WorldWideScience

Sample records for local strand separation

  1. Hyperchromicity and strand separation in bacterial DNA.

    Science.gov (United States)

    FREIFELDER, D; DAVISON, P F

    1962-05-01

    Studies of the per cent of strand separation of N(14)-N(15) hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions.

  2. Hyperchromicity and Strand Separation in Bacterial DNA

    Science.gov (United States)

    Freifelder, David; Davison, Peter F.

    1962-01-01

    Studies of the per cent of strand separation of N14-N15 hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions. PMID:13894962

  3. Separability of local reactivity descriptors

    Indian Academy of Sciences (India)

    Akhilesh Tanwar; Sourav Pal

    2005-09-01

    The size-dependence of different local reactivity descriptors of dimer A2 and AB type of systems is discussed. We derive analytic results of these descriptors calculated using finite difference approximation. In particular, we studied Fukui functions, relative electrophilicity and relative nucleophilicity, local softness and local philicity. The results are explained using the example of the dimer of BH3NH3.

  4. Bayesian Source Separation and Localization

    CERN Document Server

    Knuth, K H

    1998-01-01

    The problem of mixed signals occurs in many different contexts; one of the most familiar being acoustics. The forward problem in acoustics consists of finding the sound pressure levels at various detectors resulting from sound signals emanating from the active acoustic sources. The inverse problem consists of using the sound recorded by the detectors to separate the signals and recover the original source waveforms. In general, the inverse problem is unsolvable without additional information. This general problem is called source separation, and several techniques have been developed that utilize maximum entropy, minimum mutual information, and maximum likelihood. In previous work, it has been demonstrated that these techniques can be recast in a Bayesian framework. This paper demonstrates the power of the Bayesian approach, which provides a natural means for incorporating prior information into a source model. An algorithm is developed that utilizes information regarding both the statistics of the amplitudes...

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

    Energy Technology Data Exchange (ETDEWEB)

    Pagratis, N.; Revel, H.R. (Univ. of Chicago, IL (USA))

    1990-07-01

    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.

  6. Numerical analysis of the non-metallic inclusions distribution and separation in a two-strand tundish

    Directory of Open Access Journals (Sweden)

    T. Merder

    2013-04-01

    Full Text Available The tundish plays an important role in the challenging task of a “clean steel” production process. The flow of the liquid steel in tundish has a crucial influence on non-metallic inclusions distribution and separation. The article presents computational studies of non-metallic inclusions separation in a two-strand industrial tundish during steady-state casting. Tundish capacity is 7,5 t. First, flow structure in the tundish was investigated using water model of the industrial tundish in a 1:2 scale. The experimental results, regarding RTD characteristics were used to validate numerical model. With validated model, particle distribution and separation in the two-strand tundish were investigated numerically. For modelling the separation of particles at the fluid surface, a modified boundary condition has been implemented.

  7. Label-Free and Separation-Free Atomic Fluorescence Spectrometry-Based Bioassay: Sensitive Determination of Single-Strand DNA, Protein, and Double-Strand DNA.

    Science.gov (United States)

    Chen, Piaopiao; Wu, Peng; Chen, Junbo; Yang, Peng; Zhang, Xinfeng; Zheng, Chengbin; Hou, Xiandeng

    2016-02-16

    Based on selective and sensitive determination of Hg(2+) released from mercury complex by cold vapor generation (CVG) atomic fluorescence spectrometry (AFS) using SnCl2 as a reductant, a novel label-free and separation-free strategy was proposed for DNA and protein bioassay. To construct the DNA bioassay platform, an Hg(2+)-mediated molecular beacon (hairpin) without labeling but possessing several thymine (T) bases at both ends was employed as the probe. It is well-known that Hg(2+) could trigger the formation of the hairpin structure through T-Hg(2+)-T connection. In the presence of a specific target, the hairpin structure could be broken and the captured Hg(2+) was released. Interestingly, it was found that SnCl2 could selectively reduce only free Hg(2+) to Hg(0) vapor in the presence of T-Hg(2+)-T complex, which could be separated from sample matrices for sensitive AFS detection. Three different types of analyte, namely, single-strand DNA (ssDNA), protein, and double-strand DNA (dsDNA), were investigated as the target analytes. Under the optimized conditions, this bioassay provided high sensitivity for ssDNA, protein, and dsDNA determination with the limits of detection as low as 0.2, 0.08, and 0.3 nM and the linear dynamic ranges of 10-150, 5-175, and 1-250 nM, respectively. The analytical performance for these analytes compares favorably with those by previously reported methods, demonstrating the potential usefulness and versatility of this new AFS-based bioassay. Moreover, the bioassay retains advantages of simplicity, cost-effectiveness, and sensitivity compared to most of the conventional methods.

  8. Labeling of double-stranded DNA by ROX-dideoxycytosine triphosphate using terminal deoxynucleotidyl transferase and separation by capillary electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Figeys, D.; Renborg, A.; Dovichi, N.J. (Univ. of Alberta, Edmonton, Alberta (Canada))

    1994-12-01

    Terminal transferase is used to add a single fluorescently labeled dideoxynucleotide to double-stranded DNA prepared by restriction endonuclease action on a bacteriophage. The product is separated by capillary electrophoresis with both hydroxypropylmethylcellulose and non-cross-linked polyacrylamide. The reaction products generate single peaks for each fragment with hydroxypropylmethylcellulose. However, the higher resolution separation produced by non-cross-linked polyacrylamide shows that the product contains two components for each restriction digest fragment. This labeling technique should be useful in restriction fragment length polymorphism studies. 9 refs., 2 figs.

  9. Localized degradation of foreign DNA strands in cells: Only excising the first nucleotide of 5' region.

    Science.gov (United States)

    Li, Hui; Shen, Wei; Lam, Michael Hon-Wah; Liang, Haojun

    2017-09-15

    Intracellular delivery of foreign DNA probes sharply increases the efficiency of various biodetection protocols. Spherical nucleic acid (SNA) conjugate is a new type of probe that consists of a dense oligonucleotide shell attached typically to a gold nanoparticle core. They are widely used as novel labels for in vitro biodetection and intracellular assay. However, the degradation of foreign DNA still remains a challenge that can cause significant signal leakage (false positive signal). Hence, the site and behavior of intracellular degradation need to be investigated. Herein, we discover a localized degradation behavior that only excises the first nucleotide of 5' terminal from a DNA strand, whereas the residual portion of this strand is unbroken in MCF-7 cell. This novel degradation action totally differs from previous opinion that foreign DNA strand would be digested into tiny fragments or even individual nucleotides in cellular environment. On the basis of these findings, we propose a simple and effective way to avoid degradation-caused false positive that one can bypass the degradable site and choose a secure region to label fluorophore along the DNA stand, when using DNA probes for intracellular biodetection. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Super-resolution mbPAINT for optical localization of single-stranded DNA.

    Science.gov (United States)

    Chen, Jixin; Bremauntz, Alberto; Kisley, Lydia; Shuang, Bo; Landes, Christy F

    2013-10-09

    We demonstrate the application of superlocalization microscopy to identify sequence-specific portions of single-stranded DNA (ssDNA) with sequence resolution of 50 nucleotides, corresponding to a spatial resolution of 30 nm. Super-resolution imaging was achieved using a variation of a single-molecule localization method, termed as "motion blur" point accumulation for imaging in nanoscale topography (mbPAINT). The target ssDNA molecules were immobilized on the substrate. Short, dye-labeled, and complementary ssDNA molecules stochastically bound to the target ssDNA, with repeated binding events allowing super-resolution. Sequence specificity was demonstrated via the use of a control, noncomplementary probe. The results support the possibility of employing relatively inexpensive short ssDNAs to identify gene sequence specificity with improved resolution in comparison to the existing methods.

  11. Separation and quantification of viral double-stranded RNA fragments by capillary electrophoresis in hydroxyethylcellulose polymer solutions.

    Science.gov (United States)

    Shambaugh, C L; Bodmer, J L; Hsu, D; Ranucci, C S

    2004-10-01

    Capillary electrophoresis (CE) is an analytical technique widely utilized to resolve complex mixtures of nucleic acids. CE uses a variety of polymers in solution that act as a molecular sieve to separate nucleic acid fragments according to size. It has been shown previously that purified dsDNA can be resolved efficiently by solutions of hydroxyethylcellulose (HEC) polymer, providing a rapid and high resolution method of separation. We have applied this separation technique to viral double-stranded (ds) RNA segments derived from rotavirus process samples. HEC polymers of various molecular masses and concentrations were identified and compared for their ability to separate dsRNA based on the extent of expected polymer network formation. The HEC polymer exhibiting the most desirable separation characteristics was then used for subsequent optimization of various method parameters, such as, injection time, electric field strength, dye concentration and capillary equilibration. The optimized method was then applied to the quantification of genome concentration based on a representative segment of the rotavirus genome. This study demonstrated that purified viral dsRNA material of known concentration could be used to generate an external standard curve relating concentration to peak area. This standard curve was used to determine the concentration of unknown samples by interpolation. This novel RNA quantification assay is likely to be applicable to other types of virus, including those containing dsDNA.

  12. Response of axisymmetric separated flow to its spatially localized perturbation

    Science.gov (United States)

    Dovgal, A. V.; Zanin, B. Yu.; Sorokin, A. M.

    2016-11-01

    The flow past an axisymmetric body with laminar boundary-layer separation in a low-velocity air stream has been studied. The hot-wire technique was employed to identify the variation of velocity field induced by a local stationary perturbation of separation region at the stern of the experimental model. A large-scale influence upon the near-wall flow due to a cylinder roughness element provided on the model surface was observed. The obtained data substantiate the possibility of controlling the laminar boundary-layer separation on an axisymmetric body using a local external forcing.

  13. 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

  14. Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions.

    Directory of Open Access Journals (Sweden)

    Anatoly S Glukhov

    Full Text Available The complete sequence of the 46,267 bp genome of the lytic bacteriophage tf specific to Pseudomonas putida PpG1 has been determined. The phage genome has two sets of convergently transcribed genes and 186 bp long direct terminal repeats. The overall genomic architecture of the tf phage is similar to that of the previously described Pseudomonas aeruginosa phages PaP3, LUZ24 and phiMR299-2, and 39 out of the 72 products of predicted tf open reading frames have orthologs in these phages. Accordingly, tf was classified as belonging to the LUZ24-like bacteriophage group. However, taking into account very low homology levels between tf DNA and that of the other phages, tf should be considered as an evolutionary divergent member of the group. Two distinguishing features not reported for other members of the group were found in the tf genome. Firstly, a unique end structure--a blunt right end and a 4-nucleotide 3'-protruding left end--was observed. Secondly, 14 single-chain interruptions (nicks were found in the top strand of the tf DNA. All nicks were mapped within a consensus sequence 5'-TACT/RTGMC-3'. Two nicks were analyzed in detail and were shown to be present in more than 90% of the phage population. Although localized nicks were previously found only in the DNA of T5-like and phiKMV-like phages, it seems increasingly likely that this enigmatic structural feature is common to various other bacteriophages.

  15. A DNA double-strand break kinetic rejoining model based on the local effect model.

    Science.gov (United States)

    Tommasino, F; Friedrich, T; Scholz, U; Taucher-Scholz, G; Durante, M; Scholz, M

    2013-11-01

    We report here on a DNA double-strand break (DSB) kinetic rejoining model applicable to a wide range of radiation qualities based on the DNA damage pattern predicted by the local effect model (LEM). In the LEM this pattern is derived from the SSB and DSB yields after photon irradiation in combination with an amorphous track structure approach. Together with the assumption of a giant-loop organization to describe the higher order chromatin structure this allows the definition of two different classes of DSB. These classes are defined by the level of clustering on a micrometer scale, i.e., "isolated DSB" (iDSB) are characterized by a single DSB in a giant loop and "clustered DSB" (cDSB) by two or more DSB in a loop. Clustered DSB are assumed to represent a more difficult challenge for the cell repair machinery compared to isolated DSB, and we thus hypothesize here that the fraction of isolated DSB can be identified with the fast component of rejoining, whereas clustered DSB are identified with the slow component of rejoining. The resulting predicted bi-exponential decay functions nicely reproduce the experimental curves of DSB rejoining over time obtained by means of gel electrophoresis elution techniques as reported by different labs, involving different cell types and a wide spectrum of radiation qualities. New experimental data are also presented aimed at investigating the effects of the same ion species accelerated at different energies. The results presented here further support the relevance of the proposed two classes of DSB as a basis for understanding cell response to ion irradiation. Importantly the density of DSB within DNA giant loops of around 2 Mbp size, i.e., on a micrometer scale, is identified as a key parameter for the description of radiation effectiveness.

  16. Local Strain Measurement of Kevlar Strand with Fiber Optic Bragg Grating

    Science.gov (United States)

    Banks, Curtis E.; Grant, Joseph; Russell, Sam; Arnett, Shawn

    2008-01-01

    1987 DuPont manufactured 4560 denier Kevlar/Epoxy Strands were instrumented with nine and three sensors each. Stress tests were performed at 30,45,60,70 and 80% of ultimate strength with dwell times of 10,000 seconds. FBG showed uneven stress levels which is contrary to conventional observation.

  17. Locally optimized separability enhancement indices for urban land cover mapping

    DEFF Research Database (Denmark)

    Feyisa, Gudina L.; Meilby, Henrik; Darrel Jenerette, G.

    2016-01-01

    Landsat data were used to assess urbanization-induced dynamics in Land use/cover (LULC), surface thermal intensity, and its relationships with urban biophysical composition. The study was undertaken in Addis Ababa city, Ethiopia. Ground-based data and high resolution images were used as reference...... data in LULC classification. To more accurately quantify landscape patterns and their changes, we applied new locally optimized separability enhancement indices and decision rules (SEI–DR approach) to address commonly observed classification accuracy problems in urban environments. We tested the SEI...... classification method, use of hotspot analysis, and the investigations of the UHI for an African city fill important research gaps for studies of urban thermal variation....

  18. An autonomous surveillance system for blind sources localization and separation

    Science.gov (United States)

    Wu, Sean; Kulkarni, Raghavendra; Duraiswamy, Srikanth

    2013-05-01

    This paper aims at developing a new technology that will enable one to conduct an autonomous and silent surveillance to monitor sound sources stationary or moving in 3D space and a blind separation of target acoustic signals. The underlying principle of this technology is a hybrid approach that uses: 1) passive sonic detection and ranging method that consists of iterative triangulation and redundant checking to locate the Cartesian coordinates of arbitrary sound sources in 3D space, 2) advanced signal processing to sanitizing the measured data and enhance signal to noise ratio, and 3) short-time source localization and separation to extract the target acoustic signals from the directly measured mixed ones. A prototype based on this technology has been developed and its hardware includes six B and K 1/4-in condenser microphones, Type 4935, two 4-channel data acquisition units, Type NI-9234, with a maximum sampling rate of 51.2kS/s per channel, one NI-cDAQ 9174 chassis, a thermometer to measure the air temperature, a camera to view the relative positions of located sources, and a laptop to control data acquisition and post processing. Test results for locating arbitrary sound sources emitting continuous, random, impulsive, and transient signals, and blind separation of signals in various non-ideal environments is presented. This system is invisible to any anti-surveillance device since it uses the acoustic signal emitted by a target source. It can be mounted on a robot or an unmanned vehicle to perform various covert operations, including intelligence gathering in an open or a confined field, or to carry out the rescue mission to search people trapped inside ruins or buried under wreckages.

  19. Localized Ambient Solidity Separation Algorithm Based Computer User Segmentation

    Directory of Open Access Journals (Sweden)

    Xiao Sun

    2015-01-01

    Full Text Available Most of popular clustering methods typically have some strong assumptions of the dataset. For example, the k-means implicitly assumes that all clusters come from spherical Gaussian distributions which have different means but the same covariance. However, when dealing with datasets that have diverse distribution shapes or high dimensionality, these assumptions might not be valid anymore. In order to overcome this weakness, we proposed a new clustering algorithm named localized ambient solidity separation (LASS algorithm, using a new isolation criterion called centroid distance. Compared with other density based isolation criteria, our proposed centroid distance isolation criterion addresses the problem caused by high dimensionality and varying density. The experiment on a designed two-dimensional benchmark dataset shows that our proposed LASS algorithm not only inherits the advantage of the original dissimilarity increments clustering method to separate naturally isolated clusters but also can identify the clusters which are adjacent, overlapping, and under background noise. Finally, we compared our LASS algorithm with the dissimilarity increments clustering method on a massive computer user dataset with over two million records that contains demographic and behaviors information. The results show that LASS algorithm works extremely well on this computer user dataset and can gain more knowledge from it.

  20. Localized Ambient Solidity Separation Algorithm Based Computer User Segmentation.

    Science.gov (United States)

    Sun, Xiao; Zhang, Tongda; Chai, Yueting; Liu, Yi

    2015-01-01

    Most of popular clustering methods typically have some strong assumptions of the dataset. For example, the k-means implicitly assumes that all clusters come from spherical Gaussian distributions which have different means but the same covariance. However, when dealing with datasets that have diverse distribution shapes or high dimensionality, these assumptions might not be valid anymore. In order to overcome this weakness, we proposed a new clustering algorithm named localized ambient solidity separation (LASS) algorithm, using a new isolation criterion called centroid distance. Compared with other density based isolation criteria, our proposed centroid distance isolation criterion addresses the problem caused by high dimensionality and varying density. The experiment on a designed two-dimensional benchmark dataset shows that our proposed LASS algorithm not only inherits the advantage of the original dissimilarity increments clustering method to separate naturally isolated clusters but also can identify the clusters which are adjacent, overlapping, and under background noise. Finally, we compared our LASS algorithm with the dissimilarity increments clustering method on a massive computer user dataset with over two million records that contains demographic and behaviors information. The results show that LASS algorithm works extremely well on this computer user dataset and can gain more knowledge from it.

  1. Localized Ambient Solidity Separation Algorithm Based Computer User Segmentation

    Science.gov (United States)

    Sun, Xiao; Zhang, Tongda; Chai, Yueting; Liu, Yi

    2015-01-01

    Most of popular clustering methods typically have some strong assumptions of the dataset. For example, the k-means implicitly assumes that all clusters come from spherical Gaussian distributions which have different means but the same covariance. However, when dealing with datasets that have diverse distribution shapes or high dimensionality, these assumptions might not be valid anymore. In order to overcome this weakness, we proposed a new clustering algorithm named localized ambient solidity separation (LASS) algorithm, using a new isolation criterion called centroid distance. Compared with other density based isolation criteria, our proposed centroid distance isolation criterion addresses the problem caused by high dimensionality and varying density. The experiment on a designed two-dimensional benchmark dataset shows that our proposed LASS algorithm not only inherits the advantage of the original dissimilarity increments clustering method to separate naturally isolated clusters but also can identify the clusters which are adjacent, overlapping, and under background noise. Finally, we compared our LASS algorithm with the dissimilarity increments clustering method on a massive computer user dataset with over two million records that contains demographic and behaviors information. The results show that LASS algorithm works extremely well on this computer user dataset and can gain more knowledge from it. PMID:26221133

  2. Protein kinase CK2 localizes to sites of DNA double-strand break regulating the cellular response to DNA damage

    Directory of Open Access Journals (Sweden)

    Olsen Birgitte B

    2012-03-01

    Full Text Available Abstract Background The DNA-dependent protein kinase (DNA-PK is a nuclear complex composed of a large catalytic subunit (DNA-PKcs and a heterodimeric DNA-targeting subunit Ku. DNA-PK is a major component of the non-homologous end-joining (NHEJ repair mechanism, which is activated in the presence of DNA double-strand breaks induced by ionizing radiation, reactive oxygen species and radiomimetic drugs. We have recently reported that down-regulation of protein kinase CK2 by siRNA interference results in enhanced cell death specifically in DNA-PKcs-proficient human glioblastoma cells, and this event is accompanied by decreased autophosphorylation of DNA-PKcs at S2056 and delayed repair of DNA double-strand breaks. Results In the present study, we show that CK2 co-localizes with phosphorylated histone H2AX to sites of DNA damage and while CK2 gene knockdown is associated with delayed DNA damage repair, its overexpression accelerates this process. We report for the first time evidence that lack of CK2 destabilizes the interaction of DNA-PKcs with DNA and with Ku80 at sites of genetic lesions. Furthermore, we show that CK2 regulates the phosphorylation levels of DNA-PKcs only in response to direct induction of DNA double-strand breaks. Conclusions Taken together, these results strongly indicate that CK2 plays a prominent role in NHEJ by facilitating and/or stabilizing the binding of DNA-PKcs and, possibly other repair proteins, to the DNA ends contributing to efficient DNA damage repair in mammalian cells.

  3. Local compression properties of double-stranded DNA based on a dynamic simulation

    CERN Document Server

    Lei, Xiaoling; Fang, Haiping

    2013-01-01

    The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. The compression simulation results for the 16 nm diameter sphere tip are well consistent with the experimental results. With the diameter of the tip decreasing, the radial compressive elastic properties under external loads become sensitive to the tip size and the local DNA conformation. There appears a suddenly force break in the compression-force curve when the sphere size is less than or equal to 12 nm diameter. The analysis of the hydrogen bonds and base stacking interaction shows there is a local unwinding process occurs. During the local unwinding process, first the hydrogen bonds between complement base pairs are broken. With the compression aggregating, the local backbones in the compression center are unwound from ...

  4. The AdditionalCurriculum of Career and Technology Learning Strand onCloth Products of Local Invention for Matthayomsueksa 2

    Directory of Open Access Journals (Sweden)

    Saifon Lasudta

    2016-09-01

    development of additional curriculum in the Career and TechnologyLearning Strand on the topic of Designing Products from Local Textiles for Mathayomsueksa 2was consistent with local problems / need and contexts. It promoted students-centered learning approach. It also provided various learning activities and materials. For thesereasons, the students were successful intheir learning.

  5. 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.

  6. Novel Smad proteins localize to IR-induced double-strand breaks: interplay between TGFβ and ATM pathways

    Science.gov (United States)

    Wang, Minli; Saha, Janapriya; Hada, Megumi; Anderson, Jennifer A.; Pluth, Janice M.; O’Neill, Peter; Cucinotta, Francis A.

    2013-01-01

    Cellular damage from ionizing radiation (IR) is in part due to DNA damage and reactive oxygen species, which activate DNA damage response (DDR) and cytokine signaling pathways, including the ataxia telangiectasia mutated (ATM) and transforming growth factor (TGF)β/Smad pathways. Using classic double-strand breaks (DSBs) markers, we studied the roles of Smad proteins in DDR and the crosstalk between TGFβ and ATM pathways. We observed co-localization of phospho-Smad2 (pSmad2) and Smad7 with DSB repair proteins following low and high linear energy transfer (LET) radiation in human fibroblasts and epithelial cells. The decays of both foci were similar to that of γH2AX foci. Irradiation with high LET particles induced pSmad2 and Smad7 foci tracks indicating the particle trajectory through cells. pSmad2 foci were absent in S phase cells, while Smad7 foci were present in all phases of cell cycle. pSmad2 (but not Smad7) foci were completely abolished when ATM was depleted or inactivated. In contrast, a TGFβ receptor 1 (TGFβR1) inhibitor abrogated Smad7, but not pSmad2 foci at DSBs sites. In summary, we suggest that Smad2 and Smad7 contribute to IR-induced DSB signaling in an ATM or TGFβR1-dependent manner, respectively. PMID:23221633

  7. Do Exogenous DNA Double-Strand Breaks Change Incomplete Synapsis and Chiasma Localization in the Grasshopper Stethophyma grossum?

    Science.gov (United States)

    2016-01-01

    Meiotic recombination occurs as a programmed event that initiates by the formation of DNA double-strand breaks (DSBs) that give rise to the formation of crossovers that are observed as chiasmata. Chiasmata are essential for the accurate chromosome segregation and the generation of new combinations of parental alleles. Some treatments that provoke exogenous DSBs also lead to alterations in the recombination pattern of some species in which full homologous synapsis is achieved at pachytene. We have carried out a similar approach in males of the grasshopper Stethophyma grossum, whose homologues show incomplete synapsis and proximal chiasma localization. After irradiating males with γ rays we have studied the distribution of both the histone variant γ-H2AX and the recombinase RAD51. These proteins are cytological markers of DSBs at early prophase I. We have inferred synaptonemal complex (SC) formation via identification of SMC3 and RAD 21 cohesin subunits. Whereas thick and thin SMC3 filaments would correspond to synapsed and unsynapsed regions, the presence of RAD21 is only restricted to synapsed regions. Results show that irradiated spermatocytes maintain restricted synapsis between homologues. However, the frequency and distribution of chiasmata in metaphase I bivalents is slightly changed and quadrivalents were also observed. These results could be related to the singular nuclear polarization displayed by the spermatocytes of this species. PMID:28005992

  8. Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory

    Science.gov (United States)

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

    2016-09-01

    Thermodynamic properties of water molecules around single- and double-stranded DNAs (ssDNAs and dsDNAs) with different sequences were investigated using grid inhomogeneous solvation theory. Free energies of water molecules solvating the minor groove of dsDNAs are lower than those near ssDNAs, while water molecules should be released during the formation of dsDNA. Free energies of water molecules around dsDNA are lower than those around ssDNA even in the second and third hydration shells. Our findings will help to clarify the role of water molecules in the formation of dsDNA from ssDNAs, thus facilitating the designs of drugs or nanomaterials using DNA.

  9. Co-Localization of Somatic and Meiotic Double Strand Breaks Near the Myc Oncogene on Mouse Chromosome 15

    Science.gov (United States)

    Ng, Siemon H.; Maas, Sarah A.; Petkov, Petko M.; Mills, Kevin D.; Paigen, Kenneth

    2010-01-01

    Both somatic and meiotic recombinations involve the repair of DNA double strand breaks (DSBs) that occur at preferred locations in the genome. Improper repair of DSBs during either mitosis or meiosis can lead to mutations, chromosomal aberration such as translocations, cancer and/or cell death. Currently, no model exists that explains the locations of either spontaneous somatic DSBs or programmed meiotic DSBs or relates them to each other. One common class of tumorigenic translocations arising from DSBs is chromosomal rearrangements near the Myc oncogene. Myc translocations have been associated with Burkitt lymphoma in humans, plasmacytoma in mice and immunocytoma in rats. Comparing the locations of somatic and meiotic DSBs near the mouse Myc oncogene, we demonstrated that the placement of these DSBs is not random and that both events clustered in the same short discrete region of the genome. Our work shows that both somatic and meiotic DSBs tend to occur in proximity to each other within the Myc region, suggesting that they share common originating features. It is likely that some regions of the genome are more susceptible to both somatic and meiotic DSBs, and the locations of meiotic hotspots may be an indicator of genomic regions more susceptible to DNA damage. PMID:19603522

  10. Propagation of slip pulse along frictionless contact interface with local separation between two piezoelectric solids

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The Stroh formalism of piezoelectric materials, Fourier analysis and singular integral equation technique were used to investigate the existence of a pu lse at the frictionless interface in presence of local separation between two contact piezoelectric solids.The two solids were combined together by uniaxial tractions and laid in the electric field.The problem was cast into a set of Cauchy singular integral equations, from which the closed-form solutions were derived.The numerical discussion on the existence of such a slip pulse was presented.The results show that such a slip pulse, which has square root singularities at both ends of the local separation zone, can propagate in most material combinations.And the existence of such a slip pulse will not be affected by the applied mechanical and electric fields in some special material combinations.

  11. On the role of local charge carrier mobility in the charge separation mechanism of organic photovoltaics.

    Science.gov (United States)

    Yoshikawa, Saya; Saeki, Akinori; Saito, Masahiko; Osaka, Itaru; Seki, Shu

    2015-07-21

    Although the charge separation (CS) and transport processes that compete with geminate and non-geminate recombination are commonly regarded as the governing factors of organic photovoltaic (OPV) efficiency, the details of the CS mechanism remain largely unexplored. Here we provide a systematic investigation on the role of local charge carrier mobility in bulk heterojunction films of ten different low-bandgap polymers and polythiophene analogues blended with methanofullerene (PCBM). By correlating with the OPV performances, we demonstrated that the local mobility of the blend measured by time-resolved microwave conductivity is more important for the OPV output than those of the pure polymers. Furthermore, the results revealed two separate trends for crystalline and semi-crystalline polymers. This work offers guidance in the design of high-performance organic solar cells.

  12. Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis.

    Science.gov (United States)

    Glavac, Damjan; Potocnik, Uros; Podpecnik, Darja; Zizek, Teofil; Smerkolj, Sava; Ravnik-Glavac, Metka

    2002-04-01

    We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct insight into the mechanism of CE-SSCP and showed that MFOLD prediction could be helpful in making decisions about the running temperatures and in prediction of CE-SSCP data patterns, especially for shorter (50-100 bp) DNA fragments.

  13. Separation of Radio-Frequency Sources and Localization of Partial Discharges in Noisy Environments

    Directory of Open Access Journals (Sweden)

    Guillermo Robles

    2015-04-01

    Full Text Available The detection of partial discharges (PD can help in early-warning detection systems to protect critical assets in power systems. The radio-frequency emission of these events can be measured with antennas even when the equipment is in service which reduces dramatically the maintenance costs and favours the implementation of condition-based monitoring systems. The drawback of these type of measurements is the difficulty of having a reference signal to study the events in a classical phase-resolved partial discharge pattern (PRPD. Therefore, in open-air substations and overhead lines where interferences from radio and TV broadcasting and mobile communications are important sources of noise and other pulsed interferences from rectifiers or inverters can be present, it is difficult to identify whether there is partial discharges activity or not. This paper proposes a robust method to separate the events captured with the antennas, identify which of them are partial discharges and localize the piece of equipment that is having problems. The separation is done with power ratio (PR maps based on the spectral characteristics of the signal and the identification of the type of event is done localizing the source with an array of four antennas. Several classical methods to calculate the time differences of arrival (TDOA of the emission to the antennas have been tested, and the localization is done using particle swarm optimization (PSO to minimize a distance function.

  14. Increased sister chromatid cohesion and DNA damage response factor localization at an enzyme-induced DNA double-strand break in vertebrate cells.

    LENUS (Irish Health Repository)

    Dodson, Helen

    2009-10-01

    The response to DNA damage in vertebrate cells involves successive recruitment of DNA signalling and repair factors. We used light microscopy to monitor the genetic dependencies of such localization to a single, induced DNA double strand break (DSB) in vertebrate cells. We used an inducible version of the rare-cutting I-SceI endonuclease to cut a chromosomally integrated I-SceI site beside a Tet operator array that was visualized by binding a Tet repressor-GFP fusion. Formation of gamma-H2AX foci at a single DSB was independent of ATM or Ku70. ATM-deficient cells showed normal kinetics of 53Bp1 recruitment to DSBs, but Rad51 localization was retarded. 53Bp1 and Rad51 foci formation at a single DSB was greatly reduced in H2AX-null DT40 cells. We also observed decreased inter-sister chromatid distances after DSB induction, suggesting that cohesin loading at DSBs causes elevated sister chromatid cohesion. Loss of ATM reduced DSB-induced cohesion, consistent with cohesin being an ATM target in the DSB response. These data show that the same genetic pathways control how cells respond to single DSBs and to multiple lesions induced by whole-cell DNA damage.

  15. Interferon-inducible p200-family protein IFI16, an innate immune sensor for cytosolic and nuclear double-stranded DNA: regulation of subcellular localization.

    Science.gov (United States)

    Veeranki, Sudhakar; Choubey, Divaker

    2012-01-01

    The interferon (IFN)-inducible p200-protein family includes structurally related murine (for example, p202a, p202b, p204, and Aim2) and human (for example, AIM2 and IFI16) proteins. All proteins in the family share a partially conserved repeat of 200-amino acid residues (also called HIN-200 domain) in the C-terminus. Additionally, most proteins (except the p202a and p202b proteins) also share a protein-protein interaction pyrin domain (PYD) in the N-terminus. The HIN-200 domain contains two consecutive oligosaccharide/oligonucleotide binding folds (OB-folds) to bind double stranded DNA (dsDNA). The PYD domain in proteins allows interactions with the family members and an adaptor protein ASC. Upon sensing cytosolic dsDNA, Aim2, p204, and AIM2 proteins recruit ASC protein to form an inflammasome, resulting in increased production of proinflammatory cytokines. However, IFI16 protein can sense cytosolic as well as nuclear dsDNA. Interestingly, the IFI16 protein contains a nuclear localization signal (NLS). Accordingly, the initial studies had indicated that the endogenous IFI16 protein is detected in the nucleus and within the nucleus in the nucleolus. However, several recent reports suggest that subcellular localization of IFI16 protein in nuclear versus cytoplasmic (or both) compartment depends on cell type. Given that the IFI16 protein can sense cytosolic as well as nuclear dsDNA and can initiate different innate immune responses (production of IFN-β versus proinflammatory cytokines), here we evaluate the experimental evidence for the regulation of subcellular localization of IFI16 protein in various cell types. We conclude that further studies are needed to understand the molecular mechanisms that regulate the subcellular localization of IFI16 protein. Published by Elsevier Ltd.

  16. Non-local separable solutions of two interacting particles in a harmonic trap

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Santander, C., E-mail: cglezsantander@fis.ucm.e [GISC, Departamento de Fisica de Materiales, Universidad Complutense, E-28040 Madrid (Spain); Dominguez-Adame, F. [GISC, Departamento de Fisica de Materiales, Universidad Complutense, E-28040 Madrid (Spain)

    2011-01-17

    We calculate the energy levels of two particles trapped in a harmonic potential. The actual two-body potential, assumed to be spherically symmetric, is replaced by a projective operator (non-local separable potential) to determine the energy levels in a closed form. This approach overcomes the limitations of the regularized Fermi pseudopotential when the characteristic length of the two-body interaction potential is of the order of the size of the harmonic trap. In addition, we recover the results obtained with the Fermi pseudopotential when the length of the interaction is much smaller than the size of the trap.

  17. An analytic method for separating local from regional effects on macroseismic intensity

    Directory of Open Access Journals (Sweden)

    C. Gasparini

    1995-06-01

    Full Text Available nterpretation of macroseismic data is hazardous, due to its qualitative nature. This, linked with errors in eval- uation, and the variations of local intensity, makes it difficult to draw valid conclusions. This study presents a statistical method as the basis for distinguishing the diverse components that constitute a macroseismic field. The method is based on the polar transformation of the coordinate system and on the analysis of the fractal di- mension of the intensity values, exposed to the gradually increasing action of a two-dimensional filter. The fractal dimension is shown to be an ideaI parameter with which to measure out the filtering process in order to separate the local components from the regional trend. This method has been applied to two Italian events and to an earthquake which took pIace in the Former Yugoslavian Republic of Macedonia (FYROM.

  18. Influence of nanoparticle-graphene separation on the localized surface plasmon resonances of metal nanoparticles

    CERN Document Server

    Saadabad, Reza Masoudian; Shirdel-Havar, Amir Hushang; Havar, Majid Shirdel

    2015-01-01

    We develop a theory to model the interaction of graphene substrate with localized plasmon resonances in metallic nanoparticles. The influence of a graphene substrate on the surface plasmon resonances is described using an effective background permittivity that is derived from a pseudoparticle concept using the electrostatic method. For this purpose, the interaction of metal nanoparticle with graphene sheet is studied to obtain the optical spectrum of gold nanoparticles deposited on a graphene substrate. Then, we introduce a factor based on dipole approximation to predict the influence of the separation of nanoparticles and graphene on the spectral position of the localized plasmon resonance of the nanoparticles. We applied the theory for a 4 nm radius gold nanosphere placed near 1.5 nm graphene layer. It is shown that a blue shift is emerged in the position of plasmon resonance when the nanoparticle moves away from graphene.

  19. Acoustic space learning for sound-source separation and localization on binaural manifolds.

    Science.gov (United States)

    Deleforge, Antoine; Forbes, Florence; Horaud, Radu

    2015-02-01

    In this paper, we address the problems of modeling the acoustic space generated by a full-spectrum sound source and using the learned model for the localization and separation of multiple sources that simultaneously emit sparse-spectrum sounds. We lay theoretical and methodological grounds in order to introduce the binaural manifold paradigm. We perform an in-depth study of the latent low-dimensional structure of the high-dimensional interaural spectral data, based on a corpus recorded with a human-like audiomotor robot head. A nonlinear dimensionality reduction technique is used to show that these data lie on a two-dimensional (2D) smooth manifold parameterized by the motor states of the listener, or equivalently, the sound-source directions. We propose a probabilistic piecewise affine mapping model (PPAM) specifically designed to deal with high-dimensional data exhibiting an intrinsic piecewise linear structure. We derive a closed-form expectation-maximization (EM) procedure for estimating the model parameters, followed by Bayes inversion for obtaining the full posterior density function of a sound-source direction. We extend this solution to deal with missing data and redundancy in real-world spectrograms, and hence for 2D localization of natural sound sources such as speech. We further generalize the model to the challenging case of multiple sound sources and we propose a variational EM framework. The associated algorithm, referred to as variational EM for source separation and localization (VESSL) yields a Bayesian estimation of the 2D locations and time-frequency masks of all the sources. Comparisons of the proposed approach with several existing methods reveal that the combination of acoustic-space learning with Bayesian inference enables our method to outperform state-of-the-art methods.

  20. Local microstructure evolution at shear bands in metallic glasses with nanoscale phase separation

    Science.gov (United States)

    He, Jie; Kaban, Ivan; Mattern, Norbert; Song, Kaikai; Sun, Baoan; Zhao, Jiuzhou; Kim, Do Hyang; Eckert, Jürgen; Greer, A. Lindsay

    2016-01-01

    At room temperature, plastic flow of metallic glasses (MGs) is sharply localized in shear bands, which are a key feature of the plastic deformation in MGs. Despite their clear importance and decades of study, the conditions for formation of shear bands, their structural evolution and multiplication mechanism are still under debate. In this work, we investigate the local conditions at shear bands in new phase-separated bulk MGs containing glassy nanospheres and exhibiting exceptional plasticity under compression. It is found that the glassy nanospheres within the shear band dissolve through mechanical mixing driven by the sharp strain localization there, while those nearby in the matrix coarsen by Ostwald ripening due to the increased atomic mobility. The experimental evidence demonstrates that there exists an affected zone around the shear band. This zone may arise from low-strain plastic deformation in the matrix between the bands. These results suggest that measured property changes originate not only from the shear bands themselves, but also from the affected zones in the adjacent matrix. This work sheds light on direct visualization of deformation-related effects, in particular increased atomic mobility, in the region around shear bands. PMID:27181922

  1. Local microstructure evolution at shear bands in metallic glasses with nanoscale phase separation.

    Science.gov (United States)

    He, Jie; Kaban, Ivan; Mattern, Norbert; Song, Kaikai; Sun, Baoan; Zhao, Jiuzhou; Kim, Do Hyang; Eckert, Jürgen; Greer, A Lindsay

    2016-05-16

    At room temperature, plastic flow of metallic glasses (MGs) is sharply localized in shear bands, which are a key feature of the plastic deformation in MGs. Despite their clear importance and decades of study, the conditions for formation of shear bands, their structural evolution and multiplication mechanism are still under debate. In this work, we investigate the local conditions at shear bands in new phase-separated bulk MGs containing glassy nanospheres and exhibiting exceptional plasticity under compression. It is found that the glassy nanospheres within the shear band dissolve through mechanical mixing driven by the sharp strain localization there, while those nearby in the matrix coarsen by Ostwald ripening due to the increased atomic mobility. The experimental evidence demonstrates that there exists an affected zone around the shear band. This zone may arise from low-strain plastic deformation in the matrix between the bands. These results suggest that measured property changes originate not only from the shear bands themselves, but also from the affected zones in the adjacent matrix. This work sheds light on direct visualization of deformation-related effects, in particular increased atomic mobility, in the region around shear bands.

  2. Enhancing Localized Evaporation through Separated Light Absorbing Centers and Scattering Centers.

    Science.gov (United States)

    Zhao, Dengwu; Duan, Haoze; Yu, Shengtao; Zhang, Yao; He, Jiaqing; Quan, Xiaojun; Tao, Peng; Shang, Wen; Wu, Jianbo; Song, Chengyi; Deng, Tao

    2015-11-26

    This report investigates the enhancement of localized evaporation via separated light absorbing particles (plasmonic absorbers) and scattering particles (polystyrene nanoparticles). Evaporation has been considered as one of the most important phase-change processes in modern industries. To improve the efficiency of evaporation, one of the most feasible methods is to localize heat at the top water layer rather than heating the bulk water. In this work, the mixture of purely light absorptive plasmonic nanostructures such as gold nanoparticles and purely scattering particles (polystyrene nanoparticles) are employed to confine the incident light at the top of the solution and convert light to heat. Different concentrations of both the light absorbing centers and the light scattering centers were evaluated and the evaporation performance can be largely enhanced with the balance between absorbing centers and scattering centers. The findings in this study not only provide a new way to improve evaporation efficiency in plasmonic particle-based solution, but also shed lights on the design of new solar-driven localized evaporation systems.

  3. Local Intermolecular Order Controls Photoinduced Charge Separation at Donor/Acceptor Interfaces in Organic Semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Feier, Hilary M.; Reid, Obadiah G.; Pace, Natalie A.; Park, Jaehong; Bergkamp, Jesse J.; Sellinger, Alan; Gust, Devens; Rumbles, Garry

    2016-03-23

    How free charge is generated at organic donor-acceptor interfaces is an important question, as the binding energy of the lowest energy (localized) charge transfer states should be too high for the electron and hole to escape each other. Recently, it has been proposed that delocalization of the electronic states participating in charge transfer is crucial, and aggregated or otherwise locally ordered structures of the donor or the acceptor are the precondition for this electronic characteristic. The effect of intermolecular aggregation of both the polymer donor and fullerene acceptor on charge separation is studied. In the first case, the dilute electron acceptor triethylsilylhydroxy-1,4,8,11,15,18,22,25-octabutoxyphthalocyaninatosilicon(IV) (SiPc) is used to eliminate the influence of acceptor aggregation, and control polymer order through side-chain regioregularity, comparing charge generation in 96% regioregular (RR-) poly(3-hexylthiophene) (P3HT) with its regiorandom (RRa-) counterpart. In the second case, ordered phases in the polymer are eliminated by using RRa-P3HT, and phenyl-C61-butyric acid methyl ester (PC61BM) is used as the acceptor, varying its concentration to control aggregation. Time-resolved microwave conductivity, time-resolved photoluminescence, and transient absorption spectroscopy measurements show that while ultrafast charge transfer occurs in all samples, long-lived charge carriers are only produced in films with intermolecular aggregates of either RR-P3HT or PC61BM, and that polymer aggregates are just as effective in this regard as those of fullerenes.

  4. Selective excitation for spectral editing and assignment in separated local field experiments of oriented membrane proteins.

    Science.gov (United States)

    Koroloff, Sophie N; Nevzorov, Alexander A

    2017-01-01

    Spectroscopic assignment of NMR spectra for oriented uniformly labeled membrane proteins embedded in their native-like bilayer environment is essential for their structure determination. However, sequence-specific assignment in oriented-sample (OS) NMR is often complicated by insufficient resolution and spectral crowding. Therefore, the assignment process is usually done by a laborious and expensive "shotgun" method involving multiple selective labeling of amino acid residues. Presented here is a strategy to overcome poor spectral resolution in crowded regions of 2D spectra by selecting resolved "seed" residues via soft Gaussian pulses inserted into spin-exchange separated local-field experiments. The Gaussian pulse places the selected polarization along the z-axis while dephasing the other signals before the evolution of the (1)H-(15)N dipolar couplings. The transfer of magnetization is accomplished via mismatched Hartmann-Hahn conditions to the nearest-neighbor peaks via the proton bath. By optimizing the length and amplitude of the Gaussian pulse, one can also achieve a phase inversion of the closest peaks, thus providing an additional phase contrast. From the superposition of the selective spin-exchanged SAMPI4 onto the fully excited SAMPI4 spectrum, the (15)N sites that are directly adjacent to the selectively excited residues can be easily identified, thereby providing a straightforward method for initiating the assignment process in oriented membrane proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications.

    Science.gov (United States)

    Mostofian, Barmak; Cai, Charles M; Smith, Micholas Dean; Petridis, Loukas; Cheng, Xiaolin; Wyman, Charles E; Smith, Jeremy C

    2016-08-31

    Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. To elucidate the mechanism of the THF-water interactions with cellulose, we pair simulation and experimental data demonstrating that enhanced solubilization of cellulose can be achieved by the THF-water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF-water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method.

  6. Selective excitation for spectral editing and assignment in separated local field experiments of oriented membrane proteins

    Science.gov (United States)

    Koroloff, Sophie N.; Nevzorov, Alexander A.

    2017-01-01

    Spectroscopic assignment of NMR spectra for oriented uniformly labeled membrane proteins embedded in their native-like bilayer environment is essential for their structure determination. However, sequence-specific assignment in oriented-sample (OS) NMR is often complicated by insufficient resolution and spectral crowding. Therefore, the assignment process is usually done by a laborious and expensive "shotgun" method involving multiple selective labeling of amino acid residues. Presented here is a strategy to overcome poor spectral resolution in crowded regions of 2D spectra by selecting resolved "seed" residues via soft Gaussian pulses inserted into spin-exchange separated local-field experiments. The Gaussian pulse places the selected polarization along the z-axis while dephasing the other signals before the evolution of the 1H-15N dipolar couplings. The transfer of magnetization is accomplished via mismatched Hartmann-Hahn conditions to the nearest-neighbor peaks via the proton bath. By optimizing the length and amplitude of the Gaussian pulse, one can also achieve a phase inversion of the closest peaks, thus providing an additional phase contrast. From the superposition of the selective spin-exchanged SAMPI4 onto the fully excited SAMPI4 spectrum, the 15N sites that are directly adjacent to the selectively excited residues can be easily identified, thereby providing a straightforward method for initiating the assignment process in oriented membrane proteins.

  7. Where Does the Density Localize? Convergent Behavior for Global Hybrids, Range Separation, and DFT+U

    CERN Document Server

    Gani, Terry Z H

    2016-01-01

    Approximate density functional theory (DFT) suffers from many-electron self- interaction error, otherwise known as delocalization error, that may be diagnosed and then corrected through elimination of the deviation from exact piecewise linear behavior between integer electron numbers. Although paths to correction of energetic delocalization error are well- established, the impact of these corrections on the electron density is less well-studied. Here, we compare the effect on density delocalization of DFT+U, global hybrid tuning, and range- separated hybrid tuning on a diverse test set of 32 transition metal complexes and observe the three methods to have qualitatively equivalent effects on the ground state density. Regardless of valence orbital diffuseness (i.e., from 2p to 5p), ligand electronegativity (i.e., from Al to O), basis set (i.e., plane wave versus localized basis set), metal (i.e., Ti, Fe, Ni) and spin state, or tuning method, we consistently observe substantial charge loss at the metal and gain ...

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

    Science.gov (United States)

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

    2012-10-25

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-25

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

  10. The non-singular Green tensor of Mindlin's anisotropic gradient elasticity with separable weak non-locality

    Energy Technology Data Exchange (ETDEWEB)

    Lazar, Markus, E-mail: lazar@fkp.tu-darmstadt.de [Heisenberg Research Group, Department of Physics, Darmstadt University of Technology, Hochschulstr. 6, D-64289 Darmstadt (Germany); Po, Giacomo, E-mail: gpo@ucla.edu [Department of Mechanical and Aerospace Engineering, University of California Los Angeles, Los Angeles, CA 90095 (United States)

    2015-07-31

    In this paper, we derive the Green tensor of anisotropic gradient elasticity with separable weak non-locality, a special version of Mindlin's form II anisotropic gradient elasticity theory with up to six independent length scale parameters. The framework models materials where anisotropy is twofold, namely the bulk material anisotropy and a weak non-local anisotropy relevant at the nano-scale. In contrast with classical anisotropic elasticity, it is found that both the Green tensor and its gradient are non-singular at the origin, and that they rapidly converge to their classical counterparts away from the origin. Therefore, the Green tensor of Mindlin's anisotropic gradient elasticity with separable weak non-locality can be used as a physically-based regularization of the classical Green tensor for materials with strong anisotropy. - Highlights: • Theory of Mindlin's anisotropic gradient elasticity with separable weak non-locality is presented. • The non-singular (3D) Green tensor is given. • The gradient of the non-singular Green tensor is calculated.

  11. Local Control, Democracy, and the Separation in the Public Opinion of School Finance Reform

    Science.gov (United States)

    Shelly, Bryan

    2007-01-01

    What role does a person's support for local educational control play in determining her attitude towards equity-minded school finance reform? This article reports estimations of binary and ordered probit models of two state public opinion polls and discusses newspaper coverage from the same two states to determine if and how local control has such…

  12. Separability Filter for Localizing Abnormal Pupil: Identification Criteria of Input Image

    Directory of Open Access Journals (Sweden)

    Tutik Ida Rosanti

    2013-11-01

    Full Text Available Separability filter method is a reliable method for pupil detection. However, so far this method is implemented for detecting pupil of normal eye, while for abnormal eye such as cataract and glaucoma patients; they have different characteristics of pupil such as color, shape and radius size of pupil. In this paper we propose to use separability filter for detecting pupil of abnormal patients with different characteristics. We faced a problem about radius size, shape and color of pupil; therefore we implemented Hough Transform, Blob area and Brightness for identifying input images before applying separability filter. The experiment results show that we can increase performance of pupil detection for abnormal eye to be 95.65%.

  13. Aspects of Quantum Non-Locality I: Superluminal Signalling, Action-at-a-Distance, Non-Separability and Holism

    Science.gov (United States)

    Berkovitz, Joseph

    In this paper and its sequel, I consider the significance of Jarrett's and Shimony's analyses of the so-called factorisability (Bell-locality) condition for clarifying the nature of quantum non-locality. In this paper, I focus on four types of non-locality: superluminal signalling, action-at-a-distance, non-separability and holism. In the second paper, I consider a fifth type of non-locality: superluminal causation according to 'logically weak' concepts of causation, where causal dependence requires neither action nor signalling. In this connection, I pay special attention to the difficulties that superluminal causation raises in relativistic space-time. I conclude by evaluating the relevance of Jarrett's and Shimony's analyses for clarifying the question of the compatibility of quantum non-locality with relativity theory. My main conclusions are, first: these analyses are significant for clarifying the questions of superluminal signalling in quantum phenomena and for the compatibility of these phenomena with relativity. But, second, by contrast: these analyses are not very significant for the study of action-at-a distance, superluminal causation, non-separability and holism in quantum phenomena.

  14. Finger Vein Segmentation from Infrared Images Based on a Modified Separable Mumford Shah Model and Local Entropy Thresholding

    OpenAIRE

    Marios Vlachos; Evangelos Dermatas

    2015-01-01

    A novel method for finger vein pattern extraction from infrared images is presented. This method involves four steps: preprocessing which performs local normalization of the image intensity, image enhancement, image segmentation, and finally postprocessing for image cleaning. In the image enhancement step, an image which will be both smooth and similar to the original is sought. The enhanced image is obtained by minimizing the objective function of a modified separable Mumford Shah Model. Sin...

  15. Short range DFT combined with long-range local RPA within a range-separated hybrid DFT framework

    CERN Document Server

    Chermak, E; Mussard, Bastien; Angyan, Janos

    2015-01-01

    Selecting excitations in localized orbitals to calculate long-range correlation contributions to range-separated density-functional theory can reduce the overall computational effort significantly. Beyond simple selection schemes of excited determinants, the dispersion-only approximation, which avoids counterpoise-corrected monomer calculations, is shown to be particularly interesting in this context, which we apply to the random-phase approximation. The approach has been tested on dimers of formamide, water, methane and benzene.

  16. Separation of Sperm Whale Click-Trains for Multipath Rejection and Localization

    Science.gov (United States)

    2010-03-05

    features were selected and separated into 3 groups: [kerr, perr , aerr, K.3, D-K3], [cerr, psdot, derr, Kl, K2, K4, TSTD, TM4, D-Kl, D-K4, D-TM3], [dT... perr Log power ratio aerr Log amplitude (SNR) ratio psdot Power spectrum deviation snrmin SNR off weakest click derr Incoherent correlation

  17. The evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription.

    Science.gov (United States)

    Takeuchi, Nobuto; Salazar, Laura; Poole, Anthony M; Hogeweg, Paulien

    2008-08-11

    The simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually become double-stranded and, hence, become unavailable for replication. Thus the problem of how to separate the two strands is considered a major issue for the early evolution of self-replicating RNA. One biologically plausible way to copy a double-stranded RNA is to displace a preexisting strand by a newly synthesized strand. Such copying can in principle be initiated from either the (+) or (-) strand of a double-stranded RNA. Assuming that only one of them, say (+), can act as replicase when single-stranded, strand displacement produces a new replicase if the (-) strand is the template. If, however, the (+) strand is the template, it produces a new template (but no replicase). Modern transcription exhibits extreme strand preference wherein anti-sense strands are always the template. Likewise, replication by strand displacement seems optimal if it also exhibits extreme strand preference wherein (-) strands are always the template, favoring replicase production. Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement. We first studied a simple mathematical model of the replicator dynamics. Our results indicated that if the system is well-mixed, there is no selective force acting upon strand preference per se. Next, we studied an individual-based simulation model to investigate the evolution of strand preference under finite diffusion. Interestingly, the results showed that selective forces "emerge" because of finite diffusion. Strikingly, the direction of the strand preference that evolves [i.e. (+) or (-) strand excess] is a complex non-monotonic function of the diffusion intensity. The mechanism underlying this behavior is elucidated. Furthermore, a speciation-like phenomenon is observed under

  18. The evolution of strand preference in simulated RNA replicators with strand displacement: Implications for the origin of transcription

    Directory of Open Access Journals (Sweden)

    Poole Anthony M

    2008-08-01

    Full Text Available Abstract Background The simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually become double-stranded and, hence, become unavailable for replication. Thus the problem of how to separate the two strands is considered a major issue for the early evolution of self-replicating RNA. One biologically plausible way to copy a double-stranded RNA is to displace a preexisting strand by a newly synthesized strand. Such copying can in principle be initiated from either the (+ or (- strand of a double-stranded RNA. Assuming that only one of them, say (+, can act as replicase when single-stranded, strand displacement produces a new replicase if the (- strand is the template. If, however, the (+ strand is the template, it produces a new template (but no replicase. Modern transcription exhibits extreme strand preference wherein anti-sense strands are always the template. Likewise, replication by strand displacement seems optimal if it also exhibits extreme strand preference wherein (- strands are always the template, favoring replicase production. Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement. Results We first studied a simple mathematical model of the replicator dynamics. Our results indicated that if the system is well-mixed, there is no selective force acting upon strand preference per se. Next, we studied an individual-based simulation model to investigate the evolution of strand preference under finite diffusion. Interestingly, the results showed that selective forces "emerge" because of finite diffusion. Strikingly, the direction of the strand preference that evolves [i.e. (+ or (- strand excess] is a complex non-monotonic function of the diffusion intensity. The mechanism underlying this behavior is elucidated. Furthermore, a speciation

  19. Overexpression of SETβ, a protein localizing to centromeres, causes precocious separation of chromatids during the first meiosis of mouse oocytes.

    Science.gov (United States)

    Qi, Shu-Tao; Wang, Zhen-Bo; Ouyang, Ying-Chun; Zhang, Qing-Hua; Hu, Meng-Wen; Huang, Xin; Ge, Zhaojia; Guo, Lei; Wang, Ya-Peng; Hou, Yi; Schatten, Heide; Sun, Qing-Yuan

    2013-04-01

    Chromosome segregation in mammalian oocyte meiosis is an error-prone process, and any mistake in this process may result in aneuploidy, which is the main cause of infertility, abortion and many genetic diseases. It is now well known that shugoshin and protein phosphatase 2A (PP2A) play important roles in the protection of centromeric cohesion during the first meiosis. PP2A can antagonize the phosphorylation of rec8, a member of the cohesin complex, at the centromeres and thus prevent cleavage of rec8 and so maintain the cohesion of chromatids. SETβ is a protein that physically interacts with shugoshin and inhibits PP2A activity. We thus hypothesized that SETβ might regulate cohesion protection and chromosome segregation during oocyte meiotic maturation. Here we report for the first time the expression, subcellular localization and functions of SETβ during mouse oocyte meiosis. Immunoblotting analysis showed that the expression level of SETβ was stable from the germinal vesicle stage to the MII stage of oocyte meiosis. Immunofluorescence analysis showed SETβ accumulation in the nucleus at the germinal vesicle stage, whereas it was targeted mainly to the inner centromere area and faintly localized to the interchromatid axes from germinal vesicle breakdown to MI stages. At the MII stage, SETβ still localized to the inner centromere area, but could relocalize to kinetochores in a process perhaps dependent on the tension on the centromeres. SETβ partly colocalized with PP2A at the inner centromere area. Overexpression of SETβ in mouse oocytes caused precocious separation of sister chromatids, but depletion of SETβ by RNAi showed little effects on the meiotic maturation process. Taken together, our results suggest that SETβ, even though it localizes to centromeres, might not be essential for chromosome separation during mouse oocyte meiotic maturation, although its forced overexpression causes premature chromatid separation.

  20. Design and implementation of a space domain spherical microphone array with application to source localization and separation.

    Science.gov (United States)

    Bai, Mingsian R; Yao, Yueh Hua; Lai, Chang-Sheng; Lo, Yi-Yang

    2016-03-01

    In this paper, four delay-and-sum (DAS) beamformers formulated in the modal domain and the space domain for open and solid spherical apertures are examined through numerical simulations. The resulting beampatterns reveal that the mainlobe of the solid spherical DAS array is only slightly narrower than that of the open array, whereas the sidelobes of the modal domain array are more significant than those of the space domain array due to the discrete approximation of continuous spherical Fourier transformation. To verify the theory experimentally, a three-dimensionally printed spherical array on which 32 micro-electro-mechanical system microphones are mounted is utilized for localization and separation of sound sources. To overcome the basis mismatch problem in signal separation, source localization is first carried out using minimum variance distortionless response beamformer. Next, Tikhonov regularization (TIKR) and compressive sensing (CS) are employed to extract the source signal amplitudes. Simulations and experiments are conducted to validate the proposed spherical array system. Objective perceptual evaluation of speech quality test and a subjective listening test are undertaken in performance evaluation. The experimental results demonstrate better separation quality achieved by the CS approach than by the TIKR approach at the cost of computational complexity.

  1. SEPARATION OF Ca AND Fe METAL ION IN SOURCE WATER BY ADSORPTION COLUMN TECHNIC WITH LOCAL ZEOLITE AND ACTIVE CARBON

    Directory of Open Access Journals (Sweden)

    Suyanta Suyanta

    2016-04-01

    Full Text Available This research aims are to separate of Ca and Fe metal ion in source water, with local zeolite and active carbon by adsorption column technic. Efficiency of separation are control by adsorption time and size of zeolite. Method that used was column adsorption with a flow system in which sample is applied to the filtration tube containing zeolite and active carbon. Initial and final concentrations of the samples were analyzed using Atomic Adsorption Spectrophotometer instrument. The results obtained shows that ability adsorption of zeolite to Ca and Fe metal ion are a good. Zeolite 1 (10 mesh can reduce iron concentration until 93.98 % and zeolite 2 (5mesh until 98.88% for 1 – 4 week range time. Whereas reducing of calcium concentration is not good, until 2 week period time adsorption of calcium ion is about 50%.   Keywords: adsorption, zeolite, source water

  2. DNA strand displacement system running logic programs.

    Science.gov (United States)

    Rodríguez-Patón, Alfonso; Sainz de Murieta, Iñaki; Sosík, Petr

    2014-01-01

    The paper presents a DNA-based computing model which is enzyme-free and autonomous, not requiring a human intervention during the computation. The model is able to perform iterated resolution steps with logical formulae in conjunctive normal form. The implementation is based on the technique of DNA strand displacement, with each clause encoded in a separate DNA molecule. Propositions are encoded assigning a strand to each proposition p, and its complementary strand to the proposition ¬p; clauses are encoded comprising different propositions in the same strand. The model allows to run logic programs composed of Horn clauses by cascading resolution steps. The potential of the model is demonstrated also by its theoretical capability of solving SAT. The resulting SAT algorithm has a linear time complexity in the number of resolution steps, whereas its spatial complexity is exponential in the number of variables of the formula. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  3. Finger Vein Segmentation from Infrared Images Based on a Modified Separable Mumford Shah Model and Local Entropy Thresholding

    Directory of Open Access Journals (Sweden)

    Marios Vlachos

    2015-01-01

    Full Text Available A novel method for finger vein pattern extraction from infrared images is presented. This method involves four steps: preprocessing which performs local normalization of the image intensity, image enhancement, image segmentation, and finally postprocessing for image cleaning. In the image enhancement step, an image which will be both smooth and similar to the original is sought. The enhanced image is obtained by minimizing the objective function of a modified separable Mumford Shah Model. Since, this minimization procedure is computationally intensive for large images, a local application of the Mumford Shah Model in small window neighborhoods is proposed. The finger veins are located in concave nonsmooth regions and, so, in order to distinct them from the other tissue parts, all the differences between the smooth neighborhoods, obtained by the local application of the model, and the corresponding windows of the original image are added. After that, veins in the enhanced image have been sufficiently emphasized. Thus, after image enhancement, an accurate segmentation can be obtained readily by a local entropy thresholding method. Finally, the resulted binary image may suffer from some misclassifications and, so, a postprocessing step is performed in order to extract a robust finger vein pattern.

  4. Finger Vein Segmentation from Infrared Images Based on a Modified Separable Mumford Shah Model and Local Entropy Thresholding.

    Science.gov (United States)

    Vlachos, Marios; Dermatas, Evangelos

    2015-01-01

    A novel method for finger vein pattern extraction from infrared images is presented. This method involves four steps: preprocessing which performs local normalization of the image intensity, image enhancement, image segmentation, and finally postprocessing for image cleaning. In the image enhancement step, an image which will be both smooth and similar to the original is sought. The enhanced image is obtained by minimizing the objective function of a modified separable Mumford Shah Model. Since, this minimization procedure is computationally intensive for large images, a local application of the Mumford Shah Model in small window neighborhoods is proposed. The finger veins are located in concave nonsmooth regions and, so, in order to distinct them from the other tissue parts, all the differences between the smooth neighborhoods, obtained by the local application of the model, and the corresponding windows of the original image are added. After that, veins in the enhanced image have been sufficiently emphasized. Thus, after image enhancement, an accurate segmentation can be obtained readily by a local entropy thresholding method. Finally, the resulted binary image may suffer from some misclassifications and, so, a postprocessing step is performed in order to extract a robust finger vein pattern.

  5. Chromosomal localization of mitochondrial transcription factor A (TCF6), single-stranded DNA-binding protein (SSBP), and endonuclease G (ENDOG), three human housekeeping genes involving in mitochondrial biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Tiranti, V.; Rossi, G.; DiDonato, S. [Istituto Nazionale Neurologico, Carlo Besta (Italy)] [and others

    1995-01-20

    By using a PCR-based screening of a somatic cell hybrid panel and FISH, we have assigned the loci of mitochondrial single-stranded DNA-binding protein (SSBP), mitochondrial transcription factor A (TCF6), and mitochondrial endonuclease G (ENDOG) genes to human chromosomes 7q34, 10q21, and 9q34.1, respectively. The products of these three genes are involved in fundamental aspects of mitochondrial biogenesis, such as replication and transcription of the mitochondrial genome. The chromosomal localization of these genes is important to testing whether the corresponding proteins may play a role in the etiopathogenesis of human disorders associated with qualitative or quantitative abnormalities of mitochondrial DNA. 20 refs., 1 fig., 2 tabs.

  6. 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...

  7. 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...

  8. Whale strandings: hypothesis.

    Science.gov (United States)

    Mawson, A R

    1978-01-01

    The hypothesis is presented that whales become stranded inadvertently as a consequence of seeking stimulation. The animals enter shallow water in order to roll over, bask, and rub themselves in the sand, and are trapped by the receding tide. It suggested that stimulation-seeking behavior (and stranding) reflects a general sympathetic nervous system response which may be due to a number of factors such as pain, discomfort, reproductive state, and other biorhythmic changes.

  9. Localized electron states and phase separation at the LaAlO3/SrTiO3 interface

    Science.gov (United States)

    Satpathy, S.; Shanavas, K. V.

    2012-02-01

    Even though the 2D electron gas at the polar interfaces of LAO/STO has been studied extensively, an explanation for the observed magnetic centers or the coexistence of magnetism and superconductivity is still lacking. Earlier density-functional calculations have indicated the presence of multi-bands and two types of electrons at the interface [1]. Here we propose that a combination of lattice disorder, octahedral rotations, and Jahn-Teller distortion can lead to some of these electrons to be localized near the interface and form lattice polarons. Evidence for this is presented from detailed density-functional calculations, which indicate that the energy gain associated with JT distortion and impurity or disorder induced local potentials can offset the kinetic energy cost of localization. Our model studies [2] also show the possible existence of a phase separation, thereby providing a natural explanation for the coexistence of magnetism and superconductivity [3].[4pt] [1] Z. S. Popovi'c, S. Satpathy and R. M. Martin Phys. Rev. Lett., 101, 256801 (2008)[0pt] [2] B. R. K. Nanda and S. Satpathy Phys. Rev B, 83, 195114 (2011)[0pt] [3] L. Li et. al. Nature Physics, 7, 762 (2011); J. A. Bert et. al. ibid, 767 (2011);

  10. Opening the strands of replication origins – still an open question

    Directory of Open Access Journals (Sweden)

    Dhruba Chattoraj

    2016-09-01

    Full Text Available The local separation of duplex DNA strands (strand opening is necessary for initiating basic transactions on DNA such as transcription, replication and homologous recombination. Strand opening is commonly a stage at which these processes are regulated. Many different mechanisms are used to open the DNA duplex, the details of which are of great current interest. In this review, we focus on a few well-studied cases of DNA replication origin opening in bacteria. In particular, we discuss the opening of origins that support the theta ( mode of replication, which is used by all chromosomal origins and many extra-chromosomal elements such as plasmids and phages. Although the details of opening can vary among different origins, a common theme is binding of the initiator to multiple sites at the origin, causing stress that opens an adjacent and intrinsically unstable A+T rich region. The initiator stabilizes the opening by capturing one of the open strands. How the initiator binding energy is harnessed for strand opening remains to be understood.

  11. Separation of convective and stratiform precipitation for a precipitation analysis of the local model of the German Weather Service

    Directory of Open Access Journals (Sweden)

    E. Reimer

    2007-04-01

    Full Text Available An improved independent precipitation data set with the horizontal resolution of 7×7 km grid over central Europe was generated (Free University of Berlin (FUB-precipitation analysis. For scale dependent evaluation of the Local model (LM of the German Weather service, the precipitation data were separated into convective and stratiform fractions. To analyse precipitation amounts an interpolation scheme is used which contains the data set of "present weather" (ww, rain gauges and cloud types from the WMO-network in hourly resolution from the year 1992 until 2004 together with satellite cloud types derived from Meteosat-7 data. The structural analyses of cloud classes from satellite data as well as clouds from the synoptic observations were used to develop a statistical interpolation procedure to build up an independent precipitation analysis in resolution corresponding to the LM grid.

  12. Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Yong Yang

    2008-11-01

    Full Text Available The major DNA repair pathways operate on damage in double-strand DNA because they use the intact strand as a template after damage removal. Therefore, lesions in transient single-strand stretches of chromosomal DNA are expected to be especially threatening to genome stability. To test this hypothesis, we designed systems in budding yeast that could generate many kilobases of persistent single-strand DNA next to double-strand breaks or uncapped telomeres. The systems allowed controlled restoration to the double-strand state after applying DNA damage. We found that lesions induced by UV-light and methyl methanesulfonate can be tolerated in long single-strand regions and are hypermutagenic. The hypermutability required PCNA monoubiquitination and was largely attributable to translesion synthesis by the error-prone DNA polymerase zeta. In support of multiple lesions in single-strand DNA being a source of hypermutability, analysis of the UV-induced mutants revealed strong strand-specific bias and unexpectedly high frequency of alleles with widely separated multiple mutations scattered over several kilobases. Hypermutability and multiple mutations associated with lesions in transient stretches of long single-strand DNA may be a source of carcinogenesis and provide selective advantage in adaptive evolution.

  13. Hypermutability of Damaged Single-Strand DNA Formed at Double-Strand Breaks and Uncapped Telomeres in Yeast Saccharomyces cerevisiae

    Science.gov (United States)

    Yang, Yong; Sterling, Joan; Storici, Francesca; Resnick, Michael A.; Gordenin, Dmitry A.

    2008-01-01

    The major DNA repair pathways operate on damage in double-strand DNA because they use the intact strand as a template after damage removal. Therefore, lesions in transient single-strand stretches of chromosomal DNA are expected to be especially threatening to genome stability. To test this hypothesis, we designed systems in budding yeast that could generate many kilobases of persistent single-strand DNA next to double-strand breaks or uncapped telomeres. The systems allowed controlled restoration to the double-strand state after applying DNA damage. We found that lesions induced by UV-light and methyl methanesulfonate can be tolerated in long single-strand regions and are hypermutagenic. The hypermutability required PCNA monoubiquitination and was largely attributable to translesion synthesis by the error-prone DNA polymerase ζ. In support of multiple lesions in single-strand DNA being a source of hypermutability, analysis of the UV-induced mutants revealed strong strand-specific bias and unexpectedly high frequency of alleles with widely separated multiple mutations scattered over several kilobases. Hypermutability and multiple mutations associated with lesions in transient stretches of long single-strand DNA may be a source of carcinogenesis and provide selective advantage in adaptive evolution. PMID:19023402

  14. 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

  15. Op het strand

    NARCIS (Netherlands)

    Boer, M.G. de

    2010-01-01

    SAMENVATTING Het woord spiaggia ‘strand’ wordt besproken binnen het veld van woorden die een scheiding tussen land en water aangeven. Hierbij worden historisch verschillende scenario’s (frames) onderscheiden, al naar de functie de het strand destijds had. Spiaggia wordt vergeleken met zijn synoniem

  16. 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

  17. 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.

  18. Op het strand

    NARCIS (Netherlands)

    Boer, M.G. de

    2010-01-01

    SAMENVATTING Het woord spiaggia ‘strand’ wordt besproken binnen het veld van woorden die een scheiding tussen land en water aangeven. Hierbij worden historisch verschillende scenario’s (frames) onderscheiden, al naar de functie de het strand destijds had. Spiaggia wordt vergeleken met zijn

  19. Separating Hazardous Aerosols from Ambient Aerosols: Role of Fluorescence-Spectral Determination, Aerodynamic Deflector and Pulse Aerodynamic Localizer (PAL)

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Yong-Le; Cobler, Patrick J.; Rhodes, Scott A.; Halverson, Justin; Chang, Richard K.

    2005-08-22

    An aerosol deflection technique based on the single-shot UV-laser-induced fluorescence spectrum from a flowing particle is presented as a possible front-end bio-aerosol/hazardous-aerosol sensor/identifier. Cued by the fluorescence spectra, individual flowing bio-aerosol particles (1-10 {micro}m in diameter) have been successfully deflected from a stream of ambient aerosols. The electronics needed to compare the fluorescence spectrum of a particular particle with that of a pre-determined fluorescence spectrum are presented in some detail. The deflected particles, with and without going through a funnel for pulse aerodynamic localization (PAL), were collected onto a substrate for further analyses. To demonstrate how hazardous materials can be deflected, TbCl{sub 3} {center_dot} 6H{sub 2}O (a simulant material for some chemical forms of Uranium Oxide) aerosol particles (2 {micro}m in diameter) mixed with Arizona road dust was separated and deflected with our system.

  20. Area per lipid and cholesterol interactions in membranes from separated local-field (13)C NMR spectroscopy.

    Science.gov (United States)

    Leftin, Avigdor; Molugu, Trivikram R; Job, Constantin; Beyer, Klaus; Brown, Michael F

    2014-11-18

    Investigations of lipid membranes using NMR spectroscopy generally require isotopic labeling, often precluding structural studies of complex lipid systems. Solid-state (13)C magic-angle spinning NMR spectroscopy at natural isotopic abundance gives site-specific structural information that can aid in the characterization of complex biomembranes. Using the separated local-field experiment DROSS, we resolved (13)C-(1)H residual dipolar couplings that were interpreted with a statistical mean-torque model. Liquid-disordered and liquid-ordered phases were characterized according to membrane thickness and average cross-sectional area per lipid. Knowledge of such structural parameters is vital for molecular dynamics simulations, and provides information about the balance of forces in membrane lipid bilayers. Experiments were conducted with both phosphatidylcholine (dimyristoylphosphatidylcholine (DMPC) and palmitoyloleoylphosphatidylcholine (POPC)) and egg-yolk sphingomyelin (EYSM) lipids, and allowed us to extract segmental order parameters from the (13)C-(1)H residual dipolar couplings. Order parameters were used to calculate membrane structural quantities, including the area per lipid and bilayer thickness. Relative to POPC, EYSM is more ordered in the ld phase and experiences less structural perturbation upon adding 50% cholesterol to form the lo phase. The loss of configurational entropy is smaller for EYSM than for POPC, thus favoring its interaction with cholesterol in raftlike lipid systems. Our studies show that solid-state (13)C NMR spectroscopy is applicable to investigations of complex lipids and makes it possible to obtain structural parameters for biomembrane systems where isotope labeling may be prohibitive.

  1. Saw1 Localizes to Repair Sites but is not Required for Recruitment of Rad10 to Repair Intermediates Bearing Short Non-Homologous 3′ Flaps during Single-Strand Annealing in S. cerevisiae

    OpenAIRE

    Mardirosian, Melina; Nalbandyan, Linette; Miller, Aaron D.; Phan, Claire; Kelson, Eric P.; Fischhaber, Paula L.

    2015-01-01

    SAW1 is required for efficient removal by the Rad1-Rad10 nuclease of 3′ non-homologous DNA ends (flaps) formed as intermediates during two modes of double-strand break repair in S. cerevisiae, single-strand annealing (SSA) and synthesis-dependent strand annealing (SDSA). Saw1 was shown in vitro to bind flaps with high affinity, but displayed diminished affinity when flaps were short (< 30 deoxynucleotides [nt]), consistent with it not being required for short flap cleavage. Accordingly, this ...

  2. Thermophoresis of single stranded DNA.

    Science.gov (United States)

    Reineck, Philipp; Wienken, Christoph J; Braun, Dieter

    2010-01-01

    The manipulation and analysis of biomolecules in native bulk solution is highly desired; however, few methods are available. In thermophoresis, the thermal analog to electrophoresis, molecules are moved along a microscopic temperature gradient. Its theoretical foundation is still under debate, but practical applications for analytics in biology show considerable potential. Here we measured the thermophoresis of highly diluted single stranded DNA using an all-optical capillary approach. Temperature gradients were created locally by an infrared laser. The thermal depletion of oligonucleotides of between 5 and 50 bases in length were investigated by fluorescence at various salt concentrations. To a good approximation, the previously tested capacitor model describes thermophoresis: the Soret coefficient linearly depends on the Debye length and is proportional to the DNA length to the power of 0.35, dictated by the conformation-based size scaling of the diffusion coefficient. The results form the basis for quantitative DNA analytics using thermophoresis.

  3. Computing in mammalian cells with nucleic acid strand exchange

    Science.gov (United States)

    Groves, Benjamin; Chen, Yuan-Jyue; Zurla, Chiara; Pochekailov, Sergii; Kirschman, Jonathan L.; Santangelo, Philip J.; Seelig, Georg

    2016-03-01

    DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution.

  4. Separable quantum states do not have stronger correlations than local realism A comment on quant-ph/0611126 of Z. Chen

    CERN Document Server

    Seevinck, M

    2007-01-01

    Chen (quant-ph/0611126) has recently claimed ``exponential violation of local realism by separable states", in the sense that multi-partite separable quantum states are supposed to give rise to correlations and fluctuations that violate a Bell-type inequality that Chen takes to be satisfied by local realism. However, this can not be true since all predictions (including all correlations and fluctuations) that separable quantum states give rise to have a local realistic description and thus satisfy all Bell-type inequalities, and this holds for all number of parties. Since Chen claims otherwise by presenting a new inequality, claimed to be a Bell-type one, which separable states supposedly can violate, there must be a flaw in the argumentation. I will expose this flaw, not merely for clarification of this issue, but perhaps even more importantly since it re-teaches us an old lesson John Bell taught us over 40 years ago. I will argue that this lesson provides us with a new morale especially relevant to modern r...

  5. The causes of whale strandings.

    Science.gov (United States)

    Cordes, D O

    1982-03-01

    Strandings of cetaceans (whales and dolphins) is probably the result of a sequence of events rather than a simple cause-and-effect relationship. Strandings of solitary animals are more common than massed and generally thought to be due to severe disease. Mass strandings (three to several hundred individuals) are less common, but very spectacular. Mass strandings are considered to be due to a complex of factors in which behavioural factors are probably important, severe disease making an unimportant, or negligible contribution. There may be interaction of physical conditions (weather, tides, currents, coastline) and biological conditions (predators, feeding, disturbance of echolocation and disease) which result in stranding. One postulated reason for stranding is that it is dependent on instinctive behaviour, deeply located in subcortical areas of the brain, which provokes cetaceans to seek refuge ashore when under stress.

  6. 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.

  7. Localization of Post-Translational Modifications in Peptide Mixtures via High-Resolution Differential Ion Mobility Separations Followed by Electron Transfer Dissociation

    Science.gov (United States)

    Baird, Matthew A.; Shvartsburg, Alexandre A.

    2016-12-01

    Precise localization of post-translational modifications (PTMs) on proteins and peptides is an outstanding challenge in proteomics. While electron transfer dissociation (ETD) has dramatically advanced PTM analyses, mixtures of localization variants that commonly coexist in cells often require prior separation. Although differential or field asymmetric waveform ion mobility spectrometry (FAIMS) achieves broad variant resolution, the need for standards to identify the features has limited the utility of approach. Here we demonstrate full a priori characterization of variant mixtures by high-resolution FAIMS coupled to ETD and the procedures to systematically extract the FAIMS spectra for all variants from such data.

  8. Localization of Post-Translational Modifications in Peptide Mixtures via High-Resolution Differential Ion Mobility Separations Followed by Electron Transfer Dissociation

    Science.gov (United States)

    Baird, Matthew A.; Shvartsburg, Alexandre A.

    2016-09-01

    Precise localization of post-translational modifications (PTMs) on proteins and peptides is an outstanding challenge in proteomics. While electron transfer dissociation (ETD) has dramatically advanced PTM analyses, mixtures of localization variants that commonly coexist in cells often require prior separation. Although differential or field asymmetric waveform ion mobility spectrometry (FAIMS) achieves broad variant resolution, the need for standards to identify the features has limited the utility of approach. Here we demonstrate full a priori characterization of variant mixtures by high-resolution FAIMS coupled to ETD and the procedures to systematically extract the FAIMS spectra for all variants from such data.

  9. Autonomous parvovirus LuIII encapsidates equal amounts of plus and minus DNA strands

    Energy Technology Data Exchange (ETDEWEB)

    Bates, R.C.; Snyder, C.E.; Banerjee, P.T.; Mitra, S.

    1984-02-01

    Autonomous parvoviruses are thought to uniquely encapsidate single-stranded DNA of minus polarity. In contrast, the defective adeno-associated viruses separately encapsidate equal amounts of plus and minus DNA strands. The uniqueness of minus strand encapsidation is reexamined for the autonomous parvoviruses. Although it was found that Kilham rat virus and H-1 virus encapsidate varying but small amounts of complementary-strand DNA, it was unexpected to find that LuIII virus encapsidated equal amounts of plus and minus DNA. The extracted LuIII DNA possessed properties of double-stranded replicative-form DNA, including insensitivity to S1 endonuclease, cleavage by restriction enzymes, and conversion to unit-length, single-stranded DNA when electrophoresed under denaturing conditions. However, the inability of this DNA to form single-stranded DNA circles when denatured and then renatured in the presence of formamide and the lack of double-stranded DNA circle formation after treatment with exonuclease III and reannealing shows a lack of sequence homology of the 3' and 5' termini of LuIII DNA, in contrast to adeno-associated virus DNA. Digestion of LuIII double-stranded DNA with EcoRI and HincII and separation of plus and minus DNA strands on composite agarose-acrylamide gels identified a heterogeneity present only in the plus DNA strand. These results suggest that strand specificity of viral DNA encapsidation is not a useful property for differentiation between the autonomous and defective parvoviruses. Furthermore, encapsidation by LuIII of equal amounts of complementary DNA strands in contrast to encapsidation of minus strands by H-1 virus, when propagated in the same host cell type, suggests that selection of strands for encapsidation is a virus-coded rather than host-controlled event.

  10. The structure-specific endonuclease Mus81-Eme1 promotes conversion of interstrand DNA crosslinks into double-strands breaks

    NARCIS (Netherlands)

    K. Hanada (Katsuhiro); M. Budzowska (Magdalena); M. Modesti (Mauro); A. Maas (Alex); C. Wyman (Claire); J. Essers (Jeroen); R. Kanaar (Roland)

    2006-01-01

    textabstractRepair of interstrand crosslinks (ICLs) requires multiple-strand incisions to separate the two covalently attached strands of DNA. It is unclear how these incisions are generated. DNA double-strand breaks (DSBs) have been identified as intermediates in ICL repair, but enzymes responsible

  11. 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

  12. local

    Directory of Open Access Journals (Sweden)

    Abílio Amiguinho

    2005-01-01

    Full Text Available The process of socio-educational territorialisation in rural contexts is the topic of this text. The theme corresponds to a challenge to address it having as main axis of discussion either the problem of social exclusion or that of local development. The reasons to locate the discussion in this last field of analysis are discussed in the first part of the text. Theoretical and political reasons are there articulated because the question is about projects whose intentions and practices call for the political both in the theoretical debate and in the choices that anticipate intervention. From research conducted for several years, I use contributions that aim at discuss and enlighten how school can be a potential locus of local development. Its identification and recognition as local institution (either because of those that work and live in it or because of those that act in the surrounding context are crucial steps to progressively constitute school as a partner for development. The promotion of the local values and roots, the reconstruction of socio-personal and local identities, the production of sociabilities and the equation and solution of shared problems were the dimensions of a socio-educative intervention, markedly globalising. This scenario, as it is argued, was also, intentionally, one of transformation and of deliberate change of school and of the administration of the educative territoires.

  13. Local mechanisms for the separation of optic flow-field components in the land crab, Cardisoma guanhumi: a role for motion parallax?

    Science.gov (United States)

    Johnson, Aaron P; Barnes, W Jon P; Macauley, Martin W S

    2004-01-01

    Although a number of global mechanisms have been proposed over the years that explain how crabs might separate the rotational and translational components of their optic flow field, there has been no evidence to date that local mechanisms such as motion parallax are used in this separation. We describe here a study that takes advantage of a recently developed suite of computer-generated visual stimuli that creates a three-dimensional world surrounding the crab in which we can simulate translational and rotational optic flow. We show that, while motion parallax is not the only mechanism used in flow-field separation, it does play a role in the recognition of translational optic flow fields in that, under conditions of low overall light intensity and low contrast ratio when crabs find the distinction between rotation and translation harder, smaller eye movements occur in response to translation when motion parallax cues are present than when they are absent. Thus, motion parallax is one of many cues that crabs use to separate rotational and translational optic flow by showing compensatory eye movements to only the former.

  14. 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 Nb3Sn 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 Nb3Sn. 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 considerations in ...

  15. Optimized measurements of separations and angles between intra-molecular fluorescent markers

    DEFF Research Database (Denmark)

    Mortensen, Kim; Sung, Jongmin; Flyvbjerg, Henrik;

    2015-01-01

    We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie...... molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule...... and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA...

  16. Adenovirus replication and transcription sites are spatially separated in the nucleus of infected cells.

    Science.gov (United States)

    Pombo, A; Ferreira, J; Bridge, E; Carmo-Fonseca, M

    1994-11-01

    We have visualized the intranuclear topography of adenovirus replication and transcription in infected HeLa cells. The results show that viral DNA replication occurs in multiple foci that are highly organized in the nucleoplasm. Pulse-chase experiments indicate that newly synthesized viral double-stranded DNA molecules are displaced from the replication foci and spread throughout the nucleoplasm, while the single-stranded DNA replication intermediates accumulate in adjacent sites. Double-labelling experiments and confocal microscopy show that replication occurs in foci localized at the periphery of the sites where single-stranded DNA accumulates. The simultaneous visualization of viral replication and transcription reveals that the sites of transcription are predominantly separated from the sites of replication. Transcription is detected adjacent to the replication foci and extends around the sites of single-stranded DNA accumulation. These data indicate that newly synthesized double-stranded DNA molecules are displaced from the replication foci and spread in the surrounding nucleoplasm, where they are used as templates for transcription. Splicing snRNPs are shown to co-localize with the sites of transcription and to be excluded from the sites of replication. This provides evidence that splicing of viral RNAs occurs co-transcriptionally and that the sites of viral DNA replication are spatially distinct from the sites of RNA transcription and processing.

  17. Effect of subelement spacing in RRP Nb3Sn strands

    Energy Technology Data Exchange (ETDEWEB)

    Barzi, E.; Turrioni, D.; /Fermilab; Alsharo' a, M.; /MUONS Inc., Batavia; Field, M.; Hong, S.; Parrell, J.; Yamada, R.; /Fermilab; Zhang, Y.; Zlobin, A.; /Fermilab

    2007-10-01

    The Restacked Rod Process (RRP) is the Nb{sub 3}Sn strand technology presently producing the largest critical current densities at 4.2 K and 12 T. However, when subject to plastic deformation, RRP subelements (SE) were found to merge into each other, creating larger filaments with a somewhat continuous barrier. In this case, the strand sees a larger effective filament size, d{sub eff}, and its instability can dramatically increase locally leading to cable quench. To reduce and possibly eliminate this effect, Oxford Instruments Superconducting Technology (OST) developed for FNAL a modified RRP strand design with larger Cu spacing between SE's arranged in a 60/61 array. Strand samples of this design with sizes from 0.7 to 1 mm were first evaluated for transport current properties. A comparison study was then performed between the regular 54/61 and the modified 60/61 design using 0.7 mm round and deformed strands. Finite element modeling of the deformed strands was also performed with ANSYS.

  18. E4orf6 variants with separate abilities to augment adenovirus replication and direct nuclear localization of the E1B 55-kilodalton protein.

    Science.gov (United States)

    Orlando, Joseph S; Ornelles, David A

    2002-02-01

    The E4orf6 protein of group C adenovirus is an oncoprotein that, in association with the E1B 55-kDa protein and by E1B-independent means, promotes virus replication. An arginine-faced amphipathic alpha-helix in the E4orf6 protein is required for the E4orf6 protein to direct nuclear localization of the E1B 55-kDa protein and to enhance replication of an E4 deletion virus. In this study, E4orf6 protein variants containing arginine substitutions in the amphipathic alpha-helix were analyzed. Two of the six arginine residues within the alpha-helix, arginine-241 and arginine-243, were critical for directing nuclear localization of the E1B 55-kDa protein. The four remaining arginine residues appear to provide a net positive charge for the E4orf6 protein to direct nuclear localization of the E1B 55-kDa protein. The molecular determinants of the arginine-faced amphipathic alpha-helix that were required for the functional interaction between the E4orf6 and E1B 55-kDa proteins seen in the transfected cell differed from those required to support a productive infection. Several E4orf6 protein variants with arginine-to-glutamic acid substitutions that failed to direct nuclear localization of the E1B 55-kDa protein restored replication of an E4 deletion virus. Additionally, a variant containing an arginine-to-alanine substitution at position 243 that directed nuclear localization of the E1B 55-kDa protein failed to enhance virus replication. These results indicate that the ability of the E4orf6 protein to relocalize the E1B 55-kDa protein to the nucleus can be separated from the ability of the E4orf6 protein to support a productive infection.

  19. Cryptography with DNA binary strands.

    Science.gov (United States)

    Leier, A; Richter, C; Banzhaf, W; Rauhe, H

    2000-06-01

    Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.

  20. LEKTI is localized in lamellar granules, separated from KLK5 and KLK7, and is secreted in the extracellular spaces of the superficial stratum granulosum.

    Science.gov (United States)

    Ishida-Yamamoto, Akemi; Deraison, Céline; Bonnart, Chrystelle; Bitoun, Emmanuelle; Robinson, Ross; O'Brien, Timothy J; Wakamatsu, Kotaro; Ohtsubo, Sawa; Takahashi, Hidetoshi; Hashimoto, Yoshio; Dopping-Hepenstal, Patricia J C; McGrath, John A; Iizuka, Hajime; Richard, Gabriele; Hovnanian, Alain

    2005-02-01

    Lympho-epithelial Kazal-type-related inhibitor (LEKTI) is a putative serine protease inhibitor encoded by serine protease inhibitor Kazal-type 5 (SPINK5). It is strongly expressed in differentiated keratinocytes in normal skin but expression is markedly reduced or absent in Netherton syndrome (NS), a severe ichthyosis caused by SPINK5 mutations. At present, however, both the precise intracellular localization and biological roles of LEKTI are not known. To understand the functional role of LEKTI, we examined the localization of LEKTI together with kallikrein (KLK)7 and KLK5, possible targets of LEKTI, in the human epidermis, by confocal laser scanning microscopy and immunoelectron microscopy. In normal skin, LEKTI, KLK7, and KLK5 were all found in the lamellar granule (LG) system, but were separately localized. LEKTI was expressed earlier than KLK7 and KLK5. In NS skin, LEKTI was absent and an abnormal split in the superficial stratum granulosum was seen in three of four cases. Collectively, these results suggest that in normal skin the LG system transports and secretes LEKTI earlier than KLK7 and KLK5 preventing premature loss of stratum corneum integrity/cohesion. Our data provide new insights into the biological functions of LG and the pathogenesis of NS.

  1. Double stranded nucleic acid biochips

    Energy Technology Data Exchange (ETDEWEB)

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  2. Spatial periodic contact stress and critical current of a Nb3Sn strand measured in TARSIS

    NARCIS (Netherlands)

    Nijhuis, Arend; Ilyin, Y.; Wessel, Wilhelm A.J.

    2006-01-01

    We have developed a new probe for testing the influence of local contact load from crossing superconducting Nb3Sn strands. The probe is part of the TARSIS setup for strand stress–strain characterization. The results from the TARSIS setup with different probes developed for the characterization of

  3. Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

    Science.gov (United States)

    Sedova, Ada; Banavali, Nilesh K

    2017-03-14

    Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.

  4. [Effect of single-stranded and double-stranded breaks on the melting temperature of phage T2 DNA].

    Science.gov (United States)

    Iurgaĭtis, A P; Lazurkin, Iu S; Bannikov, Iu A

    1979-01-01

    The effect of single- and double-stranded breaks in DNA phage T2, on the melting temperature of this DNA in the 0,05 M SSC solution, was investigated. The number of cleavages per 1000 nucleotide pairs varied in the range of 0 to 10. It is shown that single- and double-stranded breaks affect the melting temperature with approximately (within 20%) the same efficiency. The relationship between the melting temperature shift (delta Tm) and the number of cleavages is non-linear. The magnitude of the effect is characterized by delta Tm of 2 +/- 0.4 degrees C for the average inter-cleavage distance of 200 base pairs. It is shown that the observed melting curves are non-equilibrium ones, which is probably due to the fact that the effect of cleavages on the melting temperature is largely results from the complete and practically irreversible separation of strands.

  5. 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...

  6. ELASTIC DEFORMATION ANALYSIS OF MULTILA YERED STRANDS

    Institute of Scientific and Technical Information of China (English)

    王世文; 冯继玲; 杨兆建; 连香姣

    1999-01-01

    This paper describes a general model for the mechanical behavior studying of general wire rope strand. An exact solution of the deformation characteristics was given when the strands is under tensile and torsional loads. The theoretical results are useful in evaluating the extensional and torsional moduli of rigidity for the strands. Finally, a simple design criterion is established for the nonrotating ropes.

  7. Transient stability of LHC strands

    CERN Document Server

    Baynham, D Elwyn; Coombs, R C; Bauer, P; Wolf, R

    1999-01-01

    The Large Hadron Collider (LHC) machine will operate at 1.9 K in order to achieve the high bending fields required in the dipole magnets. The cable and coil matrix is designed to be 'porous' in order to allow the He II coolant to $9 penetrate within the cable for stability enhancement. This paper describes transient stability measurements and theoretical modelling carried out on single strands from the LHC cable. The experimental work has been carried out at the $9 Rutherford Appleton Laboratory under an agreement with CERN. The aim of the experimental work has been to measure the influence of the strand surface treatment on the quench energy. The surface treatment, oxidized copper, tin-silver, $9 nickel etc., determines the transient heat transfer coefficients to the He II under high heat flux, short timescale (approximately 20 microseconds) conditions. The test equipment, based on an inductive heating technique, is described $9 and quench energy measurements presented. The experimental results are compared ...

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

    Science.gov (United States)

    Peltier, Helene; Baagøe, Hans J; Camphuysen, Kees C J; Czeck, Richard; Dabin, Willy; Daniel, Pierre; Deaville, Rob; Haelters, Jan; Jauniaux, Thierry; Jensen, Lasse F; Jepson, Paul D; Keijl, Guido O; Siebert, Ursula; Van Canneyt, Olivier; Ridoux, Vincent

    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 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Regularities in the E.coli promoters composition in connection with the DNA strands interaction and promoter activity

    Institute of Scientific and Technical Information of China (English)

    BEREZHNOY Andrey Yu; SHCKORBATOV Yuriy G.; HISANORI Kiryu

    2006-01-01

    The energy of interaction between DNA strands in promoters is of great functional importance. Visualization of the energy of DNA strands distribution in promoter sequences was achieved. The separation of promoters in groups by their energetic properties enables evaluation of the dependence of promoter strength on the energetic properties. The analysis of groups (clusters)of promoters distributed by the energy of DNA strands interaction in -55, -35, -10 and +6 sequences indicates their connection with the transcriptional activity.

  11. Trends in Marine Turtle Strandings along the East Queensland, Australia Coast, between 1996 and 2013

    Directory of Open Access Journals (Sweden)

    Jaylene Flint

    2015-01-01

    Full Text Available In-water monitoring of marine vertebrates is usually expensive while the use of stranding data can be used to provide a cost-effective estimation of disease and mortality. Strandings for Queensland are recorded in a web based database (StrandNet managed by the Queensland Government’s Department of Environment and Heritage Protection (EHP. Data recorded in StrandNet from the east coast of Queensland between 1996 and 2013 were investigated for patterns of stranding. Significant trends in Queensland over this time were (i an increase in the number of animals reported stranded within this study site; (ii a species (loggerhead and green marine turtles prevalence; (iii a seasonal effect on different age classes stranding with most overall strandings occurring between August and November; and (iv stranding hotspots (Moreton Bay, Hervey Bay, Rockhampton region, and Cleveland Bays persisting throughout the study timeframe. This study suggested that intervention strategies, such as rehabilitation, should be able to be focussed on periods of heightened importance and specific localities to minimize health risks and contribute to sustainable use of resources.

  12. Two-Domain DNA Strand Displacement

    CERN Document Server

    Cardelli, Luca

    2010-01-01

    We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose restrictions on the single strands they interact with: we consider only two-domain single strands consisting of one toehold domain and one recognition domain. We study fork and join signal-processing gates based on these structures, and we show that these systems are amenable to formalization and to mechanical verification.

  13. Hierarchical Bayesian inference for the EEG inverse problem using realistic FE head models: depth localization and source separation for focal primary currents.

    Science.gov (United States)

    Lucka, Felix; Pursiainen, Sampsa; Burger, Martin; Wolters, Carsten H

    2012-07-16

    The estimation of the activity-related ion currents by measuring the induced electromagnetic fields at the head surface is a challenging and severely ill-posed inverse problem. This is especially true in the recovery of brain networks involving deep-lying sources by means of EEG/MEG recordings which is still a challenging task for any inverse method. Recently, hierarchical Bayesian modeling (HBM) emerged as a unifying framework for current density reconstruction (CDR) approaches comprising most established methods as well as offering promising new methods. Our work examines the performance of fully-Bayesian inference methods for HBM for source configurations consisting of few, focal sources when used with realistic, high-resolution finite element (FE) head models. The main foci of interest are the correct depth localization, a well-known source of systematic error of many CDR methods, and the separation of single sources in multiple-source scenarios. Both aspects are very important in the analysis of neurophysiological data and in clinical applications. For these tasks, HBM provides a promising framework and is able to improve upon established CDR methods such as minimum norm estimation (MNE) or sLORETA in many aspects. For challenging multiple-source scenarios where the established methods show crucial errors, promising results are attained. Additionally, we introduce Wasserstein distances as performance measures for the validation of inverse methods in complex source scenarios.

  14. The Drosophila HP1 homologue Rhino is required for transposon silencing and piRNA production by dual strand clusters

    Science.gov (United States)

    Klattenhoff, Carla; Xi, Hualin; Li, Chengjian; Lee, Soohyun; Xu, Jia; Khurana, Jaspreet S.; Zhang, Fan; Schultz, Nadine; Koppetsch, Birgit S.; Nowosielska, Anetta; Seitz, Herve; Zamore, Phillip D.; Weng, Zhiping; Theurkauf, William E.

    2009-01-01

    Summary piRNAs silence transposons and maintain genome integrity during germ-line development. In Drosophila, transposon-rich heterochromatic clusters encode piRNAs either on both genomic strands (dual-strand clusters) or predominantly one genomic strand (uni-strand clusters). Primary piRNAs derived from these clusters are proposed to drive a ping-pong amplification cycle catalyzed by proteins that localize to the perinuclear nuage. We show that the HP1 homologue Rhino is required for nuage organization, transposon silencing, and ping-pong amplification of piRNAs. rhi mutations virtually eliminate piRNAs from the dual-strand clusters and block production of putative precursor RNAs from both strands of the major 42AB dual-strand cluster, but do not block production of transcripts or piRNAs from the uni-strand clusters. Furthermore, Rhino protein associates with the 42AB dual-strand cluster, but does not bind to uni-strand cluster 2 or flamenco. Rhino thus appears to promote transcription of dual-strand clusters, leading to production of piRNAs that drive the ping-pong amplification cycle. PMID:19732946

  15. THE THREE-STRANDED CORD

    Directory of Open Access Journals (Sweden)

    Walter Redmond

    2013-11-01

    Full Text Available The Schoolmen did much of their most interesting and original philosophizing in theology. An example is the dilemma in Renaissance Scholasticism on free will: how can we act freely if God causes and knows our actions? Basic issues are involved here: the antinomy between freedom and determination, modal semantics, tense logic, the logical status of counterfacts. Mexican Jesuits Matías Blanco (d. 1734 and Antonio Peralta (d. 1736 wrote books on the subject. We describe here the “disjunctive” solution that Blanco advanced in his Funiculus triplex (The Three-Stranded Cord, published posthumously in Mexico in 1746. When someone is faced with choosing between B and C, conjectures Blanco, God does not actualize either, but rather their disjunction B-or-C. Blanco calls for a truce in the “war” among the contending schools so that they may consider his solution–for he thinks it may indeed be acceptable to all.

  16. Asymmetric Quantum Transport in a Double-Stranded Kronig-Penney Model

    Science.gov (United States)

    Cheon, Taksu; Poghosyan, Sergey S.

    2015-06-01

    We introduce a double-stranded Kronig-Penney model and analyze its transport properties. Asymmetric fluxes between two strands with suddenly alternating localization patterns are found as the energy is varied. The zero-size limit of the internal lines connecting two strands is examined using quantum graph vertices with four edges. We also consider a two-dimensional Kronig-Penney lattice with two types of alternating layer with δ and δ' connections, and show the existence of energy bands in which the quantum flux can flow only in selected directions.

  17. Control of contact resistance by strand surface coating in 36-strand NbTi CICCs

    NARCIS (Netherlands)

    Nijhuis, Arend; Kate, ten Herman H.J.; Duchateau, Jean-Luc; Decool, Patrick

    2001-01-01

    The stability and AC loss of NbTi cable-in-conduit conductors (CICCs) is largely determined by the interstrand contact resistance (Rc). Rc is predominantly established by the strand surface properties. Five 36-strand CICCs, fully identical except for the plating of the strand surface or the presence

  18. The Stranding Anomaly as Population Indicator

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...

  19. The kinetics of force-dependent hybridization and strand-peeling of short DNA fragments

    Science.gov (United States)

    Yang, ZhouJie; Yuan, GuoHua; Zhai, WeiLi; Yan, Jie; Chen, Hu

    2016-08-01

    Deoxyribonucleic acid (DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded (ss) strands, forming a double-stranded (ds) DNA with a right-handed double-helical conformation. The two strands are held together by highly specific basepairing interactions and are further stabilized by stacking between adjacent basepairs. A transition from a dsDNA to two separated ssDNA is called melting and the reverse transition is called hybridization. Applying a tensile force to a dsDNA can result in a particular type of DNA melting, during which one ssDNA strand is peeled away from the other. In this work, we studied the kinetics of strand-peeling and hybridization of short DNA under tensile forces. Our results show that the force-dependent strand-peeling and hybridization can be described with a simple two-state model. Importantly, detailed analysis of the force-dependent transition rates revealed that the transition state consists of several basepairs dsDNA.

  20. Comparison of the methods for generating single-stranded DNA in SELEX.

    Science.gov (United States)

    Liang, Chao; Li, Defang; Zhang, Guangxian; Li, Hui; Shao, Ningsheng; Liang, Zicai; Zhang, Lingqiang; Lu, Aiping; Zhang, Ge

    2015-05-21

    The generation of single-stranded DNA (ssDNA) from double-stranded PCR products is an essential step in the selection of aptamers by systematic evolution of ligands by exponential enrichment (SELEX). Magnetic separation with streptavidin-coated beads is always the most commonly used method. Recently, two size separation methods derived from unequal primers with chemical or structural modification were designed in SELEX. In this report, we made a comparison between magnetic separation and the two size separation methods for generation of ssDNA from double-stranded PCR products. Our results showed that all the methods produced ssDNA of good purity. Compared to the magnetic separation, size separation derived from unequal primers with chemical modification achieved an almost equivalent recovery rate of ssDNA, whereas size separation derived from unequal primers with structural modification showed a lower recovery rate of ssDNA. Considering the low cost, size separation derived from unequal primers with chemical modification could be a satisfactory alternative to the classic magnetic separation for the generation of ssDNA in SELEX.

  1. Modelling toehold-mediated RNA strand displacement

    CERN Document Server

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

    2014-01-01

    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 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.

  2. Single-strand conformation polymorphism analysis using capillary array electrophoresis for large-scale mutation detection.

    Science.gov (United States)

    Larsen, Lars Allan; Jespersgaard, Cathrine; Andersen, Paal Skytt

    2007-01-01

    This protocol describes capillary array electrophoresis single-strand conformation polymorphism (CAE-SSCP), a screening method for detection of unknown and previously identified mutations. The method detects 98% of mutations in a sample material and can be applied to any organism where the goal is to determine genetic variation. This protocol describes how to screen for mutations in 192 singleplex or up to 768 multiplex samples over 3 days. The protocol is based on the principle of sequence-specific mobility of single-stranded DNA in a native polymer, and covers all stages in the procedure, from initial DNA purification to final CAE-SSCP data analysis, as follows: DNA is purified, followed by PCR amplification using fluorescent primers. After PCR amplification, double-stranded DNA is heat-denatured to separate the strands and subsequently cooled on ice to avoid reannealing. Finally, samples are analyzed by capillary electrophoresis and appropriate analysis software.

  3. Stranding of Two Sperm Whales (Physeter macrocephalus) in the “North Sea Trap” at Henne Strand, Denmark

    DEFF Research Database (Denmark)

    Hansen, Mette Siv; Alstrup, Aage Kristian Olsen; 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...

  4. The invariance of the total direct DNA strand break yield

    Energy Technology Data Exchange (ETDEWEB)

    Bernal, M. A.; Almeida, C. E. de; Sampaio, C.; Incerti, S.; Champion, C.; Nieminen, P. [Laboratorio de Ciencias Radiologicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-90 (Brazil); Universite Bordeaux 1, CNRS/IN2P3, Centre d' Etudes Nucleaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan (France); Laboratoire de Physique Moleculaire et des Collisions, Universite Paul Verlaine-Metz, 1 Boulevard Arago, Technopole 2000, 57078 Metz (France); ESA-ESTEC, 2200 AG Noordwijk (Netherlands)

    2011-07-15

    Purpose: The invariance of the total direct strand break yield when DNA is irradiated by different types of particles and energies has been reported by previous works. This study is intended to explain the physical causes of this behavior. Methods: The geant4-dna extension of the geant4 general purpose Monte Carlo simulation toolkit has been used to determine direct strand break yields induced by protons and alpha particles impacting on a B-DNA geometrical model, including five organization levels of the human genetic material. The linear energy transfer (LET) of such particles ranges from 4.8 keV/{mu}m (10 MeV protons) to about 235 keV/{mu}m (2 MeV alpha particles), at 5.225 {mu}m depth (near the center of the region of interest). Direct total, single and double strand break probabilities have been determined in a liquid water homogeneous medium with a 1.06 g/cm {sup 3} density. The energetic spectra of single strand breaks (SSB), the number of energy deposition events, and the SSB/event ratio were determined. Results: The target-hit probability was found to be independent of both the type and the energy of the incident particle, even if this latter is a secondary electron. This probability is determined by the geometrical properties of the system. The total strand break yield and the number of energy deposition events required to reach a certain absorbed dose were found nearly independent of the type and energy of the incident ion (proton or alpha). In contrast, the double strand break (DSB) yield was found strongly dependent on the LET of the incident radiation. Conclusions: The SSB generation process is homogeneous and independent of the LET of the particles involved, at least within the proton and alpha particle energy range here studied. The target-hit probability is only determined by the ratio between the total volume occupied by targets and that of the ROI where the radiation deposits its energy. The maximum separation distance between two adjacent SSBs to

  5. Fluctuations of charge separation perpendicular to the event plane and local parity violation in sqrt(sNN)=200 GeV Au+Au collisions at RHIC

    CERN Document Server

    Adamczyk, L; Agakishiev, G; Aggarwal, M M; Ahammed, Z; Alekseev, I; Alford, J; Anson, C D; Aparin, A; Arkhipkin, D; Aschenauer, E; Averichev, G S; Balewski, J; Banerjee, A; Barnovska, Z; Beavis, D R; Bellwied, R; Betancourt, M J; Betts, R R; Bhasin, A; Bhati, A K; Bhattarai,; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Bordyuzhin, I G; Borowski, W; Bouchet, J; Brandin, A V; Brovko, S G; Bruna, E; Bültmann, S; Bunzarov, I; Burton, T P; Butterworth, J; Caines, H; Sánchez, M Calderón de la Barca; Cebra, D; Cendejas, R; Cervantes, M C; Chaloupka, P; Chang, Z; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, J Y; Chen, L; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Chung, P; Chwastowski, J; Codrington, M J M; Corliss, R; Cramer, J G; Crawford, H J; Cui, X; Das, S; Leyva, A Davila; De Silva, L C; Debbe, R R; Dedovich, T G; Deng, J; de Souza, R Derradi; Dhamija, S; di Ruzza, B; Didenko, L; Dilks,; Ding, F; Dion, A; Djawotho, P; Dong, X; Drachenberg, J L; Draper, J E; Du, C M; Dunkelberger, L E; Dunlop, J C; Efimov, L G; Elnimr, M; Engelage, J; Engle, K S; Eppley, G; Eun, L; Evdokimov, O; Fatemi, R; Fazio, S; Fedorisin, J; Fersch, R G; Filip, P; Finch, E; Fisyak, Y; Flores, C E; Gagliardi, C A; Gangadharan, D R; Garand, D; Geurts, F; Gibson, A; Gliske, S; Grebenyuk, O G; Grosnick, D; Guo, Y; Gupta, A; Gupta, S; Guryn, W; Haag, B; Hajkova, O; Hamed, A; Han, L-X; Haque, R; Harris, J W; Hays-Wehle, J P; Heppelmann, S; Hirsch, A; Hoffmann, G W; Hofman, D J; Horvat, S; Huang, B; Huang, H Z; Huck, P; Humanic, T J; Igo, G; Jacobs, W W; Jena, C; Judd, E G; Kabana, S; Kang, K; Kauder, K; Ke, H W; Keane, D; Kechechyan, A; Kesich, A; Kikola, D P; Kiryluk, J; Kisel, I; Kisiel, A; Koetke, D D; Kollegger, T; Konzer, J; Koralt, I; Korsch, W; Kotchenda, L; Kravtsov, P; Krueger, K; Kulakov, I; Kumar, L; Kycia, R A; Lamont, M A C; Landgraf, J M; Landry, K D; LaPointe, S; Lauret, J; Lebedev, A; Lednicky, R; Lee, J H; Leight, W; LeVine, M J; Li, C; Li, W; Li, X; Li, Y; Li, Z M; Lima, L M; Lisa, M A; Liu, F; Ljubicic, T; Llope, W J; Longacre, R S; Luo, X; Ma, G L; Ma, Y G; Don, D M M D Madagodagettige; Mahapatra, D P; Majka, R; Margetis, S; Markert, C; Masui, H; Matis, H S; McDonald, D; McShane, T S; Mioduszewski, S; Mitrovski, M K; Mohammed, Y; Mohanty, B; Mondal, M M; Munhoz, M G; Mustafa, M K; Naglis, M; Nandi, B K; Nasim, Md; Nayak, T K; Nelson, J M; Nogach, L V; Novak, J; Odyniec, G; Ogawa, A; Oh, K; Ohlson, A; Okorokov, V; Oldag, E W; Oliveira, R A N; Olson, D; Pachr, M; Page, B S; Pal, S K; Pan, Y X; Pandit, Y; Panebratsev, Y; Pawlak, T; Pawlik, B; Pei, H; Perkins, C; Peryt, W; Pile, P; Planinic, M; Pluta, J; Plyku, D; Poljak, N; Porter, J; Poskanzer, A M; Powell, C B; Pruneau, C; Pruthi, N K; Przybycien, M; Pujahari, P R; Putschke, J; Qiu, H; Ramachandran, S; Raniwala, R; Raniwala, S; Ray, R L; Riley, C K; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Ross, J F; Roy, A; Ruan, L; Rusnak, J; Sahoo, N R; Sahu, P K; Sakrejda, I; Salur, S; Sandacz, A; Sandweiss, J; Sangaline, E; Sarkar, A; Schambach, J; Scharenberg, R P; Schmah, A M; Schmidke, B; Schmitz, N; Schuster, T R; Seger, J; Seyboth, P; Shah, N; Shahaliev, E; Shao, M; Sharma, B; Sharma, M; Shen, W Q; Shi, S S; Shou, Q Y; Sichtermann, E P; Singaraju, R N; Skoby, M J; Smirnov, D; Smirnov, N; Solanki, D; Sorensen, P; deSouza, U G; Spinka, H M; Srivastava, B; Stanislaus, T D S; Stevens, J R; Stock, R; Strikhanov, M; Stringfellow, B; Suaide, A A P; Suarez, M C; Sumbera, M; Sun, X M; Sun, Y; Sun, Z; Surrow, B; Svirida, D N; Symons, T J M; de Toledo, A Szanto; Takahashi, J; Tang, A H; Tang, Z; Tarini, L H; Tarnowsky, T; Thomas, J H; Timmins, A R; Tlusty, D; Tokarev, M; Trentalange, S; Tribble, R E; Tribedy, P; Trzeciak, B A; Tsai, O D; Turnau, J; Ullrich, T; Underwood, D G; Van Buren, G; van Nieuwenhuizen, G; Vanfossen,, J A; Varma, R; Vasconcelos, G M S; Vertesi, R; Videbæk, F; Viyogi, Y P; Vokal, S; Voloshin, S A; Vossen, A; Wada, M; Walker, M; Wang, F; Wang, G; Wang, H; Wang, J S; Wang, Q; Wang, X L; Wang, Y; Webb, G; Webb, J C; Westfall, G D; Wieman, H; Wissink, S W; Witt, R; Wu, Y F; Xiao, Z; Xie, W; Xin, K; Xu, H; Xu, N; Xu, Q H; Xu, W; Xu, Y; Xu, Z; Yan,; Yang, C; Yang, Y; Yepes, P; Yi, L; Yip, K; Yoo, I-K; Zawisza, Y; Zbroszczyk, H; Zha, W; Zhang, J B; Zhang, S; Zhang, X P; Zhang, Y; Zhang, Z P; Zhao, F; Zhao, J; Zhong, C; Zhu, X; Zhu, Y H; Zoulkarneeva, Y; Zyzak, M

    2013-01-01

    Recent experimental results from the STAR collaboration suggest event-by-event charge separation fluctuations perpendicular to the event plane in non-central heavy-ion collisions. Here we present the correlator previously used split into its two component parts to reveal correlations parallel and perpendicular to the event plane. The results are from a high statistics 200 GeV Au+Au collisions data set collected by the STAR experiment at RHIC. We explicitly count units of charge separation from which we find clear evidence for more charge separation fluctuations perpendicular than parallel to the event plane. We also employ a modified correlator to study the possible P-even background in same and opposite charge correlations.

  6. Repair of alpha-particle-induced DNA double strand breaks and their localization in chromatin in human lymphocytes%α粒子照射诱发DNA双链断裂修复及其在染色质中的分布

    Institute of Scientific and Technical Information of China (English)

    张亚平; 张旭霞; 王晶; 暴一众; 李佳颖; 殷丽娜; 陈红红

    2014-01-01

    Objective To investigate the characteristics of repair of DNA double strand breaks (DSB) induced by high-LET α-particle irradiation and their relationship with chromatin structure in the G0 lymphocytes of human peripheral blood,in order to provide the experimental basis for the judgement and dose evaluation of internal α-particle radiation.Methods Peripheral whole blood were collected from four healthy adults and lymphocytes were separated.A monocellular layer of human lymphocytes attached in Mylar film were irradiated with 0 and 0.5 Gy of α-particles and the lymphocytes suspensions were irradiated with 0 and 0.5 Gy of γ-rays.The formations of γH2AX foci as a surrogate marker of DSB and Rad51 foci as a marker of homologous recombination (HR) repair and their spatial localization in chromatin structure were measured by immunofluorescence staining technique at 10 min-48 h post-irradiation.Results Linear-γH2AX foci tracks were observe at 10 min-2 h post-irradiation in lymphocytes exposed to α-particle irradiation(t =11.12,14.40,16.56,P < 0.05),and almost completely disppeared at 6 h postirradiation.The frequencies of γH2AX foci peaked at 30 min after α-particle irradiation (t =51.72,P <0.05) and then decreased rapidly during 6 h post-irradiation (t =29.83,P < 0.05).The average number of foci remained only about 16% at 24-48 h post-irradiation.Moreover,27% of γH2AX foci located at DAPI-bright heterochromatin region at 10 min after α-particle radiation,suggesting that the efficacy of DSB repair may be decreased.In contrast,at 10 min-48 h after γ-ray irradiation,no linear γH2AX foci track was observed and the γH2AX foci diffused randomly in nucleus and predominantly located in DAPI-weak euchromatin region.The numbers of formative and residual γH2AX foci after γ-ray irradiation were significantly less than those after α-particle radiation.During 30 min-2 h after α-particle and γ-ray irradiation,the frequencies of Rad51 foci slightly but not

  7. Degradation feature extraction of the hydraulic pump based on high-frequency harmonic local characteristic-scale decomposition sub-signal separation and discrete cosine transform high-order singular entropy

    Directory of Open Access Journals (Sweden)

    Jian Sun

    2016-07-01

    Full Text Available Hydraulic pump degradation feature extraction is a key step of condition-based maintenance. In this article, a novel method based on high-frequency harmonic local characteristic-scale decomposition sub-signal separation and discrete cosine transform high-order singular entropy is proposed. In order to reduce noises and other disturbances, the vibration signal is processed by the local characteristic-scale decomposition modified by the high-frequency harmonic. Sub-signal with sensitive information is obtained by blind source separation of the selected intrinsic scale components. Furthermore, the discrete cosine transform high-order spectral analysis algorithm is proposed to extract singular entropies of Shannon and Tsallis to be the degradation features of the hydraulic pump. Analysis of the hydraulic pump experiment demonstrates that the proposed method is feasible and effective in indicating the performance degradation of the hydraulic pump.

  8. Cetacean strandings in Costa Rica (1966-1999)

    OpenAIRE

    Rodríguez-Fonseca, Javier; Cubero-Pardo,Priscilla

    2014-01-01

    Cetacean strandings in Costa Rica are reported for a period of 33 years, with a total of 35 strandings, 13 species and 247 individuals involved. The vast majority of documented strandings occurred on the Pacific coast and correspond to single individuals (32 and 28 strandings respectively). The highest stranding number was in the period from 1990 to 1999 (n=24). Physeter catodon (cachalot or sperm whale) is the species with the highest frequency of strandings (n=8) and the family Delphinidae ...

  9. Marine mammal strandings in the New Caledonia region, Southwest Pacific.

    Science.gov (United States)

    Borsa, Philippe

    2006-04-01

    Four hundred twenty three marine mammals, in 72 stranding events, were recorded between 1877 and 2005 in New Caledonia, the Loyalty Islands, and Vanuatu in the southwest Pacific. Sixteen species were represented in this count, including: minke whale, Balaenoptera acutorostrata (1 single stranding), sei whale, B. borealis (1 single stranding), blue whale, B. musculus (1 single stranding), humpback whale, Megaptera novaeangliae (2 single strandings), giant sperm whale, Physeter macrocephalus (18 single strandings, 2 pair strandings), pygmy sperm whale, Kogia breviceps (5 single strandings), dwarf sperm whale, K. sima (2 single strandings, 1 triple stranding), Blainville's beaked whale, Mesoplodon densirostris (2 single strandings), short-finned pilot whale, Globicephala macrorhynchus (4 strandings, 56 individuals), melon-headed whale, Peponocephala electra (1 single stranding and 2 mass strandings totalling 231 individuals), common dolphin, Delphinus delphis (1 single stranding), spinner dolphin, Stenella longirostris (1 pair stranding and 2 mass strandings of groups of approximately 30 individuals each), Indian Ocean bottlenose dolphin, Tursiops aduncus (2 single strandings), dugong, Dugong dugon (14 single strandings), and New Zealand fur seal, Arctocephalus forsteri (3 single strandings). A stranded rorqual identified as an Antarctic minke whale (B. bonaerensis), with coloration patterns that did not match known descriptions, was also reported. Sei whale was recorded for the first time in the tropical Southwest Pacific region and Antarctic minke whale, melon-headed whale, and Indian Ocean bottlenose dolphin were recorded for the first time in New Caledonia. Strandings of sperm whales were most frequent in the spring, but also occurred in autumn months, suggesting a seasonal pattern of occurrence possibly related to seasonal migration. One stranded humpback whale bore the scars of a killer whale's attack and one dugong was injured by a shark. Scars left by

  10. 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 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...... 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....

  11. Euler buckling and nonlinear kinking of double-stranded DNA.

    Science.gov (United States)

    Fields, Alexander P; Meyer, Elisabeth A; Cohen, Adam E

    2013-11-01

    The bending stiffness of double-stranded DNA (dsDNA) at high curvatures is fundamental to its biological activity, yet this regime has been difficult to probe experimentally, and literature results have not been consistent. We created a 'molecular vise' in which base-pairing interactions generated a compressive force on sub-persistence length segments of dsDNA. Short dsDNA strands (Euler buckling'. We monitored the buckling transition via Förster Resonance Energy Transfer (FRET) between appended fluorophores. For low-to-moderate concentrations of monovalent salt (up to ∼150 mM), our results are in quantitative agreement with the worm-like chain (WLC) model of DNA elasticity, without the need to invoke any 'kinked' states. Greater concentrations of monovalent salts or 1 mM Mg(2+) induced an apparent softening of the dsDNA, which was best accounted for by a kink in the region of highest curvature. We tested the effects of all single-nucleotide mismatches on the DNA bending. Remarkably, the propensity to kink correlated with the thermodynamic destabilization of the mismatched DNA relative the perfectly complementary strand, suggesting that the kinked state is locally melted. The molecular vise is exquisitely sensitive to the sequence-dependent linear and nonlinear elastic properties of dsDNA.

  12. Alaska Marine Mammal Strandings/Entanglements

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database represents a summary of information on stranded marine mammals reported to NMFS throughout the State of Alaska in fulfillment of Title IV of the Marine...

  13. Thermodynamic Analysis of Interacting Nucleic Acid Strands

    OpenAIRE

    Dirks, Robert M.; Bois, Justin S.; Schaeffer, Joseph M.; Winfree, Erik; Pierce, Niles A.

    2007-01-01

    Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed...

  14. Bubbles in live-stranded dolphins.

    Science.gov (United States)

    Dennison, S; Moore, M J; Fahlman, A; Moore, K; Sharp, S; Harry, C T; Hoppe, J; Niemeyer, M; Lentell, B; Wells, R S

    2012-04-07

    Bubbles in supersaturated tissues and blood occur in beaked whales stranded near sonar exercises, and post-mortem in dolphins bycaught at depth and then hauled to the surface. To evaluate live dolphins for bubbles, liver, kidneys, eyes and blubber-muscle interface of live-stranded and capture-release dolphins were scanned with B-mode ultrasound. Gas was identified in kidneys of 21 of 22 live-stranded dolphins and in the hepatic portal vasculature of 2 of 22. Nine then died or were euthanized and bubble presence corroborated by computer tomography and necropsy, 13 were released of which all but two did not re-strand. Bubbles were not detected in 20 live wild dolphins examined during health assessments in shallow water. Off-gassing of supersaturated blood and tissues was the most probable origin for the gas bubbles. In contrast to marine mammals repeatedly diving in the wild, stranded animals are unable to recompress by diving, and thus may retain bubbles. Since the majority of beached dolphins released did not re-strand it also suggests that minor bubble formation is tolerated and will not lead to clinically significant decompression sickness.

  15. Study on Strand Space Model Theory

    Institute of Scientific and Technical Information of China (English)

    JI QingGuang(季庆光); QING SiHan(卿斯汉); ZHOU YongBin(周永彬); FENG DengGuo(冯登国)

    2003-01-01

    The growing interest in the application of formal methods of cryptographic pro-tocol analysis has led to the development of a number of different ways for analyzing protocol. Inthis paper, it is strictly proved that if for any strand, there exists at least one bundle containingit, then an entity authentication protocol is secure in strand space model (SSM) with some smallextensions. Unfortunately, the results of attack scenario demonstrate that this protocol and the Yahalom protocol and its modification are de facto insecure. By analyzing the reasons of failure offormal inference in strand space model, some deficiencies in original SSM are pointed out. In orderto break through these limitations of analytic capability of SSM, the generalized strand space model(GSSM) induced by some protocol is proposed. In this model, some new classes of strands, oraclestrands, high order oracle strands etc., are developed, and some notions are formalized strictly in GSSM, such as protocol attacks, valid protocol run and successful protocol run. GSSM can thenbe used to further analyze the entity authentication protocol. This analysis sheds light on why thisprotocol would be vulnerable while it illustrates that GSSM not only can prove security protocolcorrect, but also can be efficiently used to construct protocol attacks. It is also pointed out thatusing other protocol to attack some given protocol is essentially the same as the case of using themost of protocol itself.

  16. Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication

    Science.gov (United States)

    Jia, Tony Z.; Fahrenbach, Albert C.; Kamat, Neha P.; Adamala, Katarzyna P.; Szostak, Jack W.

    2016-10-01

    The non-enzymatic replication of RNA is thought to have been a critical process required for the origin of life. One unsolved difficulty with non-enzymatic RNA replication is that template-directed copying of RNA results in a double-stranded product. After strand separation, rapid strand reannealing outcompetes slow non-enzymatic template copying, which renders multiple rounds of RNA replication impossible. Here we show that oligoarginine peptides slow the annealing of complementary oligoribonucleotides by up to several thousand-fold; however, short primers and activated monomers can still bind to template strands, and template-directed primer extension can still occur, all within a phase-separated condensed state, or coacervate. Furthermore, we show that within this phase, partial template copying occurs even in the presence of full-length complementary strands. This method to enable further rounds of replication suggests one mechanism by which short non-coded peptides could have enhanced early cellular fitness, and potentially explains how longer coded peptides, that is, proteins, came to prominence in modern biology.

  17. On Separate Universes

    CERN Document Server

    Dai, Liang; Schmidt, Fabian

    2015-01-01

    The separate universe conjecture states that in General Relativity a density perturbation behaves locally (i.e. on scales much smaller than the wavelength of the mode) as a separate universe with different background density and curvature. We prove this conjecture for a spherical compensated tophat density perturbation of arbitrary amplitude and radius in $\\Lambda$CDM. We then use Conformal Fermi Coordinates to generalize this result to scalar perturbations of arbitrary configuration and scale in a general cosmology with a mixture of fluids, but to linear order in perturbations. In this case, the separate universe conjecture holds for the isotropic part of the perturbations. The anisotropic part on the other hand is exactly captured by a tidal field in the Newtonian form. We show that the separate universe picture is restricted to scales larger than the sound horizons of all fluid components. We then derive an expression for the locally measured matter bispectrum induced by a long-wavelength mode of arbitrary...

  18. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters.

    Science.gov (United States)

    Klattenhoff, Carla; Xi, Hualin; Li, Chengjian; Lee, Soohyun; Xu, Jia; Khurana, Jaspreet S; Zhang, Fan; Schultz, Nadine; Koppetsch, Birgit S; Nowosielska, Anetta; Seitz, Herve; Zamore, Phillip D; Weng, Zhiping; Theurkauf, William E

    2009-09-18

    Piwi-interacting RNAs (piRNAs) silence transposons and maintain genome integrity during germline development. In Drosophila, transposon-rich heterochromatic clusters encode piRNAs either on both genomic strands (dual-strand clusters) or predominantly one genomic strand (uni-strand clusters). Primary piRNAs derived from these clusters are proposed to drive a ping-pong amplification cycle catalyzed by proteins that localize to the perinuclear nuage. We show that the HP1 homolog Rhino is required for nuage organization, transposon silencing, and ping-pong amplification of piRNAs. rhi mutations virtually eliminate piRNAs from the dual-strand clusters and block production of putative precursor RNAs from both strands of the major 42AB dual-strand cluster, but not of transcripts or piRNAs from the uni-strand clusters. Furthermore, Rhino protein associates with the 42AB dual-strand cluster,but does not bind to uni-strand cluster 2 or flamenco. Rhino thus appears to promote transcription of dual-strand clusters, leading to production of piRNAs that drive the ping-pong amplification cycle.

  19. Separation Logic

    DEFF Research Database (Denmark)

    Reynolds, John C.

    2002-01-01

    expressions) for accessing and modifying shared structures, and for explicit allocation and deallocation of storage. Assertions are extended by introducing a "separating conjunction" that asserts that its sub-formulas hold for disjoint parts of the heap, and a closely related "separating implication". Coupled......, dynamically allocated arrays, and recursive procedures. We will also discuss promising future directions....

  20. Cetacean strandings in Costa Rica (1966-1999).

    Science.gov (United States)

    Rodríguez-Fonseca, J; Cubero-Pardo, P

    2001-06-01

    Cetacean strandings in Costa Rica are reported for a period of 33 years, with a total of 35 strandings, 13 species and 247 individuals involved. The vast majority of documented strandings occurred on the Pacific coast and correspond to single individuals (32 and 28 strandings respectively). The highest stranding number was in the period from 1990 to 1999 (n = 24). Physeter catodon (cachalot or sperm whale) is the species with the highest frequency of strandings (n = 8) and the family Delphinidae has the majority of species (n = 8) and strandings (n = 22). No other general tendencies were determined with the existing data.

  1. 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 (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.

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

    Directory of Open Access Journals (Sweden)

    Buhnnum Kyokong

    2005-09-01

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

  3. 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...

  4. Win-win measurement of stranded costs

    Energy Technology Data Exchange (ETDEWEB)

    Graniere, R.J. [Ohio State Univ., Columbus, OH (United States). National Regulatory Research Inst.

    1998-08-01

    While the underrecovery of stranded costs puts a portion of the utility`s investors` wealth at risk, the overrecovery of these costs causes the utility`s customers to shoulder an unnecessary financial burden. These opposing potential costs associated inevitably with stranded-cost recovery help insure that everyone involved in the production, sale, and use of electric power, for selfish reasons, wants to coordinate on the best measure of these costs. That is, in equilibrium, everyone in the electricity production chain does not want to deviate from a measurement approach that prevents either the overrecovery or underrecovery of stranded costs. An important task, then, is to determine the ad hoc rules that must be appended to ex ante and ex post measures of stranded costs in order to reasonably prevent overrecoveries and underrecoveries. While either ex ante or ex post measures of stranded facilities and costs can be implemented reasonably, appropriately constructed ex post measures are superior, so long as regulators follow a reasonable protocol for the securitization of these costs.

  5. Marine mammal strandings in the New Caledonia region, Southwest Pacific

    OpenAIRE

    Borsa, Philippe

    2006-01-01

    International audience; Four hundred twenty three marine mammals, in 72 stranding events, were recorded between 1877 and 2005 in New Caledonia, the Loyalty Islands, and Vanuatu in the southwest Pacific. Sixteen species were represented in this count, including: minke whale, Balaenoptera acutorostrata (1 single stranding), sei whale, B. borealis (1 single stranding), blue whale, B. musculus (1 single stranding), humpback whale, Megaptera novaeangliae (2 single strandings), giant sperm whale, P...

  6. CENTRIFUGAL SEPARATORS

    Science.gov (United States)

    Skarstrom, C.

    1959-03-10

    A centrifugal separator is described for separating gaseous mixtures where the temperature gradients both longitudinally and radially of the centrifuge may be controlled effectively to produce a maximum separation of the process gases flowing through. Tbe invention provides for the balancing of increases and decreases in temperature in various zones of the centrifuge chamber as the result of compression and expansions respectively, of process gases and may be employed effectively both to neutralize harmful temperature gradients and to utilize beneficial temperaturc gradients within the centrifuge.

  7. Prospective evaluation of a hydrogel spacer for rectal separation in dose-escalated intensity-modulated radiotherapy for clinically localized prostate cancer

    Directory of Open Access Journals (Sweden)

    Eckert Franziska

    2013-01-01

    Full Text Available Abstract Background As dose-escalation in prostate cancer radiotherapy improves cure rates, a major concern is rectal toxicity. We prospectively assessed an innovative approach of hydrogel injection between prostate and rectum to reduce the radiation dose to the rectum and thus side effects in dose-escalated prostate radiotherapy. Methods Acute toxicity and planning parameters were prospectively evaluated in patients with T1-2 N0 M0 prostate cancer receiving dose-escalated radiotherapy after injection of a hydrogel spacer. Before and after hydrogel injection, we performed MRI scans for anatomical assessment of rectal separation. Radiotherapy was planned and administered to 78 Gy in 39 fractions. Results From eleven patients scheduled for spacer injection the procedure could be performed in ten. In one patient hydrodissection of the Denonvillier space was not possible. Radiation treatment planning showed low rectal doses despite dose-escalation to the target. In accordance with this, acute rectal toxicity was mild without grade 2 events and there was complete resolution within four to twelve weeks. Conclusions This prospective study suggests that hydrogel injection is feasible and may prevent rectal toxicity in dose-escalated radiotherapy of prostate cancer. Further evaluation is necessary including the definition of patients who might benefit from this approach. Trial registration: German Clinical Trials Register DRKS00003273.

  8. 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.

  9. 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.

    2014-01-01

    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. PMID:25313033

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

    Directory of Open Access Journals (Sweden)

    Cyril Buhler

    2007-12-01

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

  11. Dynamics of single-stranded DNA tethered to a solid

    Science.gov (United States)

    Radiom, Milad; Paul, Mark R.; Ducker, William A.

    2016-06-01

    Tethering is used to deliver specific biological and industrial functions. For example, single-stranded DNA (ssDNA) is tethered to polymerases and long sequences of double-stranded DNA (dsDNA) during replication, and to solids in DNA microarrays. However, tethering ssDNA to a large object limits not only the available ssDNA conformations, but also the range of time-scales over which the mechanical responses of ssDNA are important. In this work we examine the effect of tethering by measurement of the mechanical response of ssDNA that is tethered at each end to two separate atomic force microscope cantilevers in aqueous solution. Thermal motion of the cantilevers drives the ends of the ssDNA chain at frequencies near 2 kHz. The presence of a tethered molecule makes a large difference to the asymmetric cross-correlation of two cantilevers, which enables resolution of the mechanical properties in our experiments. By analysis of the correlated motion of the cantilevers we extract the friction and stiffness of the ssDNA. We find that the measured friction is much larger than the friction that is usually associated with the unencumbered motion of ssDNA. We also find that the measured relaxation time, ∼30 μs, is much greater than prior measurements of the free-molecule relaxation time. We attribute the difference to the loss of conformational possibilities as a result of constraining the ends of the ssDNA.

  12. The Role of Cytosine Methylation on Charge Transport through a DNA Strand

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Jianqing; Govind, Niranjan; Anantram, M.P.

    2015-09-04

    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 modifi-cation 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-Buttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. Specifically, we compare the results generated with the widely used B3LYP exchange-correlation (XC) functional and CAM-B3LYP based tuned range-separated hybrid density functional. 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 with both functionals, 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 interstrand 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 (HOMO) 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 both functionals. We also study the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit. Our results suggest that the effect of the two different functionals is to alter the on-site energies of the DNA bases at the HOMO level, while the transport properties don't depend much on the two

  13. Optimized measurements of separations and angles between intra-molecular fluorescent markers

    Science.gov (United States)

    Mortensen, Kim I.; Sung, Jongmin; Flyvbjerg, Henrik; Spudich, James A.

    2015-10-01

    We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly.

  14. Opening of DNA double strands by helicases. Active versus passive opening

    CERN Document Server

    Betterton, M D

    2002-01-01

    Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA). We describe helicase opening of dsNA, based on helicases which bind single NA strands and move towards the double-stranded region, using a discrete ``hopping'' model. The interaction between the helicase and the junction where the double strand opens is characterized by an interaction potential. The form of the potential determines whether the opening is active or passive. We calculate the rate of passive opening for the helicase PcrA, and show that the rate increases when the opening is active. Finally, we examine how to choose the interaction potential to optimize the rate of strand separation. One important result is our finding that active opening can increase the unwinding rate by 7 fold compared to passive opening.

  15. 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....

  16. 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 m

  17. 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 m

  18. The Impact of Turtle Excluder Devices and Fisheries Closures on Loggerhead and Kemp's Ridley Strandings in the Western Gulf of Mexico

    Science.gov (United States)

    Lewison, R.L.; Crowder, L.B.; Shaver, D.J.

    2003-01-01

    The Sea Turtle Stranding and Salvage Network has been monitoring turtle strandings for more than 20 years in the United States. High numbers of strandings in the early to mid-1980s prompted regulations to require turtle excluder devices (TEDs) on shrimping vessels (trawlers). Following year-round TED implementation in 1991, however, stranding levels in the Gulf of Mexico increased. We evaluated the efficacy of TEDs and other management actions (e.g., fisheries closures) on loggerhead (Caretta caretta) and Kemp's ridley (Lepidochelys kempii) turtle populations by analyzing a long-term, stranding data set from the western Gulf of Mexico. Our analyses suggest that both sea turtle population growth and shrimping activity have contributed to the observed increase in strandings. Compliance with regulations requiring turtle excluder devices was a significant factor in accounting for annual stranding variability: low compliance was correlated with high levels of strandings. Our projections suggest that improved compliance with TED regulations will reduce strandings to levels that, in conjunction with other protective measures, should promote population recoveries for loggerhead and Kemp's ridley turtles. Local, seasonal fisheries closures, concurrent with TED enforcement, could reduce strandings to even lower levels. A seasonal closure adjacent to a recently established Kemp's ridley nesting beach may also reduce mortality of nesting adults and thus promote long-term population persistence by fostering the establishment of a robust secondary nesting site.

  19. Spectroscopic Separation of Solar Wind Charge Exchange, Local Bubble, and Nearby Supernova Remnant X-rays: Diffuse X-ray Spectrometer Recent Results

    Science.gov (United States)

    Morgenthaler, Jeffrey P.; Edgar, R. J.; Sanders, W. T.; Smith, R. K.; Koutroumpa, D.; Henley, D. B.; Shelton, R. L.; Robertson, I. P.; Collier, M. R.; Cravens, T. E.

    2011-05-01

    The Diffuse X-ray Spectrometer (DXS) was a Space Shuttle Payload of Opportunity that flew in 1993. DXS measured the spectrum of the diffuse X-ray background (DXRB) between 150 eV and 284 eV (the 1/4 keV band) using a Bragg crystal spectrometer. Higher order Bragg reflections included the OVII and OVIII features. The counting statistics and spectroscopic resolving power of the DXS measurements have yet to be rivaled in the 1/4 keV band. DXS had a 15°x15° FOV that was repeatedly scanned over a 140° arc in the Galactic plane centered roughly toward the Galactic anti-center. The Vela-Puppis and the Monogem ring supernova remnants were studied, as well 3 adjacent regions typical of the DXRB. During the 5-day Shuttle flight, the total sky-looking DXS count rate unexpectedly dropped by 20%, suggesting a significant and variable local source of X-rays, likely generated by the solar wind charge exchange mechanism (SWCX) in the geocorona and/or a passing coronal mass ejection. We use this unique dataset to: (1) Show that a state-of-the-art heliospheric SWCX model compares reasonably well to the DXS DXRB spectrum in the 190-284 eV range, but falls short in the 150-190 eV range. (2) Spectroscopically resolve the OVII forbidden and resonance lines, showing that the resonance line is somewhat stronger. This confirms there is a contribution to the DXRB from a source other than the SWCX. (3) Present spectra of the Vela-Puppis and Monogem regions cleaned of all foreground X-ray emission and compare to standard collisional ionization equilibrium plasma models. The discrepancies between the models and data highlight the need for continued progress in understanding the L-shell ions of Mg, Si, S and the M-shell ions of Fe. (4) Present the first isolated spectrum of the SWCX in the 1/4 keV band that resolves lines/line complexes.

  20. 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.

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

    Science.gov (United States)

    Wright, Andrew J; Maar, Marie; Mohn, Christian; Nabe-Nielsen, Jacob; Siebert, Ursula; Jensen, Lasse Fast; Baagøe, Hans J; Teilmann, Jonas

    2013-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Nurhaida

    2008-04-01

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

  3. An effective mesoscopic model of double-stranded DNA.

    Science.gov (United States)

    Jeon, Jae-Hyung; Sung, Wokyung

    2014-01-01

    Watson and Crick's epochal presentation of the double helix structure in 1953 has paved the way to intense exploration of DNA's vital functions in cells. Also, recent advances of single molecule techniques have made it possible to probe structures and mechanics of constrained DNA at length scales ranging from nanometers to microns. There have been a number of atomistic scale quantum chemical calculations or molecular level simulations, but they are too computationally demanding or analytically unfeasible to describe the DNA conformation and mechanics at mesoscopic levels. At micron scales, on the other hand, the wormlike chain model has been very instrumental in describing analytically the DNA mechanics but lacks certain molecular details that are essential in describing the hybridization, nano-scale confinement, and local denaturation. To fill this fundamental gap, we present a workable and predictive mesoscopic model of double-stranded DNA where the nucleotides beads constitute the basic degrees of freedom. With the inter-strand stacking given by an interaction between diagonally opposed monomers, the model explains with analytical simplicity the helix formation and produces a generalized wormlike chain model with the concomitant large bending modulus given in terms of the helical structure and stiffness. It also explains how the helical conformation undergoes overstretch transition to the ladder-like conformation at a force plateau, in agreement with the experiment.

  4. Millisecond analysis of double stranded DNA with fluorescent intercalator by micro-thermocontrol-device.

    Science.gov (United States)

    Arata, Hideyuki F; Gillot, Frederic; Collard, Dominique; Fujita, Hiroyuki

    2009-08-15

    Study of interaction between DNA and intercalator at molecular level is important to understand the mechanisms of DNA replication and repair. A micro-fabricated local heating thermodevice was adapted to perform denaturation experiments of DNA with fluorescent intercalator on millisecond time scale. Response time of complete unzipping of double stranded DNA, 16 microm in length, was measured to be around 5 min by commercial thermocycler. Response time of quenching of double stranded DNA with fluorescent intercalator SYBR Green was measured to be 10 ms. Thus, quenching properties owing to strand unzipping and denaturation at base pair level were distinguished. This method has provided easy access to measure this parameter and may be a powerful methodology in analyzing biomolecules on millisecond time scale.

  5. Targeting of single stranded oligonucleotides through metal-induced cyclization of short complementary strands : Targeting of single stranded oligonucleotides

    OpenAIRE

    Freville, Fabrice; Richard, Tristan; Bathany, Katell; Moreau, Serge

    2006-01-01

    International audience; A new strategy to cyclize a short synthetic oligonucleotide on a DNA or a RNA target strand is described. This one relies on a metal-mediated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2':6',2”-terpyridine moieties at their 3' and 5' ends. Cyclization following metal addition (Zn2+, Fe2+) was demonstrated using UV monitored thermal denaturation experiments, mass spectrometry analysis and gel shift assays. NMR experiments were used t...

  6. 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...

  7. Genetic evidence of multiple matrilines and spatial disruption of kinship bonds in mass strandings of long-finned pilot whales, Globicephala melas.

    Science.gov (United States)

    Oremus, Marc; Gales, Rosemary; Kettles, Helen; Baker, C Scott

    2013-01-01

    Mass strandings of whales and dolphins have puzzled biologists since Aristotle. Although environmental factors are often assumed to initiate strandings, social forces must also influence the dynamics of many of these events, particularly for the primary species involved in mass strandings, the long-finned pilot whales (Globicephala melas). Here, we test two hypotheses derived from common assumptions about the social dynamics of long-finned pilot whales by identifying maternal lineages from mtDNA haplotypes and inferring kinship from microsatellite genotypes of 490 individuals from 12 stranding events. Contrary to the "extended matriline" hypothesis, we found that multiple maternal lineages were present in at least 9 of the 12 mass strandings. Contrary to the "kinship cohesion" hypothesis, we found no correlation between spatial distribution and kinship along the stranding beach. Most notably, we documented the spatial disruption of the expected proximity between mothers and their dependent calves. These results challenge the common assumption that kinship-based behavior, such as care-giving, are a primary factor in these mass strandings. We suggest instead that disruption of kinship bonds could result from interactions among unrelated social groups during feeding or mating aggregations, perhaps playing a causal role in these events. Our finding that dependent calves were often spatially separated or absent from their mothers has important implications for humane management of rescue efforts. To improve our understanding of the social causes and consequences of mass strandings, future documentation of strandings should include exhaustive DNA sampling, with accompanying spatial and temporal records.

  8. GPS Separator

    CERN Multimedia

    2016-01-01

    Footage of the 70 degree ISOLDE GPS separator magnet MAG70 as well as the switchyard for the Central Mass and GLM (GPS Low Mass) and GHM (GPS High Mass) beamlines in the GPS separator zone. In the GPS20 vacuum sector equipment such as the long GPS scanner 482 / 483 unit, faraday cup FC 490, vacuum valves and wiregrid piston WG210 and WG475 and radiation monitors can also be seen. Also the RILIS laser guidance and trajectory can be seen, the GPS main beamgate switch box and the actual GLM, GHM and Central Beamline beamgates in the beamlines as well as the first electrostatic quadrupoles for the GPS lines. Close up of the GHM deflector plates motor and connections and the inspection glass at the GHM side of the switchyard.

  9. HRS Separator

    CERN Multimedia

    2016-01-01

    Footage of the 90 and 60 degree ISOLDE HRS separator magnets in the HRS separator zone. In the two vacuum sectors HRS20 and HRS30 equipment such as the HRS slits SL240, the HRS faraday cup FC300 and wiregrid WG210 can be spotted. Vacuum valves, turbo pumps, beamlines, quadrupoles, water and compressed air connections, DC and signal cabling can be seen throughout the video. The HRS main and user beamgate in the beamline between MAG90 and MAG60 and its switchboxes as well as all vacuum bellows and flanges are shown. Instrumentation such as the HRS scanner unit 482 / 483, the HRS WG470 wiregrid and slits piston can be seen. The different quadrupoles and supports are shown as well as the RILIS guidance tubes and installation at the magnets and the different radiation monitors.

  10. Analog Computation by DNA Strand Displacement Circuits.

    Science.gov (United States)

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

    2016-08-19

    DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include addition, subtraction, and multiplication gates. The input and output of these gates are analog, which means that they are directly represented by the concentrations of the input and output DNA strands, respectively, without requiring a threshold for converting to Boolean signals. We provide detailed domain designs and kinetic simulations of the gates to demonstrate their expected performance. On the basis of these gates, we describe how DNA circuits to compute polynomial functions of inputs can be built. Using Taylor Series and Newton Iteration methods, functions beyond the scope of polynomials can also be computed by DNA circuits built upon our architecture.

  11. DNA Strand-Displacement Timer Circuits.

    Science.gov (United States)

    Fern, Joshua; Scalise, Dominic; Cangialosi, Angelo; Howie, Dylan; Potters, Leo; Schulman, Rebecca

    2017-02-17

    Chemical circuits can coordinate elaborate sequences of events in cells and tissues, from the self-assembly of biological complexes to the sequence of embryonic development. However, autonomously directing the timing of events in synthetic systems using chemical signals remains challenging. Here we demonstrate that a simple synthetic DNA strand-displacement circuit can release target sequences of DNA into solution at a constant rate after a tunable delay that can range from hours to days. The rates of DNA release can be tuned to the order of 1-100 nM per day. Multiple timer circuits can release different DNA strands at different rates and times in the same solution. This circuit can thus facilitate precise coordination of chemical events in vitro without external stimulation.

  12. Design optimization of flow control device for multi-strand tundish

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The fluid flow phenomena in tundish have a strong influence not only on the uniform of composition and temperature ofbath, but also on the separation of non-metallic inclusions, especially for the multi-strand tundish. A water model of a multi-strandtundish has been set up based on the Froude number and Reynold number similarity criteria. The effect of dam+weir and baffle onthe uniform of composition and temperature of bath for different nozzles has been studied. The residence time distribution curves ofthe fluid flow were measured by SG800. Comparing the photos of the flow pattern in tundish, the optimum arrangement of baf-fle+dam was obtained. This new structure is benefit not only to uniform the temperature among different SENs (submerge entry noz-zles) but also to separate the non-inclusions from the liquid steel, it can be widely used in multi-strand tundish.

  13. Phase separation of myelin sheath in Triton X-114 solution: predominant localization of the 21.5-kDa isoform of myelin basic protein in the lipid raft-associated domain.

    Science.gov (United States)

    Uruse, Michihiro; Yamamoto, Masahiro; Sugawa, Makoto; Matsuura, Keiko; Sato, Yurie; Seiwa, Chika; Watanabe, Kenji; Aiso, Sadakazu; Asou, Hiroaki

    2014-04-01

    Myelin basic protein (MBP) isoforms in the myelin sheath are known to have distinct intracellular expression patterns, which are profoundly related to functional specificity. Determining the differential localization of MBP isoforms is therefore important for understanding their pathophysiological roles. In this study, we have developed a new method for phase separation of myelin. The non-ionic detergent Triton X-114 is used to solubilize myelin sheath which then undergoes phase separation to yield four fractions. The lipid raft-associated proteins and lipids in each fraction were analysed by immunoblotting and lipid analysis, respectively. The present method gives two lipid raft-enriched fractions, one of them was found to contain only lipid raft-associated galactocerebroside and cholesterol as the major lipids. The 21.5-kDa MBP isoforms (21.5 MBP), both unphosphorylated and phosphorylated, were exclusively contained in this fraction. Phosphorylated 21.5 MBP (21.5 pMBP) has been shown to specifically disappear from demyelinated loci. The present analytical method clearly indicated that disappearance of 21.5 pMBP corresponded to demyelination and its reappearance corresponded to prevention of demyelination. Demyelination was also associated with aging and was prevented by the myelin-protecting herbal medicine, Chinpi, a type of dried citrus peel.

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

    Science.gov (United States)

    2014-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Markers of Decompression Stress of Mass Stranded /Live...Caught and Released vs. Single Stranded Marine Mammals Michael Moore Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543...analyze blood samples from captive, wild-caught, and stranded marine mammals in order to compare concentrations of Microparticles (MPs). If confirmed

  15. 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

  16. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses.

    Science.gov (United States)

    Kim, Kyoung-Ho; Bae, Jin-Woo

    2011-11-01

    Investigation of viruses in the environment often requires the amplification of viral DNA before sequencing of viral metagenomes. In this study, two of the most widely used amplification methods, the linker amplified shotgun library (LASL) and multiple displacement amplification (MDA) methods, were applied to a sample from the seawater surface. Viral DNA was extracted from viruses concentrated by tangential flow filtration and amplified by these two methods. 454 pyrosequencing was used to read the metagenomic sequences from different libraries. The resulting taxonomic classifications of the viruses, their functional assignments, and assembly patterns differed substantially depending on the amplification method. Only double-stranded DNA viruses were retrieved from the LASL, whereas most sequences in the MDA library were from single-stranded DNA viruses, and double-stranded DNA viral sequences were minorities. Thus, the two amplification methods reveal different aspects of viral diversity.

  17. 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.

  18. Gulf stream separation dynamics

    Science.gov (United States)

    Schoonover, Joseph

    Climate models currently struggle with the more traditional, coarse ( O(100 km) ) representation of the ocean. In these coarse ocean simulations, western boundary currents are notoriously difficult to model accurately. The modeled Gulf Stream is typically seen exhibiting a mean pathway that is north of observations, and is linked to a warm sea-surface temperature bias in the Mid-Atlantic Bight. Although increased resolution ( O(10 km) ) improves the modeled Gulf Stream position, there is no clean recipe for obtaining the proper pathway. The 70 year history of literature on the Gulf Stream separation suggests that we have not reached a resolution on the dynamics that control the current's pathway just south of the Mid-Atlantic Bight. Without a concrete knowledge on the separation dynamics, we cannot provide a clean recipe for accurately modeling the Gulf Stream at increased resolutions. Further, any reliable parameterization that yields a realistic Gulf Stream path must express the proper physics of separation. The goal of this dissertation is to determine what controls the Gulf Stream separation. To do so, we examine the results of a model intercomparison study and a set of numerical regional terraforming experiments. It is argued that the separation is governed by local dynamics that are most sensitive to the steepening of the continental shelf, consistent with the topographic wave arrest hypothesis of Stern (1998). A linear extension of Stern's theory is provided, which illustrates that wave arrest is possible for a continuously stratified fluid.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  20. Mechanistic insight into the interaction of BLM helicase with intra-strand G-quadruplex structures

    Science.gov (United States)

    Chatterjee, Sujoy; Zagelbaum, Jennifer; Savitsky, Pavel; Sturzenegger, Andreas; Huttner, Diana; Janscak, Pavel; Hickson, Ian D.; Gileadi, Opher; Rothenberg, Eli

    2014-11-01

    Bloom syndrome is an autosomal recessive disorder caused by mutations in the RecQ family helicase BLM that is associated with growth retardation and predisposition to cancer. BLM helicase has a high specificity for non-canonical G-quadruplex (G4) DNA structures, which are formed by G-rich DNA strands and play an important role in the maintenance of genomic integrity. Here we used single-molecule FRET to define the mechanism of interaction of BLM helicase with intra-stranded G4 structures. We show that the activity of BLM is substrate dependent, and highly regulated by a short-strand DNA (ssDNA) segment that separates the G4 motif from double-stranded DNA. We demonstrate cooperativity between the RQC and HRDC domains of BLM during binding and unfolding of the G4 structure, where the RQC domain interaction with G4 is stabilized by HRDC binding to ssDNA. We present a model that proposes a unique role for G4 structures in modulating the activity of DNA processing enzymes.

  1. Detection of the strand exchange reaction using DNAzyme and Thermotoga maritima recombinase A.

    Science.gov (United States)

    Jo, Hunho; Lee, Seonghwan; Min, Kyoungin; Ban, Changill

    2012-02-01

    We have designed multiple detection systems for the DNA strand exchange process. Thermostable Thermotoga maritima recombinase A (TmRecA), a core protein in homologous recombination, and DNAzyme, a catalytic DNA that can cleave a specific DNA sequence, are introduced in this work. In a colorimetric method, gold nanoparticles (AuNPs) modified with complementary DNAs (cDNAs) were assembled by annealing. Aggregated AuNPs were then separated irreversibly by TmRecA and DNAzyme, leading to a distinct color change in the particles from purple to red. For the case of fluorometric detection, fluorescein isothiocyanate (FITC)-labeled DNA as a fluorophore and black hole quencher 1 (BHQ1)-labeled DNA as a quencher were used; successful strand exchange was clearly detected by variations in fluorescence intensity. In addition, alterations in the impedance of a gold electrode with immobilized DNA were employed to monitor the regular exchange of DNA strands. All three methods provided sufficient evidence of efficient strand exchange reactions and have great potential for applications in the monitoring of recombination, discovery of new DNAzymes, detection of DNAzymes, and measurement of other protein activities.

  2. DNA Separation by Capillary Electrophoresis with Ultraviolet Detection using Mixed Synthetic Polymers

    Institute of Scientific and Technical Information of China (English)

    Qian WANG; Xu XU

    2003-01-01

    The mixtures of two polymers, poly (N,N-dimethylacrylamide) (PDMA) and polyvinylpyrrolidone (PVP) were synthesized and used as the separation medium for double-stranded and single-stranded DNA fragments by capillary electrophoresis with UV detector. On optimal conditions, 2%w/v PDMA ( 2%w/v PVP can be used to separate the doublet 123/124bp in pBR322/Hae III Markers.

  3. 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...

  4. 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.

  5. Repair of DNA Double-Strand Breaks

    Science.gov (United States)

    Falk, Martin; Lukasova, Emilie; Kozubek, Stanislav

    The genetic information of cells continuously undergoes damage induced by intracellular processes including energy metabolism, DNA replication and transcription, and by environmental factors such as mutagenic chemicals and UV and ionizing radiation. This causes numerous DNA lesions, including double strand breaks (DSBs). Since cells cannot escape this damage or normally function with a damaged genome, several DNA repair mechanisms have evolved. Although most "single-stranded" DNA lesions are rapidly removed from DNA without permanent damage, DSBs completely break the DNA molecule, presenting a real challenge for repair mechanisms, with the highest risk among DNA lesions of incorrect repair. Hence, DSBs can have serious consequences for human health. Therefore, in this chapter, we will refer only to this type of DNA damage. In addition to the biochemical aspects of DSB repair, which have been extensively studied over a long period of time, the spatio-temporal organization of DSB induction and repair, the importance of which was recognized only recently, will be considered in terms of current knowledge and remaining questions.

  6. Magnetization measurements on LHC superconducting strands

    CERN Document Server

    Le Naour, S; Wolf, R; Puzniak, R; Szewczyk, A; Wisniewski, A; Fikis, H; Foitl, M; Kirchmayr, H

    1999-01-01

    When using superconducting magnets in particle accelerators like the LHC, persistent currents in the superconductor often determine the field quality at injection, where the magnetic field is low. This paper describes magnetization measurements made on LHC cable strands at the Technical University of Vienna and the Institute of Physics of the Polish Academy of Sciences in collaboration with CERN. Measurements were performed at T=2 K and T=4.2 K on more than 50 strands of 7 different manufacturers with NbTi filament diameter between 5 and 7 micrometer. Two different measurement set-ups were used: vibrating sample magnetometer, with a sample length of about 8 mm, and an integrating coil magnetometer, with sample length of about 1 m. The two methods were compared by measuring the same sample. Low field evidence of proximity effect is discussed. Statistics like ratio of the width of the magnetization loop at 4.2 K 2 K, and the initial slope dM/dB after cooldown are presented. Decrease of the magnetization with ti...

  7. Homologous DNA strand exchange activity of the human mitochondrial DNA helicase TWINKLE

    OpenAIRE

    Sen, Doyel; Patel, Gayatri; Smita S Patel

    2016-01-01

    A crucial component of the human mitochondrial DNA replisome is the ring-shaped helicase TWINKLE—a phage T7-gene 4-like protein expressed in the nucleus and localized in the human mitochondria. Our previous studies showed that despite being a helicase, TWINKLE has unique DNA annealing activity. At the time, the implications of DNA annealing by TWINKLE were unclear. Herein, we report that TWINKLE uses DNA annealing function to actively catalyze strand-exchange reaction between the unwinding su...

  8. DNA Strand Breaks, Neurodegeneration and Aging in the Brain

    Science.gov (United States)

    Katyal, Sachin; McKinnon, Peter J.

    2013-01-01

    Defective responses to DNA single- or double-strand breaks can result in neurological disease, underscoring the critical importance of DNA repair for neural homeostasis. Human DNA repair-deficient syndromes are generally congenital, in which brain pathology reflects the consequences of developmentally incurred DNA damage. Although, it is unclear to what degree DNA strand-break repair defects in mature neural cells contributes to disease pathology. However, DNA single-strand breaks are a relatively common lesion which if not repaired can impact cells via interference with transcription. Thus, this lesion, and probably to a lesser extent DNA double strand breaks, may be particularly relevant to aging in the neural cell population. In this review we will examine the consequences of defective DNA strand break repair towards homeostasis in the brain. Further, we also consider the utility of mouse models as reagents to understand the connection between DNA strand breaks and aging in the brain. PMID:18455751

  9. Possible involvement of DNA strand breaks in regulation of cell differentiation.

    Science.gov (United States)

    Sjakste, N; Sjakste, T

    2007-01-01

    The present review summarizes data on the accumulation of DNA strand breaks in differentiating cells. Large 50 Kbp free DNA fragments were observed by several research teams in non-apoptotic insect, mammal and plant cells. A more intensive DNA breakage was observed during maturation of spermatides, embryo development, and differentiation of myotubes, epidermal cells, lymphocytes and neutrophils. In general, accumulation of DNA strand breaks in differentiating cells cannot be attributed to decrease of the DNA repair efficiency. Poly(ADP)ribose synthesis often follows the DNA breakage in differentiating cells. We hypothesize that DNA fragmentation is an epigenetic tool for regulation of the differentiation process. Scarce data on localization of the differentiation-associated DNA strand breaks indicate their preferred accumulation in specific DNA sequences including the nuclear matrix attachment sites and repeats. Recent data on non-apoptotic functions of caspases provide more evidence for possible existence of a DNA breakage mechanism in differentiating cells resembling the initial stage of apoptosis. Excision of methylated cytosine and recombination are other possible explanations of the phenomenon. Elucidation of mechanisms of differentiation-induced DNA strand breaks appears to possess considerable research potential.

  10. TRF2 is required for repair of nontelomeric DNA double-strand breaks by homologous recombination

    Science.gov (United States)

    Mao, Zhiyong; Seluanov, Andrei; Jiang, Ying; Gorbunova, Vera

    2007-01-01

    TRF2 (telomeric repeat binding factor 2) is an essential component of the telomeric cap, where it forms and stabilizes the T-loop junctions. TRF2 forms the T-loops by stimulating strand invasion of the 3′ overhang into duplex DNA. TRF2 also has been shown to localize to nontelomeric DNA double-strand breaks, but its functional role in DNA repair has not been examined. Here, we present evidence that TRF2 is involved in homologous recombination (HR) repair of nontelomeric double-strand breaks. Depletion of TRF2 strongly inhibited HR and delayed the formation of Rad51 foci after γ-irradiation, whereas overexpression of TRF2 stimulated HR. Depletion of TRF2 had no effect on nonhomologous end-joining, and overexpression of TRF2 inhibited nonhomologous end-joining. We propose, based on our results and on the ability of TRF2 to mediate strand invasion, that TRF2 plays an essential role in HR by facilitating the formation of early recombination intermediates. PMID:17670947

  11. DNA strand breakage by bivalent metal ions and ionizing radiation.

    Science.gov (United States)

    Ayene, Iraimoudi S; Koch, Cameron J; Krisch, Robert E

    2007-03-01

    To investigate mechanisms of DNA breakage via the interaction of bivalent metal ion, thiol reducing agent and ionizing radiation, in *OH scavenging abilities comparable to those in cells. We measured the effects of 10 min exposure to 200 microM Fe2+ vs. Fe3+ on the induction of single (SSB) and double (DSB) strand breaks in unirradiated and oxically irradiated SV40 DNA, in aqueous solution containing 75 or 750 mM glycerol and/or 5 mM glutathione (GSH). Fe2+ or GSH alone produced little DNA damage. However, their combination produced a dramatic increase in the production of both SSB and DSB. Experiments with ferric ion suggest that it produces DNA damage only after partial reduction to ferrous by GSH. Induction efficiencies for SSB in the presence of Fe2+/GSH showed additivity of the effects of radiation alone with those from Fe2+/GSH. However, the corresponding induction efficiencies for DSB demonstrated a 2.5-fold enhancement. Our results are consistent with a model in which reduced bivalent metal ions plus thiols, in the presence of O2, produce DSB in DNA primarily via local clusters of hydroxyl radicals arising from site specific Fenton reactions. The synergism observed between DSB production by Fe/GSH and by ionizing radiation, also believed to occur via local clusters of hydroxyl radicals, is consistent with this model. Our results suggest that both normally present intracellular iron and ionizing radiation may be important sources of oxidative stress in cells.

  12. DNA Strand Breaks, Neurodegeneration and Aging in the Brain

    OpenAIRE

    Katyal, Sachin; McKinnon, Peter J

    2008-01-01

    Defective responses to DNA single- or double-strand breaks can result in neurological disease, underscoring the critical importance of DNA repair for neural homeostasis. Human DNA repair-deficient syndromes are generally congenital, in which brain pathology reflects the consequences of developmentally incurred DNA damage. Although, it is unclear to what degree DNA strand-break repair defects in mature neural cells contributes to disease pathology. However, DNA single-strand breaks are a relat...

  13. The multiple personalities of Watson and Crick strands

    OpenAIRE

    Graur Dan; Cartwright Reed A

    2011-01-01

    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 ...

  14. Acoustical dead zones and the spatial aggregation of whale strandings.

    Science.gov (United States)

    Sundaram, Bala; Poje, Andrew C; Veit, Richard R; Nganguia, Herve

    2006-02-21

    Cetacean strandings display a marked geographical clustering. We propose a simple, two-dimensional ray-dynamics model of cetacean echolocation to examine the role played by coastline topography in influencing the location and clustering of stranding sites. We find that a number of coastlines known to attract cetacean strandings produce acoustical "Dead Zones" where echolocation signals are severely distorted by purely geometric effects. Using available cetacean stranding data bases from four disparate areas, we show that the geographical clusters in the observations correlate strongly with the regions of distorted echolocation signals as predicted by the model.

  15. A Cobalt Supramolecular Triple-Stranded Helicate-based Discrete Molecular Cage

    Science.gov (United States)

    Mai, Hien Duy; Kang, Philjae; Kim, Jin Kyung; Yoo, Hyojong

    2017-01-01

    We report a strategy to achieve a discrete cage molecule featuring a high level of structural hierarchy through a multiple-assembly process. A cobalt (Co) supramolecular triple-stranded helicate (Co-TSH)-based discrete molecular cage (1) is successfully synthesized and fully characterized. The solid-state structure of 1 shows that it is composed of six triple-stranded helicates interconnected by four linking cobalt species. This is an unusual example of a highly symmetric cage architecture resulting from the coordination-driven assembly of metallosupramolecular modules. The molecular cage 1 shows much higher CO2 uptake properties and selectivity compared with the separate supramolecular modules (Co-TSH, complex 2) and other molecular platforms. PMID:28262690

  16. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks

    Energy Technology Data Exchange (ETDEWEB)

    Larionov, V.; Kouprina, N. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)]|[Institute of Cytology, St. Petersburg, (Russian Federation); Edlarov, M. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)]|[Center of Bioengineering, Moscow, (Russian Federation); Perkins, E.; Porter, G.; Resnick, M.A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)

    1993-12-31

    Rearrangement and deletion within plasmid DNA is commonly observed during transformation. We have examined the mechanisms of transformation-associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmid contains homologous or diverged (19%) DNA repeats separated by a genetically detectable color marker. Recombination during transformation for covalently closed circular plasmids was over 100-fold more frequent than during mitotic growth. The frequency of recombination is partly dependent on the method of transformation in that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single-strand breaks that are ligatable, as well as double-strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation-associated recombination between repeat DNA`s is under the influence of the RADS2, RADI and the RNCI genes,

  17. Compound Poisson Processes and Clustered Damage of Radiation Induced DNA Double Strand Breaks

    Science.gov (United States)

    Gudowska-Nowak, E.; Ritter, S.; Taucher-Scholz, G.; Kraft, G.

    2000-05-01

    Recent experimental data have demonstrated that DNA damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The principal constituent of DNA damage are double-strand breaks (DSB) which are formed when the breaks occur in both DNA strands and are directly opposite or separated by only a few base pairs. DSBs are believed to be most important lesions produced in chromosomes by radiation; interaction between DSBs can lead to cell killing, mutation or carcinogenesis. The paper discusses a model of clustered DSB formation viewed in terms of compound Poisson process along with the predictive essay of the formalism in application to experimental data.

  18. Conservative Repair of a Chromosomal Double-Strand Break by Single-Strand DNA through Two Steps of Annealing▿ †

    OpenAIRE

    Storici, Francesca; Snipe, Joyce R.; Chan, Godwin K.; Dmitry A Gordenin; Michael A Resnick

    2006-01-01

    The repair of chromosomal double-strand breaks (DSBs) is essential to normal cell growth, and homologous recombination is a universal process for DSB repair. We explored DSB repair mechanisms in the yeast Saccharomyces cerevisiae using single-strand oligonucleotides with homology to both sides of a DSB. Oligonucleotide-directed repair occurred exclusively via Rad52- and Rad59-mediated single-strand annealing (SSA). Even the SSA domain of human Rad52 provided partial complementation for a null...

  19. 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

  20. 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

  1. Current transfer length in multi-filamentary superconducting NbTi and Nb3Sn strands; experiments and models

    NARCIS (Netherlands)

    Zhou, Chao; Dhalle, Marc M.J.; ten Kate, Herman H.J.; Nijhuis, Arend

    2014-01-01

    The current transfer length of multi-filamentary superconducting NbTi and Nb3Sn strands was measured and analyzed. The aim is to understand and quantify the current distribution process between matrix and superconducting filaments occurring at current injection joints or shunting localized

  2. Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double-stranded helices.

    Science.gov (United States)

    Giessner-Prettre, C; Ribas Prado, F; Pullman, B; Kan, L; Kast, J R; Ts'o, P O

    1981-01-01

    A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects.

  3. Why double-stranded RNA resists condensation

    Energy Technology Data Exchange (ETDEWEB)

    Tolokh, Igor S.; Pabit, Suzette; Katz, Andrea M.; Chen, Yujie; Drozdetski, Aleksander; Baker, Nathan A.; Pollack, Lois; Onufriev, Alexey

    2014-09-15

    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to attraction between the negatively charged helices and eventually to condensation. Surprisingly, this effect is suppressed in double-stranded RNA, which carries the same charge as the DNA, but assumes a different double helical form. However, additional characterization of short (25 base-pairs) nucleic acid (NA) duplex structures by circular dichroism shows that measured differences in condensation are not solely determined by duplex helical geometry. Here we combine experiment, theory, and atomistic simulations to propose a mechanism that connects the observed variations in condensation of short NA duplexes with the spatial variation of cobalt hexammine (CoHex) binding at the NA duplex surface. The atomistic picture that emerged showed that CoHex distributions around the NA reveals two major NA-CoHex binding modes -- internal and external -- distinguished by the proximity of bound CoHex to the helical axis. Decreasing trends in experimentally observed condensation propensity of the four studied NA duplexes (from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA) are explained by the progressive decrease of a single quantity: the fraction of CoHex ions in the external binding mode. Thus, while NA condensation depends on a complex interplay between various structural and sequence features, our coupled experimental and theoretical results suggest a new model in which a single parameter connects the NA condensation propensity with geometry and sequence dependence of CoHex binding.

  4. CRISPR interference directs strand specific spacer acquisition.

    Directory of Open Access Journals (Sweden)

    Daan C Swarts

    Full Text Available BACKGROUND: CRISPR/Cas is a widespread adaptive immune system in prokaryotes. This system integrates short stretches of DNA derived from invading nucleic acids into genomic CRISPR loci, which function as memory of previously encountered invaders. In Escherichia coli, transcripts of these loci are cleaved into small RNAs and utilized by the Cascade complex to bind invader DNA, which is then likely degraded by Cas3 during CRISPR interference. RESULTS: We describe how a CRISPR-activated E. coli K12 is cured from a high copy number plasmid under non-selective conditions in a CRISPR-mediated way. Cured clones integrated at least one up to five anti-plasmid spacers in genomic CRISPR loci. New spacers are integrated directly downstream of the leader sequence. The spacers are non-randomly selected to target protospacers with an AAG protospacer adjacent motif, which is located directly upstream of the protospacer. A co-occurrence of PAM deviations and CRISPR repeat mutations was observed, indicating that one nucleotide from the PAM is incorporated as the last nucleotide of the repeat during integration of a new spacer. When multiple spacers were integrated in a single clone, all spacer targeted the same strand of the plasmid, implying that CRISPR interference caused by the first integrated spacer directs subsequent spacer acquisition events in a strand specific manner. CONCLUSIONS: The E. coli Type I-E CRISPR/Cas system provides resistance against bacteriophage infection, but also enables removal of residing plasmids. We established that there is a positive feedback loop between active spacers in a cluster--in our case the first acquired spacer--and spacers acquired thereafter, possibly through the use of specific DNA degradation products of the CRISPR interference machinery by the CRISPR adaptation machinery. This loop enables a rapid expansion of the spacer repertoire against an actively present DNA element that is already targeted, amplifying the

  5. Nonequilibrium separation of short DNA using nanoslit arrays

    Science.gov (United States)

    Strychalski, Elizabeth A.; Lau, Henry W.; Archer, Lynden A.

    2009-07-01

    A nonequilibrium regime of size-based separation was observed experimentally for double-stranded deoxyribonucleic acid (DNA) molecules with lengths below 1 kbp moving electrokinetically through nanofluidic nanoslit arrays. The breakdown of Ogston sieving was supplanted at higher electric fields to recover rapid separation with a reversed elution order and elution times one to two orders of magnitude faster than with Ogston sieving at lower fields. A simple kinetic model describes the experimental results.

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

    Science.gov (United States)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela; Gamba, Cristina; Barnett, Ross; Samaniego, José Alfredo; Madrigal, Jazmín Ramos; Orlando, Ludovic; Gilbert, M Thomas P

    2015-12-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.

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

    DEFF Research Database (Denmark)

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

    1976-01-01

    Conditions were established where the thallium-catalyzed iodination of random coil DNA proceeded 100–200 times faster than for native DNA. This reaction was explored as a probe for localized regions of disrupted base pairs in duplex DNA. A heteroduplex was constructed between DNA fragments produced......, if they existed within an otherwise helical DNA fragment 789 base pairs long. Iodination studies were performed on superhelical SV40 DNA and on linear plac DNA. Analysis of the relative amount of iodine in restriction endonuclease fragments of these DNAs revealed the absence of localized single-stranded regions....

  8. Catalysis of Strand Annealing by Replication Protein A Derives from Its Strand Melting Properties*

    OpenAIRE

    Bartos, Jeremy D.; Willmott, Lyndsay J.; Binz, Sara K.; Wold, Marc S.; Bambara, Robert A.

    2008-01-01

    Eukaryotic DNA-binding protein replication protein A (RPA) has a strand melting property that assists polymerases and helicases in resolving DNA secondary structures. Curiously, previous results suggested that human RPA (hRPA) promotes undesirable recombination by facilitating annealing of flaps produced transiently during DNA replication; however, the mechanism was not understood. We designed a series of substrates, representing displaced DNA flaps generated during ma...

  9. Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization.

    Science.gov (United States)

    Tse, Jenny; Wang, Yuanyuan; Zengeya, Thomas; Rozners, Eriks; Tan-Wilson, Anna

    2015-02-01

    We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Strategies underlying RNA silencing suppression by negative strand RNA viruses

    NARCIS (Netherlands)

    Hemmes, J.C.

    2007-01-01

    The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double strand

  11. Strategies underlying RNA silencing suppression by negative strand RNA viruses

    NARCIS (Netherlands)

    Hemmes, J.C.

    2007-01-01

    The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double strand

  12. A FORMAL SPECIFICATION LANGUAGE FOR DYNAMIC STRAND SPACE MODEL

    Institute of Scientific and Technical Information of China (English)

    刘东喜; 李晓勇; 白英彩

    2002-01-01

    Specification language is used to provide enough information for the model of the cryptographic protocol. This paper first extends strand space model to dynamic strand model, and then a formal specification language for this model is defined by using BNF grammar. Compared with those in literatures, it is simpler because of only concerning the algebraic properties of cryptographic protocols.

  13. Cetaceans stranded in the Netherlands in 2008-2014

    NARCIS (Netherlands)

    Keijl, Guido; Begeman, L.; Hiemstra, S.; IJsseldijk, L.L.; Kamminga, Pepijn

    2016-01-01

    We present a validated list of cetaceans stranded from 2008 up to and including 2014. A total of 4406 cetaceans was found on the Dutch coast during this period, comprising 4346 harbour porpoises (Phocoena phocoena) (98.6% of all strandings) and 59 individuals of twelve other species. The next most n

  14. 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 (n=6

  15. Electron spin polarization transfer to the charge-separated state from locally excited triplet configuration: theory and its application to characterization of geometry and electronic coupling in the electron donor-acceptor system.

    Science.gov (United States)

    Kobori, Yasuhiro; Fuki, Masaaki; Murai, Hisao

    2010-11-18

    We present a theoretical model of analysis of the time-resolved electron paramagnetic resonance (TREPR) spectrum of the charge-separated (CS) state generated by the photoinduced electron transfer (ET) reaction via the locally excited triplet state in an electron donor-acceptor (D-A) system with a fixed molecular orientation. We show, by the stochastic-Liouville equation, that chemically induced dynamic electron polarization (CIDEP) of the triplet mechanism is explained by lack of transfer of quantum coherence terms in the primary triplet spin state, resulting in net emissive or absorptive electron spin polarization (ESP) which is dependent on anisotropy of the singlet-triplet intersystem crossing in the precursor excited state. This disappearance of the coherence is clearly shown to occur when the photoinduced ET rate is smaller than the angular frequency of the Zeeman splitting: the transferred coherence terms are averaged to be zero due to effective quantum oscillations during the time that the chemical reaction proceeds. The above theory has been applied to elucidate the molecular geometries and spin-spin exchange interactions (2J) of the CS states for both folded and extended conformers by computer simulations of TREPR spectra of the zinc porphyrin-fullerene dyad (ZnP-C(60)) bridged by diphenyldisilane. On the extended conformation, the electronic coupling is estimated from the 2J value. It has been revealed that the coupling term is smaller than the reported electronic interactions of the porphyrin-C(60) systems bridged by diphenylamide spacers. The difference in the electronic couplings has been explained by the difference in the LUMO levels of the bridge moieties that mediate the superexchange coupling for the long-range ET reaction.

  16. Relationship between marine mammal stranding events and offshore earthquakes

    Science.gov (United States)

    Grant, Rachel; Savirina, Anna; Hoppit, Will

    2014-05-01

    The causes of marine mammal stranding events are largely unknown, but may relate to ocean currents, severe weather, anthropogenic noise pollution, and other factors. Large stranding events have been suggested to occur as a result of offshore earthquakes but there is little evidence as yet to support this hypothesis. Stranding events occur in hotspots, which are sometimes areas of high seismic activity, such as Taiwan, and other times, in areas that are removed from seismic zones, such as Cape Cod. We analyse a large and robust dataset of marine mammal stranding data collected off the coast of Washington and Oregon from 1999 to 2010, to look for statistical connections to offshore earthquakes. We looked forward, as well as backward in time from significant seismic events, to ascertain whether stranding occurrences, if connected to earthquakes, are a result of the earthquake preparation period or the earthquake itself. Possible mechanisms are discussed.

  17. The effect of base pair mismatch on DNA strand displacement

    CERN Document Server

    Broadwater, Bo

    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 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 t...

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

    Science.gov (United States)

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

    2013-01-01

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

  19. Upgrading SELEX Technology by Using Lambda Exonuclease Digestion for Single-Stranded DNA Generation

    Directory of Open Access Journals (Sweden)

    Meltem Avci-Adali

    2009-12-01

    Full Text Available The generation of single-stranded DNA (ssDNA molecules plays a key role in the SELEX (Systematic Evolution of Ligands by EXponential enrichment combinatorial chemistry process and numerous molecular biology techniques and applications, such as DNA sequencing, single-nucleotide polymorphism (SNP analysis, DNA chips, DNA single-strand conformation polymorphism (SSCP analysis and many other techniques. The purity and yield of ssDNA can affect the success of each application. This study compares the two ssDNA production methods, the strand separation by streptavidin-coated magnetic beads and alkaline denaturation and the lambda exonuclease digestion, in regard to the purity of generated ssDNA and the efficiency. Here, we demonstrate the considerable benefits of ssDNA production by lambda exonuclease digestion for in vitro selection of DNA aptamers. We believe that the generation of ssDNA aptamers using this method will greatly improve the success rate of SELEX experiments concerning the recovery of target-specific aptamers.

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

    Science.gov (United States)

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

    2016-08-02

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

  1. Detection of double-stranded RNA molecules and virus-like particles in different Mucor species.

    Science.gov (United States)

    Vágvölgyi, C; Magyar, K; Papp, T; Vastag, M; Ferenczy, L; Hornok, L; Fekete, C

    1998-02-01

    The presence of double-stranded RNA elements was examined in 123 strains representing 18 Mucor species. These genetic elements were found to be present in 6 strains: 1 M. aligarensis, 1 M. hiemalis, 2 M. corticolus, 1 M. mucedo and 1 M. ramannianus. Electrophoretic separation of the nucleic acids revealed 4 different RNA patterns, with 1 to 5 discrete dsRNA bands. The molecular weights corresponding to these bands were 1.42-4.15 x 10(6) D. Using electronmicroscopy, for the first time the presence of virus like particles in Mucor species has been revealed.

  2. An Experimental Setup to Measure the Minimum Trigger Energy for Magneto-Thermal Instability in Nb3Sn Strands

    CERN Document Server

    Takala, E; Bremer, J; Balle, C; Bottura, L; Rossi, L

    2012-01-01

    Magneto-thermal instability may affect high critical current density Nb3Sn superconducting strands that can quench even though the transport current is low compared to the critical current with important implications in the design of next generation superconducting magnets. The instability is initiated by a small perturbation energy which is considerably lower than the Minimum Quench Energy (MQE). At CERN, a new experimental setup was developed to measure the smallest perturbation energy (Minimum Trigger Energy, MTE) which is able to trigger the magneto-thermal instability in superconducting Nb3Sn-strands. The setup is based on Q-switched laser technology which is able to provide a localized perturbation in nano-second time scale. Using this technique the energy deposition into the strand is well defined and reliable. The laser is located outside the cryostat at room temperature. The beam is guided from room temperature on to the superconducting strand by using a UV-enhanced fused silica fibre. The strand is ...

  3. Double-strand break repair-adox: Restoration of suppressed double-strand break repair during mitosis induces genomic instability.

    Science.gov (United States)

    Terasawa, Masahiro; Shinohara, Akira; Shinohara, Miki

    2014-12-01

    Double-strand breaks (DSBs) are one of the severest types of DNA damage. Unrepaired DSBs easily induce cell death and chromosome aberrations. To maintain genomic stability, cells have checkpoint and DSB repair systems to respond to DNA damage throughout most of the cell cycle. The failure of this process often results in apoptosis or genomic instability, such as aneuploidy, deletion, or translocation. Therefore, DSB repair is essential for maintenance of genomic stability. During mitosis, however, cells seem to suppress the DNA damage response and proceed to the next G1 phase, even if there are unrepaired DSBs. The biological significance of this suppression is not known. In this review, we summarize recent studies of mitotic DSB repair and discuss the mechanisms of suppression of DSB repair during mitosis. DSB repair, which maintains genomic integrity in other phases of the cell cycle, is rather toxic to cells during mitosis, often resulting in chromosome missegregation and aberration. Cells have multiple safeguards to prevent genomic instability during mitosis: inhibition of 53BP1 or BRCA1 localization to DSB sites, which is important to promote non-homologous end joining or homologous recombination, respectively, and also modulation of the non-homologous end joining core complex to inhibit DSB repair. We discuss how DSBs during mitosis are toxic and the multiple safeguard systems that suppress genomic instability.

  4. Picornaviruses and nuclear functions: targeting a cellular compartment distinct from the replication site of a positive-strand RNA virus

    Directory of Open Access Journals (Sweden)

    Dylan eFlather

    2015-06-01

    Full Text Available The compartmentalization of DNA replication and gene transcription in the nucleus and protein production in the cytoplasm is a defining feature of eukaryotic cells. The nucleus functions to maintain the integrity of the nuclear genome of the cell and to control gene expression based on intracellular and environmental signals received through the cytoplasm. The spatial separation of the major processes that lead to the expression of protein-coding genes establishes the necessity of a transport network to allow biomolecules to translocate between these two regions of the cell. The nucleocytoplasmic transport network is therefore essential for regulating normal cellular functioning. The Picornaviridae virus family is one of many viral families that disrupt the nucleocytoplasmic trafficking of cells to promote viral replication. Picornaviruses contain positive-sense, single-stranded RNA genomes and replicate in the cytoplasm of infected cells. As a result of the limited coding capacity of these viruses, cellular proteins are required by these intracellular parasites for both translation and genomic RNA replication. Being of messenger RNA polarity, a picornavirus genome can immediately be translated upon entering the cell cytoplasm. However, the replication of viral RNA requires the activity of RNA-binding proteins, many of which function in host gene expression, and are consequently localized to the nucleus. As a result, picornaviruses disrupt nucleocytoplasmic trafficking to exploit protein functions normally localized to a different cellular compartment from which they translate their genome to facilitate efficient replication. Furthermore, picornavirus proteins are also known to enter the nucleus of infected cells to limit host-cell transcription and down-regulate innate antiviral responses. The interactions of picornavirus proteins and host-cell nuclei are extensive, required for a productive infection, and are the focus of this review.

  5. Picornaviruses and nuclear functions: targeting a cellular compartment distinct from the replication site of a positive-strand RNA virus.

    Science.gov (United States)

    Flather, Dylan; Semler, Bert L

    2015-01-01

    The compartmentalization of DNA replication and gene transcription in the nucleus and protein production in the cytoplasm is a defining feature of eukaryotic cells. The nucleus functions to maintain the integrity of the nuclear genome of the cell and to control gene expression based on intracellular and environmental signals received through the cytoplasm. The spatial separation of the major processes that lead to the expression of protein-coding genes establishes the necessity of a transport network to allow biomolecules to translocate between these two regions of the cell. The nucleocytoplasmic transport network is therefore essential for regulating normal cellular functioning. The Picornaviridae virus family is one of many viral families that disrupt the nucleocytoplasmic trafficking of cells to promote viral replication. Picornaviruses contain positive-sense, single-stranded RNA genomes and replicate in the cytoplasm of infected cells. As a result of the limited coding capacity of these viruses, cellular proteins are required by these intracellular parasites for both translation and genomic RNA replication. Being of messenger RNA polarity, a picornavirus genome can immediately be translated upon entering the cell cytoplasm. However, the replication of viral RNA requires the activity of RNA-binding proteins, many of which function in host gene expression, and are consequently localized to the nucleus. As a result, picornaviruses disrupt nucleocytoplasmic trafficking to exploit protein functions normally localized to a different cellular compartment from which they translate their genome to facilitate efficient replication. Furthermore, picornavirus proteins are also known to enter the nucleus of infected cells to limit host-cell transcription and down-regulate innate antiviral responses. The interactions of picornavirus proteins and host-cell nuclei are extensive, required for a productive infection, and are the focus of this review.

  6. Development of Separator for Soybeans

    NARCIS (Netherlands)

    Vries, de H.C.P.; Rijpma, P.J.; Owaa, J.S.E.

    1997-01-01

    A simple and effective separator for soybeans was developed for small-scale farmers in Uganda, to clean the seeds from foreign material, chaff, broken beans etc. as demanded by local and world markets. It will help to avoid losses during post-harvest time and to reduce human drudgery of cleaning the

  7. 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).

  8. Localized bending fatigue behavior of high-strength steel monostrands

    DEFF Research Database (Denmark)

    Winkler, Jan; Fischer, Gregor; Georgakis, Christos T.

    2012-01-01

    In this paper, the localized bending fatigue behavior of pretensioned high strength steel monostrands is investigated. Furthermore, a new methodology using an optical photogrammetry system, which can quantify surface deformations on the strand is presented. The system allows measurement of the st......In this paper, the localized bending fatigue behavior of pretensioned high strength steel monostrands is investigated. Furthermore, a new methodology using an optical photogrammetry system, which can quantify surface deformations on the strand is presented. The system allows measurement...

  9. Thirty-Year-Old Paradigm about Unpalatable Perch Egg Strands Disclaimed by the Freshwater Top-Predator, the European Catfish (Silurus glanis)

    Science.gov (United States)

    Kočvara, Luboš; Sajdlová, Zuzana; Hoang The, Son Chung; Šmejkal, Marek; Peterka, Jiří

    2017-01-01

    So far, perch egg strands have been considered unpalatable biological material. However, we repeatedly found egg strands of European perch (Perca fluviatilis) in the diet of European catfish (Silurus glanis) caught by longlines in Milada and Most Lakes, Czech Republic. The finding proves that perch egg strands compose a standard food source for this large freshwater predatory fish. It extends the present knowledge on catfish foraging plasticity, showing it as an even more opportunistic feeder. Utilization of perch egg strands broadens the catfish diet niche width and represents an advantage against other fish predators. Comparison of datasets from extensive gillnet and SCUBA diver sampling campaigns gave the evidence that at least in localities where food sources are limited, multilevel predation by catfish may have an important impact on the perch population. PMID:28060862

  10. Particle separator scroll vanes

    Energy Technology Data Exchange (ETDEWEB)

    Lastrina, F. A.; Mayer, J. C.; Pommer, L. M.

    1985-07-09

    An inlet particle separator for a gas turbine engine is provided with unique vanes distributed around an entrance to a particle collection chamber. The vanes are uniquely constructed to direct extraneous particles that enter the engine into the collection chamber and prevent the particles from rebounding back into the engine's air flow stream. The vanes are provided with several features to accomplish this function, including upstream faces that are sharply angled towards air flow stream direction to cause particles to bounce towards the collection chamber. In addition, throat regions between the vanes cause a localized air flow acceleration and a focusing of the particles that aid in directing the particles in a proper direction.

  11. Fictional Separation Logic

    DEFF Research Database (Denmark)

    Jensen, Jonas Buhrkal; Birkedal, Lars

    2012-01-01

    , separation means physical separation. In this paper, we introduce \\emph{fictional separation logic}, which includes more general forms of fictional separating conjunctions P * Q, where "*" does not require physical separation, but may also be used in situations where the memory resources described by P and Q...

  12. Programmable energy landscapes for kinetic control of DNA strand displacement.

    Science.gov (United States)

    Machinek, Robert R F; Ouldridge, Thomas E; Haley, Natalie E C; Bath, Jonathan; Turberfield, Andrew J

    2014-11-10

    DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics.

  13. DNA strand exchange and RecA homologs in meiosis.

    Science.gov (United States)

    Brown, M Scott; Bishop, Douglas K

    2014-12-04

    Homology search and DNA strand-exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand-exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand-exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved.

  14. Recovery of stranded costs under electric deregulation: The Winstar doctrine

    Energy Technology Data Exchange (ETDEWEB)

    Person, J.C. [Person and Craver, Washington, DC (United States)

    1998-12-31

    This paper explores the applicability of the Winstar doctrine to the recovery of stranded costs arising from the deregulation of the electric utility industry. Such stranded costs, which have been widely estimated to be in the $100--200 billion range, represent those utility assets whose book value exceed their market value. Not addressed in this paper are the ongoing state and federal legislative initiatives to allow for the recovery of some or all of a utility`s stranded costs, such as through the assessment of competitive transmission charges (CTCs) or through stranded cost securitization. Rather, this paper presents one of several of legal arguments that could be utilized in those situations where a legislative solution either does not exist or does not allow for full book value recovery.

  15. Interaction of DAPI with double-stranded ribonucleic acids.

    OpenAIRE

    Manzini, G.; Xodo, L; Barcellona, M L; Quadrifoglio, F

    1985-01-01

    The interaction of DAPI with natural and synthetic double-stranded polyribonucleotides was studied with different optical and calorimetric methods. The results were similar to those obtained previously with double-stranded polydeoxynucleotides, i.e. two interaction modes, the first of which shows high affinity for AU clusters and consequent strong fluorescence enhancement. The results suggest caution in the use of DAPI as selective fluorescent staining agent for DNA in the presence of RNA. A ...

  16. Mismatch repair balances leading and lagging strand DNA replication fidelity.

    Directory of Open Access Journals (Sweden)

    Scott A Lujan

    Full Text Available The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases, α, δ, and ε. Current evidence suggests that DNA polymerase ε (Pol ε is the primary leading strand replicase, whereas Pols α and δ primarily perform lagging strand replication. The fact that these polymerases differ in fidelity and error specificity is interesting in light of the fact that the stability of the nuclear genome depends in part on the ability of mismatch repair (MMR to correct different mismatches generated in different contexts during replication. Here we provide the first comparison, to our knowledge, of the efficiency of MMR of leading and lagging strand replication errors. We first use the strand-biased ribonucleotide incorporation propensity of a Pol ε mutator variant to confirm that Pol ε is the primary leading strand replicase in Saccharomyces cerevisiae. We then use polymerase-specific error signatures to show that MMR efficiency in vivo strongly depends on the polymerase, the mismatch composition, and the location of the mismatch. An extreme case of variation by location is a T-T mismatch that is refractory to MMR. This mismatch is flanked by an AT-rich triplet repeat sequence that, when interrupted, restores MMR to > 95% efficiency. Thus this natural DNA sequence suppresses MMR, placing a nearby base pair at high risk of mutation due to leading strand replication infidelity. We find that, overall, MMR most efficiently corrects the most potentially deleterious errors (indels and then the most common substitution mismatches. In combination with earlier studies, the results suggest that significant differences exist in the generation and repair of Pol α, δ, and ε replication errors, but in a generally complementary manner that results in high-fidelity replication of both DNA strands of the yeast nuclear genome.

  17. The N-terminal strand modulates immunoglobulin light chain fibrillogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Pozo-Yauner, Luis del, E-mail: ldelpozo@inmegen.gob.mx [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Wall, Jonathan S. [Departments of Radiology and Medicine, The University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN (United States); González Andrade, Martín [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Sánchez-López, Rosana [Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa Cuernavaca, Morelos C.P. 62210 (Mexico); Rodríguez-Ambriz, Sandra L. [Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle CEPROBI No. 8, Col. San Isidro, Yautepec, Morelos C.P. 62731 (Mexico); Pérez Carreón, Julio I. [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); and others

    2014-01-10

    Highlights: •We evaluated the impact of mutations in the N-terminal strand of 6aJL2 protein. •Mutations destabilized the protein in a position-dependent manner. •Destabilizing mutations accelerated the fibrillogenesis by shortening the lag time. •The effect on the kinetic of fibril elongation by seeding was of different nature. •The N-terminal strand is buried in the fibrillar state of 6aJL2 protein. -- Abstract: It has been suggested that the N-terminal strand of the light chain variable domain (V{sub L}) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stability and kinetic of fibrillogenesis of the V{sub L} protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.

  18. A model capturing novel strand symmetries in bacterial DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sobottka, Marcelo, E-mail: sobottka@mtm.ufsc.br [Departamento de Matematica, Universidade Federal de Santa Catarina (Brazil); Hart, Andrew G., E-mail: ahart@dim.uchile.cl [Departamento de Ingenieria Matematica and Centro de Modelamiento Matematico, Universidad de Chile (Chile)

    2011-07-15

    Highlights: {yields} We propose a simple stochastic model to construct primitive DNA sequences. {yields} The model provide an explanation for Chargaff's second parity rule in primitive DNA sequences. {yields} The model is also used to predict a novel type of strand symmetry in primitive DNA sequences. {yields} We extend the results for bacterial DNA sequences and compare distributional properties intrinsic to the model to statistical estimates from 1049 bacterial genomes. {yields} 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.

  19. G-Strands and Peakon Collisions on Diff(R

    Directory of Open Access Journals (Sweden)

    Darryl D. Holm

    2013-03-01

    Full Text Available A G-strand is a map g: R×R→G for a Lie group G that follows from Hamilton's principle for a certain class of G-invariant Lagrangians. Some G-strands on finite-dimensional groups satisfy 1+1 space-time evolutionary equations that admit soliton solutions as completely integrable Hamiltonian systems. For example, the SO(3-strand equations may be regarded physically as integrable dynamics for solitons on a continuous spin chain. Previous work has shown that G-strands for diffeomorphisms on the real line possess solutions with singular support (e.g. peakons. This paper studies collisions of such singular solutions of G-strands when G=Diff(R is the group of diffeomorphisms of the real line R, for which the group product is composition of smooth invertible functions. In the case of peakon-antipeakon collisions, the solution reduces to solving either Laplace's equation or the wave equation (depending on a sign in the Lagrangian and is written in terms of their solutions. We also consider the complexified systems of G-strand equations for G=Diff(R corresponding to a harmonic map g: C→Diff(R and find explicit expressions for its peakon-antipeakon solutions, as well.

  20. 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.

  1. 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

  2. Hearing loss in stranded odontocete dolphins and whales.

    Directory of Open Access Journals (Sweden)

    David Mann

    Full Text Available The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70-90 dB or profound (>90 dB hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested.

  3. Protein-free parallel triple-stranded DNA complex formation

    Science.gov (United States)

    Shchyolkina, A. K.; Timofeev, E. N.; Lysov, Yu. P.; Florentiev, V. L.; Jovin, T. M.; Arndt-Jovin, D. J.

    2001-01-01

    A 14 nt DNA sequence 5′-AGAATGTGGCAAAG-3′ from the zinc finger repeat of the human KRAB zinc finger protein gene ZNF91 bearing the intercalator 2-methoxy,6-chloro,9-amino acridine (Acr) attached to the sugar–phosphate backbone in various positions has been shown to form a specific triple helix (triplex) with a 16 bp hairpin (intramolecular) or a two-stranded (intermolecular) duplex having the identical sequence in the same (parallel) orientation. Intramolecular targets with the identical sequence in the antiparallel orientation and a non-specific target sequence were tested as controls. Apparent binding constants for formation of the triplex were determined by quantitating electrophoretic band shifts. Binding of the single-stranded oligonucleotide probe sequence to the target led to an increase in the fluorescence anisotropy of acridine. The parallel orientation of the two identical sequence segments was confirmed by measurement of fluorescence resonance energy transfer between the acridine on the 5′-end of the probe strand as donor and BODIPY-Texas Red on the 3′-amino group of either strand of the target duplex as acceptor. There was full protection from OsO4-bipyridine modification of thymines in the probe strand of the triplex, in accordance with the presumed triplex formation, which excluded displacement of the homologous duplex strand by the probe–intercalator conjugate. The implications of these results for the existence of protein-independent parallel triplexes are discussed. PMID:11160932

  4. DNA Origami with Double Stranded DNA as a Unified Scaffold

    Science.gov (United States)

    Yang, Yang; Han, Dongran; Nangreave, Jeanette; Liu, Yan; Yan, Hao

    2013-01-01

    Scaffolded DNA origami is a widely used technology for self-assembling precisely structured nanoscale objects that contain a large number of addressable features. Typical scaffolds are long, single strands of DNA (ssDNA) that are folded into distinct shapes through the action of many, short ssDNA staples that are complementary to several different domains of the scaffold. However, sources of long single stranded DNA are scarce, limiting the size and complexity of structures that can be assembled. Here we demonstrated that dsDNA scaffolds can be directly used to fabricate integrated DNA origami structures that incorporate both of the constituent ssDNA molecules. Two basic principles were employed in the design of scaffold folding paths – folding path asymmetry and periodic convergence of the two ssDNA scaffold strands. Asymmetry in the folding path minimizes unwanted complementarity between staples, and incorporating an offset between the folding paths of each ssDNA scaffold strand reduces the number of times that complementary portions of the strands are brought into close proximity with one another, both of which decrease the likelihood of dsDNA scaffold recovery. Meanwhile, the folding paths of the two ssDNA scaffold strands were designed to periodically converge to promote the assembly of a single, unified structure rather than two individual ones. Our results reveal that this basic strategy can be used to reliably assemble integrated DNA nanostructures from dsDNA scaffolds. PMID:22830653

  5. Correlation between slowly repairable double-strand breaks and thermal radiosensitization in the human HeLa S3 cell line

    NARCIS (Netherlands)

    Kampinga, HH; Hiemstra, YS; Konings, AWT; Dikomey, E

    1997-01-01

    The effect of heat on double-strand breaks (dsb) repair was compared with thermal radiosensitization using HeLa S3 cells. Cells were exposed to a combined treatment of X-irradiation followed by heat (44 degrees C, 0.5 h) separated by time intervals up to 8h. DNA dsb were measured by PFGE and surviva

  6. Separation Anxiety (For Parents)

    Science.gov (United States)

    ... Kids to Be Smart About Social Media Separation Anxiety KidsHealth > For Parents > Separation Anxiety Print A A ... both of you get through it. About Separation Anxiety Babies adapt pretty well to other caregivers. Parents ...

  7. Separation Anxiety (For Parents)

    Science.gov (United States)

    ... Feeding Your 1- to 2-Year-Old Separation Anxiety KidsHealth > For Parents > Separation Anxiety A A A ... both of you get through it. About Separation Anxiety Babies adapt pretty well to other caregivers. Parents ...

  8. Absolutely separating quantum maps and channels

    Science.gov (United States)

    Filippov, S. N.; Magadov, K. Yu; Jivulescu, M. A.

    2017-08-01

    Absolutely separable states ϱ remain separable under arbitrary unitary transformations U\\varrho {U}\\dagger . By example of a three qubit system we show that in a multipartite scenario neither full separability implies bipartite absolute separability nor the reverse statement holds. The main goal of the paper is to analyze quantum maps resulting in absolutely separable output states. Such absolutely separating maps affect the states in a way, when no Hamiltonian dynamics can make them entangled afterwards. We study the general properties of absolutely separating maps and channels with respect to bipartitions and multipartitions and show that absolutely separating maps are not necessarily entanglement breaking. We examine the stability of absolutely separating maps under a tensor product and show that {{{Φ }}}\\otimes N is absolutely separating for any N if and only if Φ is the tracing map. Particular results are obtained for families of local unital multiqubit channels, global generalized Pauli channels, and combination of identity, transposition, and tracing maps acting on states of arbitrary dimension. We also study the interplay between local and global noise components in absolutely separating bipartite depolarizing maps and discuss the input states with high resistance to absolute separability.

  9. Mathematical modeling of fluid flow, heat transfer and inclusion transport in a four strand tundish

    Institute of Scientific and Technical Information of China (English)

    Yufeng Wang; Guanghua Wen; Ping Tang; Mingmei Zhu; Yuanqing Chen; Weizhao Song

    2007-01-01

    Mathematical simulation was used for trouble-shooting and optimization.By the mathematical simulation,fluid flow and heat transfer of molten-steel in a four-strand tundish of a billet caster under different conditions (bare tundish and tundish with flow control device) were analyzed.The results showed that (1) the tundish with flow control device (FCD) has an important effect on the fluid pattern and temperature distribution; (2) the unsteady solving method was used to model the inclusion motions at different time periods,and it showed that the FCD is advantageous to separate the nonmetallic inclusions.According to the simulation results,the main problem existing in the industry production was found,and some helpful measurements were executed.Consequently,the large nonmetallic inclusions were separated,and the content of total oxygen was reduced.The quality of steel was greatly improved.

  10. SCAI promotes DNA double-strand break repair in distinct chromosomal contexts

    DEFF Research Database (Denmark)

    Hansen, Rebecca Kring; Mund, Andreas; Poulsen, Sara Lund

    2016-01-01

    DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions, whose accurate repair by non-homologous end-joining (NHEJ) or homologous recombination (HR) is crucial for genome integrity and is strongly influenced by the local chromatin environment. Here, we identify SCAI (suppressor of cancer...... in repressive chromatin environments. Moreover, we establish an important role of SCAI in meiotic recombination, as SCAI deficiency in mice leads to germ cell loss and subfertility associated with impaired retention of the DMC1 recombinase on meiotic chromosomes. Collectively, our findings uncover SCAI...

  11. Global organization of a positive-strand RNA virus genome.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    Full Text Available The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE, which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.

  12. Uncovering the microscopic mechanism of strand exchange during RecA mediated homologous recombination using all-atom molecular dynamics simulations

    Science.gov (United States)

    Shankla, Manish; Yoo, Jejoong; Aksimentiev, Aleksei

    2012-02-01

    Homologous recombination (HR) is a key step during the repair process of double-stranded DNA (dsDNA) breakage. RecA is a protein that mediates HR in bacteria. RecA monomers polymerize on a single-stranded DNA (ssDNA) separated from the broken dsDNA to form a helical filament, thus allowing strand exchange to occur. Recent crystal structures depict each RecA monomer in contact with three contiguous nucleotides called DNA triplets. Surprisingly, the conformation of each triplet is similar to that of a triplet in B-form DNA. However, in the filament the neighboring triplets are separated by loops of the RecA proteins. Single molecule experiments demonstrated that strand exchange propagation occurs in 3 base-pair increments. However, the temporal resolution of the experiments was insufficient to determine the exact molecular mechanism of the triplet propagation. Using all-atom molecular dynamics simulations, we investigated the effect of both the RecA protein and the conformation of the bound ssDNA fragment on the stability of the duplex DNA intermediate formed during the strand-exchange process. Specifically, we report simulations of force-induced unzipping of duplex DNA in the presence and absence of the RecA filament that explored the effect of the triplet ladder conformation.

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

    Energy Technology Data Exchange (ETDEWEB)

    Poeschla, Eric, E-mail: poeschla.eric@mayo.edu

    2013-06-20

    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.

  14. Separation of Isotopes via Dynamical Delocalization

    Institute of Scientific and Technical Information of China (English)

    Farhan Saif

    2008-01-01

    Based on the dynamical de-localization phenomenon we show that different isotopes of a material can be separated.We explain that the suggested scheme can be realized in the laboratory using presently available experimental facilities.

  15. Strength and reliability of Oriented Strand Lumber made from heat-treated Parawood strands

    Directory of Open Access Journals (Sweden)

    Veerapong Chotchuay

    2008-08-01

    Full Text Available This study was carried out to investigate engineering properties of one type of wood composites known as Oriented Strand Lumber (OSL. Heat-treated Parawood strands were used for producing OSL specimens (HOSL and compared to a control one (nonheat-treated or NOSL. The structural application as beams was selected to determine the effect of sheared volume to longitudinal shear strength since shear failure is a critical mode of OSL. The reliability concept was then employedto analyze the data to ensure that OSL structural members can be used for construction safely and economically. The results indicated that mean values of strength of HOSL subjected to axial loading, i.e., compression (39 MPa and tension (36 MPa parallel to the grain as well as bending in the flatwise (59 MPa and edgewise (61 MPa directions were significantly higher than those of NOSL. However, the differences between HOSL and NOSL subjected to normal loading, i.e., compression perpendicular to the grain (26 vs 25 MPa, shear parallel to the grain (4 vs 3 MPa and internal bonding (0.48 vs 0.47 MPa were non-significant. The results of shear strength studies showed that the shear strength ofHOSL beams was higher than that of NOSL beams and regression analysis revealed that the shear strength depended on sheared volume. It showed that shear strength decreased with increasing sheared volume. The results of the reliability analysis indicated that the fitted distribution of the flexural rigidity (EI could be represented well as normal. The coefficient of variation of the fitted EI distribution was found to be within the serviceability limit state required by the building codes. This implies that OSL beams can be used safely as an alternative structural material for wood construction. The safetyfactor and recommended allowable design stresses are also presented.

  16. 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.

  17. 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.

  18. Stranding Events of Kogia Whales along the Brazilian Coast.

    Science.gov (United States)

    Moura, Jailson F; Acevedo-Trejos, Esteban; Tavares, Davi C; Meirelles, Ana C O; Silva, Cristine P N; Oliveira, Larissa R; Santos, Roberta A; Wickert, Janaína C; Machado, Rodrigo; Siciliano, Salvatore; Merico, Agostino

    2016-01-01

    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.

  19. Short distance movement of genomic negative strands in a host and nonhost for Sugarcane mosaic virus (SCMV

    Directory of Open Access Journals (Sweden)

    Hernández-Vela Juan

    2011-01-01

    Full Text Available Abstract Background In order to obtain an initial and preliminary understanding of host and nonhost resistance in the initial step of potyvirus replication, both positive and negative Sugarcane mosaic virus (SCMV strands where traced in inoculated and systemic leaves in host and nonhost resistant maize and sugarcane for one Mexican potyviral isolate (SCMV-VER1. Intermediary replication forms, such as the negative viral strand, seem to only move a short distance as surveyed by RT-PCR analysis and ELISA in different leaves. Virus purification was also done in leaves and stems. Results Susceptible maize plants allowed for viral SCMV replication, cell-to-cell, and long distance movement, as indicated by the presence of the coat protein along the plant. In the host resistant maize plants for the SCMV-VER1 isolate, the virus was able to establish the disease though the initial steps of virus replication, as detected by the presence of negative strands, in the basal area of the inoculated leaves at six and twelve days post inoculation. The nonhost sugarcane for SCMV-VER1 and the host sugarcane for SCMV-CAM6 also allowed the initial steps of viral replication for the VER1 isolate in the local inoculated leaf. SCMV-VER1 virions could be extracted from stems of susceptible maize with higher titers than leaves. Conclusion Nonhost and host resistance allow the initial steps of potyvirus SCMV replication, as shown by the negative strands' presence. Furthermore, both hosts allow the negative viral strands' local movement, but not their systemic spread through the stem. The presence of larger amounts of extractable virions from the stem (as compared to the leaves in susceptible maize lines suggests their long distance movement as assembled particles. This will be the first report suggesting the long distance movement of a monocot potyvirus as a virion.

  20. Controlling Separation in Turbomachines

    Science.gov (United States)

    Evans, Simon; Himmel, Christoph; Power, Bronwyn; Wakelam, Christian; Xu, Liping; Hynes, Tom; Hodson, Howard

    2010-01-01

    Four examples of flow control: 1) Passive control of LP turbine blades (Laminar separation control). 2) Aspiration of a conventional axial compressor blade (Turbulent separation control). 3) Compressor blade designed for aspiration (Turbulent separation control). 4.Control of intakes in crosswinds (Turbulent separation control).

  1. Single strand DNA binding proteins 1 and 2 protect newly replicated telomeres

    Institute of Scientific and Technical Information of China (English)

    Peili Gu; Wei Deng; Ming Lei; Sandy Chang

    2013-01-01

    Human single-strand (ss) DNA binding proteins 1 and 2 (hSSB1 and 2) are components of the hSSB1/2-INTS3-C9orf80 heterotrimeric protein complex shown to participate in DNA damage response and maintenance of genome stability.However,their roles at telomeres remain unknown.Here,we generated murine SSB1 conditional knockout mice and cells and found that mSSB1 plays a critical role in telomere end protection.Both mSSB1 and mSSB2 localize to a subset of telomeres and are required to repair TRF2-deficient telomeres.Deletion of mSSB1 resulted in increased chromatid-type fusions involving both leading-and lagging-strand telomeric DNA,suggesting that it is required for the protection of G-overhangs.mSSB1's interaction with INTS3 is required for its localization to damaged DNA.mSSB1 interacts with Potla,but not Potlb,and its association with telomeric ssDNA requires Potla.mSSB1△/△ mice die at birth with developmental abnormalities,while mice with the hypomorphic mSSB1F/F allele are born alive and display increased sensitivity to ionizing radiation (IR).Our results suggest that mSSB1 is required to maintain genome stability,and document a previously unrecognized role for mSSB1/2 in the protection of newly replicated leading-and lagging-strand telomeres.

  2. Accurate strand-specific quantification of viral RNA.

    Directory of Open Access Journals (Sweden)

    Nicole E Plaskon

    Full Text Available The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (- strand RNA with this assay when higher levels of cDNA generated from the (+ strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (- strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR(R Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV, the recent cause of large outbreaks of disease in the Indian Ocean

  3. The superconducting strand for the CMS solenoid conductor

    CERN Document Server

    Curé, B; Campi, D; Goodrich, L F; Horváth, I L; Kircher, F; Liikamaa, R; Seppälä, J; Smith, R P; Teuho, J; Vieillard, L

    2002-01-01

    The Compact Muon Solenoid (CMS) is one of the general-purpose detectors to be provided for the LHC project at CERN. The design field of the CMS superconducting magnet is 4 T, the magnetic length is 12.5 m and the free bore is 6 m. Approximately 2000 km of superconducting strand is under procurement for the conductor of the CMS superconducting solenoid. Each strand length is required to be an integral multiple of 2.75 km. The strand is composed of copper- stabilized multifilamentary Nb-Ti with Nb barrier. Individual strands are identified by distinctive patterns of Nb-Ti filaments selected during stacking of the monofilaments. The statistics of piece length, measurements of I/sub c/, n-value, copper RRR, (Cu+Nb)/Nb-Ti ratio, as well as the results of independent cross checks of these quantities, are presented. A study was performed on the CMS strands to investigate the critical current degradation due to various heat treatments. The degradation versus annealing temperature and duration are reported. (4 refs).

  4. Heavy ion induced double strand breaks in bacteria and bacteriophages

    Science.gov (United States)

    Micke, U.; Schäfer, M.; Anton, A.; Horneck, G.; Bücker, H.

    DNA damage induced by heavy ions in bacterial cells and bacteriophages such as Bacillus subtilis, E. coli and Bacteriophage Tl were investigated by analyzing the double strand breaks in the chromosomal DNA. This kind of lesion is considered as one of the main reasons for lethal events. To analyze double strand breaks in long molecules of DNA - up to some Mbp in length - the technique of pulse field agarose gel electrophoresis has been used. This allows the detection of one double strand break per genome. Cell lysis and DNA isolation were performed in small agarose blocks directly. This procedure secured minimum DNA destruction by shearing forces. After running a gel, the DNA was stained with ethidium bromide. The light intensity of ethidium bromide fluorescence for both the outcoming (running) DNA and the remaining intact DNA were measured by scanning. The mean number of double strand breaks was calculated by determining the quotient of these intensities. Strand break induction after heavy ion and X-ray irradiation was compared.

  5. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II.

    Science.gov (United States)

    Westover, Kenneth D; Bushnell, David A; Kornberg, Roger D

    2004-02-13

    The structure of an RNA polymerase II-transcribing complex has been determined in the posttranslocation state, with a vacancy at the growing end of the RNA-DNA hybrid helix. At the opposite end of the hybrid helix, the RNA separates from the template DNA. This separation of nucleic acid strands is brought about by interaction with a set of proteins loops in a strand/loop network. Formation of the network must occur in the transition from abortive initiation to promoter escape.

  6. Preparation and separation of DNA-wrapped carbon nanotubes.

    Science.gov (United States)

    Ao, Geyou; Zheng, Ming

    2015-01-01

    Purification of single-chirality single-wall carbon nanotubes (SWCNTs) from their synthetic mixture is a prerequisite for many applications. DNA-controlled carbon nanotube (CNT) purification has evolved over a decade along with other separation techniques utilizing different types of dispersing agents such as surfactants and polymers. The size of single-stranded DNA (ssDNA) libraries affords practically unlimited ways of coating SWCNTs. Recent developments in separating surfactant-dispersed SWCNTs by polymer aqueous two-phase (ATP) extraction has enabled rapid and efficient SWCNT separation on a larger volume scale. Applying the ATP separation method to DNA-SWCNT hybrids opens a new route for effective sorting of nanotubes into each and every single-chirality species. Here, we report protocols for purifying as many as 15 single-chirality nanotube species from a synthetic mixture based on the separation of DNA-SWCNTs by the aqueous two-phase (ATP) method.

  7. PROPERTIES OF DOUBLE-STRANDED DNA AS A POLYELECTROLYTE.

    Science.gov (United States)

    OHNISHI, T

    1963-11-01

    The stability of the structure of double-stranded DNA in the salt-free solution is discussed on the basis of the polyelectrolyte theory. Assuming that DNA is an infinitely long rod, and the formation of double strands is divided into combining process and folding process, the free energy changes required in these processes are calculated by the use of the exact solutions of two-dimensional Poisson-Boltzmann equation for the one rod and the two rod systems.By strong depression of electrostatic interaction due to counter-ion condensation phenomena, the free energy change is remarkably decreased so that the double-stranded structure of DNA can be stabilized by energy of hydrogen bonds between base pairs. The increase of the activity coefficient of a counterion upon heat denaturation of DNA is also explained.

  8. Interaction of DAPI with double-stranded ribonucleic acids.

    Science.gov (United States)

    Manzini, G; Xodo, L; Barcellona, M L; Quadrifoglio, F

    1985-01-01

    The interaction of DAPI with natural and synthetic double-stranded polyribonucleotides was studied with different optical and calorimetric methods. The results were similar to those obtained previously with double-stranded polydeoxynucleotides, i.e. two interaction modes, the first of which shows high affinity for AU clusters and consequent strong fluorescence enhancement. The results suggest caution in the use of DAPI as selective fluorescent staining agent for DNA in the presence of RNA. A narrow groove binding model with hydrogen bonds between DAPI and AU pairs is proposed. An intercalation mechanism can be excluded because of the non planarity of DAPI molecule. PMID:4080554

  9. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  10. Interstrand contact resistance and AC loss of a 48-strands Nb3Sn CIC conductor with a Cr/Cr-oxide coating

    NARCIS (Netherlands)

    Nijhuis, Arend; Kate, ten Herman H.J.; Pantsyrny, Victor; Shikov, Alexander K.

    2000-01-01

    The interstrand contact resistance (Rc) between crossing strands in Cable-In-Conduit Conductors (CICC's) determines the coupling loss and the stability against local disturbances. The surface oxidation, surface roughness and micro-scale sliding of the contact surfaces are key parameters in the Rc. T

  11. Interstrand contact resistance and AC loss of a 48-strands Nb3Sn CIC conductor with a Cr/Cr-oxide coating

    NARCIS (Netherlands)

    Nijhuis, Arend; ten Kate, Herman H.J.; Pantsyrny, Victor; Shikov, Alexander K.

    2000-01-01

    The interstrand contact resistance (Rc) between crossing strands in Cable-In-Conduit Conductors (CICC's) determines the coupling loss and the stability against local disturbances. The surface oxidation, surface roughness and micro-scale sliding of the contact surfaces are key parameters in the Rc.

  12. Cross-strand coupling of a beta-hairpin peptide stabilized with an Aib-Gly turn studied using isotope-edited IR spectroscopy.

    Science.gov (United States)

    Huang, Rong; Setnicka, Vladimir; Etienne, Marcus A; Kim, Joohyun; Kubelka, Jan; Hammer, Robert P; Keiderling, Timothy A

    2007-11-01

    Isotope-edited IR spectroscopy was used to study a series of singly and doubly 13C=O-labeled beta-hairpin peptides stabilized by an Aib-Gly turn sequence. The double-labeled peptides have amide I' IR spectra that show different degrees of vibrational coupling between the 13C-labeled amides due to variations in the local geometry of the peptide structure. The single-labeled peptides provide controls to determine frequencies characteristic of the diagonal force field (FF) contributions at each position for the uncoupled 13C=O modes. Separation of diagonal FF and coupling effects on the spectra are used to explain the cross-strand labeled spectral patterns. DFT calculations based on an idealized model beta-hairpin peptide correctly predict the vibrational coupling patterns. Extending these model results by consideration of frayed ends and the hairpin conformational flexibility yields an alternate interpretation of details of the spectra. Temperature-dependent isotopically labeled IR spectra reveal differences in the thermal stabilities of the individual isotopically labeled sites. This is the first example of using an IR-based isotopic labeling technique to differentiate structural transitions at specific sites along the peptide backbone in model beta-hairpin peptides.

  13. Coccidioidomycosis and other systemic mycoses of marine mammals stranding along the central California, USA coast: 1998-2012.

    Science.gov (United States)

    Huckabone, Sara E; Gulland, Frances M D; Johnson, Suzanne M; Colegrove, Kathleen M; Dodd, Erin M; Pappagianis, Demosthenes; Dunkin, Robin C; Casper, David; Carlson, Erin L; Sykes, Jane E; Meyer, Weiland; Miller, Melissa A

    2015-04-01

    A wide range of systemic mycoses have been reported from captive and wild marine mammals from North America. Examples include regionally endemic pathogens such as Coccidioides and Blastomyces spp., and novel pathogens like Cryptococcus gattii, which appear may have been introduced to North America by humans. Stranding and necropsy data were analyzed from three marine mammal stranding and response facilities on the central California coast to assess the prevalence, host demographics, and lesion distribution of systemic mycoses affecting locally endemic marine mammals. Between 1 January 1998 and 30 June 2012, >7,000 stranded marine mammals were necropsied at the three facilities. Necropsy and histopathology records were reviewed to identify cases of locally invasive or systemic mycoses and determine the nature and distribution of fungal lesions. Forty-one animals (0.6%) exhibited cytological, culture- or histologically confirmed locally invasive or systemic mycoses: 36 had coccidioidomycosis, two had zygomycosis, two had cryptococcosis, and one was systemically infected with Scedosporium apiospermum (an Ascomycota). Infected animals included 18 California sea lions (Zalophus californianus), 20 southern sea otters (Enhydra lutris nereis), two Pacific harbor seals (Phoca vitulina richardsi), one Dall's porpoise (Phocoenoides dalli), and one northern elephant seal (Mirounga angustirostris). Coccidioidomycosis was reported from 15 sea lions, 20 sea otters, and one harbor seal, confirming that Coccidioides spp. is the most common pathogen causing systemic mycosis in marine mammals stranding along the central California coast. We also report the first confirmation of C. gattii infection in a wild marine mammal from California and the first report of coccidioidomycosis in a wild harbor seal. Awareness of these pathogenic fungi during clinical care and postmortem examination is an important part of marine mammal population health surveillance and human health protection

  14. Separation anxiety in children

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/001542.htm Separation anxiety in children To use the sharing features on this page, please enable JavaScript. Separation anxiety in children is a developmental stage in which ...

  15. Ionene membrane battery separator

    Science.gov (United States)

    Moacanin, J.; Tom, H. Y.

    1969-01-01

    Ionic transport characteristics of ionenes, insoluble membranes from soluble polyelectrolyte compositions, are studied for possible application in a battery separator. Effectiveness of the thin film of separator membrane essentially determines battery lifetime.

  16. Magnetic separation of algae

    Energy Technology Data Exchange (ETDEWEB)

    Nath, Pulak; Twary, Scott N.

    2016-04-26

    Described herein are methods and systems for harvesting, collecting, separating and/or dewatering algae using iron based salts combined with a magnetic field gradient to separate algae from an aqueous solution.

  17. Stranded pumice in the western Caribbean

    Science.gov (United States)

    Herrick, J. A.; Henton De Angelis, S.; Toscano, M. A.

    2013-12-01

    Floating and washed-up pumices have been reported by scientific expeditions along the Caribbean Sea coast of the Central American Isthmus and the northern coast of South America since at least 1947. Local coastal communities have been utilizing this resource for many years. The rounded and buffered morphology of hand specimens is consistent with water-borne transit. The volcanically active Caribbean and Central American regions provide a number of candidates for source volcanoes and eruptions. We have attempted to identify this source using samples collected from Carrie Bow Cay and Placencia Beach, Belize; Tulum Beach, Mexico; Morrosquillo Bay, Colombia; and Galeta Point, Panama. We have tracked possible transport routes through the use of river drainage and ocean current maps. The criteria for comparing the products of potential source volcanoes (including Atitlán Caldera in Guatemala and Caribbean sources such as Mt. Pelée, Martinique and Soufrière Hills, Montserrat) were developed from the whole rock major and trace element geochemistry and the compositional and textural characteristics of pumice and their constituent minerals and glasses. The largest pumice sample collected from Carrie Bow Cay, Belize, was 18.5x12 cm with the typical, rounded morphology and distinctively stretched vesicles exhibited by this pumice collection.

  18. Meningoencephalitis associated with Carnobacterium maltaromaticum-like bacteria in stranded juvenile salmon sharks (Lamna ditropis).

    Science.gov (United States)

    Schaffer, P A; Lifland, B; Van Sommeran, S; Casper, D R; Davis, C R

    2013-05-01

    Juvenile salmon sharks beach yearly along the California coast, primarily during late summer and early fall. Fresh, frozen, and formalin-fixed tissues from 19 stranded salmon sharks were collected for examination. Histopathology revealed meningitis or meningoencephalitis in 18 of 19 shark brains with intralesional bacteria observed in 6 of the affected brains. Bacterial culture of fresh or frozen brain, liver, and/or heart blood from 13 sharks yielded pure cultures characterized molecularly and/or biochemically as belonging to the genus Carnobacterium. The 16s ribosomal DNA sequence of 7 tissue isolates from 7 separate sharks was 99% homologous to C. maltaromaticum (GenBank FJ656722.1). Sequence of the large ribosomal DNA intergenic spacer region (ISR) was 97% homologous to C. maltaromaticum (AF374295.1). This is the first report of Carnobacterium infection in any shark species, and the authors posit that brain infection caused by Carnobacterium is a significant cause of morbidity and mortality in juvenile salmon sharks found stranded along the Pacific coast of California.

  19. How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases.

    Science.gov (United States)

    Kurian, P; Dunston, G; Lindesay, J

    2016-02-21

    Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism.

  20. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks

    Energy Technology Data Exchange (ETDEWEB)

    Larionov, V.; Kouprina, N. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)]|[Institute of Cytology, St. Petersburg (Russian Federation); Eldarov, M. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)]|[Center for Bioengineering, Moscow (Russian Federation); Perkins, E.; Porter, G.; Resnick, M.A. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)

    1994-10-01

    Rearrangement and deletion within plasmid DNA is commonly observed during transformation. We have examined the mechanisms of transformation-associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmid contains homologous or diverged (19%) DNA repeats separated by a genetically detectable color marker. Recombination during transformation for covalently closed circular plasmids was over 100-fold more frequent than during mitotic-growth. The frequency of recombination is partly dependent on the method of transformation In that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single-strand breaks that are ligatable, as well as double-strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation-associated recombination between repeat DNA`s is under the influence of the RAD52, RAD1 and the RNC1 genes.

  1. Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement

    CERN Document Server

    Chiniforooshan, Ehsan; Kari, Lila; Seki, Shinnosuke

    2010-01-01

    We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. The design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. The design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. This means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input sp...

  2. Kinetic Gravity Separation

    NARCIS (Netherlands)

    Van Kooy, L.; Mooij, M.; Rem, P.

    2004-01-01

    Separations by density, such as the separation of non-ferrous scrap into light and heavy alloys, are often realized by means of heavy media. In principle, kinetic gravity separations in water can be faster and cheaper, because they do not rely on suspensions or salt solutions of which the density

  3. Ligation of double-stranded and single-stranded [Oligo(dT)] DNA by vaccinia virus DNA ligase

    OpenAIRE

    1996-01-01

    Vaccinia virus DNA ligase has been expressed in Escherichia coli, purified, and biochemically characterized. The enzyme ligates double-stranded (ds) DNA substrates with either cohesive or blunt-end termini and the latter reaction is stimulated by PEG. Vaccinia virus DNA ligase can also ligate oligo(dT) when annealed to either a poly(dA) or a poly(rA) backbone and, remarkably, free oligo(dT). This ligation of a single-stranded (ss) substrate is unique among eukaryotic DNA ligases. The enzyme r...

  4. Single strand annealing and ATP-independent strand exchange activities of yeast and human DNA2: possible role in Okazaki fragment maturation.

    Science.gov (United States)

    Masuda-Sasa, Taro; Polaczek, Piotr; Campbell, Judith L

    2006-12-15

    The Dna2 protein is a multifunctional enzyme with 5'-3' DNA helicase, DNA-dependent ATPase, 3' exo/endonuclease, and 5' exo/endonuclease. The enzyme is highly specific for structures containing single-stranded flaps adjacent to duplex regions. We report here two novel activities of both the yeast and human Dna2 helicase/nuclease protein: single strand annealing and ATP-independent strand exchange on short duplexes. These activities are independent of ATPase/helicase and nuclease activities in that mutations eliminating either nuclease or ATPase/helicase do not inhibit strand annealing or strand exchange. ATP inhibits strand exchange. A model rationalizing the multiple catalytic functions of Dna2 and leading to its coordination with other enzymes in processing single-stranded flaps during DNA replication and repair is presented.

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

    Science.gov (United States)

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

    2013-04-01

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

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

    NARCIS (Netherlands)

    Baas, P.D.

    1985-01-01

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

  7. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

    During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response

  8. Polarity, Continuity, and Alignment in Plant Vascular Strands

    Institute of Scientific and Technical Information of China (English)

    Megan G. Sawchuk; Enrico Scarpella

    2013-01-01

    Plant vascular cells are joined end to end along uninterrupted lines to connect shoot organs with roots;vascular strands are thus polar, continuous, and internally aligned. What controls the formation of vascular strands with these properties? The “auxin canalization hypothesis”-based on positive feedback between auxin flow through a cell and the cell’s capacity for auxin transport-predicts the selection of continuous files of cells that transport auxin polarly, thus accounting for the polarity and continuity of vascular strands. By contrast, polar, continuous auxin transport-though required-is insufficient to promote internal alignment of vascular strands, implicating additional factors. The auxin canalization hypothesis was derived from the response of mature tissue to auxin application but is consistent with molecular and cellular events in embryo axis formation and shoot organ development. Objections to the hypothesis have been raised based on vascular organizations in callus tissue and shoot organs but seem unsupported by available evidence. Other objections call instead for further research; yet the inductive and orienting influence of auxin on continuous vascular differentiation remains unique.

  9. DNA strand exchange catalyzed by molecular crowding in PEG solutions

    KAUST Repository

    Feng, Bobo

    2010-01-01

    DNA strand exchange is catalyzed by molecular crowding and hydrophobic interactions in concentrated aqueous solutions of polyethylene glycol, a discovery of relevance for understanding the function of recombination enzymes and with potential applications to DNA nanotechnology. © 2010 The Royal Society of Chemistry.

  10. 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...

  11. Targeting DNA double-strand breaks with TAL effector nucleases.

    Science.gov (United States)

    Christian, Michelle; Cermak, Tomas; Doyle, Erin L; Schmidt, Clarice; Zhang, Feng; Hummel, Aaron; Bogdanove, Adam J; Voytas, Daniel F

    2010-10-01

    Engineered nucleases that cleave specific DNA sequences in vivo are valuable reagents for targeted mutagenesis. Here we report a new class of sequence-specific nucleases created by fusing transcription activator-like effectors (TALEs) to the catalytic domain of the FokI endonuclease. Both native and custom TALE-nuclease fusions direct DNA double-strand breaks to specific, targeted sites.

  12. 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 organizat

  13. On the Distinction between Preposition Stranding and Orphan Prepositions

    Science.gov (United States)

    Roberge, Yves

    2012-01-01

    Poplack, Zentz and Dion (PZD; Poplack, Zentz & Dion, 2011, this issue) examine the often unquestioned assumption that the existence of preposition stranding (PS) in Canadian French is linked to the presence of a contact situation with English in the North American context. Although this issue has been the topic of previous research from a…

  14. Cetaceans stranded in the Netherlands from 1998 to 2007

    NARCIS (Netherlands)

    Camphuysen, C.J.; Smeenk, C.; Addink, M.; 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, relativ

  15. 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, relativ

  16. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

    During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response

  17. Double strand break repair functions of histone H2AX

    Energy Technology Data Exchange (ETDEWEB)

    Scully, Ralph, E-mail: rscully@bidmc.harvard.edu; Xie, Anyong

    2013-10-15

    Chromosomal double strand breaks provoke an extensive reaction in neighboring chromatin, characterized by phosphorylation of histone H2AX on serine 139 of its C-terminal tail (to form “γH2AX”). The γH2AX response contributes to the repair of double strand breaks encountered in a variety of different contexts, including those induced by ionizing radiation, physiologically programmed breaks that characterize normal immune cell development and the pathological exposure of DNA ends triggered by telomere dysfunction. γH2AX also participates in the evolutionarily conserved process of sister chromatid recombination, a homologous recombination pathway involved in the suppression of genomic instability during DNA replication and directly implicated in tumor suppression. At a biochemical level, the γH2AX response provides a compelling example of how the “histone code” is adapted to the regulation of double strand break repair. Here, we review progress in research aimed at understanding how γH2AX contributes to double strand break repair in mammalian cells.

  18. Sensitive, Specific Complementary - Strand Optical Detection of Viral RNA

    Science.gov (United States)

    1997-06-01

    promise Its components have been characterized and proven to show unparalleled sensitivity; in addition, an innovative method for improving...sensing. 14. SUBJECT TERMS 15. NUMBER OF PAGES RNA, enterovirii, biosensor, evanscent waves, refractometry , 31 phase detection, complementary strand...Phase Measurements (10) Tri-Phase Detection Method . (11) Phase Detectors (12) Phase Processor Board (13) Laboratory Experim ents

  19. Rapid chemical separations

    CERN Document Server

    Trautmann, N

    1976-01-01

    A survey is given on the progress of fast chemical separation procedures during the last few years. Fast, discontinuous separation techniques are illustrated by a procedure for niobium. The use of such techniques for the chemical characterization of the heaviest known elements is described. Other rapid separation methods from aqueous solutions are summarized. The application of the high speed liquid chromatography to the separation of chemically similar elements is outlined. The use of the gas jet recoil transport method for nuclear reaction products and its combination with a continuous solvent extraction technique and with a thermochromatographic separation is presented. Different separation methods in the gas phase are briefly discussed and the attachment of a thermochromatographic technique to an on-line mass separator is shown. (45 refs).

  20. Acoustofluidic bacteria separation

    Science.gov (United States)

    Li, Sixing; Ma, Fen; Bachman, Hunter; Cameron, Craig E.; Zeng, Xiangqun; Huang, Tony Jun

    2017-01-01

    Bacterial separation from human blood samples can help with the identification of pathogenic bacteria for sepsis diagnosis. In this work, we report an acoustofluidic device for label-free bacterial separation from human blood samples. In particular, we exploit the acoustic radiation force generated from a tilted-angle standing surface acoustic wave (taSSAW) field to separate Escherichia coli from human blood cells based on their size difference. Flow cytometry analysis of the E. coli separated from red blood cells shows a purity of more than 96%. Moreover, the label-free electrochemical detection of the separated E. coli displays reduced non-specific signals due to the removal of blood cells. Our acoustofluidic bacterial separation platform has advantages such as label-free separation, high biocompatibility, flexibility, low cost, miniaturization, automation, and ease of in-line integration. The platform can be incorporated with an on-chip sensor to realize a point-of-care sepsis diagnostic device.

  1. Excited states in DNA strands investigated by ultrafast laser spectroscopy.

    Science.gov (United States)

    Chen, Jinquan; Zhang, Yuyuan; Kohler, Bern

    2015-01-01

    Ultrafast laser experiments on carefully selected DNA model compounds probe the effects of base stacking, base pairing, and structural disorder on excited electronic states formed by UV absorption in single and double DNA strands. Direct π-orbital overlap between two stacked bases in a dinucleotide or in a longer single strand creates new excited states that decay orders of magnitude more slowly than the generally subpicosecond excited states of monomeric bases. Half or more of all excited states in single strands decay in this manner. Ultrafast mid-IR transient absorption experiments reveal that the long-lived excited states in a number of model compounds are charge transfer states formed by interbase electron transfer, which subsequently decay by charge recombination. The lifetimes of the charge transfer states are surprisingly independent of how the stacked bases are oriented, but disruption of π-stacking, either by elevating temperature or by adding a denaturing co-solvent, completely eliminates this decay channel. Time-resolved emission measurements support the conclusion that these states are populated very rapidly from initial excitons. These experiments also reveal the existence of populations of emissive excited states that decay on the nanosecond time scale. The quantum yield of these states is very small for UVB/UVC excitation, but increases at UVA wavelengths. In double strands, hydrogen bonding between bases perturbs, but does not quench, the long-lived excited states. Kinetic isotope effects on the excited-state dynamics suggest that intrastrand electron transfer may couple to interstrand proton transfer. By revealing how structure and non-covalent interactions affect excited-state dynamics, on-going experimental and theoretical studies of excited states in DNA strands can advance understanding of fundamental photophysics in other nanoscale systems.

  2. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

    Directory of Open Access Journals (Sweden)

    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.

  3. A non-phenol-chloroform extraction of double-stranded RNA from plant and fungal tissues.

    Science.gov (United States)

    Balijja, Alitukiriza; Kvarnheden, Anders; Turchetti, Tullio

    2008-09-01

    Double-stranded RNA (dsRNA) molecules of viruses are found in nature at a very high frequency. Their detection in plants and fungi has been carried out with difficulty due to the complicated dsRNA extraction techniques used commonly which includes phenol-chloroform extractions. In this study, an extraction method for isolation of dsRNA is described that is free of phenol and chloroform. A lysis buffer, containing beta-mercaptoethanol and polyvinylpolypyrrolidone (PVPP-40), was added to homogenised tissues and the subsequent supernatant was filtered through a cellulose CF-11 mini-column. DsRNA molecules were separated based on the differing affinity of nucleic acids for the cellulose CF-11 resin in 20% ethanol buffer. This easy, rapid and cheap technique has been successfully tested on fungi and plants containing different dsRNA virus molecules, indicating the possibility of a wide use of the method.

  4. Critical current and strand stiffness of three types Nb3Sn strand subjected to spatial periodic bending

    NARCIS (Netherlands)

    Nijhuis, Arend; Ilyin, Y.; Wessel, Wilhelm A.J.; Abbas, Wouter

    2006-01-01

    Knowledge of the influence of bending on the critical current (Ic) of Nb3Sn strands is essential for the understanding of the reduction in performance due to transverse electromagnetic load. In particular, for the large cable-in-conduit conductors (CICCs) meant for the international thermonuclear

  5. The role of DNA double-strand breaks in spontaneous homologous recombination in S. cerevisiae.

    Directory of Open Access Journals (Sweden)

    Gaëlle Lettier

    2006-11-01

    Full Text Available Homologous recombination (HR is a source of genomic instability and the loss of heterozygosity in mitotic cells. Since these events pose a severe health risk, it is important to understand the molecular events that cause spontaneous HR. In eukaryotes, high levels of HR are a normal feature of meiosis and result from the induction of a large number of DNA double-strand breaks (DSBs. By analogy, it is generally believed that the rare spontaneous mitotic HR events are due to repair of DNA DSBs that accidentally occur during mitotic growth. Here we provide the first direct evidence that most spontaneous mitotic HR in Saccharomyces cerevisiae is initiated by DNA lesions other than DSBs. Specifically, we describe a class of rad52 mutants that are fully proficient in inter- and intra-chromosomal mitotic HR, yet at the same time fail to repair DNA DSBs. The conclusions are drawn from genetic analyses, evaluation of the consequences of DSB repair failure at the DNA level, and examination of the cellular re-localization of Rad51 and mutant Rad52 proteins after introduction of specific DSBs. In further support of our conclusions, we show that, as in wild-type strains, UV-irradiation induces HR in these rad52 mutants, supporting the view that DNA nicks and single-stranded gaps, rather than DSBs, are major sources of spontaneous HR in mitotic yeast cells.

  6. [Separation anxiety in children].

    Science.gov (United States)

    Purper-Ouakil, Diane; Franc, Nathalie

    2010-06-20

    Separation anxiety disorder can be differentiated from developmental anxiety because of its intensity, persistence and negative impact on adaptive functioning. This disorder is closely linked to other anxiety and mood disorders and can also be associated with externalizing psychopathology in children and adolescents. Severe separation anxiety can result in school refusal and intra-familial violence. Cognitive behavioral therapies have the best evidence-based support for the treatment of separation anxiety disorder in children and adolescents. In addition, it is important to detect factors associated with persistence of anxiety such as systematic avoidance of separation and parental overprotection. The role of pediatricians and general practitioners in recognizing clinical separation anxiety and encouraging appropriate care and positive parental attitudes is essential, as separation anxiety is often associated with a variety of somatic symptoms.

  7. In vivo SELEX of single-stranded domains in the HIV-1 leader RNA.

    Science.gov (United States)

    van Bel, Nikki; Das, Atze T; Berkhout, Ben

    2014-02-01

    The 5' untranslated leader region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is a strongly conserved sequence that encodes several regulatory motifs important for viral replication. Most of these motifs are exposed as hairpin structures, including the dimerization initiation signal (DIS), the major splice donor site (SD), and the packaging signal (Ψ), which are connected by short single-stranded regions. Mutational analysis revealed many functions of these hairpins, but only a few studies have focused on the single-stranded purine-rich sequences. Using the in vivo SELEX (systematic evolution of ligands by exponential enrichment) approach, we probed the sequence space in these regions that is compatible with efficient HIV-1 replication and analyzed the impact on the RNA secondary structure of the leader RNA. Our results show a strong sequence requirement for the DIS hairpin flanking regions. We postulate that these sequences are important for the binding of specific protein factors that support leader RNA-mediated functions. The sequence between the SD and Ψ hairpins seems to have a less prominent role, despite the strong conservation of the stretch of 5 A residues in natural isolates. We hypothesize that this may reflect the subtle evolutionary pressure on HIV-1 to acquire an A-rich RNA genome. In silico analyses indicate that sequences are avoided in all 3 single-stranded domains that affect the local or overall leader RNA folding. IMPORTANCE Many regulatory RNA sequences are clustered in the untranslated leader domain of the HIV-1 RNA genome. Several RNA hairpin structures in this domain have been proposed to fulfill specific roles, e.g., mediating RNA dimer formation to facilitate HIV-1 recombination. We now focus on the importance of a few well-conserved single-stranded sequences that connect these hairpins. We created libraries of HIV-1 variants in which these segments were randomized and selected the best-replicating variants. For two

  8. [Separation anxiety. Theoretical considerations].

    Science.gov (United States)

    Blandin, N; Parquet, P J; Bailly, D

    1994-01-01

    The interest in separation anxiety is nowadays increasing: this disorder appearing during childhood may predispose to the occurrence of anxiety disorders (such as panic disorder and agoraphobia) and major depression into adulthood. Psychoanalytic theories differ on the nature of separation anxiety and its place in child development. For some authors, separation anxiety must be understood as resulting from the unconscious internal conflicts inherent in the individuation process and gradual attainment of autonomy. From this point of view, the fear of loss of mother by separation is not regarded as resulting from a real danger. However, Freud considers the primary experience of separation from protecting mother as the prototype situation of anxiety and compares the situations generating fear to separation experiences. For him, anxiety originates from two factors: the physiological fact is initiated at the time of birth but the primary traumatic situation is the separation from mother. This point of view may be compared with behavioral theories. Behavioral theories suggest that separation anxiety may be conditioned or learned from innate fears. In Freud's theory, the primary situation of anxiety resulting from the separation from mother plays a role comparable to innate fears. Grappling with the problem of separation anxiety, Bowlby emphasizes then the importance of the child's attachment to one person (mother or primary caregiver) and the fact that this attachment is instinctive. This point of view, based on the watch of infants, is akin to ethological theories on behaviour of non human primates. Bowlby especially shows that the reactions of infant separated from mother evolve on three stages: the phase of protestation which may constitute the prototype of adulthood anxiety, the phase of desperation which may be the prototype of depression, and the phase of detachment. He emphasizes so the role of early separations in the development of vulnerability to depression

  9. Msh2 blocks an alternative mechanism for non-homologous tail removal during single-strand annealing in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Glenn M Manthey

    Full Text Available Chromosomal translocations are frequently observed in cells exposed to agents that cause DNA double-strand breaks (DSBs, such as ionizing radiation and chemotherapeutic drugs, and are often associated with tumors in mammals. Recently, translocation formation in the budding yeast, Saccharomyces cerevisiae, has been found to occur at high frequencies following the creation of multiple DSBs adjacent to repetitive sequences on non-homologous chromosomes. The genetic control of translocation formation and the chromosome complements of the clones that contain translocations suggest that translocation formation occurs by single-strand annealing (SSA. Among the factors important for translocation formation by SSA is the central mismatch repair (MMR and homologous recombination (HR factor, Msh2. Here we describe the effects of several msh2 missense mutations on translocation formation that suggest that Msh2 has separable functions in stabilizing annealed single strands, and removing non-homologous sequences from their ends. Additionally, interactions between the msh2 alleles and a null allele of RAD1, which encodes a subunit of a nuclease critical for the removal of non-homologous tails suggest that Msh2 blocks an alternative mechanism for removing these sequences. These results suggest that Msh2 plays multiple roles in the formation of chromosomal translocations following acute levels of DNA damage.

  10. Separation of flow

    CERN Document Server

    Chang, Paul K

    2014-01-01

    Interdisciplinary and Advanced Topics in Science and Engineering, Volume 3: Separation of Flow presents the problem of the separation of fluid flow. This book provides information covering the fields of basic physical processes, analyses, and experiments concerning flow separation.Organized into 12 chapters, this volume begins with an overview of the flow separation on the body surface as discusses in various classical examples. This text then examines the analytical and experimental results of the laminar boundary layer of steady, two-dimensional flows in the subsonic speed range. Other chapt

  11. Structure of the EMMPRIN N-terminal domain 1: Dimerization via [beta]-strand swapping

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Jinquan; Teplyakov, Alexey; Obmolova, Galina; Malia, Thomas; Wu, Sheng-Jiun; Beil, Eric; Baker, Audrey; Swencki-Underwood, Bethany; Zhao, Yonghong; Sprenkle, Justin; Dixon, Ken; Sweet, Raymond; Gilliland, Gary L.; (Centocor)

    2010-09-27

    ECD. Quite unexpectedly, ND1 forms a dimer mediated through the exchange of its last {beta}-strand (strand G). {beta}-strand swapping, which is a subset of 3D domain swapping, has been found to mediate cell-cell adhesion by cadherins. 3D domain swapping has been proposed to be a mechanism of protein oligomerization, aggregation, evolution of oligomeric proteins from single domains and amyloidogenesis. In domain swapped proteins, the same structural elements are involved in the final 3D structure, and so there is little overall energetic difference between the monomer and the swapped oligomers. However, there is often a high energy barrier for the conversion as it often goes through an unfolded state. It is also possible that strand-swapping occurs during folding of nascent polypeptide chains. Frequently, the exchange hinges contain proline-rich motifs which are often in high strain conformations. Domain swapping appears to be a strategy to resolve such local structural strain. The exchange hinge of ND1 contains a Pro-Glu-Pro tripeptide motif. Both of the proline residues adopt extended trans conformations, when compared with cis in the full-length ECD structure. Proline cis-trans isomerization may be the driving force for this exchange. Strand-exchanged dimerization may be a mechanism for the oligomerization of EMMPRIN ECD and its cis-dependent homophilic interactions in cell-cell adhesion.

  12. 蛋白质中strand-loop-strand模体的分类%THE CLASSIFICATION OF STRAND-LOOP-STRAND MOTIFS IN PROTEINS

    Institute of Scientific and Technical Information of China (English)

    高苏娟; 胡秀珍

    2009-01-01

    从蛋白质一级序列出发,以氨基酸紧邻关联为参数,用离散量的方法,采用5交叉检验,对蛋白质中的strand-loop-strand模体进行了分类.文中使用了两个数据库,采用了不同的截取方式和序列模式长,均得到了较好的预测效果.

  13. Introduction of structural affinity handles as a tool in selective nucleic acid separations

    Science.gov (United States)

    Willson, III, Richard Coale (Inventor); Cano, Luis Antonio (Inventor)

    2011-01-01

    The method is used for separating nucleic acids and other similar constructs. It involves selective introduction, enhancement, or stabilization of affinity handles such as single-strandedness in the undesired (or desired) nucleic acids as compared to the usual structure (e.g., double-strandedness) of the desired (or undesired) nucleic acids. The undesired (or desired) nucleic acids are separated from the desired (or undesired) nucleic acids due to capture by methods including but not limited to immobilized metal affinity chromatography, immobilized single-stranded DNA binding (SSB) protein, and immobilized oligonucleotides. The invention is useful to: remove contaminating genomic DNA from plasmid DNA; remove genomic DNA from plasmids, BACs, and similar constructs; selectively separate oligonucleotides and similar DNA fragments from their partner strands; purification of aptamers, (deoxy)-ribozymes and other highly structured nucleic acids; Separation of restriction fragments without using agarose gels; manufacture recombinant Taq polymerase or similar products that are sensitive to host genomic DNA contamination; and other applications.

  14. Multi-Quality Properties Capability Analysis for Prestressing Strand of Prestressed Concrete

    Institute of Scientific and Technical Information of China (English)

    Wen; Pei; Sung; Kuen; Suan; Chen; Cheer; Germ; Go

    2002-01-01

    Prestressed concrete structures are main conformati on for the construction of high way bridges. The quality of prestressed concrete s tructures is mainly affected by the tensile strength of prestressing strand. In order to attain the purpose of economic design and long life span of prestressin g strand, the less relaxation property of strand type is suitable for constructi on and usage. Thus, the research and development of prestressing strand is requi red to reach the goals of high tensile strength and ...

  15. Unusual Mortality Events of Harbor Porpoise Strandings in North Carolina, 1997–2009

    OpenAIRE

    Aleta A. Hohn; Rotstein, David S.; Byrd, Barbie L.

    2013-01-01

    A marked increase in the frequency of harbor porpoises (Phocoena phocoena) stranded in North Carolina in 2005 was declared as an Unusual Mortality Event (UME). Strandings occurred in January through May when harbor porpoises are seasonally present. Increased stranding rates were measured relative to a threshold to determine that the UME was occurring. The threshold analysis also revealed elevated strandings during 1999, an undeclared UME year. Recovered carcasses during 1999 and 2005 accounte...

  16. The separation of adult separation anxiety disorder.

    Science.gov (United States)

    Baldwin, David S; Gordon, Robert; Abelli, Marianna; Pini, Stefano

    2016-08-01

    The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) categorization of mental disorders places "separation anxiety disorder" within the broad group of anxiety disorders, and its diagnosis no longer rests on establishing an onset during childhood or adolescence. In previous editions of DSM, it was included within the disorders usually first diagnosed in infancy, childhood, or adolescence, with the requirement for an onset of symptoms before the age of 18 years: symptomatic adults could only receive a retrospective diagnosis, based on establishing this early onset. The new position of separation anxiety disorder is based upon the findings of epidemiological studies that revealed the unexpectedly high prevalence of the condition in adults, often in individuals with an onset of symptoms after the teenage years; its prominent place within the DSM-5 group of anxiety disorders should encourage further research into its epidemiology, etiology, and treatment. This review examines the clinical features and boundaries of the condition, and offers guidance on how it can be distinguished from other anxiety disorders and other mental disorders in which "separation anxiety" may be apparent.

  17. Extended minus-strand DNA as template for R-U5-mediated second-strand transfer in recombinational rescue of primer binding site-modified retroviral vectors

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Dybkaer, K

    1998-01-01

    We have previously demonstrated recombinational rescue of primer binding site (PBS)-impaired Akv murine leukemia virus-based vectors involving initial priming on endogenous viral sequences and template switching during cDNA synthesis to obtain PBS complementarity in second-strand transfer...... of reverse transcription (Mikkelsen et al., J. Virol. 70:1439-1447, 1996). By use of the same forced recombination system, we have now found recombinant proviruses of different structures, suggesting that PBS knockout vectors may be rescued through initial priming on endogenous virus RNA, read......-through of the mutated PBS during minus-strand synthesis, and subsequent second-strand transfer mediated by the R-U5 complementarity of the plus strand and the extended minus-strand DNA acceptor template. Mechanisms for R-U5-mediated second-strand transfer and its possible role in retrovirus replication and evolution...

  18. 77 FR 2958 - Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To...

    Science.gov (United States)

    2012-01-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE International Trade Administration Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of... administrative review of the antidumping duty order on prestressed concrete steel wire strand (``PC Strand...

  19. 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...

  20. 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 dynamic

  1. Folding DNA origami from a double-stranded source of scaffold

    Science.gov (United States)

    Högberg, Björn; Liedl, Tim; Shih, William M.

    2009-01-01

    Combined heat and chemical denaturation of double-stranded DNA scaffold strands in the presence of staple strands, followed by a sudden temperature drop and then stepwise dialysis to remove the chemical denaturant, leads to self-assembly of two distinct DNA-origami structures. PMID:19566089

  2. 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... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1,...

  3. 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....

  4. 75 FR 28560 - Prestressed Concrete Steel Wire Strand From the People's Republic of China: Final Determination...

    Science.gov (United States)

    2010-05-21

    ... International Trade Administration Prestressed Concrete Steel Wire Strand From the People's Republic of China... less than fair value (``LTFV'') in the antidumping investigation of prestressed concrete steel strand...'' section of this notice. \\1\\ See Prestressed Concrete Steel Wire Strand From the People's Republic of...

  5. 75 FR 32747 - Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping Duty Administrative...

    Science.gov (United States)

    2010-06-09

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE INTERNATIONAL TRADE ADMINISTRATION Prestressed Concrete Steel Wire Strand from Mexico: Rescission of Antidumping... prestressed concrete steel wire strand (``PC Strand'') from Mexico for the period January 1, 2009...

  6. Hybrid fur rendering: combining volumetric fur with explicit hair strands

    DEFF Research Database (Denmark)

    Andersen, Tobias Grønbeck; Falster, Viggo; Frisvad, Jeppe Revall

    2016-01-01

    Hair is typically modeled and rendered using either explicitly defined hair strand geometry or a volume texture of hair densities. Taken each on their own, these two hair representations have difficulties in the case of animal fur as it consists of very dense and thin undercoat hairs in combination...... with coarse guard hairs. Explicit hair strand geometry is not well-suited for the undercoat hairs, while volume textures are not well-suited for the guard hairs. To efficiently model and render both guard hairs and undercoat hairs, we present a hybrid technique that combines rasterization of explicitly...... defined guard hairs with ray marching of a prismatic shell volume with dynamic resolution. The latter is the key to practical combination of the two techniques, and it also enables a high degree of detail in the undercoat. We demonstrate that our hybrid technique creates a more detailed and soft fur...

  7. Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions.

    Science.gov (United States)

    Sawlekar, Rucha; Montefusco, Francesco; Kulkarni, Vishwesh V; Bates, Declan G

    2016-07-01

    We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs.

  8. HOMFLY polynomials in representation [3, 1] for 3-strand braids

    Science.gov (United States)

    Mironov, A.; Morozov, A.; Morozov, An.; Sleptsov, A.

    2016-09-01

    This paper is a new step in the project of systematic description of colored knot polynomials started in [1]. In this paper, we managed to explicitly find the inclusive Racah matrix, i.e. the whole set of mixing matrices in channels R ⊗3 -→ Q with all possible Q, for R = [3 , 1]. The calculation is made possible by the use of a newly-developed efficient highest-weight method, still it remains tedious. The result allows one to evaluate and investigate [3 , 1]-colored polynomials for arbitrary 3-strand knots, and this confirms many previous conjectures on various factorizations, universality, and differential expansions. We consider in some detail the next-to-twist-knots three-strand family ( n, -1 | 1 , -1) and deduce its colored HOMFLY. Also confirmed and clarified is the eigenvalue hypothesis for the Racah matrices, which promises to provide a shortcut to generic formulas for arbitrary representations.

  9. Hybrid fur rendering: combining volumetric fur with explicit hair strands

    DEFF Research Database (Denmark)

    Andersen, Tobias Grønbeck; Falster, Viggo; Frisvad, Jeppe Revall

    2016-01-01

    Hair is typically modeled and rendered using either explicitly defined hair strand geometry or a volume texture of hair densities. Taken each on their own, these two hair representations have difficulties in the case of animal fur as it consists of very dense and thin undercoat hairs in combination...... with coarse guard hairs. Explicit hair strand geometry is not well-suited for the undercoat hairs, while volume textures are not well-suited for the guard hairs. To efficiently model and render both guard hairs and undercoat hairs, we present a hybrid technique that combines rasterization of explicitly...... defined guard hairs with ray marching of a prismatic shell volume with dynamic resolution. The latter is the key to practical combination of the two techniques, and it also enables a high degree of detail in the undercoat. We demonstrate that our hybrid technique creates a more detailed and soft fur...

  10. Working with Separation

    Science.gov (United States)

    Krugman, Dorothy C.

    1971-01-01

    Discusses the role of the caseworker in providing support to children experiencing separation from their families and emphasizes the need to recognize that there are differences between those separation experiences dictated by the needs of children and those dictated by arbitrary or noncasework factors. (AJ)

  11. Separation anxiety disorder

    NARCIS (Netherlands)

    Nauta, M.H.; Emmelkamp, P.M.G.; Sturmey, P.; Hersen, M.

    2012-01-01

    Separation anxiety disorder (SAD) is the only anxiety disorder that is specific to childhood; however, SAD has hardly ever been addressed as a separate disorder in clinical trials investigating treatment outcome. So far, only parent training has been developed specifically for SAD. This particular t

  12. Social Separation in Monkeys.

    Science.gov (United States)

    Mineka, Susan; Suomi, Stephen J.

    1978-01-01

    Reviews phenomena associated with social separation from attachment objects in nonhuman primates. Evaluates four theoretical treatments of separation in light of existing data: Bowlby's attachment-object-loss theory, Kaufman's conservation-withdrawal theory, Seligman's learned helplessness theory, and Solomon and Corbit's opponent-process theory.…

  13. Nonterminal Separating Macro Grammars

    NARCIS (Netherlands)

    Hogendorp, Jan Anne; Asveld, P.R.J.; Nijholt, A.; Verbeek, Leo A.M.

    1987-01-01

    We extend the concept of nonterminal separating (or NTS) context-free grammar to nonterminal separating $m$-macro grammar where the mode of derivation $m$ is equal to "unrestricted". "outside-in' or "inside-out". Then we show some (partial) characterization results for these NTS $m$-macro grammars.

  14. 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.

  15. What Governs the Unzipping Process of Double-Stranded DNA

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Feng; LEI Xiao-Ling; FANG Hai-Ping

    2006-01-01

    @@ The unzipping process of double-stranded DNA is analysed using a discrete model at the base level [Chin. Phys.Lett. 22 (2005)1540]. The numerical results are consistent with the experimental observations on the force-displacement behaviour including the sequence-dependence. We find that the hydrogen bond interaction in a base pair is crucially important to the force-displacement profile.

  16. Electrostatic Origin of Single-Stranded Genome Packing in Viruses

    Science.gov (United States)

    Belyi, Vladimir; Muthukumar, M.

    2006-03-01

    We develop an electrostatic model for single-stranded RNA/DNA viruses that bind their genome via highly basic semiflexible peptide arms. We show that genome-capsid binding is dominated by non-specific electrostatic interactions, rather than actual amino-acid content. Proposed model explains many universal features of the viral genome. Good agreement is found with wide range of qualified wild-type and mutant viruses.

  17. Five strands of math tasks big book : grades pk-2

    CERN Document Server

    Reed, Nat; Forest, Chris

    2009-01-01

    For grades PK-2, our Common Core State Standards-based resource meets the five strands of math concepts addressed by the NCTM standards and encourages the students to learn and review the concepts in unique ways. Included are challenging problem-solving tasks which will push the boundaries of critical thought and demonstrate to students the importance of mathematical problems in Number & Operations, Geometry, Measurement, Data Analysis & Probability and Algebra using real world situations.

  18. Five strands of math drills big book : grades PK-2

    CERN Document Server

    Reed, Nat; Forest, Chris

    2011-01-01

    For grades PK-2, our Common Core State Standards-based resource meets the five strands of math concepts addressed by the NCTM standards and encourages the students to review the concepts in unique ways. Included are warm-up and timed drill activities which will push the boundaries of critical thought and demonstrate to students the importance of mathematical problems in Number & Operations, Geometry, Measurement, Data Analysis & Probability and Algebra using real world situations.

  19. Spiral microfluidic nanoparticle separators

    Science.gov (United States)

    Bhagat, Ali Asgar S.; Kuntaegowdanahalli, Sathyakumar S.; Dionysiou, Dionysios D.; Papautsky, Ian

    2008-02-01

    Nanoparticles have potential applications in many areas such as consumer products, health care, electronics, energy and other industries. As the use of nanoparticles in manufacturing increases, we anticipate a growing need to detect and measure particles of nanometer scale dimensions in fluids to control emissions of possible toxic nanoparticles. At present most particle separation techniques are based on membrane assisted filtering schemes. Unfortunately their efficiency is limited by the membrane pore size, making them inefficient for separating a wide range of sizes. In this paper, we propose a passive spiral microfluidic geometry for momentum-based particle separations. The proposed design is versatile and is capable of separating particulate mixtures over a wide dynamic range and we expect it will enable a variety of environmental, medical, or manufacturing applications that involve rapid separation of nanoparticles in real-world samples with a wide range of particle components.

  20. 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.

  1. Structure of the guide-strand-containing argonaute silencing complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yanli; Sheng, Gang; Juranek, Stefan; Tuschl, Thomas; Patel, Dinshaw J. (MSKCC); (HHMI)

    2009-01-15

    The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

  2. A novel bio-sensor based on DNA strand displacement.

    Directory of Open Access Journals (Sweden)

    Xiaolong Shi

    Full Text Available DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called "DNA neurons" are achieved, in which a "smart" way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The "DNA neuron" is bistable, that is, it can sense DNA molecules as input signals, and release "negative" or "positive" signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized "DNA neurons", which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.

  3. 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.

  4. Minimum Quench Energy and Early Quench Development in NbTi Superconducting Strands

    CERN Document Server

    Breschi, M; Boselli, M; Bottura, Luca; Devred, Arnaud; Ribani, P L; Trillaud, F

    2007-01-01

    The stability of superconducting wires is a crucial task in the design of safe and reliable superconducting magnets. These magnets are prone to premature quenches due to local releases of energy. In order to simulate these energy disturbances, various heater technologies have been developed, such as coated tips, graphite pastes, and inductive coils. The experiments studied in the present work have been performed using a single-mode diode laser with an optical fiber to illuminate the superconducting strand surface. Minimum quench energies and voltage traces at different magnetic flux densities and transport currents have been measured on an LHC-type, Cu/NbTi wire bathed in pool boiling helium I. This paper deals with the numerical analysis of the experimental data. In particular, a coupled electromagnetic and thermal model has been developed to study quench development and propagation, focusing on the influence of heat exchange with liquid helium.

  5. Molecular detection of bacterial pathogens using microparticle enhanced double-stranded DNA probes.

    Science.gov (United States)

    Riahi, Reza; Mach, Kathleen E; Mohan, Ruchika; Liao, Joseph C; Wong, Pak Kin

    2011-08-15

    Rapid, specific, and sensitive detection of bacterial pathogens is essential toward clinical management of infectious diseases. Traditional approaches for pathogen detection, however, often require time-intensive bacterial culture and amplification procedures. Herein, a microparticle enhanced double-stranded DNA probe is demonstrated for rapid species-specific detection of bacterial 16S rRNA. In this molecular assay, the binding of the target sequence to the fluorophore conjugated probe thermodynamically displaces the quencher probe and allows the fluorophore to fluoresce. By incorporation of streptavidin-coated microparticles to localize the biotinylated probes, the sensitivity of the assay can be improved by 3 orders of magnitude. The limit of detection of the assay is as few as eight bacteria without target amplification and is highly specific against other common pathogens. Its applicability toward clinical diagnostics is demonstrated by directly identifying bacterial pathogens in urine samples from patients with urinary tract infections.

  6. SCAI promotes DNA double-strand break repair in distinct chromosomal contexts

    DEFF Research Database (Denmark)

    Hansen, Rebecca Kring; Mund, Andreas; Poulsen, Sara Lund;

    2016-01-01

    DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions, whose accurate repair by non-homologous end-joining (NHEJ) or homologous recombination (HR) is crucial for genome integrity and is strongly influenced by the local chromatin environment. Here, we identify SCAI (suppressor of cancer...... cell invasion) as a 53BP1-interacting chromatin-associated protein that promotes the functionality of several DSB repair pathways in mammalian cells. SCAI undergoes prominent enrichment at DSB sites through dual mechanisms involving 53BP1-dependent recruitment to DSB-surrounding chromatin and 53BP1......-independent accumulation at resected DSBs. Cells lacking SCAI display reduced DSB repair capacity, hypersensitivity to DSB-inflicting agents and genome instability. We demonstrate that SCAI is a mediator of 53BP1-dependent repair of heterochromatin-associated DSBs, facilitating ATM kinase signalling at DSBs...

  7. Spectroscopic characterization of the interaction of phenosafranin and safranin O with double stranded, heat denatured and single stranded calf thymus DNA.

    Science.gov (United States)

    Saha, Ishita; Kumar, Gopinatha Suresh

    2011-01-01

    Interaction of phenosafranin and safranin O with double stranded, heat denatured and single stranded calf thymus DNA has been studied by fluorescence, absorbance and circular dichroic techniques. Binding to the double stranded and heat denatured DNA conformations induced strong quenching in the fluorescence spectra of both dyes. Linear Scatchard plots indicated the binding to be of one type and the affinity evaluated to be of the order of 10(5) M(-1) with double stranded and heat denatured DNAs. Fluorescence quenching was much weaker with the single stranded DNA and the binding affinity was one order lower. Ferrocyanide quenching studies revealed that the fluorescence emission of the dye molecules bound to the double stranded and heat denatured DNAs was quenched much less compared to that bound to the single stranded DNA. Further, there was significant emission polarization for the bound dyes and strong energy transfer from the DNA base pairs to the dye molecules indicating intercalative binding. Salt dependence of the binding phenomenon revealed that electrostatic forces have significant role in the binding process. The intercalation of these molecules to double stranded and heat denatured DNA and simple stacking to single strands was proved by these fluorescence techniques. Support to the fluorescence results have been derived from absorption and circular dichroic results. Phenosafranin was revealed to be a stronger binding species compared to safranin O.

  8. Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea

    Science.gov (United States)

    Pyenson, Nicholas D.; Gutstein, Carolina S.; Parham, James F.; Le Roux, Jacobus P.; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M.; Velez-Juarbe, Jorge; Santelli, Cara M.; Rogers, David Rubilar; Cozzuol, Mario A.; Suárez, Mario E.

    2014-01-01

    Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities. PMID:24573855

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

    Science.gov (United States)

    Monnet, Jordan; Kozelka, Jiří

    2012-10-01

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

  10. Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea.

    Science.gov (United States)

    Pyenson, Nicholas D; Gutstein, Carolina S; Parham, James F; Le Roux, Jacobus P; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M; Velez-Juarbe, Jorge; Santelli, Cara M; Rogers, David Rubilar; Cozzuol, Mario A; Suárez, Mario E

    2014-04-22

    Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities.

  11. Complete mitochondrial genome of Locusta migratoria migratoria (Orthoptera: Oedipodidae): three tRNA-like sequences on the N-strand.

    Science.gov (United States)

    Ye, Hai-Yan; Xiao, Li-Li; Zhou, Zhi-Jun; Huang, Yuan

    2012-02-01

    The complete 16053 bp mitochondrial genome (mitogenome) sequence of Locusta migratoria migratoria has been determined. This mitogenome contains the base compositional biases and codon usage typical of metazoans, and the RSCU values indicate a negative correlation with the C and G contents in codon. The orientation and gene order of the L. migratoria migratoria is identical to Locusta migratoria migratoiodes. An unusual feature of the L. migratoria migratoria mitogenome is the presence of three tRNA-like structures on the N-strand: one tRNA(Ile)-like and two tRNA(Leu(CUN))-like sequences. The tRNA-like sequences have proper folding structures and anticodons sequences. Two repeated DNA sequences, Rpt I and Rpt II, were found in the A+T-rich region of the L. migratoria migratoria mitogenome. Both repeated sequences have various features. In the 5' region of Rpt I, a 51 bp fragment is localized in the srRNA gene; and there are two tandemly sub-repeated DNA sequences (sub-Rpts), Rpt 1-4, within Rpt I and Rpt II. One stem-loop structure on the N-strand that may be involved in the N-strand replication initiation was found in the A+T-rich region.

  12. Bottlenose dolphin (Tursiops truncatus) strandings in South Carolina, 1992-1996

    OpenAIRE

    McFee, Wayne E.; Hopkins-Murphy, Sally R.

    2002-01-01

    From 1992 to 1996, 153 bottlenose dolphin stranded in South Carolina, accounting for 73% of all marine mammal strandings during this period. The objectives of our study were to evaluate data from these strandings to deter-mine 1) annual trends in strandings, 2) seasonal and spatial distribution trends, 3) life history parameters such as sex ratio and age classes, 3) seasonal trends in reproduction, and 4) the extent to which humans have played a role in causing these strandings (human inter-a...

  13. Cetacean stranding records in the Turkish Western Black Sea coast during October 2012 - September 2013

    Directory of Open Access Journals (Sweden)

    Arda M. Tonay

    2016-11-01

    Full Text Available Between October 2012 and September 2013, a research has been conducted on marine mammal strandings on Turkish western Black Sea coast. In total, 54 stranded cetaceans were found, which included 22 bottlenose dolphins (41%, 19 harbour porpoises (35%, 11 common dolphins (20%, and 4% unidentified individuals. Most strandings were observed in May and June. Bycaught carcases were found especially in April, June and July. The aim of the study is to collect first-hand data on the monthly stranding rates in order to understand the seasonal variation of stranding cases in a year.

  14. Experimental study on the 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 superconducting parallel conductors were experimentally investigated by using NbTi multifilamentary strands with a rectangular cross section. We prepared the simple situation that was supposed in the previous theoretical study (M Iwakuma et al 2002 Supercond. Sci. Technol. 15 1525-36). The two insulated strands were sparsely co-wound into one-layer solenoidal coils. They were transposed only once and soldered at both ends. The ac losses in the sample coils were measured by a pick-up-coil method by applying uniform ac magnetic field parallel to the coil axis and comparing it with the theoretical results. The validity of the theoretical expressions derived in the previous paper was verified by the quantitative agreement with experiment in all the aspects, i.e. the dependencies on frequency, field amplitude and the deviation length in transposition in both the non-saturation and saturation cases and also the threshold condition between them. The results obtained support the t...

  15. The isothermal amplification detection of double-stranded DNA based on a double-stranded fluorescence probe.

    Science.gov (United States)

    Shi, Chao; Shang, Fanjin; Pan, Mei; Liu, Sen; Ma, Cuiping

    2016-06-15

    Here we have developed a novel method of isothermal amplification detection of double-stranded DNA (dsDNA) based on double-stranded fluorescence probe (ds-probe). Target dsDNA repeatedly generated single-stranded DNA (ssDNA) with polymerase and nicking enzyme. The ds-probe as a primer hybridized with ssDNA and extended to its 5'-end. The displaced ssDNA served as a new detection target to initiate above-described reaction. Meanwhile, the extended ds-probe could dynamically dissociate from ssDNA and self-hybridize, converting into a turn-back structure to initiate another amplification reaction. In particular, the ds-probe played a key role in the entire experimental process, which not only was as a primer but also produced the fluorescent signal by an extension and displacement reaction. Our method could detect the pBluescript II KS(+) plasmid with a detection limit of 2.3 amol, and it was also verified to exhibit a high specificity, even one-base mismatch. Overall, it was a true isothermal dsDNA detection strategy with a strongly anti-jamming capacity and one-pot, only requiring one ds-probe, which greatly reduced the cost and the probability of contamination. With its advantages, the approach of dsDNA detection will offer a promising tool in the field of point-of-care testing (POCT).

  16. Causal and causally separable processes

    Science.gov (United States)

    Oreshkov, Ognyan; Giarmatzi, Christina

    2016-09-01

    The idea that events are equipped with a partial causal order is central to our understanding of physics in the tested regimes: given two pointlike events A and B, either A is in the causal past of B, B is in the causal past of A, or A and B are space-like separated. Operationally, the meaning of these order relations corresponds to constraints on the possible correlations between experiments performed in the vicinities of the respective events: if A is in the causal past of B, an experimenter at A could signal to an experimenter at B but not the other way around, while if A and B are space-like separated, no signaling is possible in either direction. In the context of a concrete physical theory, the correlations compatible with a given causal configuration may obey further constraints. For instance, space-like correlations in quantum mechanics arise from local measurements on joint quantum states, while time-like correlations are established via quantum channels. Similarly to other variables, however, the causal order of a set of events could be random, and little is understood about the constraints that causality implies in this case. A main difficulty concerns the fact that the order of events can now generally depend on the operations performed at the locations of these events, since, for instance, an operation at A could influence the order in which B and C occur in A’s future. So far, no formal theory of causality compatible with such dynamical causal order has been developed. Apart from being of fundamental interest in the context of inferring causal relations, such a theory is imperative for understanding recent suggestions that the causal order of events in quantum mechanics can be indefinite. Here, we develop such a theory in the general multipartite case. Starting from a background-independent definition of causality, we derive an iteratively formulated canonical decomposition of multipartite causal correlations. For a fixed number of settings and

  17. Radiochemical separation of Cobalt

    NARCIS (Netherlands)

    Erkelens, P.C. van

    1961-01-01

    A method is described for the radiochemical separation of cobalt based on the extraordinary stability of cobalt diethyldithiocarbamate. Interferences are few; only very small amounts of zinc and iron accompany cobalt, which is important in neutron-activation analysis.

  18. Electroextraction separation of dyestuffs

    Energy Technology Data Exchange (ETDEWEB)

    Luo, G.S.; Yu, M.J.; Jiang, W.B.; Zhu, S.L.; Dai, Y.Y. [Tsinghua Univ., Beijing (China). Dept. of Chemical Engineering

    1999-03-01

    Electroseparation technologies have prospects for significant growth well into the next century. Electroextraction, a coupled separation technique of solvent extraction with electrophoresis, was used to remove dyestuffs from their aqueous stream. A study on the characteristics of the separation technique was carried out with n-butanol/acid-chrom blue K/water and n-butanol/methyl blue/water as working systems. A continuous separation equipment was designed and sued in this work. The influences of two-phase flow, field strength, and concentration of the feed on the recovery of solute were studied. The results showed that much higher recovery of solute with less solvent consumption could be achieved by using this technique to remove dyes from their aqueous streams, especially for the separation of the dilute solution. When the field strength is increased, the recovery and mass flux increase. When the feed flow rate and the initial solute concentration are increased, the recovery decreases and the mass flux increases.

  19. Shoulder separation - aftercare

    Science.gov (United States)

    ... and top of your shoulder blade A severe shoulder separation You may need surgery right away if you have: Numbness in your fingers Cold fingers Muscle weakness in your arm Severe deformity of the joint

  20. Radiochemical separation of Cobalt

    NARCIS (Netherlands)

    Erkelens, P.C. van

    1961-01-01

    A method is described for the radiochemical separation of cobalt based on the extraordinary stability of cobalt diethyldithiocarbamate. Interferences are few; only very small amounts of zinc and iron accompany cobalt, which is important in neutron-activation analysis.

  1. Safe Separators for Treewidth

    NARCIS (Netherlands)

    Bodlaender, H.L.; Koster, A.M.C.A.

    2003-01-01

    A set of vertices S Í V is called a safe separator for treewidth, if S is a separator of G, and the treewidth of G equals the maximum of the treewidth over all connected components W of G - S of the graph, obtained by making S a clique in the subgraph of G, induced by W È S. We show that such safe s

  2. Hydrogen separation process

    Science.gov (United States)

    Mundschau, Michael [Longmont, CO; Xie, Xiaobing [Foster City, CA; Evenson, IV, Carl; Grimmer, Paul [Longmont, CO; Wright, Harold [Longmont, CO

    2011-05-24

    A method for separating a hydrogen-rich product stream from a feed stream comprising hydrogen and at least one carbon-containing gas, comprising feeding the feed stream, at an inlet pressure greater than atmospheric pressure and a temperature greater than 200.degree. C., to a hydrogen separation membrane system comprising a membrane that is selectively permeable to hydrogen, and producing a hydrogen-rich permeate product stream on the permeate side of the membrane and a carbon dioxide-rich product raffinate stream on the raffinate side of the membrane. A method for separating a hydrogen-rich product stream from a feed stream comprising hydrogen and at least one carbon-containing gas, comprising feeding the feed stream, at an inlet pressure greater than atmospheric pressure and a temperature greater than 200.degree. C., to an integrated water gas shift/hydrogen separation membrane system wherein the hydrogen separation membrane system comprises a membrane that is selectively permeable to hydrogen, and producing a hydrogen-rich permeate product stream on the permeate side of the membrane and a carbon dioxide-rich product raffinate stream on the raffinate side of the membrane. A method for pretreating a membrane, comprising: heating the membrane to a desired operating temperature and desired feed pressure in a flow of inert gas for a sufficient time to cause the membrane to mechanically deform; decreasing the feed pressure to approximately ambient pressure; and optionally, flowing an oxidizing agent across the membrane before, during, or after deformation of the membrane. A method of supporting a hydrogen separation membrane system comprising selecting a hydrogen separation membrane system comprising one or more catalyst outer layers deposited on a hydrogen transport membrane layer and sealing the hydrogen separation membrane system to a porous support.

  3. Separation techniques: Chromatography

    OpenAIRE

    Coskun, Ozlem

    2016-01-01

    Chromatography is an important biophysical technique that enables the separation, identification, and purification of the components of a mixture for qualitative and quantitative analysis. Proteins can be purified based on characteristics such as size and shape, total charge, hydrophobic groups present on the surface, and binding capacity with the stationary phase. Four separation techniques based on molecular characteristics and interaction type use mechanisms of ion exchange, surface adsorp...

  4. Distal humeral epiphyseal separation.

    Science.gov (United States)

    Moucha, Calin S; Mason, Dan E

    2003-10-01

    Distal humeral epiphyseal separation is an uncommon injury that is often misdiagnosed upon initial presentation. To make a timely, correct diagnosis, the treating physician must have a thorough understanding of basic anatomical relationships and an awareness of the existence of this injury. This is a case of a child who sustained a separation of the distal humeral epiphysis, as well as multiple other bony injuries, secondary to child abuse.

  5. Small Rad51 and Dmc1 Complexes Often Co-occupy Both Ends of a Meiotic DNA Double Strand Break.

    Directory of Open Access Journals (Sweden)

    M Scott Brown

    2015-12-01

    Full Text Available The Eukaryotic RecA-like proteins Rad51 and Dmc1 cooperate during meiosis to promote recombination between homologous chromosomes by repairing programmed DNA double strand breaks (DSBs. Previous studies showed that Rad51 and Dmc1 form partially overlapping co-foci. Here we show these Rad51-Dmc1 co-foci are often arranged in pairs separated by distances of up to 400 nm. Paired co-foci remain prevalent when DSBs are dramatically reduced or when strand exchange or synapsis is blocked. Super-resolution dSTORM microscopy reveals that individual foci observed by conventional light microscopy are often composed of two or more substructures. The data support a model in which the two tracts of ssDNA formed by a single DSB separate from one another by distances of up to 400 nm, with both tracts often bound by one or more short (about 100 nt Rad51 filaments and also by one or more short Dmc1 filaments.

  6. Use of 1-4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand.

    Science.gov (United States)

    Pang, Yuan-Ping

    2015-02-06

    1-4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6-12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1-4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1-4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA)3-NH2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

  7. Inmunoterapia local Local immunotherapy

    Directory of Open Access Journals (Sweden)

    E. Lasa

    2003-01-01

    Full Text Available La inmunoterapia específica, junto con la evitación del alergeno y el tratamiento sintomático, forma parte del tratamiento de la patología alérgica. La modalidad más antigua, más conocida y mejor estudiada es la inmunoterapia subcutánea (ITSC, cuya eficacia tanto a corto como a largo plazo, ha sido ampliamente demostrada en numerosos estudios. Sin embargo, a pesar de haberse demostrado segura, no está exenta de efectos adversos y precisa ser administrada bajo supervisión de personal médico. Esto ha animado a buscar nuevas vías de administración de eficacia similar, con un buen perfil de seguridad, y de buena cumplimentación por parte del paciente. De las distintas alternativas estudiadas la más relevante es la inmunoterapia sublingual (ITSL. En ésta, se administra el antígeno en forma de gotas debajo de la lengua. Existen diferentes pautas de administración en función del alergeno implicado. La dosis óptima de tratamiento está aún sin determinar, hallándose en este momento en un rango amplio de dosis respecto a la inmunoterapia subcutánea. Su mecanismo de acción es poco conocido aunque en diversos estudios se han observado cambios inmunológicos. La ITSL ha mostrado un buen perfil de seguridad con escasos efectos secundarios, habitualmente de carácter local. Asimismo se han realizado distintos ensayos clínicos en los que se ha demostrado su eficacia en el tratamiento de la alergia respiratoria tanto en niños como en adultos. Por ello, aunque aún existen datos sin resolver respecto a esta vía de administración de inmunoterapia, ha sido propuesta por la OMS como una alternativa válida a la ITSC.Specific immunotherapy, together with avoidance of the allergen and symptomatic treatment, forms part of the treatment of allergic pathology. The oldest, best known and most studied form is subcutaneous immunotherapy (SCIT, whose efficacy, both in the short and the long term, has been widely demonstrated in numerous studies

  8. Documenting localities

    CERN Document Server

    Cox, Richard J

    1996-01-01

    Now in paperback! Documenting Localities is the first effort to summarize the past decade of renewed discussion about archival appraisal theory and methodology and to provide a practical guide for the documentation of localities.This book discusses the continuing importance of the locality in American historical research and archival practice, traditional methods archivists have used to document localities, and case studies in documenting localities. These chapters draw on a wide range of writings from archivists, historians, material culture specialists, historic preservationists

  9. Single-stranded heteroduplex intermediates in λ Red homologous recombination

    Directory of Open Access Journals (Sweden)

    Zhang Youming

    2010-07-01

    Full Text Available Abstract Background The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. Results Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting the fact that Redα exonuclease activity requires a 5' phosphorylated end, or is blocked by phosphothioates. Using these substrates, we found that the most efficient configuration for dsDNA recombination occurred when the strand that can prime Okazaki-like synthesis contained both homology regions on the same ssDNA molecule. Furthermore, we show that Red recombination requires replication of the target molecule. Conclusions Hence we propose a new model for dsDNA recombination, termed 'beta' recombination, based on the formation of ssDNA heteroduplexes at the replication fork. Implications of the model were tested using (i an in situ assay for recombination, which showed that recombination generated mixed wild type and recombinant colonies; and (ii the predicted asymmetries of the homology arms, which showed that recombination is more sensitive to non-homologies attached to 5' than 3' ends. Whereas beta recombination can generate deletions in target BACs of at least 50 kb at about the same efficiency as small deletions, the converse event of insertion is very sensitive to increasing size. Insertions up to 3 kb are most efficiently achieved using beta recombination, however at greater sizes, an alternative Red-mediated mechanism(s appears to be equally efficient. These findings define a new intermediate in homologous recombination, which also has practical implications for recombineering with the Red proteins.

  10. Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes.

    Directory of Open Access Journals (Sweden)

    Maria E Morales

    Full Text Available Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR and single strand annealing (SSA, which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the "error prone" non-homologous end joining (alt-NHEJ while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.

  11. Reachability bounds for chemical reaction networks and strand displacement systems.

    Science.gov (United States)

    Condon, Anne; Kirkpatrick, Bonnie; Maňuch, Ján

    2014-01-01

    Chemical reaction networks (CRNs) and DNA strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. However, in order for some DSDs in the literature to behave in an expected manner, the initial number of copies of some reagents is required to be fixed. In this paper we show that, when multiple copies of all initial molecules are present, general types of CRNs and DSDs fail to work correctly if the length of the shortest sequence of reactions needed to produce any given molecule exceeds a threshold that grows polynomially with attributes of the system.

  12. Strand Breaks in DNA Samples Induced with LASERIX

    Science.gov (United States)

    Zielbauer, B.; Habib, J.; Kazamias, S.; Guilbaud, O.; Pittman, M.; Ros, D.; Hervé du Penhoat, M.-A.; Touati, A.; Sech, C. Le; Porcel, E.; Lacombe, S.

    Samples of plasmid DNA were irradiated with pulsed 18.9 nm radiation originating from a Mo X-ray laser pumped in GRIP configuration at the LASERIX facility [1]. Surface doses of up to 500 kGray were delivered with a repetition rate of 10 Hz and average pulse energy of 200 nJ. The occurrence of single and double strand breaks not present in controls having undergone the same treatment except for the XRL irradiation can be seen as a clear effect of the XRL irradiation. This confirms the role of direct effects in DNA damages as previously seen with low energy ions [2, 3] and electrons.

  13. Organic Separation Test Results

    Energy Technology Data Exchange (ETDEWEB)

    Russell, Renee L.; Rinehart, Donald E.; Peterson, Reid A.

    2014-09-22

    Separable organics have been defined as “those organic compounds of very limited solubility in the bulk waste and that can form a separate liquid phase or layer” (Smalley and Nguyen 2013), and result from three main solvent extraction processes: U Plant Uranium Recovery Process, B Plant Waste Fractionation Process, and Plutonium Uranium Extraction (PUREX) Process. The primary organic solvents associated with tank solids are TBP, D2EHPA, and NPH. There is concern that, while this organic material is bound to the sludge particles as it is stored in the tanks, waste feed delivery activities, specifically transfer pump and mixer pump operations, could cause the organics to form a separated layer in the tank farms feed tank. Therefore, Washington River Protection Solutions (WRPS) is experimentally evaluating the potential of organic solvents separating from the tank solids (sludge) during waste feed delivery activities, specifically the waste mixing and transfer processes. Given the Hanford Tank Waste Treatment and Immobilization Plant (WTP) waste acceptance criteria per the Waste Feed Acceptance Criteria document (24590-WTP-RPT-MGT-11-014) that there is to be “no visible layer” of separable organics in the waste feed, this would result in the batch being unacceptable to transfer to WTP. This study is of particular importance to WRPS because of these WTP requirements.

  14. Separably injective Banach spaces

    CERN Document Server

    Avilés, Antonio; Castillo, Jesús M F; González, Manuel; Moreno, Yolanda

    2016-01-01

    This monograph contains a detailed exposition of the up-to-date theory of separably injective spaces: new and old results are put into perspective with concrete examples (such as l∞/c0 and C(K) spaces, where K is a finite height compact space or an F-space, ultrapowers of L∞ spaces and spaces of universal disposition). It is no exaggeration to say that the theory of separably injective Banach spaces is strikingly different from that of injective spaces. For instance, separably injective Banach spaces are not necessarily isometric to, or complemented subspaces of, spaces of continuous functions on a compact space. Moreover, in contrast to the scarcity of examples and general results concerning injective spaces, we know of many different types of separably injective spaces and there is a rich theory around them. The monograph is completed with a preparatory chapter on injective spaces, a chapter on higher cardinal versions of separable injectivity and a lively discussion of open problems and further lines o...

  15. Separation and isolation of BTV dsRNA segments and viral proteins.

    Science.gov (United States)

    Li, Joseph K-K; Huang, I-Jen; Hayama, Emiko

    2012-05-01

    Bluetongue virus (BTV) genome contains ten double-stranded RNA segments. The sequence of the plus strand of each of the BTV genomic double-stranded RNAs is the same as that of its mRNA, which encodes for a single viral protein, except the smallest S4 segment which can encode for two nonstructural proteins, primarily for the release assistance of the viral progeny. The separation and isolation of each BTV dsRNA segment and viral protein have provided extensive data related to its viral infection, pathology, suppression of host cellular functions, and eventual apoptosis of the infected host cells. This cytoplasmic virus is also an animal killer that costs the U.S. livestock industry at least $125 million yearly. However, this virus has no known effect on humans. Thus, it is very safe to carry out investigation with the virus, preferably in a BSL-2 laboratory.

  16. 75 FR 38977 - Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China: Notice of Amended...

    Science.gov (United States)

    2010-07-07

    ... International Trade Administration Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China... concrete steel wire strand (PC strand) from the People's Republic of China (PRC). On June 22, 2010, the ITC...-Stressed Concrete Steel Wire Strand from the People's Republic of China, USITC Pub. 4162, Inv. Nos....

  17. Mechanical behaviors of multi-filament twist superconducting strand under tensile and cyclic loading

    Science.gov (United States)

    Wang, Xu; Li, Yingxu; Gao, Yuanwen

    2016-01-01

    The superconducting strand, serving as the basic unit cell of the cable-in-conduit-conductors (CICCs), is a typical multi-filament twist composite which is always subjected to a cyclic loading under the operating condition. Meanwhile, the superconducting material Nb3Sn in the strand is sensitive to strain frequently relating to the performance degradation of the superconductivity. Therefore, a comprehensive study on the mechanical behavior of the strand helps understanding the superconducting performance of the strained Nb3Sn strands. To address this issue, taking the LMI (internal tin) strand as an example, a three-dimensional structural finite element model, named as the Multi-filament twist model, of the strand with the real configuration of the LMI strand is built to study the influences of the plasticity of the component materials, the twist of the filament bundle, the initial thermal residual stress and the breakage and its evolution of the filaments on the mechanical behaviors of the strand. The effective properties of superconducting filament bundle with random filament breakage and its evolution versus strain are obtained based on the damage theory of fiber-reinforced composite materials proposed by Curtin and Zhou. From the calculation results of this model, we find that the occurrence of the hysteresis loop in the cyclic loading curve is determined by the reverse yielding of the elastic-plastic materials in the strand. Both the initial thermal residual stress in the strand and the pitch length of the filaments have significant impacts on the axial and hysteretic behaviors of the strand. The damage of the filaments also affects the axial mechanical behavior of the strand remarkably at large axial strain. The critical current of the strand is calculated by the scaling law with the results of the Multi-filament twist model. The predicted results of the Multi-filament twist model show an acceptable agreement with the experiment.

  18. Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA.

    Science.gov (United States)

    Chakraborty, Kaushik; Bandyopadhyay, Sanjoy

    2015-01-07

    Molecular dynamics simulations of the single-stranded DNA oligomer (5'-CGCGAAT TCGCG-3') in aqueous solution have been carried out at different temperatures between 160 K and 300 K. The effects of temperature on the low-frequency vibrational spectrum and local structural arrangements of water molecules hydrating the DNA strand have been explored in detail. The low-frequency density of states distributions reveal that increasingly trapped transverse water motions play a dominant role in controlling the band corresponding to O⋯O⋯O bending or transverse oscillations of hydration water at supercooled temperatures. In addition, presence of a broad band around 260 (±20) cm(-1) under supercooled conditions indicates transformation from high density liquid-like structuring of hydration water at higher temperatures to that of a low density liquid at lower temperatures. It is found that long-range correlations between the supercooled hydration water molecules arise due to such local structural transition around the DNA oligomer.

  19. Mass Separation by Metamaterials.

    Science.gov (United States)

    Restrepo-Flórez, Juan Manuel; Maldovan, Martin

    2016-02-25

    Being able to manipulate mass flow is critically important in a variety of physical processes in chemical and biomolecular science. For example, separation and catalytic systems, which requires precise control of mass diffusion, are crucial in the manufacturing of chemicals, crystal growth of semiconductors, waste recovery of biological solutes or chemicals, and production of artificial kidneys. Coordinate transformations and metamaterials are powerful methods to achieve precise manipulation of molecular diffusion. Here, we introduce a novel approach to obtain mass separation based on metamaterials that can sort chemical and biomolecular species by cloaking one compound while concentrating the other. A design strategy to realize such metamaterial using homogeneous isotropic materials is proposed. We present a practical case where a mixture of oxygen and nitrogen is manipulated using a metamaterial that cloaks nitrogen and concentrates oxygen. This work lays the foundation for molecular mass separation in biophysical and chemical systems through metamaterial devices.

  20. Phaco slice and separate.

    Science.gov (United States)

    Arshinoff, S A

    1999-04-01

    Phaco slice and separate retains the advantages of the chopping techniques of Nagahara, Koch, and Fukasaku but replaces chopping or snapping with slicing across the center of the phaco-tip-stabilized nucleus using a Nagahara chopper and then repositioning the chopper to optimally separate the divided lens halves. As the lens is rotated in the capsular bag, small pieces of the nuclear pie are sliced off, separated, emulsified, and aspirated. Emulsification and aspiration can alternatively be left until most or all the slices have been made. This technique works with a broader range of lens densities than other chopping techniques and uses no sculpting and very little phaco time. The phaco time required for this technique is relatively independent of nuclear density compared with a sculpting technique.

  1. Membrane separation of hydrocarbons

    Science.gov (United States)

    Chang, Y. Alice; Kulkarni, Sudhir S.; Funk, Edward W.

    1986-01-01

    Mixtures of heavy oils and light hydrocarbons may be separated by passing the mixture through a polymeric membrane. The membrane which is utilized to effect the separation comprises a polymer which is capable of maintaining its integrity in the presence of hydrocarbon compounds and which has been modified by being subjected to the action of a sulfonating agent. Sulfonating agents which may be employed will include fuming sulfuric acid, chlorosulfonic acid, sulfur trioxide, etc., the surface or bulk modified polymer will contain a degree of sulfonation ranging from about 15 to about 50%. The separation process is effected at temperatures ranging from about ambient to about 100.degree. C. and pressures ranging from about 50 to about 1000 psig.

  2. G-Quadruplexes Light up Localized DNA Circuits.

    Science.gov (United States)

    Mendoza, Oscar; Mergny, Jean-Louis; Aimé, Jean-Pierre; Elezgaray, Juan

    2016-01-13

    DNA circuits tethered to nanoplatforms can perform cascade reactions for signal amplification. One DNA single strand activates a strand-displacement cascade generating numerous outputs, and therefore amplifying the signal. These localized circuits present, however, an important limitation: the spontaneous activation of the cascade reaction. Current methods to stabilize these circuits employ combination of protective DNA strands, which need to be removed to activate the device. This protection-deprotection process generates an important amount of unwanted side reactions. This is indeed an important limitation for the large potential application of these amplification circuits. In the present work, G-quadruplex DNA structures were used to stabilize localized DNA circuits. This new protocol generates nanoplatforms that no longer requires protective-deprotective systems and is therefore completely neutral to the sample. In addition, cations such as Pb(2+) or Ca(2+) can be also employed to activate the device enlarging the potential applications from biosensors devices to metal detector sensors.

  3. The variable routes of rafting: stranding dynamics of floating bull kelp Durvillaea antarctica (Fucales, Phaeophyceae) on beaches in the SE Pacific.

    Science.gov (United States)

    López, Boris A; Macaya, Erasmo C; Tala, Fadia; Tellier, Florence; Thiel, Martin

    2017-02-01

    Dispersal on floating seaweeds depends on availability, viability, and trajectories of the rafts. In the southern hemisphere, the bull kelp Durvillaea antarctica is one of the most common floating seaweeds, but phylogeographic studies had shown low connectivity between populations from continental Chile, which could be due to limitations in local supply and dispersal of floating kelps. To test this hypothesis, the spatiotemporal dynamics of kelp strandings were examined in four biogeographic districts along the Chilean coast (28°-42°S). We determined the biomass and demography of stranded individuals on 33 beaches for three subsequent years (2013, 2014, 2015) to examine whether rafting is restricted to certain districts and seasons (winter or summer). Stranded kelps were found on all beaches. Most kelps had only one stipe (one individual), although we also frequently found coalesced holdfasts with mature males and females, which would facilitate successful rafting dispersal, gamete release, and reproduction upon arrival. High biomasses of stranded kelps occurred in the northern-central (30°S-33°S) and southernmost districts (37°S-42°S), and lower biomasses in the northernmost (28°S-30°S) and southern-central districts (33°S-37°S). The highest percentages and sizes of epibionts (Lepas spp.), indicative of prolonged floating periods, were found on stranded kelps in the northernmost and southernmost districts. Based on these results, we conclude that rafting dispersal can vary regionally, being more common in the northernmost and southernmost districts, depending on intrinsic (seaweed biology) and extrinsic factors (shore morphology and oceanography) that affect local supply of kelps and regional hydrodynamics.

  4. The biomechanics of Kansal Separator: A ‘2 in 1’ self-secured orthodontic spring separator

    Science.gov (United States)

    Kumar, Arun; Kansal, Sudhanshu; Thareja, Vimal; Singh, Gurkeerat; Kumar, Piush

    2014-01-01

    Background: An important stage at the very beginning of orthodontic therapy is the separation of teeth where space is created for banding of the molars. A dislodged separator may create problems if ingested or it may get wedged between the adjacent teeth causing acute localized periodontitis. In order to overcome these shortcomings of conventional separators, the Kansal Separator was conceptualized. This separator has been designed as a single device that acts simultaneously on both mesial and distal aspects of tooth, causing adequate separation. In addition to separator's independent 2 in 1 action, the self-locking connecting bar prevents the premature dislodgement of the separator. Aim: To determine the force vectors produced by Kansal separator. Materials and Methods: A prototype model was created to study the forces produced. Results: The separator's unique design is based on sound biomechanical principles that explicate the proof of concept and allows the separator to be distinctly effective and efficient in variable clinical situations, thus amplifying its uniqueness. Discussion: The Kansal Separator, a 2 in 1 orthodontic tooth separator, has a unique design enabling the device to simultaneously separate the teeth on the mesial and distal aspect of the tooth to be banded. Conclusion: Kansal Separator's unique design is based on sound biomechanical principles that explicate the proof of concept and allows the separator to be distinctly effective and efficient in variable clinical situations, thus amplifying its uniqueness. PMID:24987658

  5. Gas separation membranes

    Science.gov (United States)

    Schell, William J.

    1979-01-01

    A dry, fabric supported, polymeric gas separation membrane, such as cellulose acetate, is prepared by casting a solution of the polymer onto a shrinkable fabric preferably formed of synthetic polymers such as polyester or polyamide filaments before washing, stretching or calendering (so called griege goods). The supported membrane is then subjected to gelling, annealing, and drying by solvent exchange. During the processing steps, both the fabric support and the membrane shrink a preselected, controlled amount which prevents curling, wrinkling or cracking of the membrane in flat form or when spirally wound into a gas separation element.

  6. Separation membrane development

    Energy Technology Data Exchange (ETDEWEB)

    Lee, M.W. [Savannah River Technology Center, Aiken, SC (United States)

    1998-08-01

    A ceramic membrane has been developed to separate hydrogen from other gases. The method used is a sol-gel process. A thin layer of dense ceramic material is coated on a coarse ceramic filter substrate. The pore size distribution in the thin layer is controlled by a densification of the coating materials by heat treatment. The membrane has been tested by permeation measurement of the hydrogen and other gases. Selectivity of the membrane has been achieved to separate hydrogen from carbon monoxide. The permeation rate of hydrogen through the ceramic membrane was about 20 times larger than Pd-Ag membrane.

  7. Separation techniques: Chromatography

    Science.gov (United States)

    Coskun, Ozlem

    2016-01-01

    Chromatography is an important biophysical technique that enables the separation, identification, and purification of the components of a mixture for qualitative and quantitative analysis. Proteins can be purified based on characteristics such as size and shape, total charge, hydrophobic groups present on the surface, and binding capacity with the stationary phase. Four separation techniques based on molecular characteristics and interaction type use mechanisms of ion exchange, surface adsorption, partition, and size exclusion. Other chromatography techniques are based on the stationary bed, including column, thin layer, and paper chromatography. Column chromatography is one of the most common methods of protein purification. PMID:28058406

  8. Learning Isometric Separation Maps

    CERN Document Server

    Vasiloglou, Nikolaos; Anderson, David V

    2008-01-01

    Maximum Variance Unfolding (MVU) and its variants have been very successful in embedding data-manifolds in lower dimensionality spaces, often revealing the true intrinsic dimensions. In this paper we show how to also incorporate supervised class information into an MVU-like method without breaking its convexity. We call this method the Isometric Separation Map and we show that the resulting kernel matrix can be used for a binary/multiclass Support Vector Machine in a semi-supervised (transductive) framework. We also show that the method always finds a kernel matrix that linearly separates the training data exactly without projecting them in infinite dimensional spaces.

  9. Separators for electrochemical cells

    Science.gov (United States)

    Carlson, Steven Allen; Anakor, Ifenna Kingsley

    2014-11-11

    Provided are separators for use in an electrochemical cell comprising (a) an inorganic oxide and (b) an organic polymer, wherein the inorganic oxide comprises organic substituents. Preferably, the inorganic oxide comprises an hydrated aluminum oxide of the formula Al.sub.2O.sub.3.xH.sub.2O, wherein x is less than 1.0, and wherein the hydrated aluminum oxide comprises organic substituents, preferably comprising a reaction product of a multifunctional monomer and/or organic carbonate with an aluminum oxide, such as pseudo-boehmite and an aluminum oxide. Also provided are electrochemical cells comprising such separators.

  10. Fibrillar structures formed by covalently bound, short, β-stranded peptides on self-assembled monolayers.

    Science.gov (United States)

    Dugger, Jason W; Webb, Lauren J

    2015-03-24

    The ability to maintain or reproduce biomolecular structures on inorganic substrates has the potential to impact diverse fields such as sensing and molecular electronics, as well as the study of biological self-assembly and structure-function relationships. Because the structure and self-assembly of biomolecules are exquisitely sensitive to their local chemical and electrostatic environment, the goal of reproducing or mimicking biological function in an abiological environment, including at a surface, is challenging. However, simple and well-characterized chemical modifications of prepared surfaces can be used to tune surface chemistry, structure, electrostatics, and reactivity of inorganic materials to facilitate biofunctionalization and function. Here, we describe the covalent attachment of 13-residue β-stranded peptides containing alkyne groups to a flat gold surface functionalized with an azide-terminated self-assembled monolayer through a Huisgen cycloaddition, or "click", reaction. The chemical composition and structural morphology of these surfaces were characterized using X-ray photoelectron spectroscopy, grazing incidence angle reflection-absorption infrared spectroscopy, surface circular dichroism, and atomic force microscopy. The surface-bound β-strands self-assemble into antiparallel β-sheets to form fibrillar structures 24.9 ± 1.6 nm in diameter and 2.83 ± 0.74 nm in height on the reactive surface. The results herein provide a platform for studying and controlling the self-assembly process of biomolecules into larger supermolecular structures while allowing tunable control through chemical functionalization of the surface. Interest in the mechanisms of formation of fibrillar structures has most commonly been associated with neurodegenerative diseases, such as Alzheimer's and Parkinson's, but fibrils may actually represent the thermodynamic low-energy conformation of a much larger class of peptides and proteins. The protocol developed here is an

  11. Binding by TRBP-dsRBD2 Does Not Induce Bending of Double-Stranded RNA.

    Science.gov (United States)

    Acevedo, Roderico; Evans, Declan; Penrod, Katheryn A; Showalter, Scott A

    2016-06-21

    Protein-nucleic acid interactions are central to a variety of biological processes, many of which involve large-scale conformational changes that lead to bending of the nucleic acid helix. Here, we focus on the nonsequence-specific protein TRBP, whose double-stranded RNA-binding domains (dsRBDs) interact with the A-form geometry of double-stranded RNA (dsRNA). Crystal structures of dsRBD-dsRNA interactions suggest that the dsRNA helix must bend in such a way that its major groove expands to conform to the dsRBD's binding surface. We show through isothermal titration calorimetry experiments that dsRBD2 of TRBP binds dsRNA with a temperature-independent observed binding affinity (KD ∼500 nM). Furthermore, a near-zero observed heat capacity change (ΔCp = 70 ± 40 cal·mol(-1)·K(-1)) suggests that large-scale conformational changes do not occur upon binding. This result is bolstered by molecular-dynamics simulations in which dsRBD-dsRNA interactions generate only modest bending of the RNA along its helical axis. Overall, these results suggest that this particular dsRBD-dsRNA interaction produces little to no change in the A-form geometry of dsRNA in solution. These results further support our previous hypothesis, based on extensive gel-shift assays, that TRBP preferentially binds to sites of nearly ideal A-form structure while being excluded from sites of local deformation in the RNA helical structure. The implications of this mechanism for efficient micro-RNA processing will be discussed.

  12. Activation of 2'-5' oligoadenylate synthetase by single-stranded and double-stranded RNA aptamers

    DEFF Research Database (Denmark)

    Hartmann, R; Norby, P L; Martensen, P M

    1998-01-01

    A number of small RNA molecules that are high affinity ligands for the 46-kDa form of human 2'-5' oligoadenylate synthetase have been identified by the SELEX method. Surface plasmon resonance analysis indicates that these RNAs bind to the enzyme with dissociation constants in the nanomolar range......-stranded RNA, can also be activated by RNA ligands with little secondary structure. Since 2'-5' oligoadenylate synthetase possesses no homology to other known RNA-binding proteins, the development of small specific ligands by SELEX should facilitate studies of RNA-protein interactions and may reveal novel...

  13. Protection of DNA strand breakage by radiation exposure

    Energy Technology Data Exchange (ETDEWEB)

    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{sub 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 {gamma}-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

  14. Charge Migration in DNA: A Double Stranded Model

    Institute of Scientific and Technical Information of China (English)

    BAO, Han; LU, Jing; FAN, Kang-Nian

    2006-01-01

    In particular, charge migration phenomena in DNA have attracted much interest because of relevance to the generation of damage and mutations which play important roles in most of life processes. In this paper a theory method was presented in which the DNA chain was treated as a double-stranded system, and the charge migration in DNA based on the donor-bridge-acceptor system was investigated by this model. After having obtained the Hamiltonian, the effects of the surrounding were explained and calculated. The double-strand calculation could lead to good exponential decay curves and this time two different falloff parameters were found respectively before and after 3 or 4 AT base pair bridge lengths as prediction. Lately theoretical study showed this result by addition of more parameter, and sequence effect was then concentrated on. The difference of transfer integral caused the different decay rate of unlike sequences, but bridge length was still proved to be the main factor on the decay rates.

  15. The RNA synthesis machinery of negative-stranded RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-15

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

  16. 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.

  17. Single-Stranded DNA Curtains for Studying Homologous Recombination.

    Science.gov (United States)

    Ma, C J; Steinfeld, J B; Greene, E C

    2017-01-01

    Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51. © 2017 Elsevier Inc. All rights reserved.

  18. Tip Heater for Minimum Quench Energy Measurements on Superconducting Strands

    CERN Document Server

    Bauer, P; Oberli, L R

    1999-01-01

    Superconducting strands can be characterized by their Minimum Quench Energy (MQE), i.e. the minimum heat pulse needed to trigger a quench in operation conditions (field, temperature, current), in the limit of a (temporally and spatially) d-shaped disturbance. The sub-mm/µs range of perturbation space has only recently been achieved using the electrical graphite-paste heater technique [1]. The present work has put this technique into practice for the strands of the LHC main magnets, which are designed to operate at 1.9K in peak fields of up to 9T [1]. No way has been found yet to calibrate MQE measurements. To make relative statements on the MQE of different samples possible, the reproducibility of the measurements was emphasized. First heater prototypes did not come up to this stipulation. Finally the tip-heater configuration was found to meet the requirements. It generates a heat pulse in a thin resistive graphite paste deposit on top of a small tip that is pressed against the sample with a clamp. The clamp...

  19. Disseminated mycobacteriosis in a stranded loggerhead sea turtle (Caretta caretta).

    Science.gov (United States)

    Nardini, Giordano; Florio, Daniela; Di Girolamo, Nicola; Gustinelli, Andrea; Quaglio, Francesco; Fiorentini, Laura; Leopardi, Stefania; Fioravanti, Maria Letizia

    2014-06-01

    A loggerhead sea turtle (Caretta caretta) was found stranded alive along the Adriatic coast close to Ancona, Italy, displaying obtundation, tachypnea, and increased respiratory effort. It died a few hours after admission, and a postmortem examination was immediately performed. Miliary yellowish nodules were evident in the liver, and a lower number in the heart, stomach, and gut wall. Hundreds of whitish nodules were scattered in the lungs, with the majority of the pulmonary parenchyma being replaced by the lesions. Histologically, all nodular lesions consisted of a small central area of necrosis with acid-fast bacilli surrounded by epithelioid cells, macrophages, and lymphocytes. Giant cells were found in the spleen and the liver. Kidneys, lungs, liver, spleen, brain, and skin lesions were inoculated aseptically onto general isolation media and selective isolation media for mycobacteria. The isolate showed a restriction pattern identical to Mycobacterium chelonae by polymerase chain reaction-restriction fragment length polymorphism. To the best of the authors' knowledge, this is the first description of a disseminated infection caused by a potentially pathogenic mycobacteria in a stranded, free-ranging loggerhead sea turtle. Veterinary staff and biologists who handle sea turtles with suspected mycobacterial disease should protect themselves appropriately.

  20. Separation vortices and pattern formation

    DEFF Research Database (Denmark)

    Andersen, Anders Peter; Bohr, Tomas; Schnipper, Teis

    2010-01-01

    In this paper examples are given of the importance of flow separation for fluid patterns at moderate Reynolds numbers—both in the stationary and in the time-dependent domain. In the case of circular hydraulic jumps, it has been shown recently that it is possible to generalise the Prandtl–Kármán–P...... results for the vortex patterns behind a flapping foil in a flowing soap film, which shows the interaction and competition between the vortices shed from the round leading edge (like the von Kármán vortex street) and those created at the sharp trailing edge.......-time evolution of the sand ripple pattern, which has the surprising features that it breaks the local sand conservation and has long-range interaction, features that can be underpinned by experiments. Very similar vortex dynamics takes place around oscillating structures such as wings and fins. Here, we present...

  1. Nonadditivity in the recognition of single-stranded DNA by the schizosaccharomyces pombe protection of telomeres 1 DNA-binding domain, Pot1-DBD.

    Science.gov (United States)

    Croy, Johnny E; Altschuler, Sarah E; Grimm, Nicole E; Wuttke, Deborah S

    2009-07-28

    The Schizosaccharomyces pombe protection of telomeres 1 (SpPot1) protein recognizes the 3' single-stranded ends of telomeres and provides essential protective and regulatory functions. The ssDNA-binding activity of SpPot1 is conferred by its ssDNA-binding domain, Pot1-DBD (residues 1-389), which can be further separated into two distinct domains, Pot1pN (residues 1-187) and Pot1pC (residues 188-389). Here we show that Pot1pC, like Pot1pN, can function independently of Pot1-DBD and binds specifically to a minimal nonameric oligonucleotide, d(GGTTACGGT), with a K(D) of 400 +/- 70 nM (specifically recognized nucleotides in bold). NMR chemical shift perturbation analysis indicates that the overall structures of the isolated Pot1pN and Pot1pC domains remain intact in Pot1-DBD. Furthermore, alanine scanning reveals modest differences in the ssDNA-binding contacts provided by isolated Pot1pN and within Pot1-DBD. Although the global character of both Pot1pN and Pot1pC is maintained in Pot1-DBD, chemical shift perturbation analysis highlights localized structural differences within the G1/G2 and T3/T4 binding pockets of Pot1pN in Pot1-DBD, which correlate with its distinct ssDNA-binding activity. Furthermore, we find evidence for a putative interdomain interface on Pot1pN that mediates interactions with Pot1pC that ultimately result in the altered ssDNA-binding activity of Pot1-DBD. Together, these data provide insight into the mechanisms underlying the activity and regulation of SpPot1 at the telomere.

  2. Experimental Limits on Local Realism with Separable and Entangled Photons

    Science.gov (United States)

    2011-01-01

    a photon received by Bob triggers a device which acts questionably on the unsuspecting feline ). There is only a single time slot available for the... feline fate information would not be available to her until after her photon reaches the (very remote) intrusive polarizer, and she had made a

  3. diffusive phase separation

    Directory of Open Access Journals (Sweden)

    Nobuyuki Kenmochi

    1996-01-01

    w is constrained to have double obstacles σ*≤w≤σ* (i.e., σ* and σ* are the threshold values of w. The objective of this paper is to discuss the semigroup {S(t} associated with the phase separation model, and construct its global attractor.

  4. Phase separation micro molding

    NARCIS (Netherlands)

    Vogelaar, Laura

    2005-01-01

    The research described in this thesis concerns the development of a new microfabrication method, Phase Separation Micro Molding (PSμM). While microfabrication is still best known from semiconductor industry, where it is used to integrate electrical components on a chip, the scope has immensely expan

  5. Fathering After Marital Separation

    Science.gov (United States)

    Keshet, Harry Finkelstein; Rosenthal, Kristine M.

    1978-01-01

    Deals with experiences of a group of separated or divorced fathers who chose to remain fully involved in the upbringing of their children. As they underwent transition from married parenthood to single fatherhood, these men learned that meeting demands of child care contributed to personal stability and growth. (Author)

  6. Isotope hydrograph separation

    Energy Technology Data Exchange (ETDEWEB)

    Fritz, P. [UFZ-Umweltforschungszentrum, Centre of Environmental Research Leipzig-Halle, Leipzig (Germany)

    2000-07-01

    Storm-runoff thus reflects the complex hydraulic behaviour of drainage basins and water-links of such systems. Water of different origin may participate in the events and in this lecture, the application of isotope techniques to separate storm hydrographs into different components will be presented.

  7. Unity Through Separation

    DEFF Research Database (Denmark)

    Dabelsteen, Hans B.

    This PhD thesis asks how we can conceptualize the current separation doctrine of religion and politics in a country like Denmark, where the structure of the established church and peoplehood overlap. In order to answer this question, Hans Bruun Dabelsteen maps the current discussion of secularism...

  8. Acromioclavicular Joint Separations

    Science.gov (United States)

    2013-01-01

    Published online: 16 December 2012 # Springer Science+Business Media New York 2012 Abstract Acromioclavicular (AC) joint separations are common...injuries. The sports most likely to cause AC joint dislocations are football, soccer , hockey, rugby, and skiing, among others [9, 28, 29]. The major cause

  9. Pre-Separation Guide

    Science.gov (United States)

    1992-03-04

    SEPARATEES Defense Outplacement Referral System (DORS) Since most of us are not independently wealthy, we will need a job after separation. DORS is...Job Assistance SPOUSES OF ALL SEPARATEES As a spouse you may take advantage of preparing Standard Form 17 1’s and resu- the outplacement services

  10. Separation of Powers.

    Science.gov (United States)

    Bill of Rights in Action, 1987

    1987-01-01

    The dimensions of the separation of powers principle are explored through three lessons in the subject areas of U.S. history, U.S. government, and world history. In 1748, a French nobleman, Baron de Montesquieu, wrote a book called "The Spirit of the Laws," in which he argued that there could be no liberty when all government power was…

  11. 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.

  12. Simulation of 125I induced DNA strand breaks in a CAP-DNA complex.

    Science.gov (United States)

    Li, W; Friedland, W; Jacob, P; Paretzke, H G; Panyutin, I; Neumann, R D

    2002-01-01

    The E. coli catabolite gene activator protein (CAP)-DNA complex with 125I located at the position of the H5 atom of the cytosine near the centre was incorporated into the PARTRAC track structure code. DNA strand breaks due to irradiation were calculated by track structure and radical attack simulations; strand breaks due to neutralisation of the highly charged 125Te ion were derived from a semi-empirical distribution. According to the calculations, the neutralisation effect dominates the strand breakage frequency at 2 bases away from the 125I decay site on both strands. The first breakage distribution counted from a 32P labelled end on the strand with 125I agreed well with experimental data, but on the opposite strand, the calculated distribution is more concentrated around the decay site and its yield is about 20% larger than the measured data.

  13. 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.

  14. Experimental investigation of inhomogeneities, nanoscopic phase separation, and magnetism in arc melted Fe-Cu metals with equal atomic ratio of the constituents

    KAUST Repository

    Hassnain Jaffari, G.

    2015-12-16

    Composition gradient and phase separation at the nanoscale have been investigated for arc-melted and solidified with equiatomic Fe-Cu. Diffraction studies revealed that Fe and Cu exhibited phase separation with no trace of any mixing. Microscopy studies revealed that immiscible Fe-Cu form dense bulk nanocomposite. The spatial distribution of Fe and Cu showed existence of two distinct regions, i.e., Fe-rich and Cu-rich regions. Fe-rich regions have Cu precipitates of various sizes and different shapes, with Fe forming meshes or channels greater than 100 nm in size. On the other hand, the matrix of Cu-rich regions formed strips with fine strands of nanosized Fe. Macromagnetic response of the system showed ferromagnetic behavior with a magnetic moment being equal to about 2.13 μB/Fe atom and a bulk like negligible value of coercivity over the temperature range of 5–300 K. Anisotropy constant has been calculated from various laws of approach to saturation, and its value is extracted to be equal to 1350 J/m3. Inhomogeneous strain within the Cu and Fe crystallites has been calculated for the (unannealed) sample solidified after arc-melting. Annealed sample also exhibited local inhomogeneity with removal of inhomogeneous strain and no appreciable change in magnetic character. However, for the annealed sample phase separated Fe exhibited homogenous strain.

  15. Local architecture

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Local architecture refers to structures built in the countryside,such as temples,memorial halls,residences, stores,pavilions, bridges,decorated archways, and wells. Because these structures were all built by focal craftsmen and villagers in the traditional local style, they are generally called local architecture.

  16. OsRAD51C Is Essential for Double Strand Break Repair in Rice Meiosis

    Directory of Open Access Journals (Sweden)

    Ding eTang

    2014-05-01

    Full Text Available RAD51C is one of the RAD51 paralogs that plays an important role in DNA double-strand break repair by homologous recombination. Here, we identified and characterized OsRAD51C, the rice homolog of human RAD51C. The Osrad51c mutant plant is normal in vegetative growth but exhibits complete male and female sterility. Cytological investigation revealed that homologous pairing and synapsis were severely disrupted. Massive chromosome fragmentation occurred during metaphase I in Osrad51c meiocytes, and was fully suppressed by the CRC1 mutation. Immunofluorescence analysis showed that OsRAD51C localized onto the chromosomes from leptotene to early pachytene during prophase I, and that normal loading of OsRAD51C was dependent on OsREC8, PAIR2, and PAIR3. Additionally, ZEP1 did not localize properly in Osrad51c, indicating that OsRAD51C is required for synaptonemal complex assembly. Our study also provided evidence in support of a functional divergence in RAD51C among organisms.

  17. ATM release at resected double-strand breaks provides heterochromatin reconstitution to facilitate homologous recombination.

    Directory of Open Access Journals (Sweden)

    Verena Geuting

    Full Text Available Non-homologous end-joining (NHEJ and homologous recombination (HR represent the two main pathways for repairing DNA double-strand breaks (DSBs. During the G2 phase of the mammalian cell cycle, both processes can operate and chromatin structure is one important factor which determines DSB repair pathway choice. ATM facilitates the repair of heterochromatic DSBs by phosphorylating and inactivating the heterochromatin building factor KAP-1, leading to local chromatin relaxation. Here, we show that ATM accumulation and activity is strongly diminished at DSBs undergoing end-resection during HR. Such DSBs remain unrepaired in cells devoid of the HR factors BRCA2, XRCC3 or RAD51. Strikingly, depletion of KAP-1 or expression of phospho-mimic KAP-1 allows repair of resected DSBs in the absence of BRCA2, XRCC3 or RAD51 by an erroneous PARP-dependent alt-NHEJ process. We suggest that DSBs in heterochromatin elicit initial local heterochromatin relaxation which is reversed during HR due to the release of ATM from resection break ends. The restored heterochromatic structure facilitates HR and prevents usage of error-prone alternative processes.

  18. Sp1 facilitates DNA double-strand break repair through a nontranscriptional mechanism.

    Science.gov (United States)

    Beishline, Kate; Kelly, Crystal M; Olofsson, Beatrix A; Koduri, Sravanthi; Emrich, Jacqueline; Greenberg, Roger A; Azizkhan-Clifford, Jane

    2012-09-01

    Sp1 is a ubiquitously expressed transcription factor that is phosphorylated by ataxia telangiectasia mutated kinase (ATM) in response to ionizing radiation and H(2)O(2). Here, we show by indirect immunofluorescence that Sp1 phosphorylated on serine 101 (pSp1) localizes to ionizing radiation-induced foci with phosphorylated histone variant γH2Ax and members of the MRN (Mre11, Rad50, and Nbs1) complex. More precise analysis of occupancy of DNA double-strand breaks (DSBs) by chromatin immunoprecipitation (ChIP) shows that Sp1, like Nbs1, resides within 200 bp of DSBs. Using laser microirradiation of cells, we demonstrate that pSp1 is present at DNA DSBs by 7.5 min after induction of damage and remains at the break site for at least 8 h. Depletion of Sp1 inhibits repair of site-specific DNA breaks, and the N-terminal 182-amino-acid peptide, which contains targets of ATM kinase but lacks the zinc finger DNA binding domain, is phosphorylated, localizes to DSBs, and rescues the repair defect resulting from Sp1 depletion. Together, these data demonstrate that Sp1 is rapidly recruited to the region immediately adjacent to sites of DNA DSBs and is required for DSB repair, through a mechanism independent of its sequence-directed transcriptional effects.

  19. Strand Burner Results of AFP-001 Propellant with Inert Coating for Temperature Compensation

    Science.gov (United States)

    2015-10-01

    ARL-MR-0907 ● OCT 2015 US Army Research Laboratory Strand Burner Results of AFP -001 Propellant with Inert Coating for Temperature...Laboratory Strand Burner Results of AFP -001 Propellant with Inert Coating for Temperature Compensation by John J Ritter and Anthony Canami...COVERED (From - To) February 2015 4. TITLE AND SUBTITLE Strand Burner Results of AFP -001 Propellant with Inert Coating for Temperature Compensation

  20. A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology.

    OpenAIRE

    Marcel Ander; Sivaraman Subramaniam; Karim Fahmy; Francis Stewart, A.; Erik Schäffer

    2015-01-01

    Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recog...

  1. Analysis of Cable-in-Conduit Conductors' DC Performance in Light of Strand's Experimental Properties

    Institute of Scientific and Technical Information of China (English)

    TAN Yunfei; WENG Peide; LIU Fang; LI Shaolei

    2007-01-01

    Conductor qualification will be carried out with four Cable-in-Conduit Conductor (CICC) samples made of superconducting strands. The direct current (DC) performance of these samples will be tested in the SULTAN facility. The critical current densities of the strands can be well simulated by empirical equations. In this paper, a model is illustrated to predict the DC behaviour of the cable in light of the single strand's experimental properties. The simulation results were compared with experimental results.

  2. Interpreting the spatio-temporal patterns of sea turtle strandings: Going with the flow

    Science.gov (United States)

    Hart, K.M.; Mooreside, P.; Crowder, L.B.

    2006-01-01

    Knowledge of the spatial and temporal distribution of specific mortality sources is crucial for management of species that are vulnerable to human interactions. Beachcast carcasses represent an unknown fraction of at-sea mortalities. While a variety of physical (e.g., water temperature) and biological (e.g., decomposition) factors as well as the distribution of animals and their mortality sources likely affect the probability of carcass stranding, physical oceanography plays a major role in where and when carcasses strand. Here, we evaluate the influence of nearshore physical oceanographic and wind regimes on sea turtle strandings to decipher seasonal trends and make qualitative predictions about stranding patterns along oceanfront beaches. We use results from oceanic drift-bottle experiments to check our predictions and provide an upper limit on stranding proportions. We compare predicted current regimes from a 3D physical oceanographic model to spatial and temporal locations of both sea turtle carcass strandings and drift bottle landfalls. Drift bottle return rates suggest an upper limit for the proportion of sea turtle carcasses that strand (about 20%). In the South Atlantic Bight, seasonal development of along-shelf flow coincides with increased numbers of strandings of both turtles and drift bottles in late spring and early summer. The model also predicts net offshore flow of surface waters during winter - the season with the fewest relative strandings. The drift bottle data provide a reasonable upper bound on how likely carcasses are to reach land from points offshore and bound the general timeframe for stranding post-mortem (strandings follow a seasonal regime predictable from physical oceanography and mimicked by drift bottle experiments. Managers can use these findings to reevaluate incidental strandings limits and fishery takes for both nearshore and offshore mortality sources. ?? 2005 Elsevier Ltd. All rights reserved.

  3. Analysis of heavy-ion-induced DNA strand breaks in plasmid pUC18

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Plasmid DNA was irradiated or implanted by mixed particle field(CR) or lithium-ion-beam to detect strand breaks.The primary results showed that mixed particle field could induce single and double strand breaks with positive linear-dose-effects;most of sequence changes induced by CR were point mutant.Lithium-ion-beam could induce strand breaks also,but it was only at dose of 20Gy.

  4. Edwardsiella tarda sepsis in a live-stranded sperm whale (Physeter macrocephalus).

    Science.gov (United States)

    Cools, Piet; Haelters, Jan; Lopes dos Santos Santiago, Guido; Claeys, Geert; Boelens, Jerina; Leroux-Roels, Isabel; Vaneechoutte, Mario; Deschaght, Pieter

    2013-09-27

    Whale strandings remain poorly understood, although bacterial infections have been suggested to contribute. We isolated Edwardsiella tarda from the blood of a stranded sperm whale. The pathogen was identified with MALDI-TOF MS, confirmed by 16S rRNA gene sequencing and quantified in blood by qPCR. We report the first case of sepsis in a sperm whale. The zoonotic potential of E. tarda and the possible role of bacterial infections in the enigmatic strandings of cetaceans are discussed.

  5. Refinement of Propellant Strand Burning Method to Suit Aluminised Composite Rocket Propellant

    Science.gov (United States)

    2014-12-01

    ABSTRACT An epoxy coating was trialled as an inhibitor for composite rocket propellant strands burned in a Crawford–style bomb . The epoxy coating...into the Crawford bomb and pressurised with nitrogen to the specified pressure. Once pressure and temperature were stable at the required set- point...aggressive propellant. This method involved the coating of strands of propellant with a two-part epoxy polymer. Strands were dipped into a bath of epoxy

  6. The Caenorhabditis elegans homolog of Gen1/Yen1 resolvases links DNA damage signaling to DNA double-strand break repair.

    Directory of Open Access Journals (Sweden)

    Aymeric P Bailly

    2010-07-01

    Full Text Available DNA double-strand breaks (DSBs can be repaired by homologous recombination (HR, which can involve Holliday junction (HJ intermediates that are ultimately resolved by nucleolytic enzymes. An N-terminal fragment of human GEN1 has recently been shown to act as a Holliday junction resolvase, but little is known about the role of GEN-1 in vivo. Holliday junction resolution signifies the completion of DNA repair, a step that may be coupled to signaling proteins that regulate cell cycle progression in response to DNA damage. Using forward genetic approaches, we identified a Caenorhabditis elegans dual function DNA double-strand break repair and DNA damage signaling protein orthologous to the human GEN1 Holliday junction resolving enzyme. GEN-1 has biochemical activities related to the human enzyme and facilitates repair of DNA double-strand breaks, but is not essential for DNA double-strand break repair during meiotic recombination. Mutational analysis reveals that the DNA damage-signaling function of GEN-1 is separable from its role in DNA repair. GEN-1 promotes germ cell cycle arrest and apoptosis via a pathway that acts in parallel to the canonical DNA damage response pathway mediated by RPA loading, CHK1 activation, and CEP-1/p53-mediated apoptosis induction. Furthermore, GEN-1 acts redundantly with the 9-1-1 complex to ensure genome stability. Our study suggests that GEN-1 might act as a dual function Holliday junction resolvase that may coordinate DNA damage signaling with a late step in DNA double-strand break repair.

  7. 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).

  8. Genetic requirements for the single-strand annealing pathway of double-strand break repair in Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, E.L.; Sugawara, N.; Haber, J.E. [Brandeis Univ., Waltham, MA (United States)] [and others

    1996-03-01

    HO endonuclease-induced double-strand breaks (DSBs) within a direct duplication of Escherichia coli lacZ genes are repaired either by gene conversion or by single-strand annealing (SSA), with >80% being SSA. Previously it was demonstrated that the RAD52 gene is required for DSB-induced SSA. In the present study, the effects of other genes belonging to the RAD52 epistasis group were analyzed. We show that RAD51, RAD54, RAD55, and RAD57 genes are not required for SSA irrespective of whether recombination occurred in plasmid or chromosomal DNA. In both plasmid and chromosomal constructs with homologous sequences in direct orientation, the proportion of SSA events over gene conversion was significantly elevated in the mutant strains. However, gene conversion was not affected when the two lacZ sequences were in inverted orientation. These results suggest that there is a competition between SSA and gene conversion processes that favors SSA in the absence of RAD51, RAD54, RAD55 and RAD57. Mutations in RAD50 and XRS2 genes do not prevent the completion, but markedly retard the kinetics, of DSB repair by both mechanisms in the lacZ direct repeat plasmid, a result resembling the effects of these genes during mating-type (MAT) switching. 43 refs., 8 figs., 3 tabs.

  9. Transport AC loss characteristics of a nine strand YBCO Roebel cable

    Science.gov (United States)

    Jiang, Zhenan; Badcock, R. A.; Long, N. J.; Staines, Mike; Thakur, K. P.; Lakshmi, L. S.; Wright, A.; Hamilton, K.; Sidorov, G. N.; Buckley, R. G.; Amemiya, Naoyuki; Caplin, A. D.

    2010-02-01

    Transport AC loss in a short length of 9/2 YBCO Roebel cable (nine 2 mm wide strands) is measured. The AC loss data are compared with those in a 5/2 YBCO Roebel cable (five 2 mm wide strands) as well as that in a single strand. All the strands composing the cables and the single strand are insulated and cut from the same stock material. The validity of the measurement method was reconfirmed by results at a range of frequencies. At a wide range of It/Ic, the normalized AC losses in the Roebel cable were around 6.2-6.7 times of those in the single strand. This is less than the nine times predicted for a tight bundle of nine conductors. The normalized transport AC losses in the 5/2 Roebel cable are much smaller than those in the 9/2 Roebel. This should be due to larger superposition of magnetic field in the 9/2 Roebel. The Ic of the 9/2 and 5/2 Roebel cables is determined by serial connection of the strands. This eliminates the effect where differing resistances in the current terminations cause uneven current sharing between strands when the strands are connected in parallel.

  10. Sequence Conversion by Single Strand Oligonucleotide Donors via Non-homologous End Joining in Mammalian Cells*

    OpenAIRE

    Liu, Jia; Majumdar, Alokes; Liu, Jilan; Thompson, Lawrence H.; Seidman, Michael M.

    2010-01-01

    Double strand breaks (DSBs) can be repaired by homology independent nonhomologous end joining (NHEJ) pathways involving proteins such as Ku70/80, DNAPKcs, Xrcc4/Ligase 4, and the Mre11/Rad50/Nbs1 (MRN) complex. DSBs can also be repaired by homology-dependent pathways (HDR), in which the MRN and CtIP nucleases produce single strand ends that engage homologous sequences either by strand invasion or strand annealing. The entry of ends into HDR pathways underlies protocols for genomic manipulatio...

  11. Sequence conversion by single strand oligonucleotide donors via non-homologous end joining in mammalian cells.

    Science.gov (United States)

    Liu, Jia; Majumdar, Alokes; Liu, Jilan; Thompson, Lawrence H; Seidman, Michael M

    2010-07-23

    Double strand breaks (DSBs) can be repaired by homology independent nonhomologous end joining (NHEJ) pathways involving proteins such as Ku70/80, DNAPKcs, Xrcc4/Ligase 4, and the Mre11/Rad50/Nbs1 (MRN) complex. DSBs can also be repaired by homology-dependent pathways (HDR), in which the MRN and CtIP nucleases produce single strand ends that engage homologous sequences either by strand invasion or strand annealing. The entry of ends into HDR pathways underlies protocols for genomic manipulation that combine site-specific DSBs with appropriate informational donors. Most strategies utilize long duplex donors that participate by strand invasion. Work in yeast indicates that single strand oligonucleotide (SSO) donors are also active, over considerable distance, via a single strand annealing pathway. We examined the activity of SSO donors in mammalian cells at DSBs induced either by a restriction nuclease or by a targeted interstrand cross-link. SSO donors were effective immediately adjacent to the break, but activity declined sharply beyond approximately 100 nucleotides. Overexpression of the resection nuclease CtIP increased the frequency of SSO-mediated sequence modulation distal to the break site, but had no effect on the activity of an SSO donor adjacent to the break. Genetic and in vivo competition experiments showed that sequence conversion by SSOs in the immediate vicinity of the break was not by strand invasion or strand annealing pathways. Instead these donors competed for ends that would have otherwise entered NHEJ pathways.

  12. 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...

  13. Flexural behavior of bonded post-tensioned concrete beams under strand corrosion

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xuhui [College of Civil Engineering and Mechanics, Xiangtan University, 411105 Xiangtan (China); School of Civil Engineering and Architecture, Changsha University of Science & Technology, 410114 Changsha (China); Industry Key Laboratory of Traffic Infrastructure Security Risk Management (CSUST), 410114 Changsha (China); Wang, Lei, E-mail: leiwlei@hotmail.com [School of Civil Engineering and Architecture, Changsha University of Science & Technology, 410114 Changsha (China); Industry Key Laboratory of Traffic Infrastructure Security Risk Management (CSUST), 410114 Changsha (China); Zhang, Jianren; Ma, Yafei [School of Civil Engineering and Architecture, Changsha University of Science & Technology, 410114 Changsha (China); Industry Key Laboratory of Traffic Infrastructure Security Risk Management (CSUST), 410114 Changsha (China); Liu, Yongming [School for Engineering of Matter, Transport and Energy, Arizona State University, 85281 Tempe, AZ (United States)

    2017-03-15

    Highlights: • Flexural behavior of bonded PT beams with strand corrosion is experimental tested. • Cracking, stiffness, ultimate strength, failure & ductility of beams are clarified. • A coefficient is proposed to measure incompatible strain between strand & concrete. - Abstract: An experimental test is performed to investigate the flexural behavior of bonded post-tensioned concrete beams under strand corrosion. Eight beams are designed and subjected to accelerated method to different corrosion levels. The initial stiffness of beams is observed by cyclic loading-unloading test during the corrosion procedure. Corrosion effects on concrete cracking, post-cracking stiffness, ultimate strength, failure mode and ductility are then clarified by the flexural test. And, a coefficient is introduced to quantify the incompatible strain between corroded strand and concrete. Results show that the prestress force loss of strand has almost the linear relation with corrosion loss. Strand corrosion affects slightly the initial stiffness of beam before flexural cracking, but degrades significantly the post-cracking stiffness of beam as the corrosion loss exceeds 27.0%. Slight corrosion of strand has little effects on beams flexural behavior. The severe corrosion, however, decreases the number of crack, changes the failure mode form the concrete crushing to strand rupture, degrades the ductility and the ultimate strength of beams, and leads to the incompatible strain between strand and concrete. In the present test, the incompatible strain decreases about 20% of the flexural strength as the corrosion loss exceeds 27.0%.

  14. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication.

    Science.gov (United States)

    Price, Morgan N; Alm, Eric J; Arkin, Adam P

    2005-01-01

    In bacteria, most genes are on the leading strand of replication, a phenomenon attributed to collisions between the DNA and RNA polymerases. In Escherichia coli, these collisions slow the movement of the replication fork through actively transcribed genes only if they are coded on the lagging strand. For genes on both strands, however, these collisions sever nascent transcripts and interrupt gene expression. Based on these observations, we propose a new theory to explain strand bias: genes whose expression is important for fitness are selected to the leading strand because this reduces the duration of these interruptions. Our theory predicts that multi-gene operons, which are subject to longer interruptions, should be more strongly selected to the leading strand than singleton transcripts. We show that this is true even after controlling for the tendency for essential genes, which are strongly biased to the leading strand, to occur in operons. Our theory also predicts that other factors that are associated with strand bias should have stronger effects for genes that are in operons. We find that expression level and phylogenetic ubiquity are correlated with strand bias for both essential and non-essential genes, but only for genes in operons.

  15. Workshop on effects of chromium coating on Nb{sub 3}Sn superconductor strand: Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    1994-04-12

    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{sub 3}Sn strand.

  16. 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...

  17. Polycation graft copolymers accelerating DNA strand exchange: involvement of ionic interaction.

    Science.gov (United States)

    Kim, W J; Ishihara, T; Akaike, T; Maruyama, A

    2001-01-01

    In the previous study (Chem. Eur. J., 7, 176 (2001)) we demonstrated that the comb-type polycationic copolymer (PLL-g-Dex) which is composed of poly (L-lysine) backbone and dextran graft chains expedited the DNA strand exchange reaction. In this study, fluorescence resonance energy transfer (FRET) was employed to explore the copolymer-mediated DNA strand exchange with higher time-resolution. To initiate strand exchange reaction the duplex prepared from 3'-fluorescein isothiocyanate (FITC)--and 5'-carboxytetramethylrhodamine(TAMRA)-labeled complementary DNAs was added to its non-labeled complementary single strand. DNA strand exchange was monitored by observing the recovery of the FITC quenching. More than 20,000 times increase in strand exchange rate at 37 degrees C by the copolymer was estimated. To investigate the accelerating mechanisms of the copolymer, the same reactions but at various ionic strenghts were studied. With increasing ionic strengths the strand exchange rate in the absence of the copolymer increased, suggesting that ionic repulsion among DNAs is unfavorable for the strand exchange to occur. Hence, alleviation of the electrostatic repulsion through interpolyelectrolyte complex formation is probably a role of the copolymer for accelerating the strand exchange reaction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sedgwick, B.; Setlow, J.K.

    1976-02-01

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

  19. A euryarchaeal histone modulates strand displacement synthesis by replicative DNA polymerases.

    Science.gov (United States)

    Sun, Fei; Huang, Li

    2016-07-01

    Euryarchaeota and Crenarchaeota, the two main lineages of the domain Archaea, encode different chromatin proteins and differ in the use of replicative DNA polymerases. Crenarchaea possess a single family B DNA polymerase (PolB), which is capable of strand displacement modulated by the chromatin proteins Cren7 and Sul7d. Euryarchaea have two distinct replicative DNA polymerases, PolB and PolD, a family D DNA polymerase. Here we characterized the strand displacement activities of PolB and PolD from the hyperthermophilic euryarchaeon Pyrococcus furiosus and investigated the influence of HPfA1, a homolog of eukaryotic histones from P. furiosus, on these activities. We showed that both PolB and PolD were efficient in strand displacement. HPfA1 inhibited DNA strand displacement by both DNA polymerases but exhibited little effect on the displacement of a RNA strand annealed to single-stranded template DNA. This is consistent with the finding that HPfA1 bound more tightly to double-stranded DNA than to a RNA:DNA hybrid. Our results suggest that, although crenarchaea and euryarchaea differ in chromosomal packaging, they share similar mechanisms in modulating strand displacement by DNA polymerases during lagging strand DNA synthesis.

  20. Microgravity Passive Phase Separator

    Science.gov (United States)

    Paragano, Matthew; Indoe, William; Darmetko, Jeffrey

    2012-01-01

    A new invention disclosure discusses a structure and process for separating gas from liquids in microgravity. The Microgravity Passive Phase Separator consists of two concentric, pleated, woven stainless- steel screens (25-micrometer nominal pore) with an axial inlet, and an annular outlet between both screens (see figure). Water enters at one end of the center screen at high velocity, eventually passing through the inner screen and out through the annular exit. As gas is introduced into the flow stream, the drag force exerted on the bubble pushes it downstream until flow stagnation or until it reaches an equilibrium point between the surface tension holding bubble to the screen and the drag force. Gas bubbles of a given size will form a front that is moved further down the length of the inner screen with increasing velocity. As more bubbles are added, the front location will remain fixed, but additional bubbles will move to the end of the unit, eventually coming to rest in the large cavity between the unit housing and the outer screen (storage area). Owing to the small size of the pores and the hydrophilic nature of the screen material, gas does not pass through the screen and is retained within the unit for emptying during ground processing. If debris is picked up on the screen, the area closest to the inlet will become clogged, so high-velocity flow will persist farther down the length of the center screen, pushing the bubble front further from the inlet of the inner screen. It is desired to keep the velocity high enough so that, for any bubble size, an area of clean screen exists between the bubbles and the debris. The primary benefits of this innovation are the lack of any need for additional power, strip gas, or location for venting the separated gas. As the unit contains no membrane, the transport fluid will not be lost due to evaporation in the process of gas separation. Separation is performed with relatively low pressure drop based on the large surface

  1. Second Home Owners, Locals and Their Perspectives on Rural Development

    Science.gov (United States)

    Farstad, Maja; Rye, Johan Fredrik

    2013-01-01

    Dominating strands within the research literature on second homes explain social conflicts between rural hosting and visiting second home populations by describing their differing perspectives on rural development. Such presentations suggest that locals are likely to welcome new developments in order to enhance the economic viability of their…

  2. GPS Separator HD

    CERN Multimedia

    2016-01-01

    Footage of the 70 degree ISOLDE GPS separator magnet MAG70 as well as the switchyard for the Central Mass and GLM (GPS Low Mass) and GHM (GPS High Mass) beamlines in the GPS separator zone. In the GPS20 vacuum sector equipment such as the long GPS scanner 482 / 483 unit, faraday cup FC 490, vacuum valves and wiregrid piston WG210 and WG475 and radiation monitors can also be seen. Also the RILIS laser guidance and trajectory can be seen, the GPS main beamgate switch box and the actual GLM, GHM and Central Beamline beamgates in the beamlines as well as the first electrostatic quadrupoles for the GPS lines. Close up of the GHM deflector plates motor and connections and the inspection glass at the GHM side of the switchyard.

  3. HRS Separator HD

    CERN Multimedia

    2016-01-01

    Footage of the 90 and 60 degree ISOLDE HRS separator magnets in the HRS separator zone. In the two vacuum sectors HRS20 and HRS30 equipment such as the HRS slits SL240, the HRS faraday cup FC300 and wiregrid WG210 can be spotted. Vacuum valves, turbo pumps, beamlines, quadrupoles, water and compressed air connections, DC and signal cabling can be seen throughout the video. The HRS main and user beamgate in the beamline between MAG90 and MAG60 and its switchboxes as well as all vacuum bellows and flanges are shown. Instrumentation such as the HRS scanner unit 482 / 483, the HRS WG470 wiregrid and slits piston can be seen. The different quadrupoles and supports are shown as well as the RILIS guidance tubes and installation at the magnets and the different radiation monitors.

  4. Nylon separators. [thermal degradation

    Science.gov (United States)

    Lim, H. S.

    1977-01-01

    A nylon separator was placed in a flooded condition in K0H solution and heated at various high temperatures ranging from 60 C to 110 C. The weight decrease was measured and the molecular weight and decomposition product were analyzed to determine: (1) the effect of K0H concentration on the hydrolysis rate; (2) the effect of K0H concentration on nylon degradation; (3) the activation energy at different K0H concentrations; and (4) the effect of oxygen on nylon degradation. The nylon hydrolysis rate is shown to increase as K0H concentration is decreased 34%, giving a maximum rate at about 16%. Separator hydrolysis is confirmed by molecular weight decrease in age of the batteries, and the reaction of nylon with molecular oxygen is probably negligible, compared to hydrolysis. The extrapolated rate value from the high temperature experiment correlates well with experimental values at 35 degrees.

  5. Battery separator manufacturing process

    Energy Technology Data Exchange (ETDEWEB)

    Palmer, N.I.; Sugarman, N.

    1974-12-27

    A battery with a positive plate, a negative plate, and a separator of polymeric resin having a degree of undesirable hydrophobia, solid below 180/sup 0/F, extrudable as a hot melt, and resistant to degradation by at least either acids or alkalies positioned between the plates is described. The separator comprises a nonwoven mat of fibers, the fibers being comprised of the polymeric resin and a wetting agent in an amount of 0.5 to 20 percent by weight based on the weight of the resin with the amount being incompatible with the resin below the melting point of the resin such that the wetting agent will bloom over a period of time at ambient temperatures in a battery, yet being compatible with the resin at the extrusion temperature and bringing about blooming to the surface of the fibers when the fibers are subjected to heat and pressure.

  6. Unity Through Separation

    DEFF Research Database (Denmark)

    Dabelsteen, Hans B.

    analysis, Dabelsteen study Danish secularism as an ideological concept. He finds that the conceptual structure of Danish secularism holds separation-as-principled distance at its core. Institutionally this particularly pertains to the establishment arrangement, and in practice it translates...... and proposes two conceptual expansions. The first is to include modest establishment in a framework of secularism defensible by political liberalism, and the second is to consider secularism in close connection to a theory of peoplehood. Methodologically positioned between interpretive realism and policy...... into the principle of treating everybody equally (with religious freedom, equality and Danish peoplehood as the most important principles adjacent to secularism). In a study of the historical roots of the separation doctrine and two current policy cases (same-sex marriage and reforms of church governance...

  7. Acoustophoresis separation method

    Science.gov (United States)

    Heyman, Joseph S. (Inventor)

    1993-01-01

    A method and apparatus are provided for acoustophoresis, i.e., the separation of species via acoustic waves. An ultrasonic transducer applies an acoustic wave to one end of a sample container containing at least two species having different acoustic absorptions. The wave has a frequency tuned to or harmonized with the point of resonance of the species to be separated. This wave causes the species to be driven to an opposite end of the sample container for removal. A second ultrasonic transducer may be provided to apply a second, oppositely directed acoustic wave to prevent undesired streaming. In addition, a radio frequency tuned to the mechanical resonance and coupled with a magnetic field can serve to identify a species in a medium comprising species with similar absorption coefficients, whereby an acoustic wave having a frequency corresponding to this gyrational rate can then be applied to sweep the identified species to one end of the container for removal.

  8. A Core Language for Separate Variability Modeling

    DEFF Research Database (Denmark)

    Iosif-Lazăr, Alexandru Florin; Wasowski, Andrzej; Schaefer, Ina

    2014-01-01

    Separate variability modeling adds variability to a modeling language without requiring modifications of the language or the supporting tools. We define a core language for separate variability modeling using a single kind of variation point to define transformations of software artifacts in object...... hierarchical dependencies between variation points via copying and flattening. Thus, we reduce a model with intricate dependencies to a flat executable model transformation consisting of simple unconditional local variation points. The core semantics is extremely concise: it boils down to two operational rules...

  9. Separation of enantiomers

    CERN Document Server

    Todd , Matthew H

    2014-01-01

    In one handy volume this handbook summarizes the most common synthetic methods for the separation of racemic mixtures, allowing an easy comparison of the different strategies described in the literature.Alongside classical methods, the authors also consider kinetic resolutions, dynamic kinetic resolutions, divergent reactions of a racemic mixture, and a number of ""neglected"" cases not covered elsewhere, such as the use of circularly polarized light, polymerizations, ""ripening"" processes, dynamic combinatorial chemistry, and several thermodynamic processes. The result is a thorough introdu

  10. Separation Logic and Concurrency

    Science.gov (United States)

    Bornat, Richard

    Concurrent separation logic is a development of Hoare logic adapted to deal with pointers and concurrency. Since its inception, it has been enhanced with a treatment of permissions to enable sharing of data between threads, and a treatment of variables as resource alongside heap cells as resource. An introduction to the logic is given with several examples of proofs, culminating in a treatment of Simpson's 4-slot algorithm, an instance of racy non-blocking concurrency.

  11. Innovative Separations Technologies

    Energy Technology Data Exchange (ETDEWEB)

    J. Tripp; N. Soelberg; R. Wigeland

    2011-05-01

    Reprocessing used nuclear fuel (UNF) is a multi-faceted problem involving chemistry, material properties, and engineering. Technology options are available to meet a variety of processing goals. A decision about which reprocessing method is best depends significantly on the process attributes considered to be a priority. New methods of reprocessing that could provide advantages over the aqueous Plutonium Uranium Reduction Extraction (PUREX) and Uranium Extraction + (UREX+) processes, electrochemical, and other approaches are under investigation in the Fuel Cycle Research and Development (FCR&D) Separations Campaign. In an attempt to develop a revolutionary approach to UNF recycle that may have more favorable characteristics than existing technologies, five innovative separations projects have been initiated. These include: (1) Nitrogen Trifluoride for UNF Processing; (2) Reactive Fluoride Gas (SF6) for UNF Processing; (3) Dry Head-end Nitration Processing; (4) Chlorination Processing of UNF; and (5) Enhanced Oxidation/Chlorination Processing of UNF. This report provides a description of the proposed processes, explores how they fit into the Modified Open Cycle (MOC) and Full Recycle (FR) fuel cycles, and identifies performance differences when compared to 'reference' advanced aqueous and fluoride volatility separations cases. To be able to highlight the key changes to the reference case, general background on advanced aqueous solvent extraction, advanced oxidative processes (e.g., volumetric oxidation, or 'voloxidation,' which is high temperature reaction of oxide UNF with oxygen, or modified using other oxidizing and reducing gases), and fluorination and chlorination processes is provided.

  12. Colour Separation and Aversion

    Directory of Open Access Journals (Sweden)

    Sarah M Haigh

    2012-05-01

    Full Text Available Aversion to achromatic patterns is well documented but relatively little is known about discomfort from chromatic patterns. Large colour differences are uncommon in the natural environment and deviation from natural statistics makes images uncomfortable (Fernandez and Wilkins 2008, Perception, 37(7, 1098–113; Juricevic et al 2010, Perception, 39(7, 884–899. We report twelve studies documenting a linear increase in aversion to chromatic square-wave gratings as a function of the separation in UCS chromaticity between the component bars, independent of their luminance contrast. Two possible explanations for the aversion were investigated: (1 accommodative response, or (2 cortical metabolic demand. We found no correlation between chromaticity separation and accommodative lag or variance in lag, measured using an open-field autorefractor. However, near infrared spectroscopy of the occipital cortex revealed a larger oxyhaemoglobin response to patterns with large chromaticity separation. The aversion may be cortical in origin and does not appear to be due to accommodation.

  13. Molecular dynamics simulations of a single stranded (ss) DNA

    CERN Document Server

    Chatterjee, Subhasish; Thakur, Siddarth; Burin, Alexander

    2012-01-01

    The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) of the nucleic acid backbone of the ssDNA were studied using molecular dynamics (MD) simulations. The AMBER program was used for building the structural model of the ssDNA, and atomistic MD simulations in three different ensembles were carried out using the NAMD program. The microcanonical (NVE), conical (NVT) and isobaric-isothermal (NPT) ensembles were employed to compare the equilibrium characteristics of ssDNA in aqueous solutions. Our results indicate that the conformational stability of the ssDNA is dependent on the thermodynamic conditions.

  14. Using both strands: The fundamental nature of antisense transcription.

    Science.gov (United States)

    Murray, Struan C; Mellor, Jane

    2016-01-01

    Non-coding transcription across the antisense strands of genes is an abundant, pervasive process in eukaryotes from yeast to humans, however its biological function remains elusive. Here, we provide commentary on a recent study of ours, which demonstrates a genome-wide role for antisense transcription: establishing a unique, dynamic chromatin architecture over genes. Antisense transcription increases the level of nucleosome occupancy and histone acetylation at the promoter and body of genes, without necessarily modulating the level of protein-coding sense transcription. It is also associated with high levels of histone turnover. By allowing genes to sample a wider range of chromatin configurations, antisense transcription could serve to make genes more sensitive to changing signals, priming them for responses to developmental programs or stressful cellular environments. Given the abundance of antisense transcription and the breadth of these chromatin changes, we propose that antisense transcription represents a fundamental, canonical feature of eukaryotic genes.

  15. Electronic transport in double-strand DNA segments

    Science.gov (United States)

    Albuquerque, E. L.; Mauriz, P. W.; Moreira, D. A.

    2008-03-01

    We report in this work a numerical study of the electronic density of states in π-stacked arrays of DNA double-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for a genomic DNA sequence, considering a segment of the first sequenced human chromosome 22 (Ch 22), with those of two artificial sequences forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Our theoretical method uses an electronic tight-binding Hamiltonian suitable to describe the DNA segments modeled by the quasiperiodic chains.

  16. Current-voltage characteristics of double-strand DNA sequences

    Science.gov (United States)

    Bezerril, L. M.; Moreira, D. A.; Albuquerque, E. L.; Fulco, U. L.; de Oliveira, E. L.; de Sousa, J. S.

    2009-09-01

    We use a tight-binding formulation to investigate the transmissivity and the current-voltage (I-V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for the genomic DNA sequence with those of artificial sequences (the long-range correlated Fibonacci and Rudin-Shapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same first neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I-V curves seem to be mostly influenced by the short-range correlations.

  17. Regulatory RNA design through evolutionary computation and strand displacement.

    Science.gov (United States)

    Rostain, William; Landrain, Thomas E; Rodrigo, Guillermo; Jaramillo, Alfonso

    2015-01-01

    The discovery and study of a vast number of regulatory RNAs in all kingdoms of life over the past decades has allowed the design of new synthetic RNAs that can regulate gene expression in vivo. Riboregulators, in particular, have been used to activate or repress gene expression. However, to accelerate and scale up the design process, synthetic biologists require computer-assisted design tools, without which riboregulator engineering will remain a case-by-case design process requiring expert attention. Recently, the design of RNA circuits by evolutionary computation and adapting strand displacement techniques from nanotechnology has proven to be suited to the automated generation of DNA sequences implementing regulatory RNA systems in bacteria. Herein, we present our method to carry out such evolutionary design and how to use it to create various types of riboregulators, allowing the systematic de novo design of genetic control systems in synthetic biology.

  18. Stranded cost recovery presents stumbling block to open access

    Energy Technology Data Exchange (ETDEWEB)

    Del Roccili, J.A.

    1996-04-01

    Much of the impetus for the movement to competitive power markets is a result of the tremendous variance in energy prices across the country. Large commercial and industrial customers are becoming increasingly aware of these discrepancies and are marshaling the market and political forces required to guarantee the eventual development of a national open-access transmission policy. Such a policy will facilitate competition and equalize prices on a regional, and to some extent, national level. The stumbling block, however, is the recovery of stranded investment. Under traditional regulation, historical costs could be collected through approved rates for a bundled service. With the protection of a monopoly franchise, average electricity prices provide the possibility of cost recovery for assets that might not be recoverable in a competitive market.

  19. Membranous Replication Factories Induced by Plus-Strand RNA Viruses

    Directory of Open Access Journals (Sweden)

    Inés Romero-Brey

    2014-07-01

    Full Text Available In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+ RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments.

  20. Phosphorylation: The Molecular Switch of Double-Strand Break Repair

    Directory of Open Access Journals (Sweden)

    K. C. Summers

    2011-01-01

    Full Text Available Repair of double-stranded breaks (DSBs is vital to maintaining genomic stability. In mammalian cells, DSBs are resolved in one of the following complex repair pathways: nonhomologous end-joining (NHEJ, homologous recombination (HR, or the inclusive DNA damage response (DDR. These repair pathways rely on factors that utilize reversible phosphorylation of proteins as molecular switches to regulate DNA repair. Many of these molecular switches overlap and play key roles in multiple pathways. For example, the NHEJ pathway and the DDR both utilize DNA-PK phosphorylation, whereas the HR pathway mediates repair with phosphorylation of RPA2, BRCA1, and BRCA2. Also, the DDR pathway utilizes the kinases ATM and ATR, as well as the phosphorylation of H2AX and MDC1. Together, these molecular switches regulate repair of DSBs by aiding in DSB recognition, pathway initiation, recruitment of repair factors, and the maintenance of repair mechanisms.

  1. Electronic transport in double-strand DNA segments

    Energy Technology Data Exchange (ETDEWEB)

    Albuquerque, E L; Moreira, D A [Departamento de Fisica, Universidade Federal do Rio Grande do Norte 59072-970 Natal-RN (Brazil); Mauriz, P W [Departamento de Ciencias Exatas, Centro Federal de Educacao Tecnologica do Maranhao 65025-001 Sao Luis-MA (Brazil)], E-mail: eudenilson@dfte.ufrn.br

    2008-03-15

    We report in this work a numerical study of the electronic density of states in {pi}-stacked arrays of DNA double-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for a genomic DNA sequence, considering a segment of the first sequenced human chromosome 22 (Ch 22), with those of two artificial sequences forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Our theoretical method uses an electronic tight-binding Hamiltonian suitable to describe the DNA segments modeled by the quasiperiodic chains.

  2. Current-voltage characteristics of double-strand DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bezerril, L.M.; Moreira, D.A. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@dfte.ufrn.b [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Fulco, U.L. [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Oliveira, E.L. de; Sousa, J.S. de [Departamento de Fisica, Universidade Federal do Ceara, 60455-760, Fortaleza-CE (Brazil)

    2009-09-07

    We use a tight-binding formulation to investigate the transmissivity and the current-voltage (I-V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for the genomic DNA sequence with those of artificial sequences (the long-range correlated Fibonacci and Rudin-Shapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same first neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I-V curves seem to be mostly influenced by the short-range correlations.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-07

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

  4. $Local^{3}$ Index Theorem

    CERN Document Server

    Teleman, Nicolae

    2011-01-01

    $Local^{3}$ Index Theorem means $Local(Local(Local \\;Index \\; Theorem)))$. $Local \\; Index \\; Theorem$ is the Connes-Moscovici local index theorem \\cite{Connes-Moscovici1}, \\cite{Connes-Moscovici2}. The second "Local" refers to the cyclic homology localised to a certain separable subring of the ground algebra, while the last one refers to Alexander-Spanier type cyclic homology. The Connes-Moscovici work is based on the operator $R(A) = \\mathbf{P} - \\mathbf{e}$ associated to the elliptic pseudo-differential operator $A$ on the smooth manifold $M$, where $\\mathbf{P}$, $\\mathbf{e}$ are idempotents, see \\cite{Connes-Moscovici1}, Pg. 353. The operator $R(A)$ has two main merits: it is a smoothing operator and its distributional kernel is situated in an arbitrarily small neighbourhood of the diagonal in $M \\times M$. The operator $R(A)$ has also two setbacks: -i) it is not an idempotent (and therefore it does not have a genuine Connes-Chern character); -ii) even if it were an idempotent, its Connes-Chern character ...

  5. Molecular detection of plant pathogenic bacteria using polymerase chain reaction single-strand conformation polymorphism.

    Science.gov (United States)

    Srinivasa, Chandrashekar; Sharanaiah, Umesha; Shivamallu, Chandan

    2012-03-01

    The application of polymerase chain reaction (PCR) technology to molecular diagnostics holds great promise for the early identification of agriculturally important plant pathogens. Ralstonia solanacearum, Xanthomoans axonopodis pv. vesicatoria, and Xanthomonas oryzae pv. oryzae are phytopathogenic bacteria, which can infect vegetables, cause severe yield loss. PCR-single-strand conformation polymorphism (PCR-SSCP) is a simple and powerful technique for identifying sequence changes in amplified DNA. The technique of PCR-SSCP is being exploited so far, only to detect and diagnose human bacterial pathogens in addition to plant pathogenic fungi. Selective media and serology are the commonly used methods for the detection of plant pathogens in infected plant materials. In this study, we developed PCR-SSCP technique to identify phytopathogenic bacteria. The PCR product was denatured and separated on a non-denaturing polyacrylamide gel. SSCP banding patterns were detected by silver staining of nucleic acids. We tested over 56 isolates of R. solanacearum, 44 isolates of X. axonopodis pv. vesicatoria, and 20 isolates of X. oryzae pv. oryzae. With the use of universal primer 16S rRNA, we could discriminate such species at the genus and species levels. Species-specific patterns were obtained for bacteria R. solanacearum, X. axonopodis pv. vesicatoria, and X. oryzae pv. oryzae. The potential use of PCR-SSCP technique for the detection and diagnosis of phytobacterial pathogens is discussed in the present paper.

  6. Rapid discrimination of Salmonella isolates by single-strand conformation polymorphism analysis.

    Science.gov (United States)

    Al-Adhami, Batol H; Huby-Chilton, Florence; Blais, Burton W; Martinez-Perez, Amalia; Chilton, Neil B; Gajadhar, Alvin A

    2008-10-01

    A molecular typing technique was developed for the differentiation of Salmonella isolates based on single-strand conformation polymorphism (SSCP) analysis of amplicons generated by PCR. Amplicons from parts of the fimA (both the 5' and 3' ends), mdh, invA, and atpD genes were generated separately from a panel of Salmonella strains representing Salmonella bongori, and four subspecies and 17 serovars of Salmonella enterica. These amplicons were subjected to SSCP analysis for differentiation of the salmonellae on the basis of different conformational forms arising due to nucleotide sequence variations in the target genes. Several distinct SSCP banding patterns (a maximum of 14 each for atpD and fimA 3' end) were observed with this panel of Salmonella strains for amplicons generated from each target gene. The best discrimination of Salmonella subspecies and serovar was achieved from the SSCP analysis of a combination of at least three gene targets: atpD, invA, and either mdh or fimA 3' end. This demonstrates the applicability of SSCP analysis as an important additional method to classical typing approaches for the differentiation of foodborne Salmonella isolates. SSCP is simple to perform and should be readily transferable to food microbiology laboratories with basic PCR capability.

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

    Science.gov (United States)

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

    2012-09-01

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

  8. Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation.

    Science.gov (United States)

    Gasser, Robin B; Hu, Min; Chilton, Neil B; Campbell, Bronwyn E; Jex, Aaron J; Otranto, Domenico; Cafarchia, Claudia; Beveridge, Ian; Zhu, Xingquan

    2006-01-01

    The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations. Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR amplification of target sequences, through to the gel-based separation of amplicons and scanning for mutations by SSCP (either by the analysis of radiolabeled amplicons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point mutations for amplicon sizes of up to 450-500 bp, and usually takes 1-2 days to carry out. This user-friendly, low-cost, potentially high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be applied to any gene of any organism.

  9. Molecular detection of plant pathogenic bacteria using polymerase chain reaction single-strand conformation polymorphism

    Institute of Scientific and Technical Information of China (English)

    Chandrashekar Srinivasa; Umesha Sharanaiah; Chandan Shivamallu

    2012-01-01

    The application of polymerase chain reaction (PCR) technology to molecular diagnostics holds great promise for the early identification of agriculturally important plant pathogens.Ralstonia solanacearum,Xanthomoans axonopodis pv.vesicatoria,and Xanthomonas oryzae pv.oryzae are phytopathogenic bacteria,which can infect vegetables,cause severe yield loss.PCR-single-strand conformation polymorphism (PCR-SSCP) is a simple and powerful technique for identifying sequence changes in amplified DNA.The technique of PCR-SSCP is being exploited so far,only to detect and diagnose human bacterial pathogens in addition to plant pathogenic fungi.Selective media and serology are the commonly used methods for the detection of plant pathogens in infected plant materials.In this study,we developed PCR-SSCP technique to identify phytopathogenic bacteria.The PCR product was denatured and separated on a non-denaturing polyacrylamide gel.SSCP banding patterns were detected by silver staining of nucleic acids.We tested over 56 isolates of R. solanacearum,44 isolates of X. axonopodis pv.vesicatoria,and 20 isolates of X.oryzae pv.oryzae.With the use of universal primer 16S rRNA,we could discriminate such species at the genus and species levels.Speciesspecific patterns were obtained for bacteria R.solanacearum,X.axonopodis pv.vesicatoria,and X.oryzae pv.oryzae.The potential use of PCR-SSCP technique for the detection and diagnosis of phytobacterial pathogens is discussed in the present paper.

  10. Discovery of a novel circular single-stranded DNA virus from porcine faeces.

    Science.gov (United States)

    Sikorski, Alyssa; Argüello-Astorga, Gerardo R; Dayaram, Anisha; Dobson, Renwick C J; Varsani, Arvind

    2013-01-01

    A large number of novel single-stranded DNA (ssDNA) viruses have been characterised from various environmental sources in the last 5 years. The bulk of these have been from faecal sources, and faecal sampling is an ideal non-invasive pathogen sampling method. We characterised a novel ssDNA from a porcine faecal sample from Cass Basin of the South Island of New Zealand. The novel viral genome has two large open reading frames (ORFs), which are bidirectionally transcribed and separated by intergenic regions. The largest ORF has some degree of similarity (DNA virus (PigSCV), whereas the second-largest ORF has high similarity to the putative replication-associated protein (Rep) of ChiSCV (~50 %) and bovine stool-associated circular DNA virus (BoSCV; ~30 %). Based on genome architecture, location of putative stem-loop like elements, and maximum-likelihood phylogenetic analysis of the gene encoding the Rep protein, the novel isolate belongs to the same family of ssDNA viruses as ChiSCV and BoSCV.

  11. Transcription-induced mutational strand bias and its effect on substitution rates in human genes.

    Science.gov (United States)

    Mugal, Carina F; von Grünberg, Hans-Hennig; Peifer, Martin

    2009-01-01

    If substitution rates are not the same on the two complementary DNA strands, a substitution is considered strand asymmetric. Such substitutional strand asymmetries are determined here for the three most frequent types of substitution on the human genome (C --> T, A --> G, and G --> T). Substitution rate differences between both strands are estimated for 4,590 human genes by aligning all repeats occurring within the introns with their ancestral consensus sequences. For 1,630 of these genes, both coding strand and noncoding strand rates could be compared with rates in gene-flanking regions. All three rates considered are found to be on average higher on the coding strand and lower on the transcribed strand in comparison to their values in the gene-flanking regions. This finding points to the simultaneous action of rate-increasing effects on the coding strand--such as increased adenine and cytosine deamination--and transcription-coupled repair as a rate-reducing effect on the transcribed strand. The common behavior of the three rates leads to strong correlations of the rate asymmetries: Whenever one rate is strand biased, the other two rates are likely to show the same bias. Furthermore, we determine all three rate asymmetries as a function of time: the A --> G and G --> T rate asymmetries are both found to be constant in time, whereas the C --> T rate asymmetry shows a pronounced time dependence, an observation that explains the difference between our results and those of an earlier work by Green et al. (2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet. 33:514-517.). Finally, we show that in addition to transcription also the replication process biases the substitution rates in genes.

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

    Directory of Open Access Journals (Sweden)

    Zhenghe Li

    2010-11-01

    Full Text Available Replication of plus-strand RNA viruses depends on host factors that are recruited into viral replicase complexes. Previous studies showed that eukaryotic translation elongation factor (eEF1A is one of the resident host proteins in the highly purified tombusvirus replicase complex. Using a random library of eEF1A mutants, we identified one mutant that decreased and three mutants that increased Tomato bushy stunt virus (TBSV replication in a yeast model host. Additional in vitro assays with whole cell extracts prepared from yeast strains expressing the eEF1A mutants demonstrated several functions for eEF1A in TBSV replication: facilitating the recruitment of the viral RNA template into the replicase complex; the assembly of the viral replicase complex; and enhancement of the minus-strand synthesis by promoting the initiation step. These roles for eEF1A are separate from its canonical role in host and viral protein translation, emphasizing critical functions for this abundant cellular protein during TBSV replication.

  13. ISI支付协议的Strand Space模型及其公平性分析%Strand Space Model of ISI Payment Protocol and Its Fairness Analysis

    Institute of Scientific and Technical Information of China (English)

    陈浩; 程娜; 何大可

    2006-01-01

    文章利用Strand Space模型对ISI支付协议进行了分析,得出了与卿_周逻辑分析方法相同的结论,并将Strand Space模型对认证协议协定性的分析方法应用到了电子商务协议公平性的分析.

  14. Local Helioseismology

    Directory of Open Access Journals (Sweden)

    Gizon Laurent

    2005-11-01

    Full Text Available We review the current status of local helioseismology, covering both theoretical and observational results. After a brief introduction to solar oscillations and wave propagation through inhomogeneous media, we describe the main techniques of local helioseismology: Fourier-Hankel decomposition, ring-diagram analysis, time-distance helioseismology, helioseismic holography, and direct modeling. We discuss local helioseismology of large-scale flows, the solar-cycle dependence of these flows, perturbations associated with regions of magnetic activity, and solar supergranulation.

  15. Eddy current separation apparatus, separation module, separation method and method for adjusting an eddy current separation apparatus

    NARCIS (Netherlands)

    Rem, P.C.; Bakker, M.C.M.; Berkhout, S.P.M.; Rahman, M.A.

    2012-01-01

    Eddy current separation apparatus (1) for separating particles (20) from a particle stream (w), wherein the apparatus (1) comprises a separator drum (4) adapted to create a first particle fraction (21) and a second particle fraction (23), a feeding device (2) upstream of the separator drum (4) for s

  16. Simple design criteria and efficiency of hydrodynamic vortex separators.

    Science.gov (United States)

    Gronowska-Szneler, M A; Sawicki, J M

    2014-01-01

    Vortex separators still draw attention from specialists investigating the process of removing particles suspended in liquids. The devices are locally applied for waste water treatment in different systems - from storm waste water sewerage to water circulation in fish ponds. However, the methods for separator design presented in the literature are questionable. The paper presents two simple and functional criteria that were employed to construct a laboratory test stand. The test results gave positive feedback on the efficiency of vortex separators.

  17. Interpolatability distinguishes LOCC from separable von Neumann measurements

    Energy Technology Data Exchange (ETDEWEB)

    Childs, Andrew M.; Leung, Debbie; Mančinska, Laura [Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada); Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada); Ozols, Maris [Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada); Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada); IBM TJ Watson Research Center, Yorktown Heights, New York 10598 (United States)

    2013-11-15

    Local operations with classical communication (LOCC) and separable operations are two classes of quantum operations that play key roles in the study of quantum entanglement. Separable operations are strictly more powerful than LOCC, but no simple explanation of this phenomenon is known. We show that, in the case of von Neumann measurements, the ability to interpolate measurements is an operational principle that sets apart LOCC and separable operations.

  18. SEPARATION OF PLUTONIUM

    Science.gov (United States)

    Maddock, A.G.; Smith, F.

    1959-08-25

    A method is described for separating plutonium from uranium and fission products by treating a nitrate solution of fission products, uranium, and hexavalent plutonium with a relatively water-insoluble fluoride to adsorb fission products on the fluoride, treating the residual solution with a reducing agent for plutonium to reduce its valence to four and less, treating the reduced plutonium solution with a relatively insoluble fluoride to adsorb the plutonium on the fluoride, removing the solution, and subsequently treating the fluoride with its adsorbed plutonium with a concentrated aqueous solution of at least one of a group consisting of aluminum nitrate, ferric nitrate, and manganous nitrate to remove the plutonium from the fluoride.

  19. POLONIUM SEPARATION PROCESS

    Science.gov (United States)

    Karraker, D.G.

    1959-07-14

    A liquid-liquid extraction process is presented for the recovery of polonium from lead and bismuth. According to the invention an acidic aqueous chloride phase containing the polonium, lead, and bismuth values is contacted with a tributyl phosphate ether phase. The polonium preferentially enters the organic phase which is then separated and washed with an aqueous hydrochloric solution to remove any lead or bismuth which may also have been extracted. The now highly purified polonium in the organic phase may be transferred to an aqueous solution by extraction with aqueous nitric acid.

  20. PLUTONIUM SEPARATION METHOD

    Science.gov (United States)

    Beaufait, L.J. Jr.; Stevenson, F.R.; Rollefson, G.K.

    1958-11-18

    The recovery of plutonium ions from neutron irradiated uranium can be accomplished by bufferlng an aqueous solutlon of the irradiated materials containing tetravalent plutonium to a pH of 4 to 7, adding sufficient acetate to the solution to complex the uranyl present, adding ferric nitrate to form a colloid of ferric hydroxide, plutonlum, and associated fission products, removing and dissolving the colloid in aqueous nitric acid, oxldizlng the plutonium to the hexavalent state by adding permanganate or dichromate, treating the resultant solution with ferric nitrate to form a colloid of ferric hydroxide and associated fission products, and separating the colloid from the plutonlum left in solution.

  1. Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines.

    Science.gov (United States)

    Wang, Shoushan; Zhao, Peiwen; Zhang, Changzhe; Bu, Yuxiang

    2016-03-17

    Experimental studies showed that high energy radiation induced base release and DNA backbone breaks mainly occur at the neighboring 5' nucleotide when a single-stranded DNA is modified by radiosensitizing 5-halogenated deoxyuridines. However, no mechanism can be used to interpret these experimental observations. To better understand the radiosensitivity of 5-halogenated deoxyuridines, mechanisms involving hydrogen abstraction by the uracil-5-yl radical from the C2' and C3' positions of an adjacent nucleotide separately followed by the C3'-O3' or N-glycosidic bond rupture and the P-O3' bond breakage are investigated in the DNA sequence 5'-TU(•)-3' employing density functional theory calculations in the present study. It is found that hydrogen abstractions from both positions are comparable with the one from the C2' site slightly more favorable. The N-glycosidic bond cleavage in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is estimated to have the lowest activation free energies, indicating that the adjacent 5' base release dominates electron induced damage to single-stranded DNA incorporated by 5-halogenated deoxyuridines. Relative to the P-O3' bond breakage after the internucleotide C3'-H abstraction, the C3'-O3' bond rupture in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is predicted to have a lower activation free energy, implying that single-stranded DNA backbone breaks are prone to occur at the C3'-O3' bond site. The 5'-TU(•)-3' species has substantial electron affinity and can even capture a hydrated electron, forming the 5'-TU(-)-3' anion. However, the electron induced C3'-O3' bond rupture in 5'-TU(-)-3' anion via a pathway of internucleotide proton abstraction is only minor in both the gas phase and aqueous solution. The present theoretical predictions can interpret rationally experimental observations, thereby demonstrating that the mechanisms proposed here are responsible for high

  2. Quintessential Scale Dependence from Separate Universe Simulations

    CERN Document Server

    Chiang, Chi-Ting; Hu, Wayne; LoVerde, Marilena

    2016-01-01

    By absorbing fluctuations into a local background, separate universe simulations provide a powerful technique to characterize the response of small-scale observables to the long-wavelength density fluctuations, for example those of the power spectrum and halo mass function which lead to the squeezed-limit $n$-point function and halo bias, respectively. Using quintessence dark energy as the paradigmatic example, we extend these simulation techniques to cases where non-gravitational forces in other sectors establish a Jeans scale across which the growth of density fluctuations becomes scale dependent. By characterizing the separate universes with matching background expansion histories, we show that the power spectrum and mass function responses depend on whether the long-wavelength mode is above or below the Jeans scale. Correspondingly, the squeezed bispectrum and halo bias also become scale dependent. Models of bias that are effectively local in the density field at a single epoch, initial or observed, canno...

  3. Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

    DEFF Research Database (Denmark)

    Nielsen, L.M.; Pedersen, S.O.; Kirketerp, M.-B.S.;

    2012-01-01

    strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (~3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar...

  4. 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.

    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 po

  5. 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

  6. 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

  7. Antibiotic efficacy in eliminating leptospiruria in California sea lions (Zalophus californianus) stranding with leptospirosis

    Science.gov (United States)

    Infection of California sea lions with leptospirosis can result in stranding and death of the animals. Shedding of the infectious organism contributes to spread of the disease to other animals and also poses a threat to human health. This is both for the public interacting with stranded animals and ...

  8. Unusual Mortality Events of Harbor Porpoise Strandings in North Carolina, 1997–2009

    Directory of Open Access Journals (Sweden)

    Aleta A. Hohn

    2013-01-01

    Full Text Available A marked increase in the frequency of harbor porpoises (Phocoena phocoena stranded in North Carolina in 2005 was declared as an Unusual Mortality Event (UME. Strandings occurred in January through May when harbor porpoises are seasonally present. Increased stranding rates were measured relative to a threshold to determine that the UME was occurring. The threshold analysis also revealed elevated strandings during 1999, an undeclared UME year. Recovered carcasses during 1999 and 2005 accounted for 39% of 261 strandings during 1997–2009. During 2005, of 43 strandings, primary or secondary causes of mortality included fishery interactions, emaciation, and interspecific aggression. Apart from small but significant differences in timing and condition of strandings, composition of strandings during UME and non-UME years was similar, with most being young-of-the-year and occurring during March and April, north of Cape Hatteras. Porpoises had high levels of parasitic infestation typical for this species. However, no indication of infectious disease and no cause of the 2005 event were found from gross and histologic findings. Response to UMEs is challenging, particularly along the expanses of North Carolina beaches, requiring additional effort to obtain carcasses in sufficiently fresh condition to determine the cause of these events.

  9. 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

  10. Dolphin Morbillivirus Associated with a Mass Stranding of Sperm Whales, Italy

    Science.gov (United States)

    Centelleghe, Cinzia; Di Provvido, Andrea; Di Renzo, Ludovica; Cardeti, Giusy; Cersini, Antonella; Fichi, Gianluca; Petrella, Antonio; Di Francesco, Cristina Esmeralda; Mignone, Walter; Casalone, Cristina; Di Guardo, Giovanni

    2017-01-01

    In September 2014, seven sperm whales were stranded along Italy’s Adriatic coastline. Postmortem investigations on 3 female adult whales and 1 male fetus carried by the largest female revealed molecular and immunohistochemical evidence of dolphin morbillivirus infection. A possible role of the virus in the stranding event was considered. PMID:27983493

  11. Parasitism as a factor (?) in single strandings of southern California cetaceans.

    Science.gov (United States)

    Dailey, M D; Walker, W A

    1978-08-01

    From 1970 to 1976 a total of 91 cetaceans was examined for parasites and associated pathology. Sixty of the animals were found stranded along a 100-mile section of southern California coastline while 31 were taken at sea. Parasites from 5 species of cetaceans are reported along with their possible role as a contributing factor in stranding behavior.

  12. 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.

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

    DEFF Research Database (Denmark)

    Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie;

    2014-01-01

    sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections...

  14. 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 synthesiz

  15. Orbiter Repair Maneuver Contingency Separation Methods and Analysis

    Science.gov (United States)

    Machula, Michael

    2005-01-01

    Repairing damaged thermal protection system tile requires the Space Shuttle to be oriented such that repair platform access from the International Space Station (ISS) is possible. To do this, the Space Shuttle uses the Orbiter Repair Maneuver (ORM), which utilizes the Shuttle Remote Manipulator System (SRMS) to rotate the Space Shuttle in relation to the ISS, for extended periods of time. These positions cause difficulties and challenges to performing a safe separation (no collision or thruster plume damage to sensitive ISS structures) should an inadvertent release occur or a contingency procedure require it. To help protect for an SRMS failure or other failures, a method for separating without collision and the ability to redock to ISS from the ORM configuration was needed. The contingency ORM separation solution elegantly takes advantage of orbital mechanics between ISS and the separating Space Shuttle. By pitching the ISS down approximately 45 degrees, in a majority of the ORM repair positions, the altitude difference between the ISS and Space Shuttle center of gravity is maximized. This altitude difference results in different orbital energies (orbital periods) causing objects to separate from each other without requiring translational firings. Using this method, a safe contingency ORM separation is made possible in many odd positions even though some separation positions point high powered thrusters directly at fragile ISS and Soyuz solar arrays. Documented in this paper are the development simulations and procedures of the contingency ORM separation and the challenges encountered with large constraints to work around. Lastly, a method of returning to redock with the ISS to pick up the stranded crew members (or transfer the final crew members) is explained as well as the thruster and ISS loads analysis.

  16. Separation anxiety: stress, tension and cytokinesis.

    Science.gov (United States)

    Mohan, Krithika; Iglesias, Pablo A; Robinson, Douglas N

    2012-07-15

    Cytokinesis, the physical separation of a mother cell into two daughter cells, progresses through a series of well-defined changes in morphology. These changes involve distinct biochemical and mechanical processes. Here, we review the mechanical features of cells during cytokinesis, discussing both the material properties as well as sources of stresses, both active and passive, which lead to the observed changes in morphology. We also describe a mechanosensory feedback control system that regulates protein localization and shape progression during cytokinesis.

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

    Science.gov (United States)

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

    2017-04-01

    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 involved eight different strand suppliers all over the world, of which four are using the bronze route (BR) process and four the internal-tin (IT) process. In total more than 500 tons have been produced including excess material covering losses during the conductor manufacturing process, in particular the cabling. The procurement is based on a functional specification where the main strand requirements like critical current, hysteresis losses, Cu ratio and residual resistance ratio are specified but not the strand production process or layout. This paper presents the analysis on the data acquired during the quality control (QC) process that was carried out to ensure the same conductor performance requirements are met by the different strand suppliers regardless of strand design. The strand QC is based on 100% billet testing and on applying statistical process control (SPC) limits. Throughout the production, samples adjacent to the strand pieces tested by the suppliers are cross-checked (‘verified’) by their respective DAs reference labs. The level of verification was lowered from 100% at the beginning of the procurement progressively to approximately 25% during the final phase of production. Based on the complete dataset of the TF strand production, an analysis of the SPC limits of the critical strand parameters is made and the related process capability indices are calculated. In view of the large-scale production and costs, key manufacturing parameters such as billet yield, number of breakages and piece-length distribution are also discussed. The results are compared among all the strand suppliers, focusing on the difference between BR and IT processes. Following

  18. Printed Spacecraft Separation System

    Energy Technology Data Exchange (ETDEWEB)

    Holmans, Walter [Planetary Systems Corporation, Silver Springs, MD (United States); Dehoff, Ryan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-10-01

    In this project Planetary Systems Corporation proposed utilizing additive manufacturing (3D printing) to manufacture a titanium spacecraft separation system for commercial and US government customers to realize a 90% reduction in the cost and energy. These savings were demonstrated via “printing-in” many of the parts and sub-assemblies into one part, thus greatly reducing the labor associated with design, procurement, assembly and calibration of mechanisms. Planetary Systems Corporation redesigned several of the components of the separation system based on additive manufacturing principles including geometric flexibility and the ability to fabricate complex designs, ability to combine multiple parts of an assembly into a single component, and the ability to optimize design for specific mechanical property targets. Shock absorption was specifically targeted and requirements were established to attenuate damage to the Lightband system from shock of initiation. Planetary Systems Corporation redesigned components based on these requirements and sent the designs to Oak Ridge National Laboratory to be printed. ORNL printed the parts using the Arcam electron beam melting technology based on the desire for the parts to be fabricated from Ti-6Al-4V based on the weight and mechanical performance of the material. A second set of components was fabricated from stainless steel material on the Renishaw laser powder bed technology due to the improved geometric accuracy, surface finish, and wear resistance of the material. Planetary Systems Corporation evaluated these components and determined that 3D printing is potentially a viable method for achieving significant cost and savings metrics.

  19. Virus separation using membranes.

    Science.gov (United States)

    Grein, Tanja A; Michalsky, Ronald; Czermak, Peter

    2014-01-01

    Industrial manufacturing of cell culture-derived viruses or virus-like particles for gene therapy or vaccine production are complex multistep processes. In addition to the bioreactor, such processes require a multitude of downstream unit operations for product separation, concentration, or purification. Similarly, before a biopharmaceutical product can enter the market, removal or inactivation of potential viral contamination has to be demonstrated. Given the complexity of biological solutions and the high standards on composition and purity of biopharmaceuticals, downstream processing is the bottleneck in many biotechnological production trains. Membrane-based filtration can be an economically attractive and efficient technology for virus separation. Viral clearance, for instance, of up to seven orders of magnitude has been reported for state of the art polymeric membranes under best conditions.This chapter summarizes the fundamentals of virus ultrafiltration, diafiltration, or purification with adsorptive membranes. In lieu of an impractical universally applicable protocol for virus filtration, application of these principles is demonstrated with two examples. The chapter provides detailed methods for production, concentration, purification, and removal of a rod-shaped baculovirus (Autographa californica M nucleopolyhedrovirus, about 40 × 300 nm in size, a potential vector for gene therapy, and an industrially important protein expression system) or a spherical parvovirus (minute virus of mice, 22-26 nm in size, a model virus for virus clearance validation studies).

  20. Acute hypoxia and hypoxic exercise induce DNA strand breaks and oxidative DNA damage in humans

    DEFF Research Database (Denmark)

    Møller, P; Loft, S; Lundby, C

    2001-01-01

    ; lymphocytes were isolated for analysis of DNA strand breaks and oxidatively altered nucleotides, detected by endonuclease III and formamidipyridine glycosylase (FPG) enzymes. Urine was collected for 24 h periods for analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a marker of oxidative DNA damage....... Urinary excretion of 8-oxodG increased during the first day in altitude hypoxia, and there were more endonuclease III-sensitive sites on day 3 at high altitude. The subjects had more DNA strand breaks in altitude hypoxia than at sea level. The level of DNA strand breaks further increased immediately after...... exercise in altitude hypoxia. Exercise-induced generation of DNA strand breaks was not seen at sea level. In both environments, the level of FPG and endonuclease III-sensitive sites remained unchanged immediately after exercise. DNA strand breaks and oxidative DNA damage are probably produced by reactive...