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.

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.

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.

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...

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

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

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 ...

Fault Sample Generation for Virtual Testability Demonstration Test Subject to Minimal Maintenance and Scheduled Replacement

Directory of Open Access Journals (Sweden)

Yong Zhang

2015-01-01

Full Text Available Virtual testability demonstration test brings new requirements to the fault sample generation. First, fault occurrence process is described by stochastic process theory. It is discussed that fault occurrence process subject to minimal repair is nonhomogeneous Poisson process (NHPP. Second, the interarrival time distribution function of the next fault event is proposed and three typical kinds of parameterized NHPP are discussed. Third, the procedure of fault sample generation is put forward with the assumptions of minimal maintenance and scheduled replacement. The fault modes and their occurrence time subject to specified conditions and time period can be obtained. Finally, an antenna driving subsystem in automatic pointing and tracking platform is taken as a case to illustrate the proposed method. Results indicate that both the size and structure of the fault samples generated by the proposed method are reasonable and effective. The proposed method can be applied to virtual testability demonstration test well.

Repair of Impact-Damaged Prestressed Bridge Girders Using Strand Splices and Fabric Reinforced Cementitious Matrix

OpenAIRE

Jones, Mark Stevens

2017-01-01

This thesis investigates the repair of impact-damaged prestressed concrete bridge girders with strand splices and fabric-reinforced cementitious matrix systems, specifically for repair of structural damage to the underside of an overpass bridge girder due to an overheight vehicle collision. Collision damage to bridges can range from minor to catastrophic, potentially requiring repair or replacement of a bridge girder. This thesis investigates the performance of two different types of repair...

Analysis of Nb$_{3}$Sn Rutherford cable production and strand deformations

CERN Document Server

Peggiani, Sonia; Beghi, Marco

The development of cutting-edge 11-12 T superconducting magnets made from Nb$_{3}$Sn technology is one of the major milestones for the upgrade of the Large Hadron Collider at CERN. The upgrade, called High Luminosity LHC Project, was planned in order to reach higher luminosity and discover new particles. Replacing the NbTi superconductor with the Nb$_{3}$Sn makes it possible to reach a practical operating magnetic field limit of up to 16 T. The superconducting coils are formed by Nb$_{3}$Sn Rutherford cables with a trapezoidal cross section and composed of 40 strands. Since the superconducting phase of Nb$_{3}$Sn is very brittle and it is reached after a thermal cycle, the Nb$_{3}$Sn Rutherford cable needs to be wound in a coil before the thermal treatment. The cabling process is a delicate step in the production of high performing cables that need different systems to control their quality. This work aims to provide practical tools to analyze the Nb$_{3}$Sn Rutherford cable production and the strands defo...

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.

Second-strand cDNA synthesis: classical method

International Nuclear Information System (INIS)

Gubler, U.

1987-01-01

The classical scheme for the synthesis of double-stranded cDNA as it was reported in 1976 is described. Reverse transcription of mRNA with oligo(dT) as the primer generates first strands with a small loop at the 3' end of the cDNA (the end that corresponds to the 5' end of the mRNA). Subsequent removal of the mRNA by alkaline hydrolysis leaves single-stranded cDNA molecules again with a small 3' loop. This loop can be used by either reverse transcriptase or Klenow fragment of DNA polymerase I as a primer for second-strand synthesis. The resulting products are double-stranded cDNA molecules that are covalently closed at the end corresponding to the 5' end of the original mRNA. Subsequent cleavage of the short piece of single-stranded cDNA within the loop with the single-strand-specific S 1 nuclease generate open double-stranded molecules that can be used for molecular cloning in plasmids or in phage. Useful variations of this scheme have been described

Detection of negative and positive RNA strand of poliovirus Sabin 1 and echovirus E19 by a stem-loop reverse transcription PCR.

Science.gov (United States)

Fikatas, A; Dimitriou, T G; Kyriakopoulou, Z; Moschonas, G D; Amoutzias, G D; Mossialos, D; Gartzonika, C; Levidiotou-Stefanou, S; Markoulatos, P

2017-09-01

In this report a strand specific RT-PCR was established for the detection of the replicative negative RNA strand of poliovirus sabin 1 (Sabin1) and Echovirus 19 (E19) strains. The key for the successful conduction of the assay was the use of a specific reverse transcription primer targeting the 5'-UTR of enteroviruses that consisted of a stem-loop structure at the 5'-end and an enteroviral-specific sequence at the 3'-end. The stem loop RT-PCR was found to be an accurate and sensitive method, detecting even 10 -2 CCID 50 of poliovirus sabin 1 (Sabin1) and E19 strains 6 h postinfection (p.i.), while CPE appeared 3 days later. This assay was also validated in SiHa and Caski cell lines that are not used for the detection of enteroviruses. The negative RNA strand was detected 6 h and 12 h p.i. in SiHa and Caski cells, when these cell lines were inoculated with 10 5 and 1 CCID 50 respectively, whereas CPE was observed 5 days p.i for SiHa cells and 8 days p.i for Caski cells and that only at 10 5 CCID 50 . The results show that this approach may be used for replacing the time-consuming cell cultures in order to detect the active replication of enteroviruses. Enteroviruses are positive stranded RNA viruses that may cause severe diseases. The conventional method for detection of active viral replication involves virus isolation in sensitive cell cultures followed by titration and seroneutralization. In this report, we describe the use of a stem-loop secondary structured oligonucleotide in RT-PCR assay for the detection of the replicative negative strand of the positive-stranded RNA of poliovirus sabin 1 and E19 strains. This approach proved to be a useful tool that may be used for replacing the time-consuming cell culture assays in order to detect the active replication of enteroviruses. © 2017 The Society for Applied Microbiology.

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.

Inhibition of APOBEC3G activity impedes double-stranded DNA repair.

Science.gov (United States)

Prabhu, Ponnandy; Shandilya, Shivender M D; Britan-Rosich, Elena; Nagler, Adi; Schiffer, Celia A; Kotler, Moshe

2016-01-01

The cellular cytidine deaminase APOBEC3G (A3G) was first described as an anti-HIV-1 restriction factor, acting by directly deaminating reverse transcripts of the viral genome. HIV-1 Vif neutralizes the activity of A3G, primarily by mediating degradation of A3G to establish effective infection in host target cells. Lymphoma cells, which express high amounts of A3G, can restrict Vif-deficient HIV-1. Interestingly, these cells are more stable in the face of treatments that result in double-stranded DNA damage, such as ionizing radiation and chemotherapies. Previously, we showed that the Vif-derived peptide (Vif25-39) efficiently inhibits A3G deamination, and increases the sensitivity of lymphoma cells to ionizing radiation. In the current study, we show that additional peptides derived from Vif, A3G, and APOBEC3F, which contain the LYYF motif, inhibit deamination activity. Each residue in the Vif25-39 sequence moderately contributes to the inhibitory effect, whereas replacing a single residue in the LYYF motif completely abrogates inhibition of deamination. Treatment of A3G-expressing lymphoma cells exposed to ionizing radiation with the new inhibitory peptides reduces double-strand break repair after irradiation. Incubation of cultured irradiated lymphoma cells with peptides that inhibit double-strand break repair halts their propagation. These results suggest that A3G may be a potential therapeutic target that is amenable to peptide and peptidomimetic inhibition. © 2015 FEBS.

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.

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...

A periodic inspection and replacement policy for systems subject to competing failure modes due to degradation and traumatic events

Energy Technology Data Exchange (ETDEWEB)

Huynh, K.T., E-mail: tuan.huynh@utt.f [Universite de technologie de Troyes, Institut Charles Delaunay and STMR UMR CNRS 6279-12, rue Marie Curie, BP2060, 10010 Troyes cedex (France); Barros, A., E-mail: anne.barros@utt.f [Universite de technologie de Troyes, Institut Charles Delaunay and STMR UMR CNRS 6279-12, rue Marie Curie, BP2060, 10010 Troyes cedex (France); Berenguer, C., E-mail: christophe.berenguer@utt.f [Universite de technologie de Troyes, Institut Charles Delaunay and STMR UMR CNRS 6279-12, rue Marie Curie, BP2060, 10010 Troyes cedex (France); Castro, I.T., E-mail: inmatorres@unex.e [Departamento de Matematicas, Escuela Politecnica, 10071 Caceres (Spain)

2011-04-15

This paper deals with the condition-based maintenance of single-unit systems which are subject to the competing and dependent failures due deterioration and traumatic shock events. The main aim is to provide a model to assess the value of condition monitoring information for the maintenance decision-making. A condition-based periodic inspection/replacement policy is developed and compared with a benchmark time-based block replacement policy. Numerical results show that it is indeed useful to follow closely the actual evolution of the system to adapt the maintenance decisions to the true system state to improve the performance of maintenance policies. The analysis of the maintenance costs savings can be used to justify or not the choice to implement a policy based on condition monitoring information and to invest in condition monitoring devices.

A periodic inspection and replacement policy for systems subject to competing failure modes due to degradation and traumatic events

International Nuclear Information System (INIS)

Huynh, K.T.; Barros, A.; Berenguer, C.; Castro, I.T.

2011-01-01

This paper deals with the condition-based maintenance of single-unit systems which are subject to the competing and dependent failures due deterioration and traumatic shock events. The main aim is to provide a model to assess the value of condition monitoring information for the maintenance decision-making. A condition-based periodic inspection/replacement policy is developed and compared with a benchmark time-based block replacement policy. Numerical results show that it is indeed useful to follow closely the actual evolution of the system to adapt the maintenance decisions to the true system state to improve the performance of maintenance policies. The analysis of the maintenance costs savings can be used to justify or not the choice to implement a policy based on condition monitoring information and to invest in condition monitoring devices.

Normal rejoining of DNA strand breaks in ataxia telangiectasia fibroblast lines after low x-ray exposure

International Nuclear Information System (INIS)

Hariharan, P.V.; Eleczko, S.; Smith, B.P.; Paterson, M.C.

1981-01-01

The alkaline elution method was used to measure the enzymatic repair of x-ray-induced DNA strand breaks in skin fibroblasts derived from human subjects afflicted with ataxia telangiectasia (AT). Monolayer cultures of normal control and AT cell lines were exposed acutely to moderately lethal (250-rad) and highly lethal (1250-rad) doses of 250-kV x rays under aerobic conditions. Upon receiving 250 rad, the control fibroblasts from a clinically normal donor rejoined all detectable single-strand breaks (plus alkali-labile bonds) within 30 to 60 min of incubation. When challenged with 1250 rad the kinetics of strand rejoining by the normal control cells were biphasic. For both exposures, no significant difference in either the rate or the extent of strand rejoining was detected between the normal cell line (GM38) and three mutant cell lines (AT2BE, AT3BI, AT4BI) belonging to the three known genetic complementation groups in AT. It would thus appear that the enhanced radiosensitivity of cultured AT cells does not stem from faulty rejoining of radiogenic DNA strand breaks

Double strand DNA breaks response in Huntington´s disease

Czech Academy of Sciences Publication Activity Database

Šolc, Petr; Valášek, Jan; Rausová, Petra; Juhásová, Jana; Juhás, Štefan; Motlík, Jan

2015-01-01

Roč. 78, Suppl 2 (2015), s. 15-15 ISSN 1210-7859. [Conference on Animal Models for neurodegenerative Diseases /3./. 08.11.2015-10.11.2015, Liblice] R&D Projects: GA MŠk ED2.1.00/03.0124; GA MŠk(CZ) 7F14308 Institutional support: RVO:67985904 Keywords : Huntington ´s disease * DNA damage * double strand DNA breaks Subject RIV: FH - Neurology

Identification of cis-acting elements on positive-strand subgenomic mRNA required for the synthesis of negative-strand counterpart in bovine coronavirus.

Science.gov (United States)

Yeh, Po-Yuan; Wu, Hung-Yi

2014-07-30

It has been demonstrated that, in addition to genomic RNA, sgmRNA is able to serve as a template for the synthesis of the negative-strand [(-)-strand] complement. However, the cis-acting elements on the positive-strand [(+)-strand] sgmRNA required for (-)-strand sgmRNA synthesis have not yet been systematically identified. In this study, we employed real-time quantitative reverse transcription polymerase chain reaction to analyze the cis-acting elements on bovine coronavirus (BCoV) sgmRNA 7 required for the synthesis of its (-)-strand counterpart by deletion mutagenesis. The major findings are as follows. (1) Deletion of the 5'-terminal leader sequence on sgmRNA 7 decreased the synthesis of the (-)-strand sgmRNA complement. (2) Deletions of the 3' untranslated region (UTR) bulged stem-loop showed no effect on (-)-strand sgmRNA synthesis; however, deletion of the 3' UTR pseudoknot decreased the yield of (-)-strand sgmRNA. (3) Nucleotides positioned from -15 to -34 of the sgmRNA 7 3'-terminal region are required for efficient (-)-strand sgmRNA synthesis. (4) Nucleotide species at the 3'-most position (-1) of sgmRNA 7 is correlated to the efficiency of (-)-strand sgmRNA synthesis. These results together suggest, in principle, that the 5'- and 3'-terminal sequences on sgmRNA 7 harbor cis-acting elements are critical for efficient (-)-strand sgmRNA synthesis in BCoV.

Fair Exchange in Strand Spaces

Directory of Open Access Journals (Sweden)

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.

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.

Identification of Cis-Acting Elements on Positive-Strand Subgenomic mRNA Required for the Synthesis of Negative-Strand Counterpart in Bovine Coronavirus

Directory of Open Access Journals (Sweden)

Po-Yuan Yeh

2014-07-01

Full Text Available It has been demonstrated that, in addition to genomic RNA, sgmRNA is able to serve as a template for the synthesis of the negative-strand [(−-strand] complement. However, the cis-acting elements on the positive-strand [(+-strand] sgmRNA required for (−-strand sgmRNA synthesis have not yet been systematically identified. In this study, we employed real-time quantitative reverse transcription polymerase chain reaction to analyze the cis-acting elements on bovine coronavirus (BCoV sgmRNA 7 required for the synthesis of its (−-strand counterpart by deletion mutagenesis. The major findings are as follows. (1 Deletion of the 5'-terminal leader sequence on sgmRNA 7 decreased the synthesis of the (−-strand sgmRNA complement. (2 Deletions of the 3' untranslated region (UTR bulged stem-loop showed no effect on (−-strand sgmRNA synthesis; however, deletion of the 3' UTR pseudoknot decreased the yield of (−-strand sgmRNA. (3 Nucleotides positioned from −15 to −34 of the sgmRNA 7 3'-terminal region are required for efficient (−-strand sgmRNA synthesis. (4 Nucleotide species at the 3'-most position (−1 of sgmRNA 7 is correlated to the efficiency of (−-strand sgmRNA synthesis. These results together suggest, in principle, that the 5'- and 3'-terminal sequences on sgmRNA 7 harbor cis-acting elements are critical for efficient (−-strand sgmRNA synthesis in BCoV.

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

Criteria for the replacement of restorations

DEFF Research Database (Denmark)

Wilson, Nairn; Lynch, Christopher; Brunton, Paul Brunton

2016-01-01

The replacement of a restoration is one of the most common procedures in dentistry. However, the criteria for such intervention, excluding catastrophic failure and persistent discomfort and pain, continue to be the subject of considerable debate. The decision-making process remains subjective...... on the part of the treating clinician, while the evidence base for refurbishment and repair rather than replacement for the management of defective and failing restorations continues to grow and strengthen. This article, prepared as an Academy of Operative Dentistry European Section consensus publication...

A Walnut-Enriched Diet Reduces Lipids in Healthy Caucasian Subjects, Independent of Recommended Macronutrient Replacement and Time Point of Consumption: a Prospective, Randomized, Controlled Trial.

Science.gov (United States)

Bamberger, Charlotte; Rossmeier, Andreas; Lechner, Katharina; Wu, Liya; Waldmann, Elisa; Stark, Renée G; Altenhofer, Julia; Henze, Kerstin; Parhofer, Klaus G

2017-10-06

Studies indicate a positive association between walnut intake and improvements in plasma lipids. We evaluated the effect of an isocaloric replacement of macronutrients with walnuts and the time point of consumption on plasma lipids. We included 194 healthy subjects (134 females, age 63 ± 7 years, BMI 25.1 ± 4.0 kg/m²) in a randomized, controlled, prospective, cross-over study. Following a nut-free run-in period, subjects were randomized to two diet phases (8 weeks each). Ninety-six subjects first followed a walnut-enriched diet (43 g walnuts/day) and then switched to a nut-free diet. Ninety-eight subjects followed the diets in reverse order. Subjects were also randomized to either reduce carbohydrates ( n = 62), fat ( n = 65), or both ( n = 67) during the walnut diet, and instructed to consume walnuts either as a meal or as a snack. The walnut diet resulted in a significant reduction in fasting cholesterol (walnut vs. -8.5 ± 37.2 vs. -1.1 ± 35.4 mg/dL; p = 0.002), non-HDL cholesterol (-10.3 ± 35.5 vs. -1.4 ± 33.1 mg/dL; p ≤ 0.001), LDL-cholesterol (-7.4 ± 32.4 vs. -1.7 ± 29.7 mg/dL; p = 0.029), triglycerides (-5.0 ± 47.5 vs. 3.7 ± 48.5 mg/dL; p = 0.015) and apoB (-6.7 ± 22.4 vs. -0.5 ± 37.7; p ≤ 0.001), while HDL-cholesterol and lipoprotein (a) did not change significantly. Neither macronutrient replacement nor time point of consumption significantly affected the effect of walnuts on lipids. Thus, 43 g walnuts/d improved the lipid profile independent of the recommended macronutrient replacement and the time point of consumption.

Effects of lifestyle intervention and meal replacement on glycaemic and body-weight control in Chinese subjects with impaired glucose regulation: a 1-year randomised controlled trial.

Science.gov (United States)

Xu, Dan-Feng; Sun, Jian-Qin; Chen, Min; Chen, Yan-Qiu; Xie, Hua; Sun, Wei-Jia; Lin, Yi-Fan; Jiang, Jing-Jing; Sun, Wei; Chen, Ai-Fang; Tang, Qian-Ru

2013-02-14

The purpose of the present study was to evaluate the impact of a lifestyle intervention programme, combined with a daily low-glycaemic index meal replacement, on body-weight and glycaemic control in subjects with impaired glucose regulation (IGR). Subjects with IGR were randomly assigned to an intervention group (n 46) and a control group (n 42). Both groups received health counselling at baseline. The intervention group also received a daily meal replacement and intensive lifestyle intervention to promote healthy eating habits during the first 3 months of the study, and follow-up visits performed monthly until the end of the 1-year study. Outcome measurements included changes in plasma glucose, glycated Hb (HbA1c), plasma lipids, body weight, blood pressure and body composition (such as body fat mass and visceral fat area). The results showed that body-weight loss after 1 year was significant in the intervention group compared with the control group (-1·8 (SEM 0·35) v. -0·6 (SEM 0·40) 2·5 kg, Pmeal replacement is beneficial in promoting IGR to NGR.

Defective processing of methylated single-stranded DNA by E. coli alkB mutants

Science.gov (United States)

Dinglay, Suneet; Trewick, Sarah C.; Lindahl, Tomas; Sedgwick, Barbara

2000-01-01

Escherichia coli alkB mutants are very sensitive to DNA methylating agents. Despite these mutants being the subject of many studies, no DNA repair or other function has been assigned to the AlkB protein or to its human homolog. Here, we report that reactivation of methylmethanesulfonate (MMS)-treated single-stranded DNA phages, M13, f1, and G4, was decreased dramatically in alkB mutants. No such decrease occurred when using methylated λ phage or M13 duplex DNA. These data show that alkB mutants have a marked defect in processing methylation damage in single-stranded DNA. Recombinant AlkB protein bound more efficiently to single- than double-stranded DNA. The single-strand damage processed by AlkB was primarily cytotoxic and not mutagenic and was induced by SN2 methylating agents, MMS, DMS, and MeI but not by SN1 agent N-methyl-N-nitrosourea or by γ irradiation. Strains lacking other DNA repair activities, alkA tag, xth nfo, uvrA, mutS, and umuC, were not defective in reactivation of methylated M13 phage and did not enhance the defect of an alkB mutant. A recA mutation caused a small but additive defect. Thus, AlkB functions in a novel pathway independent of these activities. We propose that AlkB acts on alkylated single-stranded DNA in replication forks or at transcribed regions. Consistent with this theory, stationary phase alkB cells were less MMS sensitive than rapidly growing cells. PMID:10950872

Mechanical characterization of glass fiber (woven roving/chopped strand mat E-glass fiber) reinforced polyester composites

Science.gov (United States)

Bhaskar, V. Vijaya; Srinivas, Kolla

2017-07-01

Polymer reinforced composites have been replacing most of the engineering material and their applications become more and more day by day. Polymer composites have been analyzing from past thirty five years for their betterment for adapting more applications. This paper aims at the mechanical properties of polyester reinforced with glass fiber composites. The glass fiber is reinforced with polyester in two forms viz Woven Rovings (WRG) and Chopped Strand Mat (CSMG) E-glass fibers. The composites are fabricated by hand lay-up technique and the composites are cut as per ASTM Standard sizes for corresponding tests like flexural, compression and impact tests, so that flexural strength, compression strength, impact strength and inter laminar shear stress(ILSS) of polymer matrix composites are analyzed. From the tests and further calculations, the polyester composites reinforced with Chopped Strand Mat glass fiber have shown better performance against flexural load, compression load and impact load than that of Woven Roving glass fiber.

DNA strand breaks, repair, and survival in x-irradiated mammalian cells

International Nuclear Information System (INIS)

Dugle, D.L.; Gillespie, C.J.; Chapman, J.D.

1976-01-01

The yields of unrepairable single- and double-strand breaks in the DNA of x-irradiated Chinese hamster cells were measured by low-speed neutral and alkaline sucrose density gradient sedimentation in order to investigate the relation between these lesions and reproductive death. After maximal single-strand rejoining, at all doses, the number of residual single-strand breaks was twice the number of residual double-strand breaks. Both double-strand and unrepairable single-strand breaks were proportional to the square of absorbed dose, in the range 10-50 krad. No rejoining of double-strand breaks was observed. These observations suggest that, in mammalian cells, most double-strand breaks are not repairable, while all single-strand breaks are repaired except those that are sufficiently close on complementary strands to constitute double-strand breaks. Comparison with cell survival measurements at much lower doses suggests that loss of reproductive capacity corresponds to induction of approximately one double-strand break

Replacing penalties

Directory of Open Access Journals (Sweden)

Vitaly Stepashin

2017-01-01

Full Text Available УДК 343.24The subject. The article deals with the problem of the use of "substitute" penalties.The purpose of the article is to identify criminal and legal criteria for: selecting the replacement punishment; proportionality replacement leave punishment to others (the formalization of replacement; actually increasing the punishment (worsening of legal situation of the convicted.Methodology.The author uses the method of analysis and synthesis, formal legal method.Results. Replacing the punishment more severe as a result of malicious evasion from serving accused designated penalty requires the optimization of the following areas: 1 the selection of a substitute punishment; 2 replacement of proportionality is serving a sentence other (formalization of replacement; 3 ensuring the actual toughening penalties (deterioration of the legal status of the convict. It is important that the first two requirements pro-vide savings of repression in the implementation of the replacement of one form of punishment to others.Replacement of punishment on their own do not have any specifics. However, it is necessary to compare them with the contents of the punishment, which the convict from serving maliciously evaded. First, substitute the punishment should assume a more significant range of restrictions and deprivation of certain rights of the convict. Second, the perfor-mance characteristics of order substitute the punishment should assume guarantee imple-mentation of the new measures.With regard to replacing all forms of punishment are set significant limitations in the application that, in some cases, eliminates the possibility of replacement of the sentence, from serving where there has been willful evasion, a stricter measure of state coercion. It is important in the context of the topic and the possibility of a sentence of imprisonment as a substitute punishment in cases where the original purpose of the strict measures excluded. It is noteworthy that the

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

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

Connecting localized DNA strand displacement reactions

Science.gov (United States)

Mullor Ruiz, Ismael; Arbona, Jean-Michel; Lad, Amitkumar; Mendoza, Oscar; Aimé, Jean-Pierre; Elezgaray, Juan

2015-07-01

Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/C5NR02434J

Southeast US Historical Marine Mammal Stranding Database

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Data on marine mammal strandings are collected by the Southeast Marine Mammal Stranding Network. Basic data on the location, species identification, animal...

The stranding anomaly as population indicator

DEFF Research Database (Denmark)

Peltier, Helene; Baagøe, Hans J.; Camphuysen, Kees C. J.

2013-01-01

Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistica...... surveys, mostly SCANS surveys (1994 and 2005). This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna....... credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform...

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

The importance of becoming double-stranded: Innate immunity and the kinetic model of HIV-1 central plus strand synthesis

International Nuclear Information System (INIS)

Poeschla, Eric

2013-01-01

Central initiation of plus strand synthesis is a conserved feature of lentiviruses and certain other retroelements. This complication of the standard reverse transcription mechanism produces a transient “central DNA flap” in the viral cDNA, which has been proposed to mediate its subsequent nuclear import. This model has assumed that the important feature is the flapped DNA structure itself rather than the process that produces it. Recently, an alternative kinetic model was proposed. It posits that central plus strand synthesis functions to accelerate conversion to the double-stranded state, thereby helping HIV-1 to evade single-strand DNA-targeting antiviral restrictions such as APOBEC3 proteins, and perhaps to avoid innate immune sensor mechanisms. The model is consistent with evidence that lentiviruses must often synthesize their cDNAs when dNTP concentrations are limiting and with data linking reverse transcription and uncoating. There may be additional kinetic advantages for the artificial genomes of lentiviral gene therapy vectors. - Highlights: • Two main functional models for HIV central plus strand synthesis have been proposed. • In one, a transient central DNA flap in the viral cDNA mediates HIV-1 nuclear import. • In the other, multiple kinetic consequences are emphasized. • One is defense against APOBEC3G, which deaminates single-stranded DNA. • Future questions pertain to antiviral restriction, uncoating and nuclear import

Alaska Beluga Strandings

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — NMFS is mandated by the Marine Mammal Protection Act (MMPA) to collect reports of marine mammal stranding events. This particular catalogue item is specific to the...

Low-residue euthanasia of stranded mysticetes.

Science.gov (United States)

Harms, Craig A; McLellan, William A; Moore, Michael J; Barco, Susan G; Clarke, Elsburgh O; Thayer, Victoria G; Rowles, Teresa K

2014-01-01

Euthanasia of stranded large whales poses logistic, safety, pharmaceutical, delivery, public relations, and disposal challenges. Reasonable arguments may be made for allowing a stranded whale to expire naturally. However, slow cardiovascular collapse from gravitational effects outside of neutral buoyancy, often combined with severely debilitating conditions, motivate humane efforts to end the animal's suffering. The size of the animal and prevailing environmental conditions often pose safety concerns for stranding personnel, which take priority over other considerations. When considering chemical euthanasia, the size of the animal also necessitates large quantities of euthanasia agents. Drug residues are a concern for relay toxicity to scavengers, particularly for pentobarbital-containing euthanasia solutions. Pentobarbital is also an environmental concern because of its stability and long persistence in aquatic environments. We describe a euthanasia technique for stranded mysticetes using readily available, relatively inexpensive, preanesthetic and anesthetic drugs (midazolam, acepromazine, xylazine) followed by saturated KCl delivered via custom-made needles and a low-cost, basic, pressurized canister. This method provides effective euthanasia while moderating personnel exposure to hazardous situations and minimizing drug residues of concern for relay toxicity.

Stranded Specimen Data

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Marine Mammal and Turtle Division collects data about individual cetaceans and sea turtles that come ashore, or strand on the beach. The date and location of...

Comparison of Energy Dissipation, Stiffness, and Damage of Structural Oriented Strand Board (OSB, Conventional Gypsum, and Viscoelastic Gypsum Shearwalls Subjected to Cyclic Loads

Directory of Open Access Journals (Sweden)

Andrew S. Blasetti

2012-06-01

Full Text Available A key element in the seismic load resisting system of a wood framed structure is the shear wall which is typically sheathed on one side with plywood or oriented strand board (OSB and gypsum on the other. The shear capacity of gypsum sheathed shear walls is typically neglected in high seismic areas due to the susceptibility of conventional drywall screw connections to damage caused by earthquakes. The earthquake resistance of an innovative viscoelastic (VE gypsum shearwall is evaluated and compared to conventional structural and non-structural walls. Ten 8 ft × 8 ft wood framed wall specimens of three configurations [nailed-OSB, screw-gypsum, and VE polymer-gypsum] were subjected to a cyclic test protocol. The energy dissipation, stiffness, and damage characteristics of all shearwalls are reported herein. Testing results indicate the VE-gypsum walls can dissipate more energy than the OSB structural panels and 500% more energy that the conventional gypsum sheathed walls and contains a constant source of energy dissipation not seen in the structural and non-structural walls. The wall stiffness of the OSB wall degrades at a far greater rate that the VE gypsum wall and at continued cycling degrades below the VE wall stiffness. Unlike both of the conventional wall types, the VE wall showed no visible or audible signs of damage when subjected to shear displacements up to 1.

A complex method of equipment replacement planning. An advanced plan for the replacement of medical equipment.

Science.gov (United States)

Dondelinger, Robert M

2004-01-01

This complex method of equipment replacement planning is a methodology; it is a means to an end, a process that focuses on equipment most in need of replacement, rather than the end itself. It uses data available from the maintenance management database, and attempts to quantify those subjective items important [figure: see text] in making equipment replacement decisions. Like the simple method of the last issue, it is a starting point--albeit an advanced starting point--which the user can modify to fit their particular organization, but the complex method leaves room for expansion. It is based on sound logic, documented facts, and is fully defensible during the decision-making process and will serve your organization well as provide a structure for your equipment replacement planning decisions.

Current redistribution in cables made of insulated, soldered, or oxidized strands

International Nuclear Information System (INIS)

Turck, B.

1979-07-01

Current redistributions are compared in cables made of insulated strands, soldered, or oxidized strands and insulated strands with periodic joints. After discussing the different current redistributions in the cases of a rapidly changing current and a dc current, several particular situations are investigated: what happens if a strand is broken, or if a local normal zone appears that does not affect all the strands equally, the detection of this normal zone, and the influence of short circuits between strands

Strand SPA & Konverentsikeskus

Index Scriptorium Estoniae

2008-01-01

Strand SPA & Konverentsikeskus on Pärnu suurim äri- ja konverentsiklientidele suunatud hotell, mis klientide seas on hinnatud just selle kompleksuse tõttu, kuna kõik, mida külaline vajab ja soovib, on olemas ühe katuse all

A shock and wear system under environmental conditions subject to internal failures, repair, and replacement

International Nuclear Information System (INIS)

Montoro-Cazorla, Delia; Pérez-Ocón, Rafael

2012-01-01

A system in a random environment is considered. The influence of the external conditions is governed by a Markovian arrival process. The internal structure of failure and repair are governed by phase-type distributions. The maintenance is performed by policy N. Under these assumptions, the Markov process governing the system is constructed, and it is studied in transient and stationary regime, calculating the availability and the rate of occurrence of failures. The renewal process due to the replacements of the system is studied, and expressions for the number of replacements and for the number of repairs between replacements are calculated. This paper extends other previously published since it incorporates a shock arrival process with dependence among the interarrival times and the renewal process associated to the replacements. A numerical application illustrates the calculations.

Development of strand burner for solid propellant burning rate studies

International Nuclear Information System (INIS)

Aziz, A; Mamat, R; Ali, W K Wan

2013-01-01

It is well-known that a strand burner is an apparatus that provides burning rate measurements of a solid propellant at an elevated pressure in order to obtain the burning characteristics of a propellant. This paper describes the facilities developed by author that was used in his studies. The burning rate characteristics of solid propellant have be evaluated over five different chamber pressures ranging from 1 atm to 31 atm using a strand burner. The strand burner has a mounting stand that allows the propellant strand to be mounted vertically. The strand was ignited electrically using hot wire, and the burning time was recorded by electronic timer. Wire technique was used to measure the burning rate. Preliminary results from these techniques are presented. This study shows that the strand burner can be used on propellant strands to obtain accurate low pressure burning rate data

Double-Stranded Peptide Nucleic Acids

DEFF Research Database (Denmark)

2001-01-01

A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.......A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

What is DNA damage? Risk of double-strand break and its individual variation

International Nuclear Information System (INIS)

Hanaoka, Fumio

2011-01-01

The author discusses about the title subject in an aspect of possible spreading of Fukushima radioactive substances mainly in eastern north area of Japan where carcinogenic incidence may be increased as the ionizing radiation injures the gene (DNA). At first, explained is that cancer is a disease of genes with infinitive proliferation of cells, there are systems to prevent it by repairing the damaged DNA and by other mechanisms like exclusion of cells damaged too much or killing cancer cells with immunity, and individual difference of the repairing capability exists. DNA is always damaged even under ordinary living conditions by sunlight UV ray, cosmic radiation and chemicals externally and by active oxygen species and thermal water movement internally. Concomitantly, DNA damaged by many mechanisms like deletion, dimmer formation, chemical modification of bases, single and double strand breaks is always repaired by concerned enzymes. Double-strand damage by high-energy radiation like gamma ray is quite risky because its repair sometimes accompanies error as concerned enzymes are from more multiple genes. There are many syndromes derived from gene deficit of those repairing enzymes. The diseases concerned with repair of the double-strand damage teach that fetus and infant are more sensitive to radiation than adult as their young body cells are more actively synthesizing DNA, during which, if DNA is injured by radiation, risk of repairing error is higher as the double strand break more frequently occurs. It cannot be simply said that a certain radiation dose limit is generally permissible. There is an individual difference of radiation sensitivity and a possible method to find out an individual weak to radiation is the lymphocyte screening in vitro using anticancer bleomycin which breaks the double strand. (T.T.)

The (not so) immortal strand hypothesis.

Science.gov (United States)

Tomasetti, Cristian; Bozic, Ivana

2015-03-01

Non-random segregation of DNA strands during stem cell replication has been proposed as a mechanism to minimize accumulated genetic errors in stem cells of rapidly dividing tissues. According to this hypothesis, an "immortal" DNA strand is passed to the stem cell daughter and not the more differentiated cell, keeping the stem cell lineage replication error-free. After it was introduced, experimental evidence both in favor and against the hypothesis has been presented. Using a novel methodology that utilizes cancer sequencing data we are able to estimate the rate of accumulation of mutations in healthy stem cells of the colon, blood and head and neck tissues. We find that in these tissues mutations in stem cells accumulate at rates strikingly similar to those expected without the protection from the immortal strand mechanism. Utilizing an approach that is fundamentally different from previous efforts to confirm or refute the immortal strand hypothesis, we provide evidence against non-random segregation of DNA during stem cell replication. Our results strongly suggest that parental DNA is passed randomly to stem cell daughters and provides new insight into the mechanism of DNA replication in stem cells. Copyright © 2015. Published by Elsevier B.V.

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs

Energy Technology Data Exchange (ETDEWEB)

Mutisya, Daniel; Hardcastle, Travis; Cheruiyot, Samwel K.; Pallan, Pradeep S.; Kennedy, Scott D.; Egli, Martin; Kelley, Melissa L.; Smith, Anja van Brabant; Rozners, Eriks

2017-06-27

While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA–DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs.

DNA strand breakage by 125I-decay in oligoDNA

International Nuclear Information System (INIS)

Lobachevsky, P.; Martin, R.F.

1996-01-01

Full text: A double-stranded oligodeoxynucleotide containing 125 I-dC in a defined location, with 5'- or 3'- 32 P-end-labelling of either strand, was used to investigate DNA strand breakage resulting from 125 I decay. Samples of the 32 P-end-labelled and 125 I-dC containing oligoDNA were incubated in 20 mM phosphate buffer (PB), or PB + 2 M dimethylsulphoxide (DMSO) at 4 deg during 18-20 days. The 32 P-end-labelled DNA fragments produced by 125 I decays were separated on denaturing polyacrylamide gels, and the 3P activity in each fragment was determined by scintillation counting after elution from the gel. The fragment size distribution was then converted to a distribution of single stranded break probabilities at each nucleotide position. The results indicate that each 125 I decay event produces at least one break in the 125 I-dC containing strand, and causes breakage of the opposite strand in 75-80% of events. Thus, the double stranded break is produced by 125 I decay with probability ∼0.8. Most of single stranded breaks (around 90%) occurred within 5-6 nucleotides of the 125 I-dC, however DNA breaks were detected up to 18-20 nucleotides from the decay site. The average numbers of single stranded breaks per decay are 3.7 (PB) and 3.3 (PB+DMSO) in 125 I-dC containing strand, and 1.5 (PB) and 1.3 (PB+DMSO) in the opposite strand. Deconvolution of strand break probabilities as a function of separation from the 125 I, in terms of both distance (to target deoxyribosyl carbon atoms, in B-DNA) and nucleotide number, show that the latter is an important parameter for the shorter-range damage. This could indicate a role for attenuation/dissipation of damage through the stacked bases. In summary, the results represent a much more extensive set of data than available from earlier experiments on DNA breakage from l25 I-decay, and may provide new mechanistic insights

Southeast Region Level A Marine Mammal Stranding Data

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Data on marine mammal strandings are collected by the Southeast Marine Mammal Stranding Network. Basic data on the location, species identification, animal...

A methodology to identify stranded generation facilities and estimate stranded costs for Louisiana's electric utility industry

Science.gov (United States)

Cope, Robert Frank, III

1998-12-01

The electric utility industry in the United States is currently experiencing a new and different type of growing pain. It is the pain of having to restructure itself into a competitive business. Many industry experts are trying to explain how the nation as a whole, as well as individual states, will implement restructuring and handle its numerous "transition problems." One significant transition problem for federal and state regulators rests with determining a utility's stranded costs. Stranded generation facilities are assets which would be uneconomic in a competitive environment or costs for assets whose regulated book value is greater than market value. At issue is the methodology which will be used to estimate stranded costs. The two primary methods are known as "Top-Down" and "Bottom-Up." The "Top-Down" approach simply determines the present value of the losses in revenue as the market price for electricity changes over a period of time into the future. The problem with this approach is that it does not take into account technical issues associated with the generation and wheeling of electricity. The "Bottom-Up" approach computes the present value of specific strandable generation facilities and compares the resulting valuations with their historical costs. It is regarded as a detailed and difficult, but more precise, approach to identifying stranded assets and their associated costs. This dissertation develops a "Bottom-Up" quantitative, optimization-based approach to electric power wheeling within the state of Louisiana. It optimally evaluates all production capabilities and coordinates the movement of bulk power through transmission interconnections of competing companies in and around the state. Sensitivity analysis to this approach is performed by varying seasonal consumer demand, electric power imports, and transmission inter-connection cost parameters. Generation facility economic dispatch and transmission interconnection bulk power transfers, specific

Replacement research reactor for Australia

International Nuclear Information System (INIS)

Miller, Ross

1998-01-01

In 1992, the Australian Government commissioned a review into the need for a replacement research reactor. That review concluded that in about years, if certain conditions were met, the Government could make a decision in favour of a replacement reactor. A major milestone was achieved when, on 3 September 1997, the Australian Government announced the construction of a replacement research reactor at the site of Australia's existing research reactor HIFAR, subject to the satisfactory outcome of an environmental assessment process. The reactor will be have the dual purpose of providing a first class facility for neutron beam research as well as providing irradiation facilities for both medical isotope production and commercial irradiations. The project is scheduled for completion before the end of 2005. (author)

Effect of Twist Pitch in the Strands on the Saturation and Losses in the Nb3Sn Strands for the ITER TF CICC

International Nuclear Information System (INIS)

Martovetsky, N.N.

2007-01-01

ITER TF coils will see a significant longitudinal magnetic field in the event of the plasma disruption. This abrupt change of magnetic fields results in the appearance of an additional electrical field in the strands. The mechanism of this electrical field is the induced currents that expel the flux from the strands. This effect was known since the late 1970's [1-3] and most of the details necessary for the analyses given in this report are presented in [4]. Let's assume for simplicity a zero transport current in the strand. When a longitudinal pulsed field is applied, the outer filaments will carry an induced current repelling the change of flux. The current density of this current is 'critical' in the simplification of Bean's critical state model, where superconducting transition is represented as j=j c at any non-zero electrical field and zero where the electrical field has not penetrated. In reality, since the current density is roughly logarithmic with the electrical field, E=E c *exp[(j-j c )/jo], Bean's model is just a simplification, and current density is slightly nonuniform in the outer filament and more so for the interior strands. The inner portion of the filaments will carry a current of the opposite sign. Even in the Bean's model it is not uniform, but the assumption that it is uniform and less than critical simplifies mathematics significantly and does not deviate far from the real current density distribution. In certain circumstances, the average electrical field in the strands will be high enough to exceed the take-off electrical field averaged across the cross section. In this case, the multifilamentary strand will become unstable and will experience transition to the normal state. With zero transport current, it will eventually recover, of course. This phenomenon is analogous to the flux jump. If the strand carries a transport current, the situation becomes more complicated. If it goes unstable and the transport current is higher than the

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.

Fragmentation in DNA double-strand breaks

International Nuclear Information System (INIS)

Wei Zhiyong; Suzhou Univ., Suzhou; Zhang Lihui; Li Ming; Fan Wo; Xu Yujie

2005-01-01

DNA double strand breaks are important lesions induced by irradiations. Random breakage model or quantification supported by this concept is suitable to analyze DNA double strand break data induced by low LET radiation, but deviation from random breakage model is more evident in high LET radiation data analysis. In this work we develop a new method, statistical fragmentation model, to analyze the fragmentation process of DNA double strand breaks. After charged particles enter the biological cell, they produce ionizations along their tracks, and transfer their energies to the cells and break the cellular DNA strands into fragments. The probable distribution of the fragments is obtained under the condition in which the entropy is maximum. Under the approximation E≅E 0 + E 1 l + E 2 l 2 , the distribution functions are obtained as exp(αl + βl 2 ). There are two components, the one proportional to exp(βl 2 ), mainly contributes to the low mass fragment yields, the other component, proportional to exp(αl), decreases slowly as the mass of the fragments increases. Numerical solution of the constraint equations provides parameters α and β. Experimental data, especially when the energy deposition is higher, support the statistical fragmentation model. (authors)

Manufacture of Strand Board Bonded with Disposal Expanded Polystyrene as Binder

OpenAIRE

Hermawan, Andi; Ohuchi, Takeshi; Fujimoto, Noboru; 大内, 毅; 藤本, 登留

2010-01-01

The objective of this study was to evaluate the physical and mechanical properties of strand board bonded with disposal expanded polystyrene (EPS) as binder. The strand board was manufactured using strand made from Douglas-fir beams selected from construction scrap wood. The strands were oriented, and two types of three-layer (face-core-face) strand board were manufactured: one in which the board bounded with only disposal EPS (P board), and the other in which the board bonded with disposal...

Four-Strand Core Suture Improves Flexor Tendon Repair Compared to Two-Strand Technique in a Rabbit Model

Directory of Open Access Journals (Sweden)

Alice Wichelhaus

2016-01-01

Full Text Available Introduction. This study was designed to investigate the influence of the amount of suture material on the formation of peritendinous adhesions of intrasynovial flexor tendon repairs. Materials and Methods. In 14 rabbits, the flexor tendons of the third and the fourth digit of the right hind leg were cut and repaired using a 2- or 4-strand core suture technique. The repaired tendons were harvested after three and eight weeks. The range of motion of the affected toes was measured and the tendons were processed histologically. The distance between the transected tendon ends, the changes in the peritendinous space, and cellular and extracellular inflammatory reaction were quantified by different staining. Results. A 4-strand core suture resulted in significantly less gap formation. The 2-strand core suture showed a tendency to less adhesion formation. Doubling of the intratendinous suture material was accompanied by an initial increase in leukocyte infiltration and showed a greater amount of formation of myofibroblasts. From the third to the eighth week after flexor tendon repair, both the cellular and the extracellular inflammation decreased significantly. Conclusion. A 4-strand core suture repair leads to a significantly better tendon healing process with less diastasis between the sutured tendon ends despite initially pronounced inflammatory response.

Control of DNA strand displacement kinetics using toehold exchange.

Science.gov (United States)

Zhang, David Yu; Winfree, Erik

2009-12-02

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.

Electro-mechanical behaviors of composite superconducting strand with filament breakage

International Nuclear Information System (INIS)

Wang, Xu; Gao, Yuanwen; Zhou, Youhe

2016-01-01

Highlights: • The electromechanical behaviors of the superconducting (SC) strand are investigated. • A 3D FEM model for bending behaviors and electric properties of strand is developed. • The influence of breakage of filaments on the critical current of SC strand is calculated. • The impact of current transfer length on the electric properties of SC strand is discussed. - Abstract: The bending behaviors of superconducting strand with typical multi-filament twist configuration are investigated based on a three-dimensional finite element method (FEM) model, named as the Multi-filament twist model, of the strand. In this 3D FEM model, the impacts of initial thermal residual stress, filament-breakage and its evaluation are taken into accounts. The mechanical responses of the strand under bending load are studied with the factors taken into consideration one by one. The distribution of the damage of the filaments and its evolution and the movement of the neutral axis caused by it are studied and displayed in detail. Besides, taking the advantages of the Multi-filament twist model, the normalized critical current of the strand under bending load is also calculated based on the invariant temperature and field strain functions. In addition, the non-negligible influences of the pitch length of the filaments on both the mechanical behaviors and the normalized critical current are discussed. The stress-strain characteristics of the strand under tensile load and the normalized critical current of it under axial and bending loads resulting from the Multi-filament twist model show good agreement with the experimental data.

Electro-mechanical behaviors of composite superconducting strand with filament breakage

Energy Technology Data Exchange (ETDEWEB)

Wang, Xu [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Gao, Yuanwen, E-mail: ywgao@lzu.edu.cn [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Zhou, Youhe [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China)

2016-10-15

Highlights: • The electromechanical behaviors of the superconducting (SC) strand are investigated. • A 3D FEM model for bending behaviors and electric properties of strand is developed. • The influence of breakage of filaments on the critical current of SC strand is calculated. • The impact of current transfer length on the electric properties of SC strand is discussed. - Abstract: The bending behaviors of superconducting strand with typical multi-filament twist configuration are investigated based on a three-dimensional finite element method (FEM) model, named as the Multi-filament twist model, of the strand. In this 3D FEM model, the impacts of initial thermal residual stress, filament-breakage and its evaluation are taken into accounts. The mechanical responses of the strand under bending load are studied with the factors taken into consideration one by one. The distribution of the damage of the filaments and its evolution and the movement of the neutral axis caused by it are studied and displayed in detail. Besides, taking the advantages of the Multi-filament twist model, the normalized critical current of the strand under bending load is also calculated based on the invariant temperature and field strain functions. In addition, the non-negligible influences of the pitch length of the filaments on both the mechanical behaviors and the normalized critical current are discussed. The stress-strain characteristics of the strand under tensile load and the normalized critical current of it under axial and bending loads resulting from the Multi-filament twist model show good agreement with the experimental data.

22 CFR 42.74 - Issuance of new or replacement visas.

Science.gov (United States)

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Issuance of new or replacement visas. 42.74... IMMIGRATION AND NATIONALITY ACT, AS AMENDED Issuance of Immigrant Visas § 42.74 Issuance of new or replacement...) Replacement immigrant visa for an immediate relative or for an alien subject to numerical limitation. (1) A...

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.

The (not so) Immortal Strand Hypothesis

OpenAIRE

Tomasetti, Cristian; Bozic, Ivana

2015-01-01

Background: Non-random segregation of DNA strands during stem cell replication has been proposed as a mechanism to minimize accumulated genetic errors in stem cells of rapidly dividing tissues. According to this hypothesis, an “immortal” DNA strand is passed to the stem cell daughter and not the more differentiated cell, keeping the stem cell lineage replication error-free. After it was introduced, experimental evidence both in favor and against the hypothesis has been presented. Principal...

A new cable-in-conduit conductor magnet with insulated strands

International Nuclear Information System (INIS)

Yamaguchi, Satarou; Yamamoto, Junya; Motojima, Osamu.

1995-09-01

Many studies have used cable-in-conduit conductor (CICC) coils in trying to develop an AC superconducting magnet because of its enormous potential if AC losses were low and insulation voltage was high. The strands in the most recent CICC magnets are coated with chromium or another metal with high electrical resistance to order to induce current re-distribution among the strands and to avoid a quench caused by a current imbalance. Current re-distribution is highly complex and very difficult to analyze because the conditions of the strand surfaces and the contact areas vary greatly with the operation of the conductor. If, however, the cable currents were well-balanced, insulating the strands would be the best way to reduce AC losses. We propose a new CICC magnet structure featuring a current lead that balances the strand currents via its resistance. Having calculated current balances, we find that strand currents are well within the present parameters for nuclear fusion experiments and superconducting magnet energy storages. (author)

The risk of stranded assets for utilities in Canada

International Nuclear Information System (INIS)

Schroeder, W.

1998-01-01

The problems of dealing with stranded assets in Canada and the United States were discussed. Compared to the United States, the risk associated with stranded assets for utilities in Canada was considered to be relatively low because of the following factors: (1) low variable cost, (2) isolation, (3) lack of transmission interconnection capacity, (4) lack of tight synchronization in North America, (5) the likelihood of an increase in natural gas prices, (6) the absence of jurisdictional disputes such as FERC versus the states, (7) social considerations, (8) the learning curve, (9) politics, (10) weak balance sheets, (11) relatively low electricity prices, (12) the weak Canadian dollar, and (13) the possibility of refinancing at lower interest rates. Ontario Hydro, New Brunswick and Nova Scotia Power are the three Canadian utilities that may have stranded costs. For Ontario Hydro and New Brunswick Power the stranded costs would be related to nuclear generator problems, whereas for Nova Scotia Power, the stranded costs would be related to the thermal generating base, the threat from Sable Island Gas and the changing tax structure of the utility. Some other reasons why stranded assets could be created in Canada would include low variable costs and high fixed costs, over capacity of at least 30 per cent in generation, limited domestic energy growth, competitive threat from gas, reliability and safety of nuclear plants, and technology change. Five factors in terms of which stranded assets can be expressed are: (1) variable cost definition, (2) total cost definition, (3) operating profit definition, (4) wide geographic definition, and (5) free market definition. In calculating stranded assets, the number of years over which the assets are recovered and the discount rate are considered to be key factors. 26 tabs

A mass stranding of the squid martialia hyadesi Rochebrune and ...

African Journals Online (AJOL)

1997-02-11

Feb 11, 1997 ... All animals were immature, with females in lower stages of maturity than males. No predatory marine mammals were seen in the area during or after the stranding event. An interpretation of the stranding is presented with reference to historical reports of squid strandings worldwide. Evidence suggests some ...

Equilibrious Strand Exchange Promoted by DNA Conformational Switching

Science.gov (United States)

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

2013-01-01

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

Radiation induced strand breaks and time scale for repair of broken strands in superinfecting phage lambda DNA in Escherichia coli lysogenic for lambda

International Nuclear Information System (INIS)

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

1975-01-01

The production of the first radiation induced break in covalent lambda DNA molecules in pol + and pol A 1 lysogenic host cells was measured after exposure to electrons from a linear accelerator and transfer to alkaline detergent within 100 ms from the onset of irradiation. The results revealed the presence of an oxygen effect in DNA strand breakage. In both pol + and pol A 1 host cells the rate of production in nitrogen was 1.2x10 -12 DNA single strand breaks per rad per dalton as compared to 5x10 -12 in oxygen. The yields of strand breaks in lambda DNA in pol + host cells under oxygenated or anoxic conditions are independent of whether the cells are irradiated in buffer at room temperature, in buffer at ice temperature, or in growth medium at 37 0 C. These results indicate that enzymic repair of DNA strand breaks before analysis is insignificant in these experiments. The presence of an oxygen effect in DNA strand breakage under these conditions suggest that an actual difference exists between initial number of breaks produced in nitrogen and in oxygen. The kinetics of rejoining of broken molecules under optimal growth conditions was measured by incubating the irradiated host cells prior to lysis. In pol + host cells 50% of the lambda DNA molecules broken in presence of oxygen are rejoined within 10 to 20 seconds of incubation. A significantly lower recovery is seen in pol + host cells after irradiation in nitrogen. The rejoining of broken lambda DNA strands in pol A 1 host cells is impaired after irradiation in presence of oxygen as well as under anoxia. These results show that DNA polymerase I is needed for the rapid rejoining of radiation induced strand breaks in the DNA, and that oxygen promoted strand breaks are more easily rejoined than are those produced in nitrogen. (author)

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs.

Science.gov (United States)

Mutisya, Daniel; Hardcastle, Travis; Cheruiyot, Samwel K; Pallan, Pradeep S; Kennedy, Scott D; Egli, Martin; Kelley, Melissa L; Smith, Anja van Brabant; Rozners, Eriks

2017-08-21

While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA-DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Induction of DNA strand breaks in 14C-labelled cells

International Nuclear Information System (INIS)

Sundell-Bergman, S.; Johanson, K.J.

1979-01-01

Chinese hamster cells grown in vitro were labelled with 14 C-thymidine for 18 hours and after 3 hours in non-radioactive medium they were stored at 0 0 C for various periods ( 1 to 12 hours). During this treatment a number of DNA strand breaks were induced by 14 C decay which were not repaired at 0 0 C. The number of DNA strand breaks was determined using the DNA unwinding technique. At 0.5-1 dpm per cell a detectable number of DNA strand breaks were found. Treatment for six hours (1 dpm per cell) reduced the percentage of double-stranded DNA from 80 to 70%, corresponding to about 750 DNA strand breaks per cell. The rejoining of DNA strand breaks was studied after treatment for 12 hours at 0 0 C followed by incubation of the cells for various periods at 37 0 C. Most of the DNA strand breaks induced by 14 C decay at 0 0 C were repaired after incubation at 37 0 C for 15 minutes. Assuming an absorbed dose of 1.8 mGy per 14 C decay to the cell nucleus an RBE value close to 1 was found for internal irradiation from 14 C decay as compared with 60 Co-gamma irradiation. (author)

New views on strand asymmetry in insect mitochondrial genomes.

Directory of Open Access Journals (Sweden)

Shu-Jun Wei

Full Text Available Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera, Aleyrodidae (Hemiptera and Braconidae (Hymenoptera; the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms.

Getting Frustrated: Modelling Emotion Contagion in Stranded Passengers

NARCIS (Netherlands)

van der Wal, C. Natalie; Couwenberg, Maik; Bosse, T.

2017-01-01

Train passengers can get stranded due to a variety of events, such as a delay, technical malfunctioning or a natural disaster. Stranded passengers can get frustrated, which could escalate in misbehaviours. Examples are verbal and physical violence or dangerous behaviours such as opening emergency

Inter-strand resistance measurements in the termination of the ITER SULTAN samples

International Nuclear Information System (INIS)

Cau, F; Bruzzone, P

2009-01-01

In cabled conductors a perfect uniformity of the current among the strands is hardly reached, due to the non-homogeneity of the contact resistance distribution between the strands and the copper of the electrical terminations. In the case of large current unbalance, the overloaded strands hit the critical surface at high field early, developing a current sharing voltage, which drives the redistribution of the current, mainly in the electrical terminations where the inter-strand resistance is lower than in the high field conductor. If the inter-strand resistance in the termination is low, the voltage levels are sufficiently low to allow an effective redistribution of the current to the less loaded strands. The inter-strand resistance of three different termination layouts of ITER short length samples is measured to make a database available which can be used to qualify the layout of the joints and their capability of redistributing the current among the strands.

RRP Nb3Sn strand studies for LARP

International Nuclear Information System (INIS)

Barzi, Emanuela; Bossert, Rodger; Caspi, Shlomo; Dietderich, Daniel R.; Ferracin, Paolo; Ghosh, Arup; Turrioni, Daniele

2006-01-01

The Nb 3 Sn strand chosen for the next step in the magnet R and D of the U.S. LHC Accelerator Research Program is the 54/61 sub-element Restacked Rod Process by Oxford Instruments, Superconducting Technology. To ensure that the 0.7 mm RRP strands to be used in the upcoming LARP magnets are suitable, extensive studies were performed. Measurements included the critical current, e , using the voltage-current (V-I) method, the stability current, I S , as the minimal quench current obtained with the voltage-field (V-H) method, and RRR. Magnetization was measured at low and high fields to determine the effective filament size and to detect flux jumps. Effects of heat treatment temperature and durations on I e and I S were also studied. Using strand billet qualification and tests of strands extracted from cables, the short sample limits of magnet performance were obtained. The details and the results of this investigation are herein described

RRP Nb3Sn Strand Studies for LARP

International Nuclear Information System (INIS)

Barzi, Emanuela; Bossert, Rodger; Caspi, Shlomo; Dietderich, Daniel R.; Ferracin, Paolo; Ghosh, Arup; Turrioni, Daniele

2007-01-01

The Nb 3 Sn strand chosen for the next step in the magnet R and D of the U.S. LHC Accelerator Research Program is the 54/61 sub-element Restacked Rod Process by Oxford Instruments, Superconducting Technology. To ensure that the 0.7 mm RRP strands to be used in the upcoming LARP magnets are suitable, extensive studies were performed. Measurements included the critical current, I c , using the voltage-current (V-I) method, the stability current, I S , as the minimal quench current obtained with the voltage-field (V-H) method, and RRR. Magnetization was measured at low and high fields to determine the effective filament size and to detect flux jumps. Effects of heat treatment temperature and durations on I c and I S were also studied. Using strand billet qualification and tests of strands extracted from cables, the short sample limits of magnet performance were obtained. The details and the results of this investigation are herein described

LHC superconducting strand

CERN Multimedia

Patrice Loiez

1999-01-01

This cross-section through a strand of superconducting matieral as used in the LHC shows the 8000 Niobium-Titanium filaments embedded like a honeycomb in copper. When cooled to 1.9 degrees above absolute zero in the LHC accelerator, these filaments will have zero resistance and so will carry a high electric current with no energy loss.

A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement

Directory of Open Access Journals (Sweden)

Xin Li

2015-01-01

Full Text Available DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement.

A Stress Measurement Method for Steel Strands Based on LC Oscillation

Directory of Open Access Journals (Sweden)

Dongjun Chen

2018-01-01

Full Text Available The prestress loss is one of the main factors affecting the safety of prestressed concrete structure. While the detecting signals like sound and light are difficult to spread in steel strands, there is no effective method for prestress detection of the bonded prestressed steel strands in existing structures yet. In this paper, taking into consideration that the electromagnetic oscillation characteristic can make the signal propagate effectively on the bonded prestressed steel strands, a nondestructive prestress detection method based on the electromagnetic effect to detect oscillation frequency is proposed. In a detection circuit, the steel strands are simulated as an inductance component, in which an induced electromagnetic signal passes through the steel strands to form resonance. And then, a frequency meter is used to detect the oscillation frequency of the resonant circuit. The oscillation frequency is supposed to have relationship with the prestress loading on the steel strands. A section of steel strands with a length of 1.2 m is adopted to test the correlation of stress and oscillation frequency. Both the theoretical and experimental results show that the resonant frequency of the circuit decreases with the increase of the stress of the strand and is linear in a certain range.

A model capturing novel strand symmetries in bacterial DNA

International Nuclear Information System (INIS)

Sobottka, Marcelo; Hart, Andrew G.

2011-01-01

Highlights: → We propose a simple stochastic model to construct primitive DNA sequences. → The model provide an explanation for Chargaff's second parity rule in primitive DNA sequences. → The model is also used to predict a novel type of strand symmetry in primitive DNA sequences. → We extend the results for bacterial DNA sequences and compare distributional properties intrinsic to the model to statistical estimates from 1049 bacterial genomes. → We find out statistical evidences that the novel type of strand symmetry holds for bacterial DNA sequences. -- Abstract: Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for double-stranded DNA genomes and fails to hold for single-stranded genomes. While Chargaff's first parity rule is fully explained by the Watson-Crick pairing in the DNA double helix, a definitive explanation for the second parity rule has not yet been determined. In this work, we propose a model based on a hidden Markov process for approximating the distributional structure of primitive DNA sequences. Then, we use the model to provide another possible theoretical explanation for Chargaff's second parity rule, and to predict novel distributional aspects of bacterial DNA sequences.

Sub-ensemble monitoring of DNA strand displacement using multiparameter single-molecule FRET

OpenAIRE

Baltierra Jasso, Laura; Morten, Michael; Magennis, Steven William

2018-01-01

Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constan...

Stranding Events of Kogia Whales along the Brazilian Coast.

Directory of Open Access Journals (Sweden)

Jailson F Moura

Full Text Available The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST, water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast.

Radiobiological study on DNA strand breaks and repair using single cell gel electrophoresis

International Nuclear Information System (INIS)

Ikushima, Takaji

1994-01-01

Single cell gel electrophoresis (SCGE) provides a novel method to measure DNA damage in individual cells and more importantly, to assess heterogeneity in response within a mixed population of cells. Cells embedded in agarose are lysed, subjected to electrophoresis, stained with a fluorescent DNA-specific dye, and viewed under a fluorescence microscope. Damaged cells display 'comets', broken DNA migrating farther to the anode in the electric field. We have previously used this technique to quantify DNA damage induced by moderate doses of low and high LET radiations in cultured Chinese hamster cells. The assay has been optimized in terms of lysing and electrophoresis conditions, and applied to analyse the DNA strand breaks, their repair kinetics and heterogeneity in response in individual Chinese hamster cells exposed to gamma-rays, and to KUR thermal neutrons with and without 10 B or to KEK PF monochromatic soft X-rays as well as to a radio-mimetic agent, neocarzinostatin. The DNA double-strand breaks induced by boron-neutron captured reactions were repaired at a slower rate, but a heterogeneity in response might not contribute to the difference. The neocarzinostatin-induced DNA damage were efficiently repaired in a dose-dependent fashion. The initial amount of gamma-ray induced DNA double-strand breaks was not significantly altered in cells pre-exposed to very low adapting dose. (author)

Prioritizing equipment for replacement.

Science.gov (United States)

Capuano, Mike

2010-01-01

It is suggested that clinical engineers take the lead in formulating evaluation processes to recommend equipment replacement. Their skill, knowledge, and experience, combined with access to equipment databases, make them a logical choice. Based on ideas from Fennigkoh's scheme, elements such as age, vendor support, accumulated maintenance cost, and function/risk were used.6 Other more subjective criteria such as cost benefits and efficacy of newer technology were not used. The element of downtime was also omitted due to the data element not being available. The resulting Periop Master Equipment List and its rationale was presented to the Perioperative Services Program Council. They deemed the criteria to be robust and provided overwhelming acceptance of the list. It was quickly put to use to estimate required capital funding, justify items already thought to need replacement, and identify high-priority ranked items for replacement. Incorporating prioritization criteria into an existing equipment database would be ideal. Some commercially available systems do have the basic elements of this. Maintaining replacement data can be labor-intensive regardless of the method used. There is usually little time to perform the tasks necessary for prioritizing equipment. However, where appropriate, a clinical engineering department might be able to conduct such an exercise as shown in the following case study.

Device for the replacement of a component subject to radioactive irradiation

International Nuclear Information System (INIS)

Schoening, J.; Handel, H.; Landwehr, H.; Fink, H.

1979-01-01

A component is situated in a cut-out of the loading plant, which is accessible from the side away from the reactor. It can be replaced by a new component by a magazine with several channels, which are of the same crossection as the cut-out and using a gripping tool. The gripping tool pulls the component into one of the channels, after the magazine was moved sideways, it presses the new component from another channel into the cut-out. (DG) [de

75 FR 36678 - Prestressed Concrete Steel Wire Strand From China; Determinations

Science.gov (United States)

2010-06-28

... prestressed concrete steel wire strand (PC strand), provided for in subheading 7312.10.30 of the Harmonized... Publication 4162 (June 2010), entitled Prestressed Concrete Steel Wire Strand from China: Investigation Nos... INTERNATIONAL TRADE COMMISSION [Investigation Nos. 701-TA-464 and 731-TA-1160 (Final)] Prestressed...

Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand*

Science.gov (United States)

Teasley, Daniel C.; Parajuli, Shankar; Nguyen, Mai; Moore, Hayley R.; Alspach, Elise; Lock, Ying Jie; Honaker, Yuchi; Saharia, Abhishek; Piwnica-Worms, Helen; Stewart, Sheila A.

2015-01-01

The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer. PMID:25922071

Characteristics of Cu stabilized Nb3Al strands with low Cu ratio

Energy Technology Data Exchange (ETDEWEB)

Kikuchi, A.; Yamada, R.; Barzi, E.; Kobayashi, M.; Lamm, M.; Nakagawa, K.; Sasaki, K.; Takeuchi, T.; Turrioni, D.; Zlobin, A.V.; /NIMC, Tsukuba /Fermilab /Hitachi, Tsuchiura Works /KEK, Tsukuba

2008-12-01

Characteristics of recently developed F4-Nb{sub 3}Al strand with low Cu ratio are described. The overall J{sub c} of the Nb{sub 3}Al strand could be easily increased by decreasing of the Cu ratio. Although the quench of a pulse-like voltage generation is usually observed in superconducting unstable conductor, the F4 strand with a low Cu ratio of 0.61 exhibited an ordinary critical transition of gradual voltage generation. The F4 strand does not have magnetic instabilities at 4.2 K because of the tantalum interfilament matrix. The overall J{sub c} of the F4 strand achieved was 80-85% of the RRP strand. In the large mechanical stress above 100 MPa, the overall J{sub c} of the F4 strand might be comparable to that of high J{sub c} RRP-Nb{sub 3}Sn strands. The Rutherford cable with a high packing factor of 86.5% has been fabricated using F4 strands. The small racetrack magnet, SR07, was also fabricated by a 14 m F4 cable. The quench current, I{sub q}, of SR07 were obtained 22.4 kA at 4.5 K and 25.2 kA at 2.2 K. The tantalum matrix Nb{sub 3}Al strands are promising for the application of super-cooled high-field magnets as well as 4.2 K operation magnets.

Characterization of a parallel-stranded DNA hairpin

International Nuclear Information System (INIS)

Germann, M.W.; Vogel, H.J.; Pon, R.T.; van de Sande, J.H.

1989-01-01

Recently, the authors have shown that synthetic DNA containing homooligomeric A-T base pairs can form a parallel-stranded intramolecular hairpin structure. In the present study, they have employed NMR and optical spectroscopy to investigate the structure of the parallel-stranded (PS) DNA hairpin 3'-d(T) 8 C 4 (A) 8 -3' and the related antiparallel (APS) hair 5'-d(T) 8 C 4 (A) 8 -3'. The parallel orientation of the strands in the PS oligonucleotide is achieved by introducing a 5'-5' phosphodiester linkage in the hairpin loop. Ultraviolet spectroscopic and fluorescence data of drug binding are consistent with the formation of PS and APS structures, respectively, in these two hairpins. Vacuum circular dichroism measurements in combination with theoretical CD calculations indicate that the PS structure forms a right-handed helix. 31 P NMR measurements indicate that the conformation of the phosphodiester backbone of the PS structure is not drastically different from that of the APS control. The presence of slowly exchanging imino protons at 14 ppm and the observation of nuclear Overhauser enhancement between imino protons and the AH-2 protons demonstrate that similar base pairing and base stacking between T and A residues occur in both hairpins. On the basis of NOESY measurements, they find that the orientation of the bases is in the anti region and that the sugar puckering is in the 2'-endo range. The results indicate a B-like conformation for each of the strands in the stem part of the PS hairpin and reverse Watson-Crick base pairing between the T and A residues. These data are consistent with a previously calculated structure for parallel-stranded DNA

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.

Replacement of core components in the Advanced Test Reactor

International Nuclear Information System (INIS)

Durney, J.L.; Croucher, D.W.

1990-01-01

The core internals of the Advanced Test Reactor are subjected to very high neutron fluences resulting in significant aging. The most irradiated components have been replaced on several occasions as a result of the neutron damage. The surveillance program to monitor the aging developed the needed criteria to establish replacement schedules and maximize the use of the reactor. The methods to complete the replacements with minimum radiation exposures to workers have been developed using the experience gained from each replacement. The original design of the reactor core and associated components allows replacements to be completed without special equipment. The plant has operated for about 20 years and is expected to continue operation for at least and additional 25 years. Aging evaluations are in progress to address additional replacements that may be needed during this period

Replacement of core components in the Advanced Test Reactor

International Nuclear Information System (INIS)

Durney, J.L.; Croucher, D.W.

1989-01-01

The core internals of the Advanced Test Reactor are subjected to very high neutron fluences resulting in significant aging. The most irradiated components have been replaced on several occasions as a result of the neutron damage. The surveillance program to monitor the aging developed the needed criteria to establish replacement schedules and maximize the use of the reactor. Methods to complete the replacements with minimum radiation exposures to workers have been developed using the experience gained from each replacement. The original design of the reactor core and associated components allows replacements to be completed without special equipment. The plant has operated for about 20 years and will continue operation for perhaps another 20 years. Aging evaluations are in program to address additional replacements that may be needed during this extended time period. 3 figs

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

Czech Academy of Sciences Publication Activity Database

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

2006-01-01

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

Torsional regulation of hRPA-induced unwinding of double-stranded DNA

NARCIS (Netherlands)

De Vlaminck, I.; Vidic, I.; Van Loenhout, M.T.J.; Kanaar, R.; Lebbink, J.H.G.; Dekker, C.

2010-01-01

All cellular single-stranded (ss) DNA is rapidly bound and stabilized by single stranded DNA-binding proteins (SSBs). Replication protein A, the main eukaryotic SSB, is able to unwind double-stranded (ds) DNA by binding and stabilizing transiently forming bubbles of ssDNA. Here, we study the

Role of stranded gas in increasing global gas supplies

Science.gov (United States)

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

2013-01-01

This report synthesizes the findings of three regional studies in order to evaluate, at the global scale, the contribution that stranded gas resources can make to global natural gas supplies. Stranded gas, as defined for this study, is natural gas in discovered conventional gas and oil fields that is currently not commercially producible for either physical or economic reasons. The regional studies evaluated the cost of bringing the large volumes of undeveloped gas in stranded gas fields to selected markets. In particular, stranded gas fields of selected Atlantic Basin countries, north Africa, Russia, and central Asia are screened to determine whether the volumes are sufficient to meet Europe’s increasing demand for gas imports. Stranded gas fields in Russia, central Asia, Southeast Asia, and Australia are also screened to estimate development, production, and transport costs and corresponding gas volumes that could be supplied to Asian markets in China, India, Japan, and South Korea. The data and cost analysis presented here suggest that for the European market and the markets examined in Asia, the development of stranded gas provides a way to meet projected gas import demands for the 2020-to-2040 period. Although this is a reconnaissance-type appraisal, it is based on volumes of gas that are associated with individual identified fields. Individual field data were carefully examined. Some fields were not evaluated because current technology was insufficient or it appeared the gas was likely to be held off the export market. Most of the evaluated stranded gas can be produced and delivered to markets at costs comparable to historical prices. Moreover, the associated volumes of gas are sufficient to provide an interim supply while additional technologies are developed to unlock gas diffused in shale and hydrates or while countries transition to making a greater use of renewable energy sources.

Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking.

Science.gov (United States)

Nakamura, Shigetaka; Hashimoto, Hirokazu; Kobayashi, Satoshi; Fujimoto, Kenzo

2017-10-18

DNA strand displacement is an essential reaction in genetic recombination, biological processes, and DNA nanotechnology. In particular, various DNA nanodevices enable complicated calculations. However, it takes time before the output is obtained, so acceleration of DNA strand displacement is required for a rapid-response DNA nanodevice. Herein, DNA strand displacement by using DNA photo-crosslinking to accelerate this displacement is evaluated. The DNA photo-crosslinking of 3-cyanovinylcarbazole ( CNV K) was accelerated at least 20 times, showing a faster DNA strand displacement. The rate of photo-crosslinking is a key factor and the rate of DNA strand displacement is accelerated through ultrafast photo-crosslinking. The rate of DNA strand displacement was regulated by photoirradiation energy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Corrosion characteristics of unprotected post-tensioning strands under stress.

Science.gov (United States)

2014-05-01

An investigation was conducted to determine the effect of stress condition : and environmental exposure on corrosion of post-tensioned strands during ungrouted periods. : Exposures for periods of up to 4 weeks of stressed, as-received strand placed i...

Stranded cost recovery in electricity market reforms in the US

International Nuclear Information System (INIS)

Woo, C.K.; Lloyd, D.; Karimov, R.; Tishler, A.

2003-01-01

An important element of an electricity market reform is stranded cost recovery. This paper explains the cause of stranded costs, describes four recovery mechanisms, evaluates these mechanisms using the criteria of recovery certainty, economic efficiency and equity, reviews the financial performance of 12 utilities in the US in connection to stranded cost recovery, and shows why the mechanism used in California has contributed to the reform failure in that state. (Author)

A novel single fluorophore-labeled double-stranded oligonucleotide probe for fluorescence-enhanced nucleic acid detection based on the inherent quenching ability of deoxyguanosine bases and competitive strand-displacement reaction.

Science.gov (United States)

Zhang, Yingwei; Tian, Jingqi; Li, Hailong; Wang, Lei; Sun, Xuping

2012-01-01

We develop a novel single fluorophore-labeled double-stranded oligonucleotide (OND) probe for rapid, nanostructure-free, fluorescence-enhanced nucleic acid detection for the first time. We further demonstrate such probe is able to well discriminate single-base mutation in nucleic acid. The design takes advantage of an inherent quenching ability of guanine bases. The short strand of the probe is designed with an end-labeled fluorophore that is placed adjacent to two guanines as the quencher located on the long opposite strand, resulting in great quenching of dye fluorescence. In the presence of a target complementary to the long strand of the probe, a competitive strand-displacement reaction occurs and the long strand forms a more stable duplex with the target, resulting in the two strands of the probe being separated from each other. As a consequence of this displacement, the fluorophore and the quencher are no longer in close proximity and dye fluorescence increases, signaling the presence of target.

Bioprinting Using Mechanically Robust Core-Shell Cell-Laden Hydrogel Strands.

Science.gov (United States)

Mistry, Pritesh; Aied, Ahmed; Alexander, Morgan; Shakesheff, Kevin; Bennett, Andrew; Yang, Jing

2017-06-01

The strand material in extrusion-based bioprinting determines the microenvironments of the embedded cells and the initial mechanical properties of the constructs. One unmet challenge is the combination of optimal biological and mechanical properties in bioprinted constructs. Here, a novel bioprinting method that utilizes core-shell cell-laden strands with a mechanically robust shell and an extracellular matrix-like core has been developed. Cells encapsulated in the strands demonstrate high cell viability and tissue-like functions during cultivation. This process of bioprinting using core-shell strands with optimal biochemical and biomechanical properties represents a new strategy for fabricating functional human tissues and organs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand.

Science.gov (United States)

Teasley, Daniel C; Parajuli, Shankar; Nguyen, Mai; Moore, Hayley R; Alspach, Elise; Lock, Ying Jie; Honaker, Yuchi; Saharia, Abhishek; Piwnica-Worms, Helen; Stewart, Sheila A

2015-06-12

The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

DNA strand breaks induced by soft X-ray pulses from a compact laser plasma source

Czech Academy of Sciences Publication Activity Database

Adjei, D.; Wiechec, A.; Wachulak, P.; Ayele, M. G.; Lekki, J.; Kwiatek, W. M.; Bartnik, A.; Davídková, Marie; Vyšín, Luděk; Juha, Libor; Pina, L.; Fiedorowicz, H.

2016-01-01

Roč. 120, MAR (2016), s. 17-25 ISSN 0969-806X R&D Projects: GA ČR GA13-28721S; GA ČR(CZ) GBP108/12/G108 EU Projects: European Commission(XE) 284464 - LASERLAB-EUROPE Institutional support: RVO:68378271 ; RVO:61389005 Keywords : laser-produced plasma * soft X-rays * radiobiology * gas puff target * water window * DNA strand break Subject RIV: BO - Biophysics Impact factor: 1.315, year: 2016

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

Directory of Open Access Journals (Sweden)

Simon Roux

2016-12-01

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

Feasibility and antihypertensive effect of replacing regular salt with mineral salt -rich in magnesium and potassium- in subjects with mildly elevated blood pressure

Directory of Open Access Journals (Sweden)

Sarkkinen Essi S

2011-09-01

Full Text Available Abstract Background High salt intake is linked to hypertension whereas a restriction of dietary salt lowers blood pressure (BP. Substituting potassium and/or magnesium salts for sodium chloride (NaCl may enhance the feasibility of salt restriction and lower blood pressure beyond the sodium reduction alone. The aim of this study was to determine the feasibility and effect on blood pressure of replacing NaCl (Regular salt with a novel mineral salt [50% sodium chloride and rich in potassium chloride (25%, magnesium ammonium potassium chloride, hydrate (25%] (Smart Salt. Methods A randomized, double-blind, placebo-controlled study was conducted with an intervention period of 8-weeks in subjects (n = 45 with systolic (SBP 130-159 mmHg and/or diastolic (DBP 85-99 mmHg. During the intervention period, subjects consumed processed foods salted with either NaCl or Smart Salt. The primary endpoint was the change in SBP. Secondary endpoints were changes in DBP, daily urine excretion of sodium (24-h dU-Na, potassium (dU-K and magnesium (dU-Mg. Results 24-h dU-Na decreased significantly in the Smart Salt group (-29.8 mmol; p = 0.012 and remained unchanged in the control group: resulting in a 3.3 g difference in NaCl intake between the groups. Replacement of NaCl with Smart Salt resulted in a significant reduction in SBP over 8 weeks (-7.5 mmHg; p = 0.016. SBP increased (+3.8 mmHg, p = 0.072 slightly in the Regular salt group. The difference in the change of SBP between study groups was significant (p Conclusions The substitution of Smart Salt for Regular salt in subjects with high normal or mildly elevated BP resulted in a significant reduction in their daily sodium intake as well as a reduction in SBP. Trial Registration ISRCTN: ISRCTN01739816

Cetacean strandings along the coast of Izmir Bay, Turkey

NARCIS (Netherlands)

Guclusoy, H.; Veryeri, N.; Cirik, S.

2004-01-01

The present paper provides information on the stranding of cetaceans in Izmir Bay, Aegean Sea, between 1992 and 2004. The data were collected opportunistically during sightings and stranding data collection for Monk Seals. A total of 12 cetaceans, namely Bottle-nosed Dolphin, Tursiops truncatus

DNA turnover and strand breaks in Escherichia coli

International Nuclear Information System (INIS)

Hanawalt, P.; Grivell, A.; Nakayama, H.

1975-01-01

The extent of DNA turnover has been measured in a dnaB mutant of Escherichia coli, temperature sensitive for semiconservative DNA replication. At the nonpermissive temperature about 0.02 percent of the deoxynucleotides in DNA are exchanged per generation period. This turnover rate is markedly depressed in the presence of rifampicin. During thymine starvation strand breaks accumulate in the DNA of E. coli strains that are susceptible to thymineless death. Rifampicin suppresses the appearance of these breaks, consistent with our hypothesis that transcription may be accompanied by repairable single-strand breaks in DNA. DNA turnover is enhanced severalfold in strands containing 5-bromodeoxyuridine in place of thymidine, possibly because the analog (or the deoxyuridine, following debromination) is sometimes recognized and excised

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.

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...

Improving strand quality of upland oaks for use in oriented strand board

Science.gov (United States)

David B. DeValliance; Jody D. Gray; Shawn T. Grushecky

2013-01-01

Past research estimates that more than 1 million tons of oak logging residues go unused in West Virginia each year. Much research has been done investigating potential products and markets for this underutilized resource. West Virginia is home to an oriented strand board (OSB) producer that consumes large volumes of small diameter, low quality round wood. However, the...

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.

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.

Development of a 10 m quasi-isotropic strand assembled from 2G wires

Science.gov (United States)

Kan, Changtao; Wang, Yinshun; Hou, Yanbing; Li, Yan; Zhang, Han; Fu, Yu; Jiang, Zhe

2018-03-01

Quasi-isotropic strands made of second generation (2G) high temperature superconducting (HTS) wires are attractive to applications of high-field magnets at low temperatures and power transmission cables at liquid nitrogen temperature in virtue of their high current carrying capability and well mechanical property. In this contribution, a 10 m length quasi-isotropic strand is manufactured and successfully tested in liquid nitrogen to verify the feasibility of an industrial scale production of the strand by the existing cabling technologies. The strand with copper sheath consists of 72 symmetrically assembled 2G wires. The uniformity of critical properties of long quasi-isotropic strands, including critical current and n-value, is very important for their using. Critical currents as well as n-values of the strand are measured every 1 m respectively and compared with the simulation results. Critical current and n-value of the strand are calculated basing on the self-consistent model solved by the finite element method (FEM). Effects of self-field on the critical current and n-value distributions in wires of the strand are analyzed in detail. The simulation results show good agreement with the experimental data and the 10 m quasi-isotropic strand has good critical properties uniformity.

Corrosion characteristics of post-tensioning strands in ungrouted ducts : summary.

Science.gov (United States)

2011-01-01

To prevent corrosion of post-tensioning strands, FDOT construction specifications currently require post-tensioning ducts to be grouted within seven calendar days of strand installation. This period challenges construction schedules on large projects...

Forces of Faith: Endurance, Flourishing, and the Queer Religious Subject

NARCIS (Netherlands)

van Doorn, N.

2015-01-01

This essay examines what it means for queer subjects to cultivate a concern for their lives and the lives of others in the face of debilitating circumstances, when these efforts are maintained through religious practices and attachments. Taking cues from a small yet growing strand of social science

Liquid and Solid Meal Replacement Products Differentially Affect Postprandial Appetite and Food Intake in Older Adults

Science.gov (United States)

Stull, April J.; Apolzan, John W.; Thalacker-Mercer, Anna E.; Iglay, Heidi B.; Campbell, Wayne W.

2008-01-01

Liquid and solid foods are documented to elicit differential appetitive and food intake responses. This study was designed to assess the influences of liquid vs solid meal replacement products on postprandial appetite ratings and subsequent food intake in healthy older adults. This study used a randomized and crossover design with two 1-day trials (1 week between trials), and 24 adults (12 men and 12 women) aged 50 to 80 years with body mass index (calculated as kg/m2) between 22 and 30 participated. After an overnight fast, the subjects consumed meal replacement products as either a beverage (liquid) or a bar (solid). The meal replacement products provided 25% of each subject's daily estimated energy needs with comparable macro-nutrient compositions. Subjects rated their appetite on a 100 mm quasilogarithmic visual analog scale before and 15, 30, 45, 60, 90, 120, and 150 minutes after consuming the meal replacement product. At minute 120, each subject consumed cooked oatmeal ad libitum to a “comfortable level of fullness.” Postprandial composite (area under the curve from minute 15 to minute 120) hunger was higher (P=0.04) for the liquid vs solid meal replacement products and desire to eat (P=0.15), preoccupation with thoughts of food (P=0.07), and fullness (P=0.25) did not differ for the liquid vs solid meal replacement products. On average, the subjects consumed 13.4% more oatmeal after the liquid vs solid (P=0.006) meal replacement product. These results indicate that meal replacement products in liquid and solid form do not elicit comparable appetitive and ingestive behavior responses and that meal replacement products in liquid form blunt the postprandial decline in hunger and increase subsequent food intake in older adults. PMID:18589034

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.

Stem cell identity and template DNA strand segregation.

Science.gov (United States)

Tajbakhsh, Shahragim

2008-12-01

The quest for stem cell properties to distinguish their identity from that of committed daughters has led to a re-investigation of the notion that DNA strands are not equivalent, and 'immortal' DNA strands are retained in stem cells whereas newly replicated DNA strands segregate to the differentiating daughter cell during mitosis. Whether this process occurs only in stem cells, and also in all tissues, remains unclear. That individual chromosomes can be also partitioned non-randomly raises the question if this phenomenon is related to the immortal DNA hypothesis, and it underscores the need for high-resolution techniques to observe these events empirically. Although initially postulated as a mechanism to avoid DNA replication errors, alternative views including epigenetic regulation and sister chromatid silencing may provide insights into this process.

Mechanical behavior of Nb{sub 3}Sn strands under transverse electromagnetic loads

Energy Technology Data Exchange (ETDEWEB)

Ru, Yanyun; Yong, Huadong, E-mail: yonghd@lzu.edu.cn; Zhou, Youhe

2016-11-15

Highlights: • The contact forces between the strands under transverse electromagnetic load are considered. • The indentation depth for two-dimensional contact problem is calculated. • The strand damage for different layers is presented. • We discuss the effect of bending wavelength on the Nb{sub 3}Sn strand. - Abstract: The performance of Nb{sub 3}Sn cable-in-conduit-conductor (CICC) shows a significant degradation with increasing electromagnetic load in the International Thermonuclear Experimental Reactor (ITER). As the strand is under the compression caused by adjacent strands, the strand damage may occur for high contact force. In this paper, we present a 3D helix model based on the TEMLOP and FEMCAM to simulate the contact force among the strands under transverse load. The maximum linear strain and indentation depth induced by contact stress are calculated with two-dimensional contact model of cylinder. The numerical results are compared with the experimental values. Finally, the indentation depth is discussed for different layers and cross angles based on two models. With the increasing of layer number, the degradation of performance will occur. The short bending wavelength leads to small indentation depth.

Sub-Ensemble Monitoring of DNA Strand Displacement Using Multiparameter Single-Molecule FRET.

Science.gov (United States)

Baltierra-Jasso, Laura E; Morten, Michael J; Magennis, Steven W

2018-03-05

Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here, we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of 10 m -1  s -1 . We also followed the displacement from a DNA three-way junction (3WJ) by ssDNA. The presence of three internal mismatched bases in the middle of the invading strand did not prevent displacement from the 3WJ, but reduced the second-order rate constant by about 50 %. We attribute strand exchange in the dsDNA and 3WJ to a zero-toehold pathway from the blunt-ended duplex arms. The single-molecule approach demonstrated here will be useful for studying complex DNA networks. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Performance optimization of internal tin process multifilamentary Nb{sub 3}Sn strands

Energy Technology Data Exchange (ETDEWEB)

Zhang, Ke, E-mail: zhangke@c-wst.com [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China); Zhang, Pingxiang [State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China); Northwest Institute for Non-ferrous Metal Research, Xi’an, Shaanxi 710016 (China); Shi, Yigong; Liu, Jianwei; Gao, Huixian; Li, Jianfeng; Liu, Xianghong; Feng, Yong [Western Superconducting Technologies Co. Ltd, Xi’an, Shaanxi 710018 (China); State Engineering Lab. of Superconducting Material Preparation, Xi’an, Shaanxi 710018 (China)

2016-11-01

Highlights: • J{sub c} increases by adding Sn cores in the interspaces, hysteresis loss increases at the same time. • Enlarger the number of filaments with the same Sn proportion will increase J{sub c} and hysteresis loss. • Cu split adopted in each sub-element leads to a low hysteresis loss. - Abstract: In this study, internal tin process Nb{sub 3}Sn strands for the International Thermo-nuclear Experimental Reactor are developed in Western Superconducting Technologies. Short cable-in-conduit conductors manufactured with these strands have been qualified. Mass production is accomplished, and all the performances of the strands meet the requirement of ITER project. Besides, more researches on the effect of strand design on critical current density and hysteresis loss for Nb{sub 3}Sn strands are carried out. It is found that critical current density can be enhanced by reducing filament diameter and increasing Sn content, and hysteresis loss of the strands can be significantly reduced through Cu split adopted in sub-element.

Metallographic investigation of fracture behavior in ITER-style Nb$_{3}$Sn superconducting strands

CERN Document Server

Jewell, M C; Larbalestier, D C; Nijhuis, A

2009-01-01

In this work we specify the extent to which fracture in two ITER-style Nb$_{3}$Sn composite strands occurs in a collective or individual manner, under mechanical tension and bending from the TARSIS apparatus at the University of Twente. A bronze-route strand from European Advanced Superconductors (EAS), which has very uniform, well-spaced filaments, has a widely distributed (200 μm) fracture field and exhibits a composite of individual and collective cracks. An internal tin strand from Oxford Instruments – Superconducting Technology (OST) demonstrates much more localized, collective fracture behavior. The filaments in this strand are about four times larger (in area) than the filaments in the EAS strand, and also agglomerate significantly during heat treatment upon conversion of the Nb to Nb$_{3}$Sn. These results demonstrate that the architecture of the strand can play a significant role in determining the mechanical toughness of the composite, and that strand design should incorporate mechanical consider...

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.

Microwave wood strand drying: energy consumption, VOC emission and drying quality

Energy Technology Data Exchange (ETDEWEB)

Wang, S.; Du, G.; Zhang, Y. [Tennessee Univ., Knoxville, TN (United States). Dept. of Forestry, Wildlife and Fisheries

2005-07-01

The objective of this research was to develop microwave drying technology for wood strand drying for oriented strand board (OSB) manufacturing. The advantages of microwave drying included a reduction in the drying time of wood strands and a reduction in the release of volatile organic compounds (VOC) through a decrease in the thermal degradation of the wood material. Temperature and moisture content changes under different microwave drying conditions were investigated. The effects of microwave drying on VOC emissions were evaluated and analyzed using gas chromatography and mass spectrometry. Microwave power input and the mass of drying materials in the microwave oven were found to have a dominant effect on drying quality. Results indicated that an increase in microwave power input and a decrease in sample weights resulted in high drying temperatures, short drying times and a high drying rate. The effect of microwave drying on the strand surfaces was also investigated. Different strand geometries and initial moisture content resulted in varying warm-up curves, but did not influence final moisture content. VOC emissions were quantified by comparing alpha-pinene concentrations. The microwave drying resulted in lower VOC emissions compared with conventional drying methods. It was concluded that the microwave drying technique provided faster strand drying and reduced energy consumption by up to 50 per cent. In addition, the surface wettability of wood strands dried with microwaves was better than with an industrial rotary drum drier. 12 refs., 3 tabs., 5 figs.

Toxin MqsR Cleaves Single-Stranded mRNA with Various 5 Ends

Science.gov (United States)

2016-08-24

either protein ORIGINAL RESEARCH Toxin MqsR cleaves single- stranded mRNA with various 5’ ends Nityananda Chowdhury1,*, Brian W. Kwan1,*, Louise C...in which a single 5′- GCU site was predicted to be single- stranded (ssRNA), double- stranded (dsRNA), in the loop of a stem - loop (slRNA), or in a...single- stranded 5′- GCU sites since cleavage was approximately 20- fold higher than cleavage seen with the 5′- GCU site in the stem - loop and

World-Wide Benchmarking of ITER Nb$_{3}$Sn Strand Test Facilities

CERN Document Server

Jewell, MC; Takahashi, Yoshikazu; Shikov, Alexander; Devred, Arnaud; Vostner, Alexander; Liu, Fang; Wu, Yu; Jewell, Matthew C; Boutboul, Thierry; Bessette, Denis; Park, Soo-Hyeon; Isono, Takaaki; Vorobieva, Alexandra; Martovetsky, Nicolai; Seo, Kazutaka

2010-01-01

The world-wide procurement of Nb$_{3}$Sn and NbTi for the ITER superconducting magnet systems will involve eight to ten strand suppliers from six Domestic Agencies (DAs) on three continents. To ensure accurate and consistent measurement of the physical and superconducting properties of the composite strand, a strand test facility benchmarking effort was initiated in August 2008. The objectives of this effort are to assess and improve the superconducting strand test and sample preparation technologies at each DA and supplier, in preparation for the more than ten thousand samples that will be tested during ITER procurement. The present benchmarking includes tests for critical current (I-c), n-index, hysteresis loss (Q(hys)), residual resistivity ratio (RRR), strand diameter, Cu fraction, twist pitch, twist direction, and metal plating thickness (Cr or Ni). Nineteen participants from six parties (China, EU, Japan, South Korea, Russia, and the United States) have participated in the benchmarking. This round, cond...

Self-Field Effects in Magneto-Thermal Instabilities for Nb-Sn Strands

CERN Document Server

Bordini, B; Fehér, S; Rossi, L; Zlobin, A V

2008-01-01

Recent advancements in the critical current density (Jc) of Nb$_{3}$Sn conductors, coupled with a large effective filament size, have drawn attention to the problem of magnetothermal instabilities. At low magnetic fields, the quench current of such high Jc Nb$_{3}$Sn strands is significantly lower than their critical current because of the above-mentioned instabilities. An adiabatic model to calculate the minimum current at which a strand can quench due to magneto-thermal instabilities is developed. The model is based on an 'integral' approach already used elsewhere [1]. The main difference with respect to the previous model is the addition of the self-field effect that allows to describe premature quenches of non-magnetized Nb$_{3}$Sn strands and to better calculate the quench current of strongly magnetized strands. The model is in good agreement with experimental results at 4.2 K obtained at Fermilab using virgin Modified Jelly Roll (MJR) strands with a low Residual Resistivity Ratio (RRR) of the stabilizin...

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.

The role of cytosine methylation on charge transport through a DNA strand

Energy Technology Data Exchange (ETDEWEB)

Qi, Jianqing, E-mail: jqqi@uw.edu; Anantram, M. P., E-mail: anantmp@uw.edu [Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500 (United States); Govind, Niranjan, E-mail: niri.govind@pnnl.gov [William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

2015-09-07

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.

Ketahanan Papan Unting (Oriented Strand Board) terhadap Serangan Rayap Tanah dan Rayap Kayu Kering

OpenAIRE

Gea, Bud diman

2011-01-01

Oriented strand board is panel of wood raw material from which strand composed of cross and upright structure. In order to oriented strand board can be used for interior and exterior needs, than necessary to be applied various thenology of quality improvement like durabelities and endurance of oriented strand board. For it does found endurance oriented strand board from attack of ground termite and wood dry termite, necessary doing grave yard trial and wood dry termite trial. This research ta...

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.

Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange*

Science.gov (United States)

Borgogno, María V.; Monti, Mariela R.; Zhao, Weixing; Sung, Patrick; Argaraña, Carlos E.; Pezza, Roberto J.

2016-01-01

Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3′ end of the initiating DNA strand have a small effect, whereas most mismatches near the 5′ end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity. PMID:26709229

Checkpoint Kinase Rad53 Couples Leading- and Lagging-Strand DNA Synthesis under Replication Stress.

Science.gov (United States)

Gan, Haiyun; Yu, Chuanhe; Devbhandari, Sujan; Sharma, Sushma; Han, Junhong; Chabes, Andrei; Remus, Dirk; Zhang, Zhiguo

2017-10-19

The checkpoint kinase Rad53 is activated during replication stress to prevent fork collapse, an essential but poorly understood process. Here we show that Rad53 couples leading- and lagging-strand synthesis under replication stress. In rad53-1 cells stressed by dNTP depletion, the replicative DNA helicase, MCM, and the leading-strand DNA polymerase, Pol ε, move beyond the site of DNA synthesis, likely unwinding template DNA. Remarkably, DNA synthesis progresses further along the lagging strand than the leading strand, resulting in the exposure of long stretches of single-stranded leading-strand template. The asymmetric DNA synthesis in rad53-1 cells is suppressed by elevated levels of dNTPs in vivo, and the activity of Pol ε is compromised more than lagging-strand polymerase Pol δ at low dNTP concentrations in vitro. Therefore, we propose that Rad53 prevents the generation of excessive ssDNA under replication stress by coordinating DNA unwinding with synthesis of both strands. Copyright © 2017 Elsevier Inc. All rights reserved.

Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells.

Science.gov (United States)

Byrne, Susan M; Ortiz, Luis; Mali, Prashant; Aach, John; Church, George M

2015-02-18

Sequence-specific nucleases such as TALEN and the CRISPR/Cas9 system have so far been used to disrupt, correct or insert transgenes at precise locations in mammalian genomes. We demonstrate efficient 'knock-in' targeted replacement of multi-kilobase genes in human induced pluripotent stem cells (iPSC). Using a model system replacing endogenous human genes with their mouse counterpart, we performed a comprehensive study of targeting vector design parameters for homologous recombination. A 2.7 kilobase (kb) homozygous gene replacement was achieved in up to 11% of iPSC without selection. The optimal homology arm length was around 2 kb, with homology length being especially critical on the arm not adjacent to the cut site. Homologous sequence inside the cut sites was detrimental to targeting efficiency, consistent with a synthesis-dependent strand annealing (SDSA) mechanism. Using two nuclease sites, we observed a high degree of gene excisions and inversions, which sometimes occurred more frequently than indel mutations. While homozygous deletions of 86 kb were achieved with up to 8% frequency, deletion frequencies were not solely a function of nuclease activity and deletion size. Our results analyzing the optimal parameters for targeting vector design will inform future gene targeting efforts involving multi-kilobase gene segments, particularly in human iPSC. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Estimation of Prestress Force Distribution in the Multi-Strand System of Prestressed Concrete Structures

Directory of Open Access Journals (Sweden)

Keunhee Cho

2015-06-01

Full Text Available Prestressed concrete (PSC is one of the most reliable, durable and widely used construction materials, which overcomes the weakness of concrete in tension by the introduction of a prestress force. Smart strands enabling measurement of the prestress force have recently been developed to maintain PSC structures throughout their lifetime. However, the smart strand cannot give a representative indication of the whole prestress force when used in multi-strand systems since each strand sustains a different prestress force. In this paper, the actual distribution of the prestress force in a multi-strand system is examined using elastomagnetic (EM sensors to develop a method for tracking representative indicators of the prestress force using smart strands.

Estimation of Prestress Force Distribution in the Multi-Strand System of Prestressed Concrete Structures.

Science.gov (United States)

Cho, Keunhee; Park, Sung Yong; Cho, Jeong-Rae; Kim, Sung Tae; Park, Young-Hwan

2015-06-15

Prestressed concrete (PSC) is one of the most reliable, durable and widely used construction materials, which overcomes the weakness of concrete in tension by the introduction of a prestress force. Smart strands enabling measurement of the prestress force have recently been developed to maintain PSC structures throughout their lifetime. However, the smart strand cannot give a representative indication of the whole prestress force when used in multi-strand systems since each strand sustains a different prestress force. In this paper, the actual distribution of the prestress force in a multi-strand system is examined using elastomagnetic (EM) sensors to develop a method for tracking representative indicators of the prestress force using smart strands.

DNA strand breakage repair in ataxia telangiectasia fibroblast-like cells

Energy Technology Data Exchange (ETDEWEB)

Vincent, Jr, R A; Sheridan, III, R B; Huang, P C [Johns Hopkins Univ., Baltimore, Md. (USA). Dept. of Environmental and Biophysical Sciences

1975-12-01

Human diploid fibroblast-like cells derived from four patients with the genetic disease ataxia telangiectasia and from two non-mutant donors were examined for the repair of x-ray induced strand breaks in DNA. The ataxia telangiectasia cultures showed no significant differences from the non-mutant cultures in the kinetics and extent of strand repair. This suggests that the increased spontaneous and x-ray induced chromatid aberrations observed in ataxia telangiectasia cells are not caused by a defect in the repair of single strand breaks as might be suspected from a general model of aberration production.

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

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

Oriented-strand-board- the wave of the future- for the building trade

Science.gov (United States)

Linda Ashton

1984-01-01

Move over, plywood. Oriented-strand board is here. It's less expensive. It's as durable. It has as many uses. And it is the wave of the future. "Oriented-strand board is a direct substitute for plywood" said Jerry Buckner, plant manager for the Martco oriented-strand board plant in Lemoyen. OSB, as it is commonly called, is a structural panel made...

75 FR 62820 - Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA

Science.gov (United States)

2010-10-13

... Providers of Synthetic Double- Stranded DNA AGENCY: Department of Health and Human Services, Office of the.... Government has developed Guidance that provides a framework for screening synthetic double-stranded DNA (dsDNA). This document, the Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA...

Stress-rupture lifetimes of organic fiber-epoxy strands and pressure vessels

International Nuclear Information System (INIS)

Hahn, H.T.; Chiu, I.L.; Gates, T.L.

1979-01-01

Long-term behavior of filament-wound pressure vessels were tested, Kevlar 49 epoxy strands were studied in stress-rupture for more than a year. Because the strands are the smallest structural unit in filament winding, their behavior directly controls the performance of vessels. Five different stress levels were studied: 86, 80, 74, 68, and 50% of the mean ultimate tensile strength (UTS). At each stress level, approximately one-hundred strands were hung in a room maintained at 22 to 24 0 C and below 20% relative humidity. Failure times were automatically recorded by a data acquisition system. Lifetimes were analyzed statistically using a two-parameter Weibull distribution. The maximum-likelihood method was used to estimate the parameters. The shape parameter, which is a measure of scatter and failure-rate change, increased with decreasing stress level. Less scatter and increasing failure rates were observed at lower stresses. There was no sign of an endurance limit down to 68% UTS. At 50% UTS no failure had yet occurred after 9000 h. The strand data were compared with data on lifetimes of pressure vessels wound with the same fiber and epoxy. The strands had slightly longer characteristic lifetimes, except at 86% UTS, and slightly less scatter, except at 68% UTS. The results of this study indicate that strands can provide valuable information about the long-term performance of filament-wound pressure vessels

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.

Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: II. Significant reduction of strand movement and strand damage in short twist pitch CICCs

International Nuclear Information System (INIS)

Sanabria, Carlos; Lee, Peter J; Starch, William; Larbalestier, David C; Devred, Arnaud

2015-01-01

Prototype cable-in-conduit-conductors (CICCs) destined for use in the toroidal field and central solenoid coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3%–7% void fraction increase on the low pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb 3 Sn filament fractures observed in the longer twist pitch conductors. We report here a detailed strand-to-cable analysis of short and longer ‘baseline’ twist pitch CICCs. It was found that the use of internal tin (IT) strands in the longer ‘baseline’ twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of bronze process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the IT strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Conversely, the short twist pitch CICC made from bronze process strands preserved diffusion barrier integrity. (paper)

Late Quaternary slip history of the Mill Creek strand of the San Andreas fault in San Gorgonio Pass, southern California: The role of a subsidiary left-lateral fault in strand switching

Science.gov (United States)

Kendrick, Katherine J.; Matti, Jonathan; Mahan, Shannon

2015-01-01

The fault history of the Mill Creek strand of the San Andreas fault (SAF) in the San Gorgonio Pass region, along with the reconstructed geomorphology surrounding this fault strand, reveals the important role of the left-lateral Pinto Mountain fault in the regional fault strand switching. The Mill Creek strand has 7.1–8.7 km total slip. Following this displacement, the Pinto Mountain fault offset the Mill Creek strand 1–1.25 km, as SAF slip transferred to the San Bernardino, Banning, and Garnet Hill strands. An alluvial complex within the Mission Creek watershed can be linked to palinspastic reconstruction of drainage segments to constrain slip history of the Mill Creek strand. We investigated surface remnants through detailed geologic mapping, morphometric and stratigraphic analysis, geochronology, and pedogenic analysis. The degree of soil development constrains the duration of surface stability when correlated to other regional, independently dated pedons. This correlation indicates that the oldest surfaces are significantly older than 500 ka. Luminescence dates of 106 ka and 95 ka from (respectively) 5 and 4 m beneath a younger fan surface are consistent with age estimates based on soil-profile development. Offset of the Mill Creek strand by the Pinto Mountain fault suggests a short-term slip rate of ∼10–12.5 mm/yr for the Pinto Mountain fault, and a lower long-term slip rate. Uplift of the Yucaipa Ridge block during the period of Mill Creek strand activity is consistent with thermochronologic modeled uplift estimates.

Workshop on effects of chromium coating on Nb3Sn superconductor strand: Proceedings

International Nuclear Information System (INIS)

1994-01-01

This report discusses the following topics: Chromium coating on superconductor strand -- an overview; technology of chromium plating; comparison of wires plated by different platers; search for chromium in copper; strand manufactures' presentations; chromium plating at the Lawrence Livermore National Laboratory; a first look at a chromium plating process development project tailored for T.P.X. and I.T.E.R. strand; and influence of chromium diffusion and related phenomena on the reference ratios of bare and chromium plated Nb 3 Sn strand

Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange.

Science.gov (United States)

Borgogno, María V; Monti, Mariela R; Zhao, Weixing; Sung, Patrick; Argaraña, Carlos E; Pezza, Roberto J

2016-03-04

Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3' end of the initiating DNA strand have a small effect, whereas most mismatches near the 5' end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Performance of Nb3Sn RRP strands and cables based on a 108/127 stack design

International Nuclear Information System (INIS)

Barzi, E.; Ambrosio, G.; Andreev, N.; Bossert, R.; Carcagno, R.; Feher, S.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; Nobrega, F.; Novitski, I.; Pishalnikov, Y.; Sylvester, C.; Tartaglia, M.; Turrioni, D.; Yamada, R.; Zlobin, A.V.; Field, M.; Hong, S.; Parrell, J.; Zhang, Y.

2006-01-01

The high performance Nb 3 Sn strand produced by Oxford Superconducting Technology (OST) with the Restack Rod Process (RRP) is presently considered as a baseline conductor for the Fermilab's accelerator magnet R and D program. To improve the strand stability in the current and field range expected in magnet models, the number of subelements in the strand was increased by a factor of two (from 54 to 108), which resulted in a smaller effective filament size. The performance of the 1.0 and 0.7 mm strands of this design was studied using virgin and deformed strand samples. 27-strand Rutherford cables made of 1 mm strand were also tested using a superconducting transformer, small racetrack and 1-m shell-type dipole coils. This paper presents the RRP strand and cable parameters, and reports the results of strand, cable and coil testing

Stranding of two sperm whales (Physeter macrocephalus) in the "North Sea trap" at Henne Strand, Denmark

DEFF Research Database (Denmark)

Hansen, Mette Sif; Alstrup, Aage K. O.; Hansen, Jørgen H.

2016-01-01

In February 2014 two male sperm whales (Physeter macrocephalus) stranded at Henne Strand, Denmark. One whale (MCE 1644) was found dead, while the other (MCE 1645) was still alive, but drowned during the high tide. To increase our knowledge of sperm whales, conduct forage investigations, post......-mortem and diagnostic examinations were carried out. The decay of the carcasses progressed quickly. The whales had large (MCE 1644) or moderate (MCE 1645) numbers of squid beaks (Gonatus fabricii) in the stomachventricles, but no evidence of recentfresh feeding. Both whales had acute dermatitis probably due to trauma...... severe localized or systemic infections. The finding of large volumes of bloody pleural fluid with large quantities of C. septicum suggests that MCE 1644 died of infection. However, reservations must be taken due to the pronounced decay of the carcass. Sperm whales have strong social bonds where...

Coronavirus minus-strand RNA synthesis and effect of cycloheximide on coronavirus RNA synthesis

International Nuclear Information System (INIS)

Sawicki, S.G.; Sawicki, D.L.

1986-01-01

The temporal sequence of coronavirus plus-strand and minus-strand RNA synthesis was determined in 17CL1 cells infected with the A59 strain of mouse hepatitis virus (MHV). MHV-induced fusion was prevented by keeping the pH of the medium below pH 6.8. This had no effect on the MHV replication cycle, but gave 5- to 10-fold-greater titers of infectious virus and delayed the detachment of cells from the monolayer which permitted viral RNA synthesis to be studied conveniently until at least 10 h postinfection. Seven species of poly(A)-containing viral RNAs were synthesized at early and late times infection, in nonequal but constant ratios. MHV minus-strand RNA synthesis was first detected at about 3 h after infection and was found exclusively in the viral replicative intermediates and was not detected in 60S single-stranded form in infected cells. Early in the replication cycle, from 45 to 65% of the [ 3 H]uridine pulse-labeled RF core of purified MHV replicative intermediates was in minus-strand RNA. The rate of minus-strand synthesis peaked at 5 to 6 h postinfection and then declined to about 20% of the maximum rate. The addition of cycloheximide before 3 h postinfection prevented viral RNA synthesis, whereas the addition of cycloheximide after viral RNA synthesis had begun resulted in the inhibition of viral RNA synthesis. The synthesis of both genome and subgenomic mRNAs and of viral minus strands required continued protein synthesis, and minis-strand RNA synthesis was three- to fourfold more sensitive to inhibition of cycloheximide than was plus-strand synthesis

Strand critical current degradation in $Nb_{3}$ Sn Rutherford cables

CERN Document Server

Barzi, E; Higley, H C; Scanlan, R M; Yamada, R; Zlobin, A V

2001-01-01

Fermilab is developing 11 Tesla superconducting accelerator magnets based on Nb/sub 3/Sn superconductor. Multifilamentary Nb/sub 3/Sn strands produced using the modified jelly roll, internal tin, and powder-in-tube technologies were used for the development and test of the prototype cable. To optimize the cable geometry with respect to the critical current, short samples of Rutherford cable with packing factors in the 85 to 95% range were fabricated and studied. In this paper, the results of measurements of critical current, n-value and RRR made on the round virgin strands and on the strands extracted from the cable samples are presented. (5 refs).

Performance of Nb3Sn RRP strands and cables based on a 108/127 stack design

Energy Technology Data Exchange (ETDEWEB)

Barzi, E.; Ambrosio, G.; Andreev, N.; Bossert, R.; Carcagno, R.; Feher, S.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; Nobrega, F.; Novitski, I.; /Fermilab /Oxford Supercond. Tech., Carteret

2006-08-01

The high performance Nb{sub 3}Sn strand produced by Oxford Superconducting Technology (OST) with the Restack Rod Process (RRP) is presently considered as a baseline conductor for the Fermilab's accelerator magnet R&D program. To improve the strand stability in the current and field range expected in magnet models, the number of subelements in the strand was increased by a factor of two (from 54 to 108), which resulted in a smaller effective filament size. The performance of the 1.0 and 0.7 mm strands of this design was studied using virgin and deformed strand samples. 27-strand Rutherford cables made of 1 mm strand were also tested using a superconducting transformer, small racetrack and 1-m shell-type dipole coils. This paper presents the RRP strand and cable parameters, and reports the results of strand, cable and coil testing.

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

International Nuclear Information System (INIS)

Boye, E.; Krisch, R.E.

1980-01-01

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

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

Czech Academy of Sciences Publication Activity Database

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

2015-01-01

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

Mammalian DNA single-strand break repair: an X-ra(y)ted affair.

Science.gov (United States)

Caldecott, K W

2001-05-01

The genetic stability of living cells is continuously threatened by the presence of endogenous reactive oxygen species and other genotoxic molecules. Of particular threat are the thousands of DNA single-strand breaks that arise in each cell, each day, both directly from disintegration of damaged sugars and indirectly from the excision repair of damaged bases. If un-repaired, single-strand breaks can be converted into double-strand breaks during DNA replication, potentially resulting in chromosomal rearrangement and genetic deletion. Consequently, cells have adopted multiple pathways to ensure the rapid and efficient removal of single-strand breaks. A general feature of these pathways appears to be the extensive employment of protein-protein interactions to stimulate both the individual component steps and the overall repair reaction. Our current understanding of DNA single-strand break repair is discussed, and testable models for the architectural coordination of this important process are presented. Copyright 2001 John Wiley & Sons, Inc.

Axial and transverse stress-strain characterization of the EU dipole high current density Nb{sub 3}Sn strand

Energy Technology Data Exchange (ETDEWEB)

Nijhuis, A; Ilyin, Y; Abbas, W [Faculty of Science and Technology, Low Temperature Division, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands)], E-mail: a.nijhuis@tnw.utwente.nl

2008-06-15

We have measured the critical current (I{sub c}) of a high current density Nb{sub 3}Sn strand subjected to spatial periodic bending, periodic contact stress and uniaxial strain. The strand is destined for the cable-in-conduit conductors (CICC) of the European dipole (EDIPO) 12.5 T superconducting magnet test facility. The spatial periodic bending was applied on the strand, using the bending wavelengths from 5 to 10 mm with a peak bending strain of 1.5%, a periodic contact stress with a periodicity of 4.7 mm and a stress level exceeding 250 MPa. For the uniaxial strain characterization, the voltage-current characteristics were measured with an applied axial strain from -0.9% to +0.3%, with a magnetic field from 6 to 14 T, temperature from 4.2 to 10 K and currents up to almost 900 A. In addition the axial stiffness was determined by a tensile axial stress-strain test. The characterization of the strand is essential for understanding the behaviour of the strand under mainly axial thermal stress variation during cool down and transverse electromagnetic forces during charging, which is essential for the design of the CICC for the dipole magnet. The strand appears to be fully reversible in the compressive regime during the axial strain testing, while in the tensile regime, the behaviour is already irreversibly degraded when reaching the maximum in the critical current versus strain characteristic. The degradation is accentuated by an immediate decrease of the n value by a factor of 2. The parameters for the improved deviatoric strain description are derived from the I{sub c} data, giving the accuracy of the scaling with a standard deviation of 4 A, which is by far within the expected deviation for the large scale strand production of such a high J{sub c} strand. The I{sub c} versus the applied bending strain follows the low resistivity limit, indicative of full interfilament current transfer, while a strong decrease is observed at a peak bending strain of {approx}0

Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure.

Science.gov (United States)

Karro, J E; Peifer, M; Hardison, R C; Kollmann, M; von Grünberg, H H

2008-02-01

The distribution of guanine and cytosine nucleotides throughout a genome, or the GC content, is associated with numerous features in mammals; understanding the pattern and evolutionary history of GC content is crucial to our efforts to annotate the genome. The local GC content is decaying toward an equilibrium point, but the causes and rates of this decay, as well as the value of the equilibrium point, remain topics of debate. By comparing the results of 2 methods for estimating local substitution rates, we identify 620 Mb of the human genome in which the rates of the various types of nucleotide substitutions are the same on both strands. These strand-symmetric regions show an exponential decay of local GC content at a pace determined by local substitution rates. DNA segments subjected to higher rates experience disproportionately accelerated decay and are AT rich, whereas segments subjected to lower rates decay more slowly and are GC rich. Although we are unable to draw any conclusions about causal factors, the results support the hypothesis proposed by Khelifi A, Meunier J, Duret L, and Mouchiroud D (2006. GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol. 62:745-752.) that the isochore structure has been reshaped over time. If rate variation were a determining factor, then the current isochore structure of mammalian genomes could result from the local differences in substitution rates. We predict that under current conditions strand-symmetric portions of the human genome will stabilize at an average GC content of 30% (considerably less than the current 42%), thus confirming that the human genome has not yet reached equilibrium.

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...

Repair and gamma radiation-induced single- and double-strand breaks in DNA of Escherichia coli

International Nuclear Information System (INIS)

Petrov, S.I.

1981-01-01

Studies in the kinetics of repair of γ-radiation-induced single- and double-strand breaks in DNA of E. coli cells showed that double-strand DNA breaks are rejoined by the following two ways. The first way is conditioned by repair of single-strand breaks and represents the repair of ''oblique'' double-strand breaks in DNA, whereas the second way is conditioned by functioning of the recombination mechanisms and, to all appearance, represents the repair of ''direct'' double-strand breaks in DNA

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

Efficient immunoglobulin gene disruption and targeted replacement in rabbit using zinc finger nucleases.

Directory of Open Access Journals (Sweden)

Tatiana Flisikowska

Full Text Available Rabbits are widely used in biomedical research, yet techniques for their precise genetic modification are lacking. We demonstrate that zinc finger nucleases (ZFNs introduced into fertilized oocytes can inactivate a chosen gene by mutagenesis and also mediate precise homologous recombination with a DNA gene-targeting vector to achieve the first gene knockout and targeted sequence replacement in rabbits. Two ZFN pairs were designed that target the rabbit immunoglobulin M (IgM locus within exons 1 and 2. ZFN mRNAs were microinjected into pronuclear stage fertilized oocytes. Founder animals carrying distinct mutated IgM alleles were identified and bred to produce offspring. Functional knockout of the immunoglobulin heavy chain locus was confirmed by serum IgM and IgG deficiency and lack of IgM(+ and IgG(+ B lymphocytes. We then tested whether ZFN expression would enable efficient targeted sequence replacement in rabbit oocytes. ZFN mRNA was co-injected with a linear DNA vector designed to replace exon 1 of the IgM locus with ∼1.9 kb of novel sequence. Double strand break induced targeted replacement occurred in up to 17% of embryos and in 18% of fetuses analyzed. Two major goals have been achieved. First, inactivation of the endogenous IgM locus, which is an essential step for the production of therapeutic human polyclonal antibodies in the rabbit. Second, establishing efficient targeted gene manipulation and homologous recombination in a refractory animal species. ZFN mediated genetic engineering in the rabbit and other mammals opens new avenues of experimentation in immunology and many other research fields.

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.

Development of Nb3Sn strands for ITER in Japan

International Nuclear Information System (INIS)

Isono, T.; Nunoya, Y.; Matsui, K.; Nabara, Y.; Koizumi, N.; Takahashi, Y.; Okuno, K.

2007-01-01

Nb 3 Sn strands for ITER Toroidal Field (TF) coils and Central Solenoids (CS) are required to have both high current density (Jc) and low hysteresis loss. The required Jc at 12 T, 4.2 K and no external strain is lager than 700 A/mm 2 for bronze processed strand and lager than 800 A/mm 2 for internal tin processed one at 12 T, 4.2 K and no external strain. Upper limit of hysteresis loss is 1,000 mJ/cm 3 at 4.2 K and a cycle of ±3 T. Outer diameter is 0.82 mm and 0.83 mm for TF coils and CS, respectively. Area ratio of copper to non copper is one and outer surface is Cr plated. Japan will procure 25% of Nb 3 Sn for ITER TF coils and 100% for ITER CS. There are four Nb 3 Sn strand suppliers in Japan; three of them use bronze process and the other uses internal tin process. For bronze processed strand, increase Jc was achieved by using bronze with high tin content of 15 to 16%. To keep productivity while using the harder bronze with high tin content, Nb is used for barrier in place of Ta. The material is expected to have better adhesion to other materials such as bronze and copper. For internal tin process, size of modules, each of which has a tin rod and a lot of Nb filaments embedded in a copper cylinder, is reduced, while total amount of tin increase in order to satisfy both required high Jc and low hysteresis loss. Each supplier fabricated a strand of more than 0.1 ton for TF coils and succeeded to develop a strand satisfying the ITER requirements of Jc and hysteresis loss. (authors)

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)

Offshore Earthquakes Do Not Influence Marine Mammal Stranding Risk on the Washington and Oregon Coasts

Science.gov (United States)

Grant, Rachel A.; Savirina, Anna

2018-01-01

Simple Summary Marine mammals stranding on coastal beaches is not unusual. However, there appears to be no single cause for this, with several causes being probable, such as starvation, contact with humans (for example boat strike or entanglement with fishing gear), disease, and parasitism. We evaluated marine mammal stranding off the Washington and Oregon coasts and looked at offshore earthquakes as a possible contributing factor. Our analysis showed that offshore earthquakes did not make marine mammals more likely to strand. We also analysed a subset of data from the north of Washington State and found that non-adult animals made up a large proportion of stranded animals, and for dead animals the commonest cause of death was disease, traumatic injury, or starvation. Abstract The causes of marine mammals stranding on coastal beaches are not well understood, but may relate to topography, currents, wind, water temperature, disease, toxic algal blooms, and anthropogenic activity. Offshore earthquakes are a source of intense sound and disturbance and could be a contributing factor to stranding probability. We tested the hypothesis that the probability of marine mammal stranding events on the coasts of Washington and Oregon, USA is increased by the occurrence of offshore earthquakes in the nearby Cascadia subduction zone. The analysis carried out here indicated that earthquakes are at most, a very minor predictor of either single, or large (six or more animals) stranding events, at least for the study period and location. We also tested whether earthquakes inhibit stranding and again, there was no link. Although we did not find a substantial association of earthquakes with strandings in this study, it is likely that there are many factors influencing stranding of marine mammals and a single cause is unlikely to be responsible. Analysis of a subset of data for which detailed descriptions were available showed that most live stranded animals were pups, calves, or

Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

Directory of Open Access Journals (Sweden)

Yu Xiu-Juan

2007-10-01

Full Text Available Abstract Background The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. It is interesting to mention that almost all bacterial genomes exhibit the same kind of base asymmetry. This work aims to investigate the strand biases in Chlamydia muridarum genome and show the potential of the Z curve method for quantitatively differentiating genes on the leading and lagging strands. Results The occurrence frequencies of bases of protein-coding genes in C. muridarum genome were analyzed by the Z curve method. It was found that genes located on the two strands of replication have distinct base usages in C. muridarum genome. According to their positions in the 9-D space spanned by the variables u1 – u9 of the Z curve method, K-means clustering algorithm can assign about 94% of genes to the correct strands, which is a few percent higher than those correctly classified by K-means based on the RSCU. The base usage and codon usage analyses show that genes on the leading strand have more G than C and more T than A, particularly at the third codon position. For genes on the lagging strand the biases is reverse. The y component of the Z curves for the complete chromosome sequences show that the excess of G over C and T over A are more remarkable in C. muridarum genome than in other bacterial genomes without separating base and/or codon usages. Furthermore, for the genomes of Borrelia burgdorferi, Treponema pallidum, Chlamydia muridarum and Chlamydia trachomatis, in which distinct base and/or codon usages have been observed, closer phylogenetic distance is found compared with other bacterial genomes. Conclusion The nature of the strand biases of base composition in C. muridarum is similar to that in most other bacterial genomes. However, the base composition asymmetry between the leading and lagging strands in C. muridarum is more significant than that in

Investigations of radiation-induced strand breaks of poly(U) in aqueous solutions

International Nuclear Information System (INIS)

Lemaire, D.G.E.

1984-01-01

DNA strand breaks induced by γ irradiation were studied in polyuridylic acid (Poly(U)), a single-strand model substance with a single base. Poly(U) in diluted, aqueous solution was irradiated in a Co-γ source, and the 100 eV yields of strand breaks (Cr values) were determined on the basis of the loss of molecular weight. The molecular weight was determined by small-angle laser light scattering. (orig./PW) [de

Electron attachment to DNA single strands: gas phase and aqueous solution.

Science.gov (United States)

Gu, Jiande; Xie, Yaoming; Schaefer, Henry F

2007-01-01

The 2'-deoxyguanosine-3',5'-diphosphate, 2'-deoxyadenosine-3',5'-diphosphate, 2'-deoxycytidine-3',5'-diphosphate and 2'-deoxythymidine-3',5'-diphosphate systems are the smallest units of a DNA single strand. Exploring these comprehensive subunits with reliable density functional methods enables one to approach reasonable predictions of the properties of DNA single strands. With these models, DNA single strands are found to have a strong tendency to capture low-energy electrons. The vertical attachment energies (VEAs) predicted for 3',5'-dTDP (0.17 eV) and 3',5'-dGDP (0.14 eV) indicate that both the thymine-rich and the guanine-rich DNA single strands have the ability to capture electrons. The adiabatic electron affinities (AEAs) of the nucleotides considered here range from 0.22 to 0.52 eV and follow the order 3',5'-dTDP > 3',5'-dCDP > 3',5'-dGDP > 3',5'-dADP. A substantial increase in the AEA is observed compared to that of the corresponding nucleic acid bases and the corresponding nucleosides. Furthermore, aqueous solution simulations dramatically increase the electron attracting properties of the DNA single strands. The present investigation illustrates that in the gas phase, the excess electron is situated both on the nucleobase and on the phosphate moiety for DNA single strands. However, the distribution of the extra negative charge is uneven. The attached electron favors the base moiety for the pyrimidine, while it prefers the 3'-phosphate subunit for the purine DNA single strands. In contrast, the attached electron is tightly bound to the base fragment for the cytidine, thymidine and adenosine nucleotides, while it almost exclusively resides in the vicinity of the 3'-phosphate group for the guanosine nucleotides due to the solvent effects. The comparatively low vertical detachment energies (VDEs) predicted for 3',5'-dADP(-) (0.26 eV) and 3',5'-dGDP(-) (0.32 eV) indicate that electron detachment might compete with reactions having high activation barriers

Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands.

Science.gov (United States)

Barboiu, Mihail; Stadler, Adrian-Mihail; Lehn, Jean-Marie

2016-03-18

General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

Science.gov (United States)

Zhang, Z.; Birkedal, V.; Gothelf, K. V.

2016-05-01

The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts, which can be detected by a shift in the fluorescence resonance energy transfer signal between dyes attached to the DNA strands. In the present study we have integrated an ATP aptamer in the strand B and demonstrated the optical detection of ATP. Furthermore we explore a new readout method using a split G-quadruplex DNAzyme for colorimetric readout of the detection of streptavidin by the naked eye. Finally, we integrate the whole G-quadruplex DNAzyme system in a single DNA strand and show that it is applicable to colorimetric detection.

Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

DEFF Research Database (Denmark)

Zhang, Zhao; Birkedal, Victoria; Gothelf, Kurt Vesterager

2016-01-01

The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts, w...... G-quadruplex DNAzyme for colorimetric readout of the detection of streptavidin by the naked eye. Finally, we integrate the whole G-quadruplex DNAzyme system in a single DNA strand and show that it is applicable to colorimetric detection......., which can be detected by a shift in the fluorescence resonance energy transfer signal between dyes attached to the DNA strands. In the present study we have integrated an ATP aptamer in the strand B and demonstrated the optical detection of ATP. Furthermore we explore a new readout method using a split...

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.

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

DNA Strand Breaks in Mitotic Germ Cells of Caenorhabditis elegans Evaluated by Comet Assay

Science.gov (United States)

Park, Sojin; Choi, Seoyun; Ahn, Byungchan

2016-01-01

DNA damage responses are important for the maintenance of genome stability and the survival of organisms. Such responses are activated in the presence of DNA damage and lead to cell cycle arrest, apoptosis, and DNA repair. In Caenorhabditis elegans, double-strand breaks induced by DNA damaging agents have been detected indirectly by antibodies against DSB recognizing proteins. In this study we used a comet assay to detect DNA strand breaks and to measure the elimination of DNA strand breaks in mitotic germline nuclei of C. elegans. We found that C. elegans brc-1 mutants were more sensitive to ionizing radiation and camptothecin than the N2 wild-type strain and repaired DNA strand breaks less efficiently than N2. This study is the first demonstration of direct measurement of DNA strand breaks in mitotic germline nuclei of C. elegans. This newly developed assay can be applied to detect DNA strand breaks in different C. elegans mutants that are sensitive to DNA damaging agents. PMID:26903030

Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium.

Science.gov (United States)

Fern, Joshua; Schulman, Rebecca

2017-09-15

The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers of cell or tissue behavior. DNA-based molecular circuits, in particular DNA strand-displacement circuits, provide simple and effective biocompatible control mechanisms and sensors, but are vulnerable to digestion by nucleases present in living tissues and serum-supplemented cell culture. The stability of double-stranded and single-stranded DNA circuit components in serum-supplemented cell medium and the corresponding effect of nuclease-mediated degradation on circuit performance were characterized to determine the major routes of degradation and DNA strand-displacement circuit failure. Simple circuit design choices, such as the use of 5' toeholds within the DNA complexes used as reactants in the strand-displacement reactions and the termination of single-stranded components with DNA hairpin domains at the 3' termini, significantly increase the functional lifetime of the circuit components in the presence of nucleases. Simulations of multireaction circuits, guided by the experimentally measured operation of single-reaction circuits, enable predictive realization of multilayer and competitive-reaction circuit behavior. Together, these results provide a basic route to increased DNA circuit stability in cell culture environments.

Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic

Science.gov (United States)

Prado, Jonatas H. F.; Mattos, Paulo H.; Silva, Kleber G.; Secchi, Eduardo R.

2016-01-01

Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574), South American fur seal, (n = 3,419), South American sea lion (n = 2,049), bottlenose dolphins (n = 293) and subantarctic fur seal (n = 219) were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal) and warm-water (e.g. rough-toothed dolphin) species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to climate change

Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic.

Directory of Open Access Journals (Sweden)

Jonatas H F Prado

Full Text Available Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574, South American fur seal, (n = 3,419, South American sea lion (n = 2,049, bottlenose dolphins (n = 293 and subantarctic fur seal (n = 219 were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal and warm-water (e.g. rough-toothed dolphin species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to

Necropsy report of a fin whale (Balaenoptera physalus) stranded in Denmark in 2010

DEFF Research Database (Denmark)

Alstrup, Aage K. O.; Hedayat, Abdi; Jensen, Trine Hammer

2013-01-01

There is little detailed information on stranded fin whales (Balaenoptera physalus) in the scientific literature (Notarbartolo di Sciara et al., 2003). In Denmark, at least eight fin whales stranded between the years 1603 and 1958 (Kinze, 1995). On 16 June 2010, a live subadult or adult male fin...... whale stranded in the Bay of Vejle (55º 69' N, 9º 58' E), Denmark. Despite several attempts, it was not possible to rescue the fin whale, which was only partially exposed by the water. The fin whale succumbed after 5 d stranded in shallow water. The dead fin whale was transported to a nearby pier...

Statistical Assessment of Cetacean Stranding Events in Cape Cod (Massachusetts, USA) area.

Science.gov (United States)

Zellar, R.; Pulkkinen, A. A.; Moore, K.; Reeb, D.; Karakoylu, E.; Uritskaya, O.

2017-12-01

Cetacean (whales, dolphins and porpoises) mass strandings are a longstanding mystery in the field of marine biology that continue to be recorded in coastal environments around the world. For each of these events, anywhere from a few to several hundred otherwise healthy animals strand in onshore environments, often for no apparent reason. While the causes of these events remain unclear, anthropogenic and naturogenic mechanisms have been suggested. We present results of an inter-disciplinary study that draws expertise from space weather, marine mammal biology and ecology, and marine mammal stranding response. This study assessed 16 years of cetacean stranding events in the Cape Cod (Massachusetts, USA) area concurrently with a large dataset of meteorological, geophysical, biological, oceanographic and space weather data to produce inferences about possible causes for these unexplained events.

Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

OpenAIRE

Khodakov, Dmitriy A.; Khodakova, Anastasia S.; Huang, David M.; Linacre, Adrian; Ellis, Amanda V.

2015-01-01

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 doubl...

A delay time model for a mission-based system subject to periodic and random inspection and postponed replacement

International Nuclear Information System (INIS)

Yang, Li; Ma, Xiaobing; Zhai, Qingqing; Zhao, Yu

2016-01-01

We propose an inspection and replacement policy for a single component system that successively executes missions with random durations. The failure process of the system can be divided into two states, namely, normal and defective, following the delay time concept. Inspections are carried out periodically and immediately after the completion of each mission (random inspections). The failed state is always identified immediately, whereas the defective state can only be revealed by an inspection. If the system fails or is defective at a periodic inspection, then replacement is immediate. If, however, the system is defective at a random inspection, then replacement will be postponed if the time to the subsequent periodic inspection is shorter than a pre-determined threshold, and immediate otherwise. We derive the long run expected cost per unit time and then investigate the optimal periodic inspection interval and postponement threshold. A numerical example is presented to demonstrate the applicability of the proposed maintenance policy. - Highlights: • A delay time model of inspection is introduced for mission-based systems. • Periodic and random inspections are performed to check the state. • Replacement of the defective system at a random inspection can be postponed.

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

Strand Tension Control in Anchor Span for Suspension Bridge Using Dynamic Balance Theory

Directory of Open Access Journals (Sweden)

Da Wang

Full Text Available Abstract Strand tension control is essential in suspension bridge safety. However, few quantitative studies have examined the bending rigidity and boundary condition behavior of strands in the anchor span of suspension bridges because of their special structure and complex configuration. In this paper, a new calculation method for strand tension is explored by using dynamic balance theory to determine the effect of bending rigidity and boundary conditions. The accuracy and effectiveness of the proposed method are tested and confirmed with verification examples and application on Nanxi Yangtze Suspension Bridge in China. The results indicated that only low-order frequency calculation could be used to calculate the strand tension without considering the effect of bending rigidity to ensure control accuracy. The influence of bending rigidity on the control precision is related to the tension and the length of the strands, which is significantly determined by the specific value between the stress rigidity and the bending rigidity. The uncertain boundary conditions of the anchor span cable, which are fixed between consolidated and hinged, also have a major effect on the control accuracy. To improve the accuracy of strand tension control, the least squares method is proposed during the tension construction control of the anchor span. This approach can significantly improve the accuracy of the tension control of the main cable strand. Some recommendations for future bridge analysis are provided based on the results of this study.

Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii

OpenAIRE

Stroud, A. L.

2012-01-01

Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. The roles of RPA include stabilising and protecting single- stranded DNA from nuclease degradation during DNA replication and repair. To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA. Haloferax volcanii encodes three RPAs – RPA1, RPA2 and RPA3, of which rpa1 and rpa3 are in operons with genes encoding associated proteins (APs). ...

Genetic transformation of Neisseria gonorrhoeae shows a strand preference

OpenAIRE

Duffin, Paul M.; Seifert, H. Steven

2012-01-01

Natural transformation is the main means of horizontal genetic exchange in the obligate human pathogen Neisseria gonorrhoeae. Neisseria spp. have been shown to preferentially take up and transform their own DNA by recognizing a non-palindromic 10 or 12 nucleotide DNA uptake sequence (DUS10 or DUS12). We investigated the ability of the DUS12 to enhance single-stranded DNA (ssDNA) transformation. Given the non-palindromic nature of the DUS12, we tested whether both strands of the DUS equally en...

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.

Replacement policy in a system under shocks following a Markovian arrival process

International Nuclear Information System (INIS)

Montoro-Cazorla, Delia; Perez-Ocon, Rafael; Carmen Segovia, Maria del

2009-01-01

We present a system subject to shocks that arrive following a Markovian arrival process. The system is minimally repaired. It is replaced when a certain number of shocks arrive. A general model where the replacements are governed by a discrete phase-type distribution is studied. For this system, the Markov process governing the system is constructed, and the interarrival times between replacements and the number of replacements are calculated. A special case of this system is when it can stand a prefixed number of shocks. For this new system, the same performance measures are calculated. The systems are considered in transient and stationary regime

Replacement policy in a system under shocks following a Markovian arrival process

Energy Technology Data Exchange (ETDEWEB)

Montoro-Cazorla, Delia [Department of Statistics and Operational Research, University of Jaen (Spain); Perez-Ocon, Rafael [Department of Statistics and Operational Research, University of Granada, Granada (Spain)], E-mail: rperezo@ugr.es; Carmen Segovia, Maria del [Departamento de Estadistica e I.O., University of Granada, Granada (Spain)

2009-02-15

We present a system subject to shocks that arrive following a Markovian arrival process. The system is minimally repaired. It is replaced when a certain number of shocks arrive. A general model where the replacements are governed by a discrete phase-type distribution is studied. For this system, the Markov process governing the system is constructed, and the interarrival times between replacements and the number of replacements are calculated. A special case of this system is when it can stand a prefixed number of shocks. For this new system, the same performance measures are calculated. The systems are considered in transient and stationary regime.

Magnetization Losses of Roebel Cable Samples with 2G YBCO Coated Conductor Strands

CERN Document Server

Yang, Y.; Falorio, I.; Young, E.A.; Kario, A.; Goldacker, W.; Dhallé, M. M. J.; van Nugteren, J.; Kirby, G.; Bottura, L.; Ballarino, A.

2016-01-01

Roebel cable with 2G YBCO strands is one of the promising HTS solutions of fully transposed high current conductors for high field accelerator magnets. Following the considerable research effort on the manufacturing of Roebel cables in recent years, sample conductors are now available in useful lengths with reproducible performances to allow detailed characterizations beyond the standard critical current measurements. The ac loss and strands coupling are of significant interest for the field quality of the accelerator magnets. We report a set of systematic ac loss measurements on two different Roebel cable samples prepared for the EuCARD2 collaboration. The measurements were performed over a wide range of temperature between 5 K and 90 K and the results were analyzed in the context of strands architecture and coupling. The results show that the transposed bundles are partially decoupled and the strands in transposition sections behave as an isolated single tape if the strands are insulated.

Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions

International Nuclear Information System (INIS)

Mahapatro, Ajit K; Jeong, Kyung J; Lee, Gil U; Janes, David B

2007-01-01

This paper presents a study of sequence specific electronic conduction through short (15-base-pair) double-stranded (ds) DNA molecules, measured by immobilizing 3 ' -thiol-derivatized DNAs in nanometre scale gaps between gold electrodes. The polycation spermidine was used to stabilize the ds-DNA structure, allowing electrical measurements to be performed in a dry state. For specific sequences, the conductivity was observed to scale with the surface density of immobilized DNA, which can be controlled by the buffer concentration. A series of 15-base DNA oligonucleotide pairs, in which the centre sequence of five base pairs was changed from G:C to A:T pairs, has been studied. The conductivity per molecule is observed to decrease exponentially with the number of adjacent A:T pairs replacing G:C pairs, consistent with a barrier at the A:T sites. Conductance-based devices for short DNA sequences could provide sensing approaches with direct electrical readout, as well as label-free detection

Age Replacement and Service Rate Control of Stochastically Degrading Queues

National Research Council Canada - National Science Library

Chapin, Patrick

2004-01-01

This thesis considers the problem of optimally selecting a periodic replacement time for a multiserver queueing system in which each server is subject to degradation as a function of the mean service...

Breaks in plasmid DNA strand induced by laser radiation at a wavelength of 193 nm

International Nuclear Information System (INIS)

Gurzadyan, G.G.; Shul'te Frolinde, D.

1996-01-01

DNA of plasmid pB322 irradiated with laser at a wavelength of 193 nm was treated with an extract containing proteins from E.coli K12 AB1157 (wild-type). The enzymes were found to produce single- and double-strand DNA breaks, which was interpreted as a transformation of a portion of cyclobutane pyrimidine dimers and (6-4) photoproducts into nonrepairable single-strand DNA breaks. The products resulted from ionization of DNA, in particular, single-strand breaks, transform to double-strand breaks. A comparison of these data with the data on survival of plasmid upon transformation of E.coli K12 AB1157 enables one to assess the biological significance of single- and double-strand breaks. The inactivation of the plasmid is mainly determined by the number of directly formed laser-induced single-strand breaks. 26 refs.; 2 figs

7 CFR 301.75-15 - Funds for the replacement of commercial citrus trees.

Science.gov (United States)

2010-01-01

... 7 Agriculture 5 2010-01-01 2010-01-01 false Funds for the replacement of commercial citrus trees... trees. Subject to the availability of appropriated funds, the owner of a commercial citrus grove may be eligible to receive funds to replace commercial citrus trees in accordance with the provisions of this...

Paul Strand y las paradojas de la modernidad americana

Directory of Open Access Journals (Sweden)

Vicente Sánchez Biosca

2010-06-01

Full Text Available As contribuições de Strand para o cinema estão estreitamente relacionadas com seus trabalhos fotográficos da época e mesmo com um olhar que, apesar de suas múltiplas diferenças, possui muitos pontos em comum. Se em Manhatta (1920, Strand (em colaboração com Sheeler oferece uma síntese da natureza e da modernidade, em Redes (1934 o que predomina, em contrapartida, é a experiência da arte muralista mexicana e a influência de Eisenstein (em suas andanças por México são os fatores que determinam seus esforços na construção de uma épica dos operários. Mas sem dúvida, o projeto mais ambicioso de Strand (ao mando da produtora Frontier Films foi Native Land, o filme que atendeu às demandas do American Popular Front e as moldou nas palavras dos fundadores da pátria americana.

IHF-independent assembly of the Tn10 strand transfer transpososome: implications for inhibition of disintegration

OpenAIRE

Stewart, Barry J.; Wardle, Simon J.; Haniford, David B.

2002-01-01

The frequency of DNA transposition in transposition systems that employ a strand transfer step may be significantly affected by the occurrence of a disintegration reaction, a reaction that reverses the strand transfer event. We have asked whether disintegration occurs in the Tn10 transposition system. We show that disintegration substrates (substrates constituting one half of the strand transfer product) are assembled into a transpososome that mimics the strand transfer intermediate. This str...

Chirality induction and protonation-induced molecular motions in helical molecular strands.

Science.gov (United States)

Kolomiets, Elena; Berl, Volker; Lehn, Jean-Marie

2007-01-01

The long oligopyridinedicarboxamide strand 9, containing 15 heterocyclic rings has been synthesized and its helical structure determined by X-ray crystallography. It was shown that the shorter analogue 6 displays induced circular dichroism and amplification of induced chirality upon dissolution in an optically active solvent, diethyl-L-tartrate. A novel class of helical foldamers was prepared, strands 14-16, based on two oligopyridine carboxamide segments linked through a L-tartaric acid derived spacer. These tartro strands display internal chirality induction as well as chirality amplification. NMR spectroscopy (on 8 and 9) and circular dichroism (on 16) studies show that the oligopyridine carboxamide strands undergo reversible unfolding/folding upon protonation. The protonation-induced unfolding has been confirmed by X-ray crystallographic determination of the molecular structure of the extended protonated heptameric form 8(+). The molecular-scale mechano-chemical motions of the protonation-induced structural switching consist of a change of the length of the molecule, from 6 angstroms (6, coiled form) to 29 angstroms (8(+), uncoiled form) for the heptamer and from 12.5 angstroms (9, coiled form, X-ray structure) to 57 angstroms (9(+), uncoiled form, from modeling) for the pentadecamer. Similar unfolding/folding motional processes take place in the L-tartro strands 15 and 16 upon protonation/deprotonation, with loss of helicity-induced circular dichroism on unfolding as shown for the protonated form 16(+).

Evolutionary implications of inversions that have caused intra-strand parity in DNA

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Wei John

2007-06-01

Full Text Available Abstract Background Chargaff's rule of DNA base composition, stating that DNA comprises equal amounts of adenine and thymine (%A = %T and of guanine and cytosine (%C = %G, is well known because it was fundamental to the conception of the Watson-Crick model of DNA structure. His second parity rule stating that the base proportions of double-stranded DNA are also reflected in single-stranded DNA (%A = %T, %C = %G is more obscure, likely because its biological basis and significance are still unresolved. Within each strand, the symmetry of single nucleotide composition extends even further, being demonstrated in the balance of di-, tri-, and multi-nucleotides with their respective complementary oligonucleotides. Results Here, we propose that inversions are sufficient to account for the symmetry within each single-stranded DNA. Human mitochondrial DNA does not demonstrate such intra-strand parity, and we consider how its different functional drivers may relate to our theory. This concept is supported by the recent observation that inversions occur frequently. Conclusion Along with chromosomal duplications, inversions must have been shaping the architecture of genomes since the origin of life.

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.

Sequential strand displacement beacon for detection of DNA coverage on functionalized gold nanoparticles.

Science.gov (United States)

Paliwoda, Rebecca E; Li, Feng; Reid, Michael S; Lin, Yanwen; Le, X Chris

2014-06-17

Functionalizing nanomaterials for diverse analytical, biomedical, and therapeutic applications requires determination of surface coverage (or density) of DNA on nanomaterials. We describe a sequential strand displacement beacon assay that is able to quantify specific DNA sequences conjugated or coconjugated onto gold nanoparticles (AuNPs). Unlike the conventional fluorescence assay that requires the target DNA to be fluorescently labeled, the sequential strand displacement beacon method is able to quantify multiple unlabeled DNA oligonucleotides using a single (universal) strand displacement beacon. This unique feature is achieved by introducing two short unlabeled DNA probes for each specific DNA sequence and by performing sequential DNA strand displacement reactions. Varying the relative amounts of the specific DNA sequences and spacing DNA sequences during their coconjugation onto AuNPs results in different densities of the specific DNA on AuNP, ranging from 90 to 230 DNA molecules per AuNP. Results obtained from our sequential strand displacement beacon assay are consistent with those obtained from the conventional fluorescence assays. However, labeling of DNA with some fluorescent dyes, e.g., tetramethylrhodamine, alters DNA density on AuNP. The strand displacement strategy overcomes this problem by obviating direct labeling of the target DNA. This method has broad potential to facilitate more efficient design and characterization of novel multifunctional materials for diverse applications.

Comparison Between Nb3Al and Nb3Sn Strands and Cables for High Field Accelerator Magnets

Energy Technology Data Exchange (ETDEWEB)

Yamada, R.; Kikuchi, A.; Barzi, E.; Chlachidze, G.; Rusy, A.; Takeuchi, T.; Tartaglia, M.; Turrioni, D.; Velev, V.; Wake, M.; Zlobin, A.V.; /Fermilab

2010-01-01

The Nb{sub 3}Al small racetrack magnet, SR07, has been successfully built and tested to its short sample limit beyond 10 Tesla without any training. Thus the practical application of Nb{sub 3}Al strands for high field accelerator magnets is established. The characteristics of the representative F4 strand and cable, are compared with the typical Nb{sub 3}Sn strand and cable. It is represented by the OST high current RRP Nb{sub 3}Sn strand with 108/127 configuration. The effects of Rutherford cabling to both type strands are explained and the inherent problem of the Nb{sub 3}Sn strand is discussed. Also the test results of two representative small racetrack magnets are compared from the stand point of Ic values, and training. The maximum current density of the Nb{sub 3}Al strands is still smaller than that of the Nb{sub 3}Sn strands, but if we take into account of the stress-strain characteristics, Nb{sub 3}Al strands become somewhat favorable in some applications.

Missing Strands? Dealing with Hair Loss

Science.gov (United States)

... 2017 Print this issue Missing Strands? Dealing with Hair Loss En español Send us your comments Hair loss is often associated with men and aging, but ... or their treatments, and many other things cause hair loss. The most common type of hair loss is ...

The stranding anomaly as population indicator: the case of harbour porpoise Phocoena phocoena in North-Western Europe.

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Helene Peltier

Full Text Available Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990-2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005. This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna.

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.

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.

Study in regularities in the formation of double stranded DNA breaks in irradiated rat thymocytes

International Nuclear Information System (INIS)

Ivannik, B.P.; ProskuryakoV, S.Ya.; Ryabchenko, N.I.

1979-01-01

Using low-gradient viscosimetry of neutral detergent nuclear lysates a study was made of postradiation changes in the molecular weight of double-stranded DNA of thymocytes. It was established that 375 eV are needed for one double-stranded break to appear, and a dose of 1 rad is required for 0.275 double-stranded break to occur at the site of DNA with m.w. 10 12 dalton. The repair of double-stranded breaks is only observed when rats are exposed to a dose of 500 R. It is assumed that the absence of repair of double-stranded DNA breaks and the presence of secondary postradiation degradation of DNA are responsible for thymocyte death

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

Enzymatic induction of DNA double-strand breaks in γ-irradiated Escherichia coli K-12

International Nuclear Information System (INIS)

Bonura, T.; Smith, K.C.; Kaplan, H.S.

1975-01-01

The polA1 mutation increases the sensitivity of E. coli K-12 to killing by γ-irradiation in air by a factor of 2.9 and increases the yield of DNA double-strand breaks by a factor of 2.5. These additional DNA double-strand breaks appear to be due to the action of nucleases in the polA1 strain rather than to the rejoining of radiation-induced double-strand breaks in the pol + strain. This conclusion is based upon the observation that γ-irradiation at 3 0 did not affect the yield of DNA double-strand breaks in the pol + strain, but decreased the yield in the polA1 strain by a factor of 2.2. Irradiation of the polA1 strain at 3 0 followed by incubation at 3 0 for 20 min before plating resulted in approximately a 1.5-fold increase in the D 0 . The yield of DNA double-strand breaks was reduced by a factor of 1.5. The pol + strain, however, did not show the protective effect of the low temperature incubation upon either survival or DNA double-strand breakage. We suggest that the increased yield of DNA double-strand breaks in the polA 1 strain may be the result of the unsuccessful excision repair of ionizing radiation-induced dna base damage

Three methods to determine the yields of DNA double-strand breaks

International Nuclear Information System (INIS)

Erzgraeber, G.; Lapidus, I.L.

1985-01-01

A possibility of determining the yield of DNA double-strand breaks in cells of the Chinese hamster (V79-4) by finding the amount of DNA released as a result of breaks and by determining the relative sedimentation velocity of DNA-membrane complexes affected by ionizing radiations with different physical characteristics is discussed. Results of the analysis are compared with the data obtained by a traditional method of sedimentation in the neutral sucrose density gradient. Comparative characterization of the methods is discussed. The yields of DNA double-strand breaks determined by the suggested independent methods are in good agreement, which opens possibilities of studying induction and repair of double-strand breaks by means of simpler and more reliable methods

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

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Andronescu Mirela

2008-08-01

Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

Comparison of DNA strand-break simulated with different DNA models

International Nuclear Information System (INIS)

Xie, Wenzhang; Li, Junli; Qiu, Rui; Yan, Congchong; Zeng, Zhi; Li, Chunyan

2013-01-01

Full text of the publication follows. In Monte Carlo simulation of DNA damage, the geometric model of DNA is of great importance. To study the influence of DNA model on the simulation of DNA damage, three DNA models were created in this paper. They were a volume model and two atomic models with different parameters. Direct DNA strand-break induced by low-energy electrons were simulated respectively with the three models. The results show that most of the energy depositions in the DNA segments do not lead to strand-breaks. The simple single strand-break (SSB) tends to be the predominant damage type, and the contribution of complex double strand-break (DSB) to the total DSB cannot be neglected. Among the yields of all the three DNA target models applied here, the yields of the volume model are the highest, the yields of the atomic model with double van der Waals radii (r) take the second place, whereas the yields of the atomic model with single r come last. On average, the ratios of SSB yields are approximately equivalent to the corresponding ratios of the models' volume. However, there seems to be no clear relationship between the DSB yields and the models' volume. (authors)

Real-time monitoring of enzyme-free strand displacement cascades by colorimetric assays

Science.gov (United States)

Duan, Ruixue; Wang, Boya; Hong, Fan; Zhang, Tianchi; Jia, Yongmei; Huang, Jiayu; Hakeem, Abdul; Liu, Nannan; Lou, Xiaoding; Xia, Fan

2015-03-01

The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications.The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications. Electronic supplementary information (ESI) available: Experimental procedures and analytical data are provided. See DOI: 10.1039/c5nr00697j

Multiple pathways of DNA double-strand break processing in a mutant Indian muntjac cell line

International Nuclear Information System (INIS)

Bouffler, S.D.; Jha, B.; Johnson, R.T.

1990-01-01

DNA break processing is compared in the Indian muntjac cell lines, SVM and DM. The initial frequencies and resealing of X-ray generated single- and double-strand breaks are similar in the two cell lines. Inhibiting the repair of UV damage leads to greater double-strand breakage in SVM than in DM, and some of these breaks are not repaired; however, repair-associated single-strand breakage and resealing are normal. Dimethylsulfate also induces excess double-strand breakage in SVM, and these breaks are irreparable. Restricted plasmids are reconstituted correctly in SVM at approximately 30% of the frequency observed in DM. Thus SVM has a reduced capacity to repair certain types of double-strand break. This defect is not due to a DNA ligase deficiency. We conclude that DNA double-strand breaks are repaired by a variety of pathways within mammalian cells and that the structure of the break or its mode of formation determines its subsequent fate

Resumption of menstruation and pituitary response to gonadotropin-releasing hormone in functional hypothalamic amenorrhea subjects undertaking estrogen replacement therapy.

Science.gov (United States)

Shen, Z Q; Xu, J J; Lin, J F

2013-11-01

Functional hypothalamic amenorrhea (FHA) refers to a functional menstrual disorder with various causes and presentations. Recovery of menstrual cyclicity is common in long-term follow-up but the affecting factors remain unknown. To explore factors affecting the menstrual resumption and to evaluate the pituitary response to gonadotropin-releasing hormone (GnRH) in FHA. Thirty cases with FHA were recruited. All subjects were put on continuous 1 mg/day estradiol valerate orally and followed up monthly. Recovery was defined as the occurrence of at least three consecutive regular cycles. Responder referred to those who recovered within two years of therapy. Gonadotropin response to the 50 μg GnRH challenge was tested every three months. Nineteen (63.3%) subjects recovered with a mean time to recovery of 26.8 months. Time to recovery was negatively correlated with body mass index (BMI) before and by amenorrhea. Twentyone cases had undertaken therapy for more than two years and 10 of them recovered. BMI before and by amenorrhea were negatively correlated with the recovery. Significant increase of serum luteinizing hormone (LH) and LH response to GnRH were noted after recovery. Menstrual resumption was common in FHA undertaking estrogen replacement therapy (ERT). The likelihood of recovery was affected by their BMI before and by amenorrhea but not by the weight gain during therapy. Low serum LH and attenuated LH response to GnRH were the main features of pituitary deficiency in FHA. The menstrual resumption in FHA was accompanied by the recovery of serum LH and the LH response to GnRH.

Withdrawal Strength of Dowels in Plywood and Oriented Strand Board

OpenAIRE

ERDİL, Yusuf Z.; ECKELMAN, Carl A.

2001-01-01

Plywood and oriented strand board (OSB) are being used increasingly in the construction of upholstered furniture frames. Yet there is little information available concerning the holding strength of various fasteners, and, in particular, dowels in these materials. A study was conducted accordingly, to obtain basic information about the holding strength of dowels in both plywood and oriented strand board. Results of the tests were incorporated into predictive expressions that allow designers to...

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

Human Cell Assays for Synthesis-Dependent Strand Annealing and Crossing over During Double-Strand Break Repair.

Science.gov (United States)

Zapotoczny, Grzegorz; Sekelsky, Jeff

2017-04-03

DNA double-strand breaks (DSBs) are one of the most deleterious types of lesions to the genome. Synthesis-dependent strand annealing (SDSA) is thought to be a major pathway of DSB repair, but direct tests of this model have only been conducted in budding yeast and Drosophila To better understand this pathway, we developed an SDSA assay for use in human cells. Our results support the hypothesis that SDSA is an important DSB repair mechanism in human cells. We used siRNA knockdown to assess the roles of a number of helicases suggested to promote SDSA. None of the helicase knockdowns reduced SDSA, but knocking down BLM or RTEL1 increased SDSA. Molecular analysis of repair products suggests that these helicases may prevent long-tract repair synthesis. Since the major alternative to SDSA (repair involving a double-Holliday junction intermediate) can lead to crossovers, we also developed a fluorescent assay that detects crossovers generated during DSB repair. Together, these assays will be useful in investigating features and mechanisms of SDSA and crossover pathways in human cells. Copyright © 2017 Zapotoczny and Sekelsky.

Human Cell Assays for Synthesis-Dependent Strand Annealing and Crossing over During Double-Strand Break Repair

Directory of Open Access Journals (Sweden)

Grzegorz Zapotoczny

2017-04-01

Full Text Available DNA double-strand breaks (DSBs are one of the most deleterious types of lesions to the genome. Synthesis-dependent strand annealing (SDSA is thought to be a major pathway of DSB repair, but direct tests of this model have only been conducted in budding yeast and Drosophila. To better understand this pathway, we developed an SDSA assay for use in human cells. Our results support the hypothesis that SDSA is an important DSB repair mechanism in human cells. We used siRNA knockdown to assess the roles of a number of helicases suggested to promote SDSA. None of the helicase knockdowns reduced SDSA, but knocking down BLM or RTEL1 increased SDSA. Molecular analysis of repair products suggests that these helicases may prevent long-tract repair synthesis. Since the major alternative to SDSA (repair involving a double-Holliday junction intermediate can lead to crossovers, we also developed a fluorescent assay that detects crossovers generated during DSB repair. Together, these assays will be useful in investigating features and mechanisms of SDSA and crossover pathways in human cells.

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.

7 CFR 301.75-17 - Funds for the replacement of certified citrus nursery stock.

Science.gov (United States)

2010-01-01

... 7 Agriculture 5 2010-01-01 2010-01-01 false Funds for the replacement of certified citrus nursery... nursery stock. Subject to the availability of appropriated funds, a commercial citrus nursery may be eligible to receive funds to replace certified citrus nursery stock in accordance with the provisions of...

Fatigue Characteristic of Chopped Strand Mat/Polyester Composite

Directory of Open Access Journals (Sweden)

I Made Astika

2012-11-01

Full Text Available The application of composite as an alternatif material to substitute of metal has better properties than metal such as light, high elasticity, corrosion and fatigue resistance. Some components in its application are subjected to millions of varying stress cycles that initiated to fatigue failure such as crack, delamination and fracture. The strength of composite is influenced by construction, fiber type, orientation and fiber fraction. The objective of this experiment is to investigate the fatigue characteristic on SCM composite. Material composite to be used is glass fiber with chopped strand mat (CSM as fiber and Yukalac 157 BQTN-EX with 1% hardener (Mexpox as matrix. The mold process was built with hand lay-up. Fiber volume fractions in composite are 40, 32 and 24 %. The tests to be done on composite are fatigue and tensile test. The research show that the increasing of fiber fraction in composite affects increasing of fatigue life, endurance limit and tensile strength. Fatigue failure modes of composite are debonding, matrix cracking, delamination and fiber fracture.

Hip joint replacement

Science.gov (United States)

Hip arthroplasty; Total hip replacement; Hip hemiarthroplasty; Arthritis - hip replacement; Osteoarthritis - hip replacement ... Your hip joint is made up of 2 major parts. One or both parts may be replaced during surgery: ...

Interaction of Ddc1 and RPA with single-stranded/double-stranded DNA junctions in yeast whole cell extracts: Proteolytic degradation of the large subunit of replication protein A in ddc1Δ strains.

Science.gov (United States)

Sukhanova, Maria V; D'Herin, Claudine; Boiteux, Serge; Lavrik, Olga I

2014-10-01

To characterize proteins that interact with single-stranded/double-stranded (ss/ds) DNA junctions in whole cell free extracts of Saccharomyces cerevisiae, we used [(32)P]-labeled photoreactive partial DNA duplexes containing a 3'-ss/ds-junction (3'-junction) or a 5'-ss/ds-junction (5'-junction). Identification of labeled proteins was achieved by MALDI-TOF mass spectrometry peptide mass fingerprinting and genetic analysis. In wild-type extract, one of the components of the Ddc1-Rad17-Mec3 complex, Ddc1, was found to be preferentially photocrosslinked at a 3'-junction. On the other hand, RPAp70, the large subunit of the replication protein A (RPA), was the predominant crosslinking product at a 5'-junction. Interestingly, ddc1Δ extracts did not display photocrosslinking of RPAp70 at a 5'-junction. The results show that RPAp70 crosslinked to DNA with a 5'-junction is subject to limited proteolysis in ddc1Δ extracts, whereas it is stable in WT, rad17Δ, mec3Δ and mec1Δ extracts. The degradation of the RPAp70-DNA adduct in ddc1Δ extract is strongly reduced in the presence of the proteasome inhibitor MG 132. We also addressed the question of the stability of free RPA, using anti-RPA antibodies. The results show that RPAp70 is also subject to proteolysis without photocrosslinking to DNA upon incubation in ddc1Δ extract. The data point to a novel property of Ddc1, modulating the turnover of DNA binding proteins such as RPAp70 by the proteasome. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison of range of motion and function of subjects with reverse anatomy Bayley-Walker shoulder replacement with those of normal subjects.

Science.gov (United States)

Masjedi, Milad; Lovell, Cara; Johnson, Garth R

2011-12-01

Patients with rotator cuff tear and degenerative shoulder joint disease commonly experience severe pain and reduced performance during activities of daily living. A popular way to treat these patients is by means of reverse anatomy shoulder prosthesis. Studying the kinematics of subjects with reverse anatomy implant would be useful in order to gain knowledge about functionality of different designs. It is hypothesized that the kinematics of these subjects, in the absence of rotator cuff muscles, differs from that of normal subjects. In this study the upper limb kinematics of 12 subjects with a Bayley-Walker reverse anatomy shoulder prosthesis while performing tasks common in everyday activities and those that represent the range of motion was analyzed and compared to that of 12 normal subjects. Each patient also completed an Oxford Shoulder Score. Substantial reduction in the Bayley-Walker subjects' ranges of motion was observed compared to normal subjects. The mean abduction angle decreased from 109° (±20) for normal subjects to 64° (±25). A similar trend was observed during flexion and axial rotation tasks. Furthermore, the normal group showed less variable ranges of motion performing the standard tasks, whereas for the prosthetic group this varied greatly, which is likely to be dependent on muscle strength. Although the decreased range of motion was prominent, subjects were able to complete most of the tasks by compensating with their elbow and trunk. The most challenging task for Bayley-Walker subjects was lifting an object to head height. Copyright © 2010 Elsevier B.V. All rights reserved.

The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces

Science.gov (United States)

Mao, Xizeng; Zhang, Han; Yin, Yanbin; Xu, Ying

2012-01-01

The majority of bacterial genes are located on the leading strand, and the percentage of such genes has a large variation across different bacteria. Although some explanations have been proposed, these are at most partial explanations as they cover only small percentages of the genes and do not even consider the ones biased toward the lagging strand. We have carried out a computational study on 725 bacterial genomes, aiming to elucidate other factors that may have influenced the strand location of genes in a bacterium. Our analyses suggest that (i) genes of some functional categories such as ribosome have higher preferences to be on the leading strands; (ii) genes of some functional categories such as transcription factor have higher preferences on the lagging strands; (iii) there is a balancing force that tends to keep genes from all moving to the leading and more efficient strand and (iv) the percentage of leading-strand genes in an bacterium can be accurately explained based on the numbers of genes in the functional categories outlined in (i) and (ii), genome size and gene density, indicating that these numbers implicitly contain the information about the percentage of genes on the leading versus lagging strand in a genome. PMID:22735706

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.)

Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

DEFF Research Database (Denmark)

Nielsen, Lisbeth Munksgård; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

2012-01-01

Circular dichroism spectra (176–330 nm) of RNA adenine oligomers, (rA)n (n = 1–10, 12, 15, and 20), reveal electronic coupling between two bases in short strands. The number of interacting bases in long strands is more and larger than that reported previously for the corresponding DNA strands....

Transmission pricing and stranded costs in the electric power industry

International Nuclear Information System (INIS)

Baumol, W.J.; Sidak, J.G.

1995-09-01

Stranded costs are those costs that electric utilities are currently permitted to recover through their rates but whose recovery may be impeded or prevented by the advent of competition in the industry. Estimates of these costs run from the tens to the hundreds of billions of dollars. Should regulators permit utilities to recover stranded costs while they take steps to promote competition in the electric power industry. William Baumol and J. Gregory Sidak argue that answer to that question should be yes.The authors show that a transmission price, the price for sending electricity over the transmission grid, can be determined in a manner that is compatible with economic efficiency and clearly neutral in its effects upon all competitors in electricity generation. A correctly constructed regime of transmission pricing may in fact achieve the efficiency and equity goals that justify the recovery of stranded costs

Informal Science learning in PIBID: identifying and interpreting the strands

Directory of Open Access Journals (Sweden)

Thomas Barbosa Fejolo

2013-10-01

Full Text Available This paper presents a research on informal Science learning in the context of the Institutional Scholarship Program Initiation to Teaching (PIBID. We take as reference the strands of informal Science learning (FAC, representing six dimensions of learning, they are: 1 Development of interest in Science; 2 Understanding of scientific knowledge; 3 Engaging in scientific reasoning; 4 Reflection on Science; 5 Engagement in scientific practice; 6 Identification with Science. For the lifting data, it was used the filming record of the interactions and dialogues of undergraduate students while performing activities of Optical Spectroscopy in the laboratory. Based on the procedures of content analysis and interpretations through communication, we investigate which of the six strands were present during the action of the students in activities. As a result we have drawn a learning profile for each student by distributing communications in different strands of informal Science learning.

7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

Science.gov (United States)

2010-01-01

... 7 Agriculture 11 2010-01-01 2010-01-01 false RUS specification for seven wire galvanized steel..., ACCEPTABLE MATERIALS, AND STANDARD CONTRACT FORMS § 1755.370 RUS specification for seven wire galvanized... Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1, 1990...

Enhanced Strain Measurement Range of an FBG Sensor Embedded in Seven-Wire Steel Strands.

Science.gov (United States)

Kim, Jae-Min; Kim, Chul-Min; Choi, Song-Yi; Lee, Bang Yeon

2017-07-18

FBG sensors offer many advantages, such as a lack of sensitivity to electromagnetic waves, small size, high durability, and high sensitivity. However, their maximum strain measurement range is lower than the yield strain range (about 1.0%) of steel strands when embedded in steel strands. This study proposes a new FBG sensing technique in which an FBG sensor is recoated with polyimide and protected by a polyimide tube in an effort to enhance the maximum strain measurement range of FBG sensors embedded in strands. The validation test results showed that the proposed FBG sensing technique has a maximum strain measurement range of 1.73% on average, which is 1.73 times higher than the yield strain of the strands. It was confirmed that recoating the FBG sensor with polyimide and protecting the FBG sensor using a polyimide tube could effectively enhance the maximum strain measurement range of FBG sensors embedded in strands.

Reconstitution of a eukaryotic replisome reveals suppression mechanisms that define leading/lagging strand operation

Science.gov (United States)

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

2015-01-01

We have reconstituted a eukaryotic leading/lagging strand replisome comprising 31 distinct polypeptides. This study identifies a process unprecedented in bacterial replisomes. While bacteria and phage simply recruit polymerases to the fork, we find that suppression mechanisms are used to position the distinct eukaryotic polymerases on their respective strands. Hence, Pol ε is active with CMG on the leading strand, but it is unable to function on the lagging strand, even when Pol δ is not present. Conversely, Pol δ-PCNA is the only enzyme capable of extending Okazaki fragments in the presence of Pols ε and α. We have shown earlier that Pol δ-PCNA is suppressed on the leading strand with CMG (Georgescu et al., 2014). We propose that CMG, the 11-subunit helicase, is responsible for one or both of these suppression mechanisms that spatially control polymerase occupancy at the fork. DOI: http://dx.doi.org/10.7554/eLife.04988.001 PMID:25871847

77 FR 2958 - Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To...

Science.gov (United States)

2012-01-20

... DEPARTMENT OF COMMERCE International Trade Administration [A-549-820] Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To Request Administrative Review AGENCY... prestressed concrete steel wire strand (``PC Strand'') from Thailand. See Antidumping or Countervailing Duty...

Rigidity of the polypeptide backbone in the triple-stranded collagen molecule.

Science.gov (United States)

Nemethy, G

1981-02-01

Conformational energy computations were carried out on collagen-like triple-stranded conformations of several polytripeptides with the structure CH3CO(GXY)3NHCH3, where X and Y can be Pro, Ala, or Gly. The computed minimum-energy conformations for various sequences are compared with that computed earlier for poly(Gly-Pro-Pro). Usually, substitution of Ala or Gly residues for Pro does not cause any strain or distortion of the conformation of the triple-stranded complex. Thus, the structure is a very stable and essentially rigid one. Unfavorable interactions were found only in the case of CH3CO(Gly-Ala-Pro)NHCH3. These interactions are a consequence of differences between the residue geometry of Ala and Pro. They result in small changes of some backbone dihedral angles and in an increase of intra- and interchain energies. The presence of a single Gly-Ala-Pro tripeptide within a sequence of Gly-Pro-Pro tripeptides is not sufficient, however, to cause even a small distoration of the triple strand. No deviation of the peptide groups from planarity is required to stabilize the triple-stranded structure.

Magnetization anomaly of Nb3Al strands and instability of Nb3Al Rutherford cables

International Nuclear Information System (INIS)

Yamada, Ryuji; Kikuchi, Akihiro; Wake, Masayoshi

2006-01-01

Using a Cu stabilized Nb 3 Al strand with Nb matrix, a 30 meter long Nb 3 Al Rutherford cable was made by a collaboration of Fermilab and NIMS. Recently the strand and cable were tested. In both cases instability was observed at around 1.5 Tesla. The magnetization of this Nb 3 Al strand was measured first using a balanced coil magnetometer at 4.2 K. Strands showed an anomalously large magnetization behavior around at 1.6 T, which is much higher than the usual B c2 ∼ 0.5 Tesla (4.2 K) of Nb matrix. This result is compared with the magnetization data of short strand samples using a SQUID magnetometer, in which a flux-jump signal was observed at 0.5 Tesla, but not at higher field. As a possible explanation for this magnetization anomaly, the interfilament coupling through the thin Nb films in the strands is suggested. The instability problem observed in low field tests of the Nb 3 Al Rutherford cables is attributed to this effect

Short, multiple-stranded β-hairpin peptides have antimicrobial potency with high selectivity and salt resistance.

Science.gov (United States)

Chou, Shuli; Shao, Changxuan; Wang, Jiajun; Shan, Anshan; Xu, Lin; Dong, Na; Li, Zhongyu

2016-01-01

The β-hairpin structure has been proposed to exhibit potent antimicrobial properties with low cytotoxicity, thus, multiple β-hairpin structures have been proved to be highly stable in structures containing tightly packed hydrophobic cores. The aim of this study was to develop peptide-based synthetic strategies for generating short, but effective AMPs as inexpensive antimicrobial agents. Multiple-stranded β-hairpin peptides with the same β-hairpin unit, (WRXxRW)n where n=1, 2, 3, or 4 and Xx represent the turn sequence, were synthesized, and their potential as antimicrobial agents was evaluated. Owning to the tightly packed hydrophobic core and paired Trp of this multiple-stranded β-hairpin structure, all the 12-residues peptides exhibited high cell selectivity towards bacterial cells over human red blood cells (hRBCs), and the peptide W2 exhibited stronger antimicrobial activities with the MIC values of 2-8μM against various tested bacteria. Not only that, but W2 also showed obvious synergy with streptomycin and chloramphenicol against Escherichia coli, and displayed synergy with ciprofloxacin against Staphylococcus aureus with the FICI values ⩽0.5. Fluorescence spectroscopy and electron microscopy analyses indicated that W2 kills microbial cells by permeabilizing the cell membrane and damaging membrane integrity. Collectively, based on the multiple β-hairpin peptides, the ability to develop libraries of short and effective peptides will be a powerful approach to the discovery of novel antimicrobial agents. We successfully screened a peptide W2 ((WRPGRW)2) from a series of multiple-stranded β-hairpin antimicrobial peptides based on the "S-shaped" motif that induced the formation of a globular structure, and Trp zipper was used to replace the disulfide bonds to reduce the cost of production. This novel structure applied to AMPs improved cell selectivity and salt stability. The findings of this study will promote the development of peptide

Two-dimensional numerical simulation of flow around three-stranded rope

Science.gov (United States)

Wang, Xinxin; Wan, Rong; Huang, Liuyi; Zhao, Fenfang; Sun, Peng

2016-08-01

Three-stranded rope is widely used in fishing gear and mooring system. Results of numerical simulation are presented for flow around a three-stranded rope in uniform flow. The simulation was carried out to study the hydrodynamic characteristics of pressure and velocity fields of steady incompressible laminar and turbulent wakes behind a three-stranded rope. A three-cylinder configuration and single circular cylinder configuration are used to model the three-stranded rope in the two-dimensional simulation. The governing equations, Navier-Stokes equations, are solved by using two-dimensional finite volume method. The turbulence flow is simulated using Standard κ-ɛ model and Shear-Stress Transport κ-ω (SST) model. The drag of the three-cylinder model and single cylinder model is calculated for different Reynolds numbers by using control volume analysis method. The pressure coefficient is also calculated for the turbulent model and laminar model based on the control surface method. From the comparison of the drag coefficient and the pressure of the single cylinder and three-cylinder models, it is found that the drag coefficients of the three-cylinder model are generally 1.3-1.5 times those of the single circular cylinder for different Reynolds numbers. Comparing the numerical results with water tank test data, the results of the three-cylinder model are closer to the experiment results than the single cylinder model results.

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.)

Prediction of guide strand of microRNAs from its sequence and secondary structure

Directory of Open Access Journals (Sweden)

Ahmed Firoz

2009-04-01

Full Text Available Abstract Background MicroRNAs (miRNAs are produced by the sequential processing of a long hairpin RNA transcript by Drosha and Dicer, an RNase III enzymes, and form transitory small RNA duplexes. One strand of the duplex, which incorporates into RNA-induced silencing complex (RISC and silences the gene expression is called guide strand, or miRNA; while the other strand of duplex is degraded and called the passenger strand, or miRNA*. Predicting the guide strand of miRNA is important for better understanding the RNA interference pathways. Results This paper describes support vector machine (SVM models developed for predicting the guide strands of miRNAs. All models were trained and tested on a dataset consisting of 329 miRNA and 329 miRNA* pairs using five fold cross validation technique. Firstly, models were developed using mono-, di-, and tri-nucleotide composition of miRNA strands and achieved the highest accuracies of 0.588, 0.638 and 0.596 respectively. Secondly, models were developed using split nucleotide composition and achieved maximum accuracies of 0.553, 0.641 and 0.602 for mono-, di-, and tri-nucleotide respectively. Thirdly, models were developed using binary pattern and achieved the highest accuracy of 0.708. Furthermore, when integrating the secondary structure features with binary pattern, an accuracy of 0.719 was seen. Finally, hybrid models were developed by combining various features and achieved maximum accuracy of 0.799 with sensitivity 0.781 and specificity 0.818. Moreover, the performance of this model was tested on an independent dataset that achieved an accuracy of 0.80. In addition, we also compared the performance of our method with various siRNA-designing methods on miRNA and siRNA datasets. Conclusion In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex. This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their

Conformal geometry and invariants of 3-strand Brownian braids

International Nuclear Information System (INIS)

Nechaev, Sergei; Voituriez, Raphael

2005-01-01

We propose a simple geometrical construction of topological invariants of 3-strand Brownian braids viewed as world lines of 3 particles performing independent Brownian motions in the complex plane z. Our construction is based on the properties of conformal maps of doubly-punctured plane z to the universal covering surface. The special attention is paid to the case of indistinguishable particles. Our method of conformal maps allows us to investigate the statistical properties of the topological complexity of a bunch of 3-strand Brownian braids and to compute the expectation value of the irreducible braid length in the non-Abelian case

Possible causes of a harbour porpoise mass stranding in Danish waters in 2005.

Directory of Open Access Journals (Sweden)

Andrew J Wright

Full Text Available An unprecedented 85 harbour porpoises stranded freshly dead along approximately 100 km of Danish coastline from 7-15 April, 2005. This total is considerably above the mean weekly stranding rate for the whole of Denmark, both for any time of year, 1.23 animals/week (ranging from 0 to 20 during 2003-2008, excluding April 2005, and specifically in April, 0.65 animals/week (0 to 4, same period. Bycatch was established as the cause of death for most of the individuals through typical indications of fisheries interactions, including net markings in the skin and around the flippers, and loss of tail flukes. Local fishermen confirmed unusually large porpoise bycatch in nets set for lumpfish (Cyclopterus lumpus and the strandings were attributed to an early lumpfish season. However, lumpfish catches for 2005 were not unusual in terms of season onset, peak or total catch, when compared to 2003-2008. Consequently, human activity was combined with environmental factors and the variation in Danish fisheries landings (determined through a principal component analysis in a two-part statistical model to assess the correlation of these factors with both the presence of fresh strandings and the numbers of strandings on the Danish west coast. The final statistical model (which was forward selected using Akaike information criterion; AIC indicated that naval presence is correlated with higher rates of porpoise strandings, particularly in combination with certain fisheries, although it is not correlated with the actual presence of strandings. Military vessels from various countries were confirmed in the area from the 7th April, en route to the largest naval exercise in Danish waters to date (Loyal Mariner 2005, 11-28 April. Although sonar usage cannot be confirmed, it is likely that ships were testing various equipment prior to the main exercise. Thus naval activity cannot be ruled out as a possible contributing factor.

Untangling the Strands of the Fourteenth Amendment.

Science.gov (United States)

Lupu, Ira C.

1979-01-01

Explores trends in the Court's interpretation of the libertarian and egalitarian dimensions of the Fourteenth Amendment and offers a theory of the two strands. Available from Michigan Law Review, Hutchins Hall, Ann Arbor, MI 48109; single issues $3.50. (Author/IRT)

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.

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

Ontario electricity industry restructuring : preliminary asset valuation and calculation of stranded debt

International Nuclear Information System (INIS)

1998-01-01

The rationale for restructuring Ontario's electricity industry was restated. Financial elements of the Government's White Paper on the electrical industry included the following: (1) establishing a level playing field on taxes and regulation, (2) restructuring Ontario Hydro into new companies with clear business mandates, and (3) taking action to put the new companies on solid financial ground. To achieve these objectives requires valuation of the new companies as a key part in the restructuring process. This Ministry of Finance document contains preliminary estimates of the total debt and liabilities of Ontario Hydro ($ 39.1 billion), the value of the new generation and service companies ($ 15.8 billion), and the stranded debt ($ 23.3 billion, less the value of dedicated revenue streams of $ 15.4 billion, equal to the residual stranded debt of $ 7.9 billion). The method by which the stranded debt was calculated is also described. It is stressed that the overriding principles governing the financial restructuring plan are to achieve restructuring without increasing electricity rates, to retain maximum value in the electricity sector until stranded debt is retired, and to recover stranded debt from the electricity sector and not from taxpayers. Ministry advisors indicate that these preliminary valuations would allow the new companies to operate as commercial companies in a competitive market and receive investment grade credit ratings. 44 figs

Double Strand Break Repair, one mechanism can hide another: Alternative non-homologous end joining

International Nuclear Information System (INIS)

Rass, E.; Grabarz, A.; Bertrand, P.; Lopez, B.S.

2012-01-01

DNA double strand breaks are major cytotoxic lesions encountered by the cells. They can be induced by ionizing radiation or endogenous stress and can lead to genetic instability. Two mechanisms compete for the repair of DNA double strand breaks: homologous recombination and non-homologous end joining (NHEJ). Homologous recombination requires DNA sequences homology and is initiated by single strand resection. Recently, advances have been made concerning the major steps and proteins involved in resection. NHEJ, in contrast, does not require sequence homology. The existence of a DNA double strand break repair mechanism, independent of KU and ligase IV, the key proteins of the canonical non homologous end joining pathway, has been revealed lately and named alternative non homologous end joining. The hallmarks of this highly mutagenic pathway are deletions at repair junctions and frequent use of distal micro-homologies. This mechanism is also initiated by a single strand resection of the break. The aim of this review is firstly to present recent data on single strand resection, and secondly the alternative NHEJ pathway, including a discussion on the fidelity of NHEJ. Based on current knowledge, canonical NHEJ does not appear as an intrinsically mutagenic mechanism, but in contrast, as a conservative one. The structure of broken DNA ends actually dictates the quality repair of the alternative NHEJ and seems the actual responsible for the mutagenesis attributed beforehand to the canonical NHEJ. The existence of this novel DNA double strand breaks repair mechanism needs to be taken into account in the development of radiosensitizing strategies in order to optimise the efficiency of radiotherapy. (authors)

Shoulder replacement - discharge

Science.gov (United States)

Total shoulder arthroplasty - discharge; Endoprosthetic shoulder replacement - discharge; Partial shoulder replacement - discharge; Partial shoulder arthroplasty - discharge; Replacement - shoulder - discharge; Arthroplasty - shoulder - discharge

The general atomic strand winding machine

International Nuclear Information System (INIS)

Matt, P.

1976-01-01

In conjunction with the integrated development of their high temperature gas cooled reactors (HTGR), General Atomic of San Diego, USA, also developed a strand winding system for the horizontal prestressing of pressure vessels. The machine lay-out, its capabilities and the test program carried out in the laboratory and on a full scale pressure vessel model are described. (author)

The (not so immortal strand hypothesis

Directory of Open Access Journals (Sweden)

Cristian Tomasetti

2015-03-01

Significance: Utilizing an approach that is fundamentally different from previous efforts to confirm or refute the immortal strand hypothesis, we provide evidence against non-random segregation of DNA during stem cell replication. Our results strongly suggest that parental DNA is passed randomly to stem cell daughters and provides new insight into the mechanism of DNA replication in stem cells.

The Mismatch-Binding Factor MutSβ Can Mediate ATR Activation in Response to DNA Double-Strand Breaks

Czech Academy of Sciences Publication Activity Database

Burdová, Kamila; Mihaljevic, B.; Sturzenegger, A.; Chappidi, N.; Janščák, Pavel

2015-01-01

Roč. 59, č. 4 (2015), s. 603-614 ISSN 1097-2765 R&D Projects: GA ČR GAP305/10/0281; GA ČR(CZ) GA14-05743S Grant - others:Oncosuisse(CH) KLS-02344-02-2009; Swiss National Science Foundation(CH) 31003A_146206; Novartis Foundation for Medical and Biological Research(CH) 11A16 Institutional support: RVO:68378050 Keywords : Ataxia telangiectasia-mutated and Rad3-related (ATR) protein kinase * DNA-damage response * DNA Double-Strand Breaks Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 13.958, year: 2015

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

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

NARCIS (Netherlands)

Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it

NbTi Strands Verification for ITER PF CICC Process Qualification of CNDA

Science.gov (United States)

Liu, F.; Liu, H.; Liu, S.; Liu, B.; Lei, L.; Wu, Y.

2014-05-01

China is in charge of most of Poloidal Field (PF) conductors production for the International Thermonuclear Experimental Reactor (ITER). The execution for PF conductors shall be in three main phases. According to ITER Procurement Arrangement (PA), the Domestic Agency (DA) shall be required to verify the room and low temperature acceptance tests carried out by the strand suppliers. As the reference laboratory of Chinese DA (CNDA), the superconducting strands test laboratory of Institute of Plasma Physics, Chinese Academy of Sciences (ASIPP) was undertaking the task of strands verification for ITER conductors. The verification test includes: diameter, Nickel plating thickness, copper-to-non-copper volume ratio, twist pitch direction and length, standard critical current (IC) and resistive transition index (n), residual resistance ration (RRR), and hysteresis loss. 48 NbTi strands with 7 billets were supplied for the PF Cable-In-Conduit Conductor (CICC) process qualification. In total, 54 samples were measured. The verification level for PF CICC process qualification was 100%. The test method, facility and results of each item are described in detail in this publication.

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

OpenAIRE

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

2017-01-01

Abstract Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3?ddR5p) at the 3?-terminus of the strand break. Interestingly, this strand scission process leaves an electr...

THE INSTABILITY AND NON-EXISTENCE OF MULTI-STRANDED LOOPS WHEN DRIVEN BY TRANSVERSE WAVES

Energy Technology Data Exchange (ETDEWEB)

Magyar, N.; Van Doorsselaere, T., E-mail: norbert.magyar@wis.kuleuven.be [Centre for Mathematical Plasma Astrophysics (CmPA), KU Leuven, Celestijnenlaan 200B bus 2400, 3001 Leuven (Belgium)

2016-06-01

In recent years, omni-present transverse waves have been observed in all layers of the solar atmosphere. Coronal loops are often modeled as a collection of individual strands in order to explain their thermal behavior and appearance. We perform three-dimensional (3D) ideal magnetohydrodynamics simulations to study the effect of a continuous small amplitude transverse footpoint driving on the internal structure of a coronal loop composed of strands. The output is also converted into synthetic images, corresponding to the AIA 171 and 193 Å passbands, using FoMo. We show that the multi-stranded loop ceases to exist in the traditional sense of the word, because the plasma is efficiently mixed perpendicularly to the magnetic field, with the Kelvin–Helmholtz instability acting as the main mechanism. The final product of our simulation is a mixed loop with density structures on a large range of scales, resembling a power-law. Thus, multi-stranded loops are unstable to driving by transverse waves, and this raises strong doubts on the usability and applicability of coronal loop models consisting of independent strands.

Detection of DNA strand breaks in mammalian cells using the radioresistant bacterium PprA protein

International Nuclear Information System (INIS)

Satoh, Katsuya; Wada, Seiichi; Narumi, Issay; Kikuchi, Masahiro; Funayama, Tomoo; Kobayashi, Yasuhiko

2003-01-01

We have previously found that the PprA protein from Deinococcus radiodurans possesses ability to recognize DNA carrying strand breaks. In the present study, we attempted to visualize radiation-induced DNA strand breaks with PprA protein using immunofluorescence technique to elucidate the DNA damage response mechanism in mammalian cultured cells. As a result, colocalization of Cy2 and DAPI fluorescent signals was observed. This observation suggests that DNA strand breaks in the nucleus of CHO-K1 cells were effectively detected using the PprA protein. The amount of DNA strand breaks (integrated density of Cy2 fluorescent signals) was increased with the increase in the radiation dose. (author)

Industry participation workshop: Chromium electroplating of superconductor strand. Proceedings

International Nuclear Information System (INIS)

1994-01-01

The primary objective of the workshop was to inform US plating vendors about the opportunity to participate in the effort on Cr plating of large quantities of superconducting wires required for the ITER and the TPX projects and DOE's interest in developing several reliable and high quality suppliers of Chromium plating services for the superconducting strand industry. The objective was also to inform plating vendors about the Cr plating technology developed in LLNL and invite interested plating vendors to get the technology. Finally the workshop was intended to inform the plating vendors about the plan to get verification of capability of two to four vendors for Cr plating of superconducting strands

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....

Effects of hyperthermia on repair of radiation-induced DNA strand breaks

International Nuclear Information System (INIS)

Mills, M.D.; Meyn, R.E.

1981-01-01

Previous reports have suggested a relationship between the heat-induced changes in nucleoprotein and the hyperthermic enhancement of radiation sensitivity. In an effort to further understand these relationships, we measured the level of initial DNA strand break damage and the DNA strand break rejoining kinetics in Chinese hamster ovary cells following combined hyperthermia and ionizing radiation treatments. The amount of protein associated with DNA measured as the ratio of [ 3 H)leucine to [ 14 C]thymidine was also compared in chromatin isolated from both heated and unheated cells. The results of these experiments show that the initial level of radiation-induced DNA strand breaks is significantly enhanced by a prior hyperthermia treatment of 43 0 C for 30 min. Treatments at higher temperatures and longer treatments at the same temperature magnified this effect. Hyperthermia was also shown to cause a substantial inhibition of the DNA strand break rejoining after irradiation. Both the initial level of DNA damage and the rejoining kinetics recovered to normal levels with incubation at 37 0 C between the hyperthermia and radiation treatments. Recovery of these parameters coincided with the return of the amount of protein associated with DNA to normal values, further suggesting a relationship between the changes in nucleoprotein and the hyperthermic enhancement of radiation sensivivity

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks.

Science.gov (United States)

Chen, Yuan-Jyue; Rao, Sundipta D; Seelig, Georg

2015-11-25

DNA nanotechnology requires large amounts of highly pure DNA as an engineering material. Plasmid DNA could meet this need since it is replicated with high fidelity, is readily amplified through bacterial culture and can be stored indefinitely in the form of bacterial glycerol stocks. However, the double-stranded nature of plasmid DNA has so far hindered its efficient use for construction of DNA nanostructures or devices that typically contain single-stranded or branched domains. In recent work, it was found that nicked double stranded DNA (ndsDNA) strand displacement gates could be sourced from plasmid DNA. The following is a protocol that details how these ndsDNA gates can be efficiently encoded in plasmids and can be derived from the plasmids through a small number of enzymatic processing steps. Also given is a protocol for testing ndsDNA gates using fluorescence kinetics measurements. NdsDNA gates can be used to implement arbitrary chemical reaction networks (CRNs) and thus provide a pathway towards the use of the CRN formalism as a prescriptive molecular programming language. To demonstrate this technology, a multi-step reaction cascade with catalytic kinetics is constructed. Further it is shown that plasmid-derived components perform better than identical components assembled from synthetic DNA.

MEIOB targets single-strand DNA and is necessary for meiotic recombination.

Directory of Open Access Journals (Sweden)

Benoit Souquet

Full Text Available Meiotic recombination is a mandatory process for sexual reproduction. We identified a protein specifically implicated in meiotic homologous recombination that we named: meiosis specific with OB domain (MEIOB. This protein is conserved among metazoan species and contains single-strand DNA binding sites similar to those of RPA1. Our studies in vitro revealed that both recombinant and endogenous MEIOB can be retained on single-strand DNA. Those in vivo demonstrated the specific expression of Meiob in early meiotic germ cells and the co-localization of MEIOB protein with RPA on chromosome axes. MEIOB localization in Dmc1 (-/- spermatocytes indicated that it accumulates on resected DNA. Homologous Meiob deletion in mice caused infertility in both sexes, due to a meiotic arrest at a zygotene/pachytene-like stage. DNA double strand break repair and homologous chromosome synapsis were impaired in Meiob (-/- meiocytes. Interestingly MEIOB appeared to be dispensable for the initial loading of recombinases but was required to maintain a proper number of RAD51 and DMC1 foci beyond the zygotene stage. In light of these findings, we propose that RPA and this new single-strand DNA binding protein MEIOB, are essential to ensure the proper stabilization of recombinases which is required for successful homology search and meiotic recombination.

Protection for low current superconducting coils wound with insulated strand cable

International Nuclear Information System (INIS)

Satti, J.

1980-09-01

The insulated strand cable concept for winding of low current superconducting coil leads to an ideal quench protection by induction coupling. A superconducting secondary loop was made within a cable of a 6.2 Henry dipole coil. When quenching occurred, current was induced in the secondary strand above the critical value. The normal strand quenched the whole cable due to good thermal contact. The secondary loop works as a heater turned on as the wire becomes normal throughout the coil. With a well spread quench, the energy dissipation density is decreased thus preventing local burnout. The mechanism is possible because of close coupling that is present in the insulated cable as in bifilar winding. For the coil tested a 12 strand cable was used, thus a favorable 11 to 1 turn ratio was obtained for the primary to secondary. The superconductor in the secondary had a lower resistance until the critical current was achieved. A theoretical explanation is described for a simplified circuit. Test on the dipole coil with four individual shells showed that the one shell protected with the induced coupling heater always had a more rapid reduction of current. The induced coupling heater tested and explained in this paper works automatically and does not rely on mechanical or electrical devices

Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand.

Science.gov (United States)

Yasukawa, Takehiro; Reyes, Aurelio; Cluett, Tricia J; Yang, Ming-Yao; Bowmaker, Mark; Jacobs, Howard T; Holt, Ian J

2006-11-15

Using two-dimensional agarose gel electrophoresis, we show that mitochondrial DNA (mtDNA) replication of birds and mammals frequently entails ribonucleotide incorporation throughout the lagging strand (RITOLS). Based on a combination of two-dimensional agarose gel electrophoretic analysis and mapping of 5' ends of DNA, initiation of RITOLS replication occurs in the major non-coding region of vertebrate mtDNA and is effectively unidirectional. In some cases, conversion of nascent RNA strands to DNA starts at defined loci, the most prominent of which maps, in mammalian mtDNA, in the vicinity of the site known as the light-strand origin.

Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes

International Nuclear Information System (INIS)

Venema, J.; van Hoffen, A.; Karcagi, V.; Natarajan, A.T.; van Zeeland, A.A.; Mullenders, L.H.

1991-01-01

The authors have measured the removal of UV-induced pyrimidine dimers from DNA fragments of the adenosine deaminase (ADA) and dihydrofolate reductase (DHFR) genes in primary normal human and xeroderma pigmentosum complementation group C (XP-C) cells. Using strand-specific probes, we show that in normal cells, preferential repair of the 5' part of the ADA gene is due to the rapid and efficient repair of the transcribed strand. Within 8 h after irradiation with UV at 10 J m-2, 70% of the pyrimidine dimers in this strand are removed. The nontranscribed strand is repaired at a much slower rate, with 30% dimers removed after 8 h. Repair of the transcribed strand in XP-C cells occurs at a rate indistinguishable from that in normal cells, but the nontranscribed strand is not repaired significantly in these cells. Similar results were obtained for the DHFR gene. In the 3' part of the ADA gene, however, both normal and XP-C cells perform fast and efficient repair of either strand, which is likely to be caused by the presence of transcription units on both strands. The factor defective in XP-C cells is apparently involved in the processing of DNA damage in inactive parts of the genome, including nontranscribed strands of active genes. These findings have important implications for the understanding of the mechanism of UV-induced excision repair and mutagenesis in mammalian cells

Development and test of Nb(3)Sn cos-theta dipoles based on PIT strands

International Nuclear Information System (INIS)

Zlobin, A.V.; Ambrosio, G.; Andreev, N.; Barzi, E.; Bossert, R.; Carcagno, R.; Chichili, D.R.; Elementi, L.; Feher, S.; Kashikhin, V.V.; Lamm, M.J.; Novitski, I.; Pischalnikov, Yu.; Sylvester, C.; Tartaglia, M.; Yamada, R.

2004-01-01

Fermilab is involved in the development of new generation high-field accelerator magnets using state-of-the-art Nb 3 Sn strands produced using different technologies. Two 1-m long models--mirror configuration and dipole magnet--were fabricated recently at Fermilab based on powder-in-tube (PIT) Nb 3 Sn strands with small effective filament size. This paper describes the parameters of superconducting strands and cable, the details of magnet design and fabrication procedure, and reports the results of PIT coil testing

Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs.

Science.gov (United States)

Santamaría-Díaz, Noelia; Méndez-Arriaga, José M; Salas, Juan M; Galindo, Miguel A

2016-05-17

The oligonucleotide d(TX)9 , which consists of an octadecamer sequence with alternating non-canonical 7-deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double-stranded DNA through the formation of hydrogen-bonded Watson-Crick base pairs. dsDNA with metal-mediated base pairs was then obtained by selectively replacing W-C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag(+) ions, and its stability is significantly enhanced in the presence of Ag(+) ions while its double-helix structure is retained. Temperature-dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)-mediated base pairs. This strategy could become useful for preparing stable metallo-DNA-based nanostructures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of Cellular Decapping Activators by Positive-Strand RNA Viruses

Directory of Open Access Journals (Sweden)

Jennifer Jungfleisch

2016-12-01

Full Text Available Positive-strand RNA viruses have evolved multiple strategies to not only circumvent the hostile decay machinery but to trick it into being a priceless collaborator supporting viral RNA translation and replication. In this review, we describe the versatile interaction of positive-strand RNA viruses and the 5′-3′ mRNA decay machinery with a focus on the viral subversion of decapping activators. This highly conserved viral trickery is exemplified with the plant Brome mosaic virus, the animal Flock house virus and the human hepatitis C virus.

On the linearity of the dose-effect relationship of DNA double strand breaks

International Nuclear Information System (INIS)

Chadwick, K.H.; Leenhouts, H.P.

1994-01-01

Most radiation biologists believe that DNA double-strand breaks are induced linearly with radiation dose for all types of radiation. Since 1985, with the advent of elution and gel electrophoresis techniques which permit the measurement of DNA double-strand breaks induced in mammalian cells at doses having radiobiological relevance, the true nature of the dose-effect relationship has been brought into some doubt. Many investigators measured curvilinear dose-effect relationships and a few found good correlations between the induction of the DNA double-strand breaks and cell survival. We approach the problem pragmatically by assuming that the induction of DNA double-strand breaks by 125 I Auger electron emitters incorporated into the DNA of the cells is a linear function of the number of 125 I decays, and by comparing the dose-effect relationship for sparsely ionizing radiation against this standard. The conclusion drawn that the curvilinear dose-effect relationships and the correlations with survival are real. (Author)

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.

Hole hopping rates in single strand oligonucleotides

Energy Technology Data Exchange (ETDEWEB)

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

2014-08-31

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

Development of a three-dimensional high-order strand-grids approach

Science.gov (United States)

Tong, Oisin

Development of a novel high-order flux correction method on strand grids is presented. The method uses a combination of flux correction in the unstructured plane and summation-by-parts operators in the strand direction to achieve high-fidelity solutions. Low-order truncation errors are cancelled with accurate flux and solution gradients in the flux correction method, thereby achieving a formal order of accuracy of 3, although higher orders are often obtained, especially for highly viscous flows. In this work, the scheme is extended to high-Reynolds number computations in both two and three dimensions. Turbulence closure is achieved with a robust version of the Spalart-Allmaras turbulence model that accommodates negative values of the turbulence working variable, and the Menter SST turbulence model, which blends the k-epsilon and k-o turbulence models for better accuracy. A major advantage of this high-order formulation is the ability to implement traditional finite volume-like limiters to cleanly capture shocked and discontinuous flows. In this work, this approach is explored via a symmetric limited positive (SLIP) limiter. Extensive verification and validation is conducted in two and three dimensions to determine the accuracy and fidelity of the scheme for a number of different cases. Verification studies show that the scheme achieves better than third order accuracy for low and high-Reynolds number flows. Cost studies show that in three-dimensions, the third-order flux correction scheme requires only 30% more walltime than a traditional second-order scheme on strand grids to achieve the same level of convergence. In order to overcome meshing issues at sharp corners and other small-scale features, a unique approach to traditional geometry, coined "asymptotic geometry," is explored. Asymptotic geometry is achieved by filtering out small-scale features in a level set domain through min/max flow. This approach is combined with a curvature based strand shortening

MO-AB-BRA-04: Radiation Measurements with a DNA Double-Strand-Break Dosimeter

Energy Technology Data Exchange (ETDEWEB)

Obeidat, M; Cline, K; Stathakis, S; Papanikolaou, N; Rasmussen, K; Gutierrez, A; Ha, CS; Lee, SE; Shim, EY; Kirby, N [University of Texas HSC SA, San Antonio, TX (United States)

2016-06-15

Purpose: Many types of dosimeters are used to measure radiation, but none of them directly measures the biological effect of this dose. The purpose here is to create a dosimeter that can measure the probability of double-strand breaks (DSB) for DNA, which is directly related to the biological effect of radiation. Methods: The dosimeter has DNA strands, which are labeled on one end with biotin and on the other with fluorescein. The biotin attaches these strands to magnetic beads. We suspended the DNA dosimeter in phosphate-buffered saline (PBS) as it matches the internal environment of the body. We placed small volumes (50µL) of the DNA dosimeter into tubes and irradiated these samples in a water-equivalent plastic phantom with several doses (three samples per dose). After irradiating the samples, a magnet was placed against the tubes. The fluorescein attached to broken DNA strands was extracted (called the supernatant) and placed into a different tube. The fluorescein on the unbroken strands remained attached to the beads in the tube and was re-suspended with 50µL of PBS. A fluorescence reader was used to measure the fluorescence for both the re-suspended beads and supernatant. To prove that we are measuring DSB, we tested dosimeter response with two different lengths of attached DNA strands (1 and 4 kilo-base pair). Results: The probability of DSB at the dose levels of 5, 10, 25, and 50 Gy were 0.05, 0.08, 0.12, and 0.19, respectively, while the coefficients of variation were 0.14, 0.07, 0.02, and 0.01, respectively. The 4 kilo-base-pair dosimeter produced 5.3 times the response of the 1 kilo-base-pair dosimeter. Conclusion: The DNA dosimeter yields a measurable response to dose that scales with the DNA strand length. The goal now is to refine the dosimeter fabrication to reproducibly create a low coefficient of variation for the lower doses. This work was supported in part by Yarmouk University (Irbid, Jordan) and CPRIT (RP140105)

MO-AB-BRA-04: Radiation Measurements with a DNA Double-Strand-Break Dosimeter

International Nuclear Information System (INIS)

Obeidat, M; Cline, K; Stathakis, S; Papanikolaou, N; Rasmussen, K; Gutierrez, A; Ha, CS; Lee, SE; Shim, EY; Kirby, N

2016-01-01

Purpose: Many types of dosimeters are used to measure radiation, but none of them directly measures the biological effect of this dose. The purpose here is to create a dosimeter that can measure the probability of double-strand breaks (DSB) for DNA, which is directly related to the biological effect of radiation. Methods: The dosimeter has DNA strands, which are labeled on one end with biotin and on the other with fluorescein. The biotin attaches these strands to magnetic beads. We suspended the DNA dosimeter in phosphate-buffered saline (PBS) as it matches the internal environment of the body. We placed small volumes (50µL) of the DNA dosimeter into tubes and irradiated these samples in a water-equivalent plastic phantom with several doses (three samples per dose). After irradiating the samples, a magnet was placed against the tubes. The fluorescein attached to broken DNA strands was extracted (called the supernatant) and placed into a different tube. The fluorescein on the unbroken strands remained attached to the beads in the tube and was re-suspended with 50µL of PBS. A fluorescence reader was used to measure the fluorescence for both the re-suspended beads and supernatant. To prove that we are measuring DSB, we tested dosimeter response with two different lengths of attached DNA strands (1 and 4 kilo-base pair). Results: The probability of DSB at the dose levels of 5, 10, 25, and 50 Gy were 0.05, 0.08, 0.12, and 0.19, respectively, while the coefficients of variation were 0.14, 0.07, 0.02, and 0.01, respectively. The 4 kilo-base-pair dosimeter produced 5.3 times the response of the 1 kilo-base-pair dosimeter. Conclusion: The DNA dosimeter yields a measurable response to dose that scales with the DNA strand length. The goal now is to refine the dosimeter fabrication to reproducibly create a low coefficient of variation for the lower doses. This work was supported in part by Yarmouk University (Irbid, Jordan) and CPRIT (RP140105)

Ankle replacement

Science.gov (United States)

Ankle arthroplasty - total; Total ankle arthroplasty; Endoprosthetic ankle replacement; Ankle surgery ... Ankle replacement surgery is most often done while you are under general anesthesia. This means you will ...

Review of thirty-two years of toothed whale strandings in Santa Catarina, southern Brazil (Cetacea: Odontoceti

Directory of Open Access Journals (Sweden)

Thaís dos S. Vianna

Full Text Available ABSTRACT Marine mammal strandings provide valuable insights into local biodiversity. Strandings can be caused by both natural and anthropogenic factors. In the state of Santa Catarina, Southern Brazil, organized marine mammal collections started in the 1980s through opportunistic and non-systematic collection efforts, representing a record of over 30 years of marine biodiversity. This study aimed to perform a preliminary review of 32 years of stranding records within this region. The secondary aim was to elucidate the stranding dynamics of the three most commonly recorded species. A total of 460 records were obtained, representing 17 species of odontocetes. The species registered most frequently were the franciscana, Pontoporia blainvillei (Gervais & d' Orbigny, 1844 (n = 173, bottlenose dolphin, Tursiops truncatus (Montagu, 1821 (n = 100, and Guiana dolphin Sotalia guianensis (Van Bénéden, 1864 (n = 97. Most of the stranding records were observed in the second half of the year during the austral winter and spring. The apparent causes of death could not be determined for most of the specimens due to carcass decomposition. For the specimens in which the apparent cause of death could be determined, 27% of the strandings were compatible with anthropogenic interactions. While the focus of this study was a preliminary assessment of stranding data obtained through opportunistic collection, it is evident that future systematic monitoring efforts and stable networks of collaborators will generate more reliable coastal biodiversity inventories and will allow the knowledge of population dynamics of marine mammal species. In particular, for threatened and vulnerable species, or species with poor natural history data, strandings are a fundamental tool for the understanding of marine biodiversity. Ideally, future more refined analyses of stranding data should be used to inform conservation and management policies and to elucidate the biology and ecology of

Self-field instabilities in high-$J_{c}$ Nb$_{3}$Sn strands the effect of copper RRR

CERN Document Server

Bordini, B

2009-01-01

High critical current density (Jc) Nb$_{3}$Sn conductor is the best candidate for next generation high field (> 10 T) accelerator magnets. Although very promising, state of the art high-Jc Nb$_{3}$Sn strands suffer of magneto-thermal instabilities that can severely limit the strand performance. Recently it has been shown that at 1.9 K the self field instability is the dominating mechanism that limits the performance of strands with a low (<10) Residual Resistivity Ratio (RRR) of the stabilizing copper. At CERN several state of the art high–Jc Nb$_{3}$Sn wires have been tested at 4.2 K and 1.9 K to study the effects on strand self-field instability of: RRR and strand impregnation with stycast. To study the effect of the RRR value on magneto-thermal instabilities, a new 2-D finite element model was also developed at CERN. This model simulates the whole development of the flux jump in the strand cross section also taking into account the heat and current diffusion in the stabilizing copper. In this paper th...

Normal formation and repair of γ-radiation-induced single and double strand DNA breaks in Down syndrome fibroblasts

International Nuclear Information System (INIS)

Steiner, M.E.; Woods, W.G.

1982-01-01

Fibroblasts from patients with Down syndrome (Trisomy 21) were examined for repair capability of γ-radiation-induced single strand and double strand DNA breaks. Formation and repair of DNA breaks were determined by DNA alkaline and non-denaturing elution techniques. Down syndrome fibroblasts were found to repair single strand and double strand breaks as well as fibroblasts from normal controls. (orig.)

Development and test of Nb(3)Sn cos-theta dipoles based on PIT strands

Energy Technology Data Exchange (ETDEWEB)

Zlobin, A.V.; Ambrosio, G.; Andreev, N.; Barzi, E.; Bossert, R.; Carcagno, R.; Chichili, D.R.; Elementi, L.; Feher, S.; Kashikhin, V.V.; Lamm, M.J.; Novitski, I.; Pischalnikov, Yu.; Sylvester, C.; Tartaglia, M.; Yamada, R.; /Fermilab

2004-11-01

Fermilab is involved in the development of new generation high-field accelerator magnets using state-of-the-art Nb{sub 3}Sn strands produced using different technologies. Two 1-m long models--mirror configuration and dipole magnet--were fabricated recently at Fermilab based on powder-in-tube (PIT) Nb{sub 3}Sn strands with small effective filament size. This paper describes the parameters of superconducting strands and cable, the details of magnet design and fabrication procedure, and reports the results of PIT coil testing.

Association of DNA repair polymorphisms with DNA repair functional outcomes in healthy human subjects

Czech Academy of Sciences Publication Activity Database

Vodička, Pavel; Štětina, R.; Poláková, Veronika; Tulupová, Elena; Naccarati, Alessio; Vodičková, Ludmila; Kumar, R.; Hánová, Monika; Pardini, Barbara; Slyšková, Jana; Musak, L.; De Palma, G.; Souček, P.; Hemminki, K.

2007-01-01

Roč. 28, č. 3 (2007), s. 657-664 ISSN 0143-3334 R&D Projects: GA MZd NR8563; GA ČR GA310/05/2626 Institutional research plan: CEZ:AV0Z50390512 Keywords : Base excision DNA * Single-strand breaks * Peripheral blood lymphocytes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.406, year: 2007

Nicotine replacement therapy

Science.gov (United States)

Smoking cessation - nicotine replacement; Tobacco - nicotine replacement therapy ... Before you start using a nicotine replacement product, here are some things to know: The more cigarettes you smoke, the higher the dose you may need to ...

Hip Replacement Surgery

Science.gov (United States)

... Outreach Initiative Breadcrumb Home Health Topics English Español Hip Replacement Surgery Basics In-Depth Download Download EPUB ... PDF What is it? Points To Remember About Hip Replacement Surgery Hip replacement surgery removes damaged or ...

Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes

Science.gov (United States)

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

2015-01-01

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

Heavy metals in tissues of stranded short-finned pilot whales

International Nuclear Information System (INIS)

Stoneburner, D.L.

1978-01-01

Selected tissues from four short-finned pilot whales that stranded at Cumberland Island National Seashore were analyzed for total cadmium, mercury and selenium by neutron activation. Cadmium reached a maximum mean wet weight concentration of 31.4 ppm in the kidney tissues. Maximum mean wet weight concentrations of mercury, 230.9 ppm, and selenium, 44.2 ppm, were found in the liver tissues. The lowest concentration of each metal was found in the blubber. Postmortem examination showed that the whales had no food in their stomachs. The whales must have been utilizing metabolic reserves, contaminated with residual concentrations of heavy metals, prior to beaching. This utilization of reserves probably resulted in the high concentrations of cadmium, mercury and selenium found in the liver and kidney tissues. Since the heavy metal concentrations were three to four times greater in the stranded whales, as compared to apparently healthy whales of the same species, it is suggested that heavy metal toxicosis may have been a factor contributing to this particular stranding. (Auth.)

X-ray induced DNA double strand break production and repair in mammalian cells as measured by neutral filter elution

Energy Technology Data Exchange (ETDEWEB)

Bradley, M O; Kohn, K W [National Institutes of Health, Bethesda, MD (USA)

1979-10-01

A neutral filter elution method was used for detecting DNA double strand breaks in mouse L1210 cells after X-ray. The assay detected the number of double strand breaks induced by as little as 1000 rad of X-ray. The rate of DNA elution through the filters under neutral conditions increased with X-ray dose. Certain conditions for deproteinization, pH, and filter type were shown to increase the assay's sensitivity. Hydrogen peroxide and Bleomycin also induced apparent DNA double strand breaks, although the ratios of double to single strand breaks varied from those produced by X-ray. The introduction of double strand cuts by HpA I restriction endonuclease in DNA lysed on filters resulted in a rapid rate of elution under neutral conditions, implying that the method can detect double strand breaks if they exist in the DNA. The eluted DNA banded with a double stranded DNA marker in cesium chloride. This evidence suggested that the assay detected DNA double strand breaks. L1210 cells were shown to rejoin most of the DNA double strand breaks induced by 5-10 krad of X-ray with a half-time of about 40 minutes. (author).

Recent Progress in Application of Internal Oxidation Technique in Nb3Sn Strands

Energy Technology Data Exchange (ETDEWEB)

Xu, Xingchen [Fermilab; Peng, Xuan [Hyper Tech Research Inc.; Sumption, Michael [Ohio State U.; Collings, E. W. [Ohio State U.

2016-10-13

The internal oxidation technique can generate ZrO2 nano particles in Nb3Sn strands, which markedly refine the Nb3Sn grain size and boost the high-field critical current density (Jc). This article summarizes recent efforts on implementing this technique in practical Nb3Sn wires and adding Ti as a dopant. It is demonstrated that this technique can be readily incorporated into the present Nb3Sn conductor manufacturing technology. Powder-in-tube (PIT) strands with fine subelements (~25 µm) based on this technique were successfully fabricated, and proper heat treatments for oxygen transfer were explored. Future work for producing strands ready for applications is proposed.

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.

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...

SAKAMATA : A tool to avoid whale strandings

NARCIS (Netherlands)

Benders, F.P.A.; Beerens, S.P.; Verboom, W.C.

2004-01-01

World-wide a concern exists about the influence of man-made noise on marine life, and particularly of high power sonar. Most concern lies with marine mammals that use acoustics for hunting, communication and/or navigation. This concern is fed by recent strandings of whales that could be related to

SAKAMATA : A tool to avoid whale strandings

NARCIS (Netherlands)

Benders, F.P.A.; Beerens, S.P.; Verboom, W.C.

2002-01-01

World-wide a concern exists about the influence of man-made noise on marine life, and particularly of high power sonar. Most concern lies with marine mammals that use acoustics for hunting, communication and/or navigation. This concern is fed by recent strandings of whales that could be related to

Language Profile in Congenital Hypothyroid Children Receiving Replacement Therapy.

Science.gov (United States)

Soliman, Hend; Abdel Hady, Aisha Fawzy; Abdel Hamid, Asmaa; Mahmoud, Heba

2016-01-01

The aim of this work was to evaluate receptive and expressive language skills in children with congenital hypothyroidism receiving early hormonal replacement treatment before the age of 3 months and to identify any subtle areas of weaknesses in their language development to check the necessity for future language intervention. The study was conducted on 30 hypothyroid children receiving hormonal replacement. They were subdivided into group I (5-8 years 11 months; 12 cases) and group II (9-12 years 11 months; 18 cases). All patients were subjected to a protocol of assessment applied in the Diabetes, Endocrine and Metabolism Pediatric Unit (DEMPU) and evaluation of language skills by the REAL scale. The younger group reached average Arabic language scores, while the older group showed moderate language delay. Early replacement therapy supports language development in young children. However, longitudinal and follow-up studies are required to identify difficulties presenting at older ages that may affect children in the academic settings. © 2016 S. Karger AG, Basel.

Fracture behavior of filament in Nb_3Sn strands with crack-bridging model

International Nuclear Information System (INIS)

Yong, Huadong; Yang, Penglei; Xue, Cun; Zhou, Youhe

2016-01-01

Highlights: • The crack-bridging model is used to study the fracture behavior of filaments. • Two different fracture modes are characterized by the number of bridging bronzes. • Short twist pitch has better mechanical stability for the tensile loadings. • The widths of bridging bronze and filament have different effects for the central crack and two collinear cracks. - Abstract: The Nb_3Sn strands which have high critical field are used in cable-in-conduit conductors (CICCs). The superconducting strands are twisted multistage and experience complex thermal and electromagnetic loadings. Due to their brittleness, the cracking of the Nb_3Sn filaments will occur under mechanical loading. In this paper, based on the linear elastic fracture theory, we study the effects of tension loading on the fracture behavior of central crack firstly. The strain energy release rates for different twist pitches and cabling stages are presented. As the triplet is subjected to the uniaxial strain, the cracking probability will increase with the twist pitch. The crack number increases with the applied strain, and wider filament or bronze can lead to smaller crack number under the same applied strain. In addition, multistage cabling has better mechanical stability. Next, the two collinear crack problem is considered. The variations of microcrack number show that the wider bronze can provide more resistance for the propagating of the large cracks. We can conclude that the bronze plays an important role in improving the stability and strength.

Testing of CFC replacement fluids for arc-induced toxic by-products

Energy Technology Data Exchange (ETDEWEB)

Cravey, W.R.; Goerz, D.A.; Hawley-Fedder, R.A.

1993-06-01

The authors have developed a unique test-stand for quantifying the generation of perfluoroisobutylene (PFIB) in chlorofluorocarbon (CFC) replacement fluids when they are subjected to high electrical stress/breakdown environments. PFIB is an extremely toxic gas with a threshold limit value of 10 ppbv as set by the American Conference of Governmental Industrial Hygienists. They have tested several new fluids from various manufacturers for their potential to generate PFIB. Their goal is to determine breakdown characteristics and quantify toxic by-products of these replacement fluids to determine a safe, usable alternative for present CFC`s.

I-SceI-mediated double-strand break does not increase the frequency of homologous recombination at the Dct locus in mouse embryonic stem cells.

Science.gov (United States)

Fenina, Myriam; Simon-Chazottes, Dominique; Vandormael-Pournin, Sandrine; Soueid, Jihane; Langa, Francina; Cohen-Tannoudji, Michel; Bernard, Bruno A; Panthier, Jean-Jacques

2012-01-01

Targeted induction of double-strand breaks (DSBs) at natural endogenous loci was shown to increase the rate of gene replacement by homologous recombination in mouse embryonic stem cells. The gene encoding dopachrome tautomerase (Dct) is specifically expressed in melanocytes and their precursors. To construct a genetic tool allowing the replacement of Dct gene by any gene of interest, we generated an embryonic stem cell line carrying the recognition site for the yeast I-SceI meganuclease embedded in the Dct genomic segment. The embryonic stem cell line was electroporated with an I-SceI expression plasmid, and a template for the DSB-repair process that carried sequence homologies to the Dct target. The I-SceI meganuclease was indeed able to introduce a DSB at the Dct locus in live embryonic stem cells. However, the level of gene targeting was not improved by the DSB induction, indicating a limited capacity of I-SceI to mediate homologous recombination at the Dct locus. These data suggest that homologous recombination by meganuclease-induced DSB may be locus dependent in mammalian cells.

Coordinated leading and lagging strand DNA synthesis by using the herpes simplex virus 1 replication complex and minicircle DNA templates.

Science.gov (United States)

Stengel, Gudrun; Kuchta, Robert D

2011-01-01

The origin-specific replication of the herpes simplex virus 1 genome requires seven proteins: the helicase-primase (UL5-UL8-UL52), the DNA polymerase (UL30-UL42), the single-strand DNA binding protein (ICP8), and the origin-binding protein (UL9). We reconstituted these proteins, excluding UL9, on synthetic minicircular DNA templates and monitored leading and lagging strand DNA synthesis using the strand-specific incorporation of dTMP and dAMP. Critical features of the assays that led to efficient leading and lagging stand synthesis included high helicase-primase concentrations and a lagging strand template whose sequence resembled that of the viral DNA. Depending on the nature of the minicircle template, the replication complex synthesized leading and lagging strand products at molar ratios varying between 1:1 and 3:1. Lagging strand products (∼0.2 to 0.6 kb) were significantly shorter than leading strand products (∼2 to 10 kb), and conditions that stimulated primer synthesis led to shorter lagging strand products. ICP8 was not essential; however, its presence stimulated DNA synthesis and increased the length of both leading and lagging strand products. Curiously, human DNA polymerase α (p70-p180 or p49-p58-p70-p180), which improves the utilization of RNA primers synthesized by herpesvirus primase on linear DNA templates, had no effect on the replication of the minicircles. The lack of stimulation by polymerase α suggests the existence of a macromolecular assembly that enhances the utilization of RNA primers and may functionally couple leading and lagging strand synthesis. Evidence for functional coupling is further provided by our observations that (i) leading and lagging strand synthesis produce equal amounts of DNA, (ii) leading strand synthesis proceeds faster under conditions that disable primer synthesis on the lagging strand, and (iii) conditions that accelerate helicase-catalyzed DNA unwinding stimulate decoupled leading strand synthesis but not

Knee Replacement

Science.gov (United States)

Knee replacement is surgery for people with severe knee damage. Knee replacement can relieve pain and allow you to ... Your doctor may recommend it if you have knee pain and medicine and other treatments are not ...

Comparison of the electrophoretic method with the sedimentation method for the analysis of DNA strand breaks

International Nuclear Information System (INIS)

Yamamoto, Osamu; Ogawa, Masaaki; Hoshi, Masaharu

1982-01-01

Application of electrophoresis to the analysis of DNA strand breaks was studied comparing with the sedimentation analysis. A BRL gel electrophoresis system (Type V16) was used for this study. Calf thymus DNA (1 mg/ml) irradiated with 60 Co gamma-rays in SSC solution was applied to both the electrophoretic analysis and the sedimentation analysis. Lamda phage DNA and its fragments were employed as the standard size molecules. In a range from 1 k base pairs to 6 k base pairs in length for double stranded DNA or from 2 k bases to 12 k bases for single stranded DNA, the calculated average molecular weight from the electrophoresis coincided with that from the sedimentation. Number of single strand breaks and double strand breaks were 1.34 x 10 11 breaks/mg/rad (G = 0.215) and 0.48 x 10 5 breaks/mg/rad 2 , respectively. (author)

DNA-imprinted polymer nanoparticles with monodispersity and prescribed DNA-strand patterns

Science.gov (United States)

Trinh, Tuan; Liao, Chenyi; Toader, Violeta; Barłóg, Maciej; Bazzi, Hassan S.; Li, Jianing; Sleiman, Hanadi F.

2018-02-01

As colloidal self-assembly increasingly approaches the complexity of natural systems, an ongoing challenge is to generate non-centrosymmetric structures. For example, patchy, Janus or living crystallization particles have significantly advanced the area of polymer assembly. It has remained difficult, however, to devise polymer particles that associate in a directional manner, with controlled valency and recognition motifs. Here, we present a method to transfer DNA patterns from a DNA cage to a polymeric nanoparticle encapsulated inside the cage in three dimensions. The resulting DNA-imprinted particles (DIPs), which are 'moulded' on the inside of the DNA cage, consist of a monodisperse crosslinked polymer core with a predetermined pattern of different DNA strands covalently 'printed' on their exterior, and further assemble with programmability and directionality. The number, orientation and sequence of DNA strands grafted onto the polymeric core can be controlled during the process, and the strands are addressable independently of each other.

Evaluation of a new methodology to simulate damage and wear of polyethylene hip replacements subjected to edge loading in hip simulator testing.

Science.gov (United States)

Partridge, Susan; Tipper, Joanne L; Al-Hajjar, Mazen; Isaac, Graham H; Fisher, John; Williams, Sophie

2018-05-01

Wear and fatigue of polyethylene acetabular cups have been reported to play a role in the failure of total hip replacements. Hip simulator testing under a wide range of clinically relevant loading conditions is important. Edge loading of hip replacements can occur following impingement under extreme activities and can also occur during normal gait, where there is an offset deficiency and/or joint laxity. This study evaluated a hip simulator method that assessed wear and damage in polyethylene acetabular liners that were subjected to edge loading. The liners tested to evaluate the method were a currently manufactured crosslinked polyethylene acetabular liner and an aged conventional polyethylene acetabular liner. The acetabular liners were tested for 5 million standard walking cycles and following this 5 million walking cycles with edge loading. Edge loading conditions represented a separation of the centers of rotation of the femoral head and the acetabular liner during the swing phase, leading to loading of the liner rim on heel strike. Rim damage and cracking was observed in the aged conventional polyethylene liner. Steady-state wear rates assessed gravimetrically were lower under edge loading compared to standard loading. This study supports previous clinical findings that edge loading may cause rim cracking in liners, where component positioning is suboptimal or where material degradation is present. The simulation method developed has the potential to be used in the future to test the effect of aging and different levels of severity of edge loading on a range of cross-linked polyethylene materials. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1456-1462, 2018. © 2017 Wiley Periodicals, Inc.

Vegetables and PUFA-rich plant oil reduce DNA strand breaks in individuals with type 2 diabetes

DEFF Research Database (Denmark)

Müllner, Elisabeth; Brath, Helmut; Pleifer, Simone

2013-01-01

SCOPE: Type 2 diabetes is a multifactorial disease associated with increased oxidative stress, which may lead to increased DNA damage. The aim of this study was to investigate the effect of a healthy diet on DNA oxidation in diabetics and nondiabetics. METHODS AND RESULTS: Seventy-six diabetic...... and 21 nondiabetic individuals participated in this study. All subjects received information about the benefits of a healthy diet, while subjects randomly assigned to the intervention group received additionally 300 g of vegetables and 25 mL PUFA-rich plant oil per day. DNA damage in mononuclear cells...... increase in plasma antioxidant concentrations. Diabetic individuals of the intervention group showed a significant reduction in HbA1c and DNA strand breaks. Levels of HbA1c were also improved in diabetics of the information group, but oxidative damage to DNA was not altered. Urinary 8-oxodG and 8-oxo...

Status of European manufacture of Toroidal Field conductor and strand for JT-60SA project

Energy Technology Data Exchange (ETDEWEB)

Zani, Louis, E-mail: louis.zani@jt60sa.org [Fusion for Energy, D-85748 Garching (Germany); CEA, IRFM, F-13108 Saint-Paul-lez-Durance (France); Barabaschi, Pietro; Di Pietro, Enrico [Fusion for Energy, D-85748 Garching (Germany)

2013-10-15

In the framework of the JT-60SA project, part of the Broader Approach (BA) agreement, EURATOM provides to Japan, the Toroidal Field (TF) magnet system, consisting of 18 superconducting coils. The procurement of the conductor for the TF coils is managed by Fusion for Energy, acting as EU representative in the BA agreement. The TF conductor procurement is split into two contracts, one dedicated to the production of Niobium Titanium (NbTi) and Cu strand and the other to TF conductor production through strand cabling and cable jacketing operations. The TF conductor is a rectangular-shaped cable-in-conduit conductor formed by 486 (0.81 mm diameter) strands (2/3 NbTi–1/3 Cu) wrapped in a stainless steel foil and embedded into a stainless steel jacket. The 18 TF coils require (including spares) 115 ‘Unit Lengths’ (UL) of such conductor, each 240 m long for a total of about 28 km. Correspondingly about 10,000 km for NbTi and 5000 km for Cu strand are produced. The Japanese company Furukawa Electric Co. (FEC) is in charge of TF strand manufacture while the Italian company Italian Consortium for Applied Superconductivity (ICAS) is in charge of cabling and jacketing of TF conductor ULs. In the paper, we provide information on the production stages presently achieved in TF strand and conductor contracts.

Advanced materials, strands, and conductors for particle accelerators. Technical report for the year 1994

International Nuclear Information System (INIS)

1994-01-01

The authors research for the Division of High Energy Physics (HEP) began with studies of both the superconducting and matrix components of multifilamentary composites, viz (1) attempts to increase the flux-pinning strength in NbTi, and (2) a method of suppressing proximity effect coupling in fine-filament strands. The latter was fully successful, and stands ready to be invoked as soon as the need arises to: (a) very closely space the filaments in the interests of quality, or (b) re-introduce fine-filament composites for strand-magnetization reduction or AC-loss minimization. But there were also many spin-offs during the life of the program, as indicated in the complete list of publications (copy available on request). For instance, the various other effects and properties that were studied and published over the period of this association with HEP include: (i) reduction in T c due to proximity effect between thin αphase precipitates and the NbTi matrix, (ii) critical field enhancement with reduction of filament diameter in fine-filament composites, (iii) studies and systematics of AC loss in composite strands, (iv) compensation of strand magnetization by means of Ni plating or filament substitution, (v) hysteretic loss due to surface pinning in multifilamentary NbTi, (vi) flux creep in SSC-type strands, (vii) temperature and field dependence of eddy current decay, (vii) influence of Mn doping on the properties of NbTi, (viii) transverse and longitudinal resistivities (including a size-effect contribution) in strands with various filament/matrix configurations

Slow conduction in mixed cultured strands of primary ventricular cells and stem cell-derived cardiomyocytes

Directory of Open Access Journals (Sweden)

Jan Pavel Kucera

2015-09-01

Full Text Available Modern concepts for the treatment of myocardial diseases focus on novel cell therapeutic strategies involving stem cell-derived cardiomyocytes (SCMs. However, functional integration of SCMs requires similar electrophysiological properties as primary cardiomyocytes (PCMs and the ability to establish intercellular connections with host myocytes in order to contribute to the electrical and mechanical activity of the heart. The aim of this project was to investigate the properties of cardiac conduction in a co-culture approach using SCMs and PCMs in cultured cell strands. Murine embryonic SCMs were pooled with fetal ventricular cells and seeded in predefined proportions on microelectrode arrays to form patterned strands of mixed cells. Conduction velocity (CV was measured during steady state pacing. SCM excitability was estimated from action potentials measured in single cells using the patch clamp technique. Experiments were complemented with computer simulations of conduction using a detailed model of cellular architecture in mixed cell strands.CV was significantly lower in strands composed purely of SCMs (5.5±1.5 cm/s, n=11 as compared to PCMs (34.9±2.9 cm/s, n=21 at similar refractoriness (100% SCMs: 122±25 ms, n=9; 100% PCMs: 139±67 ms, n=14. In mixed strands combining both cell types, CV was higher than in pure SCMs strands, but always lower than in 100% PCM strands. Computer simulations demonstrated that both intercellular coupling and electrical excitability limit CV.These data provide evidence that in cultures of murine ventricular cardiomyocytes, SCMs cannot restore CV to control levels resulting in slow conduction, which may lead to reentry circuits and arrhythmias.

STRUCTURAL AND FUNCTIONAL-ANALYSIS OF THE SINGLE-STRAND ORIGIN OF REPLICATION FROM THE LACTOCOCCAL PLASMID PWVO1

NARCIS (Netherlands)

SEEGERS, JFML; ZHAO, AC; MEIJER, WJJ; KHAN, SA; VENEMA, G; BRON, S

1995-01-01

The single-strand origin (SSO) of the rolling-circle (RC), broad-host-range lactococcal plasmid pWVO1 was functionally characterized. The activity of this SSO in the conversion of single-stranded DNA to double-stranded DNA was tested both in vivo and in vitro. In addition, the effect of this SSO on

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

NARCIS (Netherlands)

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

1984-01-01

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

Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre

DEFF Research Database (Denmark)

Lisby, M.; Mortensen, Uffe Hasbro; Rothstein, R.

2003-01-01

DNA double-strand break repair (DSBR) is an essential process for preserving genomic integrity in all organisms. To investigate this process at the cellular level, we engineered a system of fluorescently marked DNA double-strand breaks (DSBs) in the yeast Saccharomyces cerevisiae to visualize in ...

78 FR 54867 - Proposed Information Collection; Comment Request; Marine Mammal Health and Stranding Response...

Science.gov (United States)

2013-09-06

... Collection; Comment Request; Marine Mammal Health and Stranding Response Program, Level A Stranding and... governments; not-for-profit institutions; business or other for-profit organizations. Estimated Number of... collection; they also will become a matter of public record. Dated: August 30, 2013. Gwellnar Banks...

Use of seismic experience data for technical evaluation of commercial grade replacement items

International Nuclear Information System (INIS)

Cushing, R.W.; Campbell, R.D.

1991-01-01

This paper reports that the purchase of commercial grade replacement items which are dedicated for use in nuclear safety related systems requires a technical evaluation for those items which cannot be purchased as like-for-like replacements. One of the requirements for performing a technical evaluation is verification of seismic adequacy. Studying the performance and failure modes of equipment which has been subjected to strong motion earthquakes has provided the industry with the ability to predict the behavior characteristics of many types of commonly replaced components and parts. The use of Seismic Experience Data has developed into an efficient means of satisfying the seismic adequacy requirement

Heterochromatinization associated with cell differentiation as a model to study DNA double strand break induction and repair in the context of higher-order chromatin structure

Czech Academy of Sciences Publication Activity Database

Falk, Martin; Lukášová, Emilie; Štefančíková, Lenka; Baranová, E.; Falková, Iva; Ježková, L.; Davídková, Marie; Bačíková, Alena; Vachelová, Jana; Michaelidesová, Anna; Kozubek, Stanislav

2014-01-01

Roč. 83, Jan (2014), s. 177-185 ISSN 0969-8043 R&D Projects: GA MŠk(CZ) LD12039 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : DNA double strand break (DSB) repair * Immature and terminally differentiated granulocytes * gamma H2AX/53BP1 repair foci Subject RIV: BO - Biophysics; BO - Biophysics (UJF-V) Impact factor: 1.231, year: 2014

Implementation of a method to visualize noise-induced hearing loss in mass stranded cetaceans

Science.gov (United States)

Morell, Maria; Brownlow, Andrew; McGovern, Barry; Raverty, Stephen A.; Shadwick, Robert E.; André, Michel

2017-02-01

Assessment of the impact of noise over-exposure in stranded cetaceans is challenging, as the lesions that lead to hearing loss occur at the cellular level and inner ear cells are very sensitive to autolysis. Distinguishing ante-mortem pathology from post-mortem change has been a major constraint in diagnosing potential impact. Here, we outline a methodology applicable to the detection of noise-induced hearing loss in stranded cetaceans. Inner ears from two mass strandings of long-finned pilot whales in Scotland were processed for scanning electron microscopy observation. In one case, a juvenile animal, whose ears were fixed within 4 hours of death, revealed that many sensory cells at the apex of the cochlear spiral were missing. In this case, the absence of outer hair cells would be compatible with overexposure to underwater noise, affecting the region which transduces the lowest frequencies of the pilot whales hearing spectrum. Perfusion of cochlea with fixative greatly improved preservation and enabled diagnostic imaging of the organ of Corti, even 30 hours after death. This finding supports adopting a routine protocol to detect the pathological legacy of noise overexposure in mass stranded cetaceans as a key to understanding the complex processes and implications that lie behind such stranding events.

A Co-Opted DEAD-Box RNA helicase enhances tombusvirus plus-strand synthesis.

Directory of Open Access Journals (Sweden)

Nikolay Kovalev

2012-02-01

Full Text Available Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV. To separate the role of Ded1p in viral protein translation from its putative replication function, we utilized a cell-free TBSV replication assay and recombinant Ded1p. The in vitro data show that Ded1p plays a role in enhancing plus-strand synthesis by the viral replicase. We also find that Ded1p is a component of the tombusvirus replicase complex and Ded1p binds to the 3'-end of the viral minus-stranded RNA. The data obtained with wt and ATPase deficient Ded1p mutants support the model that Ded1p unwinds local structures at the 3'-end of the TBSV (-RNA, rendering the RNA compatible for initiation of (+-strand synthesis. Interestingly, we find that Ded1p and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, which is another host factor for TBSV, play non-overlapping functions to enhance (+-strand synthesis. Altogether, the two host factors enhance TBSV replication synergistically by interacting with the viral (-RNA and the replication proteins. In addition, we have developed an in vitro assay for Flock house virus (FHV, a small RNA virus of insects, that also demonstrated positive effect on FHV replicase activity by the added Ded1p helicase. Thus, two small RNA viruses, which do not code for their own helicases, seems to recruit a host RNA helicase to aid their replication in infected cells.

Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets.

Science.gov (United States)

Indu, S; Kochat, V; Thakurela, S; Ramakrishnan, C; Varadarajan, Raghavan

2011-01-01

Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel β-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T(m). All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG⁰ = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. © 2010 Wiley-Liss, Inc.

Influence of RNA Strand Rigidity on Polyion Complex Formation with Block Catiomers.

Science.gov (United States)

Hayashi, Kotaro; Chaya, Hiroyuki; Fukushima, Shigeto; Watanabe, Sumiyo; Takemoto, Hiroyasu; Osada, Kensuke; Nishiyama, Nobuhiro; Miyata, Kanjiro; Kataoka, Kazunori

2016-03-01

Polyion complexes (b-PICs) are prepared by mixing single- or double-stranded oligo RNA (aniomer) with poly(ethylene glycol)-b-poly(L-lysine) (PEG-PLL) (block catiomer) to clarify the effect of aniomer chain rigidity on association behaviors at varying concentrations. Here, a 21-mer single-stranded RNA (ssRNA) (persistence length: 1.0 nm) and a 21-mer double-stranded RNA (small interfering RNA, siRNA) (persistence length: 62 nm) are compared. Both oligo RNAs form a minimal charge-neutralized ionomer pair with a single PEG-PLL chain, termed unit b-PIC (uPIC), at low concentrations (<≈ 0.01 mg mL(-1)). Above the critical association concentration (≈ 0.01 mg mL(-1)), ssRNA b-PICs form secondary associates, PIC micelles, with sizes up to 30-70 nm, while no such multimolecular assembly is observed for siRNA b-PICs. The entropy gain associated with the formation of a segregated PIC phase in the multimolecular PIC micelles may not be large enough for rigid siRNA strands to compensate with appreciably high steric repulsion derived from PEG chains. Chain rigidity appears to be a critical parameter in polyion complex association. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Method for detecting DNA strand breaks in mammalian cells using the Deinococcus radiodurans PprA protein

International Nuclear Information System (INIS)

Satoh, Katsuya; Wada, Seiichi; Kikuchi, Masahiro; Funayama, Tomoo; Narumi, Issay; Kobayashi, Yasuhiko

2006-01-01

In a previous study, we identified the novel protein PprA that plays a critical role in the radiation resistance of Deinococcus radiodurans. In this study, we focussed on the ability of PprA protein to recognize and bind to double-stranded DNA carrying strand breaks, and attempted to visualize radiation-induced DNA strand breaks in mammalian cultured cells by employing PprA protein using an immunofluorescence technique. Increased PprA protein binding to CHO-K1 nuclei immediately following irradiation suggests the protein is binding to DNA strand breaks. By altering the cell permeabilization conditions, PprA protein binding to CHO-K1 mitochondria, which is probably resulted from DNA strand break immediately following irradiation, was also detected. The method developed and detailed in this study will be useful in evaluating DNA damage responses in cultured cells, and could also be applicable to genotoxic tests in the environmental and pharmaceutical fields

Genome-wide mapping of DNA strand breaks.

Directory of Open Access Journals (Sweden)

Frédéric Leduc

Full Text Available Determination of cellular DNA damage has so far been limited to global assessment of genome integrity whereas nucleotide-level mapping has been restricted to specific loci by the use of specific primers. Therefore, only limited DNA sequences can be studied and novel regions of genomic instability can hardly be discovered. Using a well-characterized yeast model, we describe a straightforward strategy to map genome-wide DNA strand breaks without compromising nucleotide-level resolution. This technique, termed "damaged DNA immunoprecipitation" (dDIP, uses immunoprecipitation and the terminal deoxynucleotidyl transferase-mediated dUTP-biotin end-labeling (TUNEL to capture DNA at break sites. When used in combination with microarray or next-generation sequencing technologies, dDIP will allow researchers to map genome-wide DNA strand breaks as well as other types of DNA damage and to establish a clear profiling of altered genes and/or intergenic sequences in various experimental conditions. This mapping technique could find several applications for instance in the study of aging, genotoxic drug screening, cancer, meiosis, radiation and oxidative DNA damage.

Formation of plasmid DNA strand breaks induced by low-energy ion beam: indication of nuclear stopping effects

International Nuclear Information System (INIS)

Chen Yu; Jiang Bingyao; Chen Youshan; Ding Xingzhao; Liu Xianghuai; Chen Ceshi; Guo Xinyou; Yin Guanglin

1998-01-01

Plasmid pGEM 3zf(+) was irradiated by nitrogen ion beam with energies between 20 and 100 keV and the fluence kept as 1 x 10 12 ions/cm 2 . The irradiated plasmid was assayed by neutral electrophoresis and quantified by densitometry. The yields of DNA with single-strand and double-strand breaks first increased then decreased with increasing ion energy. There was a maximal yield value in the range of 20-100 keV. The relationship between DNA double-strand breaks (DSB) cross-section and linear energy transfer (LET) also showed a peak-shaped distribution. To understand the physical process during DNA strand breaks, a Monte Carlo calculation code known as TRIM (Transport of Ions in Matter) was used to simulate energy losses due to nuclear stopping and to electronic stopping. It can be assumed that nuclear stopping plays a more important role in DNA strand breaks than electronic stopping in this energy range. The physical mechanisms of DNA strand breaks induced by a low-energy ion beam are also discussed. (orig.)

Correlation of superconductor strand, cable, and dipole critical currents in CBA magnets

International Nuclear Information System (INIS)

Tannenbaum, M.J.; Garber, M.; Sampson, W.B.

1982-01-01

A calibration between vendor critical current data for 0.0268'' diameter superconductor strand supplied to Fermilab, and the BNL 10 -12 Ωcm critical current specification is presented. Vendor critical current data for over 400 Fermilab type billets are shown, both as supplied by the vendor and converted to BNL units. Predictions of cable critical current are made using the sum of the critical currents of the 23 strands, where all strands from the same half billet are assigned the same critical current. The measured critical current shows excellent correlation to the predicted value and is approximately 14 +- 2 percent below it. Colliding Beam Accelerator (CBA) full length dipoles reach the conductor critical current limit, essentially without training. Magnet performance is predictable from the measured critical current of a short sample of cable to within 2%

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.

Dynamic protein assembly by programmable DNA strand displacement

Science.gov (United States)

Chen, Rebecca P.; Blackstock, Daniel; Sun, Qing; Chen, Wilfred

2018-03-01

Inspired by the remarkable ability of natural protein switches to sense and respond to a wide range of environmental queues, here we report a strategy to engineer synthetic protein switches by using DNA strand displacement to dynamically organize proteins with highly diverse and complex logic gate architectures. We show that DNA strand displacement can be used to dynamically control the spatial proximity and the corresponding fluorescence resonance energy transfer between two fluorescent proteins. Performing Boolean logic operations enabled the explicit control of protein proximity using multi-input, reversible and amplification architectures. We further demonstrate the power of this technology beyond sensing by achieving dynamic control of an enzyme cascade. Finally, we establish the utility of the approach as a synthetic computing platform that drives the dynamic reconstitution of a split enzyme for targeted prodrug activation based on the sensing of cancer-specific miRNAs.

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

Science.gov (United States)

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

2017-11-01

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

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.

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)

Solving probability reasoning based on DNA strand displacement and probability modules.

Science.gov (United States)

Zhang, Qiang; Wang, Xiaobiao; Wang, Xiaojun; Zhou, Changjun

2017-12-01

In computation biology, DNA strand displacement technology is used to simulate the computation process and has shown strong computing ability. Most researchers use it to solve logic problems, but it is only rarely used in probabilistic reasoning. To process probabilistic reasoning, a conditional probability derivation model and total probability model based on DNA strand displacement were established in this paper. The models were assessed through the game "read your mind." It has been shown to enable the application of probabilistic reasoning in genetic diagnosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

International Nuclear Information System (INIS)

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

2000-01-01

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

Negative-strand RNA viruses: The plant-infecting counterparts

NARCIS (Netherlands)

Kormelink, R.J.M.; Garcia, M.L.; Goodin, M.; Sasaya, T.; Haenni, A.L.

2011-01-01

While a large number of negative-strand (-)RNA viruses infect animals and humans, a relative small number have plants as their primary host. Some of these have been classified within families together with animal/human infecting viruses due to similarities in particle morphology and genome

DNA double-strand breaks & poptosis in the testis

NARCIS (Netherlands)

Hamer, Geert

2003-01-01

During spermatogenesis, DNA damage is a naturally occurring event. At a certain stage, during the first meiotic prophase, DNA breaks are endogenously induced and even required for meiotic recombination. We studied these DNA breaks but also used ionizing radiation (IR) to induce DNA double-strand

Design and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation Using Autocatalytic Amplifiers.

Science.gov (United States)

Song, Tianqi; Garg, Sudhanshu; Mokhtar, Reem; Bui, Hieu; Reif, John

2018-01-19

A main goal in DNA computing is to build DNA circuits to compute designated functions using a minimal number of DNA strands. Here, we propose a novel architecture to build compact DNA strand displacement circuits to compute a broad scope of functions in an analog fashion. A circuit by this architecture is composed of three autocatalytic amplifiers, and the amplifiers interact to perform computation. We show DNA circuits to compute functions sqrt(x), ln(x) and exp(x) for x in tunable ranges with simulation results. A key innovation in our architecture, inspired by Napier's use of logarithm transforms to compute square roots on a slide rule, is to make use of autocatalytic amplifiers to do logarithmic and exponential transforms in concentration and time. In particular, we convert from the input that is encoded by the initial concentration of the input DNA strand, to time, and then back again to the output encoded by the concentration of the output DNA strand at equilibrium. This combined use of strand-concentration and time encoding of computational values may have impact on other forms of molecular computation.

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

Quantitation of the repair of gamma-radiation-induced double-strand DNA breaks in human fibroblasts

International Nuclear Information System (INIS)

Woods, W.G.

1981-01-01

The quantitation and repair of double-strand DNA breaks in human fibroblasts has been determined using a method involving the nondenaturing elution of DNA from a filter. DNA from cells from two human fibroblast lines exposed to γ-radiation from 0 to 10000 rad showed increasing retention on a filter with decreasing radiation dose, and the data suggest a linear relationship between double-strand breaks induced and radiation dose. The ability of normal human fibroblasts to repair double-strand breaks with various doses of radiation was demonstrated, with a tsub(1/2) of 10 min for repair of 5000 rad exposure and 39 min for repair of 10000 rad damage. The kinetics of the DNA rejoining were not linear and suggest that, as in the repair of single-strand breaks, both an initial fast and a later slow mechanism may be involved. (Auth.)

Defining line replaceable units

NARCIS (Netherlands)

Parada Puig, J. E.; Basten, R. J I

2015-01-01

Defective capital assets may be quickly restored to their operational condition by replacing the item that has failed. The item that is replaced is called the Line Replaceable Unit (LRU), and the so-called LRU definition problem is the problem of deciding on which item to replace upon each type of

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)

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds.

Science.gov (United States)

Liu, Shuangna; Peng, Pai; Wang, Huihui; Shi, Lili; Li, Tao

2017-12-01

A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson-Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state. A similar mechanism is also demonstrated in antiparallel DNA duplexes where several motifs of two consecutive G•G wobble base pairs are incorporated and serve as the active pockets for ThT binding. The insight into the interactions of ThT with non-G-quadruplex DNAs allows us to introduce a new concept for constructing DNA-based sensors and devices. As proof-of-concept experiments, we design a DNA triplex containing GA motifs in its Hoogsteen hydrogen-bonded two parallel strands as a pH-driven nanoswitch and two GA-containing parallel duplexes as novel metal sensing platforms where C-C and T-T mismatches are included. This work may find further applications in biological systems (e.g. disease gene detection) where parallel duplex or triplex stretches are involved. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

75 FR 32747 - Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping Duty Administrative...

Science.gov (United States)

2010-06-09

... DEPARTMENT OF COMMERCE INTERNATIONAL TRADE ADMINISTRATION [A-201-831] Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping Duty Administrative Review AGENCY: Import... request an administrative review of the antidumping duty order on prestressed concrete steel wire strand...

Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells.

Science.gov (United States)

Guo, Weilong; Chung, Wen-Yu; Qian, Minping; Pellegrini, Matteo; Zhang, Michael Q

2014-03-01

DNA methylation is an important defense and regulatory mechanism. In mammals, most DNA methylation occurs at CpG sites, and asymmetric non-CpG methylation has only been detected at appreciable levels in a few cell types. We are the first to systematically study the strand-specific distribution of non-CpG methylation. With the divide-and-compare strategy, we show that CHG and CHH methylation are not intrinsically different in human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We also find that non-CpG methylation is skewed between the two strands in introns, especially at intron boundaries and in highly expressed genes. Controlling for the proximal sequences of non-CpG sites, we show that the skew of non-CpG methylation in introns is mainly guided by sequence skew. By studying subgroups of transposable elements, we also found that non-CpG methylation is distributed in a strand-specific manner in both short interspersed nuclear elements (SINE) and long interspersed nuclear elements (LINE), but not in long terminal repeats (LTR). Finally, we show that on the antisense strand of Alus, a non-CpG site just downstream of the A-box is highly methylated. Together, the divide-and-compare strategy leads us to identify regions with strand-specific distributions of non-CpG methylation in humans.

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

Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates.

Science.gov (United States)

Werner, Benjamin; Sottoriva, Andrea

2018-06-01

The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand, thus avoiding accumulating somatic mutations. However, quantitating the extent of non-random DNA strand segregation in human stem cells remains difficult in vivo. Here we show that the change of the mean and variance of the mutational burden with age in healthy human tissues allows estimating strand segregation probabilities and somatic mutation rates. We analysed deep sequencing data from healthy human colon, small intestine, liver, skin and brain. We found highly effective non-random DNA strand segregation in all adult tissues (mean strand segregation probability: 0.98, standard error bounds (0.97,0.99)). In contrast, non-random strand segregation efficiency is reduced to 0.87 (0.78,0.88) in neural tissue during early development, suggesting stem cell pool expansions due to symmetric self-renewal. Healthy somatic mutation rates differed across tissue types, ranging from 3.5 × 10-9/bp/division in small intestine to 1.6 × 10-7/bp/division in skin.

Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates.

Directory of Open Access Journals (Sweden)

Benjamin Werner

2018-06-01

Full Text Available The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand, thus avoiding accumulating somatic mutations. However, quantitating the extent of non-random DNA strand segregation in human stem cells remains difficult in vivo. Here we show that the change of the mean and variance of the mutational burden with age in healthy human tissues allows estimating strand segregation probabilities and somatic mutation rates. We analysed deep sequencing data from healthy human colon, small intestine, liver, skin and brain. We found highly effective non-random DNA strand segregation in all adult tissues (mean strand segregation probability: 0.98, standard error bounds (0.97,0.99. In contrast, non-random strand segregation efficiency is reduced to 0.87 (0.78,0.88 in neural tissue during early development, suggesting stem cell pool expansions due to symmetric self-renewal. Healthy somatic mutation rates differed across tissue types, ranging from 3.5 × 10-9/bp/division in small intestine to 1.6 × 10-7/bp/division in skin.

Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef.

Science.gov (United States)

Ahasan, Md Shamim; Waltzek, Thomas B; Huerlimann, Roger; Ariel, Ellen

2017-12-01

Green turtles (Chelonia mydas) are endangered marine herbivores that break down food particles, primarily sea grasses, through microbial fermentation. However, the microbial community and its role in health and disease is still largely unexplored. In this study, we investigated and compared the fecal bacterial communities of eight wild-captured green turtles to four stranded turtles in the central Great Barrier Reef regions that include Bowen and Townsville. We used high-throughput sequencing analysis targeting the hypervariable V1-V3 regions of the bacterial 16S rRNA gene. At the phylum level, Firmicutes predominated among wild-captured green turtles, followed by Bacteroidetes and Proteobacteria. In contrast, Proteobacteria (Gammaproteobacteria) was the most significantly dominant phylum among all stranded turtles, followed by Bacteroidetes and Firmicutes. In addition, Fusobacteria was also significantly abundant in stranded turtles. No significant differences were found between the wild-captured turtles in Bowen and Townsville. At the family level, the core bacterial community consisted of 25 families that were identified in both the wild-captured and stranded green turtles, while two unique sets of 14 families each were only found in stranded or wild-captured turtles. The predominance of Bacteroides in all groups indicates the importance of these bacteria in turtle gut health. In terms of bacterial diversity and richness, wild-captured green turtles showed a higher bacterial diversity and richness compared with stranded turtles. The marked differences in the bacterial communities between wild-captured and stranded turtles suggest the possible dysbiosis in stranded turtles in addition to potential causal agents. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Determining Optimal Replacement Policy with an Availability Constraint via Genetic Algorithms

Directory of Open Access Journals (Sweden)

Shengliang Zong

2017-01-01

Full Text Available We develop a model and a genetic algorithm for determining an optimal replacement policy for power equipment subject to Poisson shocks. If the time interval of two consecutive shocks is less than a threshold value, the failed equipment can be repaired. We assume that the operating time after repair is stochastically nonincreasing and the repair time is exponentially distributed with a geometric increasing mean. Our objective is to minimize the expected average cost under an availability requirement. Based on this average cost function, we propose the genetic algorithm to locate the optimal replacement policy N to minimize the average cost rate. The results show that the GA is effective and efficient in finding the optimal solutions. The availability of equipment has significance effect on the optimal replacement policy. Many practical systems fit the model developed in this paper.

Test Station for Magnetization Measurements on Large Quantities of Superconducting Strands

CERN Document Server

Le Naour, S; Billan, J; Genest, J

2001-01-01

In the superconducting main magnets of the Large Hadron Collider (LHC), persistent currents in the superconductor determine the field quality at injection field. For this reason it is necessary to check the magnetization of the cable strands during their production. During four years, this requires measurements of the width of the strand magnetization hysteresis loop at 0.5 T, 1.9 K, at a rate of up to eight samples per day. This paper describes the design, construction and the first results of a magnetization test station built for this purpose. The samples are cooled in a cryostat, with a 2-m long elliptic tail. This tail is inserted in a normal conducting dipole magnet with a field between ± 1.5 T. Racetrack pick-up coils, integrated in the cryostat, detect the voltage due to flux change, which is then integrated numerically. The sample holder can contain eight strand samples, each 20 cm long. The test station operates in two modes: either the sample is fixed while the external field is changed, or the sa...

Fracture behavior of filament in Nb{sub 3}Sn strands with crack-bridging model

Energy Technology Data Exchange (ETDEWEB)

Yong, Huadong, E-mail: yonghd@lzu.edu.cn; Yang, Penglei; Xue, Cun; Zhou, Youhe

2016-01-15

Highlights: • The crack-bridging model is used to study the fracture behavior of filaments. • Two different fracture modes are characterized by the number of bridging bronzes. • Short twist pitch has better mechanical stability for the tensile loadings. • The widths of bridging bronze and filament have different effects for the central crack and two collinear cracks. - Abstract: The Nb{sub 3}Sn strands which have high critical field are used in cable-in-conduit conductors (CICCs). The superconducting strands are twisted multistage and experience complex thermal and electromagnetic loadings. Due to their brittleness, the cracking of the Nb{sub 3}Sn filaments will occur under mechanical loading. In this paper, based on the linear elastic fracture theory, we study the effects of tension loading on the fracture behavior of central crack firstly. The strain energy release rates for different twist pitches and cabling stages are presented. As the triplet is subjected to the uniaxial strain, the cracking probability will increase with the twist pitch. The crack number increases with the applied strain, and wider filament or bronze can lead to smaller crack number under the same applied strain. In addition, multistage cabling has better mechanical stability. Next, the two collinear crack problem is considered. The variations of microcrack number show that the wider bronze can provide more resistance for the propagating of the large cracks. We can conclude that the bronze plays an important role in improving the stability and strength.

Double-strand break repair and colorectal cancer: gene variants within 3' UTRs and microRNAs binding as modulators of cancer risk and clinical outcome.

Czech Academy of Sciences Publication Activity Database

Naccarati, Alessio; Rosa, F.; Vymetálková, Veronika; Barone, E.; Jirásková, Kateřina; Gaetano, C.; Novotný, J.; Levý, M.; Vodičková, Ludmila; Gemignani, F.; Buchler, T.; Landi, S.; Vodička, Pavel; Pardini, B.

2016-01-01

Roč. 7, č. 17 (2016), s. 23156-23169 ISSN 1949-2553 R&D Projects: GA MZd(CZ) NV15-26535A; GA ČR(CZ) GAP304/12/1585; GA ČR(CZ) GA15-14789S Institutional support: RVO:68378041 Keywords : 3'UTR polymorphisms * colorectal cancer risk and clinical outcomes * double-strand break repair (DSBR) genes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.168, year: 2016

Reconstitution of DNA strand exchange mediated by Rhp51 recombinase and two mediators.

Directory of Open Access Journals (Sweden)

Yumiko Kurokawa

2008-04-01

Full Text Available In the fission yeast Schizosaccharomyces pombe, genetic evidence suggests that two mediators, Rad22 (the S. pombe Rad52 homolog and the Swi5-Sfr1 complex, participate in a common pathway of Rhp51 (the S. pombe Rad51 homolog-mediated homologous recombination (HR and HR repair. Here, we have demonstrated an in vitro reconstitution of the central step of DNA strand exchange during HR. Our system consists entirely of homogeneously purified proteins, including Rhp51, the two mediators, and replication protein A (RPA, which reflects genetic requirements in vivo. Using this system, we present the first robust biochemical evidence that concerted action of the two mediators directs the loading of Rhp51 onto single-stranded DNA (ssDNA precoated with RPA. Dissection of the reaction reveals that Rad22 overcomes the inhibitory effect of RPA on Rhp51-Swi5-Sfr1-mediated strand exchange. In addition, Rad22 negates the requirement for a strict order of protein addition to the in vitro system. However, despite the presence of Rad22, Swi5-Sfr1 is still essential for strand exchange. Importantly, Rhp51, but neither Rad22 nor the Swi5-Sfr1 mediator, is the factor that displaces RPA from ssDNA. Swi5-Sfr1 stabilizes Rhp51-ssDNA filaments in an ATP-dependent manner, and this stabilization is correlated with activation of Rhp51 for the strand exchange reaction. Rad22 alone cannot activate the Rhp51 presynaptic filament. AMP-PNP, a nonhydrolyzable ATP analog, induces a similar stabilization of Rhp51, but this stabilization is independent of Swi5-Sfr1. However, hydrolysis of ATP is required for processive strand transfer, which results in the formation of a long heteroduplex. Our in vitro reconstitution system has revealed that the two mediators have indispensable, but distinct, roles for mediating Rhp51 loading onto RPA-precoated ssDNA.

Short-term hunger intensity changes following ingestion of a meal replacement bar for weight control.

Science.gov (United States)

Rothacker, Dana Q; Watemberg, Salo

2004-05-01

Meal replacement products for weight loss are popular and safe for most unsupervised consumers desiring to lose weight. Previously we reported that the thickness of meal replacement diet shakes had a direct and significant effect on hunger intensity during the first 2 h and that hunger intensity scores for liquid meal replacements were significantly below baseline for 3 h following consumption (Mattes & Rothacker, 2001) This study uses the same protocol to investigate meal replacement bars designed for overweight consumers. Subjects were prescreened to include only those that normally ate breakfast and liked chocolate. The bar used in this study contained 250 calories (about 30 more than most liquid diet shakes), 4 g dietary fiber, 14 g protein and 8 g fat. Subjects were instructed to consume the entire bar with a glass of water following an overnight fast when they would normally consume their first meal of the day and to assess their hunger on a 1 (not hungry at all) to 9 (as hungry as I have ever felt) scale before consumption, immediately after and hourly for 6 h (only on typical weekdays). Similar assessments were made for the perception of stomach fullness (1=empty, 9=extremely full), strength of the desire to eat (1=no desire, 9=extremely strong) and thirst (1=not at all thirsty, 9=extremely thirsty). One-hundred and eight subjects (23 male and 85 female) completed the study. No gender satiety differences were found. Hunger ratings and desire to eat remained significantly below baseline for 5 h following consumption. Stomach fullness scores were significantly above baseline for 5 h. Thirst scores were significantly below baseline for 3 h. In conclusion, although the meal replacement diet bars contained only 30 additional calories than liquids, they provided an additional 2 h of hunger suppression from baseline that may have an impact on overall weightloss success. These results support superior short-term hunger control with solid meal replacements.

Induction of double-strand breaks in DNA of prokaryotes and eukaryotes and their repair. 1. Application of elastoviscosimetry for studying double-strand breaks in DNA of Escherichia coli induced by. gamma. -irradiation

Energy Technology Data Exchange (ETDEWEB)

Bresler, S E; Noskin, L A; Suslov, A V [AN SSSR, Leningrad. Inst. Yadernoj Fiziki

1980-11-01

It is shown that the method of elastoviscosimetry gives a possibility to record the formation of DNA double-strand breaks in Escherichia coli cells induced by ..gamma.. irradiation at doses close to D/sub 37/. The dependence of changes of elastoviscosity parameter on the dose (tau/sub 0/) passes through the maximum. It is shown that the ascending section of this curve (at minimum ..gamma.. irradiation doses) characterizes the relaxation process of the superspiralised chromosome in nucleotide of the E. coli. This relaxation is observed due to ..gamma.. induced damages which are not double-strand breaks. By the maximum position one can judge on a dose yield of the first DNA double-strand break, the descending part of the dose curve describes the kinetics of accumulation of breaks with the dose increase. The analysis of the data obtained gives the possibility to come to the conclusion that when applying a usual technique of irradiation and lysis of cells not providing for special measures on inhibition of endo-and exonuclease activity in ..gamma.. irradiated cells, the dose yield of double-strand breaks noticeably increases (by 4.2 times). In the case of an essential, though incomplete, inhibition of nuclease activities in ..gamma.. irradiated cells the dose yield of breaks approximately corresponds to the dose curve of inactivation of these cells (D/sub 37/12.5+-3.0 krad, the first double-strand break -at 14.5+-2.4 krad).

Induction of double-strand breaks in DNA of prokaryotes and eukaryotes and their repair. 1. Application of elastoviscosimetry for studying double-strand breaks in DNA of Escherichia coli induced by γ-irradiation

International Nuclear Information System (INIS)

Bresler, S.E.; Noskin, L.A.; Suslov, A.V.

1980-01-01

It is shown that the method of elastoviscosimetry gives a possibility to record the formation of DNA double-strand breaks in Escherichia coli cells induced by γ irradiation at doses close to D 37 . The dependence of changes of elastoviscosity parameter on the dose (tau 0 ) passes through the maximum. It is shown that the ascending section of this curve (at minimum γ irradiation doses) characterizes the relaxation process of the superspiralised chromosome in nucleotide of the E. coli. This relaxation is observed due to γ induced damages which are not double-strand breaks. By the maximum position one can judge on a dose yield of the first DNA double-strand break, the descending part of the dose curve describes the kinetics of accumulation of breaks with the dose increase. The analysis of the data obtained gives the possibility to come to the conclusion that when applying a usual technique of irradiation and lysis of cells not providing for special measures on inhibition of endo-and exonuclease activity in γ irradiated cells, the dose yield of double-strand breaks noticeably increases (by 4.2 times). In the case of an essential, though incomplete, inhibition of nuclease activities in γ irradiated cells the dose yield of breaks approximately corresponds to the dose curve of inactivation of these cells (D 37 12.5+-3.0 krad, the first double-strand break -at 14.5+-2.4 krad)

DNA single strand break in fibroblast from Down syndrome patients

International Nuclear Information System (INIS)

Rozga, B.

1992-01-01

The radiosensitivity of tree trisomic (trisomia +21) strains of human fibroblasts to gamma radiation has been investigated in vitro and the causes of induction and repair of single strand DNA breaks in these cells have been estimated. The single strand breaks in DNA of normal and trisomic cells have been found to be ameliorated with an approximately equal efficiency. Repair has been found to be three times slower in trisomic cells compared to their normal relevant, most likely due to their elevated sensitivity to ionizing radiation and the following mortality of trisomic cells, and/or the potential occurrence of a great number of chromosome aberrations in cells irradiated in vitro. (author). 28 refs, 4 figs, 1 tab

Low-Energy Electron-Induced Strand Breaks in Telomere-Derived DNA Sequences-Influence of DNA Sequence and Topology.

Science.gov (United States)

Rackwitz, Jenny; Bald, Ilko

2018-03-26

During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5'-(TTA GGG) 2 is more sensitive to low-energy electrons than an intermixed sequence 5'-(TGT GTG A) 2 confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5'-(GGG ATT) 2 to 5'-(GGG ATT) 4 ), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K + ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulating mechanisms for dispersal, production and stranding of small forage fish in temporary wetland habitats

Science.gov (United States)

Yurek, Simeon; DeAngelis, Donald L.; Trexler, Joel C.; Jopp, Fred; Donalson, Douglas D.

2013-01-01

Movement strategies of small forage fish (wetland habitats affect their overall population growth and biomass concentrations, i.e., availability to predators. These fish are often the key energy link between primary producers and top predators, such as wading birds, which require high concentrations of stranded fish in accessible depths. Expansion and contraction of seasonal wetlands induce a sequential alternation between rapid biomass growth and concentration, creating the conditions for local stranding of small fish as they move in response to varying water levels. To better understand how landscape topography, hydrology, and fish behavior interact to create high densities of stranded fish, we first simulated population dynamics of small fish, within a dynamic food web, with different traits for movement strategy and growth rate, across an artificial, spatially explicit, heterogeneous, two-dimensional marsh slough landscape, using hydrologic variability as the driver for movement. Model output showed that fish with the highest tendency to invade newly flooded marsh areas built up the largest populations over long time periods with stable hydrologic patterns. A higher probability to become stranded had negative effects on long-term population size, and offset the contribution of that species to stranded biomass. The model was next applied to the topography of a 10 km × 10 km area of Everglades landscape. The details of the topography were highly important in channeling fish movements and creating spatiotemporal patterns of fish movement and stranding. This output provides data that can be compared in the future with observed locations of fish biomass concentrations, or such surrogates as phosphorus ‘hotspots’ in the marsh.

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)

Round and Extracted Nb3Sn Strand Tests for LARP Magnet R and D

International Nuclear Information System (INIS)

Barzi, Emanuela; Bossert, Rodger; Caspi, Shlomo; Dietderich, Dan; Ferracin, Paolo; Ghosh, Arup; Turrioni, Daniele; Yamada, Ryuji; Zlobin, Alexander V.

2006-01-01

The first step in the magnet R and D of the U.S. LHC Accelerator Research Program (LARP) is fabrication of technology quadrupoles TQS01 and TQC01. These are two-layer magnets which use cables of same geometry made of 0.7 mm MJR Nb 3 Sn. Through strand billet qualification and tests of strands extracted from the cables, predictions of magnet performance are made. Measurements included the critical current, I c , using the voltage-current (VI) method at constant field, the stability current, I S , as the minimal quench current obtained with the voltage-field (VH) method at constant current in the sample, and RRR. Magnetization was measured at low and high fields to determine the effective filament size and to detect flux jumps. Effects of heat treatment duration and temperature on I c and I S were also studied. The Nb 3 Sn strand and cable samples, the equipment, measurement procedures, and results are described. Based on these results, strand specifications were formulated for next LARP quadrupole models

Efficacy of low-calorie, partial meal replacement diet plans on weight and abdominal fat in obese subjects with metabolic syndrome: a double-blind, randomised controlled trial of two diet plans - one high in protein and one nutritionally balanced.

Science.gov (United States)

Lee, K; Lee, J; Bae, W K; Choi, J K; Kim, H J; Cho, B

2009-02-01

Little is known about the relative efficacy of high-protein vs. conventional diet plans that include partial meal replacements on body fat loss in obese subjects with metabolic syndrome. We aimed to evaluate the efficacy of two low-calorie diets with partial meal replacement plans-a high-protein plan (HP) and a nutritionally balanced conventional (C) plan-on reducing obesity in obese subjects with metabolic syndrome. In a 12-week, double-blind study, we randomised 75 participants to either the HP- or the C-plan group. We recorded key metrics at 0 and 12 weeks. The overall mean weight loss was 5 kg in the HP-plan group and 4.9 kg in the C-plan group (p = 0.72). Truncal fat mass decreased 1.6 kg in the HP-plan group (p or = 70% dietary compliance, however, truncal and whole body fat mass decreased more in the HP-plan group (Delta 2.2 kg and Delta 3.5 kg respectively) than in the C-plan group (Delta 1.3 kg and Delta 2.3 [corrected] kg respectively) (p < 0.05). The HP- and C-plans had a similar effect on weight and abdominal fat reduction, but the HP-plan was more effective in reducing body fat among compliant subjects.

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

International Nuclear Information System (INIS)

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

2007-01-01

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

Transcatheter aortic valve replacement

Science.gov (United States)

... gov/ency/article/007684.htm Transcatheter aortic valve replacement To use the sharing features on this page, please enable JavaScript. Transcatheter aortic valve replacement (TAVR) is surgery to replace the aortic valve. ...

The Human L1 Element Causes DNA Double-Strand Breaks in Breast Cancer

Science.gov (United States)

2006-08-01

cancer is complex. However, defects in DNA repair genes in the double-strand break repair pathway are cancer predisposing. My lab has characterized...a new potentially important source of double-strand breaks (DSBs) in human cells and are interested in characterizing which DNA repair genes act on...this particular source of DNA damage. Selfish DNA accounts for 45% of the human genome. We have recently demonstrated that one particular selfish

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.

Effects of 18 months of L-T4 replacement in women with subclinical hypothyroidism.

LENUS (Irish Health Repository)

Adrees, M

2012-02-01

CONTEXT: Some of the cardiovascular and renal abnormalities seen in overt hypothyroidism have also been reported in subclinical hypothyroidism (SCH). Short-term L-T4 replacement in SCH improves cardiovascular risk markers and reduces carotid intima-media thickness (CIMT), a surrogate marker of atherosclerosis. The haemodynamic and renal effects of L-T4 replacement in SCH are poorly understood. OBJECTIVES: To compare cardiovascular risk factors and renal variables in women with SCH and normal women. To study the effects of L-T4 replacement in SCH subjects on these variables and on structural and functional changes in common carotid and brachial arteries. DESIGN: Fifty-six women with SCH before and after L-T4 replacement for 18 months and 56 normal women of similar age distribution were studied. Blood Pressure (BP), plasma lipids and homocysteine were measured and renal function evaluated [estimation of glomerular filtration rate (eGFR) using standard equations and measurement of serum Cystatin-C] in women with SCH before and after 18 months of l-T4, and in healthy women. CIMT and endothelial function (using brachial artery ultrasound) were studied before and after L-T4 in a subgroup of women with SCH. RESULTS: Systolic and diastolic BP, total cholesterol, triglyceride, LDL-cholesterol, lipoprotein(a) and homocysteine were greater in SCH (P < 0.05), and following L-T4 replacement decreased (P < 0.05) to levels that no longer differed from normal subjects. Estimated GFR was reduced and serum Cystatin-C increased (P < 0.05) in SCH. These variables also normalized following L-T4. Following L-T4 replacement the carotid artery baseline diameter increased by 7.1% and CIMT decreased by a mean value of 13%, while brachial artery diameter increased basally by 12.5% and following endothelium-dependent vasodilatation by 17.5% (P < 0.05). However, the increment following reactive hyperaemia did not differ before or following L-T4 replacement. CONCLUSION: Normalization of

Radiation dose response of strand breaks in SINPV-DNA

International Nuclear Information System (INIS)

Zhang Chunxiang; Luo Daling; Li Mianfeng; Liu Xiaowei; Zeng Rong; Wang Xunzhang

1995-01-01

The Spodoplera litura Nuclear Polyhedrosis Viruses (SINPV) is a kind of insectile virus with a simple structure, in which a double helix DNA is encapsulated in a protein coat and there is no function of enzymatic repair. The SINPV samples in dry powdered form held in sealed plastic tube were irradiated by 1-100 kGy gamma rays. The single strand breaks (SSB) and double strand breaks (DSB) induced in SINPV after irradiation were measured by neutral and alkaline agarose gel electrophoresis. A dose-response function combining the responses of one-hit and two-hit events was used to describe the SSB and DSB dose-response curves. It is shown that the SSB are one-hit events and the DSB are the combination of both one-hit, and two-hit events, and two-hit events are predominant in the DSB process

Statistical analysis of the Nb3Sn strand production for the ITER toroidal field coils

NARCIS (Netherlands)

Vostner, A.; Jewell, M.C.; Pong, I.; Sullivan, N.; Devred, A.; Bessette, D.; Bevillard, G.; Mitchell, N.; Romano, G.; Zhou, Chao

2017-01-01

The ITER toroidal field (TF) strand procurement initiated the largest Nb3Sn superconducting strand production hitherto. The industrial-scale production started in Japan in 2008 and finished in summer 2015. Six ITER partners (so-called Domestic Agencies, or DAs) are in charge of the procurement and

Effect of current imbalance on stability of a cable-in-conduit conductor consisting of chrome-plated strands

International Nuclear Information System (INIS)

Koizumi, Norikiyo; Takahashi, Yoshikazu; Nishi, Masataka; Isono, Takaaki; Tsuji, Hiroshi; Ono, Michitaka; Hamajima, Takataro; Fujioka, Tsutomu.

1997-02-01

The effect of an unbalanced current distribution in a conductor consisting of chrome plated strands on stability was investigated using a cable-in-conduit conductor (CICC) consisting of 27 NbTi chrome-plated strands. In addition, the quench behavior when a non-uniform current distribution was produced in the conductor was studied from the experimental results. Moreover, impedance of the chrome-plated strands was measured using the sample conductor. The results show that the stability is determined by the largest strand current when it is sufficiently large otherwise by the transport current when it is not high enough. It was found that it took a long time to make the conductor quench from the onset of the normal transition of the strand carrying the large current. This is explained by the good diffusivity of the coolant temperature in the conductor's cross section. Since the ramp-rate limitation cannot probably take place if the coolant temperature is diffused well in the conductor's cross section, it is expected the ramp-rate limitation can be prevented using this effect. It is also shown that the chrome-plated strands come into contact with one another with uniform transverse conductance on the order of 10 3 S/m. (author)

Effects of carbon concentration and filament number on advanced internal Mg infiltration-processed MgB2 strands

International Nuclear Information System (INIS)

Li, G Z; Sumption, M D; Zwayer, J B; Susner, M A; Collings, E W; Rindfleisch, M A; Thong, C J; Tomsic, M J

2013-01-01

In this paper we show that an advanced internal Mg infiltration method (AIMI) is effective in producing superconducting wires containing dense MgB 2 layers with high critical current densities. The in-field critical current densities of a series of AIMI-fabricated MgB 2 strands were investigated in terms of C doping levels, heat treatment (HT) time and filament numbers. The highest layer J c for our monofilamentary AIMI strands was 1.5 × 10 5 A cm −2 at 10 T, 4.2 K, when the C concentration was 3 mol% and the strand was heat-treated at 675 ° C for 4 h. Transport critical currents were also measured at 4.2 K on short samples and 1 m segments of 18-filament C doped AIMI strands. The layer J c s reached 4.3 × 10 5 A cm −2 at 5 T and 7.1 × 10 4 A cm −2 at 10 T, twice as high as those of the best powder-in-tube strands. The analysis of these results indicates that the AIMI strands, possessing both high layer J c s and engineering J e s after further optimization, have strong potential for commercial applications. (paper)

Mass strandings of various ommastrephid squid species have been ...

African Journals Online (AJOL)

spamer

escape reaction, to jet backwards at speed, is commonly observed. Appearing to ... on the occasion of a single mass stranding (La Pylaie, as cited in Lane 1957). ..... have also been associated with the displacement of major water masses ...

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

Directory of Open Access Journals (Sweden)

Amy eStroud

2012-06-01

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

Marine mammal strandings and environmental changes: a 15-year study in the St. Lawrence ecosystem.

Directory of Open Access Journals (Sweden)

Marie-Hélène Truchon

Full Text Available Understanding the effects of climatic variability on marine mammals is challenging due to the complexity of ecological interactions. We used general linear models to analyze a 15-year database documenting marine mammal strandings (1994-2008; n = 1,193 and nine environmental parameters known to affect marine mammal survival, from regional (sea ice to continental scales (North Atlantic Oscillation, NAO. Stranding events were more frequent during summer and fall than other seasons, and have increased since 1994. Poor ice conditions observed during the same period may have affected marine mammals either directly, by modulating the availability of habitat for feeding and breeding activities, or indirectly, through changes in water conditions and marine productivity (krill abundance. For most species (75%, n = 6 species, a low volume of ice was correlated with increasing frequency of stranding events (e.g. R(2adj = 0.59, hooded seal, Cystophora cristata. This likely led to an increase in seal mortality during the breeding period, but also to increase habitat availability for seasonal migratory cetaceans using ice-free areas during winter. We also detected a high frequency of stranding events for mysticete species (minke whale, Balaenoptera acutorostrata and resident species (beluga, Delphinapterus leucas, correlated with low krill abundance since 1994. Positive NAO indices were positively correlated with high frequencies of stranding events for resident and seasonal migratory cetaceans, as well as rare species (R(2adj = 0.53, 0.81 and 0.34, respectively. This contrasts with seal mass stranding numbers, which were negatively correlated with a positive NAO index. In addition, an unusual multiple species mortality event (n = 114, 62% of total annual mortality in 2008 was caused by a harmful algal bloom. Our findings provide an empirical baseline in understanding marine mammal survival when faced with climatic variability. This is a

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)

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

Science.gov (United States)

Piantanida, Ivo; Mašić, Lozika; Rusak, Gordana

2009-04-01

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

Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations

International Nuclear Information System (INIS)

Yoon, Gwonchan; Lee, Myeongsang; Kim, Kyungwoo; In Kim, Jae; Joon Chang, Hyun; Baek, Inchul; Na, Sungsoo; Eom, Kilho

2015-01-01

Amyloid fibrils are responsible for pathogenesis of various diseases and exhibit the structural feature of an ordered, hierarchical structure such as multi-stranded helical structure. As the multi-strandedness of amyloid fibrils has recently been found to be highly correlated with their toxicity and infectivity, it is necessary to study how the hierarchical (i.e. multi-stranded) structure of amyloid fibril is formed. Moreover, although it has recently been reported that the nanomechanics of amyloid proteins plays a key role on the amyloid-induced pathogenesis, a critical role that the multi-stranded helical structure of the fibrils plays in their nanomechanical properties has not fully characterized. In this work, we characterize the morphology and mechanical properties of multi-stranded amyloid fibrils by using equilibrium molecular dynamics simulation and elastic network model. It is shown that the helical pitch of multi-stranded amyloid fibril is linearly proportional to the number of filaments comprising the amyloid fibril, and that multi-strandedness gives rise to improving the bending rigidity of the fibril. Moreover, we have also studied the morphology and mechanical properties of a single protofilament (filament) in order to understand the effect of cross-β structure and mutation on the structures and mechanical properties of amyloid fibrils. Our study sheds light on the underlying design principles showing how the multi-stranded amyloid fibril is formed and how the structure of amyloid fibrils governs their nanomechanical properties. (paper)

Cetaceans stranded in the Netherlands from 1998 to 2007

NARCIS (Netherlands)

Camphuysen, C.J.; Smeenk, C.; Addink, M.; Grouw, van H.; Jansen, O.E.

2008-01-01

Between 1998 and 2007, 2063 cetaceans were found stranded in the Netherlands, representing at least 14 species. Two species, humpback whale (Megaptera novaeangliae) and Blainville's beaked whale (Mesoplodon densirostris), are additions to the Dutch list. Apart from the first humpback whales,

New Insight into Combined Model and Revised Model for RTD Curves in a Multi-strand Tundish

Science.gov (United States)

Lei, Hong

2015-12-01

The analysis for the residence time distribution (RTD) curve is one of the important experimental technologies to optimize the tundish design. But there are some issues about RTD analysis model. Firstly, the combined (or mixed) model and the revised model give different analysis results for the same RTD curve. Secondly, different upper limits of integral in the numerator for the mean residence time give different results for the same RTD curve. Thirdly, the negative dead volume fraction sometimes appears at the outer strand of the multi-strand tundish. In order to solve the above problems, it is necessary to have a deep insight into the RTD curve and to propose a reasonable method to analyze the RTD curve. The results show that (1) the revised model is not appropriate to treat with the RTD curve; (2) the conception of the visual single-strand tundish and the combined model with the dimensionless time at the cut-off point are applied to estimate the flow characteristics in the multi-strand tundish; and that (3) the mean residence time at each exit is the key parameter to estimate the similarity of fluid flow among strands.

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

OpenAIRE

Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

2012-01-01

DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it possible to map SCEs at orders-of-magnitude greater resolution than was previously possible. On average, murine embryonic stem (mES) cells exhibit eight SCEs, which are detected at a resolution of up...

Repair of double-strand breaks in Micrococcus radiodurans

International Nuclear Information System (INIS)

Burrell, A.D.; Dean, C.J.

1975-01-01

Micrococcus radiodurans has been shown to sustain double-strand breaks in its DNA after exposure to x-radiation. Following sublethal doses of x-rays (200 krad in oxygen or less), the cells were able to repair these breaks, and an intermediate fast-sedimenting DNA component seemed to be involved in the repair process

Kinetics of end-to-end collision in short single-stranded nucleic acids.

Science.gov (United States)

Wang, Xiaojuan; Nau, Werner M

2004-01-28

A novel fluorescence-based method, which entails contact quenching of the long-lived fluorescent state of 2,3-diazabicyclo[2.2.2]-oct-2-ene (DBO), was employed to measure the kinetics of end-to-end collision in short single-stranded oligodeoxyribonucleotides of the type 5'-DBO-(X)n-dG with X = dA, dC, dT, or dU and n = 2 or 4. The fluorophore was covalently attached to the 5' end and dG was introduced as an efficient intrinsic quencher at the 3' terminus. The end-to-end collision rates, which can be directly related to the efficiency of intramolecular fluorescence quenching, ranged from 0.1 to 9.0 x 10(6) s(-1). They were strongly dependent on the strand length, the base sequence, as well as the temperature. Oligonucleotides containing dA in the backbone displayed much slower collision rates and significantly higher positive activation energies than strands composed of pyrimidine bases, suggesting a higher intrinsic rigidity of oligoadenylate. Comparison of the measured collision rates in short single-stranded oligodeoxyribonucleotides with the previously reported kinetics of hairpin formation indicates that the intramolecular collision is significantly faster than the nucleation step of hairpin closing. This is consistent with the configurational diffusion model suggested by Ansari et al. (Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc.Natl. Acad. Sci. USA 2001, 98, 7771-7776), in which the formation of misfolded loops is thought to slow hairpin formation.

Dissimilar kinetic behavior of electrically manipulated single- and double-stranded DNA tethered to a gold surface.

Science.gov (United States)

Rant, Ulrich; Arinaga, Kenji; Tornow, Marc; Kim, Yong Woon; Netz, Roland R; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard

2006-05-15

We report on the electrical manipulation of single- and double-stranded oligodeoxynucleotides that are end tethered to gold surfaces in electrolyte solution. The response to alternating repulsive and attractive electric surface fields is studied by time-resolved fluorescence measurements, revealing markedly distinct dynamics for the flexible single-stranded and stiff double-stranded DNA, respectively. Hydrodynamic simulations rationalize this finding and disclose two different kinetic mechanisms: stiff polymers undergo rotation around the anchoring pivot point; flexible polymers, on the other hand, are pulled onto the attracting surface segment by segment.

Ankle replacement - discharge

Science.gov (United States)

... total - discharge; Total ankle arthroplasty - discharge; Endoprosthetic ankle replacement - discharge; Osteoarthritis - ankle ... You had an ankle replacement. Your surgeon removed and reshaped ... an artificial ankle joint. You received pain medicine and were ...

75 FR 28560 - Prestressed Concrete Steel Wire Strand From the People's Republic of China: Final Determination...

Science.gov (United States)

2010-05-21

... DEPARTMENT OF COMMERCE International Trade Administration [A-570-945] Prestressed Concrete Steel... antidumping investigation of prestressed concrete steel strand (``PC strand'') from the People's Republic of... are shown in the ``Final Determination Margins'' section of this notice. \\1\\ See Prestressed Concrete...

Getting it right: Filling the gaps in FERC's stranded cost policies

International Nuclear Information System (INIS)

Gordon, K.; Olson, W.P.

1999-01-01

FERC is currently at a cross-road: It must implement its stranded cost policies properly or the comprehensive approach that Order 888 represents will not be credible. In this context, it is important to remember that public policies aimed at introducing competition into electricity markets will proceed more quickly and effectively if the regulatory bargain is kept. Thus, any plan to introduce competition in electricity must honor existing commitments and provide utilities with a reasonable opportunity to recover prudently incurred investments. By closing the gaps in its stranded cost recovery policies in economically appropriate ways, FERC can reaccelerate the movement to efficient competition in generation markets

Patients Unicondylar Knee Replacement vs. Total Knee Replacement

OpenAIRE

Hedra Eskander

2017-01-01

The aim of this review article is to analyse the clinical effectiveness of total knee replacement (TKR) compared to unicondylar knee replacement (UKR) on patients. In terms of survival rates, revision rates and postoperative complications. The keywords used were: knee arthroplasty. Nearly three thousand articles were found on 25 August 2016. Of those, only twenty-five were selected and reviewed because they were strictly focused on the topic of this article. Compared with those who have TKR, ...

A hybrid deterministic-probabilistic approach to model the mechanical response of helically arranged hierarchical strands

Science.gov (United States)

Fraldi, M.; Perrella, G.; Ciervo, M.; Bosia, F.; Pugno, N. M.

2017-09-01

Very recently, a Weibull-based probabilistic strategy has been successfully applied to bundles of wires to determine their overall stress-strain behaviour, also capturing previously unpredicted nonlinear and post-elastic features of hierarchical strands. This approach is based on the so-called "Equal Load Sharing (ELS)" hypothesis by virtue of which, when a wire breaks, the load acting on the strand is homogeneously redistributed among the surviving wires. Despite the overall effectiveness of the method, some discrepancies between theoretical predictions and in silico Finite Element-based simulations or experimental findings might arise when more complex structures are analysed, e.g. helically arranged bundles. To overcome these limitations, an enhanced hybrid approach is proposed in which the probability of rupture is combined with a deterministic mechanical model of a strand constituted by helically-arranged and hierarchically-organized wires. The analytical model is validated comparing its predictions with both Finite Element simulations and experimental tests. The results show that generalized stress-strain responses - incorporating tension/torsion coupling - are naturally found and, once one or more elements break, the competition between geometry and mechanics of the strand microstructure, i.e. the different cross sections and helical angles of the wires in the different hierarchical levels of the strand, determines the no longer homogeneous stress redistribution among the surviving wires whose fate is hence governed by a "Hierarchical Load Sharing" criterion.

Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels.

Science.gov (United States)

Si, Dong; He, Jing

2014-01-01

Electron cryo-microscopy (Cryo-EM) technique produces 3-dimensional (3D) density images of proteins. When resolution of the images is not high enough to resolve the molecular details, it is challenging for image processing methods to enhance the molecular features. β-barrel is a particular structure feature that is formed by multiple β-strands in a barrel shape. There is no existing method to derive β-strands from the 3D image of a β-barrel at medium resolutions. We propose a new method, StrandRoller, to generate a small set of possible β-traces from the density images at medium resolutions of 5-10Å. StrandRoller has been tested using eleven β-barrel images simulated to 10Å resolution and one image isolated from the experimentally derived cryo-EM density image at 6.7Å resolution. StrandRoller was able to detect 81.84% of the β-strands with an overall 1.5Å 2-way distance between the detected and the observed β-traces, if the best of fifteen detections is considered. Our results suggest that it is possible to derive a small set of possible β-traces from the β-barrel cryo-EM image at medium resolutions even when no separation of the β-strands is visible in the images.

Primary resistance to integrase strand-transfer inhibitors in Europe.

NARCIS (Netherlands)

M. Casadellá; P.M. van Ham (Petra); M. Noguera-Julian; A. van Kessel; C. Pou; L.M. Hofstra (Marije); G.A. Metcalf (Ginger A.); F. Garcia; D. Struck (Daniel); I. Alexiev (Ivailo); A.M. Bakken Kran; A.I.M. Hoepelman; L.G. Kostrikis (Leondios); S. Somogyi; K. Liitsola (Kirsi); M. Linka (Marek); C. Nielsen; D. Otelea (Dan); D. Paraskevis (Dimitrios); M. Poljak (Mario); E. Puchhammer-Stöckl (Elisabeth); D. Stanekova (Danica); M. Stanojevic (Maja); K. Van Laethem (Kristel); S. Zidovec Lepej (Snjezana); B. Clotet; C.A.B. Boucher (Charles); R. Paredes (Roger); A.M.J. Wensing (Annemarie)

2015-01-01

markdownabstractThe objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. This was a multicentre, cross-sectional study within the European SPREAD

Primary resistance to integrase strand-transfer inhibitors in Europe

NARCIS (Netherlands)

Casadella, M.; van Ham, P. M.; Noguera-Julian, M.; van Kessel, A.; Pou, C.; Hofstra, L. M.; Santos, J. R.; Garcia, F.; Struck, D.; Alexiev, I.; Kran, A. M. Bakken; Hoepelman, A. I.; Kostrikis, L. G.; Somogyi, S.; Liitsola, K.; Linka, M.; Nielsen, C.; Otelea, D.; Paraskevis, D.; Poljak, M.; Puchhammer-Stoeckl, E.; Stanekova, D.; Stanojevic, M.; Van Laethem, K.; Lepej, S. Zidovec; Clotet, B.; Boucher, C. A. B.; Paredes, R.; Wensing, A. M. J.; Schuurman, R

2015-01-01

Objectives: The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. Methods: This was a multicentre, cross-sectional study within the European

Relationship between mitochondrial gene rearrangements and stability of the origin of light strand replication

Directory of Open Access Journals (Sweden)

Miguel M. Fonseca

2008-01-01

Full Text Available Mitochondrial gene rearrangements are much more frequent in vertebrates than initially thought. It has been suggested that the origin of light strand replication could have an important role in the process of gene rearrangements, but this hypothesis has never been tested before. We used amphibians to test the correlation between light-strand replication origin thermodynamic stability and the occurrence of gene rearrangements. The two variables were correlated in a non-phylogenetic approach, but when tested in a phylogenetically based comparative method the correlation was not significant, although species with unstable light-strand replication origins were much more likely to have undergone gene rearrangements. This indicates that within amphibians there are stable and unstable phylogenetic groups regarding mitochondrial gene order. The species analyzed showed variability in the thermodynamic stability of the secondary structure, in the length of its stem and loop, and several species did not present the 5’-GCCGG-3’ motif reported to be necessary for efficient mitochondrial DNA replication. Future studies should focus on the role of the light-strand replication origin in mitochondrial DNA replication and gene rearrangements mechanisms.

Artificial Disc Replacement

Science.gov (United States)

... Spondylolisthesis BLOG FIND A SPECIALIST Treatments Artificial Disc Replacement (ADR) Patient Education Committee Jamie Baisden The disc ... Disc An artificial disc (also called a disc replacement, disc prosthesis or spine arthroplasty device) is a ...

Protection of free-radical induced DNA strand breaks in vitro by flavonoids

International Nuclear Information System (INIS)

Fisher, L.; Anderson, R.F.

1998-01-01

Full text: We have used both plasmid and cosmid test systems to assay the effect of antioxidant flavonoids (AO) on DNA strand breakage in supercoiled closed circular DNA (DNA SC ) following the formation oxidative radical damage on DNA (DNA OXID + . ) in aqueous solution. Single strand breaks in DNA SC result in the formation of the relaxed circular form (DNA RC ) and double strand breaks give linear DNA (DNA L ). Dose response curves were constructed for the log of the loss of [DNA S C] against dose (0-600 Gy). The D 37 (dose for 37% unchanged DNA SC ) values determined in the presence of increasing amounts of flavonoids were compared as ratios to the D 37 control value to give dose modification factor (DMF). Irradiations were carried out under 'constant scavenging' conditions to separate out the effect of direct radical scavenging from the possible electron transfer reaction. Control irradiation experiments, were performed in aerated TRIS buffer, concentration 10 mM, which has a scavenging capacity, k s (defined as the summation of the rate constants for the reaction of OH radicals with all species in solution, multiplied by their concentrations) of 1.5 x 10 7 s -1 . The concentration of TRIS was reduced upon addition of AO to maintain k s at this level. Data will be presented for examples from all four major types of flavonoids (flavonols, isoflavones, flavones and flavon-3-ols) showing DMF values plateau at near 2.0 even at low concentrations (ca. 20 μM) of the flavonoids. Increased DNA strand breaks following post irradiation incubation with endo III protein was unaffected by having the flavonoids present at the time of irradiation. This result suggests that the protection afforded by the flavonoids is unlikely to be in repairing radical damage on pyrimidine bases that are precursors of DNA strand breaks. Overall these studies provide evidence for an additional mechanism of antioxidant activity

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.

Product Platform Replacements

DEFF Research Database (Denmark)

Sköld, Martin; Karlsson, Christer

2012-01-01

. To shed light on this unexplored and growing managerial concern, the purpose of this explorative study is to identify operational challenges to management when product platforms are replaced. Design/methodology/approach – The study uses a longitudinal field-study approach. Two companies, Gamma and Omega...... replacement was chosen in each company. Findings – The study shows that platform replacements primarily challenge managers' existing knowledge about platform architectures. A distinction can be made between “width” and “height” in platform replacements, and it is crucial that managers observe this in order...... to challenge their existing knowledge about platform architectures. Issues on technologies, architectures, components and processes as well as on segments, applications and functions are identified. Practical implications – Practical implications are summarized and discussed in relation to a framework...

DNA strand scission by the novel antitumor antibiotic leinamycin

International Nuclear Information System (INIS)

Hara, Mitsunobu; Saitoh, Yutaka; Nakano, Hirofumi

1990-01-01

Leinamycin is a recently discovered antitumor antibiotic with an unusual 1,3-dioxo-1,2-dithiolane structure. It preferentially inhibits the incorporation of [ 3 H]thymidine into the acid-insoluble fraction of Bacillus subtilis. In vitro, leinamycin causes single-strand cleavage of supercoiled double-helical pBR322 DNA in the presence of thiol cofactors. Scavengers of oxygen radical did not suppress the DNA-cleaving activity. Thiol-activated leinamycin binds calf thymus DNA at 4 degree C and thermal treatment of the leinamycin-DNA adduct released a chemically modified leinamycin from the complex. The lack of cytotoxicity and DNA-cleaving activity for S-deoxyleinamycin indicates that the 1,3-dioxo-1,2-dithiolane moiety is essential for the activity of leinamycin. Thus, the primary cellular target of leinamycin appears to be DNA. It binds DNA and causes single-strand break at low concentrations, which may account for the potent antitumor activity

Single-strand DNA molecule translocation through nanoelectrode gaps

International Nuclear Information System (INIS)

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

2007-01-01

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

Protection of DNA strand breakage by radiation exposure

International Nuclear Information System (INIS)

Lee, Jeong Ho; Kim, In Gyu; Lee, Kang Suk; Kim, Kug Chan; Shim, Hae Won

1997-12-01

Human ceruloplasmin, the plasma copper containing protein, is thought to play an essential role in iron metabolism, but it also has antioxidant properties. Ceruloplasmin directly scavenged hydroxyl radicals (.OH) generated in dithiothreitol/FeCl 3 system besides inhibitory function of hydroxyl radical formation and lipid peroxidation. Polyamines, spermidine and spermine, significantly protected the supercoiled DNA strand breakage by hydroxyl radicals and DNA strand breakage by UV was highly protected by all four polyamines used in this study. In polyamine deficient mutant KL527. It was shown that cell survivability following UV irradiation was slightly increased by exogenous polyamines putrescine and spermidine supplement. However the cell survivability of wild type (MG 1655) was not influenced by polyamine supplement. In γ-irradiated cells, cell survivability of polyamine-deficient mutant strain KL527 was significantly increased by exogenous putrescine supplement and that of wild type strain MG1655 was similar irrespective of polyamine supplement. These results implicate the possibility that polyamines play a potent role in radioprotection of cell and DNA level. (author). 32 refs., 8 figs

An extended optimal replacement model for a deteriorating system with inspections

International Nuclear Information System (INIS)

Sheu, Shey-Huei; Tsai, Hsin-Nan; Wang, Fu-Kwun; Zhang, Zhe George

2015-01-01

This study considers a generalized replacement model for a deteriorating system in which failures can only be detected by inspection. The system is assumed to have two types of failures and is replaced at the occurrence of the Nth type I failure (minor failure), or the first type II failure (catastrophic failure), or at working age T, whichever occurs first. The probability of a type I or type II failure depends on the number of type I failures since the previous replacement. Such a system can be repaired after a type I failure, but is deteriorating stochastically. That is, the operating intervals are decreasing stochastically, whereas the durations of the repairs are increasing stochastically. Based on these assumptions, we determine the expected net cost rate and discuss various special cases of the model. Finally, we develop a computational algorithm for finding the optimal policy and present a numerical example to show the properties of the proposed model. - Highlight: • Replacement policy for system subject two types of failures or the system's working age. • Failures detected by inspections. • Decreasing operating times and increasing repair times. • Derive a cost function. • Determine the cost minimization policy

Inhibition of APOBEC3G Activity Impedes Double-Strand DNA Repair

Science.gov (United States)

Prabhu, Ponnandy; Shandilya, Shivender; Britan-Rosich, Elena; Nagler, Adi; Schiffer, Celia A.; Kotler, Moshe

2015-01-01

The cellular cytidine deaminase APOBEC3G (A3G) was first described as an anti-HIV-1 restriction factor by directly deaminating reverse transcripts of the viral genome. HIV-1 Vif neutralizes the activity of A3G, primarily by mediating degradation of A3G to establish effective infection in host target cells. Lymphoma cells, which express high amounts of A3G, can restrict Vif-deficient HIV-1. Interestingly, these cells are more stable in the face of treatments that result in dsDNA damage, such as ionizing irradiation (IR) and chemotherapies. Previously, we showed that the Vif-derived peptide (Vif25-39) efficiently inhibits A3G deamination, and increases sensitivity of lymphoma cells to IR. In the current study, we show that additional peptides derived from Vif, A3G and A3F, which contain the LYYF motif, inhibit deamination activity. Each residue in the Vif25-39 sequence moderately contributes to the inhibitory effect, while, replacing a single amino acid in the LYYF motif completely abrogate inhibition of deamination. Treatment of A3G-expressing lymphoma cells exposed to ionizing radiation with the new inhibitory peptides reduces double-strand break (DSB) repair after radiation. Incubation of cultured irradiated lymphoma cells with peptides that inhibit DSB repair halts their propagation. These results suggest that A3G may be a potential therapeutic target amenable to peptide and peptidomimetic inhibition. PMID:26460502

Replacement

Directory of Open Access Journals (Sweden)

S. Radhakrishnan

2014-03-01

Full Text Available The fishmeal replaced with Spirulina platensis, Chlorella vulgaris and Azolla pinnata and the formulated diet fed to Macrobrachium rosenbergii postlarvae to assess the enhancement ability of non-enzymatic antioxidants (vitamin C and E, enzymatic antioxidants (superoxide dismutase (SOD and catalase (CAT and lipid peroxidation (LPx were analysed. In the present study, the S. platensis, C. vulgaris and A. pinnata inclusion diet fed groups had significant (P < 0.05 improvement in the levels of vitamins C and E in the hepatopancreas and muscle tissue. Among all the diets, the replacement materials in 50% incorporated feed fed groups showed better performance when compared with the control group in non-enzymatic antioxidant activity. The 50% fishmeal replacement (best performance diet fed groups taken for enzymatic antioxidant study, in SOD, CAT and LPx showed no significant increases when compared with the control group. Hence, the present results revealed that the formulated feed enhanced the vitamins C and E, the result of decreased level of enzymatic antioxidants (SOD, CAT and LPx revealed that these feeds are non-toxic and do not produce any stress to postlarvae. These ingredients can be used as an alternative protein source for sustainable Macrobrachium culture.

Use of Tranexamic Acid during Total Endoprosthetic Replacement of the Hip Joint

Directory of Open Access Journals (Sweden)

D. D. Selivanov

2010-01-01

Full Text Available Objective: to evaluate the blood-saving activity, efficacy, and safety of tranexamic acid. Subjects and methods. Thirty-seven patients allocated into two groups were enrolled in the study of the efficacy of tranexamic acid as an agent in reducing blood loss during hip joint replacement. Group 2 patients were injected tranexamic acid, 10 mg/kg body weight, 20—30 minutes before and 3 hours after surgery in the same dosage. This resulted in a significant (48.5% reduction in total blood loss (from 1089.6 to 560.8 ml (p<0.05. No tranexamic acid-induced complications were found. The administration of tranexamic acid during total endoprosthetic replacement of the hip joint could reduce blood loss by 35 and 59.4% in the intraoperative and postoperative periods, respectively, and total blood loss by 48.4%. The use of tranexamic acid allows one to refuse transfusion of blood components during total endoprosthetic replacement of the hip joint. Key words: hip joint replacement, blood loss, tranexamic acid.

Binding to the minor groove of the double-strand, tau protein prevents DNA from damage by peroxidation.

Science.gov (United States)

Wei, Yan; Qu, Mei-Hua; Wang, Xing-Sheng; Chen, Lan; Wang, Dong-Liang; Liu, Ying; Hua, Qian; He, Rong-Qiao

2008-07-02

Tau, an important microtubule associated protein, has been found to bind to DNA, and to be localized in the nuclei of both neurons and some non-neuronal cells. Here, using electrophoretic mobility shifting assay (EMSA) in the presence of DNA with different chain-lengths, we observed that tau protein favored binding to a 13 bp or a longer polynucleotide. The results from atomic force microscopy also showed that tau protein preferred a 13 bp polynucleotide to a 12 bp or shorter polynucleotide. In a competitive assay, a minor groove binder distamycin A was able to replace the bound tau from the DNA double helix, indicating that tau protein binds to the minor groove. Tau protein was able to protect the double-strand from digestion in the presence of DNase I that was bound to the minor groove. On the other hand, a major groove binder methyl green as a negative competitor exhibited little effect on the retardation of tau-DNA complex in EMSA. This further indicates the DNA minor groove as the binding site for tau protein. EMSA with truncated tau proteins showed that both the proline-rich domain (PRD) and the microtubule-binding domain (MTBD) contributed to the interaction with DNA; that is to say, both PRD and MTBD bound to the minor groove of DNA and bent the double-strand, as observed by electron microscopy. To investigate whether tau protein is able to prevent DNA from the impairment by hydroxyl free radical, the chemiluminescence emitted by the phen-Cu/H(2)O(2)/ascorbate was measured. The emission intensity of the luminescence was markedly decreased when tau protein was present, suggesting a significant protection of DNA from the damage in the presence of hydroxyl free radical.

A link between double-strand break-related repair and V(D)J recombination: the scid mutation

International Nuclear Information System (INIS)

Hendrickson, E.A.; Qin, X.Q.; Bump, E.A.; Schatz, D.G.; Oettinger, M.; Weaver, D.T.

1991-01-01

We show here that mammalian site-specific recombination and DNA-repair pathways share a common factor. The effects of DNA-damaging agents on cell lines derived from mice homozygous for the scid (severe combined immune deficiency) mutation were studied. Surprisingly, all scid cell lines exhibited a profound hypersensitivity to DNA-damaging agents that caused double-strand breaks (x-irradiation and bleomycin) but not to other chemicals that caused single-strand breaks or cross-links. Neutral filter elution assays demonstrated that the x-irradiation hypersensitivity could be correlated with a deficiency in repairing double-strand breaks. These data suggest that the scid gene product is involved in two pathways: DNA repair of random double-strand breaks and the site-specific and lymphoid-restricted variable-(diversity)-joining [V(D)J] DNA rearrangement process. We propose that the scid gene product performs a similar function in both pathways and may be a ubiquitous protein

RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans.

Science.gov (United States)

Steiner, Florian A; Okihara, Kristy L; Hoogstrate, Suzanne W; Sijen, Titia; Ketting, René F

2009-02-01

RNA interference (RNAi) is a process in which double-stranded RNA is cleaved into small interfering RNAs (siRNAs) that induce the destruction of homologous single-stranded mRNAs. Argonaute proteins are essential components of this silencing process; they bind siRNAs directly and can cleave RNA targets using a conserved RNase H motif. In Caenorhabditis elegans, the Argonaute protein RDE-1 has a central role in RNAi. In animals lacking RDE-1, the introduction of double-stranded RNA does not trigger any detectable level of RNAi. Here we show that RNase H activity of RDE-1 is required only for efficient removal of the passenger strand of the siRNA duplex and not for triggering the silencing response at the target-mRNA level. These results uncouple the role of the RDE-1 RNase H activity in small RNA maturation from its role in target-mRNA silencing in vivo.

Comparing damage on retrieved total elbow replacement bushings with lab worn specimens subjected to varied loading conditions.

Science.gov (United States)

Willing, Ryan

2018-01-09

Complication rates following total elbow replacement (TER) with conventional implants are relatively high due to mechanical failure involving the UHMWPE bushings. Unfortunately, there are no standardized pre-clinical durability testing protocols for assessing the durability of TER components. This study examines the damage observed on retrieved humeral bushings, and then uses in vitro durability testing with two different loading protocols to compare resulting damage. Damage on 25 pairs of retrieved humeral bushings was characterized using micro-computed tomographic imaging techniques. The damage was compared with that of in vitro test specimens which were subjected to 200 K cycles of either high joint reaction force (high JRF) or high varus moment (high VM) loading. Material removal (mass loss) from bushing components was measured using gravimetric techniques. Thinning was less for retrieved bushings which were still assembled in their humeral component, versus bushings which were loose (0.3 ± 0.3 mm vs. 0.6 ± 0.3 mm, p = 0.02). Comparing in vitro test specimens, thinning due to high VM loading was 0.9 ± 0.3 mm, versus 0.2 ± 0.0 mm for high JRF loading (p = 0.08); however, the actual material removal rates from the humeral bushings were not different between the two protocols (48 ± 5 mm 3 /Mc vs. 43 ± 2 mm 3 /Mc, p = 1). Neither loading protocol could produce damage patterns fully representative of the spectrum of damage patterns observed on clinical retrievals. Pre-clinical testing should employ multiple loading protocols to characterize implant performance under a broader spectrum of usage. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Meta-analysis of DNA double-strand break response kinetics

NARCIS (Netherlands)

Kochan, Jakub A.; Desclos, Emilie C. B.; Bosch, Ruben; Meister, Luna; Vriend, Lianne E. M.; Attikum, Haico V.; Krawczyk, Przemek M.

2017-01-01

Most proteins involved in the DNA double-strand break response (DSBR) accumulate at the damage sites, where they perform functions related to damage signaling, chromatin remodeling and repair. Over the last two decades, studying the accumulation of many DSBR proteins provided information about their

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.

The transport of 3H and 14C in phloem strands of Heracleum lanatum and polyester threads

International Nuclear Information System (INIS)

Hoddinott, J.; Gorham, P.R.

1976-01-01

Experiments are described which show a great similarity in the profiles of rapid movement of tritium after external application of 3 H 2 O to a small segment of a phloem strand of Heracleum lanatum and a water-soaked polyester thread. Efflux of rapidly transported tritium from phloem strands and polyester threads was also similar. No rapid movement of radioisotope from (U- 14 C)sucrose, (6,6'- 3 H)sucrose, or (6- 3 H)glucose along phloem strands was observed. A possible explanation for the rapid movement of tritium in terms of proton transfer is offered. It is concluded that the rapid movement of tritium in a phloem strand which occurs when 3 H 2 O is applied externally to a segment is an artifact and that no normal translocation is occurring. (author)

$Nb_{3}Sn macrostructure, microstructure, and property comparisons for bronze and internal Sn process strands

CERN Document Server

Lee, P J; Larbalestier, D C

2000-01-01

The variation in irreversibility field, B*(T), with temperature has been measured for Nb/sub 3/Sn superconducting strands manufactured for ITER using vibrating sample and SQUID magnetometers. The high performance strands were developed for both high transport critical current density, J/sub c/, and low hysteresis loss. Despite a wide variety of designs and components, the strands could be split into two distinctive groups, based on the extrapolated irreversibility fields, which lie about 10% lower than the upper critical field. "Bronze-process" strands exhibited consistently higher B*(T) (28 T to 31 T) compared with "internal Sn" process (24 T to 26 T) conductors. The intrinsic critical current density of the superconductor, J/sub c (sc)/, and the specific pinning force of the grain boundaries, Q/sub gb/, were evaluated using the measured J/sub c/, and image analysis of the macro- and micro-structures. A bronze-processed Nb(-Ta)/sub 3 /Sn was found to have a higher J/sub c(sc)/ but lower Q/sub gb/ than Nb/sub...

Quench performance of Nb3Sn cos-theta coils made of 108/127 RRP strands

International Nuclear Information System (INIS)

Zlobin, A.V.; Ambrosio, G.; Andreev, N.; Barzi, E.; Bossert, R.; Carcagno, R.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; Nobrega, F.; Novitski, I.

2007-01-01

A series of 1-m long Nb 3 Sn dipole models has been built at Fermilab in an attempt to refine the wind-and-react technology for Nb3Sn accelerator magnets. Three models made with Powder-in-Tube Nb 3 Sn strand reached their design field of 10 T demonstrating a good reproducibility of magnet quench performance and field quality. Recently a new dipole 'mirror' model based on Nb 3 Sn coil made of improved Restack Rod Process strand was constructed and tested reaching the maximum field above 11 T. This paper describes the parameters of the RRP strand and cable used as well as the design, fabrication and test results of this magnet

Double strand breaks in DNA in vivo and in vitro after 60Co-γ-irradiation

International Nuclear Information System (INIS)

Huelsewede, J.W.

1985-01-01

The questions of what the correlation is between double strand breaks in DNA in the cell and lethal radiation damage and by means of which possible mechanisms DNA double strand breaks could occur were studied. E. coli served as test system. In addition to this the molecular weight of the DNA from irradiated E. coli as a function of the radiation dose under various conditions was measured. This data was compared on the one hand to the survival of the cell and on the other hand to the formation of DNA double strand breaks in an aqueous buffer system, which in its ionic characteristics was similar to cell fluids. (orig./MG) [de

Yield of single-strand breaks in the DNA of E. coli 10 msec after irradiation

Energy Technology Data Exchange (ETDEWEB)

Fox, R A; Fielden, E M; Sapora, O [Institute of Cancer Research, Sutton (UK). Surrey Branch

1976-04-01

The rapid mixing of 0.3M alkali with a suspension of E.coli B/r 6 +- 3 and 144 +- 3 msec after irradiation with electrons (4.3 MeV, 0 to 50 krad) has been used to make a comparison of the yields of single strand breaks in the presence and absence of oxygen. No significant difference was observed between the numbers of single strand breaks appearing at 6 and 144 msec after irradiation. Assuming that mixing with alkali inactivates the cellular repair enzymes within several milliseconds, these results indicate that enzymic repair does not operate within this time scale. It seems probable that radiation chemical processes are responsible for the initial oxygen effect on single strand breaks.

Don't get bogged down by stranded assets - McCready

International Nuclear Information System (INIS)

Anon.

1996-01-01

Remarks made at the December 1995 IPPSO Conference by TransAlta CEO Ken McCready were summarized to the effect that the benefits of competition are too important to let stranded assets delay things much longer. He was reported as saying that government and industry have choices to make in terms of how they deal with stranded assets, but there is no excuse for limiting the range of policy options that are now available. A transformation in the utility industry has been brought about by advances in technology and by the separation of energy supply from the common carrier. In Mr. McCready's view, these factors, combined with government capital requirements and the need for more efficient management of power systems, have brought about a state of affairs that makes privatization of public utilities inevitable

Capital Equipment Replacement Decisions

OpenAIRE

Batterham, Robert L.; Fraser, K.I.

1995-01-01

This paper reviews the literature on the optimal replacement of capital equipment, especially farm machinery. It also considers the influence of taxation and capital rationing on replacement decisions. It concludes that special taxation provisions such as accelerated depreciation and investment allowances are unlikely to greatly influence farmers' capital equipment replacement decisions in Australia.

Colonic stem cell data are consistent with the immortal model of stem cell division under non-random strand segregation.

Science.gov (United States)

Walters, K

2009-06-01

Colonic stem cells are thought to reside towards the base of crypts of the colon, but their numbers and proliferation mechanisms are not well characterized. A defining property of stem cells is that they are able to divide asymmetrically, but it is not known whether they always divide asymmetrically (immortal model) or whether there are occasional symmetrical divisions (stochastic model). By measuring diversity of methylation patterns in colon crypt samples, a recent study found evidence in favour of the stochastic model, assuming random segregation of stem cell DNA strands during cell division. Here, the effect of preferential segregation of the template strand is considered to be consistent with the 'immortal strand hypothesis', and explore the effect on conclusions of previously published results. For a sample of crypts, it is shown how, under the immortal model, to calculate mean and variance of the number of unique methylation patterns allowing for non-random strand segregation and compare them with those observed. The calculated mean and variance are consistent with an immortal model that incorporates non-random strand segregation for a range of stem cell numbers and levels of preferential strand segregation. Allowing for preferential strand segregation considerably alters previously published conclusions relating to stem cell numbers and turnover mechanisms. Evidence in favour of the stochastic model may not be as strong as previously thought.

High incidence of non-random template strand segregation and asymmetric fate determination in dividing stem cells and their progeny.

Science.gov (United States)

Conboy, Michael J; Karasov, Ariela O; Rando, Thomas A

2007-05-01

Decades ago, the "immortal strand hypothesis" was proposed as a means by which stem cells might limit acquiring mutations that could give rise to cancer, while continuing to proliferate for the life of an organism. Originally based on observations in embryonic cells, and later studied in terms of stem cell self-renewal, this hypothesis has remained largely unaccepted because of few additional reports, the rarity of the cells displaying template strand segregation, and alternative interpretations of experiments involving single labels or different types of labels to follow template strands. Using sequential pulses of halogenated thymidine analogs (bromodeoxyuridine [BrdU], chlorodeoxyuridine [CldU], and iododeoxyuridine [IdU]), and analyzing stem cell progeny during induced regeneration in vivo, we observed extraordinarily high frequencies of segregation of older and younger template strands during a period of proliferative expansion of muscle stem cells. Furthermore, template strand co-segregation was strongly associated with asymmetric cell divisions yielding daughters with divergent fates. Daughter cells inheriting the older templates retained the more immature phenotype, whereas daughters inheriting the newer templates acquired a more differentiated phenotype. These data provide compelling evidence of template strand co-segregation based on template age and associated with cell fate determination, suggest that template strand age is monitored during stem cell lineage progression, and raise important caveats for the interpretation of label-retaining cells.

High incidence of non-random template strand segregation and asymmetric fate determination in dividing stem cells and their progeny.

Directory of Open Access Journals (Sweden)

Michael J Conboy

2007-05-01

Full Text Available Decades ago, the "immortal strand hypothesis" was proposed as a means by which stem cells might limit acquiring mutations that could give rise to cancer, while continuing to proliferate for the life of an organism. Originally based on observations in embryonic cells, and later studied in terms of stem cell self-renewal, this hypothesis has remained largely unaccepted because of few additional reports, the rarity of the cells displaying template strand segregation, and alternative interpretations of experiments involving single labels or different types of labels to follow template strands. Using sequential pulses of halogenated thymidine analogs (bromodeoxyuridine [BrdU], chlorodeoxyuridine [CldU], and iododeoxyuridine [IdU], and analyzing stem cell progeny during induced regeneration in vivo, we observed extraordinarily high frequencies of segregation of older and younger template strands during a period of proliferative expansion of muscle stem cells. Furthermore, template strand co-segregation was strongly associated with asymmetric cell divisions yielding daughters with divergent fates. Daughter cells inheriting the older templates retained the more immature phenotype, whereas daughters inheriting the newer templates acquired a more differentiated phenotype. These data provide compelling evidence of template strand co-segregation based on template age and associated with cell fate determination, suggest that template strand age is monitored during stem cell lineage progression, and raise important caveats for the interpretation of label-retaining cells.

RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans.

NARCIS (Netherlands)

Steiner, F.A.; Okihara, K.L.; Hoogstrate, S.W.; Sijen, T.; Ketting, R.F.

2009-01-01

RNA interference (RNAi) is a process in which double-stranded RNA is cleaved into small interfering RNAs (siRNAs) that induce the destruction of homologous single-stranded mRNAs. Argonaute proteins are essential components of this silencing process; they bind siRNAs directly and can cleave RNA

Theoretical investigation of the production of strand breaks in DNA by water radicals

International Nuclear Information System (INIS)

Chatterjee, A.; Magee, J.L.

1985-01-01

A calculation has been made of the indirect action of radiation on SV40 DNA in dilute aqueous solution, including the extent of OH reaction with both the sugar moiety and the bases. A realistic DNA model is used along with a track model that gives the correct decay rates of hydrated electrons and OH radicals in pure water with the same calculational techniques. It was found, in agreement with experiment, that 80% of the OH attack on DNA is on the bases and 20% is on the sugar. It is estimated that the probability is almost non-existent ( -6 ) for two OH radicals from the same track or from two tracks to reach sugars on opposite strands within 12 base pairs from each other. Thus double strand breaks that depend linearly on the dose (as we find in a companion experimental programme) must arise from some other mechanism. The calculated single strand break probabilities are in good agreement with experiment. (author)

Replacing lactose from calf milk replacers : effects on digestion and post-absorptive metabolism

NARCIS (Netherlands)

Gilbert, M.S.

2015-01-01

Summary PhD thesis Myrthe S. Gilbert

Replacing lactose from calf milk replacers – Effects on digestion and post-absorptive metabolism

Veal calves are fed milk replacer (MR) and solid feed. The largest part of the energy provided to veal calves

Repair of single-strand breaks induced in the DNA of Proteus mirabilis by excision repair after UV-irradiation

International Nuclear Information System (INIS)

Stoerl, K.; Mund, C.

1977-01-01

Single-strand breaks have been produced in the DNA of P. mirabilis after UV-irradiation in dependence on the incident UV-doses. It has been found that there exists a discrepancy between the single-strand breaks estimated from sedimentation in alkaline sucrose gradients and the expected single-strand breaks approximated from measurements of dimer excision. The low number in incision breaks observed by sedimentation experiments is an indication that the cells are able to repair the excision-induced breaks as fast as they are formed. Toluenized cells have been used for investigation of the incision step independently of subsequent repair processes. In presence of NMN the appearance of more single-strand breaks in the DNA has been observed. Furthermore, the number of incision breaks in toluenized cells increased in presence of exogenous ATP. The completion of the excision repair process has been investigated by observing the rejoining of incision breaks. After irradiation with UV-doses higher than approximately 240 erg/mm 2 the number of single-strand breaks remaining unrepaired in the DNA increased. Studies of the influence of nutrition conditions on the repair process have shown approximately the same capacity for repair of single-strand breaks in growth medium as well as in buffer. Progress in the excision repair was also followed by investigation of the DNA synthesized at the template-DNA containing the pyrimidine dimers. In comparison with E. coli, P. mirabilis showed a somewhat lower efficiency for the repair of single-strand breaks during the excision repair. (author)

Efficient disruption and replacement of an effector gene in the oomycete Phytophthora sojae using CRISPR/Cas9.

Science.gov (United States)

Fang, Yufeng; Tyler, Brett M

2016-01-01

Phytophthora sojae is an oomycete pathogen of soybean. As a result of its economic importance, P. sojae has become a model for the study of oomycete genetics, physiology and pathology. The lack of efficient techniques for targeted mutagenesis and gene replacement have long hampered genetic studies of pathogenicity in Phytophthora species. Here, we describe a CRISPR/Cas9 system enabling rapid and efficient genome editing in P. sojae. Using the RXLR effector gene Avr4/6 as a target, we observed that, in the absence of a homologous template, the repair of Cas9-induced DNA double-strand breaks (DSBs) in P. sojae was mediated by non-homologous end-joining (NHEJ), primarily resulting in short indels. Most mutants were homozygous, presumably as a result of gene conversion triggered by Cas9-mediated cleavage of non-mutant alleles. When donor DNA was present, homology-directed repair (HDR) was observed, which resulted in the replacement of Avr4/6 with the NPT II gene. By testing the specific virulence of several NHEJ mutants and HDR-mediated gene replacements in soybean, we have validated the contribution of Avr4/6 to recognition by soybean R gene loci, Rps4 and Rps6, but also uncovered additional contributions to resistance by these two loci. Our results establish a powerful tool for the study of functional genomics in Phytophthora, which provides new avenues for better control of this pathogen. © 2015 THE AUTHORS. MOLECULAR PLANT PATHOLOGY PUBLISHED BY JOHN WILEY & SONS LTD AND BSPP.

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

KAUST Repository

Fornander, Louise H

2012-02-22

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

Gold nanoparticle enhanced fluorescence anisotropy for the assay of single nucleotide polymorphisms (SNPs) based on toehold-mediated strand-displacement reaction.

Science.gov (United States)

Wang, Xinyi; Zou, Mingjian; Huang, Hongduan; Ren, Yuqian; Li, Limei; Yang, Xiaoda; Li, Na

2013-03-15

We developed a highly differentiating, homogeneous gold nanoparticle (AuNP) enhanced fluorescence anisotropic method for single nucleotide polymorphism (SNP) detection at nanomolar level using toehold-mediated strand-displacement reaction. The template strand, containing a toehold domain with an allele-specific site, was immobilized on the surface of AuNPs, and the solution fluorescence anisotropy was markedly enhanced when the fluorescein-labeled blocking DNA was attached to the AuNP via hybridization. Strand-displacement by the target ssDNA strand resulted in detachment of fluorescein-labeled DNA from AuNPs, and thus decreased fluorescence anisotropy. The drastic kinetic difference in strand-displacement from toehold design was used to distinguish between the perfectly matched and the single-base mismatched strands. Free energy changes were calculated to elucidate the dependence of the differentiation ability on the mutation site in the toehold region. A solid negative signal change can be obtained for single-base mismatched strand in the dynamic range of the calibration curve, and a more than 10-fold signal difference can still be observed in a mixed solution containing 100 times the single-base mismatched strand, indicating the good specificity of the method. This proposed method can be performed with a standard spectrofluorimeter in a homogeneous and cost-effective manner, and has the potential to be extended to the application of fluorescence anisotropy method of SNP detection. Copyright © 2012 Elsevier B.V. All rights reserved.

Flued head replacement alternatives

International Nuclear Information System (INIS)

Smetters, J.L.

1987-01-01

This paper discusses flued head replacement options. Section 2 discusses complete flued head replacement with a design that eliminates the inaccessible welds. Section 3 discusses alternate flued head support designs that can drastically reduce flued head installation costs. Section 4 describes partial flued head replacement designs. Finally, Section 5 discusses flued head analysis methods. (orig./GL)

Estimating potential stranded commitments for U.S. investor-owned electric utilities

International Nuclear Information System (INIS)

Baxter, L.; Hirst, E.

1995-01-01

New technologies, low natural gas prices, and federal and state utility regions are restructuring the electricity industry. Yesterday's vertically integrated utility with a retail monopoly franchise may be a very different organization in a few years. Conferences, regulatory-commission hearings, and other industry fora are dominated by debates over the extent and form of utility deintegration, wholesale competition, and retail wheeling. A key obstacle to restructuring the electricity industry is stranded commitments. Past investments, power-purchase contracts, and public-policy-driven programs that made sense in an era of cost-of-service regulation may not be cost-effective in a competitive power market. Regulators, utilities, and other parties face tough decisions concerning the mitigation and allocation of these stranded commitments. The authors developed and applied a simple method to calculate the amount of stranded commitments facing US investor-owned electric utilities. The results obtained with this method depend strongly on a few key assumptions: (1) the fraction of utility sales that is at risk with respect to competition, (2) the market price of electric generation, and (3) the number of years during which the utility would lose money because of differences between its embedded cost of production and the market price

Corrosion performance of prestressing strands in contact with dissimilar grouts.

Science.gov (United States)

2013-01-01

To improve the corrosion protection provided to prestressing strands, anti-bleed grouts are used to fill voids in post-tensioning : ducts that result from bleeding and shrinkage of older Portland Cement grouts. Environmental differences caused by exp...

Patterns and inferred processes associated with sea turtle strandings in Paraíba State, Northeast Brazil

Directory of Open Access Journals (Sweden)

C. Poli

Full Text Available This study analysed sea turtle strandings on the coast of Paraíba State, Northeastern Brazil, from August 2009 to July 2010. A total of 124 strandings were recorded in this period: green turtle Chelonia mydas (n = 106, hawksbill Eretmochelys imbricata (n = 15, olive ridley Lepidochelys olivacea (n = 2 and loggerhead Caretta caretta (n = 1. Of all turtles for which the Curved Carapace Length (CCL was measured (n = 122, only 12 individuals (9.7% were adults. Twenty individuals had synthetic anthropogenic debris in the gastrointestinal tract. Other traces of human interactions were observed in 43 individuals, such as injuries caused by entanglement in fishing lines or nets, collisions with vessels, direct contact with oil spills and lesions caused by sharp or spiked objects. Moreover, in 28.5% of the stranded turtles, the presence of external tumors was noticed, suggestive of fibropapillomatosis and in 9.7%, shark bite marks were observed. Of the 107 individuals that were sexed, 76 were females and 31 were males. Most turtles (72.6% became stranded during the spring/summer (between October and March. We found evidence of human interactions (injuries in half of the strandings, but in most cases it was not possible to determine if such interactions were the cause of death. A logistic regression found a significant relationship between CCL, ingestion of debris and lesions caused by sharks or spiked objects. Systematic data collection from stranded sea turtles can provide useful biological information, such as seasonal and spatial patterns in their occurrence and mortality, age structure, sex ratio and diet, as well as possible mortality causes.

Heat Treatment Optimization Studies on PIT Nb$_3$Sn Strand for the NED Project

CERN Document Server

Boutboul, T; den Ouden, A; Pedrini, D; Seeber, B; Volpini, G

2009-01-01

For the Next European Dipole (NED) program, a Powder-In-Tube (PIT) strand was successfully developed by SMI. This high-performance Nb$_{3}$Sn strand presents a non-copper critical current density of ~ 2500 A/mm2 at 12 T applied field and 4.2 K and a filament diameter around 50 µm. Extensive heat treatment optimization studies were performed in order to maximize both critical current and RRR, with a plateau temperature down to 625 oC and duration up to 400 hours. It appears that a critical current enhancement of ~ 10 % can be achieved for a reaction schedule of 320 hours at 625 oC with non-copper critical current density respectively exceeding 2700 and 1500 A/mm2 at 12 and 15 T (4.2 K). Thanks to this modified heat treatment, this strand completely fulfils the NED stringent specification.

Yield of single-strand breaks in the DNA of E.coli 10 msec after irradiation

International Nuclear Information System (INIS)

Fox, R.A.; Fielden, E.M.; Sapora, O.

1976-01-01

The rapid mixing of 0.3M alkali with a suspension of E.coli B/r 6 +- 3 and 144 +- 3 msec after irradiation with electrons (4.3 MeV, 0 to 50 krad) has been used to make a comparison of the yields of single strand breaks in the presence and absence of oxygen. No significant difference was observed between the numbers of single strand breaks appearing at 6 and 144 msec after irradiation. Assuming that mixing with alkali inactivates the cellular repair enzymes within several milliseconds, these results indicate that enzymic repair does not operate within this time scale. It seems probable that radiation chemical processes are responsible for the initial oxygen effect on single strand breaks. (U.K.)

Quench performance of Nb3Sn cos-theta coils made of 108/127 RRP strands

Energy Technology Data Exchange (ETDEWEB)

Zlobin, A.V.; Ambrosio, G.; Andreev, N.; Barzi, E.; Bossert, R.; Carcagno, R.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; Nobrega, F.; Novitski, I.; /Fermilab

2007-07-01

A series of 1-m long Nb{sub 3}Sn dipole models has been built at Fermilab in an attempt to refine the wind-and-react technology for Nb3Sn accelerator magnets. Three models made with Powder-in-Tube Nb{sub 3}Sn strand reached their design field of 10 T demonstrating a good reproducibility of magnet quench performance and field quality. Recently a new dipole 'mirror' model based on Nb{sub 3}Sn coil made of improved Restack Rod Process strand was constructed and tested reaching the maximum field above 11 T. This paper describes the parameters of the RRP strand and cable used as well as the design, fabrication and test results of this magnet.

Commercial possibilities for stranded conventional gas from Alaska's North Slope

Science.gov (United States)

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

2014-01-01

Stranded gas resources are defined for this study as gas resources in discrete accumulations that are not currently commercially producible, or producible at full potential, for either physical or economic reasons. Approximately 35 trillion cubic feet (TCF) of stranded gas was identified on Alaska’s North Slope. The commercialization of this resource requires facilities to transport gas to markets where sales revenue will be sufficient to offset the cost of constructing and operating a gas delivery system. With the advent of the shale gas revolution, plans for a gas pipeline to the conterminous US have been shelved (at least temporarily) and the State and resource owners are considering a liquefied natural gas (LNG) export project that targets Asian markets. This paper focuses on competitive conditions for Asian gas import markets by estimating delivered costs of competing supplies from central Asia, Russia, Indonesia, Malaysia, and Australia in the context of a range of import gas demand projections for the period from 2020 to 2040. These suppliers’ costs are based on the cost of developing, producing, and delivering to markets tranches of the nearly 600 TCF of recoverable gas from their own conventional stranded gas fields. The results of these analyses imply that Alaska’s gas exports to Asia will likely encounter substantial competitive challenges. The sustainability of Asia’s oil-indexed LNG pricing is also discussed in light of a potentially intense level of competition.

Implementing Replacement Cost Accounting

Science.gov (United States)

1976-12-01

cost accounting Clickener, John Ross Monterey, California. Naval Postgraduate School http://hdl.handle.net/10945/17810 Downloaded from NPS Archive...Calhoun IMPLEMENTING REPLACEMENT COST ACCOUNTING John Ross CHckener NAVAL POSTGRADUATE SCHOOL Monterey, California THESIS IMPLEMENTING REPLACEMENT COST ...Implementing Replacement Cost Accounting 7. AUTHORS John Ross Clickener READ INSTRUCTIONS BEFORE COMPLETING FORM 3. RECIPIENT’S CATALOG NUMBER 9. TYRE OF

Variation in normal and tumor tissue sensitivity of mice to ionizing radiation-induced DNA strand breaks in vivo

International Nuclear Information System (INIS)

Meyn, R.E.; Jenkins, W.T.

1983-01-01

The efficiency of DNA strand break formation in normal and tumor tissues of mice was measured using the technique of alkaline elution coupled with a microfluorometric determination of DNA. This methodology allowed measurement of the DNA strand breaks produced in tissues irradiated in vivo with doses of radiation comparable to those used in radiotherapy (i.e., 1.0 gray) without the necessity for the cells to be dividing and incorporating radioactive precursors to label the DNA. The results showed that substantial differences existed among various tissues in terms of the amount of DNA strand break damage produced for a given dose of radiation. Of the normal tissues, the most breaks were produced in bone marrow and the least were produced in gut. Furthermore, strand break production was relatively inefficient in the tumor compared to the normal tissues. The efficiency of DNA strand break formation measured in the cells from the tissues irradiated in vitro was much more uniform and considerably greater than that measured in vivo, suggesting that the normal tissues in the animal may be radiobiologically hypoxic

Extensive Characterization of the 1 mm PIT Nb$_{3}$Sn strand for the 13-T FRESCA2 Magnet

CERN Document Server

Bordini, B; Mondonico, G; Oberli, L; Richter, D; Seeber, B; Senatore, C; Takala, E; Valentinis, D

2012-01-01

In the framework of the EuCARD program, CERN is participating in the development of a 13 T 100-mm-aperture dipole magnet to upgrade the superconducting cable test facility FRESCA at CERN. The conductor candidates for building this magnet are two 1-mm Nb$_{3}$Sn strands: the Powder In Tube (PIT) produced by Bruker-EAS and the 132/169 RRP by Oxford Superconducting Technology (OST). Recently the PIT strand has been extensively characterized by CERN in collaboration with the University of Geneva (UniGe). The critical current dependence on the magnetic field and on the axial strain e has been measured at different temperatures. Furthermore, the strand magnetization has been measured at different temperature using a vibrating sample magnetometer. Finally the magneto-thermal stability of this strand was studied by measuring the quench current between 0 T and 12 T at 1.9 K and 4.3 K. The experimental results are compared with an optimized scaling law for the critical current of Nb$_{3}$Sn strands. In this paper the r...

Numerical and Experimental Identification of Seven-Wire Strand Tensions Using Scale Energy Entropy Spectra of Ultrasonic Guided Waves

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Ji Qian

2018-01-01

Full Text Available Accurate identification of tension in multiwire strands is a key issue to ensure structural safety and durability of prestressed concrete structures, cable-stayed bridges, and hoist elevators. This paper proposes a method to identify strand tensions based on scale energy entropy spectra of ultrasonic guided waves (UGWs. A numerical method was first developed to simulate UGW propagation in a seven-wire strand, employing the wavelet transform to extract UGW time-frequency energy distributions for different loadings. Mode separation and frequency band loss of L(0,1 were then found for increasing tension, and UGW scale energy entropy spectra were extracted to establish a tension identification index. A good linear relationship was found between the proposed identification index and tensile force, and effects of propagation distance and propagation path were analyzed. Finally, UGWs propagation was examined experimentally for a long seven-wire strand to investigate attenuation and long distance propagation. Numerical and experimental results verified that the proposed method not only can effectively identify strand tensions but can also adapt to long distance tests for practical engineering.

Repair of single-strand breaks in normal and trisomic lymphocytes

International Nuclear Information System (INIS)

Leonard, J.C.; Merz, T.

1982-01-01

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

DNA-mediated strand displacement facilitates sensitive electronic detection of antibodies in human serums.

Science.gov (United States)

Dou, Baoting; Yang, Jianmei; Shi, Kai; Yuan, Ruo; Xiang, Yun

2016-09-15

We describe here the development of a sensitive and convenient electronic sensor for the detection of antibodies in human serums. The sensor is constructed by self-assembly formation of a mixed monolayer containing the small molecule epitope conjugated double stranded DNA probes on gold electrode. The target antibody binds the epitope on the dsDNA probe and lowers the melting temperature of the duplex, which facilitates the displacement of the antibody-linked strand of the duplex probe by an invading methylene blue-tagged single stranded DNA (MB-ssDNA) through the strand displacement reaction and leads to the capture of many MB-ssDNA on the sensor surface. Subsequent electrochemical oxidation of the methylene blue labels results in amplified current response for sensitive monitoring of the antibodies. The antibody assay conditions are optimized and the sensor exhibits a linear range between 1.0 and 25.0nM with a detection limit of 0.67nM for the target antibody. The sensor is also selective and can be employed to detect the target antibodies in human serum samples. With the advantages of using small molecule epitope as the antibody recognition element over traditional antigen, the versatile manipulability of the DNA probes and the unique properties of the electrochemical transduction technique, the developed sensor thus hold great potential for simple and sensitive detection of different antibodies and other proteins in real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Harbor porpoise Phocoena phocoena strandings on the Dutch coast: No genetic structure, but evidence of inbreeding

Science.gov (United States)

van der Plas-Duivesteijn, Suzanne J.; Smit, Femmie J. L.; van Alphen, Jacques J. M.; Kraaijeveld, Ken

2015-03-01

Conservation management in the North Sea is often motivated by the population size of marine mammals, like harbor porpoises Phocoena phocoena. In the Dutch part of the North Sea, sighting and stranding data are used to estimate population sizes, but these data give little insight into genetic structuring of the population. In this study we investigated genetic structure among animals stranded at different locations and times of year. We also tested whether there is a link between stranding and necropsy data, and genetic diversity. We made use of both mitochondrial (mtDNA) and microsatellite DNA analysis of samples from dead stranded porpoises along the Dutch coast during 2007. mtDNA analysis showed 6 variable positions in the control region, defining 3 different haplotypes. mtDNA haplotypes were not randomly distributed along the Dutch coastline. However, microsatellite analysis showed that these mtDNA haplotypes did not represent separate groups on a nuclear level. Furthermore, microsatellite analysis revealed no genotypic differences between seasons, locations or genders. The results of this study indicate that the Dutch population is panmictic. In contrast, heterozygosity levels were low, indicating some level of inbreeding in this population. However, this was not corroborated by other indices of inbreeding. This research provided insight into genetic structuring of stranded porpoises in 2007, but data from multiple years should be included to be able to help estimate population sizes.

Editing Transgenic DNA Components by Inducible Gene Replacement in Drosophila melanogaster

Science.gov (United States)

Lin, Chun-Chieh; Potter, Christopher J.

2016-01-01

Gene conversions occur when genomic double-strand DNA breaks (DSBs) trigger unidirectional transfer of genetic material from a homologous template sequence. Exogenous or mutated sequence can be introduced through this homology-directed repair (HDR). We leveraged gene conversion to develop a method for genomic editing of existing transgenic insertions in Drosophila melanogaster. The clustered regularly-interspaced palindromic repeats (CRISPR)/Cas9 system is used in the homology assisted CRISPR knock-in (HACK) method to induce DSBs in a GAL4 transgene, which is repaired by a single-genomic transgenic construct containing GAL4 homologous sequences flanking a T2A-QF2 cassette. With two crosses, this technique converts existing GAL4 lines, including enhancer traps, into functional QF2 expressing lines. We used HACK to convert the most commonly-used GAL4 lines (labeling tissues such as neurons, fat, glia, muscle, and hemocytes) to QF2 lines. We also identified regions of the genome that exhibited differential efficiencies of HDR. The HACK technique is robust and readily adaptable for targeting and replacement of other genomic sequences, and could be a useful approach to repurpose existing transgenes as new genetic reagents become available. PMID:27334272

Negative-strand RNA viruses: the plant-infecting counterparts.

Science.gov (United States)

Kormelink, Richard; Garcia, Maria Laura; Goodin, Michael; Sasaya, Takahide; Haenni, Anne-Lise

2011-12-01

While a large number of negative-strand (-)RNA viruses infect animals and humans, a relative small number have plants as their primary host. Some of these have been classified within families together with animal/human infecting viruses due to similarities in particle morphology and genome organization, while others have just recently been/or are still classified in floating genera. In most cases, at least two striking differences can still be discerned between the animal/human-infecting viruses and their plant-infecting counterparts which for the latter relate to their adaptation to plants as hosts. The first one is the capacity to modify plasmodesmata to facilitate systemic spread of infectious viral entities throughout the plant host. The second one is the capacity to counteract RNA interference (RNAi, also referred to as RNA silencing), the innate antiviral defence system of plants and insects. In this review an overview will be presented on the negative-strand RNA plant viruses classified within the families Bunyaviridae, Rhabdoviridae, Ophioviridae and floating genera Tenuivirus and Varicosavirus. Genetic differences with the animal-infecting counterparts and their evolutionary descendants will be described in light of the above processes. Copyright © 2011 Elsevier B.V. All rights reserved.

Fundamental simulations of transverse load effects on Nb3Sn strands using finite element analysis

Science.gov (United States)

Wang, T.; Chiesa, L.; Takayasu, M.

2012-06-01

A 2D finite element elasto-plastic analysis with various property values of the materials in composite Nb3Sn wires has been conducted to simulate the transverse compression effect on a single strand and a 3-strand cable as basic elements of a Cable-in-Conduit Conductor (CICC). The simulation results have been compared with previously reported experimental results. A parametric study of the stress-strain characteristics of copper at 4 K was considered. The simulation results showed that wire and cable deformations due to the transverse load are very sensitive to the elasto-plastic material properties of copper and bronze. In a triplet it is found that the strain distributions inside the superconducting strand are very different along its axis, that is, for a configuration in which two strands lined in parallel to the transverse load direction shows much higher internal strain than other configurations under the same transverse load. The simulation results agree with the reported experimental results indicating a low Young's modulus for Nb3Sn wires under transverse compression. The simulation also supports the reported contact mechanics model for critical current degradation.

75 FR 4537 - Notice of Public Hearings for the Draft Environmental Impact Statement for the Silver Strand...

Science.gov (United States)

2010-01-28

... statement to Naval Facilities Engineering Command Southwest, Attention: Mr. Kent Randall, Silver Strand... Strand Way, Coronado, CA. FOR FURTHER INFORMATION CONTACT: Naval Facilities Engineering Command Southwest, Attention: Mr. Kent Randall, SSTC EIS Project Manager, 1220 Pacific Highway, Building 1, 5th Floor, San...

Survey of IUD replacing status in Sichuan, PR China.

Science.gov (United States)

Xiaoqin, Chen; Li, Xie; Xiaoping, Pan; Chuanrong, Zhang; Shiyuan, Luo

2003-05-01

To investigate the status of copper-bearing intrauterine device (IUD) replacing inert IUD in Sichuan Province, cluster random sampling method was adopted for the survey. Questionnaires were completed and IUD were inspected through ultrasound among 12,804 subjects of 15 counties, who were inserted an IUD from 1994 to 1998. The insertion rate of copper-bearing IUD was 42.1%, in a gradually increasing trend; it was lower in mountain areas than in plain and hilly areas and increased after induced abortion and previous IUD failure. Some factors, such as lower pregnancy rate, lower expulsion rate and easy removal, etc., contributed to copper-bearing IUD use. On the other hand, other factors like longer contraception period, lower side effects and lower cost contributed to inert IUD use. The results show that the adoption of copper-bearing IUD is increasing, but those factors influencing copper-bearing IUD replacement should not be neglected.

Summary of the performance of strand produced for the 1990 SSC dipole program

International Nuclear Information System (INIS)

Christopherson, D.; Capone, D. II; Seuntjens, J.; Pollock, D.; Hannaford, C.R.

1991-01-01

In 1990 and at the beginning of 1991, more than 4 million feet of wire was delivered to support the SSC Dipole Program. This wire was fabricated to meet specification SSC-MAG-M-4141, and test results and various statistics are compiled here. Certain strengths and weaknesses in the performance of the delivered strand are discussed, including analysis of strand breakage in certain billets. Test results of cable manufactured for 40 mm dipole magnets and 50 mm dipole magnets are reported, and a brief overview of the 1991-1992 Conductor Program is included

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

International Nuclear Information System (INIS)

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

1987-01-01

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

Precise gene modification mediated by TALEN and single-stranded oligodeoxynucleotides in human cells.

Directory of Open Access Journals (Sweden)

Xiaoling Wang

Full Text Available The development of human embryonic stem cells (ESCs and induced pluripotent stem cells (iPSCs facilitates in vitro studies of human disease mechanisms, speeds up the process of drug screening, and raises the feasibility of using cell replacement therapy in clinics. However, the study of genotype-phenotype relationships in ESCs or iPSCs is hampered by the low efficiency of site-specific gene editing. Transcription activator-like effector nucleases (TALENs spurred interest due to the ease of assembly, high efficiency and faithful gene targeting. In this study, we optimized the TALEN design to maximize its genomic cutting efficiency. We showed that using optimized TALENs in conjunction with single-strand oligodeoxynucleotide (ssODN allowed efficient gene editing in human cells. Gene mutations and gene deletions for up to 7.8 kb can be accomplished at high efficiencies. We established human tumor cell lines and H9 ESC lines with homozygous deletion of the microRNA-21 (miR-21 gene and miR-9-2 gene. These cell lines provide a robust platform to dissect the roles these genes play during cell differentiation and tumorigenesis. We also observed that the endogenous homologous chromosome can serve as a donor template for gene editing. Overall, our studies demonstrate the versatility of using ssODN and TALEN to establish genetically modified cells for research and therapeutic application.

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.

siRNA-like double-stranded RNAs are specifically protected against degradation in human cell extract.

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John A H Hoerter

Full Text Available RNA interference (RNAi is a set of intracellular pathways in eukaryotes that controls both exogenous and endogenous gene expression. The power of RNAi to knock down (silence any gene of interest by the introduction of synthetic small-interfering (siRNAs has afforded powerful insight into biological function through reverse genetic approaches and has borne a new field of gene therapeutics. A number of questions are outstanding concerning the potency of siRNAs, necessitating an understanding of how short double-stranded RNAs are processed by the cell. Recent work suggests unmodified siRNAs are protected in the intracellular environment, although the mechanism of protection still remains unclear. We have developed a set of doubly-fluorophore labeled RNAs (more precisely, RNA/DNA chimeras to probe in real-time the stability of siRNAs and related molecules by fluorescence resonance energy transfer (FRET. We find that these RNA probes are substrates for relevant cellular degradative processes, including the RNase H1 mediated degradation of an DNA/RNA hybrid and Dicer-mediated cleavage of a 24-nucleotide (per strand double-stranded RNA. In addition, we find that 21- and 24-nucleotide double-stranded RNAs are relatively protected in human cytosolic cell extract, but less so in blood serum, whereas an 18-nucleotide double-stranded RNA is less protected in both fluids. These results suggest that RNAi effector RNAs are specifically protected in the cellular environment and may provide an explanation for recent results showing that unmodified siRNAs in cells persist intact for extended periods of time.

Salivary cortisol day curves in Addison's disease in patients on hydrocortisone replacement.

Science.gov (United States)

Ross, I L; Levitt, N S; Van der Walt, J S; Schatz, D A; Johannsson, G; Haarburger, D H; Pillay, T S

2013-01-01

Using salivary cortisol (SC) measurements, cortisol exposure in Addison's disease patients on hydrocortisone replacement was determined and compared with healthy controls. Cortisol pharmacokinetics was assessed in 31 patients with Addison's disease on replacement hydrocortisone doses (median daily dose 20 mg; range 5-50 mg) and 30 healthy control subjects. Saliva samples (n=16) were collected between 08:00 and 00:00 h in 1 day, using a passive drool technique. Cortisol exposure was evaluated by noncompartmental approach. In the patients, cortisol exposure was significantly higher than in controls: median inter-quartile range (IQR) peak cortisol (C(max)) 174.5 (59.3-837.0) vs. 6.50 (4.7-19.3) nmol/l, p=0.0001; area under the curve (AUC) 390.1 (177.1-928.9) vs. 21.4 (14.6-28.4) minutes*nmol/l, p=0.0001, trough cortisol level (C(min)) 0.49 (0.49-0.96) vs. 0.49 (0.49-0.49) nmol/l, p=0.02, occurring at 480.0 (0.1-660.0) vs. 405.0 (180.0-570.0) min, p=0.56. First peak cortisol was 174.5 (53.0-754.7) vs. 6.27 (3.90-8.47) nmol/l, p=0.0001 and second peak cortisol 18.90 (5.22-76.9) vs. 3.12 (1.76-4.79) nmol/l, p=0.0001. The time to first peak cortisol differed between the 2 groups, 30 (30-75) vs. 0.1 (0.1-30) minutes; p=0.0001. At doses studied, hydrocortisone replacement therapy results in cortisol pharmacokinetics being markedly different from endogenous cortisol profiles in healthy control subjects. Addison's disease patients had significantly higher SC levels compared to healthy control subjects. © Georg Thieme Verlag KG Stuttgart · New York.

Wages Paid in Kind in Self-Replacing Economies

Directory of Open Access Journals (Sweden)

Alberto Benítez Sánchez

2014-05-01

Full Text Available This paper studies the two systems of production equations corresponding respectively to wages paid entirely or partialy in kind in Sraffa's self-replacing economies. Regarding the first system, the paper introduces the concept of ρ-shaped matrix, which is relevant to the subject and allows also for the addition of a complementary remark to the theory of semi-positive square matrices. In relation to the second system, it points out some differences between the cases studied here and those where the whole wage is paid in value.

The initial bearing capacities of subchondral bone replacements considerably contributing to chondrogenesis

Czech Academy of Sciences Publication Activity Database

Petrtýl, M.; Danešová, J.; Lísal, J.; Šenolt, L.; Hulejová, H.; Polanská, M.; Bastl, Zdeněk; Kruliš, Zdeněk; Černý, P.

2010-01-01

Roč. 12, č. 3 (2010), s. 59-65 ISSN 1509-409X R&D Projects: GA ČR GA106/06/0761 Institutional research plan: CEZ:AV0Z40400503; CEZ:AV0Z40500505 Keywords : biomechanics * osteochondral defects * polymer replacement Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.432, year: 2010

Multiple modernities, modern subjectivities and social order

DEFF Research Database (Denmark)

Jung, Dietrich; Sinclair, Kirstine

2015-01-01

to modern subjectivity formation. In combining conceptual tools from these strands of social theory, we argue that the emergence of multiple modernities should be understood as a historical result of idiosyncratic social constructions combining global social imaginaries with religious and other cultural......Taking its point of departure in the conceptual debate about modernities in the plural, this article presents a heuristic framework based on an interpretative approach to modernity. The article draws on theories of multiple modernities, successive modernities and poststructuralist approaches...... traditions. In the second part of the article we illustrate this argument with three short excursions into the history of Islamic reform in the 19th and 20th centuries. In this way we interpret the modern history of Muslim societies as based on cultural conflicts between different forms of social order...

Holocene geologic slip rate for the Banning strand of the southern San Andreas Fault, southern California

Science.gov (United States)

Gold, Peter O.; Behr, Whitney M.; Rood, Dylan; Sharp, Warren D.; Rockwell, Thomas; Kendrick, Katherine J.; Salin, Aaron

2015-01-01

Northwest directed slip from the southern San Andreas Fault is transferred to the Mission Creek, Banning, and Garnet Hill fault strands in the northwestern Coachella Valley. How slip is partitioned between these three faults is critical to southern California seismic hazard estimates but is poorly understood. In this paper, we report the first slip rate measured for the Banning fault strand. We constrain the depositional age of an alluvial fan offset 25 ± 5 m from its source by the Banning strand to between 5.1 ± 0.4 ka (95% confidence interval (CI)) and 6.4 + 3.7/−2.1 ka (95% CI) using U-series dating of pedogenic carbonate clast coatings and 10Be cosmogenic nuclide exposure dating of surface clasts. We calculate a Holocene geologic slip rate for the Banning strand of 3.9 + 2.3/−1.6 mm/yr (median, 95% CI) to 4.9 + 1.0/−0.9 mm/yr (median, 95% CI). This rate represents only 25–35% of the total slip accommodated by this section of the southern San Andreas Fault, suggesting a model in which slip is less concentrated on the Banning strand than previously thought. In rejecting the possibility that the Banning strand is the dominant structure, our results highlight an even greater need for slip rate and paleoseismic measurements along faults in the northwestern Coachella Valley in order to test the validity of current earthquake hazard models. In addition, our comparison of ages measured with U-series and 10Be exposure dating demonstrates the importance of using multiple geochronometers when estimating the depositional age of alluvial landforms.

DNA strand breaking and rejoining in response to ultraviolet light in normal human and xeroderma pigmentosum cells