 5} to {beta}-FeSi{sub 2} was found to be 850degC, in which the transformation process was observed by XRD and photomicroscope as a function of T{sub 3}. (author)

Increased rate of repair of ultraviolet-induced DNA strand breaks in mitogen stimulated lymphocytes

Energy Technology Data Exchange (ETDEWEB)

Hamlet, S.M.; Lavin, M.F.; Jennings, P.A. (Queensland Univ., St. Lucia (Australia). Dept. of Biochemistry; Queensland Univ., St. Lucia (Australia). Dept. of Veterinary Pathology; Queensland Univ. St. Lucia (Australia). Dept. of Public Health)

1982-05-01

Previous results have shown that phytohaemagglutinin-stimulated bovine lymphocytes exhibit a peak of ultraviolet-induced DNA repair synthesis 3 to 4 days after addition of mitogen. The level of repair synthesis was approximately tenfold higher than that in unstimulated lymphocytes. These studies have been extended to examine the rate of repair of strand breaks in U.V.-irradiated bovine lymphocytes. The extent of breakage of DNA was shown to be the same in mitogen-stimulated and unstimulated lymphocytes from two breeds of cattle, when determined by sedimentation of nucleoids on sucrose gradients. However, in mitogen-stimulated cells the time taken to repair DNA strand breaks was 6 hours compared with 12 hours in stationary phase lymphocytes after a U.V. dose of 5 J/m/sup 2/. These results suggest that the increased rate of repair of strand breaks is due to the induction of enzymes involved at the post-incision stage of DNA repair. Thus the increased level of repair synthesis observed in earlier work correlates with an increased rate of repair of DNA strand breaks in phytohaemagglutinin-stimulated bovine lymphocytes.

Increased rate of repair of ultraviolet-induced DNA strand breaks in mitogen stimulated lymphocytes

International Nuclear Information System (INIS)

Hamlet, S.M.; Lavin, M.F.; Jennings, P.A.; Queensland Univ., St. Lucia; Queensland Univ. St. Lucia

1982-01-01

Previous results have shown that phytohaemagglutinin-stimulated bovine lymphocytes exhibit a peak of ultraviolet-induced DNA repair synthesis 3 to 4 days after addition of mitogen. The level of repair synthesis was approximately tenfold higher than that in unstimulated lymphocytes. These studies have been extended to examine the rate of repair of strand breaks in U.V.-irradiated bovine lymphocytes. The extent of breakage of DNA was shown to be the same in mitogen-stimulated and unstimulated lymphocytes from two breeds of cattle, when determined by sedimentation of nucleoids on sucrose gradients. However, in mitogen-stimulated cells the time taken to repair DNA strand breaks was 6 hours compared with 12 hours in stationary phase lymphocytes after a U.V. dose of 5 J/m 2 . These results suggest that the increased rate of repair of strand breaks is due to the induction of enzymes involved at the post-incision stage of DNA repair. Thus the increased level of repair synthesis observed in earlier work correlates with an increased rate of repair of DNA strand breaks in phytohaemagglutinin-stimulated bovine lymphocytes. (author)

DNA double strand break repair is enhanced by P53 following induction by DNA damage and is dependent on the C-terminal domain of P53

International Nuclear Information System (INIS)

Wei Tang; Powell, Simon N.

1996-01-01

repair enhancement after IR compared with 10(1)Val5 cells, which show normal repair enhancement, implying that repair enhancement is a C-terminal dependent event. 10(1)Val5 cells showed the same level of repair enhancement at both 39 deg. C (mutant) and 32 deg. C (wild-type p53) again confirming that mutations in the DNA binding domain do not affect repair enhancement. Repair enhancement was seen when staggered-ended breaks were made in the test plasmid, but not after those ends were filled to create blunt ends. Conclusions: We conclude that dsb repair is enhanced by p53 induced by DNA damage. The enhancement of repair is dependent on the C-terminal domain of p53, and is not dependent upon transactivation. Repair measured by this assay may reflect strand annealing and protection of DNA termini, rather than all double strand cleavage

Dependence of Optical Properties of SEL-Deposited Silver Gallium Selenide Thin Films on the On-Line Growth Parameter: Annealing Duration

International Nuclear Information System (INIS)

Bhuiyan, M.R.A.; Firoz Hasan, S.M.

2005-01-01

Silver gallium selenide (AGS) composite thin films were formed onto ultrasonically and chemically cleaned glass substrates by successive on-line thermal evaporation of individual elements and post-deposition annealing at 300 0 C for various durations in vacuum. The annealing duration was varied between 5 and 20 minutes. The structural and optical properties of the films were ascertained by x-ray diffraction (XRD) and uv-vis-nir spectrophotometry (photon wavelength ranging between 300 and 2500 nm), respectively. The diffractogram indicated that these films were polycrystalline in nature having tetragonal structure with lattice parameters, a ∼ 6.0034 A and c ∼ 10.9165 A. The optical transmittance and reflectance were utilized to compute the absorption coefficient, refractive index and energy gap of the films. Dependence of the optical and structural properties of the films on various annealing durations has been analyzed. The nature of the optical transitions has been direct allowed with band gap energies ranging between 1.713 and 1.757 eV and refractive indices between 1.596 and 3.351 depending on photon energy as well as annealing duration. (authors)

Roles of C-Terminal Region of Yeast and Human Rad52 in Rad51-Nucleoprotein Filament Formation and ssDNA Annealing.

Directory of Open Access Journals (Sweden)

Nilesh V Khade

Full Text Available Yeast Rad52 (yRad52 has two important functions at homologous DNA recombination (HR; annealing complementary single-strand DNA (ssDNA molecules and recruiting Rad51 recombinase onto ssDNA (recombination mediator activity. Its human homolog (hRAD52 has a lesser role in HR, and apparently lacks mediator activity. Here we show that yRad52 can load human Rad51 (hRAD51 onto ssDNA complexed with yeast RPA in vitro. This is biochemically equivalent to mediator activity because it depends on the C-terminal Rad51-binding region of yRad52 and on functional Rad52-RPA interaction. It has been reported that the N-terminal two thirds of both yRad52 and hRAD52 is essential for binding to and annealing ssDNA. Although a second DNA binding region has been found in the C-terminal region of yRad52, its role in ssDNA annealing is not clear. In this paper, we also show that the C-terminal region of yRad52, but not of hRAD52, is involved in ssDNA annealing. This suggests that the second DNA binding site is required for the efficient ssDNA annealing by yRad52. We propose an updated model of Rad52-mediated ssDNA annealing.

Role of deoxyribonucleic acid polymerases and deoxyribonucleic acid ligase in x-ray-induced repair synthesis in toluene-treated Escherichia coli K-12

International Nuclear Information System (INIS)

Billen, D.; Hellermann, G.R.

1976-01-01

Toluene-treated Escherichia coli mutants have been used to study the roles of deoxyribonucleic acid (DNA) polymerases I, II, and III, and of DNA ligase in repair synthesis and strand rejoining following X-irradiation. In cells possessing all three DNA polymerases, both a greater amount of repair synthesis (''exaggerated'' repair synthesis) and failure of ligation are observed when DNA ligase activity is inhibited. In a mutant lacking the polymerizing activity of DNA polymerase I, exaggerated repair synthesis is not observed, and strand rejoining does not occur even if DNA ligase is fully activated. In a mutant possessing the polymerizing activity of DNA polymerase I but lacking its 5' → 3' exonuclease activity, exaggerated repair synthesis is minimal. After irradiation, DNA polymerases II and III are capable of carrying out an adenosine 5'-triphosphate-dependent repair synthesis, but rejoining of strand breaks does not occur and exaggerated synthesis is not seen whether DNA ligase is active or not. These results suggest that DNA polymerase I and DNA ligase act together to limit repair synthesis after X irradiation and that both are necessary in toluene-treated cells for strand rejoining. DNA polymerases II and III apparently cannot complete chain elongation and gap filling, and therefore repair carried out by these enzymes does not respond to ligase action

Frequency and temperature dependent mobility of a charged carrier and randomly interrupted strand

International Nuclear Information System (INIS)

Kumar, N.; Jayannavar, A.M.

1981-05-01

Randomly interrupted strand model of a one-dimensional conductor is considered. Exact analytical expression is obtained for the temperature dependent as mobility for a finite segment drawn at random, taking into account the reflecting barriers at the two open ends. The real part of mobility shows a broad resonance as a function of both frequency and tempeature, and vanishes quadratically in the dc limit. The frequency (temperature) maximum shifts to higher values for higher temperatures (frequencies). (author)

Thin-film designs by simulated annealing

Science.gov (United States)

Boudet, T.; Chaton, P.; Herault, L.; Gonon, G.; Jouanet, L.; Keller, P.

1996-11-01

With the increasing power of computers, new methods in synthesis of optical multilayer systems have appeared. Among these, the simulated-annealing algorithm has proved its efficiency in several fields of physics. We propose to show its performances in the field of optical multilayer systems through different filter designs.

Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways.

Science.gov (United States)

Gupta, Richa; Barkan, Daniel; Redelman-Sidi, Gil; Shuman, Stewart; Glickman, Michael S

2011-01-01

Bacterial pathogens rely on their DNA repair pathways to resist genomic damage inflicted by the host. DNA double-strand breaks (DSBs) are especially threatening to bacterial viability. DSB repair by homologous recombination (HR) requires nucleases that resect DSB ends and a strand exchange protein that facilitates homology search. RecBCD and RecA perform these functions in Escherichia coli and constitute the major pathway of error-free DSB repair. Mycobacteria, including the human pathogen M. tuberculosis, elaborate an additional error-prone pathway of DSB repair via non-homologous end-joining (NHEJ) catalysed by Ku and DNA ligase D (LigD). Little is known about the relative contributions of HR and NHEJ to mycobacterial chromosome repair, the factors that dictate pathway choice, or the existence of additional DSB repair pathways. Here we demonstrate that Mycobacterium smegmatis has three DSB repair pathway options: HR, NHEJ and a novel mechanism of single-strand annealing (SSA). Inactivation of NHEJ or SSA is compensated by elevated HR. We find that mycobacterial RecBCD does not participate in HR or confer resistance to ionizing radiation (IR), but is required for the RecA-independent SSA pathway. In contrast, the mycobacterial helicase-nuclease AdnAB participates in the RecA-dependent HR pathway, and is a major determinant of resistance to IR and oxidative DNA damage. These findings reveal distinctive features of mycobacterial DSB repair, most notably the dedication of the RecBCD and AdnAB helicase-nuclease machines to distinct repair pathways. © 2010 Blackwell Publishing Ltd.

MDA5 Detects the Double-Stranded RNA Replicative Form in Picornavirus-Infected Cells

Directory of Open Access Journals (Sweden)

Qian Feng

2012-11-01

Full Text Available RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. Major advances have been made in identifying RIG-I ligands, but our knowledge of the ligands for MDA5 remains restricted to data from transfection experiments mostly using poly(I:C, a synthetic dsRNA mimic. Here, we dissected the IFN-α/β-stimulatory activity of different viral RNA species produced during picornavirus infection, both by RNA transfection and in infected cells in which specific steps of viral RNA replication were inhibited. Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and production of the 7.5 kbp replicative form trigger a strong IFN-α/β response. IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative intermediate. This study reports MDA5 activation by a natural RNA ligand under physiological conditions.

Dependence of boron cluster dissolution on the annealing ambient

International Nuclear Information System (INIS)

Radic, Ljubo; Lilak, Aaron D.; Law, Mark E.

2002-01-01

Boron is introduced into silicon via implantation to form p-type layers. This process creates damage in the crystal that upon annealing causes enhanced diffusion and clustering of the boron layer. Reactivation of the boron is not a well-understood process. In this letter we experimentally investigate the effect of the annealing ambient on boron reactivation kinetics. An oxidizing ambient which injects silicon interstitials is compared to an inert ambient. Contrary to published theory, an excess of interstitials does not accelerate the reactivation process

Effects of buffer layer annealing temperature on the structural and optical properties of hydrothermal grown ZnO

Energy Technology Data Exchange (ETDEWEB)

Zhao, X.Q.; Kim, C.R.; Lee, J.Y.; Heo, J.H.; Shin, C.M. [Department of Nano Systems Engineering, Center for Nano Manufacturing, Inje University, Obang-dong, Gimhae, Gyeongnam 621-749 (Korea, Republic of); Ryu, H., E-mail: hhryu@inje.ac.kr [Department of Nano Systems Engineering, Center for Nano Manufacturing, Inje University, Obang-dong, Gimhae, Gyeongnam 621-749 (Korea, Republic of); Chang, J.H. [Major of Nano Semiconductor, Korea Maritime University, 1 Dongsam-dong, Yeongdo-Ku, Busan 606-791 (Korea, Republic of); Lee, H.C. [Department of Mechatronics Engineering, Korea Maritime University, 1 Dongsam-dong, Yeongdo-Ku, Busan 606-791 (Korea, Republic of); Son, C.S. [Department of Electronic Materials Engineering, Silla University, Gwaebeop-dong, Sasang-gu, Busan 617-736 (Korea, Republic of); Lee, W.J. [Department of Nano Engineering, Dong-Eui University, 995 Eomgwangno, Busanjin-gu, Busan 614-714 (Korea, Republic of); Jung, W.G. [School of Advanced Materials Engineering, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul 136-702 (Korea, Republic of); Tan, S.T. [Institute of Microelectronics, 11 Science Park Road, Science Park II, Singapore 117685 (Singapore); Zhao, J.L. [School of Electrical and Electronic Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798 (Singapore); Sun, X.W. [Institute of Microelectronics, 11 Science Park Road, Science Park II, Singapore 117685 (Singapore); School of Electrical and Electronic Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798 (Singapore)

2009-02-01

ZnO was deposited on bare Si(1 0 0), as-deposited, and annealed ZnO/Si(1 0 0) substrates by hydrothermal synthesis. The effects of a ZnO buffer layer and its thermal annealing on the properties of the ZnO deposited by hydrothermal synthesis were studied. The grain size and root mean square (RMS) roughness values of the ZnO buffer layer increased after thermal annealing of the buffer layer. The effect of buffer layer annealing temperature on the structural and optical properties was investigated by photoluminescence, X-ray diffraction, atomic force microscopy, and scanning electron microscopy. Hydrothermal grown ZnO deposited on ZnO/Si(1 0 0) annealed at 750 deg. C with the concentration of 0.3 M exhibits the best structural and optical properties.

C-terminal phenylalanine of bacteriophage T7 single-stranded DNA-binding protein is essential for strand displacement synthesis by T7 DNA polymerase at a nick in DNA.

Science.gov (United States)

Ghosh, Sharmistha; Marintcheva, Boriana; Takahashi, Masateru; Richardson, Charles C

2009-10-30

Single-stranded DNA-binding protein (gp2.5), encoded by gene 2.5 of bacteriophage T7, plays an essential role in DNA replication. Not only does it remove impediments of secondary structure in the DNA, it also modulates the activities of the other replication proteins. The acidic C-terminal tail of gp2.5, bearing a C-terminal phenylalanine, physically and functionally interacts with the helicase and DNA polymerase. Deletion of the phenylalanine or substitution with a nonaromatic amino acid gives rise to a dominant lethal phenotype, and the altered gp2.5 has reduced affinity for T7 DNA polymerase. Suppressors of the dominant lethal phenotype have led to the identification of mutations in gene 5 that encodes the T7 DNA polymerase. The altered residues in the polymerase are solvent-exposed and lie in regions that are adjacent to the bound DNA. gp2.5 lacking the C-terminal phenylalanine has a lower affinity for gp5-thioredoxin relative to the wild-type gp2.5, and this affinity is partially restored by the suppressor mutations in DNA polymerase. gp2.5 enables T7 DNA polymerase to catalyze strand displacement DNA synthesis at a nick in DNA. The resulting 5'-single-stranded DNA tail provides a loading site for T7 DNA helicase. gp2.5 lacking the C-terminal phenylalanine does not support this event with wild-type DNA polymerase but does to a limited extent with T7 DNA polymerase harboring the suppressor mutations.

C-terminal Phenylalanine of Bacteriophage T7 Single-stranded DNA-binding Protein Is Essential for Strand Displacement Synthesis by T7 DNA Polymerase at a Nick in DNA*

Science.gov (United States)

Ghosh, Sharmistha; Marintcheva, Boriana; Takahashi, Masateru; Richardson, Charles C.

2009-01-01

Single-stranded DNA-binding protein (gp2.5), encoded by gene 2.5 of bacteriophage T7, plays an essential role in DNA replication. Not only does it remove impediments of secondary structure in the DNA, it also modulates the activities of the other replication proteins. The acidic C-terminal tail of gp2.5, bearing a C-terminal phenylalanine, physically and functionally interacts with the helicase and DNA polymerase. Deletion of the phenylalanine or substitution with a nonaromatic amino acid gives rise to a dominant lethal phenotype, and the altered gp2.5 has reduced affinity for T7 DNA polymerase. Suppressors of the dominant lethal phenotype have led to the identification of mutations in gene 5 that encodes the T7 DNA polymerase. The altered residues in the polymerase are solvent-exposed and lie in regions that are adjacent to the bound DNA. gp2.5 lacking the C-terminal phenylalanine has a lower affinity for gp5-thioredoxin relative to the wild-type gp2.5, and this affinity is partially restored by the suppressor mutations in DNA polymerase. gp2.5 enables T7 DNA polymerase to catalyze strand displacement DNA synthesis at a nick in DNA. The resulting 5′-single-stranded DNA tail provides a loading site for T7 DNA helicase. gp2.5 lacking the C-terminal phenylalanine does not support this event with wild-type DNA polymerase but does to a limited extent with T7 DNA polymerase harboring the suppressor mutations. PMID:19726688

Strong white photoluminescence from annealed zeolites

International Nuclear Information System (INIS)

Bai, Zhenhua; Fujii, Minoru; Imakita, Kenji; Hayashi, Shinji

2014-01-01

The optical properties of zeolites annealed at various temperatures are investigated for the first time. The annealed zeolites exhibit strong white photoluminescence (PL) under ultraviolet light excitation. With increasing annealing temperature, the emission intensity of annealed zeolites first increases and then decreases. At the same time, the PL peak red-shifts from 495 nm to 530 nm, and then returns to 500 nm. The strongest emission appears when the annealing temperature is 500 °C. The quantum yield of the sample is measured to be ∼10%. The PL lifetime monotonously increases from 223 μs to 251 μs with increasing annealing temperature. The origin of white PL is ascribed to oxygen vacancies formed during the annealing process. -- Highlights: • The optical properties of zeolites annealed at various temperatures are investigated. • The annealed zeolites exhibit strong white photoluminescence. • The maximum PL enhancement reaches as large as 62 times. • The lifetime shows little dependence on annealing temperature. • The origin of white emission is ascribed to the oxygen vacancies

Interaction between the cellular protein eEF1A and the 3'-terminal stem-loop of West Nile virus genomic RNA facilitates viral minus-strand RNA synthesis.

Science.gov (United States)

Davis, William G; Blackwell, Jerry L; Shi, Pei-Yong; Brinton, Margo A

2007-09-01

RNase footprinting and nitrocellulose filter binding assays were previously used to map one major and two minor binding sites for the cell protein eEF1A on the 3'(+) stem-loop (SL) RNA of West Nile virus (WNV) (3). Base substitutions in the major eEF1A binding site or adjacent areas of the 3'(+) SL were engineered into a WNV infectious clone. Mutations that decreased, as well as ones that increased, eEF1A binding in in vitro assays had a negative effect on viral growth. None of these mutations affected the efficiency of translation of the viral polyprotein from the genomic RNA, but all of the mutations that decreased in vitro eEF1A binding to the 3' SL RNA also decreased viral minus-strand RNA synthesis in transfected cells. Also, a mutation that increased the efficiency of eEF1A binding to the 3' SL RNA increased minus-strand RNA synthesis in transfected cells, which resulted in decreased synthesis of genomic RNA. These results strongly suggest that the interaction between eEF1A and the WNV 3' SL facilitates viral minus-strand synthesis. eEF1A colocalized with viral replication complexes (RC) in infected cells and antibody to eEF1A coimmunoprecipitated viral RC proteins, suggesting that eEF1A facilitates an interaction between the 3' end of the genome and the RC. eEF1A bound with similar efficiencies to the 3'-terminal SL RNAs of four divergent flaviviruses, including a tick-borne flavivirus, and colocalized with dengue virus RC in infected cells. These results suggest that eEF1A plays a similar role in RNA replication for all flaviviruses.

Effects of synthesis variables on the magnetic properties of CoFe{sub 2}O{sub 4} nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Briceno, Sarah, E-mail: sarahbriara@gmail.com [Laboratorio de Fisica de la Materia Condensada, Centro de Fisica, Instituto Venezolano de Investigaciones Cientificas (IVIC), Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); Braemer-Escamilla, Werner; Silva, Pedro [Laboratorio de Fisica de la Materia Condensada, Centro de Fisica, Instituto Venezolano de Investigaciones Cientificas (IVIC), Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); Delgado, Gerzon E. [Laboratorio de Cristalografia, Departamento de Quimica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101-A (Venezuela, Bolivarian Republic of); Plaza, Eric [Laboratorio de Microscopia Electronica. Instituto Zuliano de Investigaciones Tecnologicas. Apartado 331. Km. 15. La Canada (Venezuela, Bolivarian Republic of); Palacios, Jordana [Laboratorio de Polimeros, Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas (IVIC), Apartado 20632, Caracas 1020-A (Venezuela, Bolivarian Republic of); Canizales, Edgard [Area de Analisis Quimico Inorganico. PDVSA. INTEVEP. Los Teques 1070-A (Venezuela, Bolivarian Republic of)

2012-09-15

Cobalt ferrite nanoparticles (CoFe{sub 2}O{sub 4}) have been synthesized using precipitation in water solution with polyethylene glycol as surfactant. Influence of various synthesis variables included pH, reaction time and annealing temperature on the magnetic properties and particle sizes has also been studied. Structural identification of the samples was carried out using Thermogravimetric and Differential thermal analysis, X-ray diffraction, Fourier transform infrared spectroscopy, Scanning electron microscopy, High resolution transmission electron microscopy. Vibrating sample magnetometer was used for the magnetic investigation of the samples. Magnetic properties of nanoparticles show strong dependence on the particle size. The magnetic properties increase with pH of the precipitating medium and annealing temperature while the coercivity goes through a maximum, peaking at around 25 nm. - Highlights: Black-Right-Pointing-Pointer CoFe{sub 2}O{sub 4} have been synthesized via chemical synthesis route using PEG as surfactant. Black-Right-Pointing-Pointer Influence of various synthesis variables on the magnetic properties has been studied. Black-Right-Pointing-Pointer Magnetic properties of nanoparticles show strong dependence on the particle size. Black-Right-Pointing-Pointer Magnetic properties increase with pH and annealing temperature.

Creating Directed Double-strand Breaks with the Ref Protein: A Novel Rec A-Dependent Nuclease from Bacteriophage P1

Energy Technology Data Exchange (ETDEWEB)

Gruenig, Marielle C.; Lu, Duo; Won, Sang Joon; Dulberger, Charles L.; Manlick, Angela J.; Keck, James L.; Cox, Michael M. (UW)

2012-03-16

The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 {angstrom} resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded {beta}-hairpin that is sandwiched between several {alpha}-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.

Annealing-temperature-dependent voltage-sign reversal in all-oxide spin Seebeck devices using RuO2

Science.gov (United States)

Kirihara, Akihiro; Ishida, Masahiko; Yuge, Ryota; Ihara, Kazuki; Iwasaki, Yuma; Sawada, Ryohto; Someya, Hiroko; Iguchi, Ryo; Uchida, Ken-ichi; Saitoh, Eiji; Yorozu, Shinichi

2018-04-01

Thermoelectric converters based on the spin Seebeck effect (SSE) have attracted great attention due to their potential to offer novel applications such as energy harvesting and heat-flow sensing. For converting a SSE-induced spin current into an electric current, a transition metal film such as Pt, which exhibits large inverse spin-Hall effect (ISHE), has been typically used. In this work, we show an all-oxide SSE device using ruthenium oxide (RuO2) as a conductive film. We found that both the sign and magnitude of the SSE-induced ISHE voltage V appearing in the RuO2 film changes depending on the post annealing temperature, and that the magnitude can become larger than that of a standard SSE device using Pt. The similar sign change was also observed in Hall-resistance measurements of the RuO2 films. X-ray absorption fine structure (XAFS) spectra of as-deposited and annealed RuO2 revealed that the annealing process substantially improved the long-range crystalline order in RuO2. This suggests that change in the crystalline order may modify the dominant ISHE mechanism or electronic states in RuO2, leading to the sign reversal of V as well as the Hall coefficient. Our result demonstrates that RuO2 is an interesting material not only as a practical ISHE film but also as a testbed to study physics of spin-to-charge converters that depend on their crystalline order.

RPA coordinates DNA end resection and prevents formation of DNA hairpins.

Science.gov (United States)

Chen, Huan; Lisby, Michael; Symington, Lorraine S

2013-05-23

Replication protein A (RPA) is an essential eukaryotic single-stranded DNA binding protein with a central role in DNA metabolism. RPA directly participates in DNA double-strand break repair by stimulating 5'-3' end resection by the Sgs1/BLM helicase and Dna2 endonuclease in vitro. Here we investigated the role of RPA in end resection in vivo, using a heat-inducible degron system that allows rapid conditional depletion of RPA in Saccharomyces cerevisiae. We found that RPA depletion eliminated both the Sgs1-Dna2- and Exo1-dependent extensive resection pathways and synergized with mre11Δ to prevent end resection. The short single-stranded DNA tails formed in the absence of RPA were unstable due to 3' strand loss and the formation of fold-back hairpin structures that required resection initiation and Pol32-dependent DNA synthesis. Thus, RPA is required to generate ssDNA, and also to protect ssDNA from degradation and inappropriate annealing that could lead to genome rearrangements. Copyright © 2013 Elsevier Inc. All rights reserved.

Aqueous chemical growth of Cu{sub 2}ZnSnS{sub 4} (CZTS) thin films: Air annealing and photoelectrochemical properties

Energy Technology Data Exchange (ETDEWEB)

Shinde, N.M.; Deshmukh, P.R.; Patil, S.V. [Thin Film Physics Laboratory, Department of Physics, Shivaji University, Kolhapur 416004, M.S. (India); Lokhande, C.D., E-mail: l_chandrakant@yahoo.com [Thin Film Physics Laboratory, Department of Physics, Shivaji University, Kolhapur 416004, M.S. (India)

2013-05-15

Highlights: ► Facile and efficient route for synthesis of CZTS film. ► Effect of annealing on structural, morphological and electrical properties of CZTS films. ► Solar cell study. - Abstract: In present investigation, Cu{sub 2}ZnSnS{sub 4} (CZTS) thin films have been deposited on to glass substrates by novel chemical successive ionic layer adsorption and reaction (SILAR) method. The effect of air annealing in the temperature range between 573 and 773 K on the structural, morphological, optical and electrical properties has been studied. The X-ray diffraction studies revealed the formation of polycrystalline CZTS films. The surface morphological study showed smooth, compact and uniform film formation after annealing formation. The band gap was in between range from 1.5 to 1.8 eV depending on annealing temperature. The thermo emf measurement revealed that the CZTS exhibits p-type electrical conductivity. Further, photoactivity of CZTS thin films was tested by forming the photoelectrochemical cell.

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

NARCIS (Netherlands)

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

2009-01-01

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

Immortal DNA strand cosegregation requires p53/IMPDH-dependent asymmetric self-renewal associated with adult stem cells.

Science.gov (United States)

Rambhatla, Lakshmi; Ram-Mohan, Sumati; Cheng, Jennifer J; Sherley, James L

2005-04-15

Because they are long-lived and cycle continuously, adult stem cells (ASCs) are predicted as the most common precursor for cancers in adult mammalian tissues. Two unique attributes have been proposed to restrict the carcinogenic potential of ASCs. These are asymmetric self-renewal that limits their number and immortal DNA strand cosegregation that limits their accumulation of mutations due to DNA replication errors. Until recently, the molecular basis and regulation of these important ASC-specific functions were unknown. We developed engineered cultured cells that exhibit asymmetric self-renewal and immortal DNA strand cosegregation. These model cells were used to show that both ASC-specific functions are regulated by the p53 cancer gene. Previously, we proposed that IMP dehydrogenase (IMPDH) was an essential factor for p53-dependent asymmetric self-renewal. We now confirm this proposal and provide quantitative evidence that asymmetric self-renewal is acutely sensitive to even modest changes in IMPDH expression. These analyses reveal that immortal DNA strand cosegregation is also regulated by IMPDH and confirm the original implicit precept that immortal DNA strand cosegregation is specific to cells undergoing asymmetric self-renewal (i.e., ASCs). With IMPDH being the rate-determining enzyme for guanine ribonucleotide (rGNP) biosynthesis, its requirement implicates rGNPs as important regulators of ASC asymmetric self-renewal and immortal DNA strand cosegregation. An in silico analysis of global gene expression data from human cancer cell lines underscored the importance of p53-IMPDH-rGNP regulation for normal tissue cell kinetics, providing further support for the concept that ASCs are key targets for adult tissue carcinogenesis.

Nuclear techniques of analysis in diamond synthesis and annealing

Energy Technology Data Exchange (ETDEWEB)

Jamieson, D. N.; Prawer, S.; Gonon, P.; Walker, R.; Dooley, S.; Bettiol, A.; Pearce, J. [Melbourne Univ., Parkville, VIC (Australia). School of Physics

1996-12-31

Nuclear techniques of analysis have played an important role in the study of synthetic and laser annealed diamond. These measurements have mainly used ion beam analysis with a focused MeV ion beam in a nuclear microprobe system. A variety of techniques have been employed. One of the most important is nuclear elastic scattering, sometimes called non-Rutherford scattering, which has been used to accurately characterise diamond films for thickness and composition. This is possible by the use of a database of measured scattering cross sections. Recently, this work has been extended and nuclear elastic scattering cross sections for both natural boron isotopes have been measured. For radiation damaged diamond, a focused laser annealing scheme has been developed which produces near complete regrowth of MeV phosphorus implanted diamonds. In the laser annealed regions, proton induced x-ray emission has been used to show that 50 % of the P atoms occupy lattice sites. This opens the way to produce n-type diamond for microelectronic device applications. All these analytical applications utilize a focused MeV microbeam which is ideally suited for diamond analysis. This presentation reviews these applications, as well as the technology of nuclear techniques of analysis for diamond with a focused beam. 9 refs., 6 figs.

Nuclear techniques of analysis in diamond synthesis and annealing

Energy Technology Data Exchange (ETDEWEB)

Jamieson, D N; Prawer, S; Gonon, P; Walker, R; Dooley, S; Bettiol, A; Pearce, J [Melbourne Univ., Parkville, VIC (Australia). School of Physics

1997-12-31

Nuclear techniques of analysis have played an important role in the study of synthetic and laser annealed diamond. These measurements have mainly used ion beam analysis with a focused MeV ion beam in a nuclear microprobe system. A variety of techniques have been employed. One of the most important is nuclear elastic scattering, sometimes called non-Rutherford scattering, which has been used to accurately characterise diamond films for thickness and composition. This is possible by the use of a database of measured scattering cross sections. Recently, this work has been extended and nuclear elastic scattering cross sections for both natural boron isotopes have been measured. For radiation damaged diamond, a focused laser annealing scheme has been developed which produces near complete regrowth of MeV phosphorus implanted diamonds. In the laser annealed regions, proton induced x-ray emission has been used to show that 50 % of the P atoms occupy lattice sites. This opens the way to produce n-type diamond for microelectronic device applications. All these analytical applications utilize a focused MeV microbeam which is ideally suited for diamond analysis. This presentation reviews these applications, as well as the technology of nuclear techniques of analysis for diamond with a focused beam. 9 refs., 6 figs.

Nuclear techniques of analysis in diamond synthesis and annealing

International Nuclear Information System (INIS)

Jamieson, D. N.; Prawer, S.; Gonon, P.; Walker, R.; Dooley, S.; Bettiol, A.; Pearce, J.

1996-01-01

Nuclear techniques of analysis have played an important role in the study of synthetic and laser annealed diamond. These measurements have mainly used ion beam analysis with a focused MeV ion beam in a nuclear microprobe system. A variety of techniques have been employed. One of the most important is nuclear elastic scattering, sometimes called non-Rutherford scattering, which has been used to accurately characterise diamond films for thickness and composition. This is possible by the use of a database of measured scattering cross sections. Recently, this work has been extended and nuclear elastic scattering cross sections for both natural boron isotopes have been measured. For radiation damaged diamond, a focused laser annealing scheme has been developed which produces near complete regrowth of MeV phosphorus implanted diamonds. In the laser annealed regions, proton induced x-ray emission has been used to show that 50 % of the P atoms occupy lattice sites. This opens the way to produce n-type diamond for microelectronic device applications. All these analytical applications utilize a focused MeV microbeam which is ideally suited for diamond analysis. This presentation reviews these applications, as well as the technology of nuclear techniques of analysis for diamond with a focused beam. 9 refs., 6 figs

Reactor pressure vessel thermal annealing

International Nuclear Information System (INIS)

Lee, A.D.

1997-01-01

The steel plates and/or forgings and welds in the beltline region of a reactor pressure vessel (RPV) are subject to embrittlement from neutron irradiation. This embrittlement causes the fracture toughness of the beltline materials to be less than the fracture toughness of the unirradiated material. Material properties of RPVs that have been irradiated and embrittled are recoverable through thermal annealing of the vessel. The amount of recovery primarily depends on the level of the irradiation embrittlement, the chemical composition of the steel, and the annealing temperature and time. Since annealing is an option for extending the service lives of RPVs or establishing less restrictive pressure-temperature (P-T) limits; the industry, the Department of Energy (DOE) and the Nuclear Regulatory Commission (NRC) have assisted in efforts to determine the viability of thermal annealing for embrittlement recovery. General guidance for in-service annealing is provided in American Society for Testing and Materials (ASTM) Standard E 509-86. In addition, the American Society of Mechanical Engineers (ASME) Code Case N-557 addresses annealing conditions (temperature and duration), temperature monitoring, evaluation of loadings, and non-destructive examination techniques. The NRC thermal annealing rule (10 CFR 50.66) was approved by the Commission and published in the Federal Register on December 19, 1995. The Regulatory Guide on thermal annealing (RG 1.162) was processed in parallel with the rule package and was published on February 15, 1996. RG 1.162 contains a listing of issues that need to be addressed for thermal annealing of an RPV. The RG also provides alternatives for predicting re-embrittlement trends after the thermal anneal has been completed. This paper gives an overview of methodology and recent technical references that are associated with thermal annealing. Results from the DOE annealing prototype demonstration project, as well as NRC activities related to the

Potent Inhibitors of the Hepatitis C Virus NS3 Protease: Design and Synthesis of Macrocyclic Substrate-Based [beta]-Strand Mimics

Energy Technology Data Exchange (ETDEWEB)

Goudreau, Nathalie; Brochu, Christian; Cameron, Dale R.; Duceppe, Jean-Simon; Faucher, Anne-Marie; Ferland, Jean-Marie; Grand-Maître, Chantal; Poirier, Martin; Simoneau, Bruno; Tsantrizos, Youla S. (Boehringer)

2008-06-30

The virally encoded NS3 protease is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. The design and synthesis of 15-membered ring {beta}-strand mimics which are capable of inhibiting the interactions between the HCV NS3 protease enzyme and its polyprotein substrate will be described. The binding interactions between a macrocyclic ligand and the enzyme were explored by NMR and molecular dynamics, and a model of the ligand/enzyme complex was developed.

Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer

Science.gov (United States)

Godet, Julien; Kenfack, Cyril; Przybilla, Frédéric; Richert, Ludovic; Duportail, Guy; Mély, Yves

2013-01-01

The HIV-1 nucleocapsid protein (NCp7) is a nucleic acid chaperone required during reverse transcription. During the first strand transfer, NCp7 is thought to destabilize cTAR, the (−)DNA copy of the TAR RNA hairpin, and subsequently direct the TAR/cTAR annealing through the zipping of their destabilized stem ends. To further characterize the destabilizing activity of NCp7, we locally probe the structure and dynamics of cTAR by steady-state and time resolved fluorescence spectroscopy. NC(11–55), a truncated NCp7 version corresponding to its zinc-finger domain, was found to bind all over the sequence and to preferentially destabilize the penultimate double-stranded segment in the lower part of the cTAR stem. This destabilization is achieved through zinc-finger–dependent binding of NC to the G10 and G50 residues. Sequence comparison further revealed that C•A mismatches close to the two G residues were critical for fine tuning the stability of the lower part of the cTAR stem and conferring to G10 and G50 the appropriate mobility and accessibility for specific recognition by NC. Our data also highlight the necessary plasticity of NCp7 to adapt to the sequence and structure variability of cTAR to chaperone its annealing with TAR through a specific pathway. PMID:23511968

Manipulation of magnetic properties of glass-coated microwires by annealing

Energy Technology Data Exchange (ETDEWEB)

Zhukov, A., E-mail: arkadi.joukov@ehu.es [Dpto. Fisica de Materiales, Fac. Quimicas, UPV/EHU, 20009 San Sebastian (Spain); IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain); Chichay, K. [Immanuel Kant Baltic Federal University, 236041 Kaliningrad (Russian Federation); Talaat, A. [Dpto. Fisica de Materiales, Fac. Quimicas, UPV/EHU, 20009 San Sebastian (Spain); Rodionova, V. [Immanuel Kant Baltic Federal University, 236041 Kaliningrad (Russian Federation); National University of Science and Technology (MISIS), 119049 Moscow (Russian Federation); Blanco, J.M. [Dpto. Física Aplicada, EUPDS Basque Country University UPV/EHU (Spain); Ipatov, M.; Zhukova, V. [Dpto. Fisica de Materiales, Fac. Quimicas, UPV/EHU, 20009 San Sebastian (Spain)

2015-06-01

We demonstrated that magnetic properties (hysteresis loops, domain wall propagation and giant magnetoimpedance effect) of Fe and Co-rich amorphous microwires can be tailored by stress and conventional annealing. Observed dependences discussed considering stress relaxation, back stresses and change of the magnetostriction after samples annealing. These considerations have been proved by experimental observation of the change of the magnetostriction coefficient sign induced by annealing. - Highlights: • Manipulation of hysteresis loop of amorphous Co–Fe- rich microwires by annealing. • Coexistence of Giant magnetoimpedance effect and fast domain wall propagation in the same sample. • Evidence of annealing dependence of the magnetostriction coefficient. • Effect of stress induced anisotropy on magnetic properties and GMI effect.

Manipulation of magnetic properties of glass-coated microwires by annealing

International Nuclear Information System (INIS)

Zhukov, A.; Chichay, K.; Talaat, A.; Rodionova, V.; Blanco, J.M.; Ipatov, M.; Zhukova, V.

2015-01-01

We demonstrated that magnetic properties (hysteresis loops, domain wall propagation and giant magnetoimpedance effect) of Fe and Co-rich amorphous microwires can be tailored by stress and conventional annealing. Observed dependences discussed considering stress relaxation, back stresses and change of the magnetostriction after samples annealing. These considerations have been proved by experimental observation of the change of the magnetostriction coefficient sign induced by annealing. - Highlights: • Manipulation of hysteresis loop of amorphous Co–Fe- rich microwires by annealing. • Coexistence of Giant magnetoimpedance effect and fast domain wall propagation in the same sample. • Evidence of annealing dependence of the magnetostriction coefficient. • Effect of stress induced anisotropy on magnetic properties and GMI effect

The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis

Science.gov (United States)

Jette, Nicholas; Lees-Miller, Susan P.

2015-01-01

The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemistry, structure and function of DNA-PK, its roles in DNA double strand break repair and its newly described roles in mitosis and other cellular processes. PMID:25550082

Mathematical foundation of quantum annealing

International Nuclear Information System (INIS)

Morita, Satoshi; Nishimori, Hidetoshi

2008-01-01

Quantum annealing is a generic name of quantum algorithms that use quantum-mechanical fluctuations to search for the solution of an optimization problem. It shares the basic idea with quantum adiabatic evolution studied actively in quantum computation. The present paper reviews the mathematical and theoretical foundations of quantum annealing. In particular, theorems are presented for convergence conditions of quantum annealing to the target optimal state after an infinite-time evolution following the Schroedinger or stochastic (Monte Carlo) dynamics. It is proved that the same asymptotic behavior of the control parameter guarantees convergence for both the Schroedinger dynamics and the stochastic dynamics in spite of the essential difference of these two types of dynamics. Also described are the prescriptions to reduce errors in the final approximate solution obtained after a long but finite dynamical evolution of quantum annealing. It is shown there that we can reduce errors significantly by an ingenious choice of annealing schedule (time dependence of the control parameter) without compromising computational complexity qualitatively. A review is given on the derivation of the convergence condition for classical simulated annealing from the view point of quantum adiabaticity using a classical-quantum mapping

RPA Stabilization of Single-Stranded DNA Is Critical for Break-Induced Replication.

Science.gov (United States)

Ruff, Patrick; Donnianni, Roberto A; Glancy, Eleanor; Oh, Julyun; Symington, Lorraine S

2016-12-20

DNA double-strand breaks (DSBs) are cytotoxic lesions that must be accurately repaired to maintain genome stability. Replication protein A (RPA) plays an important role in homology-dependent repair of DSBs by protecting the single-stranded DNA (ssDNA) intermediates formed by end resection and by facilitating Rad51 loading. We found that hypomorphic mutants of RFA1 that support intra-chromosomal homologous recombination are profoundly defective for repair processes involving long tracts of DNA synthesis, in particular break-induced replication (BIR). The BIR defects of the rfa1 mutants could be partially suppressed by eliminating the Sgs1-Dna2 resection pathway, suggesting that Dna2 nuclease attacks the ssDNA formed during end resection when not fully protected by RPA. Overexpression of Rad51 was also found to suppress the rfa1 BIR defects. We suggest that Rad51 binding to the ssDNA formed by excessive end resection and during D-loop migration can partially compensate for dysfunctional RPA. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Facile Synthesis of Calcium Borate Nanoparticles and the Annealing Effect on Their Structure and Size

Directory of Open Access Journals (Sweden)

Manizheh Navasery

2012-11-01

Full Text Available Calcium borate nanoparticles have been synthesized by a thermal treatment method via facile co-precipitation. Differences of annealing temperature and annealing time and their effects on crystal structure, particle size, size distribution and thermal stability of nanoparticles were investigated. The formation of calcium borate compound was characterized by X-ray diffraction (XRD and Fourier Transform Infrared spectroscopy (FTIR, Transmission electron microscopy (TEM, and Thermogravimetry (TGA. The XRD patterns revealed that the co-precipitated samples annealed at 700 °C for 3 h annealing time formed an amorphous structure and the transformation into a crystalline structure only occurred after 5 h annealing time. It was found that the samples annealed at 900 °C are mostly metaborate (CaB2O4 nanoparticles and tetraborate (CaB4O7 nanoparticles only observed at 970 °C, which was confirmed by FTIR. The TEM images indicated that with increasing the annealing time and temperature, the average particle size increases. TGA analysis confirmed the thermal stability of the annealed samples at higher temperatures.

The annealing temperature dependences of microstructures and magnetic properties in electro-chemical deposited CoNiFe thin films

International Nuclear Information System (INIS)

Suharyadi, Edi; Riyanto, Agus; Abraha, Kamsul

2016-01-01

CoNiFe thin films with various compositions had been successfully fabricated using electro-chemical deposition method. The crystal structure of Co_6_5Ni_1_5Fe_2_0, Co_6_2Ni_1_5Fe_2_3, and Co_5_5Ni_1_5Fe_3_0 thin films was fcc, bcc-fcc mix, and bcc, respectively. The difference crystal structure results the difference in magnetic properties. The saturation magnetic flux density (Bs) of Co_6_5Ni_1_5Fe_2_0, Co_6_2Ni_1_5Fe_2_3, and Co_5_5Ni_1_5Fe_3_0 thin films was 1.89 T, 1.93 T, and 2.05 T, respectively. An optimal annealing temperature was determined for controlling the microstructure and magnetic properties of CoNiFe thin films. Depending on annealing temperature, the ratio of bcc and fcc structure varied without changing the film composition. By annealing at temperature of T ≥ 350°C, the intensity ratio of X-ray diffraction peaks for bcc(110) to fcc(111) increased. The increase of phase ratio of bcc(110) to fcc(111) caused the increase of Bs, from 1.89 T to 1.95 T. Coercivity (Hc) also increased after annealing, from 2.6 Oe to 18.6 Oe for fcc phase thin films, from 2.0 Oe to 12.0 Oe for fcc-bcc mix phase thin films, and 7.8 Oe to 8 Oe for bcc phase thin films. The changing crystal structures during annealing process indicated that the thermal treatment at high temperature cause the changing crystallinity and atomic displacement. The TEM bright-field images with corresponding selected-area electron diffraction (SAED) patterns showed that there are strongly effects of thermal annealing on the size of fcc and bcc phase crystalline grain as described by size of individual spot and discontinuous rings. The size of crystalline grains increased by thermal annealing. The evolution of bcc and fcc structures of CoNiFe during annealing is though to be responsible for the change of magnetic properties.

Annealing time dependent up-conversion luminescence enhancement in magnesium–tellurite glass

Energy Technology Data Exchange (ETDEWEB)

Amjad, Raja J., E-mail: rajajunaid25@gmail.com [Advanced Optical Material Research Group, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor bahru 81310 (Malaysia); Centre for Solid State Physics, University of the Punjab, QAC, Lahore 54590 (Pakistan); Sahar, M.R.; Ghoshal, S.K.; Dousti, M.R. [Advanced Optical Material Research Group, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor bahru 81310 (Malaysia); Riaz, S. [Centre for Solid State Physics, University of the Punjab, QAC, Lahore 54590 (Pakistan); Samavati, A.R.; Arifin, R. [Advanced Optical Material Research Group, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor bahru 81310 (Malaysia); Naseem, S. [Centre for Solid State Physics, University of the Punjab, QAC, Lahore 54590 (Pakistan)

2013-04-15

Silver nanoparticles (NPs) embedded Er{sup 3+} ions doped magnesium–tellurite glasses are prepared using melt quenching technique. Heat treatment with different time intervals above the glass transition temperature is applied in order to reduce the silver ions (Ag{sup +}) to silver NPs (Ag{sup o}). The transmission electron microscopy (TEM), differential thermal analyses (DTA), UV–vis-NIR absorption spectroscopy and photoluminescence (PL) spectroscopy are used to examine annealing time dependent structural and optical properties. The characteristics temperatures such as glass transition temperature (T{sub g}), crystallization temperature (T{sub c}) and melting temperature (T{sub m}) obtained from DTA for an as prepared sample are 322 °C, 450 °C and 580 °C, respectively. TEM image clearly shows the homogeneous distribution of silver NPs with an average diameter ∼12 nm. The observed localized surface plasmon resonance (LSPR) band is evidenced at 534 nm. Furthermore, the infrared to visible frequency up-conversion (UC) emission under 786 nm excitation exhibits three emission bands centered at 532 nm, 554 nm and 634 nm corresponding to {sup 2}H{sub 11/2}→{sup 4}I{sub 15/2}, {sup 4}S{sub 3/2}→{sup 4}I{sub 15/2} and {sup 4}F{sub 9/2}→{sup 4}I{sub 15/2} transitions of Er{sup 3+}, respectively. Intensity of all the bands is found to enhance by increasing the annealing time up to 24 h. However, further increase in the annealing time duration (∼40 h) reduces the intensity. Enhancement in the luminescence intensity is understood in terms of the local field effect of the silver NPs whereas the quenching is attributed to the energy transfer from Er{sup 3+} ions to silver NPs. -- Highlights: ► Er{sup 3+}-doped silver NPs embedded magnesium–tellurite glasses are prepared. ► TEM confirms the successful precipitation of spherical NPs by heat treatment (HT). ► Luminescence is enhanced due to the growth of NPs after HT up to 24 h. ► With HT>24 h (40 h

An oligonucleotide complementary to the SL-B1 domain in the 3'-end of the minus-strand RNA of the hepatitis C virus inhibits in vitro initiation of RNA synthesis by the viral polymerase

International Nuclear Information System (INIS)

Reigadas, Sandrine; Ventura, Michel; Andreola, Marie-Line; Michel, Justine; Gryaznov, Sergei; Tarrago-Litvak, Laura; Litvak, Simon; Astier-Gin, Therese

2003-01-01

We describe oligonucleotides (ODNs) that inhibit hepatitis C virus (HCV) RNA synthesis in vitro. From a series of 13 ODNs complementary to the 3'-end of the minus-strand HCV RNA, only 4 inhibited RNA synthesis with IC 50 values lower than 1 μM. The inhibition was sequence-specific, since no effect was observed when the ODNs were used with a noncomplementary template. The introduction of a 2'-O-methyl modification increased the inhibitor activity 11-fold (IC 50 = 50 nM) in just 1 (ODN7) of the 4 inhibitory ODNs. ODNs did not inhibit RNA synthesis by interfering with the elongation process as no short RNAs products were detected. We also show that ODN7 did not prevent binding of NS5B to the template or cause polymerase trapping by the duplex RNA/ODN. Our data demonstrate that ODN7 inhibits the initiation process, most probably by modifying structural features present at the 3'-end of the minus-strand RNA

Growth of monodisperse nanocrystals of cerium oxide during synthesis and annealing

International Nuclear Information System (INIS)

Ghosh, Swapankumar; Divya, Damodaran; Remani, Kottayilpadi C.; Sreeremya, Thadathil S.

2010-01-01

Monodisperse cerium oxide nanocrystals have been successfully synthesised using simple ammonia precipitation technique from cerium(III) nitrate solution at different temperatures in the range 35-80 o C. The activation energy for growth of CeO 2 nanocrystals during the precipitation is calculated as 11.54 kJ/mol using Arrhenius plot. Average crystal diameter was obtained from XRD analysis, HR-TEM and light scattering (PCS). The analysis of size data from HR-TEM images and PCS clearly indicated the formation of highly crystalline CeO 2 particles in narrow size range. CeO 2 nanocrystals precipitated at 35 o C were further annealed at temperatures in the range 300-700 o C. The activation energy for crystal growth during annealing is also calculated and is close to the reported values. An effort is made to predict the mechanism of crystal growth during the precipitation and annealing.

Radiobiology of DNA strand breakage

International Nuclear Information System (INIS)

Johansen, I.

1975-01-01

The yield of single-strand breaks in lambda DNA within lysogenic host bacteria was measured after exposure to 4-MeV electrons (50 msec) and rapid transfer (45 msec) to alkaline detergent. In nitrogen anoxia the yield was 1.2 x 10 -12 DNA single-strand breaks per rad per dalton, and under full oxygenation the yield increased to 5 x 10 -12 breaks per rad per dalton. A search for the presence of fast repair mechanisms failed to demonstrate the presence of any mechanism for repair of strand breaks operating within a fraction of a second. Strand breaks produced in the presence of oxygen were repaired in 30--40 sec, while breaks produced under anoxia were rejoined even slower. A functional product from the polAl gene was needed for the rejoining of the broken molecules. Intermediate levels of DNA strand breakage seen at low concentrations of oxygen are dependent on the concentration of cellular sulfhydryl compounds, suggesting that in strand breakage oxygen and hydrogen donors compete for reactions with radiation-induced transients in the DNA. Intercomparisons of data on radiation-induced lethality of cells and single-strand breaks in episomal DNA allow the distinction between two classes of radiation-induced radicals, R 1 and R 2 , with different chemical properties; R 1 reacts readily with oxygen and N-oxyls under formation of potentially lethal products. The reactivity of oxygen in this reaction is 30--40 times higher than that of TMPN. R 2 reacts 16 times more readily than R 1 with oxygen under formation of single-strand breaks in the DNA. R 2 does not react with N-oxyls

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.

Growth of monodisperse nanocrystals of cerium oxide during synthesis and annealing

Energy Technology Data Exchange (ETDEWEB)

Ghosh, Swapankumar, E-mail: swapankumar.ghosh2@mail.dcu.ie; Divya, Damodaran [National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR) (India); Remani, Kottayilpadi C. [Sree Neelakanda Government Sanskrit College, Department of Chemistry (India); Sreeremya, Thadathil S. [National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR) (India)

2010-06-15

Monodisperse cerium oxide nanocrystals have been successfully synthesised using simple ammonia precipitation technique from cerium(III) nitrate solution at different temperatures in the range 35-80 {sup o}C. The activation energy for growth of CeO{sub 2} nanocrystals during the precipitation is calculated as 11.54 kJ/mol using Arrhenius plot. Average crystal diameter was obtained from XRD analysis, HR-TEM and light scattering (PCS). The analysis of size data from HR-TEM images and PCS clearly indicated the formation of highly crystalline CeO{sub 2} particles in narrow size range. CeO{sub 2} nanocrystals precipitated at 35 {sup o}C were further annealed at temperatures in the range 300-700 {sup o}C. The activation energy for crystal growth during annealing is also calculated and is close to the reported values. An effort is made to predict the mechanism of crystal growth during the precipitation and annealing.

Annealing Temperature Dependent Structural and Optical Properties of RF Sputtered ZnO Thin Films.

Science.gov (United States)

Sharma, Shashikant; Varma, Tarun; Asokan, K; Periasamy, C; Boolchandani, Dharmendar

2017-01-01

This work investigates the effect of annealing temperature on structural and optical properties of ZnO thin films grown over Si 100 and glass substrates using RF sputtering technique. Annealing temperature has been varied from 300 °C to 600 °C in steps of 100, and different microstructural parameters such as grain size, dislocation density, lattice constant, stress and strain have been evaluated. The structural and surface morphological characterization has been done using X-ray Diffraction (XRD) and Scanning Electron Microscope (SEM). XRD analysis reveals that the peak intensity of 002 crystallographic orientation increases with increased annealing temperature. Optical characterization of deposited films have been done using UV-Vis-NIR spectroscopy and photoluminescence spectrometer. An increase in optical bandgap of deposited ZnO thin films with increasing annealing temperature has been observed. The average optical transmittance was found to be more than 85% for all deposited films. Photoluminiscense spectra (PL) suggest that the crystalline quality of deposited film has increased at higher annealing temperature.

Germanium nanoislands grown by radio frequency magnetron sputtering: Annealing time dependent surface morphology and photoluminescence

International Nuclear Information System (INIS)

Samavati, Alireza; Othaman, Z.; Ghoshal, S. K.; Amjad, R. J.

2013-01-01

Structural and optical properties of ∼ 20 nm Ge nanoislands grown on Si(100) by radio frequency (rf) magnetron sputtering under varying annealing conditions are reported. Rapid thermal annealing at a temperature of 600°C for 30 s, 90 s, and 120 s are performed to examine the influence of annealing time on the surface morphology and photoluminescence properties. X-ray diffraction spectra reveal prominent Ge and GeO 2 peaks highly sensitive to the annealing time. Atomic force microscope micrographs of the as-grown sample show pyramidal nanoislands with relatively high-density 10 11 cm −2) ). The nanoislands become dome-shaped upon annealing through a coarsening process mediated by Oswald ripening. The room temperature photoluminescence peaks for both as-grown 3.29 eV) and annealed 3.19 eV) samples consist of high intensity and broad emission, attributed to the effect of quantum confinement. The red shift (∼0.10 eV) of the emission peak is attributed to the change in the size of the Ge nanoislands caused by annealing. Our easy fabrication method may contribute to the development of Ge nanostructure-based optoelectronics. (interdisciplinary physics and related areas of science and technology)

Annealing temperature dependence of photoluminescent characteristics of silicon nanocrystals embedded in silicon-rich silicon nitride films grown by PECVD

International Nuclear Information System (INIS)

Chao, D.S.; Liang, J.H.

2013-01-01

Recently, light emission from silicon nanostructures has gained great interest due to its promising potential of realizing silicon-based optoelectronic applications. In this study, luminescent silicon nanocrystals (Si–NCs) were in situ synthesized in silicon-rich silicon nitride (SRSN) films grown by plasma-enhanced chemical vapor deposition (PECVD). SRSN films with various excess silicon contents were deposited by adjusting SiH 4 flow rate to 100 and 200 sccm and keeping NH 3 one at 40 sccm, and followed by furnace annealing (FA) treatments at 600, 850 and 1100 °C for 1 h. The effects of excess silicon content and post-annealing temperature on optical properties of Si–NCs were investigated by photoluminescence (PL) and Fourier transform infrared spectroscopy (FTIR). The origins of two groups of PL peaks found in this study can be attributed to defect-related interface states and quantum confinement effects (QCE). Defect-related interface states lead to the photon energy levels almost kept constant at about 3.4 eV, while QCE results in visible and tunable PL emission in the spectral range of yellow and blue light which depends on excess silicon content and post-annealing temperature. In addition, PL intensity was also demonstrated to be highly correlative to the excess silicon content and post-annealing temperature due to its corresponding effects on size, density, crystallinity, and surface passivation of Si–NCs. Considering the trade-off between surface passivation and structural properties of Si–NCs, an optimal post-annealing temperature of 600 °C was suggested to maximize the PL intensity of the SRSN films

Surface Impedance of Copper MOB Depending on the Annealing Temperature and Deformation Degree

International Nuclear Information System (INIS)

Kutovoj, V.A.; Nikolaenko, A.A.; Stoev, P.I.; Vinogradov, D.V.

2006-01-01

Results of researches of influence of annealing temperature and deformation degree on mechanical features of copper MOB are presented. It is shown that minimal surface resistance is observed in copper samples that were subject to pre-deformation and were annealed in the range of temperatures 873...923 K

Post-deposition annealing temperature dependence TiO_2-based EGFET pH sensor sensitivity

International Nuclear Information System (INIS)

Zulkefle, M. A.; Rahman, R. A.; Yusoff, K. A.; Abdullah, W. F. H.; Rusop, M.; Herman, S. H.

2016-01-01

EGFET pH sensor is one type of pH sensor that is used to measure and determine pH of a solution. The sensing membrane of EGFET pH sensor plays vital role in the overall performance of the sensor. This paper studies the effects of different annealing temperature of the TiO_2 sensing membranes towards sensitivity of EGFET pH sensor. Sol-gel spin coating was chosen as TiO_2 deposition techniques since it is cost-effective and produces thin film with uniform thickness. Deposited TiO_2 thin films were then annealed at different annealing temperatures and then were connected to the gate of MOSFET as a part of the EGFET pH sensor structure. The thin films now act as sensing membranes of the EGFET pH sensor and sensitivity of each sensing membrane towards pH was measured. From the results it was determined that sensing membrane annealed at 300 °C gave the highest sensitivity followed by sample annealed at 400 °C and 500 °C.

Resistance and magnetoresistance of annealed amorphous carbon films containing Fe3C nanograins

International Nuclear Information System (INIS)

Lee Yuhua; Han Taichun; Wur, C.-S.

2004-01-01

The temperature-dependent resistance and the field-dependent magnetoresistance were measured for films annealed at temperatures from 250 deg. C to 550 deg. C for a period of 60 min. Results of temperature-dependent resistance show electrical tunneling conductance in the films annealed at T a =250 deg. C and 350 deg. C only. The largest magnetoresistance ratio (MR) of 23% at temperature T=2 K was observed for T a =350 deg. C. The variations of both the temperature dependence of resistance and the magnetoresistance with the annealing temperature are discussed

Purification of Single-Stranded cDNA Based on RNA Degradation Treatment and Adsorption Chromatography.

Science.gov (United States)

Trujillo-Esquivel, Elías; Franco, Bernardo; Flores-Martínez, Alberto; Ponce-Noyola, Patricia; Mora-Montes, Héctor M

2016-08-02

Analysis of gene expression is a common research tool to study networks controlling gene expression, the role of genes with unknown function, and environmentally induced responses of organisms. Most of the analytical tools used to analyze gene expression rely on accurate cDNA synthesis and quantification to obtain reproducible and quantifiable results. Thus far, most commercial kits for isolation and purification of cDNA target double-stranded molecules, which do not accurately represent the abundance of transcripts. In the present report, we provide a simple and fast method to purify single-stranded cDNA, exhibiting high purity and yield. This method is based on the treatment with RNase H and RNase A after cDNA synthesis, followed by separation in silica spin-columns and ethanol precipitation. In addition, our method avoids the use of DNase I to eliminate genomic DNA from RNA preparations, which improves cDNA yield. As a case report, our method proved to be useful in the purification of single-stranded cDNA from the pathogenic fungus Sporothrix schenckii.

Tensile and dimensional properties of wood strands made from plantation southern pine lumber

Science.gov (United States)

Qinglin Wu; Zhiyong Cai; Jong N. Lee

2005-01-01

Working stresses and performance of strand composite lumber largely depend upon the properties of each individual strand. Southern pine strands from plantation lumber grown in southern Louisiana were investigated in this study in order to understand strand behaviors. The effects of hot-pressing and resin application on tensile modulus, strength, and dimensional...

Toscana virus NSs protein promotes degradation of double-stranded RNA-dependent protein kinase.

Science.gov (United States)

Kalveram, Birte; Ikegami, Tetsuro

2013-04-01

Toscana virus (TOSV), which is transmitted by Phlebotomus spp. sandflies, is a major etiologic agent of aseptic meningitis and encephalitis in the Mediterranean. Like other members of the genus Phlebovirus of the family Bunyaviridae, TOSV encodes a nonstructural protein (NSs) in its small RNA segment. Although the NSs of Rift Valley fever virus (RVFV) has been identified as an important virulence factor, which suppresses host general transcription, inhibits transcription from the beta interferon promoter, and promotes the proteasomal degradation of double-stranded RNA-dependent protein kinase (PKR), little is known about the functions of NSs proteins encoded by less-pathogenic members of this genus. In this study we report that TOSV is able to downregulate PKR with similar efficiency as RVFV, while infection with the other phleboviruses-i.e., Punta Toro virus, sandfly fever Sicilian virus, or Frijoles virus-has no effect on cellular PKR levels. In contrast to RVFV, however, cellular transcription remains unaffected during TOSV infection. TOSV NSs protein promotes the proteasome-dependent downregulation of PKR and is able to interact with kinase-inactive PKR in infected cells.

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

International Nuclear Information System (INIS)

Shavitt, O.; Livneh, Z.

1989-01-01

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

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.

Controllably annealed CuO-nanoparticle modified ITO electrodes: Characterisation and electrochemical studies

Energy Technology Data Exchange (ETDEWEB)

Wang, Tong; Su, Wen; Fu, Yingyi [College of Chemistry, Beijing Normal University, Beijing 100875 (China); Hu, Jingbo, E-mail: hujingbo@bnu.edu.cn [College of Chemistry, Beijing Normal University, Beijing 100875 (China); Key Laboratory of Beam Technology and Material Modification of Ministry of Education, Beijing Normal University, Beijing 100875 (China)

2016-12-30

Graphical abstract: We report a simple and controllable synthesis of CuO-nanoparticle-modified ITO by employing a combination of ion-implantation and annealing methods for the first time. The optimum CuO/ITO electrode shows uniform morphology, highly accessible surface area, long-term stability and excellent electrochemical performance towards biomolecules such as glucose in alkaline solution. - Highlights: • Controllably annealed CuO/ITO electrode was synthesized for the first time. • The generation mechanism of CuO nanoparticles is revealed. • The optimum CuO/ITO electrode shows excellent electrochemical performance. • A reference for the controllable preparation of other metal oxide nanoparticles. - Abstract: In this paper, we report a facile and controllable two-step approach to produce indium tin oxide electrodes modified by copper(II) oxide nanoparticles (CuO/ITO) through ion implantation and annealing methods. After annealing treatment, the surface morphology of the CuO/ITO substrate changed remarkably and exhibited highly electroactive sites and a high specific surface area. The effects of annealing treatment on the synthesis of CuO/ITO were discussed based on various instruments’ characterisations, and the possible mechanism by which CuO nanoparticles were generated was also proposed in this work. Cyclic voltammetric results indicated that CuO/ITO electrodes exhibited effective catalytic responses toward glucose in alkaline solution. Under optimal experimental conditions, the proposed CuO/ITO electrode showed sensitivity of 450.2 μA cm{sup −2} mM{sup −1} with a linear range of up to ∼4.4 mM and a detection limit of 0.7 μM (S/N = 3). Moreover, CuO/ITO exhibited good poison resistance, reproducibility, and stability properties.

Genetics of x-ray induced double strand break repair in saccharomyces cerevisiae

International Nuclear Information System (INIS)

Budd, M.E.

1982-07-01

The possible fates of x-ray-induced double-strand breaks in Saccharomyces cerevisiae were examined. One possible pathway which breaks can follow, the repair pathway, was studied by assaying strains with mutations in the RAD51, RAD54, and RAD57 loci for double-strand break repair. In order of increasing radiation sensitivity one finds: rad57-1(23 0 )> rad51-1(30 0 )> rad54-3(36 0 ). At 36 0 , rad54-3 cells cannot repair double-strand breaks, while 23 0 , they can. Strains with the rad57-1 mutation can rejoin broken chromosomes at both temperatures. However, the low survival at 36 0 shows that the assay is not distinguishing large DNA fragments which allow cell survival from those which cause cell death. A rad51-1 strain could also rejoin broken chromosomes, and was thus capable of incomplete repair. The data can be explained with the hypothesis that rad54-3 cells are blocked in an early step of repair, while rad51-1 and rad57-1 strains are blocked in a later step of repair. The fate of double-strand breaks when they are left unrepaired was investigated with the rad54-3 mutation. If breaks are prevented from entering the RAD54 repair pathway they become uncommitted lesions. These lesions are repaired slower than the original breaks. One possible fate for an uncommitted lesion is conversion into a fixed lesion, which is likely to be an unrepairable or misrepaired double-strand break. The presence of protein synthesis after irradiation increases the probability that a break will enter the repair pathway. Evidence shows that increased probability of repair results from enhanced synthesis of repair proteins shortly after radiation

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

Science.gov (United States)

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

2017-01-01

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

Unified model of damage annealing in CMOS, from freeze-in to transient annealing

International Nuclear Information System (INIS)

Sander, H.H.; Gregory, B.L.

Results of an experimental study at 76 0 K, are presented showing that radiation-produced holes in SiO 2 are immobile at this temperature. If an electric field is present in the SiO 2 during low temperature (76 0 K) irradiation to sweep out the mobile electrons, the holes will virtually all be trapped where created and produce a uniform positive charge density in the oxide. These results are the basis for concluding that if a complimentary p,n metal-oxide semiconductor (CMOS) device is irradiated for sufficient time at 76 0 K to build-in an appreciable field, further irradiation with gate bias removed will produce very little additional change in V/sub th/, since the field in the oxide tends to keep all generated electrons in the oxide where they recombine with trapped holes. Hence the hole trapping rate = the hole annihilation rate. The room-temperature annealing following a pulsed gamma exposure occurs in two regimes. The first recovery of V/sub th/ occurs prior to 10 -4 seconds. The magnitude of this very early-time recovery, at room temperature, is oxide-dependent, and oxide process dependent. The rate-of-annealing is what is truly different between a rad-hard and a rad-soft device, since annealing in the hardest devices occurs very quickly at room temperature. (U.S.)

Excitation intensity dependent photoluminescence of annealed two-dimensional MoS_2 grown by chemical vapor deposition

International Nuclear Information System (INIS)

Kaplan, D.; Swaminathan, V.; Mills, K.; Lee, J.; Torrel, S.

2016-01-01

Here, we present detailed results of Raman and photoluminescence (PL) characterization of monolayers of MoS_2 grown by chemical vapor deposition (CVD) on SiO_2/Si substrates after thermal annealing at 150 °C, 200 °C, and 250 °C in an argon atmosphere. In comparison to the as-grown monolayers, annealing in the temperature range of 150–250 °C brings about significant changes in the band edge luminescence. It is observed that annealing at 150 °C gives rise to a 100-fold increase in the PL intensity and produces a strong band at 1.852 eV attributed to a free-to-bound transition that dominates over the band edge excitonic luminescence. This band disappears for the higher annealing temperatures. The improvement in PL after the 200 °C anneal is reduced in comparison to that obtained after the 150 °C anneal; this is suggested to arise from a decrease in the non-radiative lifetime caused by the creation of sulfur di-vacancies. Annealing at 250 °C degrades the PL in comparison to the as-grown sample because of the onset of disorder/decomposition of the sample. It is clear that the PL features of the CVD-grown MoS_2 monolayer are profoundly affected by thermal annealing in Ar atmosphere. However, further detailed studies are needed to identify, unambiguously, the role of native defects and/or adsorbed species in defining the radiative channels in annealed samples so that the beneficial effect of improvement in the optical efficiency of the MoS_2 monolayers can be leveraged for various device applications.

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 ...

Translation elongation factor 1A facilitates the assembly of the tombusvirus replicase and stimulates minus-strand synthesis.

OpenAIRE

Zhenghe Li; Judit Pogany; Steven Tupman; Anthony M Esposito; Terri Goss Kinzy; Peter D Nagy

2010-01-01

Replication of plus-strand RNA viruses depends on host factors that are recruited into viral replicase complexes. Previous studies showed that eukaryotic translation elongation factor (eEF1A) is one of the resident host proteins in the highly purified tombusvirus replicase complex. Using a random library of eEF1A mutants, we identified one mutant that decreased and three mutants that increased Tomato bushy stunt virus (TBSV) replication in a yeast model host. Additional in vitro assays with w...

Improved behavior of cooper-amine complexes during thermal annealing for conductive thin film synthesis

Energy Technology Data Exchange (ETDEWEB)

Ayag, Kevin Ray; Panama, Gustavo; Paul, Shrabani; Kim, Hong Doo [Dept. of Advanced Materials Engineering for Information and Electronics, Kyung Hee University, Yongin (Korea, Republic of)

2017-02-15

Previous studies successfully produced conductive thin films from organo-metallic-compounds-based inks. Some inks like those made from copper salt and amines, however, tend to move during thermal annealing and, thus, affect the conductive pattern on the substrate. In this study, conductive inks were synthesized by forming complexes of copper with amines and/or blended amines. To build-up an organo-metallic framework and preserve the pattern throughout the annealing period, diamine was added to the complex in different proportions. The prepared inks were coated on glass substrate and were annealed on a hot plate at 170°C under the gaseous mixture of formic acid and alcohol for 5 min. The metallic film was observed to retain the original pattern of the ink during and after annealing. Adhesion on the substrate was also improved. Inks with blended amines produced films with lower resistivities. The lowest electrical resistivity recorded was 4.99 μΩ cm, three times that of bulk copper.

Synthesis of borides in molybdenum implanted by B+ ions under thermal and electron annealing

International Nuclear Information System (INIS)

Kazdaev, Kh.R.; Akchulakov, M.T.; Bayadilov, E.M.; Ehngel'ko, V.I.; Lazarenko, A.V.; Chebukov, E.S.

1989-01-01

The possibility of formation of borides in the near surface layers of monocrystalline molybdenum implanted by boron ions at 35 keV energy under thermal and pulsed electron annealing by an electon beam at 140 keV energy is investigated. It is found that implantation of boron ions into molybdenum with subsequent thermal annealing permits to produce both molybdenum monoboride (α-MoB) and boride (γ-Mo 2 B) with rather different formation mechanisms. Formation of the α-MoB phase occurs with the temperature elevation from the centers appeared during implantation, while the γ-Mo 2 B phase appears only on heating the implanted layers up to definite temperature as a result of the phase transformation of the solid solution into a chemical compound. Pulsed electron annealing instead of thermal annealing results mainly in formation of molybdenum boride (γ-Mo 2 B), the state of structure is determined by the degree of heating of implanted layers and their durable stay at temperatures exceeding the threshold values

Principal and secondary luminescence lifetime components in annealed natural quartz

International Nuclear Information System (INIS)

Chithambo, M.L.; Ogundare, F.O.; Feathers, J.

2008-01-01

Time-resolved luminescence spectra from quartz can be separated into components with distinct principal and secondary lifetimes depending on certain combinations of annealing and measurement temperature. The influence of annealing on properties of the lifetimes related to irradiation dose and temperature of measurement has been investigated in sedimentary quartz annealed at various temperatures up to 900 deg. C. Time-resolved luminescence for use in the analysis was pulse stimulated from samples at 470 nm between 20 and 200 deg. C. Luminescence lifetimes decrease with measurement temperature due to increasing thermal effect on the associated luminescence with an activation energy of thermal quenching equal to 0.68±0.01eV for the secondary lifetime but only qualitatively so for the principal lifetime component. Concerning the influence of annealing temperature, luminescence lifetimes measured at 20 deg. C are constant at about 33μs for annealing temperatures up to 600 0 C but decrease to about 29μs when the annealing temperature is increased to 900 deg. C. In addition, it was found that lifetime components in samples annealed at 800 deg. C are independent of radiation dose in the range 85-1340 Gy investigated. The dependence of lifetimes on both the annealing temperature and magnitude of radiation dose is described as being due to the increasing importance of a particular recombination centre in the luminescence emission process as a result of dynamic hole transfer between non-radiative and radiative luminescence centres

Iron phthalocyanine on Cu(111): Coverage-dependent assembly and symmetry breaking, temperature-induced homocoupling, and modification of the adsorbate-surface interaction by annealing.

Science.gov (United States)

Snezhkova, Olesia; Bischoff, Felix; He, Yuanqin; Wiengarten, Alissa; Chaudhary, Shilpi; Johansson, Niclas; Schulte, Karina; Knudsen, Jan; Barth, Johannes V; Seufert, Knud; Auwärter, Willi; Schnadt, Joachim

2016-03-07

We have examined the geometric and electronic structures of iron phthalocyanine assemblies on a Cu(111) surface at different sub- to mono-layer coverages and the changes induced by thermal annealing at temperatures between 250 and 320 °C by scanning tunneling microscopy, x-ray photoelectron spectroscopy, and x-ray absorption spectroscopy. The symmetry breaking observed in scanning tunneling microscopy images is found to be coverage dependent and to persist upon annealing. Further, we find that annealing to temperatures between 300 and 320 °C leads to both desorption of iron phthalocyanine molecules from the surface and their agglomeration. We see clear evidence of temperature-induced homocoupling reactions of the iron phthalocyanine molecules following dehydrogenation of their isoindole rings, similar to what has been observed for related tetrapyrroles on transition metal surfaces. Finally, spectroscopy indicates a modified substrate-adsorbate interaction upon annealing with a shortened bond distance. This finding could potentially explain a changed reactivity of Cu-supported iron phthalocyanine in comparison to that of the pristine compound.

Post-deposition annealing temperature dependence TiO{sub 2}-based EGFET pH sensor sensitivity

Energy Technology Data Exchange (ETDEWEB)

Zulkefle, M. A., E-mail: alhadizulkefle@gmail.com; Rahman, R. A., E-mail: rohanieza.abdrahman@gmail.com; Yusoff, K. A., E-mail: khairul.aimi.yusof@gmail.com [NANO-ElecTronic Centre (NET), Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor (Malaysia); Abdullah, W. F. H., E-mail: wanfaz@salam.uitm.edu.my [Faculty of Electrical Engineering, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor (Malaysia); Rusop, M., E-mail: rusop@salam.uitm.edu.my [NANO-Science Technology (NST), Institute of Science (IOS), Faculty of Applied Sciences, Universiti Teknologi MARA - UiTM, 40450 Shah Alam, Selangor (Malaysia); Herman, S. H., E-mail: hana1617@salam.uitm.edu.my [Core of Frontier Materials & Industry Applications, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor (Malaysia)

2016-07-06

EGFET pH sensor is one type of pH sensor that is used to measure and determine pH of a solution. The sensing membrane of EGFET pH sensor plays vital role in the overall performance of the sensor. This paper studies the effects of different annealing temperature of the TiO{sub 2} sensing membranes towards sensitivity of EGFET pH sensor. Sol-gel spin coating was chosen as TiO{sub 2} deposition techniques since it is cost-effective and produces thin film with uniform thickness. Deposited TiO{sub 2} thin films were then annealed at different annealing temperatures and then were connected to the gate of MOSFET as a part of the EGFET pH sensor structure. The thin films now act as sensing membranes of the EGFET pH sensor and sensitivity of each sensing membrane towards pH was measured. From the results it was determined that sensing membrane annealed at 300 °C gave the highest sensitivity followed by sample annealed at 400 °C and 500 °C.

Dependence of the annealing kinetics of A centers and divacancies on temperature, particle energy, and irradiation dose for n-Si crystals

International Nuclear Information System (INIS)

Pagava, T.A.

2002-01-01

n-Si crystals grown by the float-zone method with a phosphorus concentration of ∼6 x 10 13 cm -3 and irradiated with 2-MeV electrons and 25-MeV protons were studied. It is shown that the kinetics of the isochronous annealing of the A centers and divacancies (the annealing temperature and the rearrangement of radiation defects in the situation where the dissociation of one type of defects gives rise to more stable defects) depends in a complicated way on the energy, dose, and temperature of irradiation; i.e., this kinetics depends on the relation between the concentrations of various radiation defects and on the charge state of reacting primary radiation defects when they interact with each other, with impurity atoms, and with disordered regions. An increase in the concentration of divacancies in the temperature range of 180-210 deg. C is attributed to the dissociation of disordered regions

Resistivity behavior in isothermal annealing of Pd-H(D) alloys around 50 K

International Nuclear Information System (INIS)

Yamakawa, Kohji; Maeta, Hiroshi

2004-01-01

The behavior of electrical resistivity during hydrogen (deuterium) ordering is investigated for Pd-H(D) alloys of various hydrogen concentrations around 50 K. The disordered hydrogen (deuterium) atoms are introduced by quenching from 100 K into liquid helium immediately before isothermal annealings. The disordered atoms order by migration of the atoms during the heating-up of the specimens. On the isothermal curves of the resistivity in the high temperature range, the resistivity increases at first and then adopts a constant value dependent on the annealing temperature. On the other hand, the resistivity increases and then decreases during isothermal annealing in the low temperature range, nevertheless the ordering is progressing. The annealing time, at which the resistivity maximum appears, and the resistivity value of the maximum increase with decreasing annealing temperature. Furthermore, the decreasing resistivity after the maximum saturates to a value dependent on each annealing temperature. Therefore, it becomes clear that an equilibrium amount of ordering depends on the temperature and the resistivity increases in the early stage of hydrogen (deuterium) ordering and decreases in the later stage. The resistivity maximum in the isothermal annealing curve is caused by the nucleation and growth of ordered domains of hydrogen (deuterium) atoms

Characterization of purified Sindbis virus nsP4 RNA-dependent RNA polymerase activity in vitro

International Nuclear Information System (INIS)

Rubach, Jon K.; Wasik, Brian R.; Rupp, Jonathan C.; Kuhn, Richard J.; Hardy, Richard W.; Smith, Janet L.

2009-01-01

The Sindbis virus RNA-dependent RNA polymerase (nsP4) is responsible for the replication of the viral RNA genome. In infected cells, nsP4 is localized in a replication complex along with the other viral non-structural proteins. nsP4 has been difficult to homogenously purify from infected cells due to its interactions with the other replication proteins and the fact that its N-terminal residue, a tyrosine, causes the protein to be rapidly turned over in cells. We report the successful expression and purification of Sindbis nsP4 in a bacterial system, in which nsP4 is expressed as an N-terminal SUMO fusion protein. After purification the SUMO tag is removed, resulting in the isolation of full-length nsP4 possessing the authentic N-terminal tyrosine. This purified enzyme is able to produce minus-strand RNA de novo from plus-strand templates, as well as terminally add adenosine residues to the 3' end of an RNA substrate. In the presence of the partially processed viral replicase polyprotein, P123, purified nsP4 is able to synthesize discrete template length minus-strand RNA products. Mutations in the 3' CSE or poly(A) tail of viral template RNA prevent RNA synthesis by the replicase complex containing purified nsP4, consistent with previously reported template requirements for minus-strand RNA synthesis. Optimal reaction conditions were determined by investigating the effects of time, pH, and the concentrations of nsP4, P123 and magnesium on the synthesis of RNA

Annealing effects on magnetic properties of silicone-coated iron-based soft magnetic composites

International Nuclear Information System (INIS)

Wu Shen; Sun Aizhi; Zhai Fuqiang; Wang Jin; Zhang Qian; Xu Wenhuan; Logan, Philip; Volinsky, Alex A.

2012-01-01

This paper focuses on novel iron-based soft magnetic composites synthesis utilizing high thermal stability silicone resin to coat iron powder. The effect of an annealing treatment on the magnetic properties of synthesized magnets was investigated. The coated silicone insulating layer was characterized by scanning electron microscopy and energy dispersive X-ray spectroscopy. Silicone uniformly coated the powder surface, resulting in a reduction of the imaginary part of the permeability, thereby increasing the electrical resistivity and the operating frequency of the synthesized magnets. The annealing treatment increased the initial permeability, the maximum permeability, and the magnetic induction, and decreased the coercivity. Annealing at 580 °C increased the maximum permeability by 72.5%. The result of annealing at 580 °C shows that the ferromagnetic resonance frequency increased from 2 kHz for conventional epoxy resin coated samples to 80 kHz for the silicone resin insulated composites. - Highlights: ► Silicone uniformly coated the powder, increased the operating frequency of SMCs. ► The annealing treatment increased the DC properties of SMCs. ► Annealing at 580 °C increased the maximum permeability by 72.5%. ► Compared with epoxy coated, the SMCs had higher resistivity annealing at 580 °C.

Annealing effects on magnetic properties of silicone-coated iron-based soft magnetic composites

Science.gov (United States)

Wu, Shen; Sun, Aizhi; Zhai, Fuqiang; Wang, Jin; Zhang, Qian; Xu, Wenhuan; Logan, Philip; Volinsky, Alex A.

2012-03-01

This paper focuses on novel iron-based soft magnetic composites synthesis utilizing high thermal stability silicone resin to coat iron powder. The effect of an annealing treatment on the magnetic properties of synthesized magnets was investigated. The coated silicone insulating layer was characterized by scanning electron microscopy and energy dispersive X-ray spectroscopy. Silicone uniformly coated the powder surface, resulting in a reduction of the imaginary part of the permeability, thereby increasing the electrical resistivity and the operating frequency of the synthesized magnets. The annealing treatment increased the initial permeability, the maximum permeability, and the magnetic induction, and decreased the coercivity. Annealing at 580 °C increased the maximum permeability by 72.5%. The result of annealing at 580 °C shows that the ferromagnetic resonance frequency increased from 2 kHz for conventional epoxy resin coated samples to 80 kHz for the silicone resin insulated composites.

DNA repair synthesis dependent on the uvrA,B gene products

International Nuclear Information System (INIS)

Moses, R.E.; Moody, E.E.M.

1975-01-01

Ultraviolet irradiation of toluene-treated Escherichia coli causes an inhibition of replicative DNA synthesis. This is followed by the appearance of nonconservative DNA repair synthesis which does not require either the polymerase or 5' → 3' exonucleolytic activities of DNA polymerase I. The repair synthesis may be catalyzed by DNA polymerase III activity but does not require a functional DNA polymerase II. The ultraviolet-induced synthesis requires ATP and is dependent on a functional uvrA and uvrB gene product. However, other uvr gene products are not required for the synthesis. The recB function is also not required

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

Science.gov (United States)

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

2017-06-20

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

Late Protein Synthesis-Dependent Phases in CTA Long-Term Memory: BDNF Requirement

Science.gov (United States)

Martínez-Moreno, Araceli; Rodríguez-Durán, Luis F.; Escobar, Martha L.

2011-01-01

It has been proposed that long-term memory (LTM) persistence requires a late protein synthesis-dependent phase, even many hours after memory acquisition. Brain-derived neurotrophic factor (BDNF) is an essential protein synthesis product that has emerged as one of the most potent molecular mediators for long-term synaptic plasticity. Studies in the rat hippocampus have been shown that BDNF is capable to rescue the late-phase of long-term potentiation as well as the hippocampus-related LTM when protein synthesis was inhibited. Our previous studies on the insular cortex (IC), a region of the temporal cortex implicated in the acquisition and storage of conditioned taste aversion (CTA), have demonstrated that intracortical delivery of BDNF reverses the deficit in CTA memory caused by the inhibition of IC protein synthesis due to anisomycin administration during early acquisition. In this work, we first analyze whether CTA memory storage is protein synthesis-dependent in different time windows. We observed that CTA memory become sensible to protein synthesis inhibition 5 and 7 h after acquisition. Then, we explore the effect of BDNF delivery (2 μg/2 μl per side) in the IC during those late protein synthesis-dependent phases. Our results show that BDNF reverses the CTA memory deficit produced by protein synthesis inhibition in both phases. These findings support the notion that recurrent rounds of consolidation-like events take place in the neocortex for maintenance of CTA memory trace and that BDNF is an essential component of these processes. PMID:21960964

Late protein synthesis-dependent phases in CTA long-term memory: BDNF requirement

Directory of Open Access Journals (Sweden)

Araceli eMartínez-Moreno

2011-09-01

Full Text Available It has been proposed that long-term memory persistence requires a late protein synthesis-dependent phase, even many hours after memory acquisition. Brain-derived neurotrophic factor (BDNF is an essential protein synthesis product that has emerged as one of the most potent molecular mediators for long-term synaptic plasticity. Studies in the rat hippocampus have been shown that BDNF is capable to rescue the late-phase of long-term potentiation as well as the hippocampus-related long-term memory when protein synthesis was inhibited. Our previous studies on the insular cortex (IC, a region of the temporal cortex implicated in the acquisition and storage of conditioned taste aversion (CTA, have demonstrated that intracortical delivery of BDNF reverses the deficit in CTA memory caused by the inhibition of IC protein synthesis due to anisomycin administration during early acquisition. In this work, we first analyze whether CTA memory storage is protein synthesis dependent in different time-windows. We observed that CTA memory become sensible to protein synthesis inhibition 5 and 7 hours after acquisition. Then, we explore the effect of BDNF delivery (2 μg/2 μl per side in the IC during those late protein synthesis-dependent phases. Our results show that BDNF reverses the CTA memory deficit produced by protein synthesis inhibition in both phases. These findings support the notion that recurrent rounds of consolidation-like events take place in the neocortex for maintenance of CTA memory trace and that BDNF is an essential component of these processes.

Late Protein Synthesis-Dependent Phases in CTA Long-Term Memory: BDNF Requirement.

Science.gov (United States)

Martínez-Moreno, Araceli; Rodríguez-Durán, Luis F; Escobar, Martha L

2011-01-01

It has been proposed that long-term memory (LTM) persistence requires a late protein synthesis-dependent phase, even many hours after memory acquisition. Brain-derived neurotrophic factor (BDNF) is an essential protein synthesis product that has emerged as one of the most potent molecular mediators for long-term synaptic plasticity. Studies in the rat hippocampus have been shown that BDNF is capable to rescue the late-phase of long-term potentiation as well as the hippocampus-related LTM when protein synthesis was inhibited. Our previous studies on the insular cortex (IC), a region of the temporal cortex implicated in the acquisition and storage of conditioned taste aversion (CTA), have demonstrated that intracortical delivery of BDNF reverses the deficit in CTA memory caused by the inhibition of IC protein synthesis due to anisomycin administration during early acquisition. In this work, we first analyze whether CTA memory storage is protein synthesis-dependent in different time windows. We observed that CTA memory become sensible to protein synthesis inhibition 5 and 7 h after acquisition. Then, we explore the effect of BDNF delivery (2 μg/2 μl per side) in the IC during those late protein synthesis-dependent phases. Our results show that BDNF reverses the CTA memory deficit produced by protein synthesis inhibition in both phases. These findings support the notion that recurrent rounds of consolidation-like events take place in the neocortex for maintenance of CTA memory trace and that BDNF is an essential component of these processes.

Annealing dependent evolution of columnar nanostructures in RF magnetron sputtered PTFE films for hydrophobic applications

Science.gov (United States)

Tripathi, S.; De, Rajnarayan; Maidul Haque, S.; Divakar Rao, K.; Misal, J. S.; Prathap, C.; Das, S. C.; Patidar, Manju M.; Ganesan, V.; Sahoo, N. K.

2018-01-01

Present communication focuses on a relatively less explored direction of producing rough polytetrafluoroethylene (PTFE) surfaces for possible hydrophobic applications. The experiments were carried out to make rough PTFE films without losing much of the transmission, which is an important factor while designing futuristic solar cell protection covers. After annealing temperature optimization, as grown RF magnetron sputtered PTFE films (prepared at 160 W RF power) were subjected to vacuum annealing at 200 °C for different time durations ranging from 1 to 4 h. The films show morphological evolution exhibiting formation and growth of columnar nanostructures that are responsible for roughening of the films due to annealing induced molecular migration and rearrangement. In agreement with this, qualitative analysis of corresponding x-ray reflectivity data shows modification in film thickness, which may again be attributed to the growth of columns at the expense of the atoms of remaining film molecules. However, the observations reveal that the film annealed at 200 °C for 2 h gives a combination of patterned columnar structures and reasonable transmission of >85% (in 500-1000 nm wavelength range), both of which are deteriorated when the films are annealed either at high temperature beyond 200 °C or for long durations >3 h. In addition, attenuated total reflection-Fourier transform infrared spectroscopy results reveal that the molecular bonds remain intact upon annealing at any temperature within the studied range indicating the stable nature of the films.

Synthesis and characterization of iron cobalt (FECO) nanorods ...

African Journals Online (AJOL)

Synthesis and characterization of iron cobalt (FECO) nanorods prepared by simple ... shaped by increasing annealing temperature from room temperature to 800 ... Keywords: FeCo nanoparticles, sodium borohydrid, CTAB, chemical synthesis ...

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

Science.gov (United States)

Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

2013-12-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

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)

Effects of Thermal Annealing Conditions on Cupric Oxide Thin Film

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyo Seon; Oh, Hee-bong; Ryu, Hyukhyun [Inje University, Gimhae (Korea, Republic of); Lee, Won-Jae [Dong-Eui University, Busan (Korea, Republic of)

2015-07-15

In this study, cupric oxide (CuO) thin films were grown on fluorine doped tin oxide(FTO) substrate by using spin coating method. We investigated the effects of thermal annealing temperature and thermal annealing duration on the morphological, structural, optical and photoelectrochemical properties of the CuO film. From the results, we could find that the morphologies, grain sizes, crystallinity and photoelectrochemical properties were dependent on the annealing conditions. As a result, the maximum photocurrent density of -1.47 mA/cm{sup 2} (vs. SCE) was obtained from the sample with the thermal annealing conditions of 500 ℃ and 40 min.

Effects of DNA double-strand and single-strand breaks on intrachromosomal recombination events in cell-cycle-arrested yeast cells

International Nuclear Information System (INIS)

Galli, A.; Schiestl, R.H.

1998-01-01

Intrachromosomal recombination between repeated elements can result in deletion (DEL recombination) events. We investigated the inducibility of such intrachromosomal recombination events at different stages of the cell cycle and the nature of the primary DNA lesions capable of initiating these events. Two genetic systems were constructed in Saccharomyces cerevisiae that select for DEL recombination events between duplicated alleles of CDC28 and TUB2. We determined effects of double-strand breaks (DSBs) and single-strand breaks (SSBs) between the duplicated alleles on DEL recombination when induced in dividing cells or cells arrested in G1 or G2. Site-specific DSBs and SSBs were produced by overexpression of the I-Sce I endonuclease and the gene II protein (gIIp), respectively. I-Sce I-induced DSBs caused an increase in DEL recombination frequencies in both dividing and cell-cycle-arrested cells, indicating that G1- and G2-arrested cells are capable of completing DSB repair. In contrast, gIIp-induced SSBs caused an increase in DEL recombination frequency only in dividing cells. To further examine these phenomena we used both γ-irradiation, inducing DSBs as its most relevant lesion, and UV, inducing other forms of DNA damage. UV irradiation did not increase DEL recombination frequencies in G1 or G2, whereas γ-rays increased DEL recombination frequencies in both phases. Both forms of radiation, however, induced DEL recombination in dividing cells. The results suggest that DSBsbut not SSBs induce DEL recombination, probably via the single-strand annealing pathway. Further, DSBs in dividing cells may result from the replication of a UV or SSB-damaged template. Alternatively, UV induced events may occur by replication slippage after DNA polymerase pausing in front of the damage. (author)

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

Science.gov (United States)

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

2015-11-19

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

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.

Electrochemical synthesis of self-organized TiO2 crystalline nanotubes without annealing

Science.gov (United States)

Giorgi, Leonardo; Dikonimos, Theodoros; Giorgi, Rossella; Buonocore, Francesco; Faggio, Giuliana; Messina, Giacomo; Lisi, Nicola

2018-03-01

This work demonstrates that upon anodic polarization in an aqueous fluoride-containing electrolyte, TiO2 nanotube array films can be formed with a well-defined crystalline phase, rather than an amorphous one. The crystalline phase was obtained avoiding any high temperature annealing. We studied the formation of nanotubes in an HF/H2O medium and the development of crystalline grains on the nanotube wall, and we found a facile way to achieve crystalline TiO2 nanotube arrays through a one-step anodization. The crystallinity of the film was influenced by the synthesis parameters, and the optimization of the electrolyte composition and anodization conditions (applied voltage and time) were carried out. For comparison purposes, crystalline anatase TiO2 nanotubes were also prepared by thermal treatment of amorphous nanotubes grown in an organic bath (ethylene glycol/NH4F/H2O). The morphology and the crystallinity of the nanotubes were studied by field emission gun-scanning electron microscopy (FEG-SEM) and Raman spectroscopy, whereas the electrochemical and semiconducting properties were analyzed by means of linear sweep voltammetry, impedance spectroscopy, and Mott-Schottky plots. X-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS) allowed us to determine the surface composition and the electronic structure of the samples and to correlate them with the electrochemical data. The optimal conditions to achieve a crystalline phase with high donor concentration are defined.

Magnetization and loss measurements on Nb3Sn and NbTi strands for ITER and LHC

International Nuclear Information System (INIS)

Foitl, M.

2001-05-01

this work, magnetization and loss measurements on 20 different strand samples which were taken from different billets supplied by two manufacturers of NbTi strands are reported, which with the use of an Integrating Coil Magnetometer as well as micro Hall sensors magnetization loops of single strands were studied. Variations in the strand magnetization could be either correlated with systematical irregularities in the strand characteristics (e.g. filament diameter) or with variations of the strand's critical current density jC. The second part of this work is related to the annealing process of superconducting magnets manufactured from internal tin Nb3Sn strands to be used for the magnetic confinement of fusion plasma. After the successful generation of plasma burning pulses of several seconds duration (Joint European Torus, JET), magnetic fusion energy research has reached a point where a tokamak burning plasma facility, in which the thermonuclear heating balances transport and radiation losses for periods of 500 s or longer, can be seriously contemplated as a next step. Achieving this goal would be a major step forward, both in science and technology, towards the ultimate goal of magnetic fusion generation of electrical power. Therefore the main objectives of the International Thermonuclear Experimental Reactor (ITER) will be the demonstration of the scientific and technological feasibility of fusion energy on a scale close to that of an eventual thermonuclear power reactor. The magnitude of the magnetic field (∼ 11.8 T) needed to confine stable a plasma of sufficient pressure to generate ∼ 0.5 GW of fusion power is comparable to the limiting magnetic fields that a toroidal superconducting magnet system can produce. In order to achieve the best magnet performance possible, the toroidal field (TF) coils made of superconducting Nb3Sn cable-in-conduit type conductors have to be optimized with respect to the maximum transport current and transient field losses

MgO magnetic tunnel junctions of enduring F-type upon annealing

International Nuclear Information System (INIS)

Schleicher, F; Halisdemir, U; Urbain, E; Gallart, M; Boukari, S; Beaurepaire, E; Gilliot, P; Bowen, M; Lacour, D; Montaigne, F; Hehn, M

2015-01-01

The authors performed magnetotransport experiments to determine whether annealing alters the oxygen vacancy-mediated tunnelling potential landscape of the central portion of a MgO ultrathin film within sputtered CoFeB/MgO/CoFeB magnetic tunnel junctions. Using the Î rel method reveals a temperature-dependent tunnelling barrier height for a non-annealed barrier that arises from single oxygen vacancies (F centres) and is qualitatively identical to that found for its partly and fully annealed counterparts. Thus these MTJs with F centres remain of F-type upon annealing. This explicitly confirms that the large tunnel-magnetoresistance (TMR) increase upon annealing results mainly from structural modifications of MgO and CoFeB and not from vacancy pairing within the barrier. Photoluminescence spectra performed on both annealed and non-annealed thin MgO films grown on CoFeB electrodes support this conclusion. This work should promote renewed scrutiny over the precise impact of annealing on tunnelling magnetotransport across MgO. (paper)

Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication.

Science.gov (United States)

Feng, Wenyi; Collingwood, David; Boeck, Max E; Fox, Lindsay A; Alvino, Gina M; Fangman, Walton L; Raghuraman, Mosur K; Brewer, Bonita J

2006-02-01

During DNA replication one or both strands transiently become single stranded: first at the sites where initiation of DNA synthesis occurs (known as origins of replication) and subsequently on the lagging strands of replication forks as discontinuous Okazaki fragments are generated. We report a genome-wide analysis of single-stranded DNA (ssDNA) formation in the presence of hydroxyurea during DNA replication in wild-type and checkpoint-deficient rad53 Saccharomyces cerevisiae cells. In wild-type cells, ssDNA was first observed at a subset of replication origins and later 'migrated' bi-directionally, suggesting that ssDNA formation is associated with continuously moving replication forks. In rad53 cells, ssDNA was observed at virtually every known origin, but remained there over time, suggesting that replication forks stall. Telomeric regions seemed to be particularly sensitive to the loss of Rad53 checkpoint function. Replication origins in Schizosaccharomyces pombe were also mapped using our method.

Excitation intensity dependent photoluminescence of annealed two-dimensional MoS{sub 2} grown by chemical vapor deposition

Energy Technology Data Exchange (ETDEWEB)

Kaplan, D.; Swaminathan, V. [U.S. Army RDECOM-ARDEC, Fuze Precision Armaments and Technology Directorate, Picatinny Arsenal, New Jersey 07806 (United States); Mills, K. [U.S. Army RDECOM-ARDEC, Energetics, Warheads and Manufacturing Technology Directorate, Picatinny Arsenal, New Jersey 07806 (United States); Lee, J. [Agency for Defense Development, Yuseong, P.O. Box 35, Daejeon, 305-600 (Korea, Republic of); Torrel, S. [Department of Materials Science and Engineering, Piscataway, Rutgers, The State University of New Jersey, New Jersey 08854 (United States)

2016-06-07

Here, we present detailed results of Raman and photoluminescence (PL) characterization of monolayers of MoS{sub 2} grown by chemical vapor deposition (CVD) on SiO{sub 2}/Si substrates after thermal annealing at 150 °C, 200 °C, and 250 °C in an argon atmosphere. In comparison to the as-grown monolayers, annealing in the temperature range of 150–250 °C brings about significant changes in the band edge luminescence. It is observed that annealing at 150 °C gives rise to a 100-fold increase in the PL intensity and produces a strong band at 1.852 eV attributed to a free-to-bound transition that dominates over the band edge excitonic luminescence. This band disappears for the higher annealing temperatures. The improvement in PL after the 200 °C anneal is reduced in comparison to that obtained after the 150 °C anneal; this is suggested to arise from a decrease in the non-radiative lifetime caused by the creation of sulfur di-vacancies. Annealing at 250 °C degrades the PL in comparison to the as-grown sample because of the onset of disorder/decomposition of the sample. It is clear that the PL features of the CVD-grown MoS{sub 2} monolayer are profoundly affected by thermal annealing in Ar atmosphere. However, further detailed studies are needed to identify, unambiguously, the role of native defects and/or adsorbed species in defining the radiative channels in annealed samples so that the beneficial effect of improvement in the optical efficiency of the MoS{sub 2} monolayers can be leveraged for various device applications.

Application of annealing for extension of WWER vessel lives

International Nuclear Information System (INIS)

Badanin, V.; Dragunow, Yu.G.; Fedorov, V.; Gorynin, I.; Nickolaev, V.

1992-01-01

The safe operation of nuclear power plants (NPP) is dependent upon the assurance that the reactor pressure vessel will not fail in a brittle manner when the effects of radiation embrittlement are taken into account. The recovery of the properties of the irradiated materials is an important way of extending the operating life of a reactor vessel. The intent of this paper is to demonstrate the efficiency of thermal annealing for the recovery of reactor vessel material properties and to present the implications for extended service life. In order to substantiate the application of annealing to the extensior of the service life of vessels, detailed investigations were conducted which involved thermal annealing temperature and time, fast neutron fluence, and metallurgical factors (i.e. impurity contents) on the recovery of properties after the annealing of irradiated materials. Similar studies were continued to determine predictive methods for radiation embrittlement after repeated annealings. In May 1987 the first pilot annealing of a commercial reactor vessel (Novo-Voronezhskaya, III, NPP) was performed. The development of the annealing equipment and investigations performed to test the annealing process proved successful, and an improved safe operation for the reactor vessel was thus atttained providing for an extended service life. (orig.)

Isothermal annealing of silicon implanted with 50 keV 10B ions

International Nuclear Information System (INIS)

Weidner, B.; Zaschke, G.

1974-01-01

Isothermal annealing characteristics of silicon implanted with boron were measured and compared with calculated results. Implantation was performed with 50 keV 10 B ions in the dose range of 7.5 x 10 12 cm -2 to 2.0 x 10 15 cm -2 . Annealing temperatures ranged from 700 to 900 0 C. Maximum annealing time was 10 4 minutes. Annealing time strongly increases with increasing dose and decreasing temperature. Assuming that there is only one activation energy the isothermal annealing curves of constant dose and different temperatures were combined to a reduced annealing curve and the reduced isothermal annealing curve calculated. Starting from first order kinetics, considering the doping profile of boron in silicon and assuming a depth-dependent decay constant the experimentally determined annealing curves could be easily described over the total dose and time range

Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription

NARCIS (Netherlands)

Berkhout, B.; Vastenhouw, N. L.; Klasens, B. I.; Huthoff, H.

2001-01-01

Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer is facilitated by terminal repeat (R) elements in the viral genome. This strand-transfer reaction depends on base pairing between the cDNA of the 5'R and the 3'R. There

Strain relaxation near high-k/Si interface by post-deposition annealing

International Nuclear Information System (INIS)

Emoto, T.; Akimoto, K.; Yoshida, Y.; Ichimiya, A.; Nabatame, T.; Toriumi, A.

2005-01-01

We studied the effect of post-deposition annealing on a HfO 2 /Si interface of by extremely asymmetric X-ray diffraction. Comparing the rocking curves before annealing the sample with those of the annealed sample, it is found that an interfacial layer with a density of 3 g/cm 3 grows at the interface between the HfO 2 layer and the substrate during post-deposition annealing. The wavelength dependency of the integrated intensities of the rocking curve for the as-deposited sample fluctuated with the observation position. This fluctuation was suppressed by annealing. From these results we concluded that the strain introduced into the substrate becomes homogeneous by annealing. Moreover, a quantitative estimation of the strain by curve fitting reveals the existence of compressive strain under the HfO 2 layer

The Effect of Basepair Mismatch on DNA Strand Displacement

OpenAIRE

Broadwater, D.?W.?Bo; Kim, Harold?D.

2016-01-01

DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single base pair mismatch. The apparent displacement rate varied si...

The effects of incomplete annealing on the temperature dependence of sheet resistance and gage factor in aluminum and phosphorus implanted silicon on sapphire

Science.gov (United States)

Pisciotta, B. P.; Gross, C.

1976-01-01

Partial annealing of damage to the crystal lattice during ion implantation reduces the temperature coefficient of resistivity of ion-implanted silicon, while facilitating controlled doping. Reliance on this method for temperature compensation of the resistivity and strain-gage factor is discussed. Implantation conditions and annealing conditions are detailed. The gage factor and its temperature variation are not drastically affected by crystal damage for some crystal orientations. A model is proposed to account for the effects of electron damage on the temperature dependence of resistivity and on silicon piezoresistance. The results are applicable to the design of silicon-on-sapphire strain gages with high gage factors.

Long lasting protein synthesis- and activity-dependent spine shrinkage and elimination after synaptic depression.

Directory of Open Access Journals (Sweden)

Yazmín Ramiro-Cortés

Full Text Available Neuronal circuits modify their response to synaptic inputs in an experience-dependent fashion. Increases in synaptic weights are accompanied by structural modifications, and activity dependent, long lasting growth of dendritic spines requires new protein synthesis. When multiple spines are potentiated within a dendritic domain, they show dynamic structural plasticity changes, indicating that spines can undergo bidirectional physical modifications. However, it is unclear whether protein synthesis dependent synaptic depression leads to long lasting structural changes. Here, we investigate the structural correlates of protein synthesis dependent long-term depression (LTD mediated by metabotropic glutamate receptors (mGluRs through two-photon imaging of dendritic spines on hippocampal pyramidal neurons. We find that induction of mGluR-LTD leads to robust and long lasting spine shrinkage and elimination that lasts for up to 24 hours. These effects depend on signaling through group I mGluRs, require protein synthesis, and activity. These data reveal a mechanism for long lasting remodeling of synaptic inputs, and offer potential insights into mental retardation.

Enhancement of RNA synthesis by promoter duplication in tombusviruses

International Nuclear Information System (INIS)

Panavas, T.; Panaviene, Z.; Pogany, J.; Nagy, P.D.

2003-01-01

Replication of tombusviruses, small plus-strand RNA viruses of plants, is regulated by cis-acting elements present in the viral RNA. The role of cis-acting elements can be studied in vitro by using a partially purified RNA-dependent RNA polymerase (RdRp) preparation obtained from tombusvirus-infected plants , Virology 276, 279- 288). Here, we demonstrate that the minus-strand RNA of tombusviruses contains, in addition to the 3'-terminal minimal plus-strand initiation promoter, a second cis-acting element, termed the promoter proximal enhancer (PPE). The PPE element enhanced RNA synthesis by almost threefold from the adjacent minimal promoter in the in vitro assay. The sequence of the PPE element is 70% similar to the minimal promoter, suggesting that sequence duplication of the minimal promoter may have been the mechanism leading to the generation of the PPE. Consistent with this proposal, replacement of the PPE element with the minimal promoter, which resulted in a perfectly duplicated promoter region, preserved its enhancer-like function. In contrast, mutagenesis of the PPE element or its replacement with an artificial G/C-rich sequence abolished its stimulative effect on initiation of RNA synthesis in vitro. In vivo experiments are also consistent with the role of the PPE element in enhancement of tombusvirus replication. Sequence comparison of several tombusviruses and related carmoviruses further supports the finding that duplication of minimal promoter sequences may have been an important mechanism during the evolution of cis-acting elements in tombusviruses and related RNA viruses

Effects of carcinogen treatment on rat liver DNA synthesis in vivo and on nascent DNA synthesis and elongation in cultured hepatocytes

International Nuclear Information System (INIS)

Zurlo, J.; Mignano, J.E.; Eustice, D.C.; Poirier, M.C.; Yager, J.D.

1986-01-01

One objective of this study was to determine the effects of N-hydroxy-2-acetylaminofluorene (N-OH-AAF) treatment on DNA synthesis in regenerating rat liver. It was found that N-OH-AAF caused a dose-dependent inhibition of [ 3 H]thymidine incorporation into liver DNA. This inhibition was followed by a gradual, but incomplete recovery. The second objective of the study was to determine the effects of DNA damage on the size distribution and elongation of nascent hepatocyte DNA. Hepatocytes, which have been shown to demonstrate a pattern of inhibition and subsequent recovery of DNA synthesis following UV irradiation similar to that seen in vivo upon treatment with N-OH-AAF were cultured. The size distribution of nascent DNA after UV irradiation was determined by pH step gradient alkaline elution analysis. The results show that UV irradiation caused a dose-dependent decrease in the size distribution of nascent DNA suggesting an inhibition of elongation. The results show that resumption of DNA synthesis and nascent strand elongation occur on damaged templates. These observations along with previous studies support the idea that DNA damage leading to inhibition of DNA synthesis may induce SOS-type processes which if mutagenic may play a role in the initiation of carcinogenesis. (Auth.)

NSs protein of rift valley fever virus induces the specific degradation of the double-stranded RNA-dependent protein kinase.

Science.gov (United States)

Habjan, Matthias; Pichlmair, Andreas; Elliott, Richard M; Overby, Anna K; Glatter, Timo; Gstaiger, Matthias; Superti-Furga, Giulio; Unger, Hermann; Weber, Friedemann

2009-05-01

Rift Valley fever virus (RVFV) continues to cause large outbreaks of acute febrile and often fatal illness among humans and domesticated animals in Africa, Saudi Arabia, and Yemen. The high pathogenicity of this bunyavirus is mainly due to the viral protein NSs, which was shown to prevent transcriptional induction of the antivirally active type I interferons (alpha/beta interferon [IFN-alpha/beta]). Viruses lacking the NSs gene induce synthesis of IFNs and are therefore attenuated, whereas the noninducing wild-type RVFV strains can only be inhibited by pretreatment with IFN. We demonstrate here in vitro and in vivo that a substantial part of the antiviral activity of IFN against RVFV is due to a double-stranded RNA-dependent protein kinase (PKR). PKR-mediated virus inhibition, however, was much more pronounced for the strain Clone 13 with NSs deleted than for the NSs-expressing strain ZH548. In vivo, Clone 13 was nonpathogenic for wild-type (wt) mice but could regain pathogenicity if mice lacked the PKR gene. ZH548, in contrast, killed both wt and PKR knockout mice indiscriminately. ZH548 was largely resistant to the antiviral properties of PKR because RVFV NSs triggered the specific degradation of PKR via the proteasome. The NSs proteins of the related but less virulent sandfly fever Sicilian virus and La Crosse virus, in contrast, had no such anti-PKR activity despite being efficient suppressors of IFN induction. Our data suggest that RVFV NSs has gained an additional anti-IFN function that may explain the extraordinary pathogenicity of this virus.

Influence of multi-deposition multi-annealing on time-dependent dielectric breakdown characteristics of PMOS with high-k/metal gate last process

International Nuclear Information System (INIS)

Wang Yan-Rong; Yang Hong; Xu Hao; Wang Xiao-Lei; Luo Wei-Chun; Qi Lu-Wei; Zhang Shu-Xiang; Wang Wen-Wu; Yan Jiang; Zhu Hui-Long; Zhao Chao; Chen Da-Peng; Ye Tian-Chun

2015-01-01

A multi-deposition multi-annealing technique (MDMA) is introduced into the process of high-k/metal gate MOSFET for the gate last process to effectively reduce the gate leakage and improve the device’s performance. In this paper, we systematically investigate the electrical parameters and the time-dependent dielectric breakdown (TDDB) characteristics of positive channel metal oxide semiconductor (PMOS) under different MDMA process conditions, including the deposition/annealing (D and A) cycles, the D and A time, and the total annealing time. The results show that the increases of the number of D and A cycles (from 1 to 2) and D and A time (from 15 s to 30 s) can contribute to the results that the gate leakage current decreases by about one order of magnitude and that the time to fail (TTF) at 63.2% increases by about several times. However, too many D and A cycles (such as 4 cycles) make the equivalent oxide thickness (EOT) increase by about 1 Å and the TTF of PMOS worsen. Moreover, different D and A times and numbers of D and A cycles induce different breakdown mechanisms. (paper)

Effect of annealing on the mechanical and scratch properties of BCN films obtained by magnetron sputtering deposition

Energy Technology Data Exchange (ETDEWEB)

Xu, Shuyan, E-mail: xsynefu@126.com [Key Laboratory of Forest Sustainable Management and Environmental Microorganism Engineering of Heilongjiang Province, Northeast Forestry University, Harbin 150040 (China); Ma, Xinxin [School of Material Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Wen, Huiying [Key Laboratory of Forest Sustainable Management and Environmental Microorganism Engineering of Heilongjiang Province, Northeast Forestry University, Harbin 150040 (China); Tang, Guangze [School of Material Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Li, Chunwei [Key Laboratory of Forest Sustainable Management and Environmental Microorganism Engineering of Heilongjiang Province, Northeast Forestry University, Harbin 150040 (China)

2014-09-15

Highlights: • The amorphous BCN films were annealed at different temperatures under vacuum condition. • The order degree increases with the annealing temperature increasing, and the films do not decompose even the annealing temperature rise to 1000 °C. • The nano-hardness and modulus of the films decrease with the increasing of annealing temperatures. • The critical load of BCN films is not affected by the annealing temperature, and the films have good interfacial adhesion. • The scratch resistance properties of BCN film are improved by annealing at 600 °C. - Abstract: Boron-carbon-nitride (BCN) films have been fabricated by direct current unbalanced magnetron sputtering. Boron carbide/graphite compound and a mixture of nitrogen and argon are used as target and carrier gas, respectively, during BCN synthesis. The obtained BCN films are annealed at different temperatures under vacuum condition. The effect of annealing temperature on the structure, mechanical properties and scratch behavior of the BCN films has been investigated. The results indicate that no decomposition products are found even the BCN films are annealed at 1000 °C. The hardness and elastic modulus of the films decrease with the increase of annealing temperatures. The BCN film annealed at 600 °C has the strongest scratch resistance. The friction coefficient of all BCN films is in range of 0.05 to 0.15.

Effect of annealing on the mechanical and scratch properties of BCN films obtained by magnetron sputtering deposition

International Nuclear Information System (INIS)

Xu, Shuyan; Ma, Xinxin; Wen, Huiying; Tang, Guangze; Li, Chunwei

2014-01-01

Highlights: • The amorphous BCN films were annealed at different temperatures under vacuum condition. • The order degree increases with the annealing temperature increasing, and the films do not decompose even the annealing temperature rise to 1000 °C. • The nano-hardness and modulus of the films decrease with the increasing of annealing temperatures. • The critical load of BCN films is not affected by the annealing temperature, and the films have good interfacial adhesion. • The scratch resistance properties of BCN film are improved by annealing at 600 °C. - Abstract: Boron-carbon-nitride (BCN) films have been fabricated by direct current unbalanced magnetron sputtering. Boron carbide/graphite compound and a mixture of nitrogen and argon are used as target and carrier gas, respectively, during BCN synthesis. The obtained BCN films are annealed at different temperatures under vacuum condition. The effect of annealing temperature on the structure, mechanical properties and scratch behavior of the BCN films has been investigated. The results indicate that no decomposition products are found even the BCN films are annealed at 1000 °C. The hardness and elastic modulus of the films decrease with the increase of annealing temperatures. The BCN film annealed at 600 °C has the strongest scratch resistance. The friction coefficient of all BCN films is in range of 0.05 to 0.15

Dependency of annealing behaviour on grain size in Al–TiC ...

Indian Academy of Sciences (India)

This work investigates the effect of grain size on annealing behaviour in both coarse-grained and ultrafinegrained Al–TiC composite processed by accumulative roll bonding (ARB). Microstructural analysis indicates that annealingbehaviour of the specimens are essentially determined by the level of strain accumulation or ...

Rapid thermal pulse annealing

International Nuclear Information System (INIS)

Miller, M.G.; Koehn, B.W.; Chaplin, R.L.

1976-01-01

Characteristics of recovery processes have been investigated for cases of heating a sample to successively higher temperatures by means of isochronal annealing or by using a rapid pulse annealing. A recovery spectra shows the same features independent of which annealing procedure is used. In order to determine which technique provides the best resolution, a study was made of how two independent first-order processes are separated for different heating rates and time increments of the annealing pulses. It is shown that the pulse anneal method offers definite advantages over isochronal annealing when annealing for short time increments. Experimental data by means of the pulse anneal techniques are given for the various substages of stage I of aluminium. (author)

Chromatin- and temperature-dependent modulation of radiation-induced double-strand breaks.

Science.gov (United States)

Elmroth, K; Nygren, J; Stenerlöw, B; Hultborn, R

2003-10-01

To investigate the influence of chromatin organization and scavenging capacity in relation to irradiation temperature on the induction of double-strand breaks (DSB) in structures derived from human diploid fibroblasts. Agarose plugs with different chromatin structures (intact cells+/-wortmannin, permeabilized cells with condensed chromatin, nucleoids and DNA) were prepared and irradiated with X-rays at 2 or 37 degrees C and lysed using two different lysis protocols (new ice-cold lysis or standard lysis at 37 degrees C). Induction of DSB was determined by constant-field gel electrophoresis. The dose-modifying factor (DMF(temp)) for irradiation at 37 compared with 2 degrees C was 0.92 in intact cells (i.e. more DSB induced at 2 degrees C), but gradually increased to 1.5 in permeabilized cells, 2.2 in nucleoids and 2.6 in naked DNA, suggesting a role of chromatin organization for temperature modulation of DNA damage. In addition, DMF(temp) was influenced by the presence of 0.1 M DMSO or 30 mM glutathione, but not by post-irradiation temperature. The protective effect of low temperature was correlated to the indirect effects of ionizing radiation and was not dependent on post-irradiation temperature. Reasons for a dose modifying factor <1 in intact cells are discussed.

Large area synthesis, characterization, and anisotropic etching of two dimensional tungsten disulfide films

International Nuclear Information System (INIS)

Mutlu, Zafer; Ozkan, Mihrimah; Ozkan, Cengiz S.

2016-01-01

Emergent properties of tungsten disulfide at the quantum confinement limit hold promise for electronic and optoelectronic applications. Here we report on the large area synthesis of atomically thin tungsten disulfide films with strong photoluminescence properties via sulfurization of the pre-deposited tungsten films. Detailed characterization of the pre-deposited tungsten films and tungsten disulfide films are performed using microscopy and spectroscopy methods. By directly heating tungsten disulfide films in air, we have shown that the films tend to be etched into a series of triangular shaped pits with the same orientations, revealing the anisotropic etching behavior of tungsten disulfide edges. Moreover, the dimensions of the triangular pits increase with the number of layers, suggesting a thickness dependent behavior of etching in tungsten disulfide films. This method offers a promising new avenue for engineering the edge structures of tungsten disulfide films. - Highlights: • Large-scale synthesis of WS_2 films is achieved via sulfurization of W films. • Annealing of W films leads to a substantial improvement in the quality of WS_2 films. • WS_2 films show laser power dependent photoluminescence characteristics. • WS_2 films are etched with well-oriented triangular pits upon annealing in air. • Anisotropic oxidative etching is greatly affected by the thickness of WS_2 films.

Simple Laboratory methods to measure cell proliferation using DNA synthesis property

Directory of Open Access Journals (Sweden)

Madhavan H N

2007-01-01

Full Text Available This is a mini-review on the techniques to measure proliferation of cells by estimation of DNA synthesis. This is not an exhaustive review of literature, but a bird’s eye view of a few selected articles which may provide the technical details to the readers.The nucleus of a cell occupies about 10-30% of the cells space, depends on the type of genetic material (DNA -DeoxyriboNucleic Acid. DNA is a long, double-stranded, helical molecule which carries the genetic information. Duplication of the DNA takes place by the phenomena of replication. One copy of double-stranded DNA molecule forms two double-stranded DNA molecules. DNA replication is the fundamental process used in all living organisms as it is the basis for biological inheritance. This process is known also as Mitosis in somatic cells. In Mitosis, the duplication process results in two genetically identical "daughter" cells from a single "parent" cell. The resulting double-stranded DNA molecules are identical; proof reading and error-checking mechanisms exist to ensure near perfect pair. Mitosis is divided into six phases: prophase, prometaphase, metaphase, anaphase, telophase, and cytokinesis.

Break-induced ATR and Ddb1-Cul4(Cdt)² ubiquitin ligase-dependent nucleotide synthesis promotes homologous recombination repair in fission yeast

DEFF Research Database (Denmark)

Moss, Jennifer; Tinline-Purvis, Helen; Walker, Carol A

2010-01-01

Nucleotide synthesis is a universal response to DNA damage, but how this response facilitates DNA repair and cell survival is unclear. Here we establish a role for DNA damage-induced nucleotide synthesis in homologous recombination (HR) repair in fission yeast. Using a genetic screen, we found...... the Ddb1-Cul4(Cdt)² ubiquitin ligase complex and ribonucleotide reductase (RNR) to be required for HR repair of a DNA double-strand break (DSB). The Ddb1-Cul4(Cdt)² ubiquitin ligase complex is required for degradation of Spd1, an inhibitor of RNR in fission yeast. Accordingly, deleting spd1(+) suppressed...

Interference effect on annealing temperature of A and E centers in silicon.

Science.gov (United States)

Fang, P. H.; Tanaka, T.

1971-01-01

The significance of recent experimental observations on the annealing defects in n-type silicon has been examined. The observed anomalous annealing temperatures of A and E centers and their impurity concentration dependence are explained by an interference between the two centers.

In-situ PXRD Study on the Annealing of SrFe12O19 Nano Particles

DEFF Research Database (Denmark)

Gjørup, Frederik; Saura-Múzquiz, Matilde; Christensen, Mogens

Nano sized strontium hexaferrite is synthesized using a hydrothermal flow synthesis, at temperature and pressure above waters critical point. The nano particles are hexagonal platelets, with the easy axis of magnetization along the short c-axis of the platelet. The nano powders are normally pressed...... and annealed to form mechanically stable pellets. This study uses In-situ Powder X-Ray Diffraction (PXRD) to examine the particle growth during annealing of the powder, with emphasis on the ratio between the axes of the platelets (a/c-ratio). By applying an external magnetic field before annealing......, the particles will align along the field lines of the external magnet, and the contact surfaces along the c-axis should increase. It will be examined whether the external magnetic field increases the growth along the c-axis relative to the a/b-axis, compared to annealing without prior magnetization....

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

Science.gov (United States)

Kringle, Loni; Sawaya, Nicolas P. D.; Widom, Julia; Adams, Carson; Raymer, Michael G.; Aspuru-Guzik, Alán; Marcus, Andrew H.

2018-02-01

Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)2 that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)2-DNA construct can be systematically varied with temperature below the ds-ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)2-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.

Inhibition and recovery of DNA synthesis in human cells after exposure to ultraviolet light

International Nuclear Information System (INIS)

Painter, R.B.

1985-01-01

The inhibition of DNA synthesis in normal human cells by UV is a complex function of fluence because it has several causes. At low fluences, inhibition of replicon initiation is most important. This is made clear by the fact that it occurs to a lesser degree in cells from patients with ataxia telangiectasia (AT). Assuming that only leading strand synthesis is blocked by UV-induced lesions, single lesions between replicons in parental strands for leading strand synthesis inhibit DNA synthesis by acting as temporary blocks until they are replicated by extension of the lagging strand of the adjacent replicon. A more severe inhibition occurs when two lesions are induced between adjacent growing replicons, because one in four possible configurations may result in a long-lived unreplicated region (LLUR). In the absence of excision repair, these may eventually be replicated by activation of an otherwise unused origin within the LLUR. The frequency of LLURs increases steeply with fluence. Activation of normally unused origins to replicate LLURs may facilitate recovery from inhibition of DNA synthesis, but repair of lesions is probably more important. In excision-repair-defective cells, an LLUR without an origin to initiate its replication may be a lethal lesion. (orig.)

Heat treatment effect on the strain dependence of the critical current for an internal-tin processed Nb3Sn strand

International Nuclear Information System (INIS)

Oh, Sangjun; Park, Soo-Hyeon; Lee, Chulhee; Choi, Heekyung; Kim, Keeman

2010-01-01

A comparative study on the effects of heat treatment, especially, the duration of the A15 reaction temperature plateau on the strain dependence of the critical current for an internal-tin processed Nb 3 Sn strand has been carried out. The strain dependence of the critical current is measured by a variable temperature Walter spiral probe that we have developed. It was shown that prolonged heat treatment can be a very effective way to improve the strain dependency. For a quantitative analysis, the measured data were analyzed with various proposed scaling laws: the scaling law based on strong-coupling theory, the modified deviatoric strain scaling law, and the interpolative scaling law. We found that there is a slight increase in the critical temperature and a substantial improvement in the maximum pinning force. The origin of improved strain dependency is further discussed.

Lingering single-strand breaks trigger Rad51-independent homology-directed repair of collapsed replication forks in the polynucleotide kinase/phosphatase mutant of fission yeast.

Directory of Open Access Journals (Sweden)

Arancha Sanchez

2017-09-01

Full Text Available The DNA repair enzyme polynucleotide kinase/phosphatase (PNKP protects genome integrity by restoring ligatable 5'-phosphate and 3'-hydroxyl termini at single-strand breaks (SSBs. In humans, PNKP mutations underlie the neurological disease known as MCSZ, but these individuals are not predisposed for cancer, implying effective alternative repair pathways in dividing cells. Homology-directed repair (HDR of collapsed replication forks was proposed to repair SSBs in PNKP-deficient cells, but the critical HDR protein Rad51 is not required in PNKP-null (pnk1Δ cells of Schizosaccharomyces pombe. Here, we report that pnk1Δ cells have enhanced requirements for Rad3 (ATR/Mec1 and Chk1 checkpoint kinases, and the multi-BRCT domain protein Brc1 that binds phospho-histone H2A (γH2A at damaged replication forks. The viability of pnk1Δ cells depends on Mre11 and Ctp1 (CtIP/Sae2 double-strand break (DSB resection proteins, Rad52 DNA strand annealing protein, Mus81-Eme1 Holliday junction resolvase, and Rqh1 (BLM/WRN/Sgs1 DNA helicase. Coupled with increased sister chromatid recombination and Rad52 repair foci in pnk1Δ cells, these findings indicate that lingering SSBs in pnk1Δ cells trigger Rad51-independent homology-directed repair of collapsed replication forks. From these data, we propose models for HDR-mediated tolerance of persistent SSBs with 3' phosphate in pnk1Δ cells.

Effect of Annealing Temperature on Broad Luminescence of Silver-Exchanged Zeolites Y and A

Science.gov (United States)

Gui, Sa Chu Rong; Lin, H.; Bao, W.; Wang, W.

2018-05-01

The annealing temperature dependence of luminescence properties of silver (Ag)-exchanged zeolites Y and A was studied. It was found that the absorbance and excitation/emission bands are strongly affected by the thermal treatments. With increase in annealing temperature, the absorbance of Ag in zeolite Y increases at first and then decreases. However, the position of the excitation/emission band in zeolite Y was found to be insensitive to the annealing temperature. In contrast, the excitation/emission bands in zeolite A are particularly sensitive to the annealing temperature. The difference of such temperature dependence in zeolites Y and A may be due to the different microporous structure of the two minerals. Moreover, the fact that this dependence is not observed in Ag-exchanged zeolite Y is likely to be due to the difficulty in dehydration of zeolite Y in air or due to the weak Ag+-Ag+ interaction in zeolite Y.

Dependence of TL-property changes of natural quartzes on aluminium contents accompanied by thermal annealing treatment

International Nuclear Information System (INIS)

Hashimoto, T.; Sakaue, S.; Aoki, H.; Ichino, M.

1994-01-01

The TL properties were investigated using both an IPDA (Intensified Photo-Diode Array) spectrometric system and a TLCI (Thermoluminescence Colour Image) method after thermal annealing treatment at several temperatures. An apparent colour change from original blue- (BTL) to red-TL(RTL) has unexpectedly occurred in a Z-cut slice of Madagascar quartz, after an annealing treatment around 1000 o C. From the TL-colour change studies of the Z-cut slice, it was confirmed that original BTL intensities are inversely proportional to the Al contents; the TLCI-patterns of the original or annealed Z-cut slice gave stripe patterns corresponding to Al impurity contents along the crystal growth direction particularly yielding an intense appearance of RTL on higher Al contents after the annealing treatment. This changeability of TL-colour towards RTL after thermal annealing treatment was found to be intimately correlated with the square of Al concentrations, although BTL clearly changed as linearly proportional to Al impurity contents. Finally, the cleavage of Al-O-Al bonds or some sites in the vicinity of Al-O-Al bonds were plausibly considered to play an important role for the formation of RTL colour centres in natural quartzes as a result of the operation of high temperature effects. (Author)

The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis

OpenAIRE

Jette, Nicholas; Lees-Miller, Susan P.

2014-01-01

The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemi...

Mechanical properties of rubberwood oriented strand lumber (OSL: The effect of strand length

Directory of Open Access Journals (Sweden)

Buhnnum Kyokong

2005-09-01

Full Text Available Effect of strand length on mechanical properties (tension, compression and bending of oriented strand lumber (OSL made of rubberwood (Hevea brasiliensis Muell. Arg. was reported. Three strand lengths of 50 mm, 100 mm, and 150 mm with 1 mm thickness and 15 mm width were used. The strands were mixed with 5% pMDI glue (weight basis in a tumble mixer. The OSL specimens were formed by hot pressing process of unidirectionally aligned strands. Average specific gravity and moisture content were 0.76 and 8.34%, respectively. Tension and compression tests were carried out for directions both parallel and perpendicular to grain while bending test was performed only in parallel direction. Ultimate stresses and moduli of elasticity were examined from the stress-strain curves. It was found that for the parallel-to-grain direction, the longer strand OSL gave higher strength. The role of the strand length did not appear for the direction normal to the grain. The relationship between the mechanical properties of OSL and strand length was well described by the modified Hankinson formula.

Gender-dependent expression of leading and passenger strand of miR-21 and miR-16 in human colorectal cancer and adjacent colonic tissues.

Science.gov (United States)

Hasáková, K; Bezakova, J; Vician, M; Reis, R; Zeman, M; Herichova, I

2017-12-30

miRNAs are small regulatory RNA molecules involved in posttranscriptional gene silencing. Their biosynthesis results in the formation of duplex consisting of a leading and a passenger strand of mature miRNA. The leading strand exhibits the main activity but recent findings indicate a certain role of the passenger strand as well. Deregulated levels of miRNA were found in many types of cancers including colorectal cancer. miR-21 and miR-16 were indicated as possible markers of colorectal cancer, however, small attention to gender differences in their expression was paid so far. Therefore, the aim of our study was to investigate the expression of miR-21-5p, miR-21-3p, miR-16-5p and miR-16-3p in human colorectal cancer tissue and compare it to the adjacent tissues taken during surgery in men and women separately. Our results showed an up-regulation of all measured miRNAs in tumor tissue compared to adjacent tissues. As expected, tumors and adjacent tissues exhibited a significantly higher expression of leading miRNAs compared to passenger strand of miR-21 and miR-16. The expression of leading and passenger strand of miR-21 and miR-16 positively correlated exhibiting the highest correlation coefficient in the distal tissue. The expression pattern showed gender-dependent differences, with higher levels of miRNA in men than in women. Our findings indicate a gender-related expression pattern of miRNA, which should be considered as an important factor in generating new prognostic or diagnostic biomarkers.

Electrical properties and annealing kinetics study of laser-annealed ion-implanted silicon

International Nuclear Information System (INIS)

Wang, K.L.; Liu, Y.S.; Kirkpatrick, C.G.; Possin, G.E.

1979-01-01

This paper describes measurements of electrical properties and the regrowth behavior of ion-implanted silicon annealed with an 80-ns (FWHM) laser pulse at 1.06 μm. The experimental results include: (1) a determination of threshold energy density required for melting using a transient optical reflectivity technique, (2) measurements of dopant distribution using Rutherford backscattering spectroscopy, (3) characterization of electrical properties by measuring reverse leakage current densities of laser-annealed and thermal-annealed mesa diodes, (4) determination of annealed junction depth using an electron-beam-induced-current technique, and (5) a deep-level-transient spectroscopic study of residual defects. In particular, by measuring these properties of a diode annealed at a condition near the threshold energy density for liquid phase epitaxial regrowth, we have found certain correlations among these various annealing behaviors and electrical properties of laser-annealed ion-implanted silicon diodes

Investigation of optimum annealing parameters for formation of dip coated Cu{sub 2}ZnSnS{sub 4} thin film

Energy Technology Data Exchange (ETDEWEB)

Chaudhari, Sushmita; Kannan, P.K.; Dey, Suhash R., E-mail: suhash@iith.ac.in

2016-08-01

Cu{sub 2}ZnSnS{sub 4} (CZTS) is most attractive absorber material for inorganic solar cell applications because of its cost effective and ecofriendly nature. To obtain phase pure CZTS film, effects of annealing parameters on synthesis of CZTS thin film are investigated. CZTS films are deposited through dip coating method followed by heat treatment to form crystalline CZTS thin films. Factors influencing the crystallinity, morphology and composition of the films such as annealing temperature, time, rate and atmosphere are studied through X-Ray Diffraction, Raman Spectroscopy, Scanning Electron Microscopy and Energy Dispersive X-Ray Spectroscopy. After numerous experiments of synthesis of CZTS in different annealing conditions and its characterization, it is observed that 1.4 eV band gap CZTS thin film of kesterite structure is obtained by annealing the film in nitrogen atmosphere for 60 min at 300 °C with 10 °C/min ramping rate. - Highlights: • Dip coated Cu{sub 2}ZnSnS{sub 4} film is developed using non-hydrazine based precursor solution. • Optimum annealing condition to achieve best crystalline film is studied. • Optimal condition is 300 °C in N{sub 2} atmosphere for 60 min at 10 °C/min ramping rate. • Bandgap of prepared films is 1.4 eV, suitable for solar cell applications.

Interlayer growth in Mo/B4C multilayered structures upon thermal annealing

International Nuclear Information System (INIS)

Nyabero, S. L.; Kruijs, R. W. E. van de; Yakshin, A. E.; Zoethout, E.; Bosgra, J.; Loch, R. A.; Blanckenhagen, G. von; Bijkerk, F.

2013-01-01

Both multilayer period thickness expansion and compaction were observed in Mo/B 4 C multilayers upon annealing, and the physical causes for this were explored in detail. Using in situ time-dependent grazing incidence X-ray reflectometry, period changes down to picometer-scale were resolved. It was shown that the changes depend on the thickness of the B 4 C layers, annealing temperature, and annealing time. Although strong stress relaxation during annealing was observed, it was excluded as a cause for period expansion. Auger electron spectroscopy and wide angle X-ray diffraction measurements revealed the growth of interlayers, with associated period changes influenced by the supply of B and C atoms to the growing compound interlayers. For multilayers with a Mo thickness of 3 nm, two regimes were recognized, depending on the deposited B 4 C thickness: in multilayers with B 4 C ≤ 1.5 nm, the supply of additional Mo into the already formed MoB x C y interlayer was dominant and led to densification, resulting in period compaction. For multilayers with B 4 C ≥ 2 nm, the B and C enrichment of interlayers formed low density compounds and yielded period expansion.

INFLUENCE OF ANNEALING ON HARDNESS OF Cr-Mn-Ni CAST IRONS

Directory of Open Access Journals (Sweden)

V. V. Netrebko

2015-01-01

Full Text Available The necessary level of material’s hardness is determined by the exploitation conditions and presence of technological operations during manufacturing of articles. Mechanical edge cutting machining of wear resistant materials is impeded because of their high hardness. It is recommended to apply annealing in order to decrease hardness and improve machinability. The purpose of the work consisted in obtaining of regression dependences of cast iron’s macrohardness on its chemical content after annealing at 730 °С. With the use of mathematical experimental design the regression dependences of cast iron’s macrohardness and structural components’ microhardness on С, Cr, Mn, Ni content have been established. The minimal hardness of 27,6 HRC after annealing at 730 °С is obtained in the cast iron containing: 3,9% С; 11,4% Cr; 0,6% Mn; 0,2% Ni. The maximal hardness of 70,4 HRC is obtained when the content is as follows: 1,1% С; 25,6% Cr; 5,4% Mn; 3,0% Ni. Annealing at 730 °С decreases the cast irons’ hardness containing the minimal amount of Cr, Mn and Ni. Annealing at 730 °С is recommended for cast irons alloyed by Mn and Ni for increasing of hardness.

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

3′-Terminal Sequence in Poliovirus Negative-Strand Templates Is the Primary cis-Acting Element Required for VPgpUpU-Primed Positive-Strand Initiation

OpenAIRE

Sharma, Nidhi; O'Donnell, Brian J.; Flanegan, James B.

2005-01-01

The 5′ cloverleaf in poliovirus RNA has a direct role in regulating the stability, translation, and replication of viral RNA. In this study, we investigated the role of stem a in the 5′ cloverleaf in regulating the stability and replication of poliovirus RNA in HeLa S10 translation-replication reactions. Our results showed that disrupting the duplex structure of stem a destabilized viral RNA and inhibited efficient negative-strand synthesis. Surprisingly, the duplex structure of stem a was no...

Reactive-inspired ball-milling synthesis of an ODS steel: study of the influence of ball-milling and annealing; Synthese et caracterisation d'un acier ODS prepare par un procede inspiredu broyage reactif: etude de l'influence des conditions de broyage et recuit

Energy Technology Data Exchange (ETDEWEB)

Brocq, M.

2010-10-15

In the context of the development of new ODS (Oxide Dispersion Strengthened) steels as core materials in future nuclear reactors, we investigated a new process inspired by reactive ball-milling which consists in using YFe{sub 3} andFe{sub 2}O{sub 3} as starting reactants instead of Y{sub 2}O{sub 3} to produce a dispersion of nano-oxides in a steel matrix and the influence of synthesis conditions on the nano-oxide characteristics were studied. For that aim, ODS steels were prepared by ball-milling and then annealed. Multi-scale characterizations were performed after each synthesis step, using notably atom probe tomography and small angle neutron scattering. The process inspired by reactive ball-milling was shown to be efficient for ODS steel synthesis, but it does not modify the nano-oxide characteristics as compared to those of oxides directly incorporated in the matrix by ball-milling. Broadly speaking, the nature of the starting oxygen bearing reactants has no influence on nano-oxide formation. Moreover, we showed that the nucleation of nano-oxides nucleation can start during milling and continues during annealing with a very fast kinetic. The final characteristics of nano-oxides formed in this way can be monitored through ball-milling parameters (intensity, temperature and atmosphere) and annealing parameters (duration and temperature). (author)

The effect of annealing on the time-dependent behavior of isotactic polypropylene at finite strains

DEFF Research Database (Denmark)

Drozdov, Aleksey D.; Christiansen, Jesper de Claville

2002-01-01

Four series of tensile relaxation tests are performed on isotactic polypropylene at elongations up to the necking point. In the first series of experiments, injection-molded samples are used without thermal pre-treatment. In the other series, the specimens are annealed for 24 h prior to testing a...... at annealing. In the post-critical region (large strains), an increase in the fraction of active amorphous domains is attributed to disintegration of primary (thick) lamellae....

A Major Role of DNA Polymerase δ in Replication of Both the Leading and Lagging DNA Strands.

Science.gov (United States)

Johnson, Robert E; Klassen, Roland; Prakash, Louise; Prakash, Satya

2015-07-16

Genetic studies with S. cerevisiae Polδ (pol3-L612M) and Polε (pol2-M644G) mutant alleles, each of which display a higher rate for the generation of a specific mismatch, have led to the conclusion that Polε is the primary leading strand replicase and that Polδ is restricted to replicating the lagging strand template. Contrary to this widely accepted view, here we show that Polδ plays a major role in the replication of both DNA strands, and that the paucity of pol3-L612M-generated errors on the leading strand results from their more proficient removal. Thus, the apparent lack of Polδ contribution to leading strand replication is due to differential mismatch removal rather than differential mismatch generation. Altogether, our genetic studies with Pol3 and Pol2 mutator alleles support the conclusion that Polδ, and not Polε, is the major DNA polymerase for carrying out both leading and lagging DNA synthesis. Copyright © 2015 Elsevier Inc. All rights reserved.

Dependence of wet etch rate on deposition, annealing conditions and etchants for PECVD silicon nitride film

International Nuclear Information System (INIS)

Tang Longjuan; Zhu Yinfang; Yang Jinling; Li Yan; Zhou Wei; Xie Jing; Liu Yunfei; Yang Fuhua

2009-01-01

The influence of deposition, annealing conditions, and etchants on the wet etch rate of plasma enhanced chemical vapor deposition (PECVD) silicon nitride thin film is studied. The deposition source gas flow rate and annealing temperature were varied to decrease the etch rate of SiN x :H by HF solution. A low etch rate was achieved by increasing the SiH 4 gas flow rate or annealing temperature, or decreasing the NH 3 and N2 gas flow rate. Concentrated, buffered, and dilute hydrofluoric acid were utilized as etchants for SiO 2 and SiN x :H. A high etching selectivity of SiO 2 over SiN x :H was obtained using highly concentrated buffered HF.

Effects of annealing on the physical properties of therapeutic proteins during freeze drying process.

Science.gov (United States)

Lim, Jun Yeul; Lim, Dae Gon; Kim, Ki Hyun; Park, Sang-Koo; Jeong, Seong Hoon

2018-02-01

Effects of annealing steps during the freeze drying process on etanercept, model protein, were evaluated using various analytical methods. The annealing was introduced in three different ways depending on time and temperature. Residual water contents of dried cakes varied from 2.91% to 6.39% and decreased when the annealing step was adopted, suggesting that they are directly affected by the freeze drying methods Moreover, the samples were more homogenous when annealing was adopted. Transition temperatures of the excipients (sucrose, mannitol, and glycine) were dependent on the freeze drying steps. Size exclusion chromatography showed that monomer contents were high when annealing was adopted and also they decreased less after thermal storage at 60°C. Dynamic light scattering results exhibited that annealing can be helpful in inhibiting aggregation and that thermal storage of freeze-dried samples preferably induced fragmentation over aggregation. Shift of circular dichroism spectrum and of the contents of etanercept secondary structure was observed with different freeze drying steps and thermal storage conditions. All analytical results suggest that the physicochemical properties of etanercept formulation can differ in response to different freeze drying steps and that annealing is beneficial for maintaining stability of protein and reducing the time of freeze drying process. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Stranded costs and exit fees

International Nuclear Information System (INIS)

2002-01-01

The New Brunswick Market Design Committee has been directed to examine the issue of stranded costs since it is a major component of restructuring within the electricity sector. When regulated monopolies are faced with competition, they could find that some of their embedded costs cannot be recovered. These costs are referred to as stranded costs. Common sources include large capital investments in uneconomic plants or expensive power purchase contracts or fuel supply contracts. In general, stranded costs do not include gains or losses associated with normal business risks experienced by regulated utilities. This report presents recommendations for mitigation of stranded costs, valuation methodologies and cost-recovery mechanisms. It also presents a summary of experience with stranded costs in other jurisdictions such as California, Rhode Island, Pennsylvania and Ontario. Stranded costs are often recovered through an obligatory charge on all customers, particularly in jurisdictions where retail competition exists. In the New Brunswick market, however, the only customers who can create stranded costs are those eligible to choose their own suppliers. It is argued that since most customers will not have a choice of electricity suppliers, they cannot generate stranded costs and therefore, should not have to pay costs stranded by others. A method to quantify stranded costs is presented, along with a review of transmission-related stranded costs in New Brunswick. Expansion of self-generation in New Brunswick could strand transmission assets. Currently, self-generators only contribute a small amount to fixed charges of the transmission system. However, under new recommended tariffs, the amount could increase. It is likely that the net amount of stranded transmission costs will not be large. 2 refs., 1 fig

On the analysis of the activation mechanisms of sub-melt laser anneals

DEFF Research Database (Denmark)

Clarysse, T.; Bogdanowicz, J.; Goosens, J.

2008-01-01

electrically active concentration level as well as the concurrent mobility is dependent on the dopant concentration level. This implies that the activation of B through the laser anneal process in the explored temperature–time space is governed by kinetic processes (i.e. the dissolution of B–I pairs......In order to fabricate carrier profiles with a junction depth (15 nm) and sheet resistance value suited for sub-32 nm Si-CMOS technology, the usage of sub-melt laser anneal is a promising route to explore. As laser annealed junctions seem to outperform standard anneal approaches, a detailed......) and not by the (temperature related) solid solubility....

Layer-by-layer composition and structure of silicon subjected to combined gallium and nitrogen ion implantation for the ion synthesis of gallium nitride

Energy Technology Data Exchange (ETDEWEB)

Korolev, D. S.; Mikhaylov, A. N.; Belov, A. I.; Vasiliev, V. K.; Guseinov, D. V.; Okulich, E. V. [Nizhny Novgorod State University (Russian Federation); Shemukhin, A. A. [Moscow State University, Skobeltsyn Institute of Nuclear Physics (Russian Federation); Surodin, S. I.; Nikolitchev, D. E.; Nezhdanov, A. V.; Pirogov, A. V.; Pavlov, D. A.; Tetelbaum, D. I., E-mail: tetelbaum@phys.unn.ru [Nizhny Novgorod State University (Russian Federation)

2016-02-15

The composition and structure of silicon surface layers subjected to combined gallium and nitrogen ion implantation with subsequent annealing have been studied by the X-ray photoelectron spectroscopy, Rutherford backscattering, electron spin resonance, Raman spectroscopy, and transmission electron microscopy techniques. A slight redistribution of the implanted atoms before annealing and their substantial migration towards the surface during annealing depending on the sequence of implantations are observed. It is found that about 2% of atoms of the implanted layer are replaced with gallium bonded to nitrogen; however, it is impossible to detect the gallium-nitride phase. At the same time, gallium-enriched inclusions containing ∼25 at % of gallium are detected as candidates for the further synthesis of gallium-nitride inclusions.

Lyn tyrosine kinase promotes silencing of ATM-dependent checkpoint signaling during recovery from DNA double-strand breaks

International Nuclear Information System (INIS)

Fukumoto, Yasunori; Kuki, Kazumasa; Morii, Mariko; Miura, Takahito; Honda, Takuya; Ishibashi, Kenichi; Hasegawa, Hitomi; Kubota, Sho; Ide, Yudai; Yamaguchi, Noritaka; Nakayama, Yuji; Yamaguchi, Naoto

2014-01-01

Highlights: • Inhibition of Src family kinases decreased γ-H2AX signal. • Inhibition of Src family increased ATM-dependent phosphorylation of Chk2 and Kap1. • shRNA-mediated knockdown of Lyn increased phosphorylation of Kap1 by ATM. • Ectopic expression of Src family kinase suppressed ATM-mediated Kap1 phosphorylation. • Src is involved in upstream signaling for inactivation of ATM signaling. - Abstract: DNA damage activates the DNA damage checkpoint and the DNA repair machinery. After initial activation of DNA damage responses, cells recover to their original states through completion of DNA repair and termination of checkpoint signaling. Currently, little is known about the process by which cells recover from the DNA damage checkpoint, a process called checkpoint recovery. Here, we show that Src family kinases promote inactivation of ataxia telangiectasia mutated (ATM)-dependent checkpoint signaling during recovery from DNA double-strand breaks. Inhibition of Src activity increased ATM-dependent phosphorylation of Chk2 and Kap1. Src inhibition increased ATM signaling both in G2 phase and during asynchronous growth. shRNA knockdown of Lyn increased ATM signaling. Src-dependent nuclear tyrosine phosphorylation suppressed ATM-mediated Kap1 phosphorylation. These results suggest that Src family kinases are involved in upstream signaling that leads to inactivation of the ATM-dependent DNA damage checkpoint

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 temperature of a quantum annealer. Such effective-temperature reduction is relevant for machine-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.

Exonuclease of human DNA polymerase gamma disengages its strand displacement function.

Science.gov (United States)

He, Quan; Shumate, Christie K; White, Mark A; Molineux, Ian J; Yin, Y Whitney

2013-11-01

Pol γ, the only DNA polymerase found in human mitochondria, functions in both mtDNA repair and replication. During mtDNA base-excision repair, gaps are created after damaged base excision. Here we show that Pol γ efficiently gap-fills except when the gap is only a single nucleotide. Although wild-type Pol γ has very limited ability for strand displacement DNA synthesis, exo(-) (3'-5' exonuclease-deficient) Pol γ has significantly high activity and rapidly unwinds downstream DNA, synthesizing DNA at a rate comparable to that of the wild-type enzyme on a primer-template. The catalytic subunit Pol γA alone, even when exo(-), is unable to synthesize by strand displacement, making this the only known reaction of Pol γ holoenzyme that has an absolute requirement for the accessory subunit Pol γB. © 2013. Published by Elsevier B.V.

X-ray diffraction investigation of self-annealing in nanocrystalline copper electrodeposits

DEFF Research Database (Denmark)

Pantleon, Karen; Somers, Marcel A. J.

2006-01-01

X-ray diffraction analysis and electrical resistivity measurements were conducted simultaneously for in-situ examination of self-annealing in copper electrodeposits. Considerable growth of the as-deposited nano-sized crystallites occurs with time and the crystallographic texture changes by multip...... twinning during self-annealing. The kinetics of self-annealing depends on the layer thickness as well as on the orientation and/or the size of the as-deposited crystallites. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.......X-ray diffraction analysis and electrical resistivity measurements were conducted simultaneously for in-situ examination of self-annealing in copper electrodeposits. Considerable growth of the as-deposited nano-sized crystallites occurs with time and the crystallographic texture changes by multiple...

Spontaneous unscheduled DNA synthesis in human lymphocytes

International Nuclear Information System (INIS)

Forell, B.; Myers, L.S. Jr.; Norman, A.

1979-01-01

The rate of spontaneous unscheduled DNA synthesis in human lymphocytes was estimated from measurements of tritiated thymidine incorporation into double-stranded DNA (ds-DNA) during incubation of cells in vitro. The contribution of scheduled DNA synthesis to the observed incorporation was reduced by inhibiting replication with hydroxyurea and by separating freshly replicated single-stranded DNA (ss-DNA) from repaired ds-DNA by column chromatography. The residual contribution of scheduled DNA synthesis was estimated by observing effects on thymidine incorporation of: (a) increasing the rate of production of apurinic sites, and alternatively, (b) increasing the number of cells in S-phase. Corrections based on estimates of endogenous pool size were also made. The rate of spontaneous unscheduled DNA synthesis is estimated to be 490 +- 120 thymidine molecules incorporated per cell per hour. These results compare favorably with estimates made from rates of depurination and depyrimidination of DNA, measured in molecular systems if we assume thymidine is incorporated by a short patch mechanism which incorporates an average of four bases per lesion

Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.

Directory of Open Access Journals (Sweden)

Laurel D Wright

2015-10-01

Full Text Available We identified a functional single strand origin of replication (sso in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Integrative and conjugative elements (ICEs, also known as conjugative transposons are DNA elements typically found integrated into a bacterial chromosome where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICEs become activated and excise from the host chromosome and can transfer to neighboring cells via the element-encoded conjugation machinery. Activated ICEBs1 undergoes autonomous rolling circle replication that is needed for the maintenance of the excised element in growing and dividing cells. Rolling circle replication, used by many plasmids and phages, generates single-stranded DNA (ssDNA. In many cases, the presence of an sso enhances the conversion of the ssDNA to double-stranded DNA (dsDNA by enabling priming of synthesis of the second DNA strand. We initially identified sso1 in ICEBs1 based on sequence similarity to the sso of an RCR plasmid. Several functional assays confirmed Sso activity. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. We found that Sso activity was important for two key aspects of the ICEBs1 lifecycle: 1 maintenance of the plasmid form of ICEBs1 in cells after excision from the chromosome, and 2 stable acquisition of ICEBs1 following transfer to a new host. We identified sequences similar to known plasmid sso's in several other ICEs. Together, our results indicate that many other ICEs contain at least one single strand origin of replication, that these ICEs likely undergo autonomous replication, and that replication contributes to the stability and spread of these elements.

Annealing time dependence of the physical, electrical and pH response characteristics of spin coated TiO2 thin films

International Nuclear Information System (INIS)

Zulkefle, M A; Rahman, R A; Yusoff, K A; Herman, S H; Abdullah, W F H; Rusop, M

2015-01-01

Titanium dioxide (TiO 2 ) thin film was deposited on indium tin oxide (ITO) substrate and used as sensing membrane of EGFET pH sensor. The thin film was fabricated using sol- gel spin coating method. All samples were annealed at 400 °C but the annealing time was varied. This is done to study the effects of annealing time on physical and electrical properties of titanium dioxide thin film. The sensitivity of each sample towards H + ion was measured and result shows that sample annealed for 45 minutes has the highest sensitivity (52.6 mV/pH). It is found that increasing annealing duration will increase the pH sensitivity but a limit will be reached at certain point. Longer annealing processes done beyond this point will results in lower pH sensitivity. (paper)

Thickness Dependence of the Dzyaloshinskii-Moriya Interaction in Co2 FeAl Ultrathin Films: Effects of Annealing Temperature and Heavy-Metal Material

Science.gov (United States)

Belmeguenai, M.; Roussigné, Y.; Bouloussa, H.; Chérif, S. M.; Stashkevich, A.; Nasui, M.; Gabor, M. S.; Mora-Hernández, A.; Nicholson, B.; Inyang, O.-O.; Hindmarch, A. T.; Bouchenoire, L.

2018-04-01

The interfacial Dzyaloshinskii-Moriya interaction (IDMI) is investigated in Co2FeAl (CFA) ultrathin films of various thicknesses (0.8 nm ≤tCFA≤2 nm ) grown by sputtering on Si substrates, using Pt, W, Ir, and MgO buffer or/and capping layers. Vibrating sample magnetometry reveals that the magnetization at saturation (Ms ) for the Pt- and Ir-buffered films is higher than the usual Ms of CFA due to the proximity-induced magnetization (PIM) in Ir and Pt estimated to be 19% and 27%, respectively. The presence of PIM in these materials is confirmed using x-ray resonant magnetic reflectivity. Moreover, while no PIM is induced in W, higher PIM is obtained with Pt when it is used as a buffer layer rather than a capping layer. Brillouin light scattering in the Damon-Eshbach geometry is used to investigate the thickness dependences of the IDMI constants from the spin-wave nonreciprocity and the perpendicular anisotropy field versus the annealing temperature. The IDMI sign is found to be negative for Pt /CFA and Ir /CFA , while it is positive for W /CFA . The thickness dependence of the effective IDMI constant for stacks involving Pt and W shows the existence of two regimes similar to that of the perpendicular anisotropy constant due to the degradation of the interfaces as the CFA thickness approaches a critical thickness. The surface IDMI and anisotropy constants of each stack are determined for the thickest samples where a linear thickness dependence of the effective IDMI constant and the effective magnetization are observed. The interface anisotropy and IDMI constants investigated for the Pt /CFA /MgO system show different trends with the annealing temperature. The decrease of the IDMI constant with increasing annealing temperature is probably due to the electronic structure changes at the interfaces, while the increase of the interface anisotropy constant is coherent with the interface quality and disorder enhancement.

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

Rapid magnetic hardening by rapid thermal annealing in NdFeB-based nanocomposites

Energy Technology Data Exchange (ETDEWEB)

Chu, K.-T.; Jin, Z Q; Chakka, Vamsi M; Liu, J P [Department of Physics, University of Texas at Arlington, Arlington, TX 76019 (United States)

2005-11-21

A systematic study of heat treatments and magnetic hardening of NdFeB-based melt-spun nanocomposite ribbons have been carried out. Comparison was made between samples treated by rapid thermal annealing and by conventional furnace annealing. Heating rates up to 200 K s{sup -1} were adopted in the rapid thermal processing. It was observed that magnetic hardening can be realized in an annealing time as short as 1 s. Coercivity of 10.2 kOe in the nanocomposites has been obtained by rapid thermal annealing for 1 s, and prolonged annealing did not give any increase in coercivity. Detailed results on the effects of annealing time, temperature and heating rate have been obtained. The dependence of magnetic properties on the annealing parameters has been investigated. Structural characterization revealed that there is a close correlation between magnetic hardening and nanostructured morphology. The coercivity mechanism was also studied by analysing the magnetization minor loops.

Effects of annealing on the corrosion behavior and mechanical properties of Ti-Al-V alloy

International Nuclear Information System (INIS)

Kim, T. K.; Choi, B. S.; Baek, J. H.; Choi, B. K.; Jeong, Y. H.; Lee, D. J.; Jang, M. H.; Jeong, Y. H.

2002-01-01

In order to determine the annealing condition after cold rolling, the effects of annealing on the corrosion behavior and mechanical properties of Ti-Al-V alloy were evaluated. The results of tensile tests at room temperature showed that the strengths and the ductility were almost independent of the annealing temperature. The results of hardness test also revealed that the hardness was independent of the annealing, However, the results of corrosion test in an ammoniated water of pH 9.98 at 360 .deg. C showed that the corrosion resistance depended on the annealing temperature, and the corrosion rate was accelerated with increasing annealing temperature. Hydrogen contents absorbed during the corrosion test of 120 days also increased with the annealing temperature. It may be attributed to the growth of α' precipitates by annealing. It is thus suggested that the lower annealing temperatures provide the better corrosion properties without degrading the tensile properties

SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair

DEFF Research Database (Denmark)

McCord, Ronald A; Michishita, Eriko; Hong, Tao

2009-01-01

-PKcs) to chromatin in response to DNA damage and stabilizes DNA-PKcs at chromatin adjacent to an induced site-specific DSB. Abrogation of these SIRT6 activities leads to impaired resolution of DSBs. Together, these findings elucidate a mechanism whereby regulation of dynamic interaction of a DNA repair factor......-dependent protein kinase) and promotes DNA DSB repair. In response to DSBs, SIRT6 associates dynamically with chromatin and is necessary for an acute decrease in global cellular acetylation levels on histone H3 Lysine 9. Moreover, SIRT6 is required for mobilization of the DNA-PK catalytic subunit (DNA......, and SIRT6 knockout cells exhibit genomic instability and DNA damage hypersensitivity. However, the molecular mechanisms underlying these defects are not fully understood. Here, we show that SIRT6 forms a macromolecular complex with the DNA double-strand break (DSB) repair factor DNA-PK (DNA...

Arranging eukaryotic nuclear DNA polymerases for replication: Specific interactions with accessory proteins arrange Pols α, δ, and ϵ in the replisome for leading-strand and lagging-strand DNA replication.

Science.gov (United States)

Kunkel, Thomas A; Burgers, Peter M J

2017-08-01

Biochemical and cryo-electron microscopy studies have just been published revealing interactions among proteins of the yeast replisome that are important for highly coordinated synthesis of the two DNA strands of the nuclear genome. These studies reveal key interactions important for arranging DNA polymerases α, δ, and ϵ for leading and lagging strand replication. The CMG (Mcm2-7, Cdc45, GINS) helicase is central to this interaction network. These are but the latest examples of elegant studies performed in the recent past that lead to a much better understanding of how the eukaryotic replication fork achieves efficient DNA replication that is accurate enough to prevent diseases yet allows evolution. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Transformation of Saccharomyces cerevisiae with UV-irradiated single-stranded plasmid.

Science.gov (United States)

Zgaga, Z

1991-08-01

UV-irradiated single-stranded replicative plasmids were used to transform different yeast strains. The low doses of UV used in this study (10-75 J/m2) caused a significant decrease in the transforming efficiency of plasmid DNA in the Rad+ strain, while they had no effect on transformation with double-stranded plasmids of comparable size. Neither the rev3 mutation, nor the rad18 or rad52 mutations influenced the efficiency of transformation with irradiated single-stranded plasmid. However, it was found to be decreased in the double rev3 rad52 mutant. Extracellular irradiation of plasmid that contains both URA3 and LEU2 genes (psLU) gave rise to up to 5% Leu- transformants among selected Ura+ ones in the repair-proficient strain. Induction of Leu- transformants was dose-dependent and only partially depressed in the rev3 mutant. These results suggest that both mutagenic and recombinational repair processes operate on UV-damaged single-stranded DNA in yeast.

The prion protein has DNA strand transfer properties similar to retroviral nucleocapsid protein.

Science.gov (United States)

Gabus, C; Auxilien, S; Péchoux, C; Dormont, D; Swietnicki, W; Morillas, M; Surewicz, W; Nandi, P; Darlix, J L

2001-04-06

The transmissible spongiform encephalopathies are fatal neurodegenerative diseases that are associated with the accumulation of a protease-resistant form of the cellular prion protein (PrP). Although PrP is highly conserved and widely expressed in vertebrates, its function remains a matter of speculation. Indeed PrP null mice develop normally and are healthy. Recent results show that PrP binds to nucleic acids in vitro and is found associated with retroviral particles. Furthermore, in mice the scrapie infectious process appears to be accelerated by MuLV replication. These observations prompted us to further investigate the interaction between PrP and nucleic acids, and compare it with that of the retroviral nucleocapsid protein (NC). As the major nucleic acid-binding protein of the retroviral particle, NC protein is tightly associated with the genomic RNA in the virion nucleocapsid, where it chaperones proviral DNA synthesis by reverse transcriptase. Our results show that the human prion protein (huPrP) functionally resembles NCp7 of HIV-1. Both proteins form large nucleoprotein complexes upon binding to DNA. They accelerate the hybridization of complementary DNA strands and chaperone viral DNA synthesis during the minus and plus DNA strand transfers necessary to generate the long terminal repeats. The DNA-binding and strand transfer properties of huPrP appear to map to the N-terminal fragment comprising residues 23 to 144, whereas the C-terminal domain is inactive. These findings suggest that PrP could be involved in nucleic acid metabolism in vivo. Copyright 2001 Academic Press.

A specific subdomain in φ29 DNA polymerase confers both processivity and strand-displacement capacity

Science.gov (United States)

Rodríguez, Irene; Lázaro, José M.; Blanco, Luis; Kamtekar, Satwik; Berman, Andrea J.; Wang, Jimin; Steitz, Thomas A.; Salas, Margarita; de Vega, Miguel

2005-01-01

Recent crystallographic studies of φ29 DNA polymerase have provided structural insights into its strand displacement and processivity. A specific insertion named terminal protein region 2 (TPR2), present only in protein-primed DNA polymerases, together with the exonuclease, thumb, and palm subdomains, forms two tori capable of interacting with DNA. To analyze the functional role of this insertion, we constructed a φ29 DNA polymerase deletion mutant lacking TPR2 amino acid residues Asp-398 to Glu-420. Biochemical analysis of the mutant DNA polymerase indicates that its DNA-binding capacity is diminished, drastically decreasing its processivity. In addition, removal of the TPR2 insertion abolishes the intrinsic capacity of φ29 DNA polymerase to perform strand displacement coupled to DNA synthesis. Therefore, the biochemical results described here directly demonstrate that TPR2 plays a critical role in strand displacement and processivity. PMID:15845765

High resolution electron microscopy study of as-prepared and annealed tungsten-carbon multilayers

International Nuclear Information System (INIS)

Nguyen, T.D.; Gronsky, R.; Kortright, J.B.

1988-12-01

A series of sputtered tungsten-carbon multilayer structures with periods ranging from 2 to 12 nm in the as-prepared state and after annealing at 500/degree/C for 4 hours has been studied with high resolution transmission electron microscopy. The evolution with annealing of the microstructure of these multilayers depends on their period. As-prepared structures appear predominantly amorphous from TEM imaging and diffraction. Annealing results in crystallization of the W-rich layers into WC in the larger period samples, and less complete or no crystallization in the smaller period samples. X-ray scattering reveals that annealing expands the period in a systematic way. The layers remain remarkably well-defined after annealing under these conditions. 12 refs., 4 figs., 1 tab

Knotting probabilities after a local strand passage in unknotted self-avoiding polygons

International Nuclear Information System (INIS)

Szafron, M L; Soteros, C E

2011-01-01

We investigate, both theoretically and numerically, the knotting probabilities after a local strand passage is performed in an unknotted self-avoiding polygon (SAP) on the simple cubic lattice. In the polygons studied, it is assumed that two polygon segments have already been brought close together for the purpose of performing a strand passage. This restricts the polygons considered to those that contain a specific pattern called Θ at a fixed location; an unknotted polygon containing Θ is called a Θ-SAP. It is proved that the number of n-edge Θ-SAPs grows exponentially (with n) at the same rate as the total number of n-edge unknotted SAPs (those with no prespecified strand passage structure). Furthermore, it is proved that the same holds for subsets of n-edge Θ-SAPs that yield a specific after-strand-passage knot-type. Thus, the probability of a given after-strand-passage knot-type does not grow (or decay) exponentially with n. Instead, it is conjectured that these after-strand-passage knot probabilities approach, as n goes to infinity, knot-type dependent amplitude ratios lying strictly between 0 and 1. This conjecture is supported by numerical evidence from Monte Carlo data generated using a composite (aka multiple) Markov chain Monte Carlo BFACF algorithm developed to study Θ-SAPs. A new maximum likelihood method is used to estimate the critical exponents relevant to this conjecture. We also obtain strong numerical evidence that the after-strand-passage knotting probability depends on the local structure around the strand-passage site. If the local structure and the crossing sign at the strand-passage site are considered, then we observe that the more 'compact' the local structure, the less likely the after-strand-passage polygon is to be knotted. This trend for compactness versus knotting probability is consistent with results obtained for other strand-passage models; however, we are the first to note the influence of the crossing-sign information. We

On the photon annealing of silicon-implanted gallium-nitride layers

International Nuclear Information System (INIS)

Seleznev, B. I.; Moskalev, G. Ya.; Fedorov, D. G.

2016-01-01

The conditions for the formation of ion-doped layers in gallium nitride upon the incorporation of silicon ions followed by photon annealing in the presence of silicon dioxide and nitride coatings are analyzed. The conditions of the formation of ion-doped layers with a high degree of impurity activation are established. The temperature dependences of the surface concentration and mobility of charge carriers in ion-doped GaN layers annealed at different temperatures are studied.

Effects of annealing on tensile property and corrosion behavior of Ti-Al-Zr alloy

International Nuclear Information System (INIS)

Kim, Tae-Kyu; Choi, Byung-Seon; Jeong, Yong-Hwan; Lee, Doo-Jeong; Chang, Moon-Hee

2002-01-01

The effects of annealing on the tensile property and corrosion behavior of Ti-Al-Zr alloy were evaluated. The annealing in the temperature range from 500 to 800 deg. C for 1 h induced the growth of the grain and the precipitate sizes. The results of tensile tests at room temperature showed that the strengths and the ductility were almost independent of the annealing temperature. However, the results of corrosion test in an ammonia aqueous solution of pH 9.98 at 360 deg. C showed that the corrosion resistance depended on the annealing temperature, and the corrosion rate was accelerated with increasing annealing temperature. Hydrogen contents absorbed during the corrosion test of 220 days also increased with the annealing temperature. It could be attributed to the growth of Fe-rich precipitates by annealing. It is thus suggested that the lower annealing temperatures provide the better corrosion properties without degrading the tensile properties

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 ...

Structural coarsening during annealing of an aluminum plate heavily deformed using ECAE

DEFF Research Database (Denmark)

Mishin, Oleg V.; Zhang, Yubin; Godfrey, A.

2015-01-01

The microstructure and softening behaviour have been investigated in an aluminum plate heavily deformed by equal channel angular extrusion and subsequently annealed at 170 °C. It is found that at this temperature the microstructure evolves by coarsening with no apparent signs of recrystallization...... even after 2 h of annealing. Both coarsening and softening are rapid within first 10 minutes of annealing followed by a slower evolution with increasing annealing duration. Evidence of triple junction (TJ) motion during coarsening is obtained by inspecting the microstructure in one region using...... the electron backscatter diffraction technique both before and after annealing for 10 minutes. The fraction of fast-migrating TJs is found to strongly depend of the type of boundaries composing a junction. The greatest fraction of fast-migrating TJs is in the group, where all boundaries forming a junction...

Annealing effect on magnetic property and recording performance of [FePt/MgO]n perpendicular magnetic recording media

International Nuclear Information System (INIS)

Suzuki, Takao; Zhang, Zhengang; Singh, Amarendra K.; Yin, Jinhua; Perumal, A.; Osawa, Hiroshi

2005-01-01

Granular-type FePt perpendicular magnetic recording media with (001)-texture, obtained by annealing FePt/MgO multilayer films, are fabricated onto 2.5-in glass discs. For the sake of spin-stand testing, the coercivity of FePt films is carefully modulated by controlling the annealing conditions. With annealing, exchange coupling between FePt grains is decreased, indicated by the reductions in α value and activation volume. FePt ordering process is dependent on initial FePt/MgO multilayer structures, which governs the optimum annealing condition regarding coercivities and α(=4π(dM/dH)H=Hc). The SNR ratio exhibits a sensitive dependence on initial FePt/MgO multilayer structures as well as annealing conditions

Temperature dependence of annealing on the contact resistance of MoS2 with graphene electrodes observed

Science.gov (United States)

Lu, Qin; Fang, Cizhe; Liu, Yan; Shao, Yao; Han, Genquan; Zhang, Jincheng; Hao, Yue

2018-04-01

Two-dimensional (2D) materials are promising candidates for atomically thin nanoelectronics. Among them, MoS2 has attracted considerable attention in the nanoscience and nanotechnology community owing to its unique characteristics including high electron mobility and intrinsic band gap. In this study, we experimentally explored the contact resistances of MoS2 films based on much layered graphene films as electrodes using the circular transmission line model (CTLM). The variation in the chemical composition of the material is thoroughly analyzed by Raman and X-ray photoelectric spectroscopy (XPS) measurements. Experimental results demonstrate that annealing followed by oxygen plasma treatment can effectively improve the contact resistance. Furthermore, the current-voltage curves measured after different annealing temperatures indicate good linear characteristics, which means a marked improvement in electrical property. Calculations show that a relatively low contact resistance of ˜4.177 kΩ (ignoring its size) without back gate voltage in a single-layer graphene/MoS2 structure at an optimal annealing temperature of 500 °C is achieved. This work about the effect of annealing temperature on contact resistance can also be employed for other 2D materials, which lays a foundation for further development of novel 2D material devices.

A quantitative model of the major pathways for radiation-induced DNA double-strand break repair

International Nuclear Information System (INIS)

Belov, O.V.; Krasavin, E.A.; Lyashko, M.S.; Batmunkh, M.; Sweilam, N.H.

2014-01-01

We have developed a model approach to simulate the major pathways of DNA double-strand break (DSB) repair in mammalian and human cells. The proposed model shows a possible mechanistic explanation of the basic regularities of DSB processing through the nonhomologous end-joining (NHEJ), homologous recombination (HR), and single-strand annealing (SSA). It reconstructs the time-courses of radiation-induced foci specific to particular repair processes including the major intermediate stages. The model is validated for ionizing radiations of a wide range of linear energy transfer (0.2-236 keV/μm) including a relatively broad spectrum of heavy ions. The appropriate set of reaction rate constants was suggested to satisfy the kinetics of DSB rejoining for the considered types of exposure. The simultaneous assessment of three repair pathways allows one to describe their possible biological relations in response to radiation. With the help of the proposed approach, we reproduce several experimental data sets on γ-H2AX foci remaining in different types of cells including those defective in NHEJ, HR, or SSA functions.

Helical self-organization and hierarchical self-assembly of an oligoheterocyclic pyridine-pyridazine strand into extended supramolecular fibers.

Science.gov (United States)

Cuccia, Louis A; Ruiz, Eliseo; Lehn, Jean-Marie; Homo, Jean-Claude; Schmutz, Marc

2002-08-02

The synthesis and characterization of an alternating pyridine-pyridazine strand comprising thirteen heterocycles are described. Spontaneous folding into a helical secondary structure is based on a general molecular self-organization process enforced by the conformational information encoded within the primary structure of the molecular strand itself. Conformational control based on heterocyclic "helicity codons" illustrates a strategy for designing folding properties into synthetic oligomers (foldamers). Strong intermolecular interactions of the highly ordered lock-washer subunits of compound 3 results in hierarchical supramolecular self-assembly into protofibrils and fibrils. Compound 3 also forms mechanically stable two-dimensional Langmuir-Blodgett and cast thin films.

Simple design for DNA nanotubes from a minimal set of unmodified strands: rapid, room-temperature assembly and readily tunable structure.

Science.gov (United States)

Hamblin, Graham D; Hariri, Amani A; Carneiro, Karina M M; Lau, Kai L; Cosa, Gonzalo; Sleiman, Hanadi F

2013-04-23

DNA nanotubes have great potential as nanoscale scaffolds for the organization of materials and the templation of nanowires and as drug delivery vehicles. Current methods for making DNA nanotubes either rely on a tile-based step-growth polymerization mechanism or use a large number of component strands and long annealing times. Step-growth polymerization gives little control over length, is sensitive to stoichiometry, and is slow to generate long products. Here, we present a design strategy for DNA nanotubes that uses an alternative, more controlled growth mechanism, while using just five unmodified component strands and a long enzymatically produced backbone. These tubes form rapidly at room temperature and have numerous, orthogonal sites available for the programmable incorporation of arrays of cargo along their length. As a proof-of-concept, cyanine dyes were organized into two distinct patterns by inclusion into these DNA nanotubes.

Double strand break rejoining by the Ku-dependent mechanism of non-homologous end-joining

International Nuclear Information System (INIS)

Jeggo, P.; Singleton, B.; Beamish, H.; Priestley, A.

1999-01-01

The DNA-dependent protein kinase functions in the repair of DNA double strand breaks (DSBs) and in V(D)J recombination. To gain insight into the function of DNA-PK in this process we have carried out a mutation analysis of Ku80 and DNA-PKcs. Mutations at multiple sites within the N-terminal two thirds of Ku80 result in loss of Ku70/80 interaction, loss of DNA end-binding activity and inability to complement Ku80 defective cell fines. In contrast, mutations in the carboxy terminal region of the protein do not impair DNA end-binding activity but decrease the ability of Ku to activate DNA-PK. To gain insight into important functional domains within DNA-PKcs, we have analysed defective mutants, including the mouse scid cell line, and the rodent mutants, ire-20 and V-3. Mutational changes in the carboxy terminal region have been identified in all cases. Our results strongly suggest that the C-terminus of DNA-PKcs is required for kinase activity. (author)

Radiation-induced strand-breaks and DNA-protein crosslinks depend predominantly on the dose, oxygen concentration and repair time

International Nuclear Information System (INIS)

Wheeler, K.T.; Miyagi, Y.; Zhang, H.

1995-01-01

It has been known for many years that the DNA damage produced by ionizing radiation depends upon the oxygen concentration around the DNA. For example, the number of DNA strand-breaks (SBs) formed per unit dose decreases at low oxygen concentrations, and the number of DNA-protein crosslinks formed per unit dose increases at low oxygen concentrations. If radiation-induced SBs and DPCs are to be useful for detecting and/or quantifying hypoxic cells in solid tumors, the formation of these lesions must depend predominantly on the oxygen concentration around the DNA. All other physical, biological, and physiological factors must either be controllable or have little influence on the assay used to measure these lesions. This paper is a summary of the authors' recent experiments to determine if the radiation-induced SBs and DPCs measured by alkaline elution may be used to estimate the hypoxic fraction or fractional hypoxic volume of solid tumors

Structure evolution and magnetic properties of annealed nanoscale Gd/Ti multilayers

Directory of Open Access Journals (Sweden)

Larrañaga A.

2013-01-01

Full Text Available The structure and magnetic properties were comparatively analyzed for [Gd/Ti]n multilayers with Gd layer thickness of 1.5 to 12 nm. Multilayers were deposited by sputtering technique at room temperature and annealed for the temperatures up to 400 ºC. It was observed that the samples are highly textured in a different way depending on the Gd layer thickness and annealing temperature. It was found that the heat treatment practically does not change the Gd grain size. The lattice parameters obtained from X-ray results change significantly only for [Gd(1.5nm/Ti]50 multilayers, but their values remain higher than for the bulk Gd. The initial slope of the temperature dependence of magnetization near Curie temperature becomes steeper and Curie temperature increases upon annealing. Curie temperature variation can be understood by taking into account both relaxation of the lattice imperfections and change in lattice constants.

The Effect of Basepair Mismatch on DNA Strand Displacement.

Science.gov (United States)

Broadwater, D W Bo; Kim, Harold D

2016-04-12

DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A Novel Leu92 Mutant of HIV-1 Reverse Transcriptase with a Selective Deficiency in Strand Transfer Causes a Loss of Viral Replication.

Science.gov (United States)

Herzig, Eytan; Voronin, Nickolay; Kucherenko, Nataly; Hizi, Amnon

2015-08-01

The process of reverse transcription (RTN) in retroviruses is essential to the viral life cycle. This key process is catalyzed exclusively by the viral reverse transcriptase (RT) that copies the viral RNA into DNA by its DNA polymerase activity, while concomitantly removing the original RNA template by its RNase H activity. During RTN, the combination between DNA synthesis and RNA hydrolysis leads to strand transfers (or template switches) that are critical for the completion of RTN. The balance between these RT-driven activities was considered to be the sole reason for strand transfers. Nevertheless, we show here that a specific mutation in HIV-1 RT (L92P) that does not affect the DNA polymerase and RNase H activities abolishes strand transfer. There is also a good correlation between this complete loss of the RT's strand transfer to the loss of the DNA clamp activity of the RT, discovered recently by us. This finding indicates a mechanistic linkage between these two functions and that they are both direct and unique functions of the RT (apart from DNA synthesis and RNA degradation). Furthermore, when the RT's L92P mutant was introduced into an infectious HIV-1 clone, it lost viral replication, due to inefficient intracellular strand transfers during RTN, thus supporting the in vitro data. As far as we know, this is the first report on RT mutants that specifically and directly impair RT-associated strand transfers. Therefore, targeting residue Leu92 may be helpful in selectively blocking this RT activity and consequently HIV-1 infectivity and pathogenesis. Reverse transcription in retroviruses is essential for the viral life cycle. This multistep process is catalyzed by viral reverse transcriptase, which copies the viral RNA into DNA by its DNA polymerase activity (while concomitantly removing the RNA template by its RNase H activity). The combination and balance between synthesis and hydrolysis lead to strand transfers that are critical for reverse transcription

Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition.

Science.gov (United States)

Borovok, Natalia; Iram, Natalie; Zikich, Dragoslav; Ghabboun, Jamal; Livshits, Gideon I; Porath, Danny; Kotlyar, Alexander B

2008-09-01

We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin-biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics.

Effect of chemical ordering annealing on martensitic transformation and superelasticity in polycrystalline Ni–Mn–Ga microwires

Energy Technology Data Exchange (ETDEWEB)

Qian, M.F. [School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Advanced Composites Centre for Innovation and Science (ACCIS), University of Bristol, Queen’s Building, University Walk, Bristol BS8 1TR (United Kingdom); Zhang, X.X., E-mail: xxzhang@hit.edu.cn [School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Wei, L.S.; Geng, L. [School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Peng, H.X., E-mail: hxpengwork@zju.edu.cn [Institute for Composites Science Innovation (InCSI), School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China)

2015-10-05

Highlights: • Chemical ordering annealing on Ni–Mn–Ga microwires was found to reduce the defect density and internal stress. • Chemical ordering annealing on Ni–Mn–Ga microwires was found to increase the MT temperatures, Curie point and saturation magnetization. • Chemical ordering annealing on Ni–Mn–Ga microwires was found to decrease the SIM stress and improve the superelastic reversibility. • Chemical ordering annealing on Ni–Mn–Ga microwires was found to weaken the temperature dependences of the superelastic stresses. - Abstract: Polycrystalline Ni–Mn–Ga microwires of diameter 30–80 μm were prepared by melt-extraction technique on a large scale. The rapidly solidified microwires exhibit a fairly high ductility and excellent shape memory property. Here, with the aim to reduce the defect density, internal stress and compositional inhomogeneity in the as-extracted microwires, a stepwise chemical ordering annealing heat treatment was carried out and the effect of annealing on martensitic transformation, magnetic properties and superelastic behavior were investigated. The results indicate that annealing increase the transformation temperature and decrease the transformation hysteresis. These are related to composition homogenization, increase of atomic ordering and decrease in internal stress and defects. During mechanical tests, the stress-induced martensite (SIM) formation took place at a much lower stress after annealing treatment. The annealed microwires also demonstrate a lower superelastic hysteresis and a higher recovery rate compared to the as-extracted microwires. The temperature dependence of SIM stress is weaker after annealing, which is related to the enthalpy change (ΔH) and phase transformation temperature change according to the Clausius–Clapeyron relation.

Mechanical behavior of multipass welded joint during stress relief annealing

International Nuclear Information System (INIS)

Ueda, Yukio; Fukuda, Keiji; Nakacho, Keiji; Takahashi, Eiji; Sakamoto, Koichi.

1978-01-01

An investigation into mechanical behavior of a multipass welded joint of a pressure vessel during stress relief annealing was conducted. The study was performed theoretically and experimentally on idealized research models. In the theoretical analysis, the thermal elastic-plastic creep theory developed by the authors was applied. The behavior of multipass welded joints during the entire thermal cycle, from welding to stress relief annealing, was consistently analyzed by this theory. The results of the analysis show a good, fundamentally coincidence with the experimental findings. The outline of the results and conclusions is as follows. (1) In the case of the material (2 1/4Cr-1Mo steel) furnished in this study, the creep strain rate during stress relief annealing below 575 0 C obeys the strain-hardening creep law using the transient creep and the one above 575 0 C obeys the power creep law using the stational creep. (2) In the transverse residual stress (σsub(x)) distribution after annealing, the location of the largest tensile stress on the top surface is about 15 mm away from the toe of weld, and the largest at the cross section is just below the finishing bead. These features are similar to those of welding residual stresses. But the stress distribution after annealing is smoother than one from welding. (3) The effectiveness of stress relief annealing depends greatly on the annealing temperature. For example, most of residual stresses are relieved at the heating stage with a heating rate of 30 0 C/hr. to 100 0 C/hr. if the annealing temperature is 650 0 C, but if the annealing temperature is 550 0 C, the annealing is not effective even with a longer holding time. (4) In the case of multipass welding residual stresses studied in this paper, the behaviors of high stresses during annealing are approximated by ones during anisothermal relaxation. (auth.)

Growth of Ge/Si(100) Nanostructures by Radio-Frequency Magnetron Sputtering: the Role of Annealing Temperature

Institute of Scientific and Technical Information of China (English)

ALIREZA Samavati; S. K. Ghoshal; Z. Othaman

2012-01-01

Surface morphologies of Ge islands deposited on Si(100) substrates are characterized and their optical properties determined.Samples are prepared by rf magnetron sputtering in a high-vacuum chamber and are annealed at 600℃,700℃ and 800℃ for 2 min at nitrogen ambient pressure.Atomic force microscopy,field emission scanning electron microscopy,visible photoluminescence (PL) and energy dispersive x-ray spectroscopy are employed.The results for the annealing temperature-dependent sample morphology and the optical properties are presented.The density,size and roughness are found to be strongly influenced by the annealing temperature.A red shift of ～0.29 eV in the PL peak is observed with increasing annealing temperature.%Surface morphologies of Ge islands deposited on Si(100) substrates are characterized and their optical properties determined. Samples are prepared by rf magnetron sputtering in a high-vacuum chamber and are annealed at 600℃, 700℃ and 800℃ for 2 min at nitrogen ambient pressure. Atomic force microscopy, field emission scanning electron microscopy, visible photoluminescence (PL) and energy dispersive x-ray spectroscopy are employed. The results for the annealing temperature-dependent sample morphology and the optical properties are presented. The density, size and roughness are found to be strongly influenced by the annealing temperature. A red shift of ~0.29 eV in the PL peak is observed with increasing annealing temperature.

Atomic scale imaging of structural changes in solid electrolyte lanthanum lithium niobate upon annealing

International Nuclear Information System (INIS)

Hu, Xiaobing; Fisher, Craig A.J.; Kobayashi, Shunsuke; Ikuhara, Yumi H.; Fujiwara, Yasuyuki; Hoshikawa, Keigo; Moriwake, Hiroki; Kohama, Keiichi; Iba, Hideki; Ikuhara, Yuichi

2017-01-01

La (1-x)/3 Li x NbO 3 (LLNbO) is a promising electrolyte material for solid-state lithium-ion batteries because it is stable in contact with Li metal and contains a high concentration of intrinsic Li-ion vacancies. One strategy for improving its ionic conductivity and making it more competitive with other solid-state Li-ion electrolytes is to disorder the Li-ion vacancies by appropriate post-synthesis heat treatment, e.g., annealing. In this study, we examine the effects of annealing on single crystals of LLNbO with Li contents x = 0.07 and 0.13 based on simultaneous atomic resolution high angle annular dark field and annular bright field imaging methods using state-of-the-art aberration corrected scanning transmission electron microscopes. It is found that La modulation within A1 layers of the cation-deficient layered perovskite structure becomes more diffuse after annealing. In addition, some La atoms move to A-site positions and O4 window positions in the nominally vacant A2 layer, while O atom columns in this layer become rumpled in the [001] p direction, indicating that the NbO 6 octahedra are more heavily distorted after annealing. The observed crystal structure differences between as-prepared and annealed single crystals explain the drop in Li-ion conductivities of LLNbO single crystals after heat treatment.

Enzymatic quantification of strand breaks of DNA induced by vacuum-UV radiation

International Nuclear Information System (INIS)

Ito, Takashi

1986-01-01

Hind3 digested plasmid DNA dried on an aluminum plate was irradiated by vacuum-UV at 160 and 195 nm using a synchrotron irradiation system. A change induced in the DNA, presumably a single strand break, was quantified by the aid of the strand break-derived stimulation of poly(ADP-ribose) synthetase activity. The end group of strand breaks so induced was recognized by the enzyme as effectively as that by DNase 1 treatment, suggesting a nicking as the major lesion inflicted on the DNA. The fluence (UV) dependent stimulation of poly(ADP-ribose) synthetase activity was much higher upon 160 nm irradiation than upon 195 nm irradiation. (Auth.)

Very fast simulated re-annealing

OpenAIRE

L. Ingber

1989-01-01

Draft An algorithm is developed to statistically find the best global fit of a nonlinear non-convex cost-function over a D-dimensional space. It is argued that this algorithm permits an annealing schedule for ‘‘temperature’’ T decreasing exponentially in annealing-time k, T = T0 exp(−ck1/D). The introduction of re-annealing also permits adaptation to changing sensitivities in the multidimensional parameter-space. This annealing schedule is faster than fast Cauchy annealing, ...

Comparative study of size dependent four-point probe sheet resistance measurement on laser annealed ultra-shallow junctions

DEFF Research Database (Denmark)

Petersen, Dirch Hjorth; Lin, Rong; Hansen, Torben Mikael

2008-01-01

have been used to characterize the sheet resistance uniformity of millisecond laser annealed USJs. They verify, both experimentally and theoretically, that the probe pitch of a four-point probe can strongly affect the measured sheet resistance. Such effect arises from the sensitivity (or "spot size......In this comparative study, the authors demonstrate the relationship/correlation between macroscopic and microscopic four-point sheet resistance measurements on laser annealed ultra-shallow junctions (USJs). Microfabricated cantilever four-point probes with probe pitch ranging from 1.5 to 500 mu m......") of an in-line four-point probe. Their study shows the benefit of the spatial resolution of the micro four-point probe technique to characterize stitching effects resulting from the laser annealing process....

The origin of the coercivity reduction of Nd–Fe–B sintered magnet annealed below an optimal temperature

International Nuclear Information System (INIS)

Akiya, T.; Sasaki, T.T.; Ohkubo, T.; Une, Y.; Sagawa, M.; Kato, H.; Hono, K.

2013-01-01

In order to understand the origin of the coercivity reduction in a sintered Nd–Fe–B magnet that is annealed below an optimal annealing temperature, we performed focused ion beam/scanning electron microscopy tomography of post-sinter annealed magnets. A number of grain boundary cracks were observed between Nd 2 Fe 14 B grains and Nd-rich phases in the sample annealed below the optimal temperature. We deduced micromagnetic parameters α and N eff by fitting the temperature dependence of the coercivity. While α was constant regardless of the annealing conditions, N eff increased in the sample annealed below the optimal temperature with the reduced coercivity. This indicates that the reduction of the coercivity is due to the local stray field at the cracks. - Highlights: • We performed FIB/SEM tomography of post-sinter annealed magnets. • A number of grain boundary cracks were observed in the low-coercivity sample. • Parameters α and N eff were deduced from the temperature dependence of coercivity. • While α was constant, N eff increased in the low-coercivity sample. • The reduction of the coercivity is due to the local stray field at the cracks

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

Influence of DNA conformation on radiation-induced single-strand breaks

International Nuclear Information System (INIS)

Barone, F.; Belli, M.; Mazzei, F.

1994-01-01

We performed experiments on two DNA fragments of about 300 bp having different conformation to test whether radiation-induced single-strand breakage is dependent on DNA conformation. Breakage analysis was carried out by denaturing polyacrylamide gel electrophoresis, which allows determination of the broken site at single nucleotide resolution. We found uniform cutting patterns in B-form regions. On the contrary, X- or γ-irradiation of curved fragments of kinetoplast DNA showed that the distribution of single-strand breaks was not uniform along the fragment, as the cleavage pattern was modulated in phase with the runs of A-T pairs. This modulation likely reflected the reduced accessibility of the sites which on hydroxyl-radical attack give rise to strand breaks. The cleavage pattern was phased with the runs of A-T pairs. Moreover, the overall yield of strand breaks was considerably lower in curved DNA fragments than in those with extended straight regions. The conformation effect found here indicates that the cleavage pattern reflects the fine structural features of DNA. (orig./MG)

Suppression of matrix protein synthesis in endothelial cells by herpes simplex virus is not dependent on viral protein synthesis

International Nuclear Information System (INIS)

Kefalides, N.A.

1986-01-01

The synthesis of matrix proteins by human endothelial cells (EC) in vitro was studied before and at various times after infection with Herpes Simplex virus Type 1 (HSV-1) or 2 (HSV-2). Monolayers of EC were either mock-infected or infected with virus for 1 hr at a multiplicity infection (MOI) of 5 to 20 at 37 0 C. Control and infected cultures were pulse-labeled for 1 or 2 hrs with either [ 14 C]proline or [ 35 S]methionine. Synthesis of labeled matrix proteins was determined by SDS-gel electrophoresis. Suppression of synthesis of fibronectin, Type IV collagen and thrombospondin began as early as 2 hrs and became almost complete by 10 hrs post-infection. The degree of suppression varied with the protein and the virus dose. Suppression of Type IV collagen occurred first followed by that of fibronectin and then thrombospondin. Infection of EC with UV irradiated HSV-1 or HSV-2 resulted in suppression of host-cell protein synthesis as well as viral protein synthesis. Infection with intact virus in the presence of actinomycin-D resulted in suppression of both host-cell and viral protein synthesis. The data indicate that infection of EC with HSV leads to suppression of matrix protein synthesis which does not depend on viral protein synthesis

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

Science.gov (United States)

Hirsch, Matthew L; Fagan, B Matthew; Dumitru, Raluca; Bower, Jacquelyn J; Yadav, Swati; Porteus, Matthew H; Pevny, Larysa H; Samulski, R Jude

2011-01-01

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.

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.

Lamellar Diblock Copolymer Thin Films during Solvent Vapor Annealing Studied by GISAXS

DEFF Research Database (Denmark)

Zhang, Jianqi; Posselt, Dorthe; Smilgies, Detlef-M.

2014-01-01

The reorientation of lamellae and the dependence of the lamellar spacing, Dlam, on polymer volume fraction, ϕP, Dlam ∝ ϕP–β, in diblock copolymer thin films during solvent vapor annealing (SVA) are examined by combining white light interferometry (WLI) and grazing-incidence small-angle X-ray scat......The reorientation of lamellae and the dependence of the lamellar spacing, Dlam, on polymer volume fraction, ϕP, Dlam ∝ ϕP–β, in diblock copolymer thin films during solvent vapor annealing (SVA) are examined by combining white light interferometry (WLI) and grazing-incidence small-angle X...

The annealing influence onto the electrical and magnetic behavior of magnetoresistive/insulator system

International Nuclear Information System (INIS)

Ahmed, A.M.; Mohamed Abd El-Mo'ez A; Mohamed, H.F.; Diab, A.K.; Mohamed Ami M; Mazen, A.E.A.

2016-01-01

This investigation is mainly concerned with the effect of annealing temperature (600, 700, 800 and 900 deg C) in air for (La 0. 7Ba 0.3 MnO 3 ) 1-x /(NiO) x with x = 0 and x = 0.10 samples. It was shown that the annealing temperature does not affect the structure and parameters of rhombohedral lattice of the samples. However, it is observed that the annealing treatment has a notable effect on the electrical resistivity and the metal-semiconductor transition temperature Tms. Temperature dependent magnetization measurements showed a decrease in Curie temperature TC with annealing temperature. In the same time, annealing process decreases the magnetoresistance of La 0.7 Ba 0.3 MnO 3 , in contrast to (La 0.7 Ba 0.3 MnO 3 ) 0.9 /(NiO) 0.1 composite.

Effect of pre-annealing on NO32- centers in synthetic hydroxyapatite

International Nuclear Information System (INIS)

Nosenko, V.V.; Vorona, I.P.; Ishchenko, S.S.; Baran, N.P.; Zatovsky, I.V.; Gorodilova, N.A.; Povarchuk, V.Yu.

2012-01-01

Effect of pre-annealing of synthetic hydroxyapatite (HAP) on properties of γ- and UV- induced NO 3 2- centers was studied by electron paramagnetic resonance (EPR). Nitrate-containing hydroxyapatite powders ((N)HAP)) and the powders with an admixture of carbonate and nitrate ions ((C,N)HAP) were annealed in the temperature range T ann = 20 °C − 600 °C before irradiation. It was found that pre-annealing of (N)HAP samples changes the parameters of NO 3 2- centers while no changes took place in (C,N)HAP. Moreover, at the pre-annealing temperatures T ann > 200 °C two new NO 3 2- centers were observed in (N)HAP samples; they are characterized by larger value of A ⊥ (3.67 and 4.41 mT) as compared to the known centers. It was also found that the dependence of NO 3 2- centers amount on T ann is non-monotonous in both types of samples. Presumably this is caused by the escape of water molecules from HAP during the annealing and essential modification of the defect subsystem of HAP.

Effects of annealing temperature in a metal alloy nano-dot memory

International Nuclear Information System (INIS)

Lee, Jung Min; Lee, Gae Hun; Song, Yun Heub; Bea, Ji Cheol; Tanaka, Tetsu

2011-01-01

The annealing temperature dependence of the capacitance-voltage (C-V) characteristic has been studied in a metal-oxide semiconductor structure containing FePt nano-dots. Several in-situ annealing temperatures from 400 to ∼700 .deg. C in a high vacuum ambience (under 1 x 10 -5 Pa) were evaluated in view of the cell's characteristics and its reliability. Here, we demonstrate that the annealing temperature is significant for memory performance in an alloy metal nano-dot structure. A higher in-situ temperature provides better retention and a more reliable memory window. In the sample with an in-situ annealing condition of 700 .deg. C for 30 min, a memory window of 9.2 V at the initial stage was obtained, and a memory window of 6.2 V after 10 years was estimated, which is reliable for a non-volatile memory. From these results, the annealing condition for an alloy metal nano-dot memory is one of the critical parameters for the memory characteristics, and should be optimized for better memory performance.

KARAKTERISTIK ORIENTED STRAND BOARD DARI KAYU AKASIA DAN AFRIKA BERDASARKAN PENYUSUNAN ARAH STRAND

Directory of Open Access Journals (Sweden)

Nurhaida

2008-04-01

Full Text Available The research objectives arc to evaluate physical and mechanical properties of OSB based on strands orientation; and to evaluate physical and mechanical properties of OSB made from akasia wood (Acacia mangium Wild and afrika wood (Maesopsis eminii Engl. Akasia and afrika wood are used for OSB strand material with phenol formaldehyde (PF as adhesives and addition of paraffin. OSB made in this research is consist of three plies whereas are differed into eight (8 strand orientations. In the making process, hot press was carried out at 160OC and pressure 25kg.cm-2 for 15 minutes. Determination of OSB physical and mechanical properties is referred to JIS A 5908-2003. Result showed that strand orientations has no affect to OSB physical properties except for linicr swelling 24h, but it significantly influence all mechanical properties of OSB. Wood species have an effect on mechanical properties of OSB in the dry test, wet MOE lengthwise test and OSB physical properties, particularly to OSB density and water absorbing capability at 2h and 24h. All of OSB physical properties arc meet JIS A 5908-2003 standard, but not all of the mechanical properties such as dry MOE lengthwise, dry MOE and MOR widthwise. The best physical and mechanical properties is presented by OSB made from akasia wood in strand orientation F, G, Band C whereas all parameters meet JIS A 5908-2003 standard. In comparation with strand orientation B that is frequent used in industry, strand orientation F and G arc proficient to raise the modulus elasticity value (MOE and strength (MOR as much as 167.81-231.65% and 89.73-109.87%, respectively; especially in widthwise board application. Furthermore, strand orientation F and G arc more flexible as structural components

Annealing temperature dependent reversible wettability switching of micro/nano structured ZnO superhydrophobic surfaces

Science.gov (United States)

Velayi, Elmira; Norouzbeigi, Reza

2018-05-01

Superhydrophobic ZnO surfaces with reversibly tunable wettability were fabricated on stainless steel meshes via a facile chemical bath deposition method just by regulating the micro/nano structured ZnO needles without using chemical post modifications. The obtained surfaces can be easily and reversibly switched between superhydrophobic and superhydrophilic/underwater superoleophobic characteristics by altering the annealing temperatures. As-prepared sample exhibited long-term superhydrophobic properties with a water contact angle (WCA) of 163.8° ± 1.8° and contact angle hysteresis (CAH) of 1.1° ± 0.8°. The SEM, XRD, XPS and Raman analyses were employed to characterize the morphological features and surface chemistry of the prepared samples. SEM images showed the formation of ZnO micro/nanoneedles with a diameter of ∼90 nm on the substrate. The superhydrophobic ZnO surface was switched to highly hydrophilic and underwater superoleophobic properties with an oil contact angle (OCA) of about 172.5° after being annealed at 400 °C in air for 30 min and restored to superhydrophobic state again by altering the annealing temperature to 150 °C. Mechanical durability of the ZnO superhydrophobic surface was tested by an abrasion test. Results confirmed that the prepared surface exhibited an excellent robustness after 20 abrasion cycles under the pressure of 4.7 kPa.

Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli.

Science.gov (United States)

Thomason, Lynn C; Costantino, Nina; Court, Donald L

2016-09-13

Recombineering, in vivo genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in Escherichia coli are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the in vivo dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion. Bacteriophage homologous recombination systems are widely used for in vivo genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand

Evolution of microstructure at hot band annealing of ferritic FeSi steels

Energy Technology Data Exchange (ETDEWEB)

Schneider, Jürgen, E-mail: juergen.schneider@t-online.de [Institute of Metal Forming, Technische Universität Bergakademie Freiberg, Bernhard-von Cotta-Str. 4, D-09596 Freiberg (Germany); Stahlzentrum Freiberg e.V., Leipziger Straße 34, D-09599 Freiberg (Germany); Li, Guangqiang [State Key Lab. of Refractories and Metallurgy, Wuhan University of Science and Technology, No. 947 Heping Avenue, Qingshan District, Wuhan 430081 (China); Franke, Armin [Stahlzentrum Freiberg e.V., Leipziger Straße 34, D-09599 Freiberg (Germany); Zhou, Bowen [State Key Lab. of Refractories and Metallurgy, Wuhan University of Science and Technology, No. 947 Heping Avenue, Qingshan District, Wuhan 430081 (China)

2017-02-15

The magnetic properties of the finally fabricated nonoriented FeSi steels critically depend on the microstructure and on the occurring crystallographic texture. The fabrication route comprises hot rolling, coiling and cooling, hot band annealing before cold rolling (optional), cold rolling and the final thermal treatment. As well known there is an interplay between the microstructure and texture during the various processing steps. For that reason, it is of interest to know more on the evolution of the microstructure at hot band annealing of hot band prepared in different ways. In this paper we will summarize our recent results on the evolution of microstructure during thermal annealing of hot band: thermal treatment following immediately the last pass of hot rolling or a hot band annealing as a separate processing step before cold rolling.

Structural features of single-stranded integron cassette attC sites and their role in strand selection.

Directory of Open Access Journals (Sweden)

Marie Bouvier

2009-09-01

Full Text Available We recently showed that cassette integration and deletion in integron platforms were occurring through unconventional site-specific recombination reactions involving only the bottom strand of attC sites. The lack of sequence conservation among attC sites led us to hypothesize that sequence-independent structural recognition determinants must exist within attC sites. The structural data obtained from a synaptic complex of the Vibrio cholerae integrase with the bottom strand of an attC site has shown the importance of extra helical bases (EHB inside the stem-loop structure formed from the bottom strand. Here, we systematically determined the contribution of three structural elements common to all known single-stranded attC site recombination substrates (the EHBs, the unpaired central spacer (UCS, and the variable terminal structure (VTS to strand choice and recombination. Their roles have been evaluated in vivo in the attIxattC reaction context using the suicide conjugation assay we previously developed, but also in an attCxattC reaction using a deletion assay. Conjugation was used to deliver the attC sites in single-stranded form. Our results show that strand choice is primarily directed by the first EHB, but the presence of the two other EHBs also serves to increase this strand selection. We found that the structure of the central spacer is essential to achieve high level recombination of the bottom strand, suggesting a dual role for this structure in active site exclusion and for hindering the reverse reaction after the first strand exchange. Moreover, we have shown that the VTS has apparently no role in strand selectivity.

Vapor annealing synthesis of non-epitaxial MgB2 films on glassy carbon

Science.gov (United States)

Baker, A. A.; Bayu Aji, L. B.; Bae, J. H.; Stavrou, E.; Steich, D. J.; McCall, S. K.; Kucheyev, S. O.

2018-05-01

We describe the fabrication and characterization of 25–800 nm thick MgB2 films on glassy carbon substrates by Mg vapor annealing of sputter-deposited amorphous B films. Results demonstrate a critical role of both the initial B film thickness and the temperature–time profile on the microstructure, elemental composition, and superconducting properties of the resultant MgB2 films. Films with thicknesses of 55 nm and below exhibit a smooth surface, with a roughness of 1.1 nm, while thicker films have surface morphology consisting of elongated nano-crystallites. The suppression of the superconducting transition temperature for thin films scales linearly with the oxygen impurity concentration and also correlates with the amount of lattice disorder probed by Raman scattering. The best results are obtained by a rapid (12 min) anneal at 850 °C with large temperature ramp and cooling rates of ∼540 °C min‑1. Such fast processing suppresses the deleterious oxygen uptake.

Strand exchange of telomeric DNA catalyzed by the Werner syndrome protein (WRN) is specifically stimulated by TRF2

Science.gov (United States)

Edwards, Deanna N.; Orren, David K.; Machwe, Amrita

2014-01-01

Werner syndrome (WS), caused by loss of function of the RecQ helicase WRN, is a hereditary disease characterized by premature aging and elevated cancer incidence. WRN has DNA binding, exonuclease, ATPase, helicase and strand annealing activities, suggesting possible roles in recombination-related processes. Evidence indicates that WRN deficiency causes telomeric abnormalities that likely underlie early onset of aging phenotypes in WS. Furthermore, TRF2, a protein essential for telomere protection, interacts with WRN and influences its basic helicase and exonuclease activities. However, these studies provided little insight into WRN's specific function at telomeres. Here, we explored the possibility that WRN and TRF2 cooperate during telomeric recombination processes. Our results indicate that TRF2, through its interactions with both WRN and telomeric DNA, stimulates WRN-mediated strand exchange specifically between telomeric substrates; TRF2's basic domain is particularly important for this stimulation. Although TRF1 binds telomeric DNA with similar affinity, it has minimal effects on WRN-mediated strand exchange of telomeric DNA. Moreover, TRF2 is displaced from telomeric DNA by WRN, independent of its ATPase and helicase activities. Together, these results suggest that TRF2 and WRN act coordinately during telomeric recombination processes, consistent with certain telomeric abnormalities associated with alteration of WRN function. PMID:24880691

Five-Strand versus Four-Strand Hamstring Tendon Graft Technique for Anterior Cruciate Ligament Reconstruction: A Biomechanical Comparison.

Science.gov (United States)

Vaillant, Eric R; Parks, Brent G; Camire, Lyn M; Hinton, Richard Y

2017-11-01

The aim of this article is to compare diameter and stiffness, displacement, and strain in a five-strand versus four-strand hamstring graft for anterior cruciate ligament reconstruction. Eight matched pairs of lower extremities underwent four-strand or five-strand hamstring graft reconstruction. Diameter was significantly higher in the five-strand versus the four-strand construct ( p  = 0.002). No significant difference was found between the groups in construct displacement or stiffness. Significantly higher strain was observed in the inner limb versus the outer limb in the four-strand construct ( p  = 0.001) and in the inner limb versus the fifth limb in the 5-strand construct ( p  = 0.004). A fifth limb added to a four-strand hamstring graft significantly increased graft diameter but did not significantly change stiffness or displacement, suggesting that attachment of additional graft material via suture did not provide for full incorporation of the added limb into the graft at time zero. The inner limb in both constructs absorbed significantly greater load than did other limbs. The use of suture to attach additional material to a four-strand hamstring graft may not contribute to improved biomechanical qualities of the graft at time zero. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

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)

Modelling Toehold-Mediated RNA Strand Displacement

OpenAIRE

Šulc, Petr; Ouldridge, Thomas E.; Romano, Flavio; Doye, Jonathan P.K.; Louis, Ard A.

2015-01-01

We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperat...

Nucleic Acid Analogue Induced Transcription of Double Stranded DNA

DEFF Research Database (Denmark)

1998-01-01

RNA is transcribed from a double stranded DNA template by forming a complex by hybridizing to the template at a desired transcription initiation site one or more oligonucleic acid analogues of the PNA type capable of forming a transcription initiation site with the DNA and exposing the complex...... to the action of a DNA dependant RNA polymerase in the presence of nucleoside triphosphates. Equal length transcripts may be obtained by placing a block to transcription downstream from the initiation site or by cutting the template at such a selected location. The initiation site is formed by displacement...... of one strand of the DNA locally by the PNA hybridization....

Late Protein Synthesis-Dependent Phases in CTA Long-Term Memory: BDNF Requirement

OpenAIRE

Martínez-Moreno, Araceli; Rodríguez-Durán, Luis F.; Escobar, Martha L.

2011-01-01

It has been proposed that long-term memory persistence requires a late protein synthesis-dependent phase, even many hours after memory acquisition. Brain-derived neurotrophic factor (BDNF) is an essential protein synthesis product that has emerged as one of the most potent molecular mediators for long-term synaptic plasticity. Studies in the rat hippocampus have been shown that BDNF is capable to rescue the late-phase of long-term potentiation as well as the hippocampus-related long-term memo...

Defect annealing in Mn/Fe-implanted TiO2 (rutile)

International Nuclear Information System (INIS)

Gunnlaugsson, H P; Svane, A; Weyer, G; Mantovan, R; Masenda, H; Naidoo, D; Mølholt, T E; Gislason, H; Ólafsson, S; Johnston, K; Bharuth-Ram, K; Langouche, G

2014-01-01

A study of the annealing processes and charge state of dilute Fe in rutile TiO 2 single crystals was performed in the temperature range 143–662 K, utilizing online 57 Fe emission Mössbauer spectroscopy following low concentrations (<10 −3  at%) implantation of 57 Mn (T 1/2  = 1.5 min). Both Fe 3+ and Fe 2+ were detected throughout the temperature range. Three annealing stages were distinguished: (i) a broad annealing stage below room temperature leading to an increased Fe 3+ fraction; (ii) a sharp annealing stage at ∼330 K characterized by conversion of Fe 3+ to Fe 2+ and changes in the hyperfine parameters of Fe 2+ , attributed to the annealing of Ti vacancies in the vicinity of the probe atoms; and (iii) an annealing stage in the temperature range from 550 to 600 K, where all Fe ions are transformed to Fe 3+ , attributed to the annealing of the nearby O vacancies. The dissociation energy of Mn Ti –V O pairs was estimated to be 1.60(15) eV. Fe 2+ is found in an environment where it can probe the lattice structure through the nuclear quadrupole interaction evidencing the extreme radiation hardness of rutile TiO 2 . Fe 3+ is found in a paramagnetic state with slow spin–lattice relaxation which follows a ∼T n temperature dependence with 4.1 < n < 6.3 at T > 350 K. (paper)

Effect of vacuum annealing on evaporated pentacene thin films for memory device applications

International Nuclear Information System (INIS)

Gayathri, A.G.; Joseph, C.M.

2016-01-01

Graphical abstract: Switching of ITO/pentacene/Al thin films for different annealing temperatures. - Highlights: • Memory device performance in pentacene improved considerably with annealing. • ON/OFF ratio of the pentacene device increases due to annealing. • Threshold voltage reduces from 2.55 V to 1.35 V due to annealing. • Structure of pentacene thin films is also dependent on annealing temperature. - Abstract: Thin films of pentacene were deposited thermally onto glass substrates and annealed at 323 K, 373 K, 423 K, 473 K and 523 K in high vacuum. Effect of annealing on the morphological and structural properties of these films was studied. X-ray diffraction patterns confirmed the crystalline nature of the films. Electrical studies for the use as write once read many (WORM) memory devices were done for the vacuum deposited pentacene thin films on indium tin oxide coated glass. Due to annealing, a sharp increase in the ON/OFF ratio of current and a decrease in threshold voltage were observed at around 373 K. This device showed a stable switching with an ON/OFF current ratio as high as 10 9 and a switching threshold voltage of 1.35 V. The performance of the device degraded above 423 K due to the changes in the crystallinity of the film.

Effect of vacuum annealing on evaporated pentacene thin films for memory device applications

Energy Technology Data Exchange (ETDEWEB)

Gayathri, A.G., E-mail: gaythri305@yahoo.com; Joseph, C.M., E-mail: cmjoseph@rediffmail.com

2016-09-15

Graphical abstract: Switching of ITO/pentacene/Al thin films for different annealing temperatures. - Highlights: • Memory device performance in pentacene improved considerably with annealing. • ON/OFF ratio of the pentacene device increases due to annealing. • Threshold voltage reduces from 2.55 V to 1.35 V due to annealing. • Structure of pentacene thin films is also dependent on annealing temperature. - Abstract: Thin films of pentacene were deposited thermally onto glass substrates and annealed at 323 K, 373 K, 423 K, 473 K and 523 K in high vacuum. Effect of annealing on the morphological and structural properties of these films was studied. X-ray diffraction patterns confirmed the crystalline nature of the films. Electrical studies for the use as write once read many (WORM) memory devices were done for the vacuum deposited pentacene thin films on indium tin oxide coated glass. Due to annealing, a sharp increase in the ON/OFF ratio of current and a decrease in threshold voltage were observed at around 373 K. This device showed a stable switching with an ON/OFF current ratio as high as 10{sup 9} and a switching threshold voltage of 1.35 V. The performance of the device degraded above 423 K due to the changes in the crystallinity of the film.

Structural and compositional evolution of carbon-doped Ge{sub 2}Sb{sub 2}Te{sub 5} film under different annealing conditions

Energy Technology Data Exchange (ETDEWEB)

Kim, Ki-Hong; Kyoung, Yong-Koo; Yun, Dong-Jin [AS group, CAS center, SAIT, Samsung Electronics Co. Ltd., Yongin 446-712 (Korea, Republic of); Choi, Sang-Jun, E-mail: sangjun5545.choi@samsung.com [Device Architecture Lab, Semiconductor R and D center, Samsung Electronics Co. Ltd., Yongin 446-712 (Korea, Republic of)

2013-12-02

Changes in the microstructural and electrical properties of carbon-doped Ge{sub 2}Sb{sub 2}Te{sub 5} during thermal annealing under N{sub 2} and air atmospheres are investigated. The occurrence of compositional and structural changes was found to depend on the annealing conditions, and in particular, on the out-diffusion of germanium atoms. The thick oxidation layer generated during air annealing prevented germanium out-diffusion, leading to structural changes but no compositional changes. In contrast, germanium out-diffusion occurred during annealing under N{sub 2}, leading to compositional changes but preventing structural changes. - Highlights: • We investigate the stability of 10% carbon-doped Ge2Sb2Te5 alloys. • The compositional and structural changes depend on the annealing conditions. • Germanium out-diffusion occurs during N2 annealing, leading to compositional changes. • The oxidation layer generated during air annealing prevents germanium out-diffusion.

Effect of synthesis conditions on the preparation of YIG powders via co-precipitation method

International Nuclear Information System (INIS)

Rashad, M.M.; Hessien, M.M.; El-Midany, A.; Ibrahim, I.A.

2009-01-01

Yttrium iron garnet (YIG) (Y 3 Fe 5 O 12 ) powders have been synthesized through a co-precipitation method in the presence of sodium bis(2-ethylhexylsulfosuccinate), AOT as an anionic surfactant. The garnet precursors produced were obtained from aqueous iron and yttrium nitrates mixtures using 5 M sodium hydroxide at pH 10. A statistical Box-Behnken experimental design was used to investigate the effect of the main parameters (i.e. AOT surfactant concentration, annealing time and temperature) on YIG powder formation, crystallite size, morphology and magnetic properties. YIG particles were investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM), and vibrating sample magnetometer. XRD revealed that the formation of single cubic phase of YIG was temperature dependent and increased by increasing the annealing temperature from 800 to 1200 o C. SEM micrographs showed that the addition of AOT surfactant promoted the microstructure of YIG in crystalline cubic-like structure. The magnetic properties were sensitive to the synthesis variables of annealing temperature, time and AOT surfactant concentration. The maximum saturation magnetization (28.13 emu/g), remanence magnetization (21.57 emu/g) and coercive force (703 Oe) were achieved at an annealing temperature of 1200 o C, time 2 h and 500 ppm of AOT surfactant concentration.

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

Dynamic dependence on ATR and ATM for double-strand break repair in human embryonic stem cells and neural descendants.

Science.gov (United States)

Adams, Bret R; Golding, Sarah E; Rao, Raj R; Valerie, Kristoffer

2010-04-02

The DNA double-strand break (DSB) is the most toxic form of DNA damage. Studies aimed at characterizing DNA repair during development suggest that homologous recombination repair (HRR) is more critical in pluripotent cells compared to differentiated somatic cells in which nonhomologous end joining (NHEJ) is dominant. We have characterized the DNA damage response (DDR) and quality of DNA double-strand break (DSB) repair in human embryonic stem cells (hESCs), and in vitro-derived neural cells. Resolution of ionizing radiation-induced foci (IRIF) was used as a surrogate for DSB repair. The resolution of gamma-H2AX foci occurred at a slower rate in hESCs compared to neural progenitors (NPs) and astrocytes perhaps reflective of more complex DSB repair in hESCs. In addition, the resolution of RAD51 foci, indicative of active homologous recombination repair (HRR), showed that hESCs as well as NPs have high capacity for HRR, whereas astrocytes do not. Importantly, the ATM kinase was shown to be critical for foci formation in astrocytes, but not in hESCs, suggesting that the DDR is different in these cells. Blocking the ATM kinase in astrocytes not only prevented the formation but also completely disassembled preformed repair foci. The ability of hESCs to form IRIF was abrogated with caffeine and siRNAs targeted against ATR, implicating that hESCs rely on ATR, rather than ATM for regulating DSB repair. This relationship dynamically changed as cells differentiated. Interestingly, while the inhibition of the DNA-PKcs kinase (and presumably non-homologous endjoining [NHEJ]) in astrocytes slowed IRIF resolution it did not in hESCs, suggesting that repair in hESCs does not utilize DNA-PKcs. Altogether, our results show that hESCs have efficient DSB repair that is largely ATR-dependent HRR, whereas astrocytes critically depend on ATM for NHEJ, which, in part, is DNA-PKcs-independent.

Enhanced exchange bias in MnN/CoFe bilayers after high-temperature annealing

Science.gov (United States)

Dunz, M.; Schmalhorst, J.; Meinert, M.

2018-05-01

We report an exchange bias of more than 2700 Oe at room temperature in MnN/CoFe bilayers after high-temperature annealing. We studied the dependence of exchange bias on the annealing temperature for different MnN thicknesses in detail and found that samples with tMnN > 32nm show an increase of exchange bias for annealing temperatures higher than TA = 400 °C. Maximum exchange bias values exceeding 2000 Oe with reasonably small coercive fields around 600 Oe are achieved for tMnN = 42, 48 nm. The median blocking temperature of those systems is determined to be 180 °C after initial annealing at TA = 525 °C. X-ray diffraction measurements and Auger depth profiling show that the large increase of exchange bias after high-temperature annealing is accompanied by strong nitrogen diffusion into the Ta buffer layer of the stacks.

Photo annealing effect on p-doped inverted organic solar cell

Energy Technology Data Exchange (ETDEWEB)

Lafalce, Evan; Toglia, Patrick; Lewis, Jason E.; Jiang, Xiaomei, E-mail: xjiang@usf.edu [Department of Physics, University of South Florida, Tampa, Florida 33620 (United States)

2014-06-28

We report the transient positive photo annealing effect in which over 600% boost of power conversion efficiency was observed in inverted organic photovoltaic devices (OPV) made from P3HT/PCBM by spray method, after 2 hrs of constant solar AM 1.5 irradiation at low temperature. This is opposite to usual photodegradation of OPV, and cannot be explained by thermal activation alone since the mere temperature effect could only account for 30% of the enhancement. We have investigated the temperature dependence, cell geometry, oxygen influence, and conclude that, for p-doped active layer at room temperature, the predominant mechanism is photo-desorption of O{sub 2}, which eliminates electron traps and reduces space charge screening. As temperature decreases, thermal activation and deep trap-state filling start to show noticeable effect on the enhancement of photocurrent at intermediate low temperature (T = 125 K). At very low temperature, the dominant mechanism for photo annealing is trap-filling, which significantly reduces recombination between free and trapped carriers. At all temperature, photo annealing effect depends on illumination direction from cathode or anode. We also explained the large fluctuation of photocurrent by the capture/reemit of trapped electrons from shallow electron traps of O{sub 2}{sup -} generated by photo-doping. Our study has demonstrated the dynamic process of photo-doping and photo-desorption, and shown that photo annealing in vacuum can be an efficient method to improve OPV device efficiency.

Citrus psorosis virus RNA 1 is of negative polarity and potentially encodes in its complementary strand a 24K protein of unknown function and 280K putative RNA dependent RNA polymerase.

Science.gov (United States)

Naum-Onganía, Gabriela; Gago-Zachert, Selma; Peña, Eduardo; Grau, Oscar; Garcia, Maria Laura

2003-10-01

Citrus psorosis virus (CPsV), the type member of genus Ophiovirus, has three genomic RNAs. Complete sequencing of CPsV RNA 1 revealed a size of 8184 nucleotides and Northern blot hybridization with chain specific probes showed that its non-coding strand is preferentially encapsidated. The complementary strand of RNA 1 contains two open reading frames (ORFs) separated by a 109-nt intergenic region, one located near the 5'-end potentially encoding a 24K protein of unknown function, and another of 280K containing the core polymerase motifs characteristic of viral RNA-dependent RNA polymerases (RdRp). Comparison of the core RdRp motifs of negative-stranded RNA viruses, supports grouping CPsV, Ranunculus white mottle virus (RWMV) and Mirafiori lettuce virus (MiLV) within the same genus (Ophiovirus), constituting a monophyletic group separated from all other negative-stranded RNA viruses. Furthermore, RNAs 1 of MiLV, CPsV and RWMV are similar in size and those of MiLV and CPsV also in genomic organization and sequence.

Magnetization, Low Field Instability and Quench of RHQT Nb(3)Al Strands

Energy Technology Data Exchange (ETDEWEB)

Yamada, R.; Wake, M.; Kikuchi, A.; Velev, V.; /Fermilab

2009-01-01

Since 2005, we made and tested three RHQT Nb{sub 3}Al strands, one with Nb matrix and two with Ta matrix, which are fully stabilized with Cu electroplating. We observed anomalously large magnetization curves extending beyond 1 to 1.5 Tesla with the F1 Nb matrix strand at 4.2 K, when we measured its magnetization with a balanced coil magnetometer. This problem was eliminated with the Ta matrix strands operating at 4.2 K. But with these strands a similar but smaller anomalous magnetization was observed at 1.9 K. We studied these phenomena with FEM. With the F1 Nb matrix strand, it is explained that at low external field, inter-filamentary coupling currents in the outer layers of sub-elements create a shielding effect. It reduces the inside field, keeps the inside Nb matrix superconductive, and stands against a higher outside field beyond the Hc of Nb. At an even higher external field, the superconductivity of the whole Nb matrix collapses and releases a large amount of energy, which may cause a big quench. Depending on the size of the energy in the strand or the cable, a magnet could quench, causing the low field instability. Some attempt to analyze the anomaly with FEM is presented.

Room temperature growth of ZnO nanorods by hydrothermal synthesis

Science.gov (United States)

Tateyama, Hiroki; Zhang, Qiyan; Ichikawa, Yo

2018-05-01

The effect of seed layer morphology on ZnO nanorod growth at room temperature was studied via hydrothermal synthesis on seed layers with different thicknesses and further annealed at different temperatures. The change in the thickness and annealing temperature enabled us to control over a diameter of ZnO nanorods which are attributed to the changing of crystallinity and roughness of the seed layers.

Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells.

Science.gov (United States)

Huh, Yang Hoon; Cohen, Justin; Sherley, James L

2013-10-15

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs "know" the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency.

Effect of annealing induced residual stress on the resonance frequency of SiO2 microcantilevers

Science.gov (United States)

Balasubramanian, S.; Prabakar, K.; Tripura Sundari, S.

2018-04-01

In the present work, effect of residual stress, induced due to annealing of SiO2 microcantilevers (MCs) on their resonance frequency is studied. SiO2MCs of various dimensions were fabricated using direct laser writer & wet chemical etching method and were annealed at 800 °C in oxygen environment, post release. The residual stress was estimated from the deflection profile of the MCs measured using 3D optical microscope, before and after annealing. Resonance frequency of the MCs was measured using nano-vibration analyzer and was found to change after annealing. Further the frequency shift was found to depend on the MC dimensions. This is attributed to the large stress gradients induced by annealing and associated stiffness changes.

Projection of the annealing behavior of irradiated Si sensors in the LHC environment

CERN Document Server

Chatterji, S; Bhardwaj, N; Chauhan, S S; Choudhary, B C; Gupta, P; Jha, M; Kumar, A; Naimuddin, M; Ranjan, K; Shivpuri, R K; Srivastava-Ajay, K

2004-01-01

The study of the radiation tolerance and subsequent annealing effects on p+-n-n+ silicon micro strip detectors has been performed as a part of R&D program for the preshower detector in the CMS experiment. CMS silicon strip sensors were irradiated with 24 GeV protons at CERN proton synchrotron (PS) to a total fluence of 3*10/sup 14/ p/cm/sup 2 /. Sensors were stored in freezer after irradiation and I-V and C-V measurements were carried out. Variation in full depletion voltage and leakage current have been studied as a function of annealing time. The breakdown performance of the device actually improves after irradiation due to the beneficial effect of type-inversion. The breakdown voltage increases further with annealing time. However, the leakage current increases tremendously just after irradiation. As the sensors are annealed, there is a drop in leakage current. The rate of annealing is observed to be temperature dependent. Hence in terms of leakage current, it seems that room temperature annealing is b...

Effects of annealing on the recombination dynamics of low-temperature grown ZnO nanorods

Energy Technology Data Exchange (ETDEWEB)

Hilker, B.; Bekeny, C.; Voss, T.; Gutowski, J. [IFP, Universitaet Bremen, 28334 Bremen (Germany); Hauschild, R.; Kalt, H. [Universitaet Karlsruhe, 76128 Karlsruhe (Germany); Postels, B.; Bakin, Andrey; Waag, A. [IHT, TU Braunschweig, 38023 Braunschweig (Germany)

2007-07-01

We present systematic temperature and excitation density dependent time-resolved photoluminescence (TRPL) measurements of as-grown and annealed ZnO nanorods fabricated by an aqueous chemical growth (ACG) technique at {proportional_to}90 C. The as-grown nanorods show strong nearband-edge and rather weak deep-level emission indicating their already good optical quality. At 4K, we find a broad emission line at 3.36 eV (line width 30 meV) which we attribute to recombination from a donor band formed through the high donor concentration. After annealing in oxygen and nitrogen atmospheres at 600-800 C well-resolved and sharper excitonic transitions are observed. To understand the recombination dynamics in the nanorods we carried out TRPL measurements using a frequency-doubled femtosecond laser and a streak camera. The as-grown sample shows a very fast monoexponential decay time of {proportional_to}10ps independent of temperature and excitation density. In contrast, the annealed samples exhibit a biexponential decay. Each a fast {tau}1 and a slow {tau}2 time constant have been determined for all annealed samples both of them significantly varying depending on the annealing atmosphere and temperature. This will be discussed on the basis of a phenomenological rate-equation model.

Influence of annealing temperature on the Dy diffusion process in NdFeB magnets

Science.gov (United States)

Hu, Sheng-qing; Peng, Kun; Chen, Hong

2017-03-01

Sintered NdFeB magnets were coated with a layer of Dy metal using electron beam evaporation method and then annealed at various temperatures to investigate the temperature dependence of Dy diffusion process in NdFeB magnets. A Dy-rich phase was observed along the grain boundaries after the grain boundary diffusion process, the diffusion coefficients of various temperatures were obtained, the diffusion coefficients of Dy along the grain boundaries at 800 °C and 900 °C were determined to be 9.8×10-8 cm2 s-1 and 2.4×10-7 cm2 s-1, respectively. The diffusion length depended on the annealing temperature and the maximum diffusion length of approximately 1.8 mm and 3.0 mm can be obtained after annealing at 800 °C and 900 °C for 8 h. Higher diffusion temperature results in the diffusion not only along the grain boundaries but also into grains and then decrease in magnetic properties. The optimum annealing conditions can be determined as 900 °C for 8 h. The coercivity was improved from 1040 kA/m to 1450 kA/m and its magnetization has no significant reduction after the grain boundary diffusion process at the optimum annealing conditions.

Temperature, stress, and annealing effects on the luminescence from electron-irradiated silicon

Science.gov (United States)

Jones, C. E.; Johnson, E. S.; Compton, W. D.; Noonan, J. R.; Streetman, B. G.

1973-01-01

Low-temperature photoluminescence spectra are presented for Si crystals which have been irradiated with high-energy electrons. Studies of isochronal annealing, stress effects, and the temperature dependences of the luminescence are used to discuss the nature of the luminescent transitions and the properties of defects. Two dominant bands present after room-temperature anneal of irradiated material are discussed, and correlations of the properties of these bands are made with known Si defects. A band between 0.8 and 1.0 eV has properties which are related to those of the divacancy, and a band between 0.6 and 0.8 eV has properties related to those of the Si-G15(K) center. Additional peaks appear in the luminescence after high-temperature anneal; the influence of impurities and the effects of annealing of these lines are discussed.

Critical current scaling and the pivot-point in Nb3Sn strands

International Nuclear Information System (INIS)

Tsui, Y; Hampshire, D P

2012-01-01

Detailed measurements are provided of the engineering critical current density (J c ) and the index of transition (n-value) of two different types of advanced ITER Nb 3 Sn superconducting strand for fusion applications. The samples consist of one internal-tin strand (OST) and two bronze-route strands (BEAS I and BEAS II—reacted using different heat treatments). Tests on different sections of these wires show that prior to applying strain, J c is homogeneous to better than 2% along the length of each strand. J c data have been characterized as a function of magnetic field (B ≤ 14.5 T), temperature (4.2 K ≤ T ≤ 12 K) and applied axial strain ( − 1% ≤ ε A ≤ 0.8%). Strain-cycling tests demonstrate that the variable strain J c data are reversible to better than 2% when the applied axial strain is in the range of − 1% ≤ ε A ≤ 0.5%. The wires are damaged when the intrinsic strain (ε I ) is ε I ≥ 0.55% and ε I ≥ 0.23% for the OST and BEAS strands, respectively. The strain dependences of the normalized J c for each type of strand are similar to those of prototype strands of similar design measured in 2005 and 2008 to about 2% which makes them candidate strands for a round-robin interlaboratory comparison. The J c data are described by Durham, ITER and Josephson-junction parameterizations to an accuracy of about 4%. For all of these scaling laws, the percentage difference between the data and the parameterization is larger when J c is small, caused by high B, T or |ε I |. The n-values can be described by a modified power law of the form n=1+rI c s , where r and s are approximately constant and I c is the critical current. It has long been known that pivot-points (or cross-overs) in J c occur at high magnetic field and temperature. Changing the magnetic field or temperature from one side of the pivot-point to the other changes the highest J c sample to the lowest J c sample and vice versa. The pivot-point follows the B–T phase boundary

Effect of high temperature annealing on defects and optical properties of ZnO single crystals

International Nuclear Information System (INIS)

Jiang, M.; Wang, D.D.; Zou, B.; Chen, Z.Q.; Kawasuso, A.; Sekiguchi, T.

2012-01-01

Hydrothermal grown ZnO single crystals were annealed in N 2 or O 2 between 900 and 1300 C. Positron lifetime measurements reveal a single lifetime in all the ZnO samples before and after annealing. The positron lifetime is about 181 ps after annealing at 900 C in either N 2 or O 2 atmosphere. However, increase of the positron lifetime is observed after further annealing the sample at higher temperatures up to 1300 C, and it has a faster increase in O 2 ambient. Temperature dependence measurements show that the positron lifetime has very slight increase with temperature for the 900 C annealed sample, while it shows notable variation for the sample annealed at 1300 C. This implied that annealing at high temperature introduces additional defects. These defects are supposed to be Zn vacancy-related defects. Cathodoluminescence (CL) measurements indicates enhancement of both UV and green emission after annealing, and the enhancement of green emission is much stronger for the samples annealed in O 2 ambient. The possible origin of green emission is tentatively discussed. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Effects of nucleic acid local structure and magnesium ions on minus-strand transfer mediated by the nucleic acid chaperone activity of HIV-1 nucleocapsid protein

OpenAIRE

Wu, Tiyun; Heilman-Miller, Susan L.; Levin, Judith G.

2007-01-01

HIV-1 nucleocapsid protein (NC) is a nucleic acid chaperone, which is required for highly specific and efficient reverse transcription. Here, we demonstrate that local structure of acceptor RNA at a potential nucleation site, rather than overall thermodynamic stability, is a critical determinant for the minus-strand transfer step (annealing of acceptor RNA to (−) strong-stop DNA followed by reverse transcriptase (RT)-catalyzed DNA extension). In our system, destabilization of a stem-loop stru...

Strand transfer and elongation of HIV-1 reverse transcription is facilitated by cell factors in vitro.

Directory of Open Access Journals (Sweden)

David Warrilow

Full Text Available Recent work suggests a role for multiple host factors in facilitating HIV-1 reverse transcription. Previously, we identified a cellular activity which increases the efficiency of HIV-1 reverse transcription in vitro. Here, we describe aspects of the activity which shed light on its function. The cellular factor did not affect synthesis of strong-stop DNA but did improve downstream DNA synthesis. The stimulatory activity was isolated by gel filtration in a single fraction of the exclusion volume. Velocity-gradient purified HIV-1, which was free of detectable RNase activity, showed poor reverse transcription efficiency but was strongly stimulated by partially purified cell proteins. Hence, the cell factor(s did not inactivate an RNase activity that might degrade the viral genomic RNA and block completion of reverse transcription. Instead, the cell factor(s enhanced first strand transfer and synthesis of late reverse transcription suggesting it stabilized the reverse transcription complex. The factor did not affect lysis of HIV-1 by Triton X-100 in the endogenous reverse transcription (ERT system, and ERT reactions with HIV-1 containing capsid mutations, which varied the biochemical stability of viral core structures and impeded reverse transcription in cells, showed no difference in the ability to be stimulated by the cell factor(s suggesting a lack of involvement of the capsid in the in vitro assay. In addition, reverse transcription products were found to be resistant to exogenous DNase I activity when the active fraction was present in the ERT assay. These results indicate that the cell factor(s may improve reverse transcription by facilitating DNA strand transfer and DNA synthesis. It also had a protective function for the reverse transcription products, but it is unclear if this is related to improved DNA synthesis.

Electron spin resonance in neutron-irradiated graphite. Dependence on temperature and effect of annealing; Resonance paramagnetique du graphite irradie aux neutrons. Variation en fonction de la temperature et experiences de recuit

Energy Technology Data Exchange (ETDEWEB)

Kester, T [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires, Laboratoire de resonance magnetique

1967-09-01

The temperature dependence of the electron spin resonance signal from neutron irradiated graphite has been studied. The results lead to an interpretation of the nature of the paramagnetic centers created by irradiation. In annealing experiments on graphite samples, which had been irradiated at low temperature, two annealing peaks and one anti-annealing peak were found. Interpretations are proposed for these peaks. (author) [French] Le graphite irradie aux neutrons a ete etudie par resonance paramagnetique electronique en fonction de la temperature. La nature des centres paramagnetiques crees par irradiation est interpretee a l'aide des resultats. Des experiences de recuit sur des echantillons de graphite irradie a 77 deg. K ont permis de mettre en evidence deux pics de recuit et un pic d'anti-recuit, pour lesquels des interpretations sont proposees. (auteur)

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)

Prebiotic Amino Acid Thioester Synthesis: Thiol-Dependent Amino Acid Synthesis from Formose substrates (Formaldehyde and Glycolaldehyde) and Ammonia

Science.gov (United States)

Weber, Arthur L.

1998-01-01

Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to react with ammonia yielding alanine and homoserine under mild aqueous conditions in the presence of thiol catalysts. Since similar reactions carried out without ammonia yielded alpha-hydroxy acid thioesters, the thiol-dependent synthesis of alanine and homoserine is presumed to occur via amino acid thioesters-intermediates capable of forming peptides. A pH 5.2 solution of 20 mM formaldehyde, 20 mM glycolaldehyde, 20 mM ammonium chloride, 23 mM 3-mercaptopropionic acid, and 23 mM acetic acid that reacted for 35 days at 40 C yielded (based on initial formaldehyde) 1.8% alanine and 0.08% homoserine. In the absence of thiol catalyst, the synthesis of alanine and homoserine was negligible. Alanine synthesis required both formaldehyde and glycolaldehyde, but homoserine synthesis required only glycolaldehyde. At 25 days the efficiency of alanine synthesis calculated from the ratio of alanine synthesized to formaldehyde reacted was 2.1%, and the yield (based on initial formaldehyde) of triose and tetrose intermediates involved in alanine and homoserine synthesis was 0.3 and 2.1%, respectively. Alanine synthesis was also seen in similar reactions containing only 10 mM each of aldehyde substrates, ammonia, and thiol. The prebiotic significance of these reactions that use the formose reaction to generate sugar intermediates that are converted to reactive amino acid thioesters is discussed.

Formation of Au nanoparticles in sapphire by using Ar ion implantation and thermal annealing

International Nuclear Information System (INIS)

Zhou, L.H.; Zhang, C.H.; Yang, Y.T.; Li, B.S.; Zhang, L.Q.; Fu, Y.C.; Zhang, H.H.

2009-01-01

In this paper, we present results of the synthesis of gold nanoclusters in sapphire, using Ar ion implantation and annealing in air. Unlike the conventional method of Au implantation followed by thermal annealing, Au was deposited on the surface of m- and a- cut sapphire single crystal samples including those pre-implanted with Ar ions. Au atoms were brought into the substrate by subsequent implantation of Ar ions to form Au nanoparticles. Samples were finally annealed stepwisely in air at temperatures ranging from 400 to 800 deg. C and then studied using UV-vis absorption spectrometry, transmission electron microscopy and Rutherford backscattered spectrometry. Evidence of the formation Au nanoparticles in the sapphire can be obtained from the characteristic surface plasmon resonance (SPR) absorption band in the optical absorption spectra or directly from the transmission electron microscopy. The results of optical absorption spectra indicate that the specimen orientations and pre-implantation also influence the size and the volume fraction of Au nanoparticles formed. Theoretical calculations using Maxwell-Garnett effective medium theory supply a good interpretation of the optical absorption results.

Effect of annealing on photoluminescence properties of neon implanted GaN

Energy Technology Data Exchange (ETDEWEB)

Majid, Abdul [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Ali, Akbar [Advance Materials Physics Laboratory, Physics Department, Quaid-i-Azam University, Islamabad (Pakistan); Zhu, J J [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Wang, Y T [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Liu, W [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Lu, G J [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Liu, W B [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Zhang, L Q [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Liu, Z S [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Zhao, D G [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Zhang, S M [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China); Jiang, D S; Yang, H [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, PO Box 912, Beijing 100083 (China)

2008-01-21

The effect of thermal annealing on the luminescence properties of neon implanted GaN thin films was studied. Low temperature photoluminescence (PL) measurements were carried out on the samples implanted with different doses ranging from 10{sup 14} to 9 x 10{sup 15} cm{sup -2} and annealed isochronally at 800 and 900 deg. C. We observed a new peak appearing at 3.44 eV in the low temperative PL spectra of all the implanted samples after annealing at 900 deg. C. This peak has not been observed in the PL spectra of implanted samples annealed at 800 deg. C except for the samples implanted with the highest dose. The intensity of the yellow luminescence (YL) band noticed in the PL spectra measured after annealing was observed to decrease with the increase in dose until it was completely suppressed at a dose of 5 x 10{sup 15} cm{sup -2}. The appearance of a new peak at 3.44 eV and dose dependent suppression of the YL band are attributed to the dissociation of V{sub Ga}O{sub N} complexes caused by high energy ion implantation.

Effect of annealing on photoluminescence properties of neon implanted GaN

International Nuclear Information System (INIS)

Majid, Abdul; Ali, Akbar; Zhu, J J; Wang, Y T; Liu, W; Lu, G J; Liu, W B; Zhang, L Q; Liu, Z S; Zhao, D G; Zhang, S M; Jiang, D S; Yang, H

2008-01-01

The effect of thermal annealing on the luminescence properties of neon implanted GaN thin films was studied. Low temperature photoluminescence (PL) measurements were carried out on the samples implanted with different doses ranging from 10 14 to 9 x 10 15 cm -2 and annealed isochronally at 800 and 900 deg. C. We observed a new peak appearing at 3.44 eV in the low temperative PL spectra of all the implanted samples after annealing at 900 deg. C. This peak has not been observed in the PL spectra of implanted samples annealed at 800 deg. C except for the samples implanted with the highest dose. The intensity of the yellow luminescence (YL) band noticed in the PL spectra measured after annealing was observed to decrease with the increase in dose until it was completely suppressed at a dose of 5 x 10 15 cm -2 . The appearance of a new peak at 3.44 eV and dose dependent suppression of the YL band are attributed to the dissociation of V Ga O N complexes caused by high energy ion implantation

Velocity and processivity of helicase unwinding of double-stranded nucleic acids

International Nuclear Information System (INIS)

Betterton, M D; Juelicher, F

2005-01-01

Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase unwinding velocity and processivity vary if the base-pair binding free energy is changed

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.

Rapid Hydrothermal Synthesis of Zinc Oxide Nanowires by Annealing Methods on Seed Layers

Directory of Open Access Journals (Sweden)

Jang Bo Shim

2011-01-01

Full Text Available Well-aligned zinc oxide (ZnO nanowire arrays were successfully synthesized on a glass substrate using the rapid microwave heating process. The ZnO seed layers were produced by spinning the precursor solutions onto the substrate. Among coatings, the ZnO seed layers were annealed at 100°C for 5 minutes to ensure particle adhesion to the glass surface in air, nitrogen, and vacuum atmospheres. The annealing treatment of the ZnO seed layer was most important for achieving the high quality of ZnO nanowire arrays as ZnO seed nanoparticles of larger than 30 nm in diameter evolve into ZnO nanowire arrays. Transmission electron microscopy analysis revealed a single-crystalline lattice of the ZnO nanowires. Because of their low power (140 W, low operating temperatures (90°C, easy fabrication (variable microwave sintering system, and low cost (90% cost reduction compared with gas condensation methods, high quality ZnO nanowires created with the rapid microwave heating process show great promise for use in flexible solar cells and flexible display devices.

Effects of post-stress hydrogen annealing on MOS oxides after 60Co irradiation or Fowler-Nordheim injection

International Nuclear Information System (INIS)

Saks, N.S.; Stahlbush, R.E.; Mrstik, B.J.; Rendell, R.W.; Klein, R.B.

1993-01-01

Changes in interface trap density D it have been determined in MOSFETs as a function of time during hydrogen annealing at 295K. Large increases in D it are observed during H 2 annealing in MOSFETs previously stressed by either 60 Co irradiation or Fowler-Nordheim electron injection. The annealing behavior is very similar for both types of stress, which suggests that the D it creation mechanism involves similar chemistry for hydrogen reactions. Studies of the time dependence of D it creation as a function of MOSFET gate length show that the time dependence is limited primarily by lateral diffusion of molecular hydrogen (H 2 ) through the gate oxide. An activation energy of 0.57 eV, which is consistent with H 2 diffusion, is obtained from the temperature dependence

Regrowth zones in laser annealed radiation damaged diamond

International Nuclear Information System (INIS)

Jamieson, D.N.; Prawer, S.; Dooley, S.P.; Kalish, R.; Technion-Israel Inst. of Tech., Haifa

1993-01-01

Focused laser annealing of ion implanted diamond with a 15 μm diameter laser spot produces as variety of effects that depend on the power density of the laser. Channeling Contrast Microscopy (CCM) provides a relatively straight forward, rapid, method to analyse the annealed regions of the diamond to characterize the effects. In order of increasing laser power density, effects that are observed include: regrowth of the end of range damage of the ion implantation, formation of a buried graphitic layer and complete graphitization of the surface of the diamond down to the bottom of the original damage layer. Information provided by CCM leads to an understanding the causes of these effects and provides insight into the carbon phase diagram in the neighbourhood of the graphite to diamond phase transition. Analysis of the effects of laser annealing by CCM are complicated by the swelling of the diamond lattice caused by the original ion implantation, compaction following regrowth and the effect of the analysis beam irradiation itself. 12 refs., 5 figs

Magnetic properties and magnetoimpedance of FeCoNi/CuBe electroplated tubes with different features of field-annealing induced magnetic anisotropy

Energy Technology Data Exchange (ETDEWEB)

El Kammouni, R.; Chlenova, A.A.; Volchkov, S.O. [Ural Federal University, Laboratory of Magnetic Sensors, Lenin Ave. 51, 620000 Ekaterinburg (Russian Federation); Kurlyandskaya, G.V., E-mail: galina@we.lc.ehu.es [Ural Federal University, Laboratory of Magnetic Sensors, Lenin Ave. 51, 620000 Ekaterinburg (Russian Federation); Departamento de Electricidad y Electrónica, Universidad del País Vasco BCMaterials (UPV/EHU), 48940 Leioa (Spain)

2017-02-01

The effect of field annealing (in direct (DC) or alternating current (AC) field) on the structure, magnetic properties and giant magnetoimpedance (GMI) of CuBe/ Fe{sub 19}Co{sub 17}Ni{sub 64} electroplated tubes was studied. The field and frequency dependences of total impedance and its real part were comparatively analyzed together with magnetization processes features. The GMI sensitivity with respect to an applied field was the subject of special attention in view of possible applications of these materials in small magnetic field sensors. The maximum GMI ratio depends strongly on the heat treatments. The DC field annealing leads to the highest total impedance GMI ratio (ΔZ/Z=250%) and real part of the total impedance GMI ratio (ΔR/R=640%), compared to as-cast and AC field annealed samples. The external field response of DC annealed samples presented a single peak GMI response as a consequence of a strong contribution of the longitudinal effective anisotropy. At the same time, the maximum obtained sensitivity of 13.5%/Oe for DC case is much lower compared to the highest sensitivity values obtained for as-prepared (28.6%/Oe) and DC field annealed (22.0%/Oe) tubes for the low frequency of 2.5 MHz. The weak dependence of ΔZ/Z ratio in the case of AC field annealed samples in the high frequency range is an important advantage for particular sensor applications. - Highlights: • CuBe/FeCoNi tubes were fabricated by electroplating. • The effect of field annealing on the structure, magnetic properties and magnetoimpedance was studied. • The maximum magnetoimpedance ( MI) ratio depends strongly on the heat treatments. • The DC field annealing leads to the highest total impedance MI ratio. • Transformation from one- to two-peaks MI curves was observed in the DC field annealed tubes.

CdO thin films based on the annealing temperature differences prepared by sol-gel method and their heterojunction devices

Science.gov (United States)

Soylu, M.; Yazici, T.

2017-12-01

Undoped CdO films were prepared on glass substrate and p-type silicon wafer using sol-gel spin coating method. The structural and optical properties of the films were investigated as a function of the annealing temperature. X-ray diffraction (XRD) patterns reveal that the films are formed from CdO with cubic crystal structure and (1 1 1) preferred orientation. It is seen that good crystallinity is due to the high annealing temperature. The surface morphology of the CdO films was found to be depending on the annealing temperature, showing cauliflower like structure. Optical band gaps for annealing temperature of 250 °C and 450 °C were found to be 2.49 eV and 2.27 eV, respectively, showing a decrease with raising temperature. Optics parameters such as extinction coefficient, refractive index, and surface-volume energy loss were determined with spectrophotometric analysis as a function of annealing temperature. CdO/p-Si heterojunction structure showed weak rectifying behavior. The diode parameters were found to be depending on annealing temperature. The results are encouraging to get better conjunction with CdO thin film component at optimize annealing temperature.

Influence of growth flux solvent on anneal-tuning of ground states in CaFe2As2

Science.gov (United States)

Roncaioli, Connor; Drye, Tyler; Saha, Shanta R.; Paglione, Johnpierre

2018-04-01

The effects of anneal-tuning of single-crystalline samples of CaFe2As2 synthesized via a molten Sn-flux method are investigated using x-ray diffraction, chemical composition, electrical transport, and magnetic susceptibility measurements in order to understand the role of growth conditions on the resultant phase diagram. Previous studies of CaFe2As2 crystals synthesized using a self-flux (FeAs) method revealed an ability to tune the structural and magnetic properties of this system by control of post-synthesis annealing conditions, resulting in an ambient pressure phase diagram that spans from tetragonal/orthorhombic antiferromagnetism to the collapsed tetragonal phase of this system. In this work, we compare previous results to those obtained on crystals synthesized via Sn flux, finding similar tunability in both self- and Sn-flux cases, but less sensitivity to annealing temperatures in the latter case, resulting in a temperature-shifted phase diagram.

Tissue-dependent paired expression of miRNAs

OpenAIRE

Ro, Seungil; Park, Chanjae; Young, David; Sanders, Kenton M.; Yan, Wei

2007-01-01

It is believed that depending on the thermodynamic stability of the 5′-strand and the 3′-strand in the stem-loop structure of a precursor microRNA (pre-miRNA), cells preferentially select the less stable one (called the miRNA or guide strand) and destroy the other one (called the miRNA* or passenger strand). However, our expression profiling analyses revealed that both strands could be co-accumulated as miRNA pairs in some tissues while being subjected to strand selection in other tissues. Ou...

Theoretical analysis on ac loss properties of two-strand parallel conductors composed of superconducting multifilamentary strands

CERN Document Server

Iwakuma, M; Funaki, K

2002-01-01

The ac loss properties of two-strand parallel conductors composed of superconducting multifilamentary strands were theoretically investigated. The constituent strands generally need to be insulated and transposed for the sake of uniform current distribution and low ac loss. In case the transposition points deviate from the optimum ones, shielding current is induced according to the interlinkage magnetic flux of the twisted loop enclosed by the insulated strands and the contact resistances at the terminals. It produces an additional ac loss. Supposing a simple situation where a two-strand parallel conductor with one-point transposition is exposed to a uniform ac magnetic field, the basic equations for the magnetic field were proposed and the theoretical expressions of the additional ac losses derived. As a result, the following features were shown. The additional ac loss in the non-saturation case, where the induced shielding current is less than the critical current of a strand, is proportional to the square ...

DNA replication and the repair of DNA strand breaks in nuclei of Physarum polycephalum. Terminal report, August 1, 1978-March 31, 1980

International Nuclear Information System (INIS)

Brewer, E.N.; Evans, T.E.

1980-01-01

Nuclei isolated from Physarum are able to replicate approximately 15% of the total genome in a manner which is qualitatively similar to the DNA replication process occurring in the intact organism. Such nuclei, however, are defective in the joining of Okazaki intermediates in vitro. Two DNA polymerase species, isolated from nuclei or intact plasmodia of this organism, can be separated by sucrose density gradient centrifugation. Total DNA polymerase activity is low in nuclei isolated during mitosis. A heat-stable glycoprotein material present in aqueous nuclear extracts stimulates DNA synthesis in well-washed nuclei. A sub-nuclear preparation active in DNA synthesis in vitro has been obtained from isolated nuclei of Physarum. Radiation-induced DNA double-strand breaks are rejoined in intact plasmodia and isolated nuclei of Physarum in a cell cycle-dependent manner. This phenomenon does not appear to be due to an intrinsic difference in nuclear DNA endonuclease activity at different times of the mitotic cycle. DNA strand breaks and repair induced by the carcinogen 4-nitroquinoline-1-oxide is similar in several respects to that resulting from exposure of the organism to ionizing radiation. Temperature sensitive strains of Physarum have been constructed and preliminary genetical and biochemical characterizations have been carried out. Two of the strains appear to be conditionally defective in DNA metabolism. An isogenic ploidal series of amoebae has been prepared and characterized as to uv and ionizing radiation sensitivity (in terms of cell survival). There is a direct relationship between ploidy and resistance to uv whereas ploidal change does not appear to affect the response to ionizing radiation

Biomolecular Specificity Regulated Synthesis of Nanocatalysts and Heterointegration of Photosynthesis Nanodevices

Science.gov (United States)

2016-01-01

Pd Nanocomposite Photocatalyst for Tandem Synthesis of Benzimidazole 2.1 Approaches: Wet -chemical synthetic routes are explored to create...nanocatalysts, and tandem catalysts systems were created through physical mixture and annealing . XRD, XPS, TEM, and STEM are used to characterized the detailed...its synergetic effect. Through annealing treatment, the metallic surface previously of segregated Au and Pd domains transforms to Au-Pd alloy. Since

DNA replication and the repair of DNA strand breaks in nuclei of Physarum polycephalum. Progress report, September 1, 1977--July 31, 1978

International Nuclear Information System (INIS)

Brewer, E.N.; Nygaard, O.F.; Kuncio, G.

1978-01-01

Isolated nuclei and intact plasmodia of Physarum contain a heat-stable stimulator of nuclear DNA replication. This substance has been purified extensively and found to contain both protein and carbohydrate. The molecular weight, estimated by gel filtration, is ca. 30,000 d. The purified material does not exhibit DNA polymerase or DNase activity, and does not stimulate DNA polymerase activity per se. In the presence of the stimulatory factor, DNA chain elongation occurs at an elevated rate, and continues for a longer time than in its absence, but G 2 nuclei are not stimulated to initiate DNA synthesis. Double-strand breaks in nuclear DNA of irradiated plasmodia are repaired in vitro to a greater extent following nuclear isolation during G 2 , and the DNA of unirradiated plasmodia is less susceptible to double-strand breakage during cell-free nuclear incubation, than is the DNA of S-phase nuclei. This correlation suggests a common basis for both observations, for example an increase in deoxyribonuclease activity or a decrease in DNA ligase activity during the S period. This, in turn, may account for the cell cycle-dependent sensitivity of this organism, in terms of mitotic delay, to ionizing radiation

Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis.

Science.gov (United States)

Beltz, Hervé; Clauss, Céline; Piémont, Etienne; Ficheux, Damien; Gorelick, Robert J; Roques, Bernard; Gabus, Caroline; Darlix, Jean-Luc; de Rocquigny, Hugues; Mély, Yves

2005-05-20

The nucleocapsid protein (NC) of human immunodeficiency virus type 1 (HIV-1) is formed of two highly conserved CCHC zinc fingers flanked by small basic domains. NC is required for the two obligatory strand transfers in viral DNA synthesis through its nucleic acid chaperoning properties. The first DNA strand transfer relies on NC's ability to bind and destabilize the secondary structure of complementary transactivation response region (cTAR) DNA, to inhibit self-priming, and to promote the annealing of cTAR to TAR RNA. To further investigate NC chaperone properties, our aim was to identify by fluorescence spectroscopy and gel electrophoresis, the NC structural determinants for cTAR binding and destabilization, and for the inhibition of self-primed DNA synthesis on a model system using a series of NC mutants and HIV-1 reverse transcriptase. NC destabilization and self-priming inhibition properties were found to be supported by the two fingers in their proper context and the basic (29)RAPRKKG(35) linker. The strict requirement of the native proximal finger suggests that its hydrophobic platform (Val13, Phe16, Thr24 and Ala25) is crucial for binding, destabilization and inhibition of self-priming. In contrast, only partial folding of the distal finger is required, probably for presenting the Trp37 residue in an appropriate orientation. Also, Trp37 and the hydrophobic residues of the proximal finger appear to be essential for the propagation of the melting from the cTAR ends up to the middle of the stem. Finally, both N-terminal and C-terminal basic domains contribute to cTAR binding but not to its destabilization.

Annealing temperature and O2 partial pressure dependence of T(sub c) in HgBa2CuO(4+delta)

Science.gov (United States)

Xiong, Q.; Cao, Y.; Chen, F.; Xue, Y. Y.; Chu, C. W.

1994-01-01

Samples of HgBa2CuO(4+delta) (Hg-1201) were annealed under various conditions. After carefully controlling annealing time, annealing temperature (T(sub a)) and O2 partial pressure (P(sub 0)), we were able to find the reversible annealing conditions for Hg-1201. Under 1 atm O2 at 260 C less than or equal to T(sub a) less than or equal to 400 C, the obtained T(sub c) is nearly the same (approximately 97 K). However, it decreases quickly with T(sub a) greater than 300 C in high vacuum (P(sub 0) approximately 10(exp -8) atm), and reaches zero at T(sub a) = 400 C. On the other hand, T(sub c) decreases with the decrease of T(sub a) in high-pressure O2 (approximately 500 atm) and reaches approximately 20 K at about 240 C. In the entire annealing region, the oxygen surplus varies significantly from 0.03 to 0.4, and a wide range of T(sub c) variation (0 goes to 97 K goes to 20 K) was obtained with anion doping alone.

Infrared absorption studies of the annealing of irradiated diamonds

International Nuclear Information System (INIS)

Woods, G.S.

1984-01-01

Natural (types Ia and IIa) and synthetic (type Ib) diamonds have been irradiated with energetic electrons and neutrons and then heated at temperatures up to 1400 deg C. Attendant changes in the infrared absorption spectra, especially above the Raman frequency (1332 cm -1 ), have been monitored. The most prominent absorption to develop in the infrared region proper, on annealing both type Ia and type Ib specimens, whether electron- or neutron-irradiated is the H1a line at 1450 cm -1 . Measurements taken of neutron-irradiated type Ia specimens show that the strength of this line is specimen-dependent, and that it is a linear function of radiation dose. Isochronal annealing studies show that the onset of the line occurs during heating at 250 deg C for type Ia specimens and at 650 deg C for type Ib specimens. The absorption begins to weaken during heating at 1100 deg C, but it is very persistent, surviving an anneal of 4 hours at 1400 deg C, albeit with diminished intensity. Three other weaker lines at 1438, 1358 and 1355 cm -1 develop with the 1450 cm -1 line, but differ from it and from each other in subsequent annealing behaviour. Other lines were observed; these are reported and discussed. (author)

Single-strand breaks in supercoiled DNA induced by vacuum-UV radiation in aqueous solution

Energy Technology Data Exchange (ETDEWEB)

Takakura, Kaoru; Ishikawa, Mitsuo; Hieda, Kotaro; Kobayashi, Katsumi; Ito, Atsushi; Ito, Takashi

1986-09-01

The induction of single-strand breaks in the DNA of plasmid pBR 322 by vacuum-UV radiation above 145 nm in aqueous solutions was studied in relation to the production of OH-radicals in water. The similarity and dissimilarity were examined on the wavelength dependence between the two effects. The maximum of single strand breaks at 150 nm could be explained by the action of OH-radicals derived from direct water photolysis: the maximum at 180 nm remains unexplained. There was no indication that the direct absorption of photon by the DNA molecule plays an important role in the production of single-strand breaks.

Single-strand breaks in supercoiled DNA induced by vacuum-UV radiation in aqueous solution

International Nuclear Information System (INIS)

Takakura, Kaoru; Ishikawa, Mitsuo; Hieda, Kotaro; Kobayashi, Katsumi; Ito, Atsushi; Ito, Takashi

1986-01-01

The induction of single-strand breaks in the DNA of plasmid pBR 322 by vacuum-UV radiation above 145 nm in aqueous solutions was studied in relation to the production of OH-radicals in water. The similarity and dissimilarity were examined on the wavelength dependence between the two effects. The maximum of single strand breaks at 150 nm could be explained by the action of OH-radicals derived from direct water photolysis: the maximum at 180 nm remains unexplained. There was no indication that the direct absorption of photon by the DNA molecule plays an important role in the production of single-strand breaks. (author)

Annealing temperature effect on structure and electrical properties of films formed of Ge nanoparticles in SiO2

International Nuclear Information System (INIS)

Stavarache, Ionel; Lepadatu, Ana-Maria; Stoica, Toma; Ciurea, Magdalena Lidia

2013-01-01

Ge–SiO 2 films with high Ge/Si atomic ratio of about 1.86 were obtained by co-sputtering of Ge and SiO 2 targets and subsequently annealed at different temperatures between 600 and 1000 °C in a conventional furnace in order to show how the annealing process influences the film morphology concerning the Ge nanocrystal and/or amorphous nanoparticle formation and to study their electrical behaviour. Atomic force microscopy (AFM) imaging, Raman spectroscopy and electrical conductance measurements were performed in order to find out the annealing effect on the film surface morphology, as well as the Ge nanoparticle formation in correlation with the hopping conductivity of the films. AFM images show that the films annealed at 600 and 700 °C present a granular surface with particle height of about 15 nm, while those annealed at higher temperatures have smoother surface. The Raman investigations evidence Ge nanocrystals (including small ones) coexisting with amorphous Ge in the films annealed at 600 °C and show that almost all Ge is crystallized in the films annealed at 700 °C. The annealing at 800 °C disadvantages the Ge nanocrystal formation due to the strong Ge diffusion. This transition in Ge nanocrystals formation process by annealing temperature increase from 700 to 800 °C revealed by AFM and Raman spectroscopy measurements corresponds to a change in the electrical transport mechanism. Thus, in the 700 °C annealed films, the current depends on temperature according to a T −1/2 law which is typical for a tunnelling mechanism between neighbour Ge nanocrystals. In the 800 °C annealed films, the current–temperature characteristic has a T −1/4 dependence showing a hopping mechanism within an electronic band of localized states related to diffused Ge in SiO 2 .

Annealing dependence of residual stress and optical properties of TiO2 thin film deposited by different deposition methods.

Science.gov (United States)

Chen, Hsi-Chao; Lee, Kuan-Shiang; Lee, Cheng-Chung

2008-05-01

Titanium oxide (TiO(2)) thin films were prepared by different deposition methods. The methods were E-gun evaporation with ion-assisted deposition (IAD), radio-frequency (RF) ion-beam sputtering, and direct current (DC) magnetron sputtering. Residual stress was released after annealing the films deposited by RF ion-beam or DC magnetron sputtering but not evaporation, and the extinction coefficient varied significantly. The surface roughness of the evaporated films exceeded that of both sputtered films. At the annealing temperature of 300 degrees C, anatase crystallization occurred in evaporated film but not in the RF ion-beam or DC magnetron-sputtered films. TiO(2) films deposited by sputtering were generally more stable during annealing than those deposited by evaporation.

Computational algorithm for molybdenite concentrate annealing

International Nuclear Information System (INIS)

Alkatseva, V.M.

1995-01-01

Computational algorithm is presented for annealing of molybdenite concentrate with granulated return dust and that of granulated molybdenite concentrate. The algorithm differs from the known analogies for sulphide raw material annealing by including the calculation of return dust mass in stationary annealing; the latter quantity varies form the return dust mass value obtained in the first iteration step. Masses of solid products are determined by distribution of concentrate annealing products, including return dust and benthonite. The algorithm is applied to computations for annealing of other sulphide materials. 3 refs

DNA unwinding by ring-shaped T4 helicase gp41 is hindered by tension on the occluded strand.

Science.gov (United States)

Ribeck, Noah; Saleh, Omar A

2013-01-01

The replicative helicase for bacteriophage T4 is gp41, which is a ring-shaped hexameric motor protein that achieves unwinding of dsDNA by translocating along one strand of ssDNA while forcing the opposite strand to the outside of the ring. While much study has been dedicated to the mechanism of binding and translocation along the ssDNA strand encircled by ring-shaped helicases, relatively little is known about the nature of the interaction with the opposite, 'occluded' strand. Here, we investigate the interplay between the bacteriophage T4 helicase gp41 and the ss/dsDNA fork by measuring, at the single-molecule level, DNA unwinding events on stretched DNA tethers in multiple geometries. We find that gp41 activity is significantly dependent on the geometry and tension of the occluded strand, suggesting an interaction between gp41 and the occluded strand that stimulates the helicase. However, the geometry dependence of gp41 activity is the opposite of that found previously for the E. coli hexameric helicase DnaB. Namely, tension applied between the occluded strand and dsDNA stem inhibits unwinding activity by gp41, while tension pulling apart the two ssDNA tails does not hinder its activity. This implies a distinct variation in helicase-occluded strand interactions among superfamily IV helicases, and we propose a speculative model for this interaction that is consistent with both the data presented here on gp41 and the data that had been previously reported for DnaB.

Survey of stranded gas and delivered costs to Europe of selected gas resources

Science.gov (United States)

Attanasi, E.D.; Freeman, P.A.

2011-01-01

Two important trends affecting the expected growth of global gas markets are (1) the shift by many industrialized countries from coal-fired electricity generation to the use of natural gas to generate electricity and (2) the industrialization of the heavily populated Asian countries of India and China. This paper surveys discovered gas in stranded conventional gas accumulations and presents estimates of the cost of developing and producing stranded gas in selected countries. Stranded gas is natural gas in discovered or identified fields that is not currently commercially producible for either physical or economic reasons. Published reserves of gas at the global level do not distinguish between volumes of gas in producing fields and volumes in nonproducing fields. Data on stranded gas reported here-that is the volumes, geographical distribution, and size distributions of stranded gas fields at the country and regional level-are based on the examination of individual-field data and represent a significant improvement in information available to industry and government decision makers. Globally, stranded gas is pervasive, but large volumes in large accumulations are concentrated in only a few areas. The cost component of the paper focuses on stranded conventional gas accumulations in Africa and South America that have the potential to augment supplies to Europe. The methods described for the computation of extraction and transport costs are innovative in that they use information on the sizes and geographical distribution of the identified stranded gas fields. The costs are based on industry data specific to the country and geologic basin where the stranded gas is located. Gas supplies to Europe can be increased significantly at competitive costs by the development of stranded gas. Net extraction costs of producing the identified gas depend critically on the natural-gas-liquids (NGLs) content, the prevailing prices of liquids, the size of the gas accumulation, and the

A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM.

Science.gov (United States)

Mouri, Kazunari; Nacher, Jose C; Akutsu, Tatsuya

2009-01-01

After IR stress, DNA double-strand breaks (DSBs) occur and repair proteins (RPs) bind to them, generating DSB-RP complexes (DSBCs), which results in repaired DSBs (RDSBs). In recent experimental studies, it is suggested that the ATM proteins detect these DNA lesions depending on the autophosphorylation of ATM which exists as a dimer before phosphorylation. Interestingly, the ATM proteins can work as a sensor for a small number of DSBs (approximately 18 DSBs in a cell after exposure to IR). Thus the ATM proteins amplify the small input signals based on the phosphorylation of the ATM dimer proteins. The true DSB-detection mechanism depending on ATM autophosphorylation has yet to be clarified. We propose a mathematical model for the detection mechanism of DSBs by ATM. Our model includes both a DSB-repair mechanism and an ATM-phosphorylation mechanism. We model the former mechanism as a stochastic process, and obtain theoretical mean values of DSBs and DSBCs. In the latter mechanism, it is known that ATM autophosphorylates itself, and we find that the autophosphorylation induces bifurcation of the phosphorylated ATM (ATM*). The bifurcation diagram depends on the total concentration of ATM, which makes three types of steady state diagrams of ATM*: monostable, reversible bistable, and irreversible bistable. Bistability exists depending on the Hill coefficient in the equation of ATM autophosphorylation, and it emerges as the total concentration of ATM increases. Combining these two mechanisms, we find that ATM* exhibits switch-like behaviour in the presence of bistability, and the detection time after DNA damage decreases when the total concentration of ATM increases. This work provides a mathematical model that explains the DSB-detection mechanism depending on ATM autophosphorylation. These results indicate that positive auto-regulation works both as a sensor and amplifier of small input signals.

Modelling toehold-mediated RNA strand displacement.

Science.gov (United States)

Šulc, Petr; Ouldridge, Thomas E; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

2015-03-10

We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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)

The flavoprotein Tah18-dependent NO synthesis confers high-temperature stress tolerance on yeast cells

International Nuclear Information System (INIS)

Nishimura, Akira; Kawahara, Nobuhiro; Takagi, Hiroshi

2013-01-01

Highlights: ► NO is produced from L-arginine in response to elevated temperature in yeast. ► Tah18 was first identified as the yeast protein involved in NO synthesis. ► Tah18-dependent NO synthesis confers tolerance to high-temperature on yeast cells. -- Abstract: Nitric oxide (NO) is a ubiquitous signaling molecule involved in the regulation of a large number of cellular functions. In the unicellular eukaryote yeast, NO may be involved in stress response pathways, but its role is poorly understood due to the lack of mammalian NO synthase (NOS) orthologues. Previously, we have proposed the oxidative stress-induced L-arginine synthesis and its physiological role under stress conditions in yeast Saccharomyces cerevisiae. Here, our experimental results indicated that increased conversion of L-proline into L-arginine led to NO production in response to elevated temperature. We also showed that the flavoprotein Tah18, which was previously reported to transfer electrons to the Fe–S cluster protein Dre2, was involved in NO synthesis in yeast. Gene knockdown analysis demonstrated that Tah18-dependent NO synthesis confers high-temperature stress tolerance on yeast cells. As it appears that such a unique cell protection mechanism is specific to yeasts and fungi, it represents a promising target for antifungal activity.

Effect of annealing and In content on the properties of electron beam evaporated ZnO films

Science.gov (United States)

Mohamed, S. H.; Ali, H. M.; Mohamed, H. A.; Salem, A. M.

2005-08-01

The effect of both annealing and In content on the properties of ZnO films prepared by electron beam evaporation were investigated. The evaporation was carried out at room temperature from bulk samples prepared by sintering technique. X-ray diffraction showed that the structure of ZnO-In{2}O{3} films depends on both the In content and annealing temperature. Amorphous, highly transparent and relatively low resistive films which can be suitable for the usage as transparent electrode of organic light-emitting diode were obtained upon annealing at 300 circC. Partially crystalline, highly transparent and highly resistive films which can be used in piezoelectric applications were obtained upon annealing at 500 circC. For each composition the refractive index has no monotonic variation upon increasing annealing temperature.

Effect of template post-annealing on Y(Dy)BaCuO nucleation on CeO2 buffered metallic tapes

Science.gov (United States)

Hu, Xuefeng; Zhong, Yun; Zhong, Huaxiao; Fan, Feng; Sang, Lina; Li, Mengyao; Fang, Qiang; Zheng, Jiahui; Song, Haoyu; Lu, Yuming; Liu, Zhiyong; Bai, Chuanyi; Guo, Yanqun; Cai, Chuanbing

2017-08-01

Substrate engineering is very significant in the synthesis of the high-temperature superconductor (HTS) coated conductor. Here we design and synthesize several distinct and stable Cerium oxide (CeO2) surface reconstructions which are used to grow epitaxial films of the HTS YBa2Cu3O7-δ (YBCO). To identify the influence of annealing and post-annealing surroundings on the nature of nucleation centers, including Ar/5%H2, humid Ar/5%H2 and O2 in high temperature annealing process, we study the well-controlled structure, surface morphology, crystal constants and surface redox processes of the ceria buffers by using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and field-emission scanning electronic microscopy (FE-SEM), respectively. The ceria film post-annealed under humid Ar/5%H2 gas shows the best buffer layer properties. Furthermore, the film absorbs more oxygen ions, which appears to contribute to oxygenation of superconductor film. The film is well-suited for ceria model studies as well as a perfect substitute for CeO2 bulk material.

The multiple personalities of Watson and Crick strands.

Science.gov (United States)

Cartwright, Reed A; Graur, Dan

2011-02-08

In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin.

The multiple personalities of Watson and Crick strands

Directory of Open Access Journals (Sweden)

Graur Dan

2011-02-01

Full Text Available Abstract Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. Reviewers This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky, and William Martin.

CO2 Laser annealing of n-doped hydrogenated amorphous silicon

International Nuclear Information System (INIS)

Bertolotti, M.; Ferrari, A.; Evangelisti, F.; Fiorini, P.; Proietti, M.G.

1985-01-01

Low power CO 2 laser annealing of n-doped a-Si:H is reported. Conductivity and its activation energy, photoconductivity, absorption coefficient and dependence of photoconductivity on light power show changes which can be interpreted as due to a better doping efficiency

Electrical behavior of amide functionalized graphene oxide and graphene oxide films annealed at different temperatures

International Nuclear Information System (INIS)

Rani, Sumita; Kumar, Mukesh; Kumar, Dinesh; Sharma, Sumit

2015-01-01

Films of graphene oxide (GO) and amide functionalized graphene oxides (AGOs) were deposited on SiO 2 /Si(100) by spin coating and were thermally annealed at different temperatures. Sheet resistance of GO and AGOs films was measured using four probe resistivity method. GO an insulator at room temperature, exhibits decrease in sheet resistance with increase in annealing temperature. However, AGOs' low sheet resistance (250.43 Ω) at room temperature further decreases to 39.26 Ω after annealing at 800 °C. It was observed that the sheet resistance of GO was more than AGOs up to 700 °C, but effect was reversed after annealing at higher temperature. At higher annealing temperatures the oxygen functionality reduces in GO and sheet resistance decreases. Sheet resistance was found to be annealing time dependent. Longer duration of annealing at a particular temperature results in decrease of sheet resistance. - Highlights: • Amide functionalized graphene oxides (AGOs) were synthesized at room temperature (RT). • AGO films have low sheet resistance at RT as compared to graphene oxide (GO). • Fast decrease in the sheet resistance of GO with annealing as compared to AGOs • AGOs were found to be highly dispersible in polar solvents

Dynamic dependence on ATR and ATM for double-strand break repair in human embryonic stem cells and neural descendants.

Directory of Open Access Journals (Sweden)

Bret R Adams

2010-04-01

Full Text Available The DNA double-strand break (DSB is the most toxic form of DNA damage. Studies aimed at characterizing DNA repair during development suggest that homologous recombination repair (HRR is more critical in pluripotent cells compared to differentiated somatic cells in which nonhomologous end joining (NHEJ is dominant. We have characterized the DNA damage response (DDR and quality of DNA double-strand break (DSB repair in human embryonic stem cells (hESCs, and in vitro-derived neural cells. Resolution of ionizing radiation-induced foci (IRIF was used as a surrogate for DSB repair. The resolution of gamma-H2AX foci occurred at a slower rate in hESCs compared to neural progenitors (NPs and astrocytes perhaps reflective of more complex DSB repair in hESCs. In addition, the resolution of RAD51 foci, indicative of active homologous recombination repair (HRR, showed that hESCs as well as NPs have high capacity for HRR, whereas astrocytes do not. Importantly, the ATM kinase was shown to be critical for foci formation in astrocytes, but not in hESCs, suggesting that the DDR is different in these cells. Blocking the ATM kinase in astrocytes not only prevented the formation but also completely disassembled preformed repair foci. The ability of hESCs to form IRIF was abrogated with caffeine and siRNAs targeted against ATR, implicating that hESCs rely on ATR, rather than ATM for regulating DSB repair. This relationship dynamically changed as cells differentiated. Interestingly, while the inhibition of the DNA-PKcs kinase (and presumably non-homologous endjoining [NHEJ] in astrocytes slowed IRIF resolution it did not in hESCs, suggesting that repair in hESCs does not utilize DNA-PKcs. Altogether, our results show that hESCs have efficient DSB repair that is largely ATR-dependent HRR, whereas astrocytes critically depend on ATM for NHEJ, which, in part, is DNA-PKcs-independent.

The PCNA-associated protein PARI negatively regulates homologous recombination via the inhibition of DNA repair synthesis

DEFF Research Database (Denmark)

Burkovics, Peter; Dome, Lili; Juhasz, Szilvia

2016-01-01

to inhibit homologous recombination (HR) events. Here, we describe a biochemical mechanism in which PARI functions as an HR regulator after replication fork stalling and during double-strand break repair. In our reconstituted biochemical system, we show that PARI inhibits DNA repair synthesis during...... recombination events in a PCNA interaction-dependent way but independently of its UvrD-like helicase domain. In accordance, we demonstrate that PARI inhibits HR in vivo, and its knockdown suppresses the UV sensitivity of RAD18-depleted cells. Our data reveal a novel human regulatory mechanism that limits...

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

The role of Frenkel defect diffusion in dynamic annealing in ion-irradiated Si

Energy Technology Data Exchange (ETDEWEB)

Wallace, J. B.; Aji, L. B. Bayu; Martin, A. A.; Shin, S. J.; Shao, L.; Kucheyev, S. O.

2017-01-06

The formation of stable radiation damage in crystalline solids often proceeds via complex dynamic annealing processes, involving migration and interaction of ballistically-generated point defects. The dominant dynamic annealing processes, however, remain unknown even for crystalline Si. Here, we use a pulsed ion beam method to study defect dynamics in Si bombarded in the temperature range from -20 to 140 °C with 500 keV Ar ions. Results reveal a defect relaxation time constant of ~10–0.2 ms, which decreases monotonically with increasing temperature. The dynamic annealing rate shows an Arrhenius dependence with two well-defined activation energies of 73 ± 5 meV and 420 ± 10 meV, below and above 60 °C, respectively. Rate theory modeling, bench-marked against this data, suggests a crucial role of both vacancy and interstitial diffusion, with the dynamic annealing rate limited by the migration and interaction of vacancies.

Influence of synthesis conditions on microstructure and phase transformations of annealed Sr2FeMoO6−x nanopowders formed by the citrate–gel method

Directory of Open Access Journals (Sweden)

Marta Yarmolich

2016-08-01

Full Text Available The sequence of phase transformations during Sr2FeMoO6−x crystallization by the citrate–gel method was studied for powders synthesized with initial reagent solutions with pH values of 4, 6 and 9. Scanning electron microscopy revealed that the as-produced and annealed powders had the largest Sr2FeMoO6−x agglomerates with diameters in the range of 0.7–1.2 µm. The average grain size of the powders in the dispersion grows from 250 to 550 nm with increasing pH value. The X-ray diffraction analysis of the powders annealed at different temperatures between 770 and 1270 K showed that the composition of the initially formed Sr2FeMoO6−x changes and the molybdenum content increases with further heating. This leads to a change in the Sr2FeMoO6−x crystal lattice parameters and a contraction of the cell volume. An optimized synthesis procedure based on an initial solution of pH 4 allowed a single-phase Sr2FeMoO6−x compound to be obtained with a grain size in the range of 50–120 nm and a superstructural ordering of iron and molybdenum cations of 88%.

Sea Turtle Stranding Network Reports

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Sea Turtle Stranding and Salvage Network (STSSN) was formally established in 1980 to collect information on and document the stranding of marine turtles along...

Influence of annealing temperature on the Dy diffusion process in NdFeB magnets

Energy Technology Data Exchange (ETDEWEB)

Hu, Sheng-qing, E-mail: joy_hsq@126.com [State Key Laboratory of Powder Metallurgy, Central South University, Changsha 410083 (China); Peng, Kun, E-mail: kpeng@hnu.edu.cn [State Key Laboratory of Powder Metallurgy, Central South University, Changsha 410083 (China); College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Chen, Hong [State Key Laboratory of Powder Metallurgy, Central South University, Changsha 410083 (China)

2017-03-15

Sintered NdFeB magnets were coated with a layer of Dy metal using electron beam evaporation method and then annealed at various temperatures to investigate the temperature dependence of Dy diffusion process in NdFeB magnets. A Dy-rich phase was observed along the grain boundaries after the grain boundary diffusion process, the diffusion coefficients of various temperatures were obtained, the diffusion coefficients of Dy along the grain boundaries at 800 °C and 900 °C were determined to be 9.8×10{sup −8} cm{sup 2} s{sup −1} and 2.4×10{sup −7} cm{sup 2} s{sup −1}, respectively. The diffusion length depended on the annealing temperature and the maximum diffusion length of approximately 1.8 mm and 3.0 mm can be obtained after annealing at 800 °C and 900 °C for 8 h. Higher diffusion temperature results in the diffusion not only along the grain boundaries but also into grains and then decrease in magnetic properties. The optimum annealing conditions can be determined as 900 °C for 8 h. The coercivity was improved from 1040 kA/m to 1450 kA/m and its magnetization has no significant reduction after the grain boundary diffusion process at the optimum annealing conditions. - Highlights: • The optimum annealing conditions can be determined as 900 °C for 8 h. • The diffusion coefficient of Dy at 900 °Care determined to be 2.4×10{sup −7} cm{sup 2} s{sup −1}. • A maximum diffusion length of about 3 mm can be obtained.

Opposing roles of RNF8/RNF168 and deubiquitinating enzymes in ubiquitination-dependent DNA double-strand break response signaling and DNA-repair pathway choice

International Nuclear Information System (INIS)

Nakada, Shinichiro

2016-01-01

The E3 ubiquitin ligases ring finger protein (RNF) 8 and RNF168 transduce the DNA double-strand break (DSB) response (DDR) signal by ubiquitinating DSB sites. The depletion of RNF8 or RNF168 suppresses the accumulation of DNA-repair regulating factors such as 53BP1 and RAP80 at DSB sites, suggesting roles for RNF8- and RNF168-mediated ubiquitination in DSB repair. This mini-review provides a brief overview of the RNF8- and RNF168-dependent DDR-signaling and DNA-repair pathways. The choice of DNA-repair pathway when RNF8- and RNF168-mediated ubiquitination-dependent DDR signaling is negatively regulated by deubiquitinating enzymes (DUBs) is reviewed to clarify how the opposing roles of RNF8/RNF168 and DUBs regulate ubiquitination-dependent DDR signaling and the choice of DNA-repair pathway

Annealing temperature dependent non-monotonic d{sup 0} ferromagnetism in pristine In{sub 2}O{sub 3} nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Cao, Haiming; Xing, Pengfei, E-mail: pfxing@tju.edu.cn; Yao, Dongsheng; Wu, Ping

2017-05-01

Cubic bixbyite In{sub 2}O{sub 3} nanoparticles with room temperature d{sup 0} ferromagnetism were prepared by sol-gel method with the air annealing temperature ranging from 500 to 900 °C. X-ray diffraction, X-ray photoelectron spectroscopy, Raman-scattering and photoluminescence were carried out to demonstrate the presence of oxygen vacancies. The lattice constant, the atomic ratio of crystal O and In, the Raman peak at 369 cm{sup −1}, the PL emission peak at 396 nm and the saturation magnetization of d{sup 0} ferromagnetism all had a consistent non-monotonic change with the increasing annealing temperature. With further considering the relation between the grain size and the distribution of oxygen vacancies, we think that d{sup 0} ferromagnetism in our samples is directly related with the singly charged oxygen vacancies at the surface of In{sub 2}O{sub 3} nanoparticles. - Highlights: • Effect of air-annealing temperature on the d{sup 0} ferromagnetism of pure In{sub 2}O{sub 3}. • Oxygen-deficiency states of all samples were detected by Raman scattering and PL. • Ferromagnetism changes non-monotonically with the increasing annealing temperature. • d{sup 0} ferromagnetism in our In{sub 2}O{sub 3} nanoparticles is related with the surface V{sub O}{sup +}.

Placement by thermodynamic simulated annealing

International Nuclear Information System (INIS)

Vicente, Juan de; Lanchares, Juan; Hermida, Roman

2003-01-01

Combinatorial optimization problems arise in different fields of science and engineering. There exist some general techniques coping with these problems such as simulated annealing (SA). In spite of SA success, it usually requires costly experimental studies in fine tuning the most suitable annealing schedule. In this Letter, the classical integrated circuit placement problem is faced by Thermodynamic Simulated Annealing (TSA). TSA provides a new annealing schedule derived from thermodynamic laws. Unlike SA, temperature in TSA is free to evolve and its value is continuously updated from the variation of state functions as the internal energy and entropy. Thereby, TSA achieves the high quality results of SA while providing interesting adaptive features

Modernizing quantum annealing using local searches

International Nuclear Information System (INIS)

Chancellor, Nicholas

2017-01-01

I describe how real quantum annealers may be used to perform local (in state space) searches around specified states, rather than the global searches traditionally implemented in the quantum annealing algorithm (QAA). Such protocols will have numerous advantages over simple quantum annealing. By using such searches the effect of problem mis-specification can be reduced, as only energy differences between the searched states will be relevant. The QAA is an analogue of simulated annealing, a classical numerical technique which has now been superseded. Hence, I explore two strategies to use an annealer in a way which takes advantage of modern classical optimization algorithms. Specifically, I show how sequential calls to quantum annealers can be used to construct analogues of population annealing and parallel tempering which use quantum searches as subroutines. The techniques given here can be applied not only to optimization, but also to sampling. I examine the feasibility of these protocols on real devices and note that implementing such protocols should require minimal if any change to the current design of the flux qubit-based annealers by D-Wave Systems Inc. I further provide proof-of-principle numerical experiments based on quantum Monte Carlo that demonstrate simple examples of the discussed techniques. (paper)

Room-temperature annealing of Si implantation damage in InP

International Nuclear Information System (INIS)

Akano, U.G.; Mitchell, I.V.

1991-01-01

Spontaneous recovery at 295 K of Si implant damage in InP is reported. InP(Zn) and InP(S) wafers of (100) orientation have been implanted at room temperature with 600 keV Si + ions to doses ranging from 3.6x10 11 to 2x10 14 cm -2 . Room-temperature annealing of the resultant damage has been monitored by the Rutherford backscattering/channeling technique. For Si doses ≤4x10 13 cm -2 , up to 70% of the initial damage (displaced atoms) annealed out over a period of ∼85 days. The degree of recovery was found to depend on the initial level of damage. Recovery is characterized by at least two time constants t 1 2 ∼100 days. Anneal rates observed between 295 and 375 K are consistent with an activation energy of 1.2 eV, suggesting that the migration of implant-induced vacancies is associated with the reordering of the InP lattice

Structural transformation of implanted diamond layers during high temperature annealing

International Nuclear Information System (INIS)

Rubanov, S.; Fairchild, B.A.; Suvorova, A.; Olivero, P.; Prawer, S.

2015-01-01

In the recent years graphitization of ion-beam induced amorphous layers became the basic tool for device fabrication in diamond. The etchable graphitic layers can be removed to form free-standing membranes into which the desired structures can be sculpted using FIB milling. The optical properties of the devices fabricated using this method are assumed on the model of sharp diamond–air interface. The real quality of this interface could depend on degree of graphitization of the amorphous damage layers after annealing. In the present work the graphitization process was studied using conventional and analytical TEM. It was found that annealing at 550 °C results in a partial graphitization of the implanted volume with formation of the nano-crystalline graphitic phase sandwiched between layers of tetrahedral amorphous carbon. Annealing at 1400 °C resulted in complete graphitization of the amorphous layers. The average size of graphite nano-crystals did not exceed 5 nm with predominant orientation of c-planes normal to the sample surface.

Ensemble annealing of complex physical systems

OpenAIRE

Habeck, Michael

2015-01-01

Algorithms for simulating complex physical systems or solving difficult optimization problems often resort to an annealing process. Rather than simulating the system at the temperature of interest, an annealing algorithm starts at a temperature that is high enough to ensure ergodicity and gradually decreases it until the destination temperature is reached. This idea is used in popular algorithms such as parallel tempering and simulated annealing. A general problem with annealing methods is th...

Comparison of pulsed electron beam-annealed and pulsed ruby laser-annealed ion-implanted silicon

International Nuclear Information System (INIS)

Wilson, S.R.; Appleton, B.R.; White, C.W.; Narayan, J.; Greenwald, A.C.

1978-11-01

Recently two new techniques, pulsed electron beam annealing and pulsed laser annealing, have been developed for processing ion-implanted silicon. These two types of anneals have been compared using ion-channeling, ion back-scattering, and transmission electron microscopy (TEM). Single crystal samples were implanted with 100 keV As + ions to a dose of approx. 1 x 10 16 ions/cm 2 and subsequently annealed by either a pulsed Ruby laser or a pulsed electron beam. Our results show in both cases that the near-surface region has melted and regrown epitaxially with nearly all of the implanted As (97 to 99%) incroporated onto lattice sites. The analysis indicates that the samples are essentially defect free and have complete electrical recovery

Annealing Kinetic Model Using Fast and Slow Metastable Defects for Hydrogenated-Amorphous-Silicon-Based Solar Cells

Directory of Open Access Journals (Sweden)

Seung Yeop Myong

2007-01-01

Full Text Available The two-component kinetic model employing “fast” and “slow” metastable defects for the annealing behaviors in pin-type hydrogenated-amorphous-silicon- (a-Si:H- based solar cells is simulated using a normalized fill factor. Reported annealing data on pin-type a-Si:H-based solar cells are revisited and fitted using the model to confirm its validity. It is verified that the two-component model is suitable for fitting the various experimental phenomena. In addition, the activation energy for annealing of the solar cells depends on the definition of the recovery time. From the thermally activated and high electric field annealing behaviors, the plausible microscopic mechanism on the defect removal process is discussed.

Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks

Science.gov (United States)

Belotserkovskii, Boris P.; Neil, Alexander J.; Saleh, Syed Shayon; Shin, Jane Hae Soo; Mirkin, Sergei M.; Hanawalt, Philip C.

2013-01-01

The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation. PMID:23275544

Structural properties of WO{sub 3} dependent of the annealing temperature deposited by hot-filament metal oxide deposition

Energy Technology Data Exchange (ETDEWEB)

Flores M, J. E. [Benemerita Universidad Autonoma de Puebla, Facultad de Ciencias de la Electronica, Av. San Claudio y 18 Sur, Ciudad Universitaria, Col. Jardines de San Manuel, 72570 Puebla (Mexico); Diaz R, J. [IPN, Centro de Investigacion en Biotecnologia Aplicada, Ex-Hacienda de San Molino Km 1.5 Tepetitla, 90700 Tlaxcala (Mexico); Balderas L, J. A., E-mail: eflores@ece.buap.mx [IPN, Unidad Profesional Interdisciplinaria de Biotecnologia, Av. Acueducto s/n, Col. Barrio la Laguna, 07340 Mexico D. F. (Mexico)

2012-07-01

In this work presents a study of the effect of the annealing temperature on structural and optical properties of WO{sub 3} that has been grown by hot-filament metal oxide deposition. The chemical stoichiometry was determined by X-ray photoelectron spectroscopy. By X-ray diffraction obtained that the as-deposited WO{sub 3} films present mainly monoclinic crystalline phase. WO{sub 3} optical band gap energy can be varied from 2.92 to 3.15 eV obtained by transmittance measurements by annealing WO{sub 3} from 100 to 500 C. The Raman spectrum of the as-deposited WO{sub 3} film shows four intense peaks that are typical Raman peaks of crystalline WO{sub 3} (m-phase) that corresponds to the stretching vibrations of the bridging oxygen that are assigned to W-O stretching ({upsilon}) and W-O bending ({delta}) modes, respectively, which enhanced and increased their intensity with the annealing temperature. (Author)

Activation of double-stranded RNA-dependent protein kinase inhibits proliferation of pancreatic β-cells

Energy Technology Data Exchange (ETDEWEB)

Chen, Shan-Shan [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Jiang, Teng [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Wang, Yi; Gu, Li-Ze [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Wu, Hui-Wen [Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing (China); Tan, Lan [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Guo, Jun, E-mail: Guoj@njmu.edu.cn [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China)

2014-01-17

Highlights: •PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in β-cells. •Activated PKR inhibited β-cell proliferation by arresting cell cycle at G1 phase. •Activated PKR fully abrogated the pro-proliferative effects of IGF-I on β-cells. -- Abstract: Double-stranded RNA-dependent protein kinase (PKR) is revealed to participate in the development of insulin resistance in peripheral tissues in type 2 diabetes (T2DM). Meanwhile, PKR is also characterized as a critical regulator of cell proliferation. To date, no study has focused on the impact of PKR on the proliferation of pancreatic β-cells. Here, we adopted insulinoma cell lines and mice islet β-cells to investigate: (1) the effects of glucolipotoxicity and pro-inflammatory cytokines on PKR activation; (2) the effects of PKR on proliferation of pancreatic β-cells and its underlying mechanisms; (3) the actions of PKR on pro-proliferative effects of IGF-I and its underlying pathway. Our results provided the first evidence that PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in pancreatic β-cells, and activated PKR significantly inhibited cell proliferation by arresting cell cycle at G1 phase. Reductions in cyclin D1 and D2 as well as increases in p27 and p53 were associated with the anti-proliferative effects of PKR, and proteasome-dependent degradation took part in the reduction of cyclin D1 and D2. Besides, PKR activation abrogated the pro-proliferative effects of IGF-I by activating JNK and disrupting IRS1/PI3K/Akt signaling pathway. These findings indicate that the anti-proliferative actions of PKR on pancreatic β-cells may contribute to the pathogenesis of T2DM.

Activation of double-stranded RNA-dependent protein kinase inhibits proliferation of pancreatic β-cells

International Nuclear Information System (INIS)

Chen, Shan-Shan; Jiang, Teng; Wang, Yi; Gu, Li-Ze; Wu, Hui-Wen; Tan, Lan; Guo, Jun

2014-01-01

Highlights: •PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in β-cells. •Activated PKR inhibited β-cell proliferation by arresting cell cycle at G1 phase. •Activated PKR fully abrogated the pro-proliferative effects of IGF-I on β-cells. -- Abstract: Double-stranded RNA-dependent protein kinase (PKR) is revealed to participate in the development of insulin resistance in peripheral tissues in type 2 diabetes (T2DM). Meanwhile, PKR is also characterized as a critical regulator of cell proliferation. To date, no study has focused on the impact of PKR on the proliferation of pancreatic β-cells. Here, we adopted insulinoma cell lines and mice islet β-cells to investigate: (1) the effects of glucolipotoxicity and pro-inflammatory cytokines on PKR activation; (2) the effects of PKR on proliferation of pancreatic β-cells and its underlying mechanisms; (3) the actions of PKR on pro-proliferative effects of IGF-I and its underlying pathway. Our results provided the first evidence that PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in pancreatic β-cells, and activated PKR significantly inhibited cell proliferation by arresting cell cycle at G1 phase. Reductions in cyclin D1 and D2 as well as increases in p27 and p53 were associated with the anti-proliferative effects of PKR, and proteasome-dependent degradation took part in the reduction of cyclin D1 and D2. Besides, PKR activation abrogated the pro-proliferative effects of IGF-I by activating JNK and disrupting IRS1/PI3K/Akt signaling pathway. These findings indicate that the anti-proliferative actions of PKR on pancreatic β-cells may contribute to the pathogenesis of T2DM

Annealing effects in solid-state track recorders

International Nuclear Information System (INIS)

Gold, R.; Roberts, J.H.; Ruddy, F.H.

1981-01-01

Current analyses of the annealing process in Solid State Track Recorders (SSTR) reveal fundamental misconceptions. The use of the Arrhenius equation to describe the decrease in track density resulting from annealing is shown to be incorrect. To overcome these deficiencies, generalized reaction rate theory is used to describe the annealing process in SSTR. Results of annealing experiments are used to guide this theoretical formulation. Within this framework, the concept of energy per etchable defect for SSTR is introduced. A general correlation between sensitivity and annealing susceptibility in SSTR is deduced. In terms of this general theory, the apparent correlation between fission track size and fission track density observed under annealing is readily explained. Based on this theoretical treatment of annealing phenomena, qualitative explanations are advanced for current enigmas in SSTR cosmic ray work

AFM, XRD and HRTEM Studies of Annealed FePd Thin Films

International Nuclear Information System (INIS)

Perzanowski, M.; Zabila, Y.; Polit, A.; Krupinski, M.; Dobrowolska, A.; Marszalek, M.; Morgiel, J.

2010-01-01

Ferromagnetic FePd L1 0 ordered alloys are highly expected as forthcoming high-density recording materials, because they reveal a large perpendicular magnetocrystalline anisotropy. The value of the magnetic anisotropy of FePd alloy strongly depends on the alloy composition, degree of alloy order as well as on the crystallographic grain orientation. In particular, to obtain the perpendicular anisotropy, it is necessary to get the films with (001) texture. One of the successful methods, which allows one to obtain highly ordered alloy, is a subsequent deposition of Fe and Pd layers, followed by an annealing at high temperature. This paper presents the study of the FePd thin alloy film structure changing in the result of high temperature annealing. During the annealing in high vacuum, the measurements of electrical resistance were performed, indicating the regions of different structure evolution. Changes in the crystal structure and surface morphology induced by thermal treatment were investigated by X-ray diffraction, atomic force microscopy, as well as high resolution transmission electron microscopy and then compared with electrical resistivity measurement. The slow thermal annealing of the deposited layers leads to the formation of L1 0 ordered FePd alloy with preferred (111) grain orientation. After the annealing at the highest used temperature, the dewetting process was observed, resulting in a creation of well oriented, regular nanoparticles. (author)

Open-System Quantum Annealing in Mean-Field Models with Exponential Degeneracy*

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Kostyantyn Kechedzhi

2016-05-01

Full Text Available Real-life quantum computers are inevitably affected by intrinsic noise resulting in dissipative nonunitary dynamics realized by these devices. We consider an open-system quantum annealing algorithm optimized for such a realistic analog quantum device which takes advantage of noise-induced thermalization and relies on incoherent quantum tunneling at finite temperature. We theoretically analyze the performance of this algorithm considering a p-spin model that allows for a mean-field quasiclassical solution and, at the same time, demonstrates the first-order phase transition and exponential degeneracy of states, typical characteristics of spin glasses. We demonstrate that finite-temperature effects introduced by the noise are particularly important for the dynamics in the presence of the exponential degeneracy of metastable states. We determine the optimal regime of the open-system quantum annealing algorithm for this model and find that it can outperform simulated annealing in a range of parameters. Large-scale multiqubit quantum tunneling is instrumental for the quantum speedup in this model, which is possible because of the unusual nonmonotonous temperature dependence of the quantum-tunneling action in this model, where the most efficient transition rate corresponds to zero temperature. This model calculation is the first analytically tractable example where open-system quantum annealing algorithm outperforms simulated annealing, which can, in principle, be realized using an analog quantum computer.

Long-term memory for instrumental responses does not undergo protein synthesis-dependent reconsolidation upon retrieval.

Science.gov (United States)

Hernandez, Pepe J; Kelley, Ann E

2004-01-01

Recent evidence indicates that certain forms of memory, upon recall, may return to a labile state requiring the synthesis of new proteins in order to preserve or reconsolidate the original memory trace. While the initial consolidation of "instrumental memories" has been shown to require de novo protein synthesis in the nucleus accumbens, it is not known whether memories of this type undergo protein synthesis-dependent reconsolidation. Here we show that low doses of the protein synthesis inhibitor anisomycin (ANI; 5 or 20 mg/kg) administered systemically in rats immediately after recall of a lever-pressing task potently impaired performance on the following daily test sessions. We determined that the nature of this impairment was attributable to conditioned taste aversion (CTA) to the sugar reinforcer used in the task rather than to mnemonic or motoric impairments. However, by substituting a novel flavored reinforcer (chocolate pellets) prior to the administration of doses of ANI (150 or 210 mg/kg) previously shown to cause amnesia, a strong CTA to chocolate was induced sparing any aversion to sugar. Importantly, when sugar was reintroduced on the following session, we found that memory for the task was not significantly affected by ANI. Thus, these data suggest that memory for a well-learned instrumental response does not require protein synthesis-dependent reconsolidation as a means of long-term maintenance.

The flavoprotein Tah18-dependent NO synthesis confers high-temperature stress tolerance on yeast cells

Energy Technology Data Exchange (ETDEWEB)

Nishimura, Akira; Kawahara, Nobuhiro [Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); Takagi, Hiroshi, E-mail: hiro@bs.naist.jp [Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan)

2013-01-04

Highlights: Black-Right-Pointing-Pointer NO is produced from L-arginine in response to elevated temperature in yeast. Black-Right-Pointing-Pointer Tah18 was first identified as the yeast protein involved in NO synthesis. Black-Right-Pointing-Pointer Tah18-dependent NO synthesis confers tolerance to high-temperature on yeast cells. -- Abstract: Nitric oxide (NO) is a ubiquitous signaling molecule involved in the regulation of a large number of cellular functions. In the unicellular eukaryote yeast, NO may be involved in stress response pathways, but its role is poorly understood due to the lack of mammalian NO synthase (NOS) orthologues. Previously, we have proposed the oxidative stress-induced L-arginine synthesis and its physiological role under stress conditions in yeast Saccharomyces cerevisiae. Here, our experimental results indicated that increased conversion of L-proline into L-arginine led to NO production in response to elevated temperature. We also showed that the flavoprotein Tah18, which was previously reported to transfer electrons to the Fe-S cluster protein Dre2, was involved in NO synthesis in yeast. Gene knockdown analysis demonstrated that Tah18-dependent NO synthesis confers high-temperature stress tolerance on yeast cells. As it appears that such a unique cell protection mechanism is specific to yeasts and fungi, it represents a promising target for antifungal activity.

Luminescence lifetimes in natural quartz annealed beyond its second phase inversion temperature

International Nuclear Information System (INIS)

Chithambo, M.L.

2015-01-01

The influence of annealing, irradiation dose, preheating and measurement temperature on luminescence lifetimes has been studied in quartz annealed at 1000 °C. The measurements were supplemented by studies on quartz annealed at 900 and 800 °C. Lifetimes increase with dose as well as with temperature and duration of annealing between 800 and 1000 °C. Preheating produces the same effect. The changes are accounted for in terms of hole-transfer from the non-radiative luminescence centre to and between radiative centres. The influence of measurement temperature on lifetimes depends on whether the stimulation is carried out from ambient to 200 °C or otherwise. This result is unlike that in quartz annealed at or below 500 °C where lifetimes are independent of the direction of heating. In particular, lifetimes decrease monotonically when measurements are made from 20 to 200 °C but not when recorded from 200 to 20 °C. The latter produces a pattern resembling that in quartz annealed up to 500 °C. The results are concluded as evidence of thermal effects on separate luminescence centres. In support of this, different values of the activation energy for thermal quenching were found for each supposed luminescence centre. The change of the corresponding luminescence intensity with temperature is also qualitatively consistent with this notion. - Highlights: • Luminescence lifetimes in natural quartz annealed beyond its second phase inversion temperature is reported. • Lifetimes increase with dose, annealing between 800 and 1000 °C, and preheating. • Lifetimes under stimulation temperature are affected by direction of heating. • Changes are accounted for in terms of hole-transfer luminescence centres.

The influence of thermal annealing on structure and oxidation of iron nanowires

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Krajewski Marcin

2015-03-01

Full Text Available Raman spectroscopy as well as Mössbauer spectroscopy were applied in order to study the phase composition of iron nanowires and its changes, caused by annealing in a neutral atmosphere at several temperatures ranging from 200°C to 800°C. As-prepared nanowires were manufactured via a simple chemical reduction in an external magnetic field. Both experimental techniques proved formation of the surface layer covered by crystalline iron oxides, with phase composition dependent on the annealing temperature (Ta. At higher Ta, hematite was the dominant phase in the nanowires.

Onset temperature for Si nanostructure growth on Si substrate during high vacuum electron beam annealing.

Science.gov (United States)

Fang, F; Markwitz, A

2009-05-01

Silicon nanostructures, called Si nanowhiskers, are successfully synthesized on Si(100) substrate by high vacuum electron beam annealing. The onset temperature and duration needed for the Si nanowhiskers to grow was investigated. It was found that the onset and growth morphology of Si nanowhiskers strongly depend on the annealing temperature and duration applied in the annealing cycle. The onset temperature for nanowhisker growth was determined as 680 degrees C using an annealing duration of 90 min and temperature ramps of +5 degrees C s(-1) for heating and -100 degrees C s(-1) for cooling. Decreasing the annealing time at peak temperature to 5 min required an increase in peak temperature to 800 degrees C to initiate the nanowhisker growth. At 900 degrees C the duration for annealing at peak temperature can be set to 0 s to grow silicon nanowhiskers. A correlation was found between the variation in annealing temperature and duration and the nanowhisker height and density. Annealing at 900 degrees C for 0 s, only 2-3 nanowhiskers (average height 2.4 nm) grow on a surface area of 5 x 5 microm, whereas more than 500 nanowhiskers with an important average height of 4.6 nm for field emission applications grow on the same surface area for a sample annealed at 970 degrees C for 0 s. Selected results are presented showing the possibility of controlling the density and height of Si nanowhisker growth for field emission applications by applying different annealing temperature and duration.

Effects of annealing temperatures on the physicochemical properties of nickel-phosphorus deposits

International Nuclear Information System (INIS)

Bai, Allen; Hu, C.-C.

2003-01-01

The dependence of physicochemical properties, including microhardness, magnetism, morphology, crystalline information, roughness factor and hydrogen evolution ability, on the phosphorus content, varying from 0 to 28 atomic percentage (at.%), of Ni-P deposits with annealing in air at eight temperatures (i.e., 100, 200, 300, 400, 500, 600, 700 and 800 deg. C) were systematically compared. The microhardness reached a maximum at 400 deg. C due to the crystallization of Ni and Ni 3 P at 400 deg. C and the significant diffusion of Cu into the Ni-P deposit at temperatures ≥500 deg. C, confirmed by the depth profiles of Ni, P, Cu and O elements. The paramagnetism of Ni-P deposit was gradually transformed into ferromagnetism at 400 deg. C, attributable to the phase separation of Ni and Ni 3 P. The roughness factor, R a , of the deposits with P contents ≤12 at.% were increased with increasing the annealing temperature at temperatures a of the deposits with 17-28 at.% of P is approximately independent of the annealing temperature. The rate of hydrogen evolution decreased with increasing the annealing temperature because the specific activity (i/R a ) of the Ni-P deposits was decreased with increasing the annealing temperature

Residual stress change by thermal annealing in amorphous Sm-Fe-B thin films

International Nuclear Information System (INIS)

Na, S.M.; Suh, S.J.; Kim, H.J.; Lim, S.H.

2002-01-01

The change in the residual stress and its effect on mechanical bending and magnetic properties of sputtered amorphous Sm-Fe-B thin films are investigated as a function of annealing temperature. Two stress components of intrinsic compressive stress and tensile stress due to the difference of the thermal expansion coefficients between the substrate and thin film are used to explain the stress state in as-deposited thin films, and the annealing temperature dependence of residual stress, mechanical bending and magnetic properties

The effect of annealing ambient on surface segregation in indium implanted sapphire

International Nuclear Information System (INIS)

Sood, D.K.; Victoria University of Technology, Melbourne; Zhou, W.; Victoria University of Technology, Melbourne; Academia Sinica, Shanghai Institute of Metallurgy; Cao, D.X.; Victoria University of Technology, Melbourne; Academia Sinica, Shanghai, SH

1991-01-01

A systematic study of the effect of annealing ambient on both indium surface segregation and lattice damage recovery of single crystal Al 2 O 3 has been done by performing 1 hour anneals at 800 deg C for the samples identically implanted with indium ions at 100keV energy to a high dose of 5x10 16 ions/cm 2 . Following solid phase epitaxial re-crystallization of amorphous layer, the indium dopant shows rapid thermal migration. The indium redistribution consists of 2 parts: 1. appreciable broadening corresponding to diffusion within the amorphous layer, and 2. indium segregation to the free surface to form In 2 O 3 , or escape out of the surface to sublime into the surrounding ambient. Lattice damage recovery depends on indium concentration profile in amorphous layer of Al 2 O 3 which is directly influenced by the annealing ambient. It is confirmed that the presence of moisture or oxygen in annealing ambient results in In 2 O 3 formation on the surface. (author). 6 refs.; 3 figs.; 1 tab

Functional interactions of nucleocapsid protein of feline immunodeficiency virus and cellular prion protein with the viral RNA.

Science.gov (United States)

Moscardini, Mila; Pistello, Mauro; Bendinelli, M; Ficheux, Damien; Miller, Jennifer T; Gabus, Caroline; Le Grice, Stuart F J; Surewicz, Witold K; Darlix, Jean-Luc

2002-04-19

All lentiviruses and oncoretroviruses examined so far encode a major nucleic-acid binding protein (nucleocapsid or NC* protein), approximately 2500 molecules of which coat the dimeric RNA genome. Studies on HIV-1 and MoMuLV using in vitro model systems and in vivo have shown that NC protein is required to chaperone viral RNA dimerization and packaging during virus assembly, and proviral DNA synthesis by reverse transcriptase (RT) during infection. The human cellular prion protein (PrP), thought to be the major component of the agent causing transmissible spongiform encephalopathies (TSE), was recently found to possess a strong affinity for nucleic acids and to exhibit chaperone properties very similar to HIV-1 NC protein in the HIV-1 context in vitro. Tight binding of PrP to nucleic acids is proposed to participate directly in the prion disease process. To extend our understanding of lentiviruses and of the unexpected nucleic acid chaperone properties of the human prion protein, we set up an in vitro system to investigate replication of the feline immunodeficiency virus (FIV), which is functionally and phylogenetically distant from HIV-1. The results show that in the FIV model system, NC protein chaperones viral RNA dimerization, primer tRNA(Lys,3) annealing to the genomic primer-binding site (PBS) and minus strand DNA synthesis by the homologous FIV RT. FIV NC protein is able to trigger specific viral DNA synthesis by inhibiting self-priming of reverse transcription. The human prion protein was found to mimic the properties of FIV NC with respect to primer tRNA annealing to the viral RNA and chaperoning minus strand DNA synthesis. Copyright 2002 Elsevier Science Ltd.

Synthesis of stable TiO2 nanotubes: effect of hydrothermal treatment, acid washing and annealing temperature.

Science.gov (United States)

López Zavala, Miguel Ángel; Lozano Morales, Samuel Alejandro; Ávila-Santos, Manuel

2017-11-01

Effect of hydrothermal treatment, acid washing and annealing temperature on the structure and morphology of TiO 2 nanotubes during the formation process was assessed. X-ray diffraction, scanning electron microscopy (SEM), transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy analysis were conducted to describe the formation and characterization of the structure and morphology of nanotubes. Hydrothermal treatment of TiO 2 precursor nanoparticles and acid washing are fundamental to form and define the nanotubes structure. Hydrothermal treatment causes a change in the crystallinity of the precursor nanoparticles from anatase phase to a monoclinic phase, which characterizes the TiO 2 nanosheets structure. The acid washing promotes the formation of high purity nanotubes due to Na + is exchanged from the titanate structure to the hydrochloric acid (HCl) solution. The annealing temperature affects the dimensions, structure and the morphology of the nanotubes. Annealing temperatures in the range of 400 °C and 600 °C are optimum to maintain a highly stable tubular morphology of nanotubes. Additionally, nanotubes conserve the physicochemical properties of the precursor Degussa P25 nanoparticles. Temperatures greater than 600 °C alter the morphology of nanotubes from tubular to an irregular structure of nanoparticles, which are bigger than those of the precursor material, i.e., the crystallinity turn from anatase phase to rutile phase inducing the collapse of the nanotubes.

Enhanced tunability of magneto-impedance and magneto-capacitance in annealed Metglas/PZT magnetoelectric composites

Science.gov (United States)

Leung, Chung Ming; Zhuang, Xin; Xu, Junran; Li, Jiefang; Zhang, Jitao; Srinivasan, G.; Viehland, D.

2018-05-01

This report is on a new class of magnetostatically tunable magneto-impedance and magneto-capacitance devices based on a composite of ferromagnetic Metglas and ferroelectric lead zirconate titanate (PZT). Layered magneto-electric (ME) composites with annealed Metglas and PZT were studied in a longitudinal in-plane magnetic field-transverse electric field (L-T) mode. It was found that the degree of tunability was dependent on the annealing temperature of Metglas. An impedance tunability (ΔZ/Z0) of ≥400% was obtained at the electromechanical resonance (EMR) frequency (fr) for a sample with Metglas layers annealed at Ta = 500oC. This tunability is a factor of two higher than for composites with Metglas annealed at 350oC. The tunability of the capacitance, (ΔC/C0), was found to be 290% and -135k% at resonance and antiresonance, respectively, for Ta = 500oC. These results provide clear evidence for improvement in static magnetic field tunability of impedance and capacitance of ME composites with the use of annealed Metglas and are of importance for their potential use in tunable electronic applications.

Analytical model of the critical current of a bent Nb3Sn strand

International Nuclear Information System (INIS)

Koizumi, Norikiyo; Murakami, Haruyuki; Hemmi, Tsutomu; Nakajima, Hideo

2011-01-01

The critical current performance of a large Nb 3 Sn cable-in-conduit conductor (CICC) was degraded by periodic bending of strands due to a large transverse electromagnetic force. The degradation of each strand due to this bending should be evaluated in calculations of the critical current of a CICC, but a suitable model has not been developed yet. Therefore, the authors have developed a new analytical model which takes into account plastic deformation of copper and bronze and filament breakage. The calculated results were compared with test results for uniformly bent Nb 3 Sn bronze-route strands. The calculated results assuming a high transverse resistance model (HTRM) show good agreement with the test results, a finding which confirms the validity of the model. Because of a much shorter calculation time than for numerical simulation, the developed model seems much more practical for use in calculating the critical current performance of a Nb 3 Sn CICC. In addition, simulation results show that since the neutral axis of a bent strand shifts to the compressive side due to plastic deformation of the copper and bronze, and/or filament breakage, the strand is elongated by bending. This elongation may enhance the strand's critical current performance. Moreover, the calculated results indicate that the dependence of the critical current on the bending strain is affected by the bending history if the strand is excessively bent, especially when filaments are broken. In a real magnet, since a strand in a CICC is normally subject to the maximum electromagnetic force prior to an evaluation of its performance at a lower electromagnetic force, the effect of over-bending should be taken into account in calculations of its critical current performance, especially when filament breakage occurs.

[Expression and purification of a novel thermophilic bacterial single-stranded DNA-binding protein and enhancement the synthesis of DNA and cDNA].

Science.gov (United States)

Jia, Xiao-Wei; Zhang, Guo-Hui; Shi, Hai-Yan

2012-12-01

Express a novel species of single-stranded DNA-binding protein (SSB) derived from Thermococcus kodakarensis KOD1, abbreviated kod-ssb. And evaluate the effect of kod-ssb on PCR-based DNA amplification and reverse transcription. We express kod-ssb with the Transrtta (DE3), and kod-ssb was purified by affinity chromatography on a Ni2+ Sepharose column, detected by SDS-PAGE. To evaluate the effect of kod-ssb on PCR-based DNA amplification, the human beta globin gene was used as template to amplify a 5-kb, 9-kb and 13-kb. And to detect the effect of kod-ssb on reverse transcription, we used RNA from flu cell culture supernatant extraction as templates to implement qRT-PCR reaction. The plasmid pET11a-kod was transformed into Transetta (DE3) and the recombinant strain Transetta (pET11 a-kod) was obtained. The kod-ssb was highly expressed when the recombinant strain Transetta(pET11a-kod) was induced by IPTG. The specific protein was detected by SDS-PAGE. To confirm that kod-ssb can enhance target DNA synthesis and reduce PCR by-products, 5-, 9-, and 13-kb human beta globin gene fragments were used as templates for PCR. When PCR reactions did not include SSB proteins, the specific PCR product was contaminated with non-specific products. When kod -ssb was added, kod-ssb significantly enhanced amplification of the 5-, 9-and 13-kb target product and minimised the non-specific PCR products. To confirm that kod-ssb can enhance target cDNA synthesis, RNA from flu cell culture supernatant extraction was used as templates for qRT-PCR reaction. The results was that when kod-ssb was added, kod-ssb significantly enhanced the synthesis of cDNA, average Ct value is 19.42, and the average Ct value without kod-ssb is 22.15. kod-ssb may in future be used to enhance DNA and cDNA amplification.

Understanding the microwave annealing of silicon

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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.

Application of annealing for WWER vessels life extension

International Nuclear Information System (INIS)

Badanin, V.I.; Gorynin, I.V.; Nickolaev, V.A.; Dragunov, Y.G.; Fedorov, V.G.

1989-01-01

Safe operation of NPP is greatly dependent on the guarantee of reactor vessel brittle failure strength with account for the effect of radiation embrittlement of vessel material. Recovery of irradiated material properties is principally important way to extend radiation life of reactor vessel. The aim of this report is to demonstrate the efficiency of annealing for recovery of vessel material properties and extension of its service-life

Intracellular generation of single-strand template increases the knock-in efficiency by combining CRISPR/Cas9 with AAV.

Science.gov (United States)

Xiao, Qing; Min, Taishan; Ma, Shuangping; Hu, Lingna; Chen, Hongyan; Lu, Daru

2018-04-18

Targeted integration of transgenes facilitates functional genomic research and holds prospect for gene therapy. The established microhomology-mediated end-joining (MMEJ)-based strategy leads to the precise gene knock-in with easily constructed donor, yet the limited efficiency remains to be further improved. Here, we show that single-strand DNA (ssDNA) donor contributes to efficient increase of knock-in efficiency and establishes a method to achieve the intracellular linearization of long ssDNA donor. We identified that the CRISPR/Cas9 system is responsible for breaking double-strand DNA (dsDNA) of palindromic structure in inverted terminal repeats (ITRs) region of recombinant adeno-associated virus (AAV), leading to the inhibition of viral second-strand DNA synthesis. Combing Cas9 plasmids targeting genome and ITR with AAV donor delivery, the precise knock-in of gene cassette was achieved, with 13-14% of the donor insertion events being mediated by MMEJ in HEK 293T cells. This study describes a novel method to integrate large single-strand transgene cassettes into the genomes, increasing knock-in efficiency by 13.6-19.5-fold relative to conventional AAV-mediated method. It also provides a comprehensive solution to the challenges of complicated production and difficult delivery with large exogenous fragments.

Fair Exchange in Strand Spaces

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Joshua D. Guttman

2009-10-01

Full Text Available Many cryptographic protocols are intended to coordinate state changes among principals. Exchange protocols coordinate delivery of new values to the participants, e.g. additions to the set of values they possess. An exchange protocol is fair if it ensures that delivery of new values is balanced: If one participant obtains a new possession via the protocol, then all other participants will, too. Fair exchange requires progress assumptions, unlike some other protocol properties. The strand space model is a framework for design and verification of cryptographic protocols. A strand is a local behavior of a single principal in a single session of a protocol. A bundle is a partially ordered global execution built from protocol strands and adversary activities. The strand space model needs two additions for fair exchange protocols. First, we regard the state as a multiset of facts, and we allow strands to cause changes in this state via multiset rewriting. Second, progress assumptions stipulate that some channels are resilient-and guaranteed to deliver messages-and some principals are assumed not to stop at certain critical steps. This method leads to proofs of correctness that cleanly separate protocol properties, such as authentication and confidentiality, from invariants governing state evolution. G. Wang's recent fair exchange protocol illustrates the approach.

Influence of oxidized purine processing on strand directionality of mismatch repair.

Science.gov (United States)

Repmann, Simone; Olivera-Harris, Maite; Jiricny, Josef

2015-04-17

Replicative DNA polymerases are high fidelity enzymes that misincorporate nucleotides into nascent DNA with a frequency lower than [1/10(5)], and this precision is improved to about [1/10(7)] by their proofreading activity. Because this fidelity is insufficient to replicate most genomes without error, nature evolved postreplicative mismatch repair (MMR), which improves the fidelity of DNA replication by up to 3 orders of magnitude through correcting biosynthetic errors that escaped proofreading. MMR must be able to recognize non-Watson-Crick base pairs and excise the misincorporated nucleotides from the nascent DNA strand, which carries by definition the erroneous genetic information. In eukaryotes, MMR is believed to be directed to the nascent strand by preexisting discontinuities such as gaps between Okazaki fragments in the lagging strand or breaks in the leading strand generated by the mismatch-activated endonuclease of the MutL homologs PMS1 in yeast and PMS2 in vertebrates. We recently demonstrated that the eukaryotic MMR machinery can make use also of strand breaks arising during excision of uracils or ribonucleotides from DNA. We now show that intermediates of MutY homolog-dependent excision of adenines mispaired with 8-oxoguanine (G(O)) also act as MMR initiation sites in extracts of human cells or Xenopus laevis eggs. Unexpectedly, G(O)/C pairs were not processed in these extracts and failed to affect MMR directionality, but extracts supplemented with exogenous 8-oxoguanine DNA glycosylase (OGG1) did so. Because OGG1-mediated excision of G(O) might misdirect MMR to the template strand, our findings suggest that OGG1 activity might be inhibited during MMR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms.

Science.gov (United States)

Tannenbaum, Emmanuel; Sherley, James L; Shakhnovich, Eugene I

2005-04-01

This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes of chromosome segregation: (1) random segregation, where the daughter chromosomes of a given parent chromosome segregate randomly into the stem cell and its differentiating sister cell and (2) "immortal DNA strand" co-segregation, for which the stem cell retains the daughter chromosomes with the oldest parent strands. Immortal strand co-segregation is a mechanism, originally proposed by [Cairns Nature (London) 255, 197 (1975)], by which stem cells preserve the integrity of their genomes. For random segregation, we develop an ordered strand pair formulation of the dynamics, analogous to the ordered strand pair formalism developed for quasispecies dynamics involving semiconservative replication with imperfect lesion repair (in this context, lesion repair is taken to mean repair of postreplication base-pair mismatches). Interestingly, a similar formulation is possible with immortal strand co-segregation, despite the fact that this segregation mechanism is age dependent. From our model we are able to mathematically show that, when lesion repair is imperfect, then immortal strand co-segregation leads to better preservation of the stem cell lineage than random chromosome segregation. Furthermore, our model allows us to estimate the optimal lesion repair efficiency for preserving an adult stem cell population for a given period of time. For human stem cells, we obtain that mispaired bases still present after replication and cell division should be left untouched, to avoid potentially fixing a mutation in both DNA strands.

Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA.

Science.gov (United States)

Khodakov, Dmitriy A; Khodakova, Anastasia S; Huang, David M; Linacre, Adrian; Ellis, Amanda V

2015-03-04

Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.

Effect of annealing on parameters of synthetic opal

International Nuclear Information System (INIS)

Gajiev, G M; Kurdyukov, D A; Travnikov, V V

2006-01-01

We report on the effect of high temperature annealing on the reflection spectra of synthetic opals. The analysis of conditions for simultaneous diffraction on the (111) planes parallel and inclined to the sample surface has shown that both annealed and unannealed opals are compressed along the growth [111] axis and the shape of the SiO 2 balls forming the opals' close packed structure can be described as spheroidal. The structure parameters were evaluated from the analysis of the angular dependences of the peak positions in the Bragg reflection spectra of unfilled and glycerol-filled samples. The major effect of annealing is due to the sintering (interpenetration) of the structural elements of opals. The maximum temperature of 1050 deg. C leads to a 10-fold increase in the degree of spheroid sintering. As a result, the interspheroid spacing decreases by over 10%, while the filling factor increases from 0.75 to 0.96 together with the effective dielectric constant of the opal as a whole (from 1.74 to 2.08). Sintering takes place not only between spheroids, but also inside spheroids between the α-SiO 2 nanoparticles constituting them. This results in a noticeable (by ∼7%) increase in the dielectric constant of opal spheroids

The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase

Directory of Open Access Journals (Sweden)

Yusuke Takezawa

2016-06-01

Full Text Available A metal-mediated base pair, composed of two ligand-bearing nucleotides and a bridging metal ion, is one of the most promising components for developing DNA-based functional molecules. We have recently reported an enzymatic method to synthesize hydroxypyridone (H-type ligand-bearing artificial DNA strands. Terminal deoxynucleotidyl transferase (TdT, a template-independent DNA polymerase, was found to oligomerize H nucleotides to afford ligand-bearing DNAs, which were subsequently hybridized through copper-mediated base pairing (H–CuII–H. In this study, we investigated the effects of a metal cofactor, MgII ion, on the TdT-catalyzed polymerization of H nucleotides. At a high MgII concentration (10 mM, the reaction was halted after several H nucleotides were appended. In contrast, at lower MgII concentrations, H nucleotides were further appended to the H-tailed product to afford longer ligand-bearing DNA strands. An electrophoresis mobility shift assay revealed that the binding affinity of TdT to the H-tailed DNAs depends on the MgII concentration. In the presence of excess MgII ions, TdT did not bind to the H-tailed strands; thus, further elongation was impeded. This is possibly because the interaction with MgII ions caused folding of the H-tailed strands into unfavorable secondary structures. This finding provides an insight into the enzymatic synthesis of longer ligand-bearing DNA strands.

Physical properties of electrically conductive Sb-doped SnO2 transparent electrodes by thermal annealing dependent structural changes for photovoltaic applications

International Nuclear Information System (INIS)

Leem, J.W.; Yu, J.S.

2011-01-01

Highlights: · The physical properties of sputtered Sb-doped SnO 2 after annealing were studied. · The figure of merit was estimated from the integral PFD and sheet resistance. · The characteristics of Sb-doped SnO 2 films were optimized by the figure of merit. · An optimized Sb-doped SnO 2 layer is promising for high efficiency photovoltaic cells. - Abstract: We have investigated the optical and electrical characteristics of antimony (Sb)-doped tin oxide (SnO 2 ) films with modified structures by thermal annealing as a transparent conductive electrode. The structural properties were analyzed from the relative void % by spectroscopic ellipsometry as well as the scanning electron microscopy images and X-ray diffraction patterns. As the annealing temperature was raised, Sb-doped SnO 2 films exhibited a slightly enhanced crystallinity with the increase of the grain size from 17.1 nm at 500 deg. C to 34.3 nm at 700 deg. C. Furthermore, the refractive index and extinction coefficient gradually decreased due to the increase in the relative void % within the film during the annealing. The resistivity decreased to 8.2 x 10 -3 Ω cm at 500 deg. C, but it increased rapidly at 700 deg. C. After thermal annealing, the optical transmittance was significantly increased. For photovoltaic applications, the photonic flux density and the figure of merit over the entire solar spectrum were obtained, indicating the highest values of 5.4 x 10 14 cm -2 s -1 nm -1 at 1.85 eV after annealing at 700 deg. C and 340.1 μA cm -2 Ω -1 at 500 deg. C, respectively.

Enhancement of thermoelectric power factor of Sr2CoMoO6 double perovskite by annealing in reducing atmosphere

Science.gov (United States)

Tanwar, Khagesh; Saxena, Mandvi; Maiti, Tanmoy

2017-10-01

In general, n-type thermoelectric materials are rather difficult to design. This study particularly pivoted on designing potential environmentally benign oxides based n-type thermoelectric material. We synthesized Sr2CoMoO6 (SCMO) polycrystalline ceramics via the solid-state synthesis route. XRD, SEM, and thermoelectric measurements were carried out for phase constitution, microstructure analysis, and to determine its potential for thermoelectric applications. As-sintered SCMO sample showed an insulator like behavior till 640 °C after which it exhibited an n-type non-degenerate semiconductor behavior followed by a p-n type conduction switching. To stabilize a high temperature n-type behavior, annealing of SCMO in reducing atmosphere (H2) at 1000 °C was carried out. After annealing, the SCMO demonstrated an n-type semiconductor behavior throughout the temperature range of measurement. The electrical conductivity (σ) and the power factor (S2σ) were found to be increased manifold in the annealed SCMO double perovskite.

The influence of predeformations and annealings on yield stress and modulus of elongation essentially yttrium doped copper

International Nuclear Information System (INIS)

Neklyudov, I.M.; Sytin, V.I.; Voevodin, V.N.

2003-01-01

The researches results of influence of predeformations and annealings on elastic and plastic characteristics of vacuum melting and yttrium doped copper are given. The interrelation between elastic and plastic characteristics has been shown. It is shown that the yield stress and modulus of elongation essentially depend on predeformations and annealings and they are the structurally sensitive characteristics

High temperature annealing effect on structural and magnetic properties of Ti/Ni multilayers

International Nuclear Information System (INIS)

Bhatt, Pramod; Ganeshan, V.; Reddy, V.R.; Chaudhari, S.M.

2006-01-01

High temperature annealing effect on structural and magnetic properties of Ti/Ni multilayer (ML) up to 600 deg. C have been studied and reported in this paper. Ti/Ni multilayer samples having constant layer thicknesses of 50 A each are deposited on float glass and Si(1 1 1) substrates using electron-beam evaporation technique under ultra-high vacuum (UHV) conditions at room temperatures. The micro-structural parameters and their evolution with temperature for as-deposited as well as annealed multilayer samples up to 600 deg. C in a step of 100 deg. C for 1 h are determined by using X-ray diffraction (XRD) and grazing incidence X-ray reflectivity techniques. The X-ray diffraction pattern recorded at 300 deg. C annealed multilayer sample shows interesting structural transformation (from crystalline to amorphous) because of the solid-state reaction (SSR) and subsequent re-crystallization at higher temperatures of annealing, particularly at ≥400 deg. C due to the formation of TiNi 3 and Ti 2 Ni alloy phases. Sample quality and surface morphology are examined by using atomic force microscopy (AFM) technique for both as-deposited as well as annealed multilayer samples. In addition to this, a temperature dependent dc resistivity measurement is also used to study the structural transformation and subsequent alloy phase formation due to annealing treatment. The corresponding magnetization behavior of multilayer samples after each stage of annealing has been investigated by using Magneto-Optical Kerr Effect (MOKE) technique and results are interpreted in terms of observed micro-structural changes

The European Nb3Sn advanced strand development programme

International Nuclear Information System (INIS)

Vostner, A.; Salpietro, E.

2005-01-01

Strands relevant for fusion with high critical current densities and moderate hysteresis losses were developed and already produced on industrial scale. Based on these achievements EFDA-CSU Garching has launched a Nb 3 Sn strand development and procurement action inside Europe in order to assess the current status of the Nb 3 Sn strand production capability. All six addressed companies have replied positively to the strand R and D programme which includes the three major Nb 3 Sn production techniques namely the bronze, internal-tin and powder-in-tube (PIT) route. According to the strand requirements for the ITER TF conductor a critical current density of 800 A/mm 2 (at 12 T, 4.2 K and 10 μV/m) and overall strand hysteresis losses below 500 kJ/m 3 have been specified as the minimum guaranteed strand performance. The second major objective of this programme is to motivate the strand manufacturers to develop and design high performance Nb 3 Sn strands optimised for the ITER conductor. For this purpose, a target critical current density of 1100 A/mm 2 has been added to the specification. This paper describes the strategy behind the strand development programme, the actual status of the strand production as well as first preliminary results obtained from the strand suppliers

Vitamin B12–dependent taurine synthesis regulates growth and bone mass

Science.gov (United States)

Roman-Garcia, Pablo; Quiros-Gonzalez, Isabel; Mottram, Lynda; Lieben, Liesbet; Sharan, Kunal; Wangwiwatsin, Arporn; Tubio, Jose; Lewis, Kirsty; Wilkinson, Debbie; Santhanam, Balaji; Sarper, Nazan; Clare, Simon; Vassiliou, George S.; Velagapudi, Vidya R.; Dougan, Gordon; Yadav, Vijay K.

2014-01-01

Both maternal and offspring-derived factors contribute to lifelong growth and bone mass accrual, although the specific role of maternal deficiencies in the growth and bone mass of offspring is poorly understood. In the present study, we have shown that vitamin B12 (B12) deficiency in a murine genetic model results in severe postweaning growth retardation and osteoporosis, and the severity and time of onset of this phenotype in the offspring depends on the maternal genotype. Using integrated physiological and metabolomic analysis, we determined that B12 deficiency in the offspring decreases liver taurine production and associates with abrogation of a growth hormone/insulin-like growth factor 1 (GH/IGF1) axis. Taurine increased GH-dependent IGF1 synthesis in the liver, which subsequently enhanced osteoblast function, and in B12-deficient offspring, oral administration of taurine rescued their growth retardation and osteoporosis phenotypes. These results identify B12 as an essential vitamin that positively regulates postweaning growth and bone formation through taurine synthesis and suggests potential therapies to increase bone mass. PMID:24911144

Modelling the behaviour of intergranular fission gas during out-of-pile annealing

International Nuclear Information System (INIS)

Valin, S.; Mocellin, A.; Eminet, G.; Ravel, S.

2002-01-01

Standard UO 2 fuel irradiated in a commercial PWR (burn-up: 14 GWd/t u ) and hyper-stoichiometric large-grained fuel irradiated in an experimental reactor (burn-up: 9 GWd/t u ) were submitted to out-of-pile annealing treatments under sweeping helium. The 85 Kr release was continuously monitored during the annealing experiments, with temperatures ranging from 1 400 to 1 760 deg C. The burst release was not systematically observed during the heating ramp but did sometimes appear during the isothermal period following the ramp. A model based on microstructural observations was developed to explain the experimental results. The release was shown to depend on gas diffusion towards grain boundaries and on temporary gas trapping in grain boundary bubbles. The gas saturation on grain boundaries, leading to release, depends on their crystallographic orientation. (authors)

Recent evaluation of 'wet' thermal annealing to resolve reactor pressure vessel embrittlement

International Nuclear Information System (INIS)

Server, W.L.; Biemiller, E.C.

1993-01-01

vessel could have continued to operate safely for at least one fuel cycle (and possibly more depending upon the degree of conservatism needed to satisfy regulators). The key elements for making this conclusion were: (1) there was approximately a 150 deg. F difference between the annealing and operating temperatures for the vessel (a key parameter), (2) there was a relatively high degree of damage in the vessel prior to annealing, and (3) the Yankee Rowe vessel materials were thought to have moderate to good recovery potential (based upon limited experimental data). For the materials in the Yankee Rowe vessel, a thermal anneal recovery of at least 40% was expected, and the lateral shift methodology for re-embrittlement after annealing was considered appropriate while maintaining at least a one sigma uncertainty similar to Regulatory Guide 1.99, Revision 2

Hormone-dependent nuclear export of estradiol receptor and DNA synthesis in breast cancer cells

Science.gov (United States)

Lombardi, Maria; Castoria, Gabriella; Migliaccio, Antimo; Barone, Maria Vittoria; Di Stasio, Rosina; Ciociola, Alessandra; Bottero, Daniela; Yamaguchi, Hiroshi; Appella, Ettore; Auricchio, Ferdinando

2008-01-01

In breast cancer cells, cytoplasmic localization of the estradiol receptor α (ERα) regulates estradiol-dependent S phase entry. We identified a nuclear export sequence (NES) in ERα and show that its export is dependent on both estradiol-mediated phosphatidylinositol-3-kinase (PI3K)/AKT activation and chromosome region maintenance 1 (CRM1). A Tat peptide containing the ERα NES disrupts ERα–CRM1 interaction and prevents nuclear export of ERα- and estradiol-induced DNA synthesis. NES-ERα mutants do not exit the nucleus and inhibit estradiol-induced S phase entry; ERα-dependent transcription is normal. ERα is associated with Forkhead proteins in the nucleus, and estradiol stimulates nuclear exit of both proteins. ERα knockdown or ERα NES mutations prevent ERα and Forkhead nuclear export. A mutant of forkhead in rhabdomyosarcoma (FKHR), which cannot be phosphorylated by estradiol-activated AKT, does not associate with ERα and is trapped in the nucleus, blocking S phase entry. In conclusion, estradiol-induced AKT-dependent phosphorylation of FKHR drives its association with ERα, thereby triggering complex export from the nucleus necessary for initiation of DNA synthesis and S phase entry. PMID:18644889

Architecture of 3D ZnCo{sub 2}O{sub 4} marigold flowers: Influence of annealing on cold emission and photocatalytic behavior

Energy Technology Data Exchange (ETDEWEB)

Kokane, Sanjay B.; Suryawanshi, Sachin R. [Center for Advanced Studies in Material Science and Condensed Matter Physics, Department of Physics, Savitribai Phule Pune University, Pune 411007 (India); Sasikala, R., E-mail: sasikala@barc.gov.in [Chemistry Division, Bhabha Atomic Research Centre, Mumbai 411085 (India); More, Mahendra A., E-mail: mam@physics.unipune.ac.in [Center for Advanced Studies in Material Science and Condensed Matter Physics, Department of Physics, Savitribai Phule Pune University, Pune 411007 (India); Sartale, Shrikrishna D., E-mail: sdsartale@physics.unipune.ac.in [Center for Advanced Studies in Material Science and Condensed Matter Physics, Department of Physics, Savitribai Phule Pune University, Pune 411007 (India)

2017-06-15

The present work demonstrates the field emission characteristics and photocatalytic behavior of ZnCo{sub 2}O{sub 4} marigold flowers synthesized via a facile hydrothermal method. The effect of annealing of these 3D porous hierarchical nanostructures on field emission and photocatalytic performances is studied. When compared with the as-synthesized sample, annealed ZnCo{sub 2}O{sub 4} exhibits a ∼2-fold improvement in photocatalytic activity for methylene blue (MB) degradation under visible light irradiation. The turn-on, threshold fields and high emission current densities are also strongly influenced as a result of annealing. The turn on field required to draw an emission current density of ∼1 μA/cm{sup 2} is found to be ∼2.4 and ∼1.8 V/μm for as-synthesized and annealed ZnCo{sub 2}O{sub 4} marigold flowers, respectively. Field-emission measurements demonstrate remarkably large field enhancement and better stability for annealed samples. The X-ray diffraction and Raman analysis reveal that annealing improves the crystallinity and also help to remove the structural defects in ZnCo{sub 2}O{sub 4}. The enhancement in the field emission and photocatalytic activity of annealed ZnCo{sub 2}O{sub 4} marigold flowers is attributed to the modification of electronic properties as a result of dehydration, crystallite growth and reduced surface defects/impurity phases. - Highlights: • 3D hierarchical porous ZnCo{sub 2}O{sub 4} marigold flowers synthesis by hydrothermal method. • Roles of CTAB as capping agent and thermal annealing are investigated. • Thermal annealing improves photocatalysis and field emission behavior drastically.

Development of a supplemental surveillance program for reactor pressure vessel thermal annealing

International Nuclear Information System (INIS)

Server, W.L.; Rosinski, S.T.

1997-01-01

The technical decision to thermally anneal a nuclear reactor pressure vessel (RPV) depends upon the level of embrittlement in the RPV steels, the amount of recovery of fracture toughness properties expected from the anneal, and the rate of re-embrittlement after the vessel is placed back into service. The recovery of Charpy impact toughness properties after annealing can be estimated initially by using a recovery model developed using experimental measurements of recovery (such as that developed by Eason et al. for U.S. vessel materials). However, actual validation measurements on plant-specific archived vessel materials (hopefully in the existing surveillance program) are needed; otherwise, irradiated surrogate materials, essentially the same as the RPV steels or bounding in expected behavior, must be utilized. The efficient use of any of these materials requires a supplemental surveillance program focused at both recovery and reirradiation embrittlement. Reconstituted Charpy specimens and new surveillance capsules will most likely be needed as part of this supplemental surveillance program. A new version of ASTM E 509 has recently been approved which provides guidance on thermal annealing in general and specifically for the development of an annealing supplemental surveillance program. The post-anneal re-embrittlement properties are crucial for continued plant operation, and the use of a re-embrittlement model, such as the lateral shift approach, may be overly conservative. This paper illustrates the new ASTM E 509 Standard Guide methodology for an annealing supplemental surveillance program. As an example, the proposed program for the Palisades RPV beltline steels is presented which covers the time from annealing to the end of operating license and beyond, if license renewal is pursued. The Palisades nuclear power plant RPV was planned to be annealed in 1998, but that plant is currently being re-evaluated. The proposed anneal was planned to be conducted at a

Sensitization of human cells by inhibitors of DNA synthesis following the action of DNA-damaging agents

Energy Technology Data Exchange (ETDEWEB)

Filatov, M.V.; Noskin, L.A. (Leningrad Inst. of Nuclear Physics, Gatchina (USSR))

1983-08-01

Inhibitors of DNA synthesis 1-..beta..-arabinofuranosylcytosine (Ac) and hydroxyurea (Hu) taken together drastically sensitized human cells to the killing effect of DNA-damaging agents. For UV-irradiation this sensitization depended on the cells' ability for excision repair. By using viscoelastometric methods of measurement of double-strand breaks (DSB) in the genome, it was established that the first DSB were generated after incubation of the damaged cells in the mixture of inhibitors at about the same dose when sensitization appeared. A scheme is proposed to describe molecular events associated with the phenomenon studied. 35 refs.

The influence of annealing atmosphere on the material properties of sol-gel derived SnO2:Sb films before and after annealing

International Nuclear Information System (INIS)

Jeng, Jiann-Shing

2012-01-01

SnO 2 films with and without Sb doping were prepared by the sol-gel spin-coating method. Material properties of the SnO 2 films with different Sb contents were investigated before and after annealing under O 2 or N 2 . When SnO 2 films are annealed under N 2 or O 2 , the resistivity decreases with increasing annealing temperature, which may be related to the increased crystallinity and reduced film defects. The intensity of SnO 2 peaks for both O 2 - and N 2 -annealed films increases as the annealing temperature increases. Small nodules are revealed on the surface of SnO 2 films after annealing in N 2 or O 2 atmospheres, and some voids are present on the surface of N 2 -annealed SnO 2 films. After doping with Sb, the resistivity of SnO 2 films after annealing in O 2 is greater than that of N 2 -annealed SnO 2 films. The surface morphology of SnO 2 films incorporating different molar ratios of Sb after annealing are similar to that of as-spun SnO 2 films with adding Sb. There were no voids found on the surfaces of N 2 -annealed SnO 2 :Sb films. In addition, the peak intensity of SnO 2 :Sb films after O 2 -annealing is higher than those films after N 2 -annealing. The chemical binding states and Hall mobility of the high-temperature annealed SnO 2 films without and with adding Sb are also related to the annealing atmospheres. This study discusses the connection among the material properties of the SnO 2 films with different Sb contents and how these properties are influenced by the Sb-doping concentration and the annealing atmospheres of SnO 2 films.

Synthesis and field emission properties of carbon nanotubes grown in ethanol flame based on a photoresist-assisted catalyst annealing process

International Nuclear Information System (INIS)

Yang Xiaoxia; Fang Guojia; Liu Nishuang; Wang Chong; Zheng Qiao; Zhou Hai; Zhao Dongshan; Long Hao; Liu Yuping; Zhao Xingzhong

2009-01-01

Carbon nanotubes (CNTs) have been grown directly on a Si substrate without a diffusion barrier in ethanol diffusion flame using Ni as the catalyst after a photoresist-assisted catalyst annealing process. The growth mechanism of as-synthesized CNTs is confirmed by scanning electron microscopy, high resolution transmission-electron microscopy and energy-dispersive spectroscopy. The photoresist is the key for the formation of active catalyst particles during annealing process, which then result in the growth of CNTs. The catalyst annealing temperature has been found to affect the morphologies and field electron emission properties of CNTs significantly. The field emission properties of as-grown CNTs are investigated with a diode structure and the obtained CNTs exhibit enhanced characteristics. This technique will be applicable to a low-cost fabrication process of electron-emitter arrays.

Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes.

Directory of Open Access Journals (Sweden)

Patricia Hingston

Full Text Available The human pathogen Listeria monocytogenes continues to pose a challenge in the food industry, where it is known to contaminate ready-to-eat foods and grow during refrigerated storage. Increased knowledge of the cold-stress response of this pathogen will enhance the ability to control it in the food-supply-chain. This study utilized strand-specific RNA sequencing and whole cell fatty acid (FA profiling to characterize the bacterium's cold stress response. RNA and FAs were extracted from a cold-tolerant strain at five time points between early lag phase and late stationary-phase, both at 4°C and 20°C. Overall, more genes (1.3× were suppressed than induced at 4°C. Late stationary-phase cells exhibited the greatest number (n = 1,431 and magnitude (>1,000-fold of differentially expressed genes (>2-fold, p<0.05 in response to cold. A core set of 22 genes was upregulated at all growth phases, including nine genes required for branched-chain fatty acid (BCFA synthesis, the osmolyte transporter genes opuCBCD, and the internalin A and D genes. Genes suppressed at 4°C were largely associated with cobalamin (B12 biosynthesis or the production/export of cell wall components. Antisense transcription accounted for up to 1.6% of total mapped reads with higher levels (2.5× observed at 4°C than 20°C. The greatest number of upregulated antisense transcripts at 4°C occurred in early lag phase, however, at both temperatures, antisense expression levels were highest in late stationary-phase cells. Cold-induced FA membrane changes included a 15% increase in the proportion of BCFAs and a 15% transient increase in unsaturated FAs between lag and exponential phase. These increases probably reduced the membrane phase transition temperature until optimal levels of BCFAs could be produced. Collectively, this research provides new information regarding cold-induced membrane composition changes in L. monocytogenes, the growth-phase dependency of its cold

Modeling active region transient brightenings observed with X-ray telescope as multi-stranded loops

Energy Technology Data Exchange (ETDEWEB)

Kobelski, Adam R.; McKenzie, David E. [Department of Physics, P.O. Box 173840, Montana State University, Bozeman, MT 59717-3840 (United States); Donachie, Martin, E-mail: kobelski@solar.physics.montana.edu [University of Glasgow, Glasgow, G128QQ, Scotland (United Kingdom)

2014-05-10

Strong evidence exists that coronal loops as observed in extreme ultraviolet and soft X-rays may not be monolithic isotropic structures, but can often be more accurately modeled as bundles of independent strands. Modeling the observed active region transient brightenings (ARTBs) within this framework allows for the exploration of the energetic ramifications and characteristics of these stratified structures. Here we present a simple method of detecting and modeling ARTBs observed with the Hinode X-Ray Telescope (XRT) as groups of zero-dimensional strands, which allows us to probe parameter space to better understand the spatial and temporal dependence of strand heating in impulsively heated loops. This partially automated method can be used to analyze a large number of observations to gain a statistical insight into the parameters of coronal structures, including the number of heating events required in a given model to fit the observations. In this article, we present the methodology and demonstrate its use in detecting and modeling ARTBs in a sample data set from Hinode/XRT. These initial results show that, in general, multiple heating events are necessary to reproduce observed ARTBs, but the spatial dependence of these heating events cannot yet be established.

Modeling active region transient brightenings observed with X-ray telescope as multi-stranded loops

International Nuclear Information System (INIS)

Kobelski, Adam R.; McKenzie, David E.; Donachie, Martin

2014-01-01

Strong evidence exists that coronal loops as observed in extreme ultraviolet and soft X-rays may not be monolithic isotropic structures, but can often be more accurately modeled as bundles of independent strands. Modeling the observed active region transient brightenings (ARTBs) within this framework allows for the exploration of the energetic ramifications and characteristics of these stratified structures. Here we present a simple method of detecting and modeling ARTBs observed with the Hinode X-Ray Telescope (XRT) as groups of zero-dimensional strands, which allows us to probe parameter space to better understand the spatial and temporal dependence of strand heating in impulsively heated loops. This partially automated method can be used to analyze a large number of observations to gain a statistical insight into the parameters of coronal structures, including the number of heating events required in a given model to fit the observations. In this article, we present the methodology and demonstrate its use in detecting and modeling ARTBs in a sample data set from Hinode/XRT. These initial results show that, in general, multiple heating events are necessary to reproduce observed ARTBs, but the spatial dependence of these heating events cannot yet be established.

A critical role for topoisomerase IIb and DNA double strand breaks in transcription.

Science.gov (United States)

Calderwood, Stuart K

2016-05-26

Recent studies have indicated a novel role for topoisomerase IIb in transcription. Transcription of heat shock genes, serum-induced immediate early genes and nuclear receptor-activated genes, each required DNA double strands generated by topoisomerase IIb. Such strand breaks seemed both necessary and sufficient for transcriptional activation. In addition, such transcription was associated with initiation of the DNA damage response pathways, including the activation of the enzymes: ataxia-telangiectasia mutated (ATM), DNA-dependent protein kinase and poly (ADP ribose) polymerase 1. DNA damage response signaling was involved both in transcription and in repair of DNA breaks generated by topoisomerase IIb.

Sleep deprivation impairs memory by attenuating mTORC1-dependent protein synthesis.

Science.gov (United States)

Tudor, Jennifer C; Davis, Emily J; Peixoto, Lucia; Wimmer, Mathieu E; van Tilborg, Erik; Park, Alan J; Poplawski, Shane G; Chung, Caroline W; Havekes, Robbert; Huang, Jiayan; Gatti, Evelina; Pierre, Philippe; Abel, Ted

2016-04-26

Sleep deprivation is a public health epidemic that causes wide-ranging deleterious consequences, including impaired memory and cognition. Protein synthesis in hippocampal neurons promotes memory and cognition. The kinase complex mammalian target of rapamycin complex 1 (mTORC1) stimulates protein synthesis by phosphorylating and inhibiting the eukaryotic translation initiation factor 4E-binding protein 2 (4EBP2). We investigated the involvement of the mTORC1-4EBP2 axis in the molecular mechanisms mediating the cognitive deficits caused by sleep deprivation in mice. Using an in vivo protein translation assay, we found that loss of sleep impaired protein synthesis in the hippocampus. Five hours of sleep loss attenuated both mTORC1-mediated phosphorylation of 4EBP2 and the interaction between eukaryotic initiation factor 4E (eIF4E) and eIF4G in the hippocampi of sleep-deprived mice. Increasing the abundance of 4EBP2 in hippocampal excitatory neurons before sleep deprivation increased the abundance of phosphorylated 4EBP2, restored the amount of eIF4E-eIF4G interaction and hippocampal protein synthesis to that seen in mice that were not sleep-deprived, and prevented the hippocampus-dependent memory deficits associated with sleep loss. These findings collectively demonstrate that 4EBP2-regulated protein synthesis is a critical mediator of the memory deficits caused by sleep deprivation. Copyright © 2016, American Association for the Advancement of Science.

Optoelectronic study and annealing stability of room temperature pulsed laser ablated ZnSe polycrystalline thin films

Energy Technology Data Exchange (ETDEWEB)

Khan, Taj Muhammad, E-mail: tajakashne@gmail.com; Zakria, M.; Ahmad, Mushtaq; Shakoor, Rana I.

2014-03-15

increased from 2.65 eV to 2.7 eV for the annealed crystalline film at 350 °C which was further decreased to 2.56 eV for the annealed amorphous film at 400 °C. The observed results manifested that room temperature pulsed laser ablated ZnSe thin film showed excellent structural, optical and morphological stability up 350 °C for optoelectronic applications. -- Highlights: • Room temperature synthesis of ZnSe thin film by PLD. • Annealing effect on Raman scattering of the deposited material. • Optical properties. • Structural properties. • Semiconductor nanostructures.

Magnetism, microstructure and First Principles calculations of atomized and annealed Ni3Al

International Nuclear Information System (INIS)

García-Escorial, A.; Crespo, P.; Hernando, A.; Lieblich, M.; Marín, P.; Velasco, V.; Ynduráin, F.

2014-01-01

Highlights: • The microstructure and order of as-atomized Ni 3 Al powder change with annealing. • The change of the magnetic properties shows the influence of the chemical order. • First Principles calculations show the effect of the density of states to the order. - Abstract: In this work Ni 3 Al powder particles obtained by atomization were characterized magnetically and microstructurally in as-atomized state and after annealing. Upon annealing the X-ray diffraction patterns show a noticeable increase of the signal of the ordered phase γ′-Ni 3 Al, L1 2 , phase and the microstructure evolves from a lamellar and dendrite to a large grain microstructure. The Curie temperature of the as-atomized powder particles is 85 K and decreases after annealing down to 50 K. First Principles calculations were carried out to correlate the experimental observations with local order of Ni and Al atoms and illustrate the importance of the local order in the density of states at the Fermi level, showing how the magnetic moment depends on the Ni and Al atomic position

Influence of initial annealing on structure evolution and magnetic properties of 3.4% Si non-oriented steel during final annealing

Energy Technology Data Exchange (ETDEWEB)

Simões Mendanha Pedrosa, Josiane [Department of Physics, Federal University of Ouro Preto, Ouro Preto MG-3540000 (Brazil); Costa Paolinelli, Sebastião da [Research Department Aperam South America, Praça Primeiro de Maio, 9, Timóteo MG-35180018 (Brazil); Barros Cota, André, E-mail: abcota@ufop.br [Department of Physics, Federal University of Ouro Preto, Ouro Preto MG-3540000 (Brazil)

2015-11-01

The effect of the initial annealing on structure evolution and magnetic properties during the final annealing of a 3.4% Si non-oriented grain steel was evaluated. Half of the samples were submitted to initial annealing at 1030 °C before cold rolling and all samples were subjected to final annealing process at temperatures from 540 °C to 1100 °C. The magnetic induction and core loss in the final samples, the microstructure by optical microscopy and the crystallographic texture by X-ray diffraction and EBSD were evaluated. The results show that the samples without initial annealing presented better magnetic properties than the samples with initial annealing, due to the higher ratio between Eta fiber and Gamma fiber volume fractions (Eta/Gamma ratio) in their structure after final annealing. - Highlights: • Texture and magnetic properties of 3.4% Si non-oriented electrical steel were measured. • Without initial annealing, better texture and magnetic properties were obtained. • Good texture and magnetic properties are obtained with Steckel hot band structure.

Direct synthesis of BiCuChO-type oxychalcogenides by mechanical alloying

Energy Technology Data Exchange (ETDEWEB)

Pele, Vincent; Barreteau, Celine [Institut de Chimie Moléculaire et des Matériaux d’Orsay, Univ. Paris-Sud, UMR 8182, Orsay F-91405 (France); CNRS, Orsay F-91405 (France); Berardan, David, E-mail: david.berardan@u-psud.fr [Institut de Chimie Moléculaire et des Matériaux d’Orsay, Univ. Paris-Sud, UMR 8182, Orsay F-91405 (France); CNRS, Orsay F-91405 (France); Zhao, Lidong; Dragoe, Nita [Institut de Chimie Moléculaire et des Matériaux d’Orsay, Univ. Paris-Sud, UMR 8182, Orsay F-91405 (France); CNRS, Orsay F-91405 (France)

2013-07-15

We report on the direct synthesis of BiCuChO based materials by mechanical alloying (Ch=Se, Te). We show that contrary to the synthesis paths used in the previous reports dealing with this family of materials, which use costly annealings in closed silica tubes under controlled atmosphere, this new synthesis route enables the synthesis of pure phase materials at room temperature under air, with reasonable milling time. This synthesis procedure is easily scalable for large scale applications. - Highlights: • Phase pure BiCuSeO doped and undoped prepared by mechanical alloying. • Synthesis performed under air at room temperature. • Electrical properties similar to that of samples synthesized by a classical path.

Ion-beam synthesis and photoluminescence of SiC nanocrystals assisted by MeV-heavy-ion-beam annealing

International Nuclear Information System (INIS)

Khamsuwan, J.; Intarasiri, S.; Kirkby, K.; Chu, P.K.; Singkarat, S.; Yu, L.D.

2012-01-01

This work explored a novel way to synthesize silicon carbide (SiC) nanocrystals for photoluminescence. Carbon ions at 90 keV were implanted in single crystalline silicon wafers at elevated temperature, followed by irradiation using xenon ion beams at an energy of 4 MeV with two low fluences of 5 × 10 13 and 1 × 10 14 ions/cm 2 at elevated temperatures for annealing. X-ray diffraction, Raman scattering, infrared spectroscopy and transmission electron microscopy were used to characterize the formation of nanocrystalline SiC. Photoluminescence was measured from the samples. The results demonstrated that MeV-heavy-ion-beam annealing could indeed induce crystallization of SiC nanocrystals and enhance emission of photoluminescence with violet bands dominance due to the quantum confinement effect.

Simulated annealing and circuit layout

NARCIS (Netherlands)

Aarts, E.H.L.; Laarhoven, van P.J.M.