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Sample records for rrp nb3sn strands

  1. Development and Test of Nb3SN Cos-Theta Coils Made of High-Jc RRP Strands

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

    A series of 1-m long Nb3Sn dipole magnets have been built at Fermilab in an attempt to refine the wind-and-react technology for Nb3Sn conductor. Models have been made with MJR and PIT strand with varying degrees of success. Subsequently two new dipole "mirror" magnets based on RRP Nb3Sn coils were constructed and tested. This paper describes the design, fabrication and test results of those magnets.

  2. Quench Performance of Nb3Sn Cos-Theta Coils Made of 108/127 Rrp Strands

    NASA Astrophysics Data System (ADS)

    Zlobin, A. V.; Ambrosio, G.; Andreev, N.; Barzi, E.; Bossert, R.; Carcagno, R.; Kashikhin, V. S.; Kashikhin, V. V.; Lamm, M. J.; Nobrega, F.; Novitski, I.; Orris, D.; Pischalnikov, Yu.; Shpakov, D.; Sylvester, C.; Tartaglia, M.; Tompkins, J. C.; Turrioni, D.; Yamada, R.; Yuan, A.

    2008-03-01

    A series of 1-m long Nb3Sn dipole models has been built at Fermilab in an attempt to refine the wind-and-react technology for Nb3Sn accelerator magnets. Three models made with Powder-in-Tube Nb3Sn strand reached their design field of 10 T demonstrating a good reproducibility of magnet quench performance and field quality. Recently a new dipole "mirror" model based on Nb3Sn coil made of improved Restack Rod Process (RRP) strand was constructed and tested reaching the maximum field above 11 T. This paper describes the parameters of the RRP strand and cable used as well as the design, fabrication and test results of this magnet.

  3. Effect of Subelement Spacing in Rrp Nb3Sn Deformed Strands

    NASA Astrophysics Data System (ADS)

    Barzi, E.; Turrioni, D.; Alsharo'a, M.; Field, M.; Hong, S.; Parrell, J.; Yamada, R.; Zhang, Y.; Zlobin, A. V.

    2008-03-01

    The Restacked Rod Process (RRP) is the Nb3Sn strand technology presently producing the largest critical current densities at 4.2 K and 12 T. However, when subject to transverse plastic deformation, RRP subelements (SE) merge into each other, creating larger filaments with a somewhat continuous barrier. In this case, the strand sees a larger effective filament size and its instability can dramatically increase locally leading to a 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.

  4. Development and test of Nb3sn cos-theta coils made of high-jc rrp strands

    SciTech Connect

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

    2005-10-01

    A series of 1-m long Nb3Sn dipole magnets have been built at Fermilab in an attempt to refine the wind-and-react technology for Nb{sub 3}Sn conductor. Models have been made with MJR and PIT strand with varying degrees of success. Subsequently two new dipole ''mirror'' magnets based on RRP Nb{sub 3}Sn coils were constructed and tested. This paper describes the design, fabrication and test results of those magnets.

  5. Effect of Subelement Size, Strand Size and RRR on Stability of RRP Nb3Sn Wires

    NASA Astrophysics Data System (ADS)

    Barzi, Emanuela; Moio, Simone; Zlobin, Alexander; Superconductor R&D Team

    2013-03-01

    Using ample statistics gathered from state-of-the-art Nb3Sn strands of different designs and sizes developed by Oxford Superconductor Technology (OST), the effects on the strand current density of subelement size, Residual Resistivity Ratio (RRR) of the copper matrix, and strand size were measured, analyzed and compared with the predictions of a stability model. The data confirmed a strong dependence of the instability current density on the subelement size, but also hinted at effects of non-uniform current distribution in the wire. The data also show that the instability current relates so weakly to RRR that it is possible to cleanly identify a common instability behavior as a function of subelement size and of strand size despite an ample range of RRR. This analysis was performed both at 4.2 K and 1.9 K.

  6. Fabrication and test of 4M long Nb3SN quadrupole coil made of RRP-114/127 strand

    NASA Astrophysics Data System (ADS)

    Bossert, Rodger; Ambrosio, G.; Andreev, Nikolai; Barzi, Emanuela; Chlachidze, Guram; Kashikhin, Vadim; Lamm, Michael; Nobrega, Alfred; Novitski, Igor; Orris, Darryl; Tartaglia, Mike; Turrioni, Daniele; Yamada, Ryuji; Zlobin, Alexander

    2012-06-01

    Fermilab is collaborating with Lawrence Berkeley National Laboratory (LBNL) and Brookhaven National Laboratory (BNL) within the US-LHC Accelerator Research Project (US-LARP collaboration) to develop a large-aperture Nb3SN superconducting quadrupole for the Large Hadron Collider (LHC) luminosity upgrade. Several two-layer quadrupole models of the 1-meter and 3.4-meter length with 90 mm apertures have been fabricated and tested by the US-LARP collaboration. High-Jc Nb3SN RRP-54/61 strand was used for nearly all models. Large flux jumps typical for this strand, due to the large sub-element diameter, limited magnet quench performance at temperatures below 2.5-3K. This paper summarizes the fabrication and test by Fermilab of LQM01, a long quadrupole coil test structure (quadrupole mirror) with the first 3.4 m quadrupole coil made of more stable RRP-114/127 strand. The coil and structure are fully instrumented with voltage taps, full bridge strain gauges and strip heaters to monitor preload, thermal properties and quench behavior. Measurements during fabrication are reported, including preload during the yoke welding process. Testing is done at 4.5 K, 1.9 K and a range of intermediate temperatures. The test results include magnet strain and quench performance during training, as well as quench studies of current ramp rate and temperature dependence from 1.9 K to 4.5 K.

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

    SciTech Connect

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

    2007-07-01

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

  8. Transport and Magnetization Properties of rolled RRP Nb3Sn Strands.

    SciTech Connect

    Ghosh,A.K.; Cooley, L.D.; Dietderich, D.R.; Sun, L.

    2007-08-27

    Restack Rod Process (RRP) strands with 54 and 108 sub-elements were rolled from 0.7 mm diameter to 0.45 mm thickness to simulate the deformation of strands at the edges of Rutherford cables. Various diagnoses were then applied to assess performance and stability. Transport measurements were used to assess the effect of rolling on the critical current. Magnetization measurements were used to probe superconducting pathway bridging between deformed sub-elements. The copper residual resistivity ratio RRR was also measured to assess tin contamination due to thinned or ruptured diffusion barriers. While systematic changes were observed in all three measurements with increasing deformation, RRR showed the strongest changes. The implications of these measurements for cable stability, and their relationship to observations of the strand cross-section by light microscopy, are discussed.

  9. Development and test of Nb3Sn cos-theta magnets based on RRP and PIT strands

    SciTech Connect

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

    2005-09-01

    As part of the High Field Magnet program at Fermilab three cos({theta}) magnets--two mirror dipole magnets utilizing RRP cable and one dipole magnet utilizing PIT cable--have been designed, fabricated and tested recently. Both mirror magnets with RRP strands only reached {approx}50-60% of their estimated critical current limit. The PIT conductor based dipole however reached its critical current limit producing over 10 T magnetic field in the bore of the magnet. This paper describes the parameters of superconducting strands and cable, the details of magnet design and fabrication procedure, and reports the results.

  10. Fabrication and test of 4m long Nb3Sn quadrupole coil made of RRP-114-127 strand

    SciTech Connect

    Bossert, R.; Ambrosio, G.; Andreev, N.; Barzi, E.; Chlachidze, G.; Kashikhin, V.V.; Lamm, M.; Nobrega, A.; Novitski, I.; Orris, D.; Tartaglia, M.; /Fermilab

    2011-06-01

    Fermilab is collaborating with LBNL and BNL (US-LARP collaboration) to develop a large-aperture Nb{sub 3}Sn superconducting quadrupole for the Large Hadron Collider (LHC) luminosity upgrade. Several two-layer quadrupole models of the 1-meter and 3.4-meter length with 90mm apertures have been fabricated and tested by the US-LARP collaboration. High-Jc RRP-54/61 strand was used for nearly all models. Large flux jumps typical for this strand due to the large sub-element diameter limited magnet quench performance at temperatures below 2.5-3K. This paper summarizes the fabrication and test by Fermilab of LQM01, a long quadrupole coil test structure (quadrupole mirror) with the first 3.4m quadrupole coil made of more stable RRP-114/127 strand. The coil and structure are fully instrumented with voltage taps, full bridge strain gauges and strip heaters to monitor preload, thermal properties and quench behavior. Measurements during fabrication are reported, including preload during the yoke welding process. Testing is done at 4.5K, 1.9K and a range of intermediate temperatures. The test results include magnet strain and quench performance during training, as well as quench studies of current ramp rate and temperature dependence from 1.9K to 4.5K.

  11. Systematic changes of the Nb-Sn reaction with time, temperature and alloying in Restacked-Rod-Process (RRP) Nb3Sn strands

    SciTech Connect

    Ghosh, A.K.; Sperry, E.A.; D'Ambra, J.; Cooley, L.D.; /Fermilab

    2008-09-01

    Reaction heat treatments spanning 605 to 750 C and 24 to {approx}400 hours were applied to several sets of RRP strands. Magnetization and transport measurements were used to track the changes of superconducting properties and the amounts of Nb{sub 3}Sn formed. The experiments showed that temperature increases of 15 C produced equivalent properties in half the time within the temperature range 620-680 C. This result was the same whether Ta or Ti was used to alloy the Nb{sub 3}Sn. The bulk pinning force Fp for Ta-alloyed wires displayed a significant drop for temperatures outside the range above, due to tin gradients at low temperatures and grain growth at high temperatures. The F{sub p} drop at high reaction temperatures prevents wire technology from taking advantage of significantly higher Kramer-plot intercept H{sub K} for high-temperature reactions. On the other hand, Ti alloying provides a quick and potent means to increase H{sub K} at reaction temperatures for which F{sub p} remains high.

  12. Development and Study of NB3SN Strands and Cables for High-Field Accelerator Magnets

    NASA Astrophysics Data System (ADS)

    Barzi, E.; Andreev, N.; Bossert, M.; Kashikhin, V. V.; Turrioni, D.; Yamada, R.; Zlobin, A. V.

    2010-04-01

    The high performance Nb3Sn strand produced by Oxford Superconducting Technology (OST) with the Restack Rod Process (RRP) and a 127 restack design is the baseline conductor presently used in the Fermilab's accelerator magnet R&D program. The original RRP-127 design was further improved in stability by increasing the Cu thickness between subelements after proving the effectiveness of this method in reducing subelement merging [1-3]. A number of RRP-127 billets of various cross sections (RRP-102/127, RRP-108/127 and RRP-114/127) were produced to optimize the design with respect to strand plastic deformation during cabling. The behavior of these new strands was studied using virgin and deformed strand samples, and compared with that of the RRP-54/61 stack design. A Rutherford cable made of 0.7 mm strands was also produced to be used in high field quadrupoles. This paper describes the RRP-127 strand development, and results of strand and cable analyses.

  13. Effect of Temperature and Deformation on Nb3Sn Strands Instabilities

    NASA Astrophysics Data System (ADS)

    Barzi, E.; Del Frate, L.; Turrioni, D.; Zlobin, A. V.

    2006-03-01

    The critical current of Nb3Sn strands used in Fermilab's high field magnets was measured at low and high fields under various experimental conditions using the voltage-current (V-I) and voltage-field (V-H) methods. The strands were commercially produced using Restack Rod Process (RRP) and Powder-in-Tube (PIT) technologies. Both round and deformed strands were studied. Measurements were performed at the Fermilab's Short Sample Test Facility using a 2-kA sample holder with a low contact resistivity. V-I characteristics at fields above 10-12T with a smooth transition from the superconducting to normal phase allowed determining strand critical current. V-I and V-H measurements at low fields showed premature quenches due to magnetic instability in strands with high critical current density and large effective filament size. The effects of strand deformation and RRR as well as test temperature were studied. This paper describes the Nb3Sn strand parameters, the equipment and measurement methods used, and the results of the critical current measurements at low and high fields. The effect of magnetic instabilities is analyzed for different measurement conditions and compared to the predictions of an instability model.

  14. Effect of cubic equiaxed grains and its Ti-stabilizing performance in Nb3Sn strands

    NASA Astrophysics Data System (ADS)

    Chaowu, Zhang; Lian, Zhou; Sulpice, Andre; Soubeyroux, Jean-Louis; Xiande, Tang; Verwaerde, Christophe; Hoang, Gia Ky

    2009-06-01

    Two kinds of multifilament internal-Sn Nb3Sn superconducting strands were fabricated through the RRP method, one with 2 wt% of Ti alloyed in an Sn core and the other just pure Sn. Four reaction temperatures of 650, 675, 700 and 725 °C and 128 h duration were applied for A15 phase formation heat treatment after a Cu-Sn alloying procedure of 210 °C/50 h+340 °C/25 h. Through the standard four-probe technique the heat-treated coil samples were examined for the transport non-Cu JC variation with applied field B which was then used to calculate the flux pinning force variation FP-B. The samples' phase microstructure were also observed by means of FESEM. The obtained results demonstrate that for fully reacted Nb3Sn superconductors the transport critical current density JC is more importantly affected by the cubic equiaxed morphology than by grain dimension, due to its much stronger flux pinning performance of the morphology. Ti addition in Sn stabilizes the cubic equiaxed grains at lower reaction temperature so that the HT temperature is effectively reduced, the flux pinning strength is largely reinforced and thus the transport non-Cu JC is substantially promoted. Funds: this research project was supported by the France-China Collaboration Research contract CNRS no. 722441 and the SUST doctoral foundation BJ07-07.

  15. Measurements of Rrr Variation in Strands Extracted from Nb3Sn-TYPE Rutherford Cables

    NASA Astrophysics Data System (ADS)

    Sumption, M. D.; Nazareth, V.; Barzi, E.; Turrioni, D.; Yamada, R.; Zlobin, A. V.; Collings, E. W.

    2008-03-01

    Modern high-Jc Nb3Sn strands and cables for use in high field accelerator magnets suffer from flux jump-related instabilities at low magnetic fields. These instabilities are determined by the values of Jc, deff, and RRR. It has been postulated that local RRR is a more relevant parameter than average RRR for stability considerations, but the range of RRR values present in a cable has not yet been quantified. Thus, longitudinal variations of RRR were estimated from multiple-tap measurements along the length of strands extracted from mixed strand cables. The cables had either 27 or 28 strands, two different keystone angles, and four different levels of compaction. One type of RRP strand was extracted from each cable, reacted, and then measured. RRR of the straight sections (on the faces) was above 100, while that at the edges of the strand was estimated to be an order of magnitude smaller ≈10. Selected regions of the strand with locally depressed RRR were examined by SEM and EDS to check for Sn leakage and examine the type of strand failure present. The implications of these measurements for stability were then discussed.

  16. Investigation of multifilamentary Nb 3Sn strand for ITER by internal Sn process

    NASA Astrophysics Data System (ADS)

    Zhang, P. X.; Zhou, L.; Tang, X. D.; Li, C. G.; Wu, Y.; Li, K.; Yan, G.; Yang, M.; Feng, Y.; Liu, X. H.; Weng, P. D.; Lu, Y. F.

    2006-10-01

    By internal Sn process we have successfully fabricated the multifilamentary Nb3Sn strand with a diameter of 0.79 mm, which has 5616-6270 filaments. A two-step heat treatment was used for the Nb3Sn strands. The first step is related to bronzing process between Cu and Sn at a temperature range of 200-600 °C, whereas the second step for the formation of superconducting Nb3Sn phase at 600-800 °C. A non-Cu Jc (12 T, 4.2 K) value of 1087 A/mm2 has been obtained. The microstructure and transport property of strands have been discussed.

  17. Nb3Sn RRP® strand and Rutherford cable development for a 15 T dipole demonstrator

    DOE PAGESBeta

    Barzi, E.; Andreev, N.; Li, P.; Lombardo, V.; Turrioni, D.; Zlobin, A. V.

    2016-03-16

    Keystoned Rutherford cables made of 28 strands and with a stainless steel core were developed and manufactured using 1 mm Nb3Sn composite wires produced by Oxford Superconducting Technology with 127 and 169 restacks using the Restacked-Rod-Process®. Furthermore, the performance and properties of these cables were studied to evaluate possible candidates for 15 T accelerator magnets.

  18. Study of Nb3Sn strands and cables for Fermilab's common coil dipole models

    NASA Astrophysics Data System (ADS)

    Barzi, E.; Ambrosio, G.; Fratini, M.; Bauer, P.; Scanlan, R. M.; Yamada, R.; Zlobin, A. V.

    2002-05-01

    Fermilab is developing 10-12 T superconducting dipole magnets for future accelerators based on Nb3Sn conductor. Within the High Field Magnet Project, a common coil design was chosen for magnet R&D using the react & wind approach. Based on cable studies in which a variety of designs were tried and tested using inexpensive ITER strands, a 41-strand cable was used for a racetrack coil, whereas a 60-strand cable was preferred for the common coil model. Multifilamentary Nb3Sn strands 0.7 mm in diameter to be respectively used in the racetrack coil and the common coil model were purchased from OST (Modified Jelly Roll technology) and IGC (Internal Tin technology). They are herein characterized by Ic, n-value, residual resistivity ratio, and magnetization. Results of cabling and bending degradation are also presented.

  19. Reduce Nb3Sn Strand Deformation when Fabricating High Jc Rutherford Cables

    SciTech Connect

    Peng, Xuan

    2012-12-17

    During Phase I, our efforts were to reduce subelements deformation when fabricating Nb3Sn Rutherford cables. Our first focus is on 217-sublement tube type strand. We successfully made a few billets in OD tube with different Cu spacing between subelements, and supplied the strands to Fermi Lab for cabling. Through the rolling test characterization, these types of strands did not have enough bonding between subelements to withstand the deformation. We saw copper cracking between subelements in the deformed strands. We scaled up the billet from OD to 1.5 OD, and made two billets. This greatly improves the bonding. There is no copper cracking in the deformed strands when we scaled up the diameter of the billets. Fermi Lab successfully made cables using one of this improved strands. In their cables, no Cu cracking and no filament bridging occurred. We also successfully made a couple of billets with hex OD and round ID subelements for 61-subelement restack. Due to the lack of bonding, we could not judge its cabling property properly. But we know through this experiment, we could keep the Nb round, once we select the proper Cu spacing.

  20. Correlation of filament distortion and RRR degradation in drawn and rolled PIT and RRP Nb3Sn wires

    NASA Astrophysics Data System (ADS)

    Brown, M.; Tarantini, C.; Starch, W.; Oates, W.; Lee, P. J.; Larbalestier, D. C.

    2016-08-01

    PIT and RRP® Nb3Sn strands are being developed for high field accelerator magnet upgrades for the high luminosity LHC. Here we report a quantitative study of the shape and position of PIT filaments and RRP® sub-elements after rolling lengths of unreacted PIT and RRP® round wires to simulate cabling deformation. In the as-drawn condition, filament shape distortion occurs preferentially in the outer ring filaments. By contrast, rolling induces non-uniform shear bands that generate greater distortion of inner ring filaments. By making a full digitization of the shapes of all filaments, we find that a critical distortion occurs for thickness reductions between 10% and 20% when filament shapes in inner filament rings heavily degrade, especially in the vicinity of the strong 45° shear bands imposed by the rolling. It is well known that maintaining diffusion barrier integrity is vital to retaining adequate RRR in the stabilizing copper needed for magnet stability. Diffusion barrier breaks occur preferentially in these distorted inner filaments and drive local Sn leakage during reaction, increasing RRR degradation.

  1. Correlation of filament distortion and RRR degradation in drawn and rolled PIT and RRP Nb 3 Sn wires

    DOE PAGESBeta

    Brown, M.; Tarantini, C.; Starch, W.; Oates, W.; Lee, P. J.; Larbalestier, D. C.

    2016-07-11

    PIT and RRP® Nb3Sn strands are being developed for high field accelerator magnet upgrades for the high luminosity LHC. Here we report a quantitative study of the shape and position of PIT filaments and RRP® sub-elements after rolling lengths of unreacted PIT and RRP® round wires to simulate cabling deformation. In the as-drawn condition, filament shape distortion occurs preferentially in the outer ring filaments. By contrast, rolling induces non-uniform shear bands that generate greater distortion of inner ring filaments. By making a full digitization of the shapes of all filaments, we find that a critical distortion occurs for thickness reductionsmore » between 10% and 20% when filament shapes in inner filament rings heavily degrade, especially in the vicinity of the strong 45° shear bands imposed by the rolling. It is well known that maintaining diffusion barrier integrity is vital to retaining adequate RRR in the stabilizing copper needed for magnet stability. Diffusion barrier breaks occur preferentially in these distorted inner filaments and drive local Sn leakage during reaction, increasing RRR degradation.« less

  2. Increasing the Jc of Tube-Type Nb3Sn Strands

    SciTech Connect

    Peng, Xuan

    2012-12-17

    In this Phase I, we successfully made strands with better Cu/Sn ratio to reduce the coarse Nb3Sn grain region, thereby providing the potential of increasing the non-Cu Jc in the Phase II and scaling up to 2 billets with 331 subelements. In order to improve the strandÃ's high field properties, we successfully doped low amount of Ti in the subelements and made a 217-subelement wire which has been drawn down to 0.7 mm without any breakage. This strand gave subelement size of 35m. We will scale up the Ti-doped billet to 271-subelement in 1.5 billet in this proposed Phase II. The hexagonal shaped subelements with round Nb-Sn have been developed for a 61-subelement restack. Thus the results indicated that for 217-subelement restack in a billet we have the potential to draw down this type of construction without problems while maintaining a good array to react more Nb to get higher non-Cu Jc in the Phase II.

  3. Texture in state-of-the-art Nb3Sn multifilamentary superconducting wires

    NASA Astrophysics Data System (ADS)

    Scheuerlein, C.; Arnau, G.; Alknes, P.; Jimenez, N.; Bordini, B.; Ballarino, A.; Di Michiel, M.; Thilly, L.; Besara, T.; Siegrist, T.

    2014-02-01

    The texture of Nb3Sn in recent multifilamentary composite wires has been studied by neutron diffraction, synchrotron x-ray diffraction and electron backscatter diffraction. In powder-in-tube (PIT) type superconductors the Nb precursor filaments exhibit a strong <110> fiber texture as a consequence of the severe cold drawing process, and a <110> texture is also observed in the Nb3Sn. In the Nb-Ta precursor of the restacked rod process (RRP) strand there is an additional texture component, and in both Ta-alloyed and Ti-alloyed RRP type conductors the Nb3Sn grains grow with a preferential <100> orientation.

  4. Critical current scaling and the pivot-point in Nb3Sn strands

    NASA Astrophysics Data System (ADS)

    Tsui, Y.; Hampshire, D. P.

    2012-05-01

    Detailed measurements are provided of the engineering critical current density (Jc) and the index of transition (n-value) of two different types of advanced ITER Nb3Sn superconducting strand for fusion applications. The samples consist of one internal-tin strand (OST) and two bronze-route strands (BEAS I and BEAS II—reacted using different heat treatments). Tests on different sections of these wires show that prior to applying strain, Jc is homogeneous to better than 2% along the length of each strand. Jc data have been characterized as a function of magnetic field (B ≤ 14.5 T), temperature (4.2 K ≤ T ≤ 12 K) and applied axial strain ( - 1% ≤ ɛA ≤ 0.8%). Strain-cycling tests demonstrate that the variable strain Jc data are reversible to better than 2% when the applied axial strain is in the range of - 1% ≤ ɛA ≤ 0.5%. The wires are damaged when the intrinsic strain (ɛI) is ɛI ≥ 0.55% and ɛI ≥ 0.23% for the OST and BEAS strands, respectively. The strain dependences of the normalized Jc for each type of strand are similar to those of prototype strands of similar design measured in 2005 and 2008 to about 2% which makes them candidate strands for a round-robin interlaboratory comparison. The Jc data are described by Durham, ITER and Josephson-junction parameterizations to an accuracy of about 4%. For all of these scaling laws, the percentage difference between the data and the parameterization is larger when Jc is small, caused by high B, T or |ɛI|. The n-values can be described by a modified power law of the form n=1+r{I}_{{c}}^{s}, where r and s are approximately constant and Ic is the critical current. It has long been known that pivot-points (or cross-overs) in Jc occur at high magnetic field and temperature. Changing the magnetic field or temperature from one side of the pivot-point to the other changes the highest Jc sample to the lowest Jc sample and vice versa. The pivot-point follows the B-T phase boundary associated with the upper

  5. Analysis of Nb3Sn Strand Microstructure After Full-size SULTAN Test of ITER TF Conductor Sample

    NASA Astrophysics Data System (ADS)

    Kaverin, D.; Potanina, L.; Shutov, K.; Vysotsky, V.; Tronza, V.; Mitin, A.; Abdyukhanov, I.; Alekseev, M.

    The study of defects generated in superconducting filaments of Nb3Sn strands under electromagnetic and thermal cycling was carried out for the TFRF3 cable-in-conduit-conductor (CICC) sample that passed final testing inthe SULTAN test facility. The TFRF3 sample was manufactured forthe qualification of the RF Toroidal Field (TF) CICC. The strand samples were taken from different locations in the cross-section of TFRF3 and different positions along its axis in relation to background magnetic field. Qualitative and quantitative analysis of defects were carried out using metallographic analysis of images obtained by Laser Scanning Microscope. We analyzed number, type, and distribution of defects in filaments of the Nb3Sn strand samples extracted from different petals of TFRF3 in dependence on thestrand location in the cross-section (the center of petal, nearby the spiral, nearby the outer jacket) in the high field zone (HFZ). The results about the defects amount and their distribution are presented and discussed.

  6. Phase transformations during the reaction heat treatment of Nb3Sn superconductors

    NASA Astrophysics Data System (ADS)

    Scheuerlein, C.; Di Michiel, M.; Thilly, L.; Buta, F.; Peng, X.; Gregory, E.; Parrell, J. A.; Pong, I.; Bordini, B.; Cantoni, M.

    2010-06-01

    The evolution of Nb containing phases during the diffusion heat treatment of three different high critical current Nb3Sn strand types is compared, based on synchrotron X-ray diffraction results that have been obtained at the ID15 beam line of the European Synchrotron Radiation Facility (ESRF). In all strands studied, Nb3Sn formation is preceded by the formation of a Cu-Nb-Sn ternary phase, NbSn2 and Nb6Sn5. As compared to the PIT and Tube Type strand, the amount of these phases formed in the RRP strand is relatively small. In the RRP strand subelements with a fine filament structure Nb3Sn grows more quickly, thereby preventing to a large extent the formation of the other higher tin phases.

  7. The effect of axial and transverse loading on the transport properties of ITER Nb3Sn strands

    NASA Astrophysics Data System (ADS)

    Nijhuis, A.; Pompe van Meerdervoort, R. P.; Krooshoop, H. J. G.; Wessel, W. A. J.; Zhou, C.; Rolando, G.; Sanabria, C.; Lee, P. J.; Larbalestier, D. C.; Devred, A.; Vostner, A.; Mitchell, N.; Takahashi, Y.; Nabara, Y.; Boutboul, T.; Tronza, V.; Park, S.-H.; Yu, W.

    2013-08-01

    The differences in thermal contraction of the composite materials in a cable in conduit conductor (CICC) for the International Thermonuclear Experimental Reactor (ITER), in combination with electromagnetic charging, cause axial, transverse contact and bending strains in the Nb3Sn filaments. These local loads cause distributed strain alterations, reducing the superconducting transport properties. The sensitivity of ITER strands to different strain loads is experimentally explored with dedicated probes. The starting point of the characterization is measurement of the critical current under axial compressive and tensile strain, determining the strain sensitivity and the irreversibility limit corresponding to the initiation of cracks in the Nb3Sn filaments for axial strain. The influence of spatial periodic bending and contact load is evaluated by using a wavelength of 5 mm. The strand axial tensile stress-strain characteristic is measured for comparison of the axial stiffness of the strands. Cyclic loading is applied for transverse loads following the evolution of the critical current, n-value and deformation. This involves a component representing a permanent (plastic) change and as well as a factor revealing reversible (elastic) behavior as a function of the applied load. The experimental results enable discrimination in performance reduction per specific load type and per strand type, which is in general different for each manufacturer involved. Metallographic filament fracture studies are compared to electromagnetic and mechanical load test results. A detailed multifilament strand model is applied to analyze the quantitative impact of strain sensitivity, intrastrand resistances and filament crack density on the performance reduction of strands and full-size ITER CICCs. Although a full-size conductor test is used for qualification of a strand manufacturer, the results presented here are part of the ITER strand verification program. In this paper, we present an

  8. Critical current scaling laws for advanced Nb3Sn superconducting strands for fusion applications with six free parameters

    NASA Astrophysics Data System (ADS)

    Lu, Xi Feng; Taylor, David M. J.; Hampshire, Damian P.

    2008-10-01

    This paper presents comprehensive measurements on three advanced ITER internal-tin Nb3Sn strands manufactured by Oxford Superconducting Technology (OST), Outokumpu Superconductors (OKSC) and Luvata Italy (OCSI) for fusion applications. The engineering critical current density (JC) at 10 µV m-1 and the index (n) characterized over the range 10-100 µV m-1 are presented as a function of magnetic field (B<=15 T in Durham and B<=28 T at the European high-field laboratory in Grenoble), temperature (2.35 K<=T<=14 K) and intrinsic strain (-1.1%<=ɛI<=0.5%). Consistency tests show that the variable strain JC data are homogeneous (± 5%) along the length of the strand, and that there is a good agreement between different samples measured in Durham and in other laboratories (at zero applied strain). Limited strain cycling (fatigue) tests demonstrate that there is no significant degradation in the critical current density in the strands due to cyclic mechanical loads. JC is accurately described by the scaling law that was derived using microscopic and phenomenological theoretical analysis and n is described by the modified power law of the form n = 1+rICs, where r and s are approximately constant. Using variable strain high magnetic field data at 2.35 K for the OCSI sample, it is demonstrated that these laws can be extended to describe data below 4.2 K. For these advanced strands, thirteen, nine and six free parameter fits to the data are considered. When thirteen or nine free parameters are used, the scaling laws fit the data very accurately. The accuracy with which the scaling law derived from fitting data taken at 4.2 K alone fits all the variable temperature data if calculated errors in fitting JC are shown to be primarily determined by uncertainties in TC. It is shown that six free parameter fits can successfully be used when, as with these advanced strands, the strain dependence of the normalized effective upper critical field at zero temperature is accurately known

  9. Increase Jc by Improving the Array of Nb3Sn strands for Fusion Application

    SciTech Connect

    Peng, Xuan

    2012-12-17

    During Phase I, our efforts were focusing on improving the array of subelement in the tube type strands by hardening the Sn core and the subelement matrix to effectively increase the Jc of the strands. Below is a summary of the results. 1) We were unsuccessful in improving the array using a Cu-Sn matrix approach. 2) We slightly improved the array using Sn with 1.5at%Ti doped core, and a 217-subelement restacked strand was made and drawn down without any breakage. 3) We greatly improved the array using the Glidcop Al-15 to replace the pure Cu sheath in the subelement, and a 217-subelement restacked strand was made and drawn down. Both strands have very good drawability and the array showed good improvement. 4) We also improved the array using improved wire drawing techniques using Hyper Tech's new caterpillar wire drawing machines to enable straight wire drawing for the entire wire drawing process. 5) The 919-subelement restack strand shows its non-Cu Jc over 2100 A/mm2 at 12 T/4.2 K and AC loss of 508 mJ/cm3.

  10. Measurement of inter-strand contact resistance in epoxy impregnated Nb3Sn Rutherford cables

    SciTech Connect

    Giorgio Ambrosio et al.

    2003-10-07

    An apparatus for the measurement, under transverse pressure, of the inter-strand contact resistance in epoxy-impregnated Nb{sub 3}Sn Rutherford cables has been recently assembled at Fermilab. Procedures have been developed to instrument and measure samples extracted from Nb{sub 3}Sn coils. Samples were extracted from coils fabricated with the Wind-and-React and the React-and-Wind technology, both presently under development at Fermilab. A ceramic binder is used to improve the insulation and to simplify the fabrication of coils using the Wind-and-React technology. Synthetic oil is used to prevent sintering during the heat treatment of coils to be wound after reaction. In order to evaluate the effects of the ceramic binder and of the synthetic oil on the inter-strand resistance, measurements of samples extracted from coils were compared with measurements of cable stacks with varying characteristics. In this paper we describe the apparatus, the sample preparation, the measurement procedure, and the results of the first series of tests.

  11. Nb3Sn cable development for the 11 T DS dipole demonstration model

    NASA Astrophysics Data System (ADS)

    Barzi, Emanuela; Lombardo, Vito; Nobrega, Alfred; Turrioni, Daniele; Yamada, Ryuji; Zlobin, Alexander; Karppinen, Mikko

    2012-06-01

    Fermilab (FNAL) and CERN have started the development of 11 T 11-m long Nb3Sn dipoles to replace a number of LHC NbTi dipoles and free space for cold collimators in the LHC DS areas. An important step in the design of these magnets is the development of the high aspecept ratio Nb3Sn cable to achieve the nominal field of 11 T at the nominal LHC operation current of 11.8 kA at 1.9 with 20% margin. Keystoned Cu wires and Nb3Sn RRP strand both mechanical stability and minimal damage to the restack design to be used in the magnet short models. Each cable was characterized electrically for transport properties degradation at high field and for low feild stability, and metallographically for internal damage.

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

    SciTech Connect

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

    2010-01-01

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

  13. Measurements of Nb3Sn conductor dimension changes during heat treatment

    NASA Astrophysics Data System (ADS)

    Bocian, D.; Ambrosio, G.; Whitson, G. M.

    2012-06-01

    During the heat treatment of Nb3Sn coils the conductor material properties change significantly. These effects together with the changes of the conductor dimensions during heat treatment may introduce large strains in the coils for accelerator magnets. The US LHC Accelerator Research Program (LARP) has initiated a study aiming at understanding the thermal expansion and contraction of Nb3Sn strands, cables and coils during heat treatment. Several measurements on OST RRP 54/61 and OST RRP 108/127 strands were performed, and a few more are in progress, in order to have sufficient inputs for finite element simulation of the dimensional changes during heat treatment. Three strand quantities were measured: diameter change, length change and twist change. The measured types of strands (OST RRP 54/61 and OST RRP 108/127) demonstrated diameter change by +2.15% and +1.88%, and length change by +0.035% and -0.045% respectively. The measured twist change after reaction was about 4%. In this paper an impact of twist change on strand length change was studied, as well. The results of measurements show a significant contribution of twist change to the strand length change.

  14. RAPID COMMUNICATION: Influence of Ti and Ta doping on the irreversible strain limit of ternary Nb3Sn superconducting wires made by the restacked-rod process

    NASA Astrophysics Data System (ADS)

    Cheggour, N.; Goodrich, L. F.; Stauffer, T. C.; Splett, J. D.; Lu, X. F.; Ghosh, A. K.; Ambrosio, G.

    2010-05-01

    Nb3Sn superconducting wires made by the restacked-rod process (RRP®) were found to have a dramatically improved resilience to axial tensile strain when alloyed with Ti as compared to Ta. Whereas Ta-alloyed Nb3Sn in RRP wires showed permanent damage to its current-carrying capacity (Ic) when tensioned beyond an intrinsic strain as small as 0.04%, Ti-doped Nb3Sn in RRP strands exhibits a remarkable reversibility up to a tensile strain of about 0.25%, conceivably making Ti-doped RRP wires more suitable for the high field magnets used in particle accelerators and nuclear magnetic resonance applications where mechanical forces are intense. A strain cycling experiment at room temperature caused a significant drop of Ic in Ta-alloyed wires, but induced an increase of Ic in the case of Ti-doped strands. Whereas either Ti or Ta doping yield a similar enhancement of the upper critical field of Nb3Sn, the much improved mechanical behavior of Ti-alloyed wires possibly makes Ti a better choice over Ta, at least for the RRP wire processing technique. Contribution of NIST, an agency of the US government, not subjected to copyright.

  15. a Study on Correlation Between Jc(4.2 k) and Current Sharing Temperature Tcs of Nb3Sn Strands and Short Sample of Conductor for Toroidal Field Coils of Iter Magnet System

    NASA Astrophysics Data System (ADS)

    Shikov, A. K.; Pantsyrny, V. I.; Kozlenkova, N. I.; Vasilyev, R. M.; Vorobieva, A. E.; Mareev, K. A.; Sudijev, S. V.

    2010-04-01

    One of the main requirements for ITER Nb3Sn Toroidal Field (TF) conductor is a temperature margin of 0.7 K under 11.8 T peak field, 68 kA operating current, and operating temperature of 5 K, i.e. current sharing temperature Tcs = 5.7 K, while the performance of Nb3Sn strands used for the fabrication of the conductor is evaluated by critical current density Jc(4.2 K, 12 T). This work represents an analysis of experimentally revealed correlation between Jc(4.2 K, 12 T) and Tcs of several Nb3Sn strands and short sample of the TF conductor RFTF2 tested in SULTAN facility (SULTAN sample). The performance of the strands used for SULTAN sample fabrication is investigated in details. The paper includes the analysis of voltage-current and voltage-temperature characteristics. An assessment of strain influence on the performance and transition parameters (n and T0) of the strands is also presented. The results obtained for strands are compared with the test results of SULTAN sample RFTF2.

  16. Measurements of Nb3Sn conductor dimension changes during heat treatment

    SciTech Connect

    Bocian, D.; Ambrosio, G.; Whitson, G.M.; /Fermilab

    2011-06-01

    During the heat treatment of Nb{sub 3}Sn coils the conductor material properties change significantly. These effects together with the changes of the conductor dimensions during heat treatment may introduce large strain in the coils for accelerator magnets. The US LHC Accelerator Research Program (LARP) has initiated a study aiming at understanding the thermal expansion and contraction of Nb3Sn strands, cables and coils during heat treatment. Several measurements on strands and cables were performed in order to have sufficient inputs for finite element simulation of the dimensional changes during heat treatment. In this paper the results of measurements of OST-RRP Nb{sub 3}Sn conductor used in the LARP magnet program are discussed.

  17. Testing of NB3SN Quadrupole Coils Using Magnetic Mirror Structure

    NASA Astrophysics Data System (ADS)

    Zlobin, A. V.; Andreev, N.; Barzi, E.; Bossert, R.; Chlachidze, G.; Kashikhin, V. S.; Kashikhin, V. V.; Lamm, M. J.; Novitski, I.; Tartaglia, M.; Tompkins, J. C.; Turrioni, D.; Yamada, R.

    2010-04-01

    This paper describes the design and parameters of a quadrupole mirror structure for testing the mechanical, thermal and quench performance of single shell-type superconducting quadrupole coils at field, current and force levels similar to that of real magnet. The concept was experimentally verified by testing two quadrupole coils, previously used in quadrupole models, in the developed mirror structure in the temperature range from 4.5 to 1.9 K. The coils were instrumented with voltage taps, heaters, and strain gauges to monitor their mechanical and thermal properties and quench performance. A new quadrupole coil made of improved Nb3Sn RRP-108/127 strand and cable insulation based on E-glass tape was also tested using this structure. The fabrication and test results of the quadrupole mirror models are reported and discussed.

  18. Test results of TQS03: A LARP shell-based Nb3Sn quadrupole using 108/127 conductor

    NASA Astrophysics Data System (ADS)

    Felice, H.; Ambrosio, G.; Bajko, M.; Barzi, E.; Bordini, B.; Bossert, R.; Caspi, S.; Dietderich, D.; Ferracin, P.; Feuvrier, J.; Ghosh, A.; Godeke, A.; Lizarazo, J.; Rossi, L.; Sabbi, G.; Wanderer, P.; Wang, X.; Zlobin, A. V.

    2010-06-01

    Future insertion quadrupoles with large apertures and high gradients will be required for the Phase II luminosity upgrade (1035 cm-2s-1) of the Large Hadron Collider (LHC). Although improved designs, based on NbTi, are being considered as an intermediate step for the Phase I upgrade, the Nb3Sn conductor is presently the best option that meets the ultimate performance goals for both operating field and temperature margin. As part of the development of Nb3Sn magnet technology, the LHC Accelerator Research Program (LARP) developed and tested several 1-meter long, 90-mm aperture Nb3Sn quadrupoles. The first two series of magnet used OST MJR 54/61 (TQ01 series) and OST RRP 54/61 (TQ02 series) strands. The third series (TQ03) used OST RRP 108/127 conductor. The larger number of sub-elements and the consequent reduction of the effective filament size, together with an increased fraction of copper and a lower Jc were expected to improve the conductor stability. The new coils were tested in the TQS03 series using a shell structure assembled with keys and bladders. The objective of the first test (TQS03a) was to evaluate the performances of the 108/127 conductor and, in particular, its behaviour at 1.9 K, while the second test (TQS03b) investigated the impact on high azimuthal pre-stress on the magnet performance. This paper reports on TQS03 fabrication, the strain gauge measurements performed during assembly, cool-down, excitation and the quench behaviour of the two magnets.

  19. Nb3Sn cable development for the 11 T dipole demonstation model

    SciTech Connect

    Barzi, E.; Lombardo, V.; Nobrega, F.; Turrioni, D.; Yamada, R.; Zlobin, A.V.; Karppinen, M.; /CERN

    2011-06-01

    Fermilab (FNAL) and CERN have started the development of 11 T 11-m long Nb{sub 3}Sn dipoles to replace a number of LHC NbTi dipoles and free space for cold collimators in the LHC DS areas. An important step in the design of these magnets is the development of the high aspect ratio Nb{sub 3}Sn cable to achieve the nominal field of 11 T at the nominal LHC operating current of 11.85 kA at 1.9 K with 20% margin. Keystoned cables with 40 and 41 strands with and without a stainless steel core were made out of hard Cu wires and Nb{sub 3}Sn RRP strand of 0.7 mm nominal diameter. The cable optimization process was aimed at achieving both mechanical stability and minimal damage to the delicate internal architecture of the Restacked-Rod-Process (RRP) Nb3Sn strands with 127 restack design to be used in the magnet short models. Each cable was characterized electrically for transport properties degradation at high field and for low field stability, and metallographically for internal damage.

  20. Cable deformation simulation and a hierarchical framework for Nb3Sn Rutherford cables

    NASA Astrophysics Data System (ADS)

    Arbelaez, D.; Prestemon, S. O.; Ferracin, P.; Godeke, A.; Dietderich, D. R.; Sabbi, G.

    2010-06-01

    Knowledge of the three-dimensional strain state induced in the superconducting filaments due to loads on Rutherford cables is essential to analyze the performance of Nb3Sn magnets. Due to the large range of length scales involved, we develop a hierarchical computational scheme that includes models at both the cable and strand levels. At the Rutherford cable level, where the strands are treated as a homogeneous medium, a three-dimensional computational model is developed to determine the deformed shape of the cable that can subsequently be used to determine the strain state under specified loading conditions, which may be of thermal, magnetic, and mechanical origins. The results can then be transferred to the model at the strand/macro-filament level for rod restack process (RRP) strands, where the geometric details of the strand are included. This hierarchical scheme can be used to estimate the three-dimensional strain state in the conductor as well as to determine the effective properties of the strands and cables from the properties of individual components. Examples of the modeling results obtained for the orthotropic mechanical properties of the Rutherford cables are presented.

  1. Stress distribution and lattice distortions in Nb3Sn multifilament wires under uniaxial tensile loading at 4.2 K

    NASA Astrophysics Data System (ADS)

    Scheuerlein, C.; Di Michiel, M.; Buta, F.; Seeber, B.; Senatore, C.; Flükiger, R.; Siegrist, T.; Besara, T.; Kadar, J.; Bordini, B.; Ballarino, A.; Bottura, L.

    2014-04-01

    The lattice parameter changes in three types of Nb3Sn superconducting wires during uniaxial stress-strain measurements at 4.2 K have been measured by high-energy synchrotron x-ray diffraction. The nearly-stress-free Nb3Sn lattice parameter has been determined using extracted filaments, and the elastic strain in the axial and transverse wire directions in the different wire phases has been calculated. The mechanical properties of the PIT and RRP wire are mainly determined by the properties of Nb3Sn and unreacted Nb. This is in contrast to the bronze route wire, where the matrix can carry substantial loads. In straight wires the axial Nb3Sn pre-strain is strongest in the bronze route wire, its value being smaller in the PIT and RRP wires. A strong reduction of the non-Cu elastic modulus of about 30% is observed during cool-down from ambient temperature to 4.2 K. The Nb3Sn Poisson ratio at 4.2 K measured in the untwisted bronze route wire is 0.35. The present study also shows that the process route has a strong influence on the Nb3Sn texture.

  2. Twisted, multifilament Nb3Sn superconductive ribbon

    NASA Technical Reports Server (NTRS)

    Coles, W. D.

    1972-01-01

    An experimental study of superconductor stabilization has resulted in the successful application of the concepts of filamentary structure and conductor twist to Nb3Sn ribbon. The Nb3Sn is formed in parallel, helical paths, which are continuous around the ribbon. Short lengths (12-18cm) of 1.27 cm wide superconductive ribbon were produced. The filamentary and twist characteristics are incorporated in the ribbon by means of an inert mask formed on the ribbon surface early in the fabrication process. Diffusion reaction of the niobium and tin is prevented at the filament boundaries. Described are the conductor methods of fabrication, and test results obtained. The technology required to adapt the processes for the production of long lengths of ribbon is available.

  3. LARP Long Nb3Sn Quadrupole Design

    SciTech Connect

    Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bossert, R.; Caspi, S.; Chlachidze, G.; Dietderich, D.; Feher, S.; Felice, H.; Ferracin, P.; /Fermilab /Brookhaven /LBL, Berkeley /Texas A-M

    2007-08-01

    A major milestone for the LHC Accelerator Research Program (LARP) is the test, by the end of 2009, of two 4m-long quadrupole magnets (LQ) wound with Nb3Sn conductor. The goal of these magnets is to be a proof of principle that Nb3Sn is a viable technology for a possible LHC luminosity upgrade. The design of the LQ is based on the design of the LARP Technological Quadrupoles, presently under development at FNAL and LBNL, with 90-mm aperture and gradient higher than 200 T/m. The design of the first LQ model will be completed by the end of 2007 with the selection of a mechanical design. In this paper we present the coil design addressing some fabrication technology issues, the quench protection study, and three designs of the support structure.

  4. Measurement of Tc distribution in Nb3Sn CICC

    NASA Astrophysics Data System (ADS)

    Calzolaio, Ciro; Bruzzone, Pierluigi; Uglietti, Davide

    2012-05-01

    Knowledge of the actual Nb3Sn filaments’ thermal strain, ɛth, in a cable-in-conduit conductor (CICC) is essential to predict the CICC performance in operation starting from the strand scaling laws for the critical current density Jc(B,T,ɛ). To obtain a measurement of ɛth under relevant conditions, i.e. at low temperature and with the mechanical constraints of a long length section of CICC, the critical temperature as a function of the applied field, Tc(B), is measured by an inductive method for the CICC in situ and for the freestanding filaments used for the cable manufacture. To deduce the thermal strain in the CICC, the Tc(B) results are compared with the Tc(B,ɛ) curve. Starting from the susceptibility curves measured for both the CICC and the filaments, it is possible to compute the Tc distribution in the CICC using a deconvolution algorithm. The first results of Tc measured on two CICCs in the SULTAN test facility suggest a broad distribution of thermal strain, peaked at negative strain, which remains almost constant during the cyclic loading. From the knowledge of both the thermal strain distribution and the actual CICC performances, it will be possible to discriminate between reversible and irreversible degradation in Nb3Sn CICC.

  5. Performance Boost in Industrial Multifilamentary Nb3Sn Wires due to Radiation Induced Pinning Centers

    PubMed Central

    Baumgartner, T.; Eisterer, M.; Weber, H. W.; Flükiger, R.; Scheuerlein, C.; Bottura, L.

    2015-01-01

    We report non-Cu critical current densities of 4 . 09 ⋅ 109 A/m2 at 12 T and 2.27 ⋅ 109 A/m2 at 15 T obtained from transport measurements on a Ti-alloyed RRP Nb3Sn wire after irradiation to a fast neutron fluence of 8.9 ⋅ 1021 m−2. These values are to our knowledge unprecedented in multifilamentary Nb3Sn, and they correspond to a Jc enhancement of approximately 60% relative to the unirradiated state. Our magnetometry data obtained on short wire samples irradiated to fast neutron fluences of up to 2.5 ⋅ 1022 m−2 indicate the possibility of an even better performance, whereas earlier irradiation studies on bronze-processed Nb3Sn wires with a Sn content further from stoichiometry attested a decline of the critical current density at such high fluences. We show that radiation induced point-pinning centers rather than an increase of the upper critical field are responsible for this Jc enhancement, and argue that these results call for further research on pinning landscape engineering. PMID:26030255

  6. Understanding Irreversible Degradation of Nb3Sn Wires with Fundamental Fracture Mechanics

    SciTech Connect

    Zhai, Yuhu; Calzolaio, Ciro; Senatore, Carmine

    2014-08-01

    Irreversible performance degradation of advanced Nb3Sn superconducting wires subjected to transverse or axial mechanical loading is a critical issue for the design of large-scale fusion and accelerator magnets such as ITER and LHC. Recent SULTAN tests indicate that most cable-in-conduit conductors for ITER coils made of Nb3Sn wires processed by various fabrication techniques show similar performance degradation under cyclic loading. The irreversible degradation due to filament fracture and local strain accumulation in Nb3Sn wires cannot be described by the existing strand scaling law. Fracture mechanic modeling combined with X-ray diffraction imaging of filament micro-crack formation inside the wires under mechanical loading may reveal exciting insights to the wire degradation mechanisms. We apply fundamental fracture mechanics with a singularity approach to study influence of wire filament microstructure of initial void size and distribution to local stress concentration and potential crack propagation. We report impact of the scale and density of the void structure on stress concentration in the composite wire materials for crack initiation. These initial defects result in an irreversible degradation of the critical current beyond certain applied stress. We also discuss options to minimize stress concentration in the design of the material microstructure for enhanced wire performance for future applications.

  7. Dimensional changes of Nb3Sn Rutherford cables during heat treatment

    DOE PAGESBeta

    Rochepault, E.; Ferracin, P.; Ambrosio, G.; Anerella, M.; Ballarino, A.; Bonasia, A.; Bordini, B.; Cheng, D.; Dietderich, D. R.; Felice, H.; et al

    2016-06-01

    In high field magnet applications, Nb3Sn coils undergo a heat treatment step after winding. During this stage, coils radially expand and longitudinally contract due to the Nb3Sn phase change. In order to prevent residual strain from altering superconducting performances, the tooling must provide the adequate space for these dimensional changes. The aim of this paper is to understand the behavior of cable dimensions during heat treatment and to provide estimates of the space to be accommodated in the tooling for coil expansion and contraction. In addition, this paper summarizes measurements of dimensional changes on strands, single Rutherford cables, cable stacks,more » and coils performed between 2013 and 2015. These samples and coils have been performed within a collaboration between CERN and the U.S. LHC Accelerator Research Program to develop Nb3Sn quadrupole magnets for the HiLumi LHC. The results are also compared with other high field magnet projects.« less

  8. Synthesis of superconducting Nb3Sn coatings on Nb substrates

    DOE PAGESBeta

    Barzi, E.; Franz, S.; Reginato, F.; Turrioni, D.; Bestetti, M.

    2015-12-01

    In the present work the electrochemical and thermal syntheses of superconductive Nb3Sn films are investigated. The Nb3Sn phase is obtained by electrodeposition of Sn layers and Cu intermediate layers onto Nb substrates followed by high temperature diffusion in inert atmosphere. Electrodeposition was performed from aqueous solutions at current densities in the 20 to 50 mA/cm2 range and at temperatures between 40 and 50°C. Subsequent thermal treatments were realized to obtain the Nb3Sn superconductive phase. Glow discharge optical emission spectrometry (GDOES) demonstrated that after thermal treatment interdiffusion of Nb and Sn occurred across a thickness of about 13 μm. Scanning Electronmore » Microscopy (SEM) allowed accurately measuring the thickness of the Nb3Sn phase, whose average for the various types of film samples was between 5.7 and 8.0 μm. X-ray diffraction (XRD) patterns confirmed the presence of a cubic Nb3Sn phase (A15 structure) having (210) preferred orientation. The maximum obtained Tc was 17.68 K and the Bc20 ranged between 22.5 T and 23.8 T. With the procedure described in the present paper, coating complex shapes cost-effectively becomes possible, which is typical of electrochemical techniques. Furthermore, this approach can be implemented in classical wire processes such as "Jelly Roll" or "Rod in Tube", or directly used for producing superconducting surfaces. In conclusion, the potential of this method for Superconducting Radiofrequency (SRF) structures is also outlined.« less

  9. INSTABILITES IN NB3SN WIRES.

    SciTech Connect

    COOLEY, L.; GHOSH, A.

    2006-04-03

    High current-density Nb{sub 3}Sn strands made by internal-tin routes are not stable against flux jumps at low fields. Since flux jumps release heat, they can initiate quenching if thermal conductivity to the liquid helium is poor. To make matters worse, tin is a potent contaminant of copper, and reaction of strands to maximize performance leads to the loss of thermal conductivity. We discuss how the root of a solution of this problem lies in optimizing two parameters, RRR and J{sub c}, instead of J{sub c} alone. An important workaround for magnet designers is controlling the balance between performance and stability by reducing the temperature or time of the final heat treatment step. This provides ample J{sub c} while also keeping RRR high. Under these conditions, the instability current density threshold J{sub s} is higher than J{sub c}. Additional factors are also available to improve the management of instabilities, including new strand designs with smaller subelements or divided subelements.

  10. FEMCAM Analysis of SULTAN Test Results for ITER Nb3SN Cable-conduit Conductors

    SciTech Connect

    Yuhu Zhai, Pierluigi Bruzzone, Ciro Calzolaio

    2013-03-19

    Performance degradation due to filament fracture of Nb3 Sn cable-in-conduit conductors (CICCs) is a critical issue in large-scale magnet designs such as ITER which is currently being constructed in the South of France. The critical current observed in most SULTAN TF CICC samples is significantly lower than expected and the voltage-current characteristic is seen to have a much broader transition from a single strand to the CICC. Moreover, most conductors exhibit the irreversible degradation due to filament fracture and strain relaxation under electromagnetic cyclic loading. With recent success in monitoring thermal strain distribution and its evolution under the electromagnetic cyclic loading from in situ measurement of critical temperature, we apply FEMCAM which includes strand filament breakage and local current sharing effects to SULTAN tested CICCs to study Nb3 Sn strain sensitivity and irreversible performance degradation. FEMCAM combines the thermal bending effect during cool down and the EM bending effect due to locally accumulating Lorentz force during magnet operation. It also includes strand filament fracture and related local current sharing for the calculation of cable n value. In this paper, we model continuous performance degradation under EM cyclic loading based on strain relaxation and the transition broadening upon cyclic loading to the extreme cases seen in SULTAN test data to better quantify conductor performance degradation.

  11. Fine Grained nb for Internal Tin NB3SN Conductors

    NASA Astrophysics Data System (ADS)

    Balachandran, S.; Barber, R. E.; Huang, Y.; Miao, H.; Parrell, J. A.; Hong, S.; Griffin, R. B.; Hartwig, K. T.

    2010-04-01

    The push to drive superconductor strand technology to reach higher critical current density (Jc) values and reduce production costs has led to innovative approaches in manufacturing technology. The Restacked Rod Process (RRP®) by Oxford Instruments is one such process which involves Nb bar extrusions in a Cu sheath. Commercially available Nb used in the initial RRP extrusion leads to nonuniform deformations of the Nb bar which in turn leads to a jagged Cu-Nb interface. This report presents a feasible methodology to remedy the problem of nonuniform deformation of Nb through severe plastic deformation (SPD) of precursor Nb to obtain smaller grains in starting Nb. Cu-Nb monocore extrusion and drawing experiments were accomplished at Oxford Instruments using Nb bars of nominal dimensions 45 mm diameter by and 78 mm long and with grain sizes in the range of μm to mm. Results of Cu-Nb interface roughness measurements show that a finer starting grain size gives a significantly lower roughness and better Nb core conformance to initial shape. Our experiments indicate that refinement of the initial Nb grain size to below ˜50μm could enable fabrication of RRP conductor with improved wire yield.

  12. Construction of TAMU3: A 14 Tesla Nb3Sn Model Dipole

    NASA Astrophysics Data System (ADS)

    Holik, Eddie; Blackburn, Raymond; Diaczenko, Nick; Elliott, Tim; Jaisle, Andrew; McInturff, Alfred; McIntyre, Peter; Sattarov, Dior

    2010-10-01

    The third phase of the Texas A&M University Accelerator Research Lab's ``Stress-Managed'' high field magnet campaign has coil modules for the assembly of TAMU3. The third phase is the high field, Bmax >= 12 -- 14 Tesla, proof of principle test of the ``Stress-Managed'' coil fabrication design philosophy. Earlier dipole phases operated in the 5 -- 8 Tesla range using NbTi and early bronze (ITER) Nb3Sn based superconductor. These third phase dipole winding modules use the tin rich multi-filament Nb3Sn/Cu composite strand with its enhanced engineering current density therefore have the possibility of producing magnetic fields > 14 Tesla, when combined with the evolution of much higher efficiency insulation. There are five modules under construction altogether, which are at various stages. The best performing pair during testing of these modules will comprise the upper and lower modules of TAMU4, a 4x2 cm aperture accelerator prototype dipole. There has also been progress in the fabrication and measurement techniques necessary to validate more accurately the ``Stress-Management'' approach.

  13. Current Progress in Fabrication of a 14 Tesla Nb3Sn Dipole

    NASA Astrophysics Data System (ADS)

    Holik, Eddie, III; Benson, Christopher; Damborsky, Kyle; Diaczenko, Nick; Elliott, Tim; Garrison, Ray; Jaisle, Andrew; McInturff, Alfred; McIntyre, Peter; Sattarov, Dior

    2012-03-01

    The Accelerator Technology Laboratory at Texas A&M is fabricating a model dipole magnet, TAMU3, designed to operate at a 14 Tesla bore field. The dipole employs an advanced internal-tin Nb3Sn/Cu composite strand with enhanced current density. The coils must be processed through a heat treatment after winding, during which the Sn within the heterogeneous strands diffuse into the Cu/Nb matrix to form high-performance superconducting layers. Heat treatment of the first coil assembly revealed tin leakage from the Sn cores that was caused by omission of a pre-anneal step in the heat treatment. We are evaluating the electrical properties of the coil, the microstructure and short-sample superconducting performance of cut-off samples of current leads to determine the extent of damage to the performance of the windings. Results of those tests and plans for construction of TAMU3 will be presented.

  14. RRP6/EXOSC10 is required for the repair of DNA double-strand breaks by homologous recombination.

    PubMed

    Marin-Vicente, Consuelo; Domingo-Prim, Judit; Eberle, Andrea B; Visa, Neus

    2015-03-15

    The exosome acts on different RNA substrates and plays important roles in RNA metabolism. The fact that short non-coding RNAs are involved in the DNA damage response led us to investigate whether the exosome factor RRP6 of Drosophila melanogaster and its human ortholog EXOSC10 play a role in DNA repair. Here, we show that RRP6 and EXOSC10 are recruited to DNA double-strand breaks (DSBs) in S2 cells and HeLa cells, respectively. Depletion of RRP6/EXOSC10 does not interfere with the phosphorylation of the histone variant H2Av (Drosophila) or H2AX (humans), but impairs the recruitment of the homologous recombination factor RAD51 to the damaged sites, without affecting RAD51 levels. The recruitment of RAD51 to DSBs in S2 cells is also inhibited by overexpression of RRP6-Y361A-V5, a catalytically inactive RRP6 mutant. Furthermore, cells depleted of RRP6 or EXOSC10 are more sensitive to radiation, which is consistent with RRP6/EXOSC10 playing a role in DNA repair. RRP6/EXOSC10 can be co-immunoprecipitated with RAD51, which links RRP6/EXOSC10 to the homologous recombination pathway. Taken together, our results suggest that the ribonucleolytic activity of RRP6/EXOSC10 is required for the recruitment of RAD51 to DSBs.

  15. Design of Nb3Sn coils for LARP long magnets

    SciTech Connect

    Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bossert, R.; Dietderich, D.; Feher, S.; Ferracin, P.; Ghosh, A.; Gourlay, S.; Kashikhin, V.V.; /Fermilab /Brookhaven /LBL, Berkeley /Texas A-M

    2006-08-01

    The LHC Accelerator Research Program (LARP) has a primary goal to develop, assemble, and test full size Nb{sub 3}Sn quadrupole magnet models for a luminosity upgrade of the Large Hadron Collider (LHC). A major milestone in this development is to assemble and test, by the end of 2009, two 4m-long quadrupole cold masses, which will be the first Nb3Sn accelerator magnet models approaching the length of real accelerator magnets. The design is based on the LARP Technological Quadrupoles (TQ), under development at FNAL and LBNL, with gradient higher than 200 T/m and aperture of 90 mm. The mechanical design will be chosen between two designs presently explored for the TQs: traditional collars and Al-shell based design (preloaded by bladders and keys). The fabrication of the first long quadrupole model is expected to start in the last quarter of 2007. Meanwhile the fabrication of 4m-long racetrack coils started this year at BNL. These coils will be tested in an Al-shell based supporting structure developed at LBNL. Several challenges have to be addressed for the successful fabrication of long Nb{sub 3}Sn coils. This paper presents these challenges with comments and solutions adopted or under study for these magnets. The coil design of these magnets, including conductor and insulation features, and quench protection studies are also presented.

  16. Development of a 15 T $Nb_3Sn$ Accelerator Dipole Demonstrator at Fermilab

    SciTech Connect

    Novitski, I.; Andreev, N.; Barzi, E.; Carmichael, J.; Kashikhin, V. V.; Turrion, D.; Yu, M.; Zlobin, A. V.

    2015-01-01

    100 TeV scale Hadron Collider (HC) with a nominal operation field of at least 15 T is being considered for the post-LHC era, which requires using the $Nb_3Sn$ technology. Practical demonstration of this field level in an accelerator-quality magnet and substantial reduction of the magnet costs are the key conditions for realization of such a machine. FNAL has started the development of a 15 T Nb3Sn dipole demonstrator for a 100 TeV scale HC. The magnet design is based on 4-layer shell type coils, graded between the inner and outer layers to maximize the performance and reduce the cost. The experience gained during the Nb3Sn magnet R&D is applied to different aspects of the magnet design. This paper describes the magnetic and structural designs and parameters of the 15 T Nb3Sn dipole and the steps towards the demonstration model fabrication.

  17. Development of a 15 T $Nb_3Sn$ Accelerator Dipole Demonstrator at Fermilab

    SciTech Connect

    Novitski, I.; Andreev, N.; Barzi, E.; Carmichael, J.; Kashikhin, V. V.; Turrion, D.; Yu, M.; Zlobin, A. V.

    2016-01-01

    100 TeV scale Hadron Collider (HC) with a nominal operation field of at least 15 T is being considered for the post-LHC era, which requires using the $Nb_3Sn$ technology. Practical demonstration of this field level in an accelerator-quality magnet and substantial reduction of the magnet costs are the key conditions for realization of such a machine. FNAL has started the development of a 15 T Nb3Sn dipole demonstrator for a 100 TeV scale HC. The magnet design is based on 4-layer shell type coils, graded between the inner and outer layers to maximize the performance and reduce the cost. The experience gained during the Nb3Sn magnet R&D is applied to different aspects of the magnet design. This paper describes the magnetic and structural designs and parameters of the 15 T Nb3Sn dipole and the steps towards the demonstration model fabrication.

  18. Finite Element Analysis of Transverse Compressive Loads on Superconducting Nb3Sn Wires Containing Voids

    NASA Astrophysics Data System (ADS)

    D'Hauthuille, Luc; Zhai, Yuhu; Princeton Plasma Physics Lab Collaboration; University of Geneva Collaboration

    2015-11-01

    High field superconductors play an important role in many large-scale physics experiments, particularly particle colliders and fusion devices such as the LHC and ITER. The two most common superconductors used are NbTi and Nb3Sn. Nb3Sn wires are favored because of their significantly higher Jc, allowing them to produce much higher magnetic fields. The main disadvantage is that the superconducting performance of Nb3Sn is highly strain-sensitive and it is very brittle. The strain-sensitivity is strongly influenced by two factors: plasticity and cracked filaments. Cracks are induced by large stress concentrators due to the presence of voids. We will attempt to understand the correlation between Nb3Sn's irreversible strain limit and the void-induced stress concentrations around the voids. We will develop accurate 2D and 3D finite element models containing detailed filaments and possible distributions of voids in a bronze-route Nb3Sn wire. We will apply a compressive transverse load for the various cases to simulate the stress response of a Nb3Sn wire from the Lorentz force. Doing this will further improve our understanding of the effect voids have on the wire's mechanical properties, and thus, the connection between the shape & distribution of voids and performance degradation.

  19. A solution for transverse load degradation in ITER Nb3Sn CICCs: verification of cabling effect on Lorentz force response

    NASA Astrophysics Data System (ADS)

    Nijhuis, A.

    2008-05-01

    We present the latest results of the novel model for transverse electromagnetic load optimization (TEMLOP) especially developed for the ITER type of cable-in-conduit conductors (CICCs). The Nb3Sn CICCs for the International Thermonuclear Experimental Reactor (ITER) showed a substantial degradation in their performance correlated with increasing electromagnetic load. Not only do the differences in the thermal contraction of the composite materials affect the critical current (Ic) and temperature margin, but electromagnetic forces cause a significant transverse strand contact and bending strain in the Nb3Sn layers, resulting in localized filament cracking and permanent degradation. The most essential feature of the a priori TEMLOP predictions presented in May 2006 is that the severe degradation in CICCs can be improved greatly and straightforwardly by increasing the pitch length in subsequent cabling stages and by reducing the void fraction. These corrective measures give more support to the strands, sufficiently reduce the strain, and therefore avoid filament damage at the strand crossover points in the cables. It was the first time that an increase of the cable twist pitches has been proposed and no experimental evidence was available at that time. A full-size European prototype TF conductor sample (TFPRO-2), manufactured in autumn 2006, was adapted according to this new insight and tested in April 2007 in SULTAN for experimental validation of the predictions. The results were outstanding: for the first time an Nb3Sn CICC conductor achieved the performance that can be expected based on the single-strand properties, with high n value and no sign of degradation. As input, besides the cable properties, the model directly uses the measured data from single strands under uni-axial stress and strain, periodic bending and contact loads. The recent test results of the ITER OST strands used for the manufacture of the TFPRO-2 obtained with the TARSIS set-up are presented

  20. Coupled mechanical electromagnetic thermal hydraulic effects in Nb3Sn cable-in-conduit conductors for ITER

    NASA Astrophysics Data System (ADS)

    Zanino, R.; Ciazynski, D.; Mitchell, N.; Savoldi Richard, L.

    2005-12-01

    The crucial multi-physics problem of how to extrapolate from the performance of an isolated Nb3Sn strand measured in the laboratory to the performance of a superconducting coil using multi-strand twisted cables is addressed here. We consider the particular case of the path going from the LMI strand to the international thermonuclear experimental reactor (ITER) toroidal field model coil (TFMC), through its associated Full Size Joint Sample, the TFMC-FSJS. Mechanical, electromagnetic and thermal-hydraulic conditions are simulated using the ANSYS, ENSIC and Mithrandir/M&M codes, respectively. At least in this case, the DC performance of the short sample turns out to be relatively close to (considering error bars) but not fully representative of that of the coil, showing higher (less compressive) effective thermal strain but also higher sensitivity to the electromechanical load.

  1. Validation of Finite-Element Models of Persistent-Current Effects in Nb3Sn Accelerator Magnets

    DOE PAGESBeta

    Wang, X.; Ambrosio, G.; Chlachidze, G.; Collings, E. W.; Dietderich, D. R.; DiMarco, J.; Felice, H.; Ghosh, A. K.; Godeke, A.; Gourlay, S. A.; et al

    2015-01-06

    Persistent magnetization currents are induced in superconducting filaments during the current ramping in magnets. The resulting perturbation to the design magnetic field leads to field quality degradation, in particular at low field where the effect is stronger relative to the main field. The effects observed in NbTi accelerator magnets were reproduced well with the critical-state model. However, this approach becomes less accurate for the calculation of the persistent-current effects observed in Nb3Sn accelerator magnets. Here a finite-element method based on the measured strand magnetization is validated against three state-of-art Nb3Sn accelerator magnets featuring different subelement diameters, critical currents, magnet designsmore » and measurement temperatures. The temperature dependence of the persistent-current effects is reproduced. Based on the validated model, the impact of conductor design on the persistent current effects is discussed. The performance, limitations and possible improvements of the approach are also discussed.« less

  2. Improvement of electromechanical properties of an ITER internal tin Nb3Sn wire

    NASA Astrophysics Data System (ADS)

    Mondonico, G.; Seeber, B.; Senatore, C.; Flükiger, R.; Corato, V.; De Marzi, G.; Muzzi, L.

    2010-11-01

    The critical current of an internal tin Nb3Sn wire developed by Oxford Instruments, Superconducting Technology for International Thermonuclear Experimental Reactor (ITER) (OST type-I, billet No. 7567) has been studied under axial strain at fields between 12 and 19 T at 4.2 K. Simulating the situation in a cable in conduit, where thermally induced compressive strain is important, a single wire (strand) was jacketed with AISI 316L stainless steel. The reinforced wire shows an important increase in ɛm, the applied strain where Ic reaches its maximum, from 0.25% to 0.57%. In addition the irreversibility limit, ɛirr, is improved from 0.50% applied strain to >1.10%. It could also be shown that the Ic at zero intrinsic strain is almost identical. This demonstrates that jacketing does not influence the physical parameters of the original wire. Experimental data of the bare wire has been well fitted by different strain functions. However, it was not possible to model the data of the jacketed wire. There are indications that only models which take into account the multidimensional character of strain are able to describe the behavior but further development is required.

  3. Effects of core type, placement, and width on the estimated interstrand coupling properties of QXF-type Nb3Sn Rutherford cables

    DOE PAGESBeta

    Collings, E. W.; Sumption, M. D.; Majoros, M.; Wang, X.; Dietderich, D. R.

    2015-01-12

    The coupling magnetization of a Rutherford cable is inversely proportional to an effective interstrand contact resistance Reff , a function of the crossing-strand resistance Rc, and the adjacent strand resistance Ra. In cored cables, Reff continuously varies with W, the core width expressed as percent interstrand cover. For a series of un-heat-treated stabrite-coated NbTi LHC-inner cables with stainless-steel (SS, insulating) cores, Reff (W) decreased smoothly as W decreased from 100%, whereas for a set of research-wound SS-cored Nb3Sn cables, Reff plummeted abruptly and remained low over most of the range. The difference is due to the controlling influence of Rcmore » - 2.5 μΩ for the stabrite/NbTi and 0.26 μΩ for Nb3Sn. The experimental behavior was replicated in the Reff (W)’s calculated by the program CUDI, which (using the basic parameters of the QXF cable) went on to show in terms of decreasing W that: 1) in QXF-type Nb3Sn cables (Rc = 0.26 μΩ), Reff dropped even more suddenly when the SS core, instead of being centered, was offset to one edge of the cable; 2) Reff decreased more gradually in cables with higher Rc’s; and 3) a suitable Reff for a Nb3Sn cable can be achieved by inserting a suitably resistive core rather than an insulating (SS) one.« less

  4. Quench protection studies of the 11-T Nb3Sn dipole for the LHC upgrade

    DOE PAGESBeta

    Bermudez, Susana Izquierdo; Auchmann, Bernhard; Bajas, Hugues; Bajko, Marta; Bordini, Bernardo; Bottura, Luca; Chlachidze, Guram; Karppinen, Mikko; Rysti, Juho; Savary, Frederic; et al

    2016-06-01

    The planned upgrade of the LHC collimation system foresees additional collimators to be installed in the dispersion suppressor areas. Fermilab and CERN are developing an 11 T Nb3Sn dipole to replace some 8.33 T-15-m-long Nb-Ti LHC main dipoles providing longitudinal space for the collimators. In case of a quench, the large stored energy and the low copper stabilizer fraction make the protection of the 11 T Nb3Sn dipoles challenging. This paper presents the results of quench protection analysis, including quench protection heater design and efficiency, quench propagation and coil heating. The numerical results are compared with the experimental data frommore » the 2-m-long Nb3Sn dipole models. Here, the validated model is used to predict the current decay and hot spot temperature under operating conditions in the LHC and the presently foreseen magnet protection scheme is discussed.« less

  5. Tests of Insulation Systems for Nb3SN Wind and React Coils

    NASA Astrophysics Data System (ADS)

    Bossert, R.; Ambrosio, G.; Andreev, N.; Whitson, G.; Zlobin, A.

    2008-03-01

    Tests were performed to assess the viability of several cable insulation systems for use in Nb3Sn accelerator magnets. Insulated stacks of cables were subjected to reaction cycles commonly used for Nb3Sn coils. After reaction and epoxy impregnation, current leakage between turns was measured at pressures up to 180 MPa and turn-to-turn potentials up to 500 V. Systems consisting of S-2 glass, ceramic fiber, and E-glass were tested. Several methods of applying the insulation were incorporated, including sleeves and various spiral wrapped configurations. Methods of sample preparation and testing are described and results are reported.

  6. Quench Protection Studies of 11T Nb$_3$Sn Dipole Models for LHC Upgrades

    SciTech Connect

    Zlobin, Alexander; Chlachidze, Guram; Nobrega, Alfred; Novitski, Igor; Karppinen, Mikko

    2014-07-01

    CERN and FNAL are developing 11 T Nb3Sn dipole magnets for the LHC collimation system upgrade. Due to the large stored energy, protection of these magnets during a quench is a challenging problem. This paper reports the results of experimental studies of key quench protection parameters including longitudinal and radial quench propagation in the coil, coil heating due to a quench, and energy extraction and quench-back effect. The studies were performed using a 1 m long 11 T Nb3Sn dipole coil tested in a magnetic mirror configuration.

  7. Status of 11 T 2-in-1 Nb$_3$Sn Dipole Development for LHC

    SciTech Connect

    Zlobin, Alexander; Andreev, Nicolai; Apollinari, Giorgio; Barzi, Emanuela; Bossert, Rodger; Buehler, Marc; Chlachidze, Guram; DiMarco, Joseph; Nobrega, Alfred; Novitski, Igor; Turrioni, Daniele; Velev, Gueorgui; Auchmann, Bernhard; Karppinen, Mikko; Rossi, Lucio; Smekens, David

    2014-07-01

    The LHC upgrade plans foresee installation of additional collimators in the LHC lattice. To provide the necessary longitudinal space for these collimators, shorter and stronger Nb3Sn dipoles compatible with the LHC lattice and main systems could be used. This paper describes the design and status of the twin-aperture Nb3Sn dipole being developed by FNAL and CERN for the LHC, and reports test results of two collared coils to be used in the first 1 m long twin-aperture dipole model.

  8. Critical current density of Nb3Sn wires after irradiation with 65MeV and 24GeV protons

    NASA Astrophysics Data System (ADS)

    Spina, T.; Scheuerlein, C.; Richter, D.; Bottura, L.; Ballarino, A.; Flükiger, R.

    2014-05-01

    Industrial Nb3Sn wires with Ti and Ta additives (RRP process) and with Ta additives (PIT process) with a diameter of 1 mm have been irradiated at room temperature with protons of 65 MeV and of 24 GeV at various fluences up to 1×1021 p/m2. A steady increase of Jc vs. fluence was observed for all the wires up to the highest fluence. The observed increase of Jc at 4.2K in all wires was quite similar in spite of the very different proton energies. With increasing fluence. the radiation induced pinning force was found to increase. the enhancement Jc/Jco after 5.04×1020 p/m2 reaching 1.4 for Ta and 1.8 for Ti alloyed wires at 10T. The present results were quantitatively analysed by assuming a radiation induced point pinning mechanism in addition to grain boundary pinning. The results are compared with those of an ongoing neutron irradiation study undertaken on the same Nb3Sn wires in collaboration with the Atominstitut Vienna. Proton irradiation was found to produce considerably higher damage than neutron irradiation.

  9. Design Concept and Parameters of a 15 T $Nb_{3}Sn$ Dipole Demonstrator for a 100 TEV Hadron Collider

    SciTech Connect

    Zlobin, A. V.; Andreev, N.; Barzi, E.; Kashikhin, V. V.; Novitski, I.

    2015-06-01

    FNAL has started the development of a 15 T $Nb_{3}Sn$ dipole demonstrator for a 100 TeV scale hadron collider. This paper describes the design concept and parameters of the 15 T $Nb_{3}Sn$ dipole demonstrator. The dipole magnetic, mechanical and quench protection concept and parameters are presented and discussed.

  10. Quench performance of a 4-m long Nb3Sn shell-type dipole coil

    SciTech Connect

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

    2008-08-01

    Fermilab has finished the first phase of Nb{sub 3}Sn technology scale up by testing 2-m and 4-m long shell-type dipole coils in a 'magnetic mirror' configuration. The 2-m long coil, made of Powder-in-Tube (PIT) Nb{sub 3}Sn strand, reached its short sample limit at a field level of 10 T. The 4-m long coil, made of advanced Nb{sub 3}Sn strand based on the Restack Rod Process (RRP) of 108/127 design, has been recently fabricated and tested. Coil test results at 4.5 K and 2.2 K are reported and discussed.

  11. Test results of a Nb3Al/Nb3Sn subscale magnet for accelerator application

    DOE PAGESBeta

    Iio, Masami; Xu, Qingjin; Nakamoto, Tatsushi; Sasaki, Ken -ichi; Ogitsu, Toru; Yamamoto, Akira; Kimura, Nobuhiro; Tsuchiya, Kiyosumi; Sugano, Michinaka; Enomoto, Shun; et al

    2015-01-28

    The High Energy Accelerator Research Organization (KEK) has been developing a Nb3Al and Nb3Sn subscale magnet to establish the technology for a high-field accelerator magnet. The development goals are a feasibility demonstration for a Nb3Al cable and the technology acquisition of magnet fabrication with Nb3Al superconductors. KEK developed two double-pancake racetrack coils with Rutherford-type cables composed of 28 Nb3Al wires processed by rapid heating, quenching, and transformation in collaboration with the National Institute for Materials Science and the Fermi National Accelerator Laboratory. The magnet was fabricated to efficiently generate a high magnetic field in a minimum-gap common-coil configuration with twomore » Nb3Al coils sandwiched between two Nb3Sn coils produced by the Lawrence Berkeley National Laboratory. A shell-based structure and a “bladder and key” technique have been used for adjusting coil prestress during both the magnet assembly and the cool down. In the first excitation test of the magnet at 4.5 K performed in June 2014, the highest quench current of the Nb3Sn coil, i.e., 9667 A, was reached at 40 A/s corresponding to 9.0 T in the Nb3Sn coil and 8.2 T in the Nb3Al coil. The quench characteristics of the magnet were studied.« less

  12. Advances in development of Nb3Sn superconducting radio-frequency cavities

    NASA Astrophysics Data System (ADS)

    Posen, Sam; Liepe, Matthias

    2014-11-01

    A 1.3 GHz Nb3Sn superconducting radio-frequency cavity prepared with a modified annealing step reached Bp k>50 mT , well above Bc 1=25 ±7 mT , without the strong Q -slope observed in previous Nb3Sn cavities. At 4.2 K, it has a Q0 of approximately 1 ×1 010 at >10 MV /m , far outperforming Nb at useable gradients. At 2 K, quench occurred at ˜55 mT , apparently due to a defect, so additional treatment may increase the maximum gradient. Material parameters of the coating were extracted from Q vs T data, including a Tc of 18.0 ±0.1 K , close to the maximum literature value. High power pulses were used to reach fields far higher than in CW measurements, and near Tc, quench fields close to the superheating field were observed. Based on a review of previous experience with Nb3Sn cavities, a speculative mechanism involving weak link grain boundaries is presented to explain how the modified annealing step could be the cause of the absence of strong Q -slope. Finally, an analysis of the progress to date provides hints that the path forward for Nb3Sn cavities should focus on minimizing defects.

  13. Development of a 15 T Nb3Sn accelerator dipole demonstrator at Fermilab

    DOE PAGESBeta

    Novitski, I.; Andreev, N.; Barzi, E.; Carmichael, J.; Kashikhin, V. V.; Turrioni, D.; Yu, M.; Zlobin, A. V.

    2016-06-01

    Here, a 100 TeV scale Hadron Collider (HC) with a nominal operation field of at least 15 T is being considered for the post-LHC era, which requires using the Nb3Sn technology. Practical demonstration of this field level in an accelerator-quality magnet and substantial reduction of the magnet costs are the key conditions for realization of such a machine. FNAL has started the development of a 15 T Nb3Sn dipole demonstrator for a 100 TeV scale HC. The magnet design is based on 4-layer shell type coils, graded between the inner and outer layers to maximize the performance and reduce themore » cost. The experience gained during the Nb3Sn magnet R&D is applied to different aspects of the magnet design. This paper describes the magnetic and structural designs and parameters of the 15 T Nb3Sn dipole and the steps towards the demonstration model fabrication.« less

  14. Development of a 15 T $Nb_3Sn$ Accelerator Dipole Demonstrator at Fermilab

    DOE PAGESBeta

    Novitski, I.; Andreev, N.; Barzi, E.; Carmichael, J.; Kashikhin, V. V.; Turrion, D.; Yu, M.; Zlobin, A. V.

    2016-01-01

    100 TeV scale Hadron Collider (HC) with a nominal operation field of at least 15 T is being considered for the post-LHC era, which requires using the $Nb_3Sn$ technology. Practical demonstration of this field level in an accelerator-quality magnet and substantial reduction of the magnet costs are the key conditions for realization of such a machine. FNAL has started the development of a 15 T Nb3Sn dipole demonstrator for a 100 TeV scale HC. The magnet design is based on 4-layer shell type coils, graded between the inner and outer layers to maximize the performance and reduce the cost. Themore » experience gained during the Nb3Sn magnet R&D is applied to different aspects of the magnet design. This paper describes the magnetic and structural designs and parameters of the 15 T Nb3Sn dipole and the steps towards the demonstration model fabrication.« less

  15. Performance of Nb3Sn Quadrupole Under High Stress

    SciTech Connect

    Felice, H.; Bajko, M.; Bingham, B.; Bordini, B.; Bottura, L.; Caspi, S.; Rijk, G. De; Dietderich, D.; Ferracin, P.; Giloux, C.; Godeke, A.; Hafalia, R.; Milanese, A.; Rossi, L.; Sabbi, G. L.

    2010-08-01

    Future upgrades of the Large Hadron Collider (LHC) will require large aperture and high gradient quadrupoles. Nb{sub 3}Sn is the most viable option for this application but is also known for its strain sensitivity. In high field magnets, with magnetic fields above 12 T, the Lorentz forces will generate mechanical stresses that may exceed 200 MPa in the windings. The existing measurements of critical current versus strain of Nb{sub 3}Sn strands or cables are not easily applicable to magnets. In order to investigate the impact of high mechanical stress on the quench performance, a series of tests was carried out within a LBNL/CERN collaboration using the magnet TQS03 (a LHC Accelerator Research Program (LARP) 1-meter long, 90-mm aperture Nb{sub 3}Sn quadrupole). The magnet was tested four times at CERN under various pre-stress conditions. The average mechanical compressive azimuthal pre-stress on the coil at 4.2 K ranged from 120 MPa to 200 MPa. This paper reports on the magnet performance during the four tests focusing on the relation between pre-stress conditions and the training plateau.

  16. Radio Frequency Magnetic Field Limits of Nb and Nb_{3}Sn.

    PubMed

    Posen, S; Valles, N; Liepe, M

    2015-07-24

    Superconducting radio frequency (srf) cavities, essential components of many large particle accelerators, rely on the metastable flux-free state of superconducting materials. In this Letter, we present results of experiments measuring the magnetic field limits of two srf materials, Nb and Nb_{3}Sn. Resonators made using these materials were probed using both high power rf pulses and dc magnetic fields. Nb, which is the current standard material for srf cavities in applications, was found to be limited by the superheating field H_{sh} when prepared using methods to avoid excessive rf dissipation at high fields. Nb_{3}Sn, which is a promising alternative material that is still in the early stages of development for srf purposes, was found to be limited between the onset field of metastability H_{c1} and H_{sh}. Analysis of the results shows that the limitation is consistent with nucleation of flux penetration at defects in the rf layer. PMID:26252705

  17. "Engineered dual NbTa barriers for higher Jc Nb3Sn superconductors"

    SciTech Connect

    Robert E. Barber; Karl T. Hartwig

    2012-07-07

    The tantalum (Ta) diffusion barrier in advanced Nb3Sn superconductors often develops a failure mode during wire drawing where the Nb and Ta layers deform non-uniformly leading to a rough interface with adjacent copper. The non-uniform deformation of these layers can lead to premature wire breakage and breaches in the barrier, and contamination of the copper stabilizer by tin (Sn). The objective of the proposed work was to demonstrate that a dual NbTa layer made from severely deformed Nb and Ta exhibits improved co-deformation behavior with pure Cu in advanced Nb3Sn superconductors. This phase I project demonstrated improved microstructural uniformity and superior mechanical property characteristics of equal channel angular extrusion (ECAE) processed and rolled Nb and Ta sheets. The results of this work point to a method for fabrication of higher field and lower cost superconducting magnets for high energy physics applications.

  18. Fabrication of 'TAMU3', a 'Wind/React' stress-managed 14T Nb3Sn block coil design

    NASA Astrophysics Data System (ADS)

    Blackburn, R.; Diaczenko, N.; Elliott, T.; Jaisle, A.; McInturff, A.; McIntyre, P.; Sattarov, A.

    2008-02-01

    The third phase of a high field dipole technology development, a full set (2+) of Stress-Managed winding modules is being fabricated. The dipole fabrication uses tooling, fixtures, procedures and technology modified and updated based on the second phase work and results reported plus new material developments and higher performance strand. The strand was furnished by the DOE HEP Nb3Sn conductor development program. The modules' cables were processed and cabled by the LBNL facility using the latest procedures developed. There were several new materials and processes introduced in this third phase to improve performance or simplify the fabrication which will be discussed. If all the performance inherent in the strand were to be achieved then the peak field should be higher than 14 T. The containment and flux return structure are the same as used in phase 2. This phase of the development will constitute the outer winding modules of a 'Collider' prototype Block dipole with Stress-Management. The lessons learned and the results obtained will be discussed.

  19. Testing of a Single 11 T $Nb_3Sn$ Dipole Coil Using a Dipole Mirror Structure

    SciTech Connect

    Zlobin, Alexander; Andreev, Nicolai; Barzi, Emanuela; Chlachidze, Guram; Kashikhin, Vadim; Nobrega, Alfred; Novitski, Igor; Turrioni, Daniele; Karppinen, Mikko; Smekens, David

    2014-07-01

    FNAL and CERN are developing an 11 T Nb3Sn dipole suitable for installation in the LHC. To optimize coil design parameters and fabrication process and study coil performance, a series of 1 m long dipole coils is being fabricated. One of the short coils has been tested using a dipole mirror structure. This paper describes the dipole mirror magnetic and mechanical designs, and reports coil parameters and test results.

  20. Magnetic and Structural Design of a 15 T $Nb_3Sn$ Accelerator Depole Model

    SciTech Connect

    Kashikhin, V. V.; Andreev, N.; Barzi, E.; Novitski, I.; Zlobin, A. V.

    2015-01-01

    Hadron Colliders (HC) are the most powerful discovery tools in modern high energy physics. A 100 TeV scale HC with a nominal operation field of at least 15 T is being considered for the post-LHC era. The choice of a 15 T nominal field requires using the Nb3Sn technology. Practical demonstration of this field level in an accelerator-quality magnet and substantial reduction of the magnet costs are the key conditions for realization of such a machine. FNAL has started the development of a 15 T $Nb_{3}Sn$ dipole demonstrator for a 100 TeV scale HC. The magnet design is based on 4-layer shell type coils, graded between the inner and outer layers to maximize the performance. The experience gained during the 11-T dipole R&D campaign is applied to different aspects of the magnet design. This paper describes the magnetic and structural designs and parameters of the 15 T $Nb_3Sn$ dipole and the steps towards the demonstration model.

  1. Nb3Sn superconducting magnets for electron cyclotron resonance ion sources.

    PubMed

    Ferracin, P; Caspi, S; Felice, H; Leitner, D; Lyneis, C M; Prestemon, S; Sabbi, G L; Todd, D S

    2010-02-01

    Electron cyclotron resonance (ECR) ion sources are an essential component of heavy-ion accelerators. Over the past few decades advances in magnet technology and an improved understanding of the ECR ion source plasma physics have led to remarkable performance improvements of ECR ion sources. Currently third generation high field superconducting ECR ion sources operating at frequencies around 28 GHz are the state of the art ion injectors and several devices are either under commissioning or under design around the world. At the same time, the demand for increased intensities of highly charged heavy ions continues to grow, which makes the development of even higher performance ECR ion sources a necessity. To extend ECR ion sources to frequencies well above 28 GHz, new magnet technology will be needed in order to operate at higher field and force levels. The superconducting magnet program at LBNL has been developing high field superconducting magnets for particle accelerators based on Nb(3)Sn superconducting technology for several years. At the moment, Nb(3)Sn is the only practical conductor capable of operating at the 15 T field level in the relevant configurations. Recent design studies have been focused on the possibility of using Nb(3)Sn in the next generation of ECR ion sources. In the past, LBNL has worked on the VENUS ECR, a 28 GHz source with solenoids and a sextupole made with NbTi operating at fields of 6-7 T. VENUS has now been operating since 2004. We present in this paper the design of a Nb(3)Sn ECR ion source optimized to operate at an rf frequency of 56 GHz with conductor peak fields of 13-15 T. Because of the brittleness and strain sensitivity of Nb(3)Sn, particular care is required in the design of the magnet support structure, which must be capable of providing support to the coils without overstressing the conductor. In this paper, we present the main features of the support structure, featuring an external aluminum shell pretensioned with water

  2. Nb3Sn superconducting magnets for electron cyclotron resonance ion sources.

    PubMed

    Ferracin, P; Caspi, S; Felice, H; Leitner, D; Lyneis, C M; Prestemon, S; Sabbi, G L; Todd, D S

    2010-02-01

    Electron cyclotron resonance (ECR) ion sources are an essential component of heavy-ion accelerators. Over the past few decades advances in magnet technology and an improved understanding of the ECR ion source plasma physics have led to remarkable performance improvements of ECR ion sources. Currently third generation high field superconducting ECR ion sources operating at frequencies around 28 GHz are the state of the art ion injectors and several devices are either under commissioning or under design around the world. At the same time, the demand for increased intensities of highly charged heavy ions continues to grow, which makes the development of even higher performance ECR ion sources a necessity. To extend ECR ion sources to frequencies well above 28 GHz, new magnet technology will be needed in order to operate at higher field and force levels. The superconducting magnet program at LBNL has been developing high field superconducting magnets for particle accelerators based on Nb(3)Sn superconducting technology for several years. At the moment, Nb(3)Sn is the only practical conductor capable of operating at the 15 T field level in the relevant configurations. Recent design studies have been focused on the possibility of using Nb(3)Sn in the next generation of ECR ion sources. In the past, LBNL has worked on the VENUS ECR, a 28 GHz source with solenoids and a sextupole made with NbTi operating at fields of 6-7 T. VENUS has now been operating since 2004. We present in this paper the design of a Nb(3)Sn ECR ion source optimized to operate at an rf frequency of 56 GHz with conductor peak fields of 13-15 T. Because of the brittleness and strain sensitivity of Nb(3)Sn, particular care is required in the design of the magnet support structure, which must be capable of providing support to the coils without overstressing the conductor. In this paper, we present the main features of the support structure, featuring an external aluminum shell pretensioned with water

  3. The Study of Single Nb3Sn Quadrupole Coils Using a Magnetic Mirror Structure

    SciTech Connect

    Chlachidze, G.; Andreev, N.; Barzi, E.; Bossert, R.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; Nobrega, N.; Novitski, I.; Orris, D.; Tartaglia, M.

    2010-07-30

    Several 90-mm quadrupole coils made of 0.7-mm Nb{sub 3}Sn strand based on the 'Restack Rod Process' (RRP) of 108/127 design, with cored and non-cored cables and different cable insulation, were fabricated and individually tested at Fermilab using a test structure designed to provide a quadrupole magnetic field environment. The coils were instrumented with voltage taps and strain gauges to study quench performance and mechanical properties. The Nb{sub 3}Sn strand and cable parameters, the coil fabrication details, the mirror model assembly procedure and test results at temperatures of 4.5 K and 1.9 K are reported and discussed.

  4. Finite-element analysis of transverse compressive and thermal loads on Nb3Sn wires with voids

    DOE PAGESBeta

    Zhai, Y.; D'Hauthuille, L.; Barth, C.; Senatore, C.

    2016-02-29

    High-field superconducting magnets play a very important role in many large-scale physics experiments, particularly particle colliders and fusion confinement devices such as Large Hadron Collider (LHC) and International Thermonuclear Experimental Reactor (ITER). The two most common superconductors used in these applications are NbTi and Nb3Sn. Nb3Sn wires are favored because of their significantly higher Jc (critical current density) for higher field applications. The main disadvantage of Nb3Sn is that the superconducting performance of the wire is highly strain sensitive and it is very brittle. This strain sensitivity is strongly influenced by two factors: plasticity and cracked filaments. Cracks are inducedmore » by large stress concentrators that can be traced to the presence of voids in the wire. We develop detailed 2-D and 3-D finite-element models containing wire filaments and different possible distributions of voids in a bronze-route Nb3Sn wire. We apply compressive transverse loads for various cases of void distributions to simulate the stress and strain response of a Nb3Sn wire under the Lorentz force. Furthermore, this paper improves our understanding of the effect voids have on the Nb3Sn wire's mechanical properties, and in so, the connection between the distribution of voids and performance degradation such as the correlation between irreversible strain limit and the void-induced local stress concentrations.« less

  5. 11 T Twin-Aperture Nb$_3$Sn Dipole Development for LHC Upgrades

    SciTech Connect

    Zlobin, A. V.; Andreev, N.; Apollinari, G.; Auchmann, B.; Barzi, E.; Izquierdo Bermudez, S.; Bossert, R.; Buehler, M.; Chlachidze, G.; DiMarco, J.; Karppinen, M.; Nobrega, F.; Novitski, I.; Rossi, L.; Smekens, D.; Tartaglia, M.; Turrioni, D.; Velev, Genadi

    2015-01-01

    FNAL and CERN are developing a twin-aperture 11 T Nb3Sn dipole suitable for installation in the LHC. This paper describes the design and parameters of the 11 T dipole developed at FNAL for the LHC upgrades in both single-aperture and twin-aperture configurations, and presents details of the constructed dipole models. Results of studies of magnet quench performance, quench protection and magnetic measurements performed using short 1 m long coils in the dipole mirror and single-aperture configurations are reported and discussed.

  6. Testing of Nb3Sn quadrupole coils using magnetic mirror structure

    SciTech Connect

    Zlobin, A.V.; Andreev, N.; Barzi, E.; Bossert, R.; Chlachidze, G.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.; Novitski, I.; Tartaglia, M.; Tompkins, J.C.; /Fermilab

    2009-07-01

    This paper describes the design and parameters of a quadrupole mirror structure for testing the mechanical, thermal and quench performance of single shell-type superconducting quadrupole coils at field, current and force levels similar to that of real magnet. The concept was experimentally verified by testing two quadrupole coils, previously used in quadrupole models, in the developed mirror structure in the temperature range from 4.5 to 1.9 K. The coils were instrumented with voltage taps, heaters, and strain gauges to monitor their mechanical and thermal properties and quench performance. A new quadrupole coil made of improved Nb{sub 3}Sn RRP-108/127 strand and cable insulation based on E-glass tape was also tested using this structure. The fabrication and test results of the quadrupole mirror models are reported and discussed.

  7. Reversible stress-induced anomalies in the strain function of Nb3Sn wires

    NASA Astrophysics Data System (ADS)

    De Marzi, G.; Corato, V.; Muzzi, L.; della Corte, A.; Mondonico, G.; Seeber, B.; Senatore, C.

    2012-02-01

    The full-matrix set of combined temperature (4.2-14 K) and applied axial strain (ɛa) data for the bulk pinning force of a technological Nb3Sn wire (OST type-I) has been studied at fields up to 19 T by combining transport (variable ɛa) and magnetic (variable T) measurements. Some length of the wire was also jacketed with AISI 316L stainless steel, in order to apply a radial strain and to simulate the thermally induced axial compressive strain that the Nb3Sn wires experience in a cable-in-conduit-conductor (CICC). Within the framework of the unified scaling law, raw scaling data for the effective upper critical field, {B}_{{c2}}^{\\ast }(T,\\varepsilon ), have been used in order to experimentally determine the strain function, s(ɛ), of both the bare and the jacketed wires. A direct testing of the various proposed models for s(ɛ) has been carried out, including the power law, the deviatoric description and the polynomial form. All models adequately fit to the s(ɛ) of the bare wire, but in the jacketed wire none of them is able to describe the tensile strain region above the Ic maximum, where the enhanced radial compression cannot be neglected. The origin of the onset of a reduced Bc2 is also discussed.

  8. Fabrication and Analysis of 150 mm Aperture Nb3Sn LARP MQXF Coils

    SciTech Connect

    Holik, E. F.; Ambrosio, G.; Anerella, M.; Bossert, R.; Cavanna, E.; Cheng, D.; Dietderich, D. R.; Ferracin, P.; Ghosh, A. K.; Izquierdo Bermudez, S.; Krave, S.; Nobrega, A.; Perez, J. C.; Pong, I.; Rochepault, Rochepault; Sabbi, G. L.; Schmalzle, J.; Yu, M.

    2016-01-01

    The US LHC Accelerator Research Program (LARP) and CERN are combining efforts for the HiLumi-LHC upgrade to design and fabricate 150 mm aperture, interaction region quadrupoles with a nominal gradient of 130 T/m using Nb3Sn. To successfully produce the necessary long MQXF triplets, the HiLumi-LHC collaboration is systematically reducing risk and design modification by heavily relying upon the experience gained from the successful 120 mm aperture LARP HQ program. First generation MQXF short (MQXFS) coils were predominately a scaling up of the HQ quadrupole design allowing comparable cable expansion during Nb3Sn formation heat treatment and increased insulation fraction for electrical robustness. A total of 13 first generation MQXFS coils were fabricated between LARP and CERN. Systematic differences in coil size, coil alignment symmetry, and coil length contraction during heat treatment are observed and likely due to slight variances in tooling and insulation/cable systems. Analysis of coil cross sections indicate that field-shaping wedges and adjacent coil turns are systematically displaced from the nominal location and the cable is expanding less than nominally designed. A second generation MQXF coil design seeks to correct the expansion and displacement discrepancies by increasing insulation and adding adjustable shims at the coil pole and midplanes to correct allowed magnetic field harmonics.

  9. Facile Synthesis of Nb3Sn Via a Hydrogen Reduction Process

    NASA Astrophysics Data System (ADS)

    Zhu, Jun; Jiao, Shuqiang; Zhang, Long; Li, Yanxiang; Zhu, Hongmin

    2016-09-01

    A controllable and facile process for the preparation of Nb3Sn intermetallic compound nanopowders using NbCl5 and SnCl2 vapors reduced by hydrogen has been developed. The vaporizing rates of the two chlorides are controlled by measuring their mass loss as a function of carrier gas (argon) flow rate at certain vaporization temperatures, respectively. X-ray diffraction (XRD) patterns indicate that hydrogenous Nb3Sn products are obtained under the vaporizing rate of 0.155 g min-1 for NbCl5 and 0.036 g min-1 for SnCl2 with the hydrogen flow rate of 2100 ml min-1 at 1273 K (1000 °C). Results of semi-quantitative analysis by X-ray fluorescence (XRF) demonstrate that the atomic ratio of Nb to Sn in the as-synthesized products is 3.48:1, and the content of (Nb + Sn) is taken up to 89.61 wt pct from the total weight of the products. The products can be purified by vacuum heat treatment. Images of transmission electron microscopy (TEM) show that the products are homogenous particles with a mean diameter of 31 nm. In addition, the reaction ratio of the chlorides and the powder yield are controllable by hydrogen flow rate.

  10. Fabrication and Analysis of 150-mm-Aperture Nb3Sn MQXF Coils

    DOE PAGESBeta

    Holik, E. F.; Ambrosio, G.; Anerella, M.; Bossert, R.; Cavanna, E.; Cheng, D.; Dietderich, D. R.; Ferracin, P.; Ghosh, A. K.; Bermudez, S. Izquierdo; et al

    2016-01-12

    The U.S. LHC Accelerator Research Program (LARP) and CERN are combining efforts for the HiLumi-LHC upgrade to design and fabricate 150-mm-aperture, interaction region quadrupoles with a nominal gradient of 130 T/m using Nb3Sn. To successfully produce the necessary long MQXF triplets, the HiLumi-LHC collaboration is systematically reducing risk and design modification by heavily relying upon the experience gained from the successful 120-mm-aperture LARP HQ program. First generation MQXF short (MQXFS) coils were predominately a scaling up of the HQ quadrupole design allowing comparable cable expansion during Nb3Sn formation heat treatment and increased insulation fraction for electrical robustness. A total ofmore » 13 first generation MQXFS coils were fabricated between LARP and CERN. Systematic differences in coil size, coil alignment symmetry, and coil length contraction during heat treatment are observed and likely due to slight variances in tooling and insulation/cable systems. Analysis of coil cross sections indicate that field-shaping wedges and adjacent coil turns are systematically displaced from the nominal location and the cable is expanding less than nominally designed. Lastly, a second generation MQXF coil design seeks to correct the expansion and displacement discrepancies by increasing insulation and adding adjustable shims at the coil pole and midplanes to correct allowed magnetic field harmonics.« less

  11. Performance of a 14-T CuNb/Nb3Sn Rutherford coil with a 300 mm wide cold bore

    NASA Astrophysics Data System (ADS)

    Oguro, Hidetoshi; Watanabe, Kazuo; Awaji, Satoshi; Hanai, Satoshi; Ioka, Shigeru; Sugimoto, Masahiro; Tsubouchi, Hirokazu

    2016-08-01

    A large-bore 14-T CuNb/Nb3Sn Rutherford coil was developed for a 25 T cryogen-free superconducting magnet. The magnet consisted of a low-temperature superconducting (LTS) magnet of NbTi and Nb3Sn Rutherford coils, and a high-temperature superconducting magnet. The Nb3Sn Rutherford coil was fabricated by the react-and-wind method for the first time. The LTS magnet reached the designed operation current of 854 A without a training quench at a 1 h ramp rate. The central magnetic field generated by the LTS magnet was measured by a Hall sensor to be 14.0 T at 854 A in a 300 mm cold bore.

  12. Summary of the Persistent Current Effect Measurements in Nb 3 Sn and NbTi Accelerator Magnets at Fermilab

    DOE PAGESBeta

    Velev, G. V.; Chlachidze, G.; DiMarco, J.; Stoynev, S. E.

    2016-01-06

    In the past 10 years, Fermilab has been executing an intensive R&D program on accelerator magnets based on Nb3Sn superconductor technology. This R&D effort includes dipole and quadrupole models for different programs, such as LARP and 11 T dipoles for the LHC high-luminosity upgrade. Before the Nb3Sn R&D program, Fermilab was involved in the production of the low-beta quadrupole magnets for LHC based on the NbTi superconductor. Additionally, during the 2003-2005 campaign to optimize the operation of the Tevatron, a large number of Tevatron magnets were re-measured. As a result of this field analysis, a systematic study of the persistentmore » current decay and snapback effect in these magnets was performed. This paper summarizes the result of this study and presents a comparison between Nb3Sn and NbTi dipoles and quadrupoles.« less

  13. Mechanical Analysis of the Nb3Sn Dipole Magnet HD1

    SciTech Connect

    Ferracin, Paolo; Bartlett, Scott E.; Caspi, Shlomo; Dietderich, Daniel R.; Gourlay, Steve A.; Hannaford, Charles R.; Hafalia, Aurelio R.; Lietzke, Alan F.; Mattafirri, Sara; Sabbi, Gianluca

    2005-06-01

    The Superconducting Magnet Group at Lawrence Berkeley National Laboratory (LBNL) has recently fabricated and tested HD1, a Nb3Sn dipole magnet. The magnet reached a 16 T field, and exhibited training quenches in the end regions and in the straight section. After the test, HD1 was disassembled and inspected, and a detailed 3D finite element mechanical analysis was done to investigate for possible quench triggers. The study led to minor modifications to mechanical structure and assembly procedure, which were verified in a second test (HD1b). This paper presents the results of the mechanical analysis, including strain gauge measurements and coil visual inspection. The adjustments implemented in the magnet structure are reported and their effect on magnet training discussed.

  14. Recent progress and tests of radiation resistant impregnation materials for Nb3Sn coils

    NASA Astrophysics Data System (ADS)

    Bossert, R.; Krave, S.; Ambrosio, G.; Andreev, N.; Chlachidze, G.; Nobrega, A.; Novitski, I.; Yu, M.; Zlobin, A. V.

    2014-01-01

    Fermilab is collaborating with Lawrence Berkeley National Laboratory (LBNL) and Brookhaven National Laboratory (BNL) (US-LARP collaboration) to develop a large-aperture Nb3Sn superconducting quadrupole for the Large Hadron Collider (LHC) luminosity upgrade. An important component of this work is the development of materials that are sufficiently radiation resistant for use in critical areas of the upgrade. This paper describes recent progress in characterization of materials, including the baseline CTD101K epoxy, cyanate ester blends, and Matrimid 5292, a bismaleimide-based system. Structural properties of "ten stacks" of cable impregnated with these materials are tested at room and cryogenic temperatures and compared to the baseline CT-101K. Experience with potting 1 and 2 meter long coils with Matrimid 5292 are described. Test results of a single 1-m coil impregnated with Matrimid 5292 are reported and compared to similar coils impregnated with the traditional epoxy.

  15. Test results of the LARP Nb$_3$Sn quadrupole HQ03a

    DOE PAGESBeta

    DiMarco, J.; G. Ambrosio; Chlachidze, G.; Bossert, R.; Holik, T.; Orris, D.; Stoynev, S.; Strauss, T.; Sylvester, C.; Tartaglia, M.; et al

    2016-03-09

    The US LHC Accelerator Research Program (LARP) has been developing $Nb_3Sn$ quadrupoles of progressively increasing performance for the high luminosity upgrade of the Large Hadron Collider. The 120 mm aperture High-field Quadrupole (HQ) models are the last step in the R&D phase supporting the development of the new IR Quadrupoles (MQXF). Three series of HQ coils were fabricated and assembled in a shell-based support structure, progressively optimizing the design and fabrication process. The final set of coils consistently applied the optimized design solutions, and was assembled in the HQ03a model. Furthermore, this paper reports a summary of the HQ03a testmore » results, including training, mechanical performance, field quality and quench studies.« less

  16. Introduction of Flux Pinning Centers for Use in Nb3Sn Superconducting Wire

    NASA Astrophysics Data System (ADS)

    Rahmani, David; Damborsky, Kyle; McIntyre, Peter; Pogue, Nathaniel

    2009-10-01

    Powder metallurgy was used to introduce a homogeneously heterogeneous distribution of nanoscale flux pinning centers in Nb rod for future use in Nb3Sn superconducting wire. The pinning centers consisted of Y, Y2O3, W, Cu, Zr, and Ti. Flux pinning centers in superconducting wire would prevent a decrease in critical current density in the presence of a high magnetic field. The blended powders were consolidated using Cold Isostatic Pressing (CIP) at 50000 PSI. The samples were analyzed and found to contain a high concentration of oxygen, which was found to be excessive for use in a superconductor and may have contributed to poor performance in CIP. Due to the high level of oxygen found in commercially available Nb powder, future attempts will require the manufacturing of Nb powder with a low oxygen content.

  17. Nb$_3$Sn High Field Magnets for the High Luminosity LHC Upgrade Project

    SciTech Connect

    Ambrosio, Giorgio

    2015-01-01

    The High Luminosity upgrade of the Large Hadron Collider at CERN requires a new generation of high field superconducting magnets. High field large aperture quadrupoles (MQXF) are needed for the low-beta triplets close to the ATLAS and CMS detectors, and high field two-in-one dipoles (11 T dipoles) are needed to make room for additional collimation. The MQXF quadrupoles, with a field gradient of 140 T/m in 150 mm aperture, have a peak coil field of 12.1 T at nominal current. The 11 T dipoles, with an aperture of 60 mm, have a peak coil field of 11.6 T at nominal current. Both magnets require Nb3Sn conductor and are the first applications of this superconductor to actual accelerator magnets.

  18. Fabrication of Nb3Sn Shell-Type Coils with Pre-Preg Ceramic Insulation

    NASA Astrophysics Data System (ADS)

    Chichili, D. R.; Andreev, N.; Kashikhin, V. S.; Zlobin, A. V.; Codell, D.; Fabian, P.; Tupper, M.

    2004-06-01

    Insulation is one of the critical components for high-field Nb3Sn magnets that follow wind-and-react approach. The insulation material has to withstand high bending stresses while winding the coil and high heat-treatment temperatures under pressure during coil reaction. At Fermilab we have developed a procedure and tested successfully the dry ceramic insulation tape with inorganic liquid binder to wind and cure the coils. Recently we have extended this to a pre-preg ceramic insulation tape, which would minimize and control the amount of binder in the coil. Several coils with various insulation patterns have been fabricated and tested at Fermilab. This paper discusses the fabrication issues of the coils with different types of cable insulation including the pre-preg ceramic insulation.

  19. Evaluation of critical current density and residual resistance ratio limits in powder in tube Nb3Sn conductors

    NASA Astrophysics Data System (ADS)

    Segal, Christopher; Tarantini, Chiara; Hawn Sung, Zu; Lee, Peter J.; Sailer, Bernd; Thoener, Manfred; Schlenga, Klaus; Ballarino, Amalia; Bottura, Luca; Bordini, Bernardo; Scheuerlein, Christian; Larbalestier, David C.

    2016-08-01

    High critical current density (J c) Nb3Sn A15 multifilamentary wires require a large volume fraction of small grain (SG), superconducting A15 phase, as well as Cu stabilizer with high Residual Resistance Ratio (RRR) to provide electromagnetic stabilization and protection. In powder-in-tube (PIT) wires the unreacted Nb7.5 wt%Ta outer layer of the tubular filaments acts as a diffusion barrier and protects the interfilamentary Cu stabilizer from Sn contamination. A high RRR requirement generally imposes a restricted A15 reaction heat treatment to prevent localized full reaction of the filament that could allow Sn to reach the Cu. In this study we investigate recent high quality PIT wires that achieve a J c (12 T, 4.2 K) up to ∼2500 A mm‑2 and find that the minimum diffusion barrier thickness decreases as the filament aspect ratio increases from ∼1 in the inner rings of filaments to 1.3 in the outer filament rings. We found that just 2–3 diffusion barrier breaches can degrade RRR from 300 to 150 or less. Using progressive etching of the Cu we also found that the RRR degradation is localized near the external filaments where deformation is highest. Consequently minimizing filament distortion during strand fabrication is important for reducing RRR degradation. The additional challenge of developing the highest possible J c must be addressed by forming the maximum fraction of high J c SG A15 and minimizing low J c large-grain (LG) A15 morphologies. In one wire we found that 15% of the filaments had a significantly enhanced SG/LG A15 ratio and no residual A15 in the core, a feature that opens a path to substantial J c improvement.

  20. Evaluation of critical current density and residual resistance ratio limits in powder in tube Nb3Sn conductors

    NASA Astrophysics Data System (ADS)

    Segal, Christopher; Tarantini, Chiara; Hawn Sung, Zu; Lee, Peter J.; Sailer, Bernd; Thoener, Manfred; Schlenga, Klaus; Ballarino, Amalia; Bottura, Luca; Bordini, Bernardo; Scheuerlein, Christian; Larbalestier, David C.

    2016-08-01

    High critical current density (J c) Nb3Sn A15 multifilamentary wires require a large volume fraction of small grain (SG), superconducting A15 phase, as well as Cu stabilizer with high Residual Resistance Ratio (RRR) to provide electromagnetic stabilization and protection. In powder-in-tube (PIT) wires the unreacted Nb7.5 wt%Ta outer layer of the tubular filaments acts as a diffusion barrier and protects the interfilamentary Cu stabilizer from Sn contamination. A high RRR requirement generally imposes a restricted A15 reaction heat treatment to prevent localized full reaction of the filament that could allow Sn to reach the Cu. In this study we investigate recent high quality PIT wires that achieve a J c (12 T, 4.2 K) up to ˜2500 A mm-2 and find that the minimum diffusion barrier thickness decreases as the filament aspect ratio increases from ˜1 in the inner rings of filaments to 1.3 in the outer filament rings. We found that just 2-3 diffusion barrier breaches can degrade RRR from 300 to 150 or less. Using progressive etching of the Cu we also found that the RRR degradation is localized near the external filaments where deformation is highest. Consequently minimizing filament distortion during strand fabrication is important for reducing RRR degradation. The additional challenge of developing the highest possible J c must be addressed by forming the maximum fraction of high J c SG A15 and minimizing low J c large-grain (LG) A15 morphologies. In one wire we found that 15% of the filaments had a significantly enhanced SG/LG A15 ratio and no residual A15 in the core, a feature that opens a path to substantial J c improvement.

  1. Evaluation of critical current density and residual resistance ratio limits in powder in tube Nb3Sn conductors

    DOE PAGESBeta

    Segal, Christopher; Tarantini, Chiara; Sung, Zu Hawn; Lee, Peter J.; Sailer, Bernd; Thoener, Manfred; Schlenga, Klaus; Ballarino, Amalia; Bottura, Luca; Bordini, Bernardo; et al

    2016-06-10

    High critical current density (Jc) Nb3Sn A15 multifilamentary wires require a large volume fraction of small grain, superconducting A15 phase, as well as Cu stabilizer with high Residual Resistance Ratio (RRR) to provide electromagnetic stabilization and protection. In Powder-in-Tube (PIT) wires the unreacted Nb7.5wt.%Ta outer layer of the tubular filaments acts as a diffusion barrier and protects the interfilamentary Cu stabilizer from Sn contamination. A high RRR requirement generally imposes a restricted A15 reaction heat treatment (HT) to prevent localized full reaction of the filament that could allow Sn to reach the Cu. In this paper we investigate recent highmore » quality PIT wires that achieve a Jc(12 T, 4.2 K) up to ~2500 A/mm-2 and find that the minimum diffusion barrier thickness decreases as the filament aspect ratio increases from ~1 in the inner rings of filaments to 1.3 in the outer filament rings. We found that just 2-3 diffusion barrier breaches can degrade RRR from 300 to 150 or less. Using progressive etching of the Cu we also found that the RRR degradation is localized near the external filaments where deformation is highest. Consequently minimizing filament distortion during strand fabrication is important for reducing RRR degradation. The additional challenge of developing the highest possible Jc must be addressed by forming the maximum fraction of high Jc small-grain (SG) A15 and minimizing low Jc large-grain (LG) A15 morphologies. Finally, in one wire we found that 15% of the filaments had a significantly enhanced SG/LG A15 ratio and no residual A15 in the core, a feature that opens a path to substantial Jc improvement.« less

  2. Influence of the heat-treatment conditions, microchemistry, and microstructure on the irreversible strain limit of a selection of Ti-doped internal-tin Nb3Sn ITER wires

    NASA Astrophysics Data System (ADS)

    Cheggour, N.; Lee, P. J.; Goodrich, L. F.; Sung, Z.-H.; Stauffer, T. C.; Splett, J. D.; Jewell, M. C.

    2014-10-01

    individual filaments are only few micrometers. All the strands contained substantial Kirkendall porosity, but we found that the quantity and distribution of the Kirkendall voids vary significantly with strand design. Luvata wires have the least porosity, followed by WST wires, and then by OST strands. However, even though the presence of cracks in the Nb3Sn filaments that are in close proximity to Kirkendall voids suggest a correlation between crack initiation and the proximity of the filaments to these voids, the porosity investigation established no definitive relationship between porosity and ɛirr,0 in the wires studied. Contribution of NIST, an agency of the US government, not subject to copyright.

  3. Design and Test of a Nb3Sn Subscale Dipole Magnet for Training Studies

    SciTech Connect

    Felice, Helene; Caspi, Shlomo; Dietderich, Daniel R.; Felice, Helene; Ferracin, Paolo; Gourlay, Steve A.; Hafalia, Aurelo R.; Lietzke, Alan F.; Mailfert, Alain; Sabbi, GainLuca; Vedrine, Pierre

    2007-06-01

    As part of a collaboration between CEA/Saclay and the Superconducting Magnet Group at LBNL, a subscale dipole structure has been developed to study training in Nb3Sn coils under variable pre-stress conditions. This design is derived from the LBNL Subscale Magnet and relies on the use of identical Nb{sub 3}Sn racetrack coils. Whereas the original LBNL subscale magnet was in a dual bore 'common-coil' configuration, the new subscale dipole magnet (SD) is assembled as a single bore dipole made of two superposed racetrack coils. The dipole is supported by a new mechanical structure developed to withstand the horizontal and axial Lorentz forces and capable of applying variable vertical, horizontal and axial preload. The magnet was tested at LBNL as part of a series of training studies aiming at understanding of the relation between pre-stress and magnet performance. Particular attention is given to the coil ends where the magnetic field peaks and stress conditions are the least understood. After a description of SD design, assembly, cool-down and tests results are reported and compared with the computations of the OPERA3D and ANSYS magnetic and mechanical models.

  4. A new generation Nb3Sn wire, and the prospects for its use inparticle accelerators

    SciTech Connect

    Scanlan, R.M.; Dietderich, D.R.; Gourlay, S.A.

    2003-09-30

    The US DOE has initiated a Conductor Development Program aimed at demonstrating a high current density, cost effective Nb3Sn conductor for use in accelerator magnets. The first goal, an increase in current density by 50%, has been achieved in a practical conductor. The program is focused at present on achieving the second goal of reduced losses. The different approaches for achieving these goals will be discussed, and the status will be presented. Magnet technology R&D has been proceeding in parallel with the conductor development efforts, and these two technologies are reaching the level required for the next step--introduction into operating accelerator magnets. An obvious point for introducing this technology is the LHC interaction region magnets, which require large apertures and high fields (or high field gradients). By upgrading the interaction region magnets, machine performance can be enhanced significantly without replacing the arc magnets, which represent most of the cost of an accelerator. Design requirements generated by recent studies and workshops will be reviewed, and a roadmap for the development of the next-generation interaction region magnets will be presented.

  5. Development and coil fabrication for the LARP 3.7-m long Nb3Sn quadruple

    SciTech Connect

    Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bossert, R.; Caspi, S.; Chlachidize, G.; Dietderich, D.; Felice, H.; Ferracin, P.; Ghosh, A.; /Fermilab /Brookhaven /LBL, Berkeley /Texas A-M

    2009-02-01

    The U.S. LHC Accelerator Research Program (LARP) has started the fabrication of 3.7-m long Nb{sub 3}Sn quadrupole models. The Long Quadrupoles (LQ) are 'Proof-of-Principle' magnets which are to demonstrate that Nb3Sn technology is mature for use in high energy particle accelerators. Their design is based on the LARP Technological Quadrupole (TQ) models, developed at FNAL and LBNL, which have design gradients higher than 200 T/m and an aperture of 90 mm. The plans for the LQ R&D and a design update are presented and discussed in this paper. The challenges of fabricating long accelerator-quality Nb{sub 3}Sn coils are presented together with the solutions adopted for the LQ coils (based on the TQ experience). During the fabrication and inspection of practice coils some problems were found and corrected. The fabrication at BNL and FNAL of the set of coils for the first Long Quadrupole is in progress.

  6. Test Results of a Nb3Sn Wind/React 'Stress-Managed' BlockDipole

    SciTech Connect

    McInturff, A.; Bish, P.; Blackburn, R.; Diaczenko, N.; Elliott,T.; Hafalia Jr., R.; Henchel, W.; Jaisle, A.; Lau, W.; Lietzke, A.; McIntyre, P.; Noyes, P.; Nyman, M.; Sattarov, A.; Sattarov, A.

    2006-08-25

    A second phase of a highfield dipole technology developmenthas been tested. A Nb3Sn block-coil model dipole was fabricated, usingmagnetic mirror geometry and wind/react coil technology. The primaryobjective of this phase was to make a first experimental test of thestress-management strategy pioneered at Texas A&M. In this strategy ahigh-strength support matrix is integrated with the windings to interceptLorentz stress from the inner winding so that it does not accumulate inthe outer winding. The magnet attained a field that was consistent withshort sample limit on the first quench; there was no training. Thedecoupling of Lorentz stress between inner and outer windings wasvalidated. In ramp rate studies the magnet exhibited a remarkablerobustness in rapid ramping operation. It reached 85 percent of shortsample(ss) current even while ramping 2-3 T/s. This robustness isattributed to the orientation of the Rutherford cables parallel to thefield in the windings, instead of the transverse orientation thatcharacterizes common dipole designs. Test results are presented and thenext development phase plans are discussed.

  7. Construction challenges and solutions in TAMU3, a 14 T stress-managed Nb3Sn dipole

    NASA Astrophysics Data System (ADS)

    Holik, E. F.; Garrison, R.; Diaczenko, N.; Elliott, T.; Jaisle, A.; McInturff, A. D.; McIntyre, P.; Sattarov, A.

    2014-01-01

    The Accelerator Research Laboratory at Texas A&M University is nearing completion of a Nb3Sn dipole that incorporates stress management directly in its windings. The windings utilize graded-cross-section cable made from 54/61 (54 out of a 61 subelement hexagonal pattern) Restacked Rod Processed® Nb3Sn/Cu conductor and fine-filament S-2 glass fabric insulation. Coil heat treatment and associated differential expansions have brought about some tin leakage, highresistance electrical shorts, and coil gaps. TAMU3b impregnation successfully increased the coil-to-ground resistance. Quench protection in TAMU3 was simulated using QUENCH. The tests of TAMU3 should provide the first examination of stress management at field intensities greater than 12 T.

  8. Embedded fiber Bragg grating sensors for true temperature monitoring in Nb3Sn superconducting magnets for high energy physics

    NASA Astrophysics Data System (ADS)

    Chiuchiolo, A.; Bajas, H.; Bajko, M.; Consales, M.; Giordano, M.; Perez, J. C.; Cusano, A.

    2016-05-01

    The luminosity upgrade of the Large Hadron Collider (HL-LHC) planned at the European Organization for Nuclear Research (CERN) requires the development of a new generation of superconducting magnets based on Nb3Sn technology. The instrumentation required for the racetrack coils needs the development of reliable sensing systems able to monitor the magnet thermo-mechanical behavior during its service life, from the coil fabrication to the magnet operation. With this purpose, Fiber Bragg Grating (FBG) sensors have been embedded in the coils of the Short Model Coil (SMC) magnet fabricated at CERN. The FBG sensitivity to both temperature and strain required the development of a solution able to separate mechanical and temperature effects. This work presents for the first time a feasibility study devoted to the implementation of an embedded FBG sensor for the measurement of the "true" temperature in the impregnated Nb3Sn coil during the fabrication process.

  9. Construction and component testing of TAMU3, a 14 Tesla stress-managed Nb3Sn model dipole

    NASA Astrophysics Data System (ADS)

    Holik, Eddie Frank, III; Benson, Chris; Blackburn, Raymond; Diaczenko, Nick; Elliott, Timothy; Jaisle, Andrew; McInturff, A.; McIntyre, P.; Sattarov, Akhdiyor

    2012-06-01

    We report the construction and testing of components of TAMU3, a 14 Tesla Nb3Sn block-coil dipole. A primary goal in developing this model dipole is to test a method of stress management in which Lorentz stress is intercepted within the coil assembly and bypassed so that it cannot accumulate to a level that would cause strain degradation in the superconducting windings. Details of the fabrication, tooling, and results of construction and magnet component testing will be presented.

  10. Development and Fabrication of Nb3Sn Rutherford Cable for the 11 T DS Dipole Demonstration Model

    SciTech Connect

    Barzi, E.; Lombardo, V.; Nobrega, F.; Turrioni, D.; Yamada, R.; Zlobin, A.V.; Karppinen, M.; /CERN

    2011-11-30

    Fermilab and CERN started the development of 11 T 11-m long Nb{sub 3}Sn dipoles to replace few regular LHC NbTi dipoles and free space for cold collimators in LHC DS areas. An important step in the design of these magnets is the development of the high aspect ratio Nb{sub 3}Sn cable to achieve the nominal field of 11 T at the nominal LHC operating current of 11.85 kA with 20% margin. The keystoned cables 14.7 mm wide with and without a stainless steel core were made out of hard Cu wires and Nb{sub 3}Sn RRP strand 0.7 mm nominal diameter. The cable optimization process was aimed at achieving both mechanical stability and minimal damage to the delicate internal architecture of the Restacked-Rod-Process (RRP) Nb{sub 3}Sn strands with 127 restack design to be used in the magnet short models. Each cable was characterized electrically for transport properties degradation at high field and for low field stability, and metallographically for internal damage.

  11. Composition and connectivity variability of the A15 phase in PIT Nb3Sn wires

    NASA Astrophysics Data System (ADS)

    Tarantini, C.; Segal, C.; Sung, Z. H.; Lee, P. J.; Oberli, L.; Ballarino, A.; Bottura, L.; Larbalestier, D. C.

    2015-09-01

    Powder-in-tube (PIT) Nb3Sn wires are competing with Restacked-Rod-Process (RRP®) for the realization of the high luminosity upgrade of the Large Hadron Collider (LHC) at CERN. These two conductors have different properties and microstructures that are in both cases averages of an inhomogeneous A15 microstructure. PIT has in general a smaller fraction of A15 in the non-Cu cross-section than RRP® and a lower non-Cu Jc (12 T, 4.2 K) (2500-2700 A mm-2 versus 2900-3000 A mm-2) but it can be made in smaller filament diameters, which is an important property for LHC magnets. Another characteristic of PIT A15 is that ˜25% is made up of ˜1-2 μm sized grains (typically ˜10 times the small grain (SG) diameter) and their contribution to transport is uncertain. Here we studied a 192 filament Ta-doped, 1 mm diameter PIT wire and combined multiple characterization techniques in order to distinguish the different wire components, to determine their individual properties and to identify which components are current-carriers. We found multiple evidence that the large A15 grains, which are also the highest-Tc grains, do not contribute to transport at high field and that the only current-carrying A15 is the SG with Tc <17.7 K. However, because of the high density of grain boundaries in the SG A15 layer, PIT has an exceptionally high SG-layer Jc and high specific grain boundary pinning force, QGB. These findings clearly show that it is essential to increase the ratio of small to large and disconnected grains in order to improve PIT performance.

  12. DESIGN, FABRICATION AND TEST OF THE REACT AND WIND, NB(3)SN, LDX FLOATING COIL CONDUCTOR.

    SciTech Connect

    SMITH,B.A.; MICHAEL,P.C.; MINERVINI,J.V.; TAKAYASU,M.; SCHULTZ,J.H.; GREGORY,E.; PYON,T.; SAMPSON,W.B.; GHOSH,A.; SCANLAN,R.

    2000-09-17

    The Levitated Dipole Experiment (LDX) is a novel approach for studying magnetic confinement of a fusion plasma. In this approach, a superconducting ring coil is magnetically levitated for up to 8 hours a day in the center of a 5 meter diameter vacuum vessel. The levitated coil, with on-board helium supply, is called the gloating Coil (F-Coil). Although the maximum field at the coil is only 5.3 tesla, a react-and-wind Nb{sub 3}Sn conductor was selected because the relatively high critical temperature will enable the coil to remain levitated while it warms from 5 K to 10 K. Since pre-reacted Nb{sub 3}Sn tape is no longer commercially available, a composite conductor was designed that contains an 18 strand Nb{sub 3}Sn Rutherford cable. The cable was reacted and then soldered into a structural copper channel that completes the conductor and also provides quench protection. The strain state of the cable was continuously controlled during fabrication steps such as: soldering into the copper channel, spooling, and coil winding, to prevent degradation of the critical current. Measurements of strand and cable critical currents are reported, as well as estimates of the effect of fabrication, winding and operating strains on critical current.

  13. Second-generation coil design of the Nb3Sn low-β quadrupole for the high luminosity LHC

    DOE PAGESBeta

    Bermudez, S. Izquierdo; Ambrosio, G.; Ballarino, A.; Cavanna, E.; Bossert, R.; Cheng, D.; Dietderich, D.; Ferracin, P.; Ghosh, A.; Hagen, P.; et al

    2016-01-18

    As part of the Large Hadron Collider Luminosity upgrade (HiLumi-LHC) program, the US LARP collaboration and CERN are working together to design and build a 150 mm aperture Nb3Sn quadrupole for the LHC interaction regions. A first series of 1.5 m long coils were fabricated and assembled in a first short model. A detailed visual inspection of the coils was carried out to investigate cable dimensional changes during heat treatment and the position of the windings in the coil straight section and in the end region. The analyses allow identifying a set of design changes which, combined with a finemore » tune of the cable geometry and a field quality optimization, were implemented in a new, second-generation, coil design. In this study, we review the main characteristics of the first generation coils, describe the modification in coil lay-out, and discuss their impact on parts design and magnet analysis.« less

  14. Assembly Tests of the First Nb 3 Sn Low-Beta Quadrupole Short Model for the Hi-Lumi LHC

    DOE PAGESBeta

    Pan, H.; Felice, H.; Cheng, D. W.; Anderssen, E.; Ambrosio, G.; Perez, J. C.; Juchno, M.; Ferracin, P.; Prestemon, S. O.

    2016-01-18

    In preparation for the high-luminosity upgrade of the Large Hadron Collider (LHC), the LHC Accelerator Research Program (LARP) in collaboration with CERN is pursuing the development of MQXF: a 150-mm-aperture high-field Nb3Sn quadrupole magnet. Moreover, the development phase starts with the fabrication and test of several short models (1.2-m magnetic length) and will continue with the development of several long prototypes. All of them are mechanically supported using a shell-based support structure, which has been extensively demonstrated on several R&D models within LARP. The first short model MQXFS-AT has been assembled at LBNL with coils fabricated by LARP and CERN.more » In our paper, we summarize the assembly process and show how it relies strongly on experience acquired during the LARP 120-mm-aperture HQ magnet series. We also present comparison between strain gauges data and finite-element model analysis. Finally, we present the implication of the MQXFS-AT experience on the design of the long prototype support structure.« less

  15. Development of MQXF: The Nb3Sn low-β quadrupole for the HiLumi LHC

    DOE PAGESBeta

    Ferracin, P.; G. Ambrosio; Anerella, M.; Ballarino, A.; Bajas, H.; Bajko, M.; Bordini, B.; Bossert, R.; Cheng, D. W.; Dietderich, D. R.; et al

    2015-12-18

    The High Luminosity (HiLumi) Large Hadron Collider (LHC) project has, as the main objective, to increase the LHC peak luminosity by a factor five and the integrated luminosity by a factor ten. This goal will be achieved mainly with a new interaction region layout, which will allow a stronger focusing of the colliding beams. The target will be to reduce the beam size in the interaction points by a factor of two, which requires doubling the aperture of the low-β (or inner triplet) quadrupole magnets. The use of Nb3Sn superconducting material and, as a result, the possibility of operating atmore » magnetic field levels in the windings higher than 11 T will limit the increase in length of these quadrupoles, called MQXF, to acceptable levels. After the initial design phase, where the key parameters were chosen and the magnet's conceptual design finalized, the MQXF project, a joint effort between the U.S. LHC Accelerator Research Program and the Conseil Europeen pour la Recherche Nucleaire (CERN), has now entered the construction and test phase of the short models. Concurrently, the preparation for the development of the full-length prototypes has been initiated. Lastly, this paper will provide an overview of the project status, describing and reporting on the performance of the superconducting material, the lessons learnt during the fabrication of superconducting coils and support structure, and the fine tuning of the magnet design in view of the start of the prototyping phase.« less

  16. Effects of neutron irradiation on pinning force scaling in state-of-the-art Nb3Sn wires

    NASA Astrophysics Data System (ADS)

    Baumgartner, T.; Eisterer, M.; Weber, H. W.; Flükiger, R.; Scheuerlein, C.; Bottura, L.

    2014-01-01

    We present an extensive irradiation study involving five state-of-the-art Nb3Sn wires which were subjected to sequential neutron irradiation up to a fast neutron fluence of 1.6 × 1022 m-2 (E > 0.1 MeV). The volume pinning force of short wire samples was assessed in the temperature range from 4.2 to 15 K in applied fields of up to 7 T by means of SQUID magnetometry in the unirradiated state and after each irradiation step. Pinning force scaling computations revealed that the exponents in the pinning force function differ significantly from those expected for pure grain boundary pinning, and that fast neutron irradiation causes a substantial change in the functional dependence of the volume pinning force. A model is presented, which describes the pinning force function of irradiated wires using a two-component ansatz involving a point-pinning contribution stemming from radiation induced pinning centers. The dependence of this point-pinning contribution on fast neutron fluence appears to be a universal function for all examined wire types.

  17. Structural analysis of the yeast exosome Rrp6p–Rrp47p complex by small-angle X-ray scattering

    SciTech Connect

    Dedic, Emil; Seweryn, Paulina; Jonstrup, Anette Thyssen; Flygaard, Rasmus Koch; Fedosova, Natalya U.; Hoffmann, Søren Vrønning; Boesen, Thomas; Brodersen, Ditlev Egeskov

    2014-07-18

    Highlights: • We show that S. cerevisiae Rrp6p and Rrp47p stabilise each other in vitro. • We determine molecular envelopes of the Rrp6p–Rrp47p complex by SAXS. • Rrp47p binds at the top of the Rrp6p exonuclease domain. • Rrp47p modulates the activity of Rrp6p on a variety of RNA substrates. • Rrp47p does not affect RNA affinity by Rrp6p. - Abstract: The RNase D-type 3′–5′ exonuclease Rrp6p from Saccharomyces cerevisiae is a nuclear-specific cofactor of the RNA exosome and associates in vivo with Rrp47p (Lrp1p). Here, we show using biochemistry and small-angle X-ray scattering (SAXS) that Rrp6p and Rrp47p associate into a stable, heterodimeric complex with an elongated shape consistent with binding of Rrp47p to the nuclease domain and opposite of the HRDC domain of Rrp6p. Rrp47p reduces the exonucleolytic activity of Rrp6p on both single-stranded and structured RNA substrates without significantly altering the affinity towards RNA or the ability of Rrp6p to degrade RNA secondary structure.

  18. Fabrication of a Short-Period Nb3Sn Superconducting Undulator

    SciTech Connect

    Dietderich, Daniel; Dietderich, Daniel; Godeke, Arno; Prestemon, Soren; Pipersky, Paul T.; Liggins, Nate L.; Higley, Hugh C.; Marks, Steve; Schlueter, Ross D.

    2007-06-01

    Lawrence Berkeley National Laboratory develops high-field Nb{sub 3}Sn magnets for HEP applications. In the past few years, this experience has been extended to the design and fabrication of undulator magnets. Some undulator applications require devices that can operate in the presence of a heat load from a beam. The use of Nb{sub 3}Sn permits operation of a device at both a marginally higher temperature (5-8K) and a higher J{sub c}, compared to NbTi devices, without requiring a larger magnetic gap. A half-undulator device consisting of 6 periods (12 coil packs) of 14.5 mm period was designed, wound, reacted, potted and tested. It reached the short sample current limit of 717A in 4 quenches. The non-Cu Jc of the strand was over 7,600 A/mm{sup 2} and the Cu current density at quench was over 8,000 A/mm{sup 2}. Magnetic field models show that if a complete device was fabricated with the same parameters one could obtain beam fields of 1.1 T and 1.6 T for pole gaps of 8 mm and 6 mm, respectively.

  19. Fabrication and test of a racetrack magnet using pre-reacted Nb3Sn cable

    SciTech Connect

    Giorgio Ambrosio et al.

    2002-12-11

    A racetrack magnet, using Nb{sub 3}Sn superconducting cable reacted before winding, has been fabricated and tested at Fermilab. It consists of two flat racetrack coils, connected in a common-coil configuration, separated by a 5 mm thick fiberglass plate. Synthetic oil was used to prevent sintering of the strands during the heat treatment. The coils were wound and vacuum impregnated in the mechanical structure. The turn-to-turn insulation, consisting of Kapton{reg_sign}and pre-impregnated fiberglass tapes as wide as the cable, was wound together with the bare cable in order to form a continuous inter-turn spacer. The coils were instrumented with voltage taps, temperature sensors, spot heaters and quench heaters. The maximum current achieved was 12675 A which is 78% of the short sample limit at 5.1 K (minimum temperature in the coil during 75 A/s ramp). Measurement of the temperature margin revealed a low degradation in the innermost turns. Quench performances at different temperatures and ramp rate effects have been measured and are presented and discussed.

  20. Kinetics of phase growth in the Cu-Sn system and application to composite Nb3Sn strands

    SciTech Connect

    Emanuela Barzi et al.1

    2002-11-18

    Nb{sub 3}Sn is the superconductor most used in the R and D of high field accelerator magnets by either the wind and react or the react and wind technique. In order to program the low temperature steps of the heat treatment, the growth kinetics of Cu-Sn intermetallics was investigated as a function of duration and temperature. The diffusion constants of {eta}, {var_epsilon} and {delta} phases between 150 and 550 C were evaluated using Cu-Sn model samples. Statistical and systematic errors were thoroughly evaluated for an accurate data analysis. Next the behavior of Internal Tin and Modified Jelly Roll Nb{sub 3}Sn composites was compared with the model predictions.

  1. Field Quality Study of a 1-m-Long Single-Aperture 11-T Nb$_3$Sn Dipole Model for LHC Upgrades

    SciTech Connect

    Chlachidze, G.; DiMarco, J.; Andreev, N.; Apollinari, G.; Auchmann, B.; Barzi, E.; Bossert, R.; Fiscarelli, L.; Karppinen, M.; Nobrega, F.; Novitski, I.; Rossi, L.; Smekens, D.; Turrioni, D.; Velev, G. V.; Zlobin, A. V.

    2014-01-01

    FNAL and CERN are carrying out a joint R&D program with the goal of building a 5.5-m-long twin-aperture 11-T Nb_3Sn dipole prototype that is suitable for installation in the LHC. An important part of the program is the development and test of a series of short single-aperture and twin-aperture dipole models with a nominal field of 11 T at the LHC operation current of 11.85 kA and 20% margin. This paper presents the results of magnetic measurements of a 1-m-long single-aperture Nb_3Sn dipole model fabricated and tested recently at FNAL, including geometrical field harmonics and effects of coil magnetization and iron yoke saturation.

  2. Successful performances of the EU-AltTF sample, a large size Nb3Sn cable-in-conduit conductor with rectangular geometry

    NASA Astrophysics Data System (ADS)

    della Corte, A.; Corato, V.; Di Zenobio, A.; Fiamozzi Zignani, C.; Muzzi, L.; Polli, G. M.; Reccia, L.; Turtù, S.; Bruzzone, P.; Salpietro, E.; Vostner, A.

    2010-04-01

    One of the design features which yet offers interesting margins for performance optimization of cable-in-conduit conductors (CICCs), is their geometry. For relatively small size Nb3Sn CICCs, operating at high electromagnetic pressure, such as those for the EDIPO project, it has been experimentally shown that a design based on a rectangular layout with higher aspect ratio leads to the best performance, especially in terms of degradation with electromagnetic loads. To extend this analysis to larger size Nb3Sn CICCs, we manufactured and tested, in the SULTAN facility, an ITER toroidal field (TF) cable, inserted into a thick stainless steel tube and then compacted to a high aspect ratio rectangular shape. Besides establishing a new record in Nb3Sn CICC performances for ITER TF type cables, the very good test results confirmed that the conductor properties improve not only by lowering the void fraction and raising the cable twist pitch, as already shown during the ITER TFPRO and the EDIPO test campaigns, but also by the proper optimization of the conductor shape with respect to the electromagnetic force distribution. The sample manufacturing steps, along with the main test results, are presented here.

  3. Significant enhancement of compositional and superconducting homogeneity in Ti rather than Ta-doped Nb3Sn

    DOE PAGESBeta

    Tarantini, C.; Sung, Z. -H.; Lee, P. J.; Ghosh, A. K.; Larbalestier, D. C.

    2016-01-25

    Nb3Sn wires are now very close to their final optimization but despite its classical nature, detailed understanding of the role of Ta and Ti doping in the A15 is not fully understood. Long thought to be essentially equivalent in their influence on Hc2, they were interchangeably applied. Here we show that Ti produces significantly more homogeneous chemical and superconducting properties. Despite Ta-doped samples having a slightly higher Tc onset in zero-field, they always have a wider Tc-distribution. In particular, whereas the Ta-doped A15 has a Tc-distribution extending from 18 down to 5-6 K (the lowest expected Tc for the binarymore » A15 phase), the Ti-doped samples have no A15 phase with Tc below ~12 K. The much narrower Tc distribution in the Ti-doped samples has a positive effect on their in-field Tc-distribution too, leading to an extrapolated μ0Hc2(0) 2 Tesla larger than the Ta-doped one. Ti-doping also appears to be very homogeneous even when the Sn content is reduced in order to inhibit breakdown of the diffusion barriers in very high Jc conductors. As a result, the enhanced homogeneity of the Ti-doped samples appears to result from its assistance of rapid diffusion of Sn into the filaments and by its incorporation into the A15 phase interchangeably with Sn on the Sn sites of the A15 phase.« less

  4. A model for the compositions of non-stoichiometric intermediate phases formed by diffusion reactions, and its application to Nb3Sn superconductors

    PubMed Central

    Xu, X.; Sumption, M. D.

    2016-01-01

    In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb3Sn superconductors. In the first part, the governing equations for the bulk diffusion and inter-phase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether it is the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that “frozen” bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Finally, we apply this model to the Nb3Sn superconductors and propose approaches to control their compositions. PMID:26754774

  5. Limits of NbTi and Nb3Sn, and Development of W&R Bi-2212 HighField Accelerator Magnets

    SciTech Connect

    Godeke, A.; Cheng, D.; Dietderich, D.R.; Ferracin, P.; Prestemon,S.O.; Sa bbi, G.; Scanlan, R.M.

    2006-09-01

    NbTi accelerator dipoles are limited to magneticfields (H)of about 10 T, due to an intrinsic upper critical field (Hc2) limitationof 14 T. To surpass this restriction, prototype Nb3Sn magnets are beingdeveloped which have reached 16 T. We show that Nb3Sn dipole technologyis practically limited to 17 to 18 T due to insufficient high fieldpinning, and intrinsically to 20 to 22 T due to Hc2 limitations.Therefore, to obtain magnetic fields approaching 20 T and higher, amaterial is required with a higher Hc2 and sufficient high field pinningcapacity. A realistic candidate for this purpose is Bi-2212, which isavailable in roundwires and sufficient lengths for the fabrication ofcoils based on Rutherford-type cables. We initiated a program to developthe required technology to construct accelerator magnets from'windand-react' (W&R) Bi-2212 coils. We outline the complicationsthat arise through the use of Bi-2212, describe the development paths toaddress these issues, and conclude with the design of W&R Bi-2212sub-scale magnets.

  6. Limits of NbTi and Nb3Sn, and Development of W&R Bi-2212 HighField Accelerator Magnets

    SciTech Connect

    Godeke, A.; Cheng, D.; Dietderich, D.R.; Ferracin, P.; Prestemon,S.O.; Sabbi, G.; Scanlan, R.M.

    2006-12-01

    NbTi accelerator dipoles are limited to magnetic fields (H)of about 10 T, due to an intrinsic upper critical field(Hc2) limitationof 14 T. To surpass this restriction, prototype Nb3Sn magnets are beingdeveloped which have reached 16 T. We show that Nb3Sn dipole technologyis practically limited to 17 to 18 T due to insufficient high fieldpinning, and intrinsically to 20 to 22 T due to Hc2 limitations.Therefore, to obtain magnetic fields approaching 20 T and higher, amaterial is required with a higher Hc2 and sufficient high field pinningcapacity. A realistic candidate for this purpose is Bi-2212, which isavailable in roundwires and sufficient lengths for the fabrication ofcoils based on Rutherford-type cables. We initiated a program to developthe required technology to construct accelerator magnets from'windand-react' (W&R) Bi-2212 coils. We outline the complicationsthat arise through the use of Bi-2212, describe the development paths toaddress these issues, and conclude with the design of W&R Bi-2212sub-scale magnets.

  7. Development and test of single-layer common coil dipole wound with reacted Nb3Sn cable

    SciTech Connect

    Vladimir Kashikhin et al.

    2004-04-27

    The first one-meter long common coil dipole model (HFDC-01) has been fabricated and is being tested at Fermilab. This magnet has several innovative features such as: single-layer racetrack coils, a 22-mm wide 59-strand Rutherford-type cable made of 0.7-mm Nb{sub 3}Sn strands, and a stainless steel coil-support structure reinforced by horizontal bridges inserted between coil blocks. The model was instrumented with voltage taps, quench heaters, temperature sensors and strain gauges in order to monitor the quench origin and propagation, and to study mechanical and quench protection issues. This paper summarizes the model design parameters, the fabrication procedures and the test results.

  8. Examination of the trade-off between intrinsic and extrinsic properties in the optimization of a modern internal tin Nb3Sn conductor

    NASA Astrophysics Data System (ADS)

    Tarantini, C.; Lee, P. J.; Craig, N.; Ghosh, A.; Larbalestier, D. C.

    2014-06-01

    In modern Nb3Sn wires there is a fundamental compromise to be made between optimizing the intrinsic properties associated with the superfluid density in the A15 phase (e.g. Tc, Hc, Hc2, all of which are composition dependent), maximizing the quantity of A15 that can be formed from a given mixture of Nb, Sn and Cu, minimizing the A15 composition gradients within each sub-element, while at the same time generating a high vortex pinning critical current density, Jc, by maximizing the grain boundary density with the additional constraint of maintaining the RRR of the Cu stabilizer above 100. Here we study these factors in a Ta-alloyed Restacked-Rod-Process (RRP®) wire with ∼70 μm diameter sub-elements. Consistent with many earlier studies, maximum non-Cu Jc(12 T, 4.2 K) requires preventing A15 grain growth, rather than by optimizing the superfluid density. In wires optimized for 12 T, 4.2 K performance, about 60% of the non-Cu cross-section is A15, 35% residual Cu and Sn core, and only 5% a residual Nb-7.5 wt% Ta diffusion barrier. The specific heat and chemical analyses show that in this 60% A15 fraction there is a wide range of Tc and chemical composition that does diminish for higher heat treatment temperatures, which, however, are impractical because of the strong RRR degradation that occurs when only about 2% of the A15 reaction front breaches the diffusion barrier. As this kind of Nb3Sn conductor design is being developed for sub-elements about half the present size, it is clear that better barriers are essential to allowing higher temperature reactions with better intrinsic A15 properties. We present here multiple and detailed intrinsic and extrinsic evaluations because we believe that only such broad and quantitative descriptions are capable of accurately tracking the limitations of individual conductor designs where optimization will always be a compromise between inherently conflicting goals.

  9. Design and Fabrication of a Single-Aperture 11T Nb3Sn Dipole Model for LHC Upgrades

    SciTech Connect

    Andreev, N.; Apollinari, G.; Barzi, E.; Bossert, R.; Nobrega, F.; Novitski, I.; Turrioni, D.; Yamada, R.; Zlobin, A.V.; Auchmann, B.; Karppinen, M.; /CERN

    2011-11-28

    The planned upgrade of the LHC collimation system includes additional collimators to be installed in the dispersion suppressor areas of points 2, 3 and 7. To provide the necessary longitudinal space for the collimators, a replacement of 8.33 T Nb-Ti LHC main dipoles with 11 T dipoles based on Nb{sub 3}Sn superconductor compatible with the LHC lattice and main systems is being considered. To demonstrate this possibility FNAL and CERN have started a joint program to develop a 2 m long single-aperture dipole magnet with the nominal field of 11 T at {approx}11.85 kA current and 60 mm bore. This paper describes the demonstrator magnet magnetic and mechanical designs and analysis, coil fabrication procedure. The Nb{sub 3}Sn strand and cable parameters and test results are also reported.

  10. Mechanical qualification of the support structure for MQXF, the Nb3Sn low-β quadrupole for the high luminosity LHC

    DOE PAGESBeta

    Juchno, M.; Ambrosio, G.; Anerella, M.; Bajas, H.; Bajko, M.; Bourcey, N.; Cheng, D. W.; Felice, H.; Ferracin, P.; Grosclaude, P.; et al

    2016-01-26

    Within the scope of the High Luminosity LHC project, the collaboration between CERN and U.S. LARP is developing new low-β quadrupoles using the Nb3Sn superconducting technology for the upgrade of the LHC interaction regions. The magnet support structure of the first short model was designed and two units were fabricated and tested at CERN and at LBNL. The structure provides the preload to the collars-coils subassembly by an arrangement of outer aluminum shells pre-tensioned with water-pressurized bladders. For the mechanical qualification of the structure and the assembly procedure, superconducting coils were replaced with solid aluminum “dummy coils”, the structure wasmore » preloaded at room temperature, and then cooled-down to 77 K. Mechanical behavior of the magnet structure was monitored with the use of strain gauges installed on the aluminum shells, the dummy coils and the axial preload system. As a result, this paper reports on the outcome of the assembly and the cool-down tests with dummy coils, which were performed at CERN and at LBNL, and presents the strain gauge measurements compared to the 3D finite element model predictions.« less

  11. Assembly and Test of HD2, a 36 mm bore high field Nb3Sn Dipole Magnet

    SciTech Connect

    Ferracin, P.; Bingham, B.; Caspi, S.; Cheng, D. W,.; Dietderich, D. R.; Felice, H.; Godeke, A.; Hafalia, A. R.; Hannaford, C. R.; Joseph, J.; Lietzke, A. F.; Lizarazo, J.; Sabbi, G.; Trillaud, F.; Wang, X.

    2008-08-17

    We report on the fabrication, assembly, and test of the Nb{sub 3}Sn dipole magnet HD2. The magnet, aimed at demonstrating the application of Nb{sub 3}Sn superconductor in high field accelerator-type dipoles, features a 36 mm clear bore surrounded by block-type coils with tilted ends. The coil design is optimized to minimize geometric harmonics in the aperture and the magnetic peak field on the conductor in the coil ends. The target bore field of 15 T at 4.3 K is consistent with critical current measurements of extracted strands. The coils are horizontally pre-stressed during assembly using an external aluminum shell pre-tensioned with water-pressurized bladders. Axial pre-loading of the coil ends is accomplished through two end plates and four aluminum tension rods. The strain in coil, shell, and rods is monitored with strain gauges during assembly, cool-down and magnet excitation, and compared with 3D finite element computations. Magnet's training performance, quench locations, and ramp-rate dependence are then analyzed and discussed.

  12. Development of multifilamentary niobium titanium and niobium tin strands for the International Thermonuclear Experimental Reactor project

    NASA Astrophysics Data System (ADS)

    Zhou, L.; Zhang, P. X.; Tang, X. D.; Liu, X. H.; Lu, Y. F.; Weng, P. D.; Grunblatt, G.; Hoang, Gia K.; Verwaerde, C.

    2007-05-01

    The International Thermonuclear Experimental Reactor(ITER) device should demonstrate the scientific and technological possibility of commercial fusion energy production in large scale in order to solve the worldwide energy problem in the future. The superconducting magnet system is the key part of the ITER device to supply high magnetic fields for confining the deuterium-tritium plasma. The multifilament NbTi and Nb3Sn strands with high quality have been studied to meet the specifications of superconducting strands for fabricating poloidal field coils (PF) and toroidal field coils (TF). For NbTi strands with 8306 filaments, Jc of 2910 A mm-2 (4.2 K, 5 T, 0.1 μV cm-1) has been obtained by a conventional process. The proposed process could be used for fabrication of long strands with a unit length more than 5000 m. By an internal tin process the multifilamentary Nb3Sn strands with a diameter of 0.79 mm and a unit length longer than 5000 m have been successfully fabricated. The highest non-Cu Jcn (12 T, 4.2 K, 0.1 μV cm-1) value of 1249 A mm-2 has been obtained. The n-value of Nb3Sn strands is larger than 20 and the residual resistance ratio (RRR) value lies between 150 and 220. The formation of the Nb3Sn superconducting phase together with the evolution of microstructure has been investigated by neutron diffraction and scanning electron microscopy. The results indicate that the properties of NbTi and Nb3Sn strands have already met basically the specifications proposed by the ITER program.

  13. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

    SciTech Connect

    Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D.

    2014-08-20

    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

  14. Final Report: MATERIALS, STRANDS, AND CABLES FOR SUPERCONDUCTING ACCELERATOR MAGNETS [Grant Number DE-SC0010312

    SciTech Connect

    Sumption, Mike D.; Collings, Edward W.

    2014-10-29

    Our program consisted of the two components: Strand Research and Cable Research, with a focus on Nb3Sn, Bi2212, and YBCO for accelerator magnet applications. We demonstrated a method to refine the grains in Nb3Sn by a factor of two, reaching 45 nm grain sizes, and layer Jcs of 6 kA/mm2 at 12 T. W also measured conductor magnetization for field quality. This has been done both with Nb3Sn conductor, as well as Bi:2212 strand. Work in support of quench studies of YBCO coils was also performed. Cable loss studies in Nb3Sn focused on connecting and comparing persistent magnetization and coupling magnetization for considering their relative impact on HEP machines. In the area of HTS cables, we have investigated both the quench in multistrand YBCO CORC cables, as well as the magnetization of these cables for use in high field magnets. In addition, we examined the magnetic and thermal properties of large (50 T) solenoids.

  15. Aluminum-stabilized NB3SN superconductor

    DOEpatents

    Scanlan, Ronald M.

    1988-01-01

    An aluminum-stabilized Nb.sub.3 Sn superconductor and process for producing same, utilizing ultrapure aluminum. Ductile components are co-drawn with aluminum to produce a conductor suitable for winding magnets. After winding, the conductor is heated to convert it to the brittle Nb.sub.3 Sn superconductor phase, using a temperature high enough to perform the transformation but still below the melting point of the aluminum. This results in reaction of substantially all of the niobium, while providing stabilization and react-in-place features which are beneficial in the fabrication of magnets utilizing superconducting materials.

  16. LARP Long Nb3Sn Quadrupole Design

    SciTech Connect

    Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bossert, R.; Caspi, S.; Chlachidize, G.; Dietderich, D.; Feher, S.; Ferracin, P.; Ghosh, A.; Hafalia, R.; Hannaford, R.; Kashikhin, V.V.; Kerby, J.; Lamm, M.; Lietzke, A.; McInturff, A.; Muratore, J.; Nobrega, F.; Novitsky, I.; Sabbi, G.L.; Schmalzle, J.; Tartaglia, M.; Turrioni, D.; Wanderer, P.; Whitson, G.; Zlobin, A.V.

    2008-06-01

    A major milestone for the LHC Accelerator Research Program (LARP) is the test, by the end of 2009, of two 4m-long quadrupole magnets (LQ) wound with Nb{sub 3}Sn conductor. The goal of these magnets is to be a proof of principle that Nb{sub 3}Sn is a viable technology for a possible LHC luminosity upgrade. The design of the LQ is based on the design of the LARP Technological Quadrupoles, presently under development at FNAL and LBNL, with 90-mm aperture and gradient higher than 200 T/m. The design of the first LQ model will be completed by the end of 2007 with the selection of a mechanical design. In this paper we present the coil design addressing some fabrication technology issues, the quench protection study, and three designs of the support structure.

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

    NASA Astrophysics Data System (ADS)

    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. Activities of human RRP6 and structure of the human RRP6 catalytic domain

    SciTech Connect

    Januszyk, Kurt; Liu, Quansheng; Lima, Christopher D.

    2011-08-29

    The eukaryotic RNA exosome is a highly conserved multi-subunit complex that catalyzes degradation and processing of coding and noncoding RNA. A noncatalytic nine-subunit exosome core interacts with Rrp44 and Rrp6, two subunits that possess processive and distributive 3'-to-5' exoribonuclease activity, respectively. While both Rrp6 and Rrp44 are responsible for RNA processing in budding yeast, Rrp6 may play a more prominent role in processing, as it has been demonstrated to be inhibited by stable RNA secondary structure in vitro and because the null allele in budding yeast leads to the buildup of specific structured RNA substrates. Human RRP6, otherwise known as PM/SCL-100 or EXOSC10, shares sequence similarity to budding yeast Rrp6 and is proposed to catalyze 3'-to-5' exoribonuclease activity on a variety of nuclear transcripts including ribosomal RNA subunits, RNA that has been poly-adenylated by TRAMP, as well as other nuclear RNA transcripts destined for processing and/or destruction. To characterize human RRP6, we expressed the full-length enzyme as well as truncation mutants that retain catalytic activity, compared their activities to analogous constructs for Saccharomyces cerevisiae Rrp6, and determined the X-ray structure of a human construct containing the exoribonuclease and HRDC domains that retains catalytic activity. Structural data show that the human active site is more exposed when compared to the yeast structure, and biochemical data suggest that this feature may play a role in the ability of human RRP6 to productively engage and degrade structured RNA substrates more effectively than the analogous budding yeast enzyme.

  19. Studies of $${\\rm Nb}_{3}{\\rm Sn}$$ Strands Based on the Restacked-Rod Process for High Field Accelerator Magnets

    DOE PAGESBeta

    Barzi, E.; Bossert, M.; Gallo, G.; Lombardo, V.; Turrioni, D.; Yamada, R.; Zlobin, A. V.

    2011-12-21

    A major thrust in Fermilab's accelerator magnet R&D program is the development of Nb3Sn wires which meet target requirements for high field magnets, such as high critical current density, low effective filament size, and the capability to withstand the cabling process. The performance of a number of strands with 150/169 restack design produced by Oxford Superconducting Technology was studied for round and deformed wires. To optimize the maximum plastic strain, finite element modeling was also used as an aid in the design. Results of mechanical, transport and metallographic analyses are presented for round and deformed wires.

  20. The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase

    PubMed Central

    Schuch, Benjamin; Feigenbutz, Monika; Makino, Debora L; Falk, Sebastian; Basquin, Claire; Mitchell, Phil; Conti, Elena

    2014-01-01

    The exosome is a conserved multi-subunit ribonuclease complex that functions in 3′ end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10-subunit core complex of the exosome (Exo-10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo-10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N-terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N-terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C-terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6–Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome. PMID:25319414

  1. Fabrication and test of LARP technological quadrupole models of TQC series

    SciTech Connect

    Bossert, R.C.; Ambrosio, G.; Andreev, N.; Barzi, E.; Chlachidze, G.; Feher, S.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.; Nobrega, A.; Novitski, I.; /Fermilab /LBL, Berkeley /Brookhaven

    2008-08-01

    In support of the development of a large-aperture Nb3Sn superconducting quadrupole for the Large Hadron Collider (LHC) luminosity upgrade, several two-layer technological quadrupole models of TQC series with 90 mm aperture and collar-based mechanical structure have been developed at Fermilab in collaboration with LBNL. This paper summarizes the results of fabrication and test of TQC02a, the second TQC model based on RRP Nb3Sn strand, and TQC02b, built with both MJR and RRP strand. The test results presented include magnet strain and quench performance during training, as well as quench studies of current ramp rate and temperature dependence from 1.9K to 4.5K.

  2. Performance Comparison of Nb3Sn Magnets at LBNL

    SciTech Connect

    Chiesa, L.; Caspi, S.; Coccoli, M.; Dietderich, D.R.; Ferracin, P.; Gourlay, S.A.; Hafalia, R.r.; Lietzke, A.F.; McInturff, A.D.; Sabbi, G.; Scanlan, R.M.

    2002-08-01

    The Superconducting Magnet group at Lawrence Berkeley National Laboratory has been successfully developing Nb{sub 3}Sn high-field dipole magnet technology for the last ten years. Noteworthy magnet tests include D20 (50mm bore, 4-layer cos{theta}, 12.8 T, accelerator quality dipole), and recent racetrack dipoles: (1) RTI (2-layer, 12 T, no bore, no training), (2) RD3b (3-layer, 14.7 T, 10mm bore), (3) RD3c (3-layer, 10 T, low-harmonics 35mm bore), and (4) some small Nb{sub 3}Sn magnets that utilized new technology. The performance of these magnets is summarized, comparing (1) cable and magnet geometry parameters, (2) training behavior, (3) ramp rate sensitivity, (4) RRR measurements, (5) peak temperatures and voltages, and (6) fast flux adjustments that occur during ramping.

  3. Developmentof the 15 T Nb3Sn dipole HD2

    SciTech Connect

    Caspi, S.; Cheng, D.W.; Dietderich, D.R.; Hafalia, A.R.; Hannaford, C.R.; Higley, H.; Lietzke, A.F.; Lizarazo, J.; McInturff, A.D.; Sabbi, G.; Ferracin, P.

    2008-06-01

    The Superconducting Magnet Program at Lawrence Berkeley National Laboratory (LBNL) is continuing the development of HD2, a 1 m long Nb{sub 3}Sn dipole generating a dipole field of 15 T in a 36 mm clear bore. With tilted (flared) ends to avoid obstructing the beam path, HD2 represents a step towards the development of cost effective accelerator quality magnets. The design has been optimized to minimize geometric harmonics and to address iron saturation and conductor magnetization effects. The support structure is based on an external aluminum shell, pre-tensioned with pressurized bladders and interference keys. Aluminum axial rods and stainless steel end plates provide longitudinal support to the coil ends during magnet excitation. This paper reports on field quality optimization and magnet parameters. The design and fabrication of the coil and structure components, and results from coil winding, reaction, and potting are also presented.

  4. Graded High Field Nb3Sn Dipole Magnets

    SciTech Connect

    Caspi, S.; Ferracin, P.; Gourlay, S.

    2007-06-01

    Dipole magnets with fields beyond 16T will require superconducting coils that are at least 40 mm thick, an applied pres-stress around 150 MPa and a protection scheme for stored energy in the range of 1-2 MJ/m. The coil size will have a direct impact on the overall magnet cost and the stored energy will raise new questions on protection. To reduce coil size and minimize risk, the coil may have to be graded. Grading is achieved by splitting the coil into several layers with current densities that match the short sample field in each layer. Grading, especially at high fields, can be effective; however it will also significantly raise the stress. In this paper we report on the results of a study on the coil size and field relation to that of the stress and stored energy. We then extend the results to graded coils and attempt to address high stress issues and ways to reduce it.

  5. Nb3Sn Quadrupole Magnets for the LHC IR

    SciTech Connect

    Sabbi, G.; Caspi, S.; Chiesa, L.; Coccoli, M.; Dietderich, D.r.; Ferracin, P.; Gourlay, S.A.; Hafalia, R.R.; Lietzke, A.F.; McInturff, A.D.; Scanlan, R.M.

    2001-08-01

    The development of insertion quadrupoles with 205 T/m gradient and 90 mm bore represents a promising strategy to achieve the ultimate luminosity goal of 2.5 x 10{sup 34} cm{sup -2}s{sup -1} at the Large Hadron Collider (LHC). At present, Nb{sub 3}Sn is the only practical conductor which can meet these requirements. Since Nb{sub 3}Sn is brittle, and considerably more strain sensitive than NbTi, the design concepts and fabrication techniques developed for NbTi magnets need to be modified appropriately. In addition, IR magnets must provide high field quality and operate reliably under severe radiation loads. The results of conceptual design studies addressing these issues are presented.

  6. Quench margin measurement in Nb3Sn quadrupole magnet

    SciTech Connect

    Kashikhin, V.V.; Bossert, R.; Chlachidze, G.; Lamm, M.; Novitski, I.; Zlobin, A.V.; /Fermilab

    2008-08-01

    One of the possible practical applications of the Nb{sub 3}Sn accelerator magnets is the LHC luminosity upgrade that involves replacing the present NbTi focusing quadrupoles in two high-luminosity interaction regions (IR). The IR magnets are exposed to strong radiation from the interaction point that requires a detailed investigation of the magnet operating margins under the expected radiation-induced heat depositions. This paper presents the results of simulation and measurement of quench limits and temperature margins for a Nb{sub 3}Sn model magnet using a special midplane strip heater.

  7. Development of a large aperture Nb3Sn racetrack quadrupolemagnet

    SciTech Connect

    Ferracin, Paolo; Bartlett, Scott E.; Caspi, Shlomo; Dietderich,Daniel R.; Gourlay, Steven A.; Hannaford, Charles R.; Hafalia, AurelioR.; Lietzke, Alan F.; Mattafirri, Sara; McInturff, Alfred D.; Nyman,Mark; Sabbi, Gianluca

    2005-04-14

    The U.S. LHC Accelerator Research Program (LARP), a collaboration between BNL, FNAL, LBNL, and SLAC, has among its major objectives the development of advanced magnet technology for an LHC luminosity upgrade. The LBNL Superconducting Magnet Group supports this program with a broad effort involving design studies, Nb{sub 3}Sn conductor development, mechanical models, and basic prototypes. This paper describes the development of a large aperture Nb{sub 3}Sn racetrack quadrupole magnet using four racetrack coils from the LBNL Subscale Magnet (SM) Program. The magnet provides a gradient of 95 T/m in a 110 mm bore, with a peak field in the conductor of 11.2 T. The coils are prestressed by a mechanical structure based on a pre-tensioned aluminum shell, and axially supported with aluminum rods. The mechanical behavior has been monitored with strain gauges and the magnetic field has been measured. Results of the test are reported and analyzed.

  8. Instrumentation and Quench Protection for LARP Nb3Sn Magnets

    SciTech Connect

    Felice, H.; Ambrosio, G.; Chlachidize, G.; Ferracin, P.; Hafalia, R.; Hannaford, R. C.; Joseph, J.; Lietzke, A.; McInturff, A.; Muratore, J.; Prestemon, S.; Sabbi, G. L.; Schmalzle, J.; Wanderer, P.; Wang, X.

    2008-08-17

    The US LHC Accelerator Research Program (LARP) is developing Nb{sub 3}Sn prototype quadrupoles for the LHC interaction region upgrades. Several magnets have been tested within this program and understanding of their behavior and performance is a primary goal. The instrumentation is consequently a key consideration, as is protection of the magnet during quenches. In all LARP magnets, the flexible circuits traces combine the instrumentation and the protection heaters. Their fabrication relies on printed circuit technology based on a laminate made of a 45-micron thick kapton sheet and a 25-micron thick foil of stainless steel. This paper reviews the protection heaters designs used in the TQ (Technology Quadrupole) and LR (Long Racetrack) series as well as the one used in LBNL HD2a high field dipole and presents the design of the traces for the Long Quadrupole (LQ), addressing challenges associated with the stored energy and the length of the magnet.

  9. Nb3Sn accelerator magnet development around the world

    SciTech Connect

    Michael J. Lamm

    2003-06-23

    During the past 30 years superconducting magnet systems have enabled accelerators to achieve energies and luminosities that would have been impractical if not impossible with resistive magnets. By far, NbTi has been the preferred conductor for this application because of its ductility and insensitivity of Jc to mechanical strain. This is despite the fact that Nb{sub 3}Sn has a more favorable Jc vs. B dependence and can operate at much higher temperatures. Unfortunately, NbTi conductor is reaching the limit of it usefulness for high field applications. Despite incremental increases in Jc and operation at superfluid temperatures, magnets are limited to approximately a 10 T field. Improvements in conductor performance combined with future requirements for accelerator magnets to have bore fields greater than 10 T or operate in areas of large beam-induced heat loads now make Nb{sub 3}Sn look attractive. Thus, laboratories in several countries are actively engaged in programs to develop Nb{sub 3}Sn accelerator magnets for future accelerator applications. A summary of this important research activity is presented along with a brief history of Nb{sub 3}Sn accelerator magnet development and a discussion of requirements for future accelerator magnets.

  10. LARP Long Nb3Sn Racetrack Coil Program

    SciTech Connect

    Wanderer, P.; Ambrosio, G.; Anerella, M.; Barzi, E.; Bossert, R.; Cheng, D.; Cozzolino, J.; Escallier, J.; Ferracin, P.; Ganetis, G.; Ghosh, A. K.; Gupta, R. C.; Hafalia, A. R.; Hannaford, C. R.; Joshi, P.; Kovach, P.; Lietzke, A. F.; Louie, W.; Marone, A.; McInturff, A. D.; Muratore, J.; Nobrega, F.; Schmalzle, J.; Thomas, R.; Turrioni, D.

    2007-06-01

    Development of high-performance Nb{sub 3}Sn quadrupoles is one of the major goals of the LHC Accelerator Research Program (LARP). As part of this program, long racetrack magnets are being made in order to check that the change in coil length that takes place during reaction is correctly accounted for in the quadrupole design and to check for length effects in implementing the 'shell' method of coil support. To check the racetrack magnet manufacturing plan, a short racetrack magnet is being made. This magnet will be the first to use restack-rod process Nb{sub 3}Sn, making it a 'long sample' test vehicle for this new material. The paper reports the reaction and characterization of the Nb{sub 3}Sn, and construction features and test results from the short racetrack magnet. The paper also reports on the status of the construction of the first long racetrack magnet.

  11. Design of Nb3Sn Coils for LARP Long Magnets

    SciTech Connect

    Ferracin, Paolo; Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bossert, R.; Ferracin, P.; Caspi, S.; Lietzke, A. F.

    2007-06-01

    The LHC Accelerator Research Program (LARP) has a primary goal to develop, assemble, and test full size Nb{sub 3}Sn quadrupole magnet models for a luminosity upgrade of the Large Hadron Collider (LHC). A major milestone in this development is to assemble and test, by the end of 2009, two 4 m-long quadrupole cold masses, which will be the first Nb{sub 3}Sn accelerator magnet models approaching the length of real accelerator magnets. The design is based on the LARP Technological Quadrupoles (TQ), under development at FNAL and LBNL, with gradient higher than 200 T/m and aperture of 90 mm. The mechanical design will be chosen between two designs presently explored for the TQs: traditional collars and Al-shell based design (preloaded by bladders and keys). The fabrication of the first long quadrupole model is expected to start in the last quarter of 2007. Meanwhile the fabrication of 4 m-long racetrack coils started this year at BNL. These coils will be tested in an Al-shell based supporting structure developed at LBNL. Several challenges have to be addressed for the successful fabrication of long Nb{sub 3}Sn coils. This paper presents these challenges with comments and solutions adopted or under study for these magnets. The coil design of these magnets, including conductor and insulation features, and quench protection studies are also presented.

  12. An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster.

    PubMed

    Eberle, Andrea B; Jordán-Pla, Antonio; Gañez-Zapater, Antoni; Hessle, Viktoria; Silberberg, Gilad; von Euler, Anne; Silverstein, Rebecca A; Visa, Neus

    2015-09-01

    RNA surveillance factors are involved in heterochromatin regulation in yeast and plants, but less is known about the possible roles of ribonucleases in the heterochromatin of animal cells. Here we show that RRP6, one of the catalytic subunits of the exosome, is necessary for silencing heterochromatic repeats in the genome of Drosophila melanogaster. We show that a fraction of RRP6 is associated with heterochromatin, and the analysis of the RRP6 interaction network revealed physical links between RRP6 and the heterochromatin factors HP1a, SU(VAR)3-9 and RPD3. Moreover, genome-wide studies of RRP6 occupancy in cells depleted of SU(VAR)3-9 demonstrated that SU(VAR)3-9 contributes to the tethering of RRP6 to a subset of heterochromatic loci. Depletion of the exosome ribonucleases RRP6 and DIS3 stabilizes heterochromatic transcripts derived from transposons and repetitive sequences, and renders the heterochromatin less compact, as shown by micrococcal nuclease and proximity-ligation assays. Such depletion also increases the amount of HP1a bound to heterochromatic transcripts. Taken together, our results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin.

  13. An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster

    PubMed Central

    Eberle, Andrea B.; Jordán-Pla, Antonio; Gañez-Zapater, Antoni; Hessle, Viktoria; Silberberg, Gilad; von Euler, Anne; Silverstein, Rebecca A.; Visa, Neus

    2015-01-01

    RNA surveillance factors are involved in heterochromatin regulation in yeast and plants, but less is known about the possible roles of ribonucleases in the heterochromatin of animal cells. Here we show that RRP6, one of the catalytic subunits of the exosome, is necessary for silencing heterochromatic repeats in the genome of Drosophila melanogaster. We show that a fraction of RRP6 is associated with heterochromatin, and the analysis of the RRP6 interaction network revealed physical links between RRP6 and the heterochromatin factors HP1a, SU(VAR)3-9 and RPD3. Moreover, genome-wide studies of RRP6 occupancy in cells depleted of SU(VAR)3-9 demonstrated that SU(VAR)3-9 contributes to the tethering of RRP6 to a subset of heterochromatic loci. Depletion of the exosome ribonucleases RRP6 and DIS3 stabilizes heterochromatic transcripts derived from transposons and repetitive sequences, and renders the heterochromatin less compact, as shown by micrococcal nuclease and proximity-ligation assays. Such depletion also increases the amount of HP1a bound to heterochromatic transcripts. Taken together, our results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin. PMID:26389589

  14. Rrp2, a prokaryotic enhancer-like binding protein, is essential for viability of Borrelia burgdorferi.

    PubMed

    Groshong, Ashley M; Gibbons, Nora E; Yang, X Frank; Blevins, Jon S

    2012-07-01

    The Lyme disease spirochete, Borrelia burgdorferi, exists in two diverse niches (i.e., an arthropod tick vector and mammalian host) during its enzootic life cycle. To effectively adapt to these unique environments, the bacterium alters the expression of numerous genes, including several major outer surface (lipo)proteins that are required for infection and transmission. An enhancer-binding protein (EBP), known as Rrp2, is one identified activator of the RpoN/RpoS alternative sigma factor cascade. Because initial efforts to generate an rrp2 deletion strain were unsuccessful, the role of Rrp2 in the activation of the RpoN/RpoS pathway was first defined using a strain of B. burgdorferi carrying an rrp2 point mutant that was defective in its ability to activate RpoN-dependent transcription. The fact that subsequent attempts to disrupt rrp2 have also been unsuccessful has led investigators to hypothesize that Rrp2 has other undefined functions which are essential for B. burgdorferi survival and independent of its EBP function. We used a lac-based inducible expression system to generate a conditional rrp2 mutant in virulent B. burgdorferi. In this strain, an isopropyl-β-D-thiogalactopyranoside-inducible copy of the rrp2 gene is expressed in trans from a borrelial shuttle vector. We found that the chromosomal copy of rrp2 could be inactivated only when rrp2 was induced, and the maintenance of rrp2 expression was required for the growth of the mutants. In addition, the overexpression of rrp2 is detrimental to B. burgdorferi growth in a manner that is independent of the RpoN/RpoS pathway. These studies provide the first direct evidence that rrp2 is an essential gene in B. burgdorferi.

  15. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    DOE PAGESBeta

    Majoros, M.; Sumption, M. D.; Collings, E. W.; Long, N. J.

    2015-04-08

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less

  16. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    DOE PAGESBeta

    sumption, Mike; Majoros, Milan; Collings, E. W.; Van der Laan, D. C.

    2014-11-07

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less

  17. Rrp6 is recruited to transcribed genes and accompanies the spliced mRNA to the nuclear pore.

    PubMed

    Hessle, Viktoria; von Euler, Anne; González de Valdivia, Ernesto; Visa, Neus

    2012-08-01

    Rrp6 is an exoribonuclease involved in the quality control of mRNA biogenesis. We have analyzed the association of Rrp6 with the Balbiani ring pre-mRNPs of Chironomus tentans to obtain insight into the role of Rrp6 in splicing surveillance. Rrp6 is recruited to transcribed genes and its distribution along the genes does not correlate with the positions of exons and introns. In the nucleoplasm, Rrp6 is bound to both unspliced and spliced transcripts. Rrp6 is released from the mRNPs in the vicinity of the nuclear pore before nucleo-cytoplasmic translocation. We show that Rrp6 is associated with newly synthesized transcripts during all the nuclear steps of gene expression and is associated with the transcripts independently of their splicing status. These observations suggest that the quality control of pre-mRNA splicing is not based on the selective recruitment of the exoribonuclease Rrp6 to unprocessed mRNAs.

  18. Is sildenafil failure in men after radical retropubic prostatectomy (RRP) due to arterial disease? Penile duplex Doppler findings in 174 men after RRP.

    PubMed

    McCullough, A; Woo, K; Telegrafi, S; Lepor, H

    2002-12-01

    Sildenafil is frequently the first-line treatment for post-radical retropubic prostatectomy (RRP) erectile dysfunction (ED) with maximum treatment satisfaction rates of 43%-80%. The etiology of erectile dysfunction after RRP has been attributed to psychogenic, vascular, veno- occlusive or nerve injury causes. The purpose of this study was to gain insight into the penile duplex Doppler arterial parameters in men with ED after RRP who failed sildenafil. The purpose was to assess whether sildenafil failure after RRP is associated with underlying corporal arterial disease. A total of 174 consecutive men presenting with sildenafil refractory ED after nerve-sparing RRP underwent color duplex penile Doppler evaluation with vasoactive injection. Mean age was 59.6 y and mean time from surgery was 11.6 months. Some 81% (141/174) of the men had no pre-operative ED (PED). Significant differences in penile duplex Doppler parameters for arterial disease were seen between men with and without PED. In men without PED, 19% (27/141) manifested arterial insufficiency. However, in men with PED, 50% (16/33) demonstrated arterial disease. Nerve sparing status did not affect the presence of arterial disease. Sildenafil refractory erectile dysfunction after RRP in men without PED is not predominantly associated with penile Doppler parameters consistent with arterial insufficiency.

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

    DOE PAGESBeta

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

    2015-10-14

    Prototype cable in conduit conductors (CICCs) destined for use in the Toroidal Field (TF) and Central Solenoid (CS) coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3 7% void fraction increase on the Low Pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb3Sn filamentmore » fractures observed in the longer twist pitch conductors. We report here a detailed strand to cable analysis of short and longer “baseline” twist pitch CICCs. It was found that the use of Internal Tin strands in the longer “baseline” twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of Bronze Process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the Internal Tin strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Furthermore, the short twist pitch CICC made from Bronze Process strands preserved diffusion barrier integrity.« less

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Prototype cable-in-conduit-conductors (CICCs) destined for use in the toroidal field and central solenoid coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3%-7% void fraction increase on the low pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb3Sn filament fractures observed in the longer twist pitch conductors. We report here a detailed strand-to-cable analysis of short and longer ‘baseline’ twist pitch CICCs. It was found that the use of internal tin (IT) strands in the longer ‘baseline’ twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of bronze process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the IT strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Conversely, the short twist pitch CICC made from bronze process strands preserved diffusion barrier integrity.

  1. Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full testing in SULTAN: 1. The mechanical role of copper strands in a CICC

    NASA Astrophysics Data System (ADS)

    Sanabria, Carlos; Lee, Peter J.; Starch, William; Blum, Timothy; Devred, Arnaud; Jewell, Matthew C.; Pong, Ian; Martovetsky, Nicolai; Larbalestier, David C.

    2015-08-01

    Cables made with Nb3Sn-based superconductor strands will provide the 13 T maximum peak magnetic field of the ITER central solenoid (CS) coils and they must survive up to 60 000 electromagnetic cycles. Accordingly, prototype designs of CS cable-in-conduit-conductors (CICC) were electromagnetically tested over multiple magnetic field cycles and warm-up-cool-down scenarios in the SULTAN facility at CRPP. We report here a post-mortem metallographic analysis of two CS CICC prototypes which exhibited some rate of irreversible performance degradation during cycling. The standard ITER CS CICC cable design uses a combination of superconducting and Cu strands, and because the Lorentz force on the strand is proportional to the transport current in the strand, removing the copper strands (while increasing the Cu:SC ratio of the superconducting strands) was proposed as one way of reducing the strand load. In this study we compare the two alternative CICCs, with and without Cu strands, keeping in mind that the degradation after the SULTAN test was lower for the CICC without Cu strands. The post-mortem metallographic evaluation revealed that the overall strand transverse movement was 20% lower in the CICC without Cu strands and that the tensile filament fractures found were less, both indications of an overall reduction in high tensile strain regions. It was interesting to see that the Cu strands in the mixed cable design (with higher degradation) helped reduce the contact stresses on the high pressure side of the CICC, but in either case, the strain reduction mechanisms were not enough to suppress cyclic degradation. Advantages and disadvantages of each conductor design are discussed here aimed to understand the sources of the degradation.

  2. Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full testing in SULTAN: 1. The mechanical role of copper strands in a CICC

    DOE PAGESBeta

    Sanabria, Carlos; Lee, Peter J.; Starch, William; Blum, Timothy; Devred, Arnaud; Jewell, Matthew C.; Pong, Ian; Martovetsky, Nicolai; Larbalestier, David C.

    2015-06-22

    Cables made with Nb3Sn-based superconductor strands will provide the 13 T maximum peak magnetic field of the ITER Central Solenoid (CS) coils and they must survive up to 60,000 electromagnetic cycles. Accordingly, prototype designs of CS cable-in-conduit-conductors (CICC) were electromagnetically tested over multiple magnetic field cycles and warm-up-cool-down scenarios in the SULTAN facility at CRPP. We report here a post mortem metallographic analysis of two CS CICC prototypes which exhibited some rate of irreversible performance degradation during cycling. The standard ITER CS CICC cable design uses a combination of superconducting and Cu strands, and because the Lorentz force on themore » strand is proportional to the transport current in the strand, removing the copper strands (while increasing the Cu:SC ratio of the superconducting strands) was proposed as one way of reducing the strand load. In this study we compare the two alternative CICCs, with and without Cu strands, keeping in mind that the degradation after SULTAN test was lower for the CICC without Cu strands. The post mortem metallographic evaluation revealed that the overall strand transverse movement was 20% lower in the CICC without Cu strands and that the tensile filament fractures found were less, both indications of an overall reduction in high tensile strain regions. Furthermore, it was interesting to see that the Cu strands in the mixed cable design (with higher degradation) helped reduce the contact stresses on the high pressure side of the CICC, but in either case, the strain reduction mechanisms were not enough to suppress cyclic degradation. Advantages and disadvantages of each conductor design are discussed here aimed to understand the sources of the degradation.« less

  3. Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.

    PubMed

    Pokharel, Yuba Raj; Saarela, Jani; Szwajda, Agnieszka; Rupp, Christian; Rokka, Anne; Lal Kumar Karna, Shibendra; Teittinen, Kaisa; Corthals, Garry; Kallioniemi, Olli; Wennerberg, Krister; Aittokallio, Tero; Westermarck, Jukka

    2015-12-01

    High content protein interaction screens have revolutionized our understanding of protein complex assembly. However, one of the major challenges in translation of high content protein interaction data is identification of those interactions that are functionally relevant for a particular biological question. To address this challenge, we developed a relevance ranking platform (RRP), which consist of modular functional and bioinformatic filters to provide relevance rank among the interactome proteins. We demonstrate the versatility of RRP to enable a systematic prioritization of the most relevant interaction partners from high content data, highlighted by the analysis of cancer relevant protein interactions for oncoproteins Pin1 and PME-1. We validated the importance of selected interactions by demonstration of PTOV1 and CSKN2B as novel regulators of Pin1 target c-Jun phosphorylation and reveal previously unknown interacting proteins that may mediate PME-1 effects via PP2A-inhibition. The RRP framework is modular and can be modified to answer versatile research problems depending on the nature of the biological question under study. Based on comparison of RRP to other existing filtering tools, the presented data indicate that RRP offers added value especially for the analysis of interacting proteins for which there is no sufficient prior knowledge available. Finally, we encourage the use of RRP in combination with either SAINT or CRAPome computational tools for selecting the candidate interactors that fulfill the both important requirements, functional relevance, and high confidence interaction detection.

  4. A novel plasmid-based microarray screen identifies suppressors of rrp6Delta in Saccharomyces cerevisiae.

    PubMed

    Abruzzi, Katharine; Denome, Sylvia; Olsen, Jens Raabjerg; Assenholt, Jannie; Haaning, Line Lindegaard; Jensen, Torben Heick; Rosbash, Michael

    2007-02-01

    Genetic screens in Saccharomyces cerevisiae provide novel information about interacting genes and pathways. We screened for high-copy-number suppressors of a strain with the gene encoding the nuclear exosome component Rrp6p deleted, with either a traditional plate screen for suppressors of rrp6Delta temperature sensitivity or a novel microarray enhancer/suppressor screening (MES) strategy. MES combines DNA microarray technology with high-copy-number plasmid expression in liquid media. The plate screen and MES identified overlapping, but also different, suppressor genes. Only MES identified the novel mRNP protein Nab6p and the tRNA transporter Los1p, which could not have been identified in a traditional plate screen; both genes are toxic when overexpressed in rrp6Delta strains at 37 degrees C. Nab6p binds poly(A)+ RNA, and the functions of Nab6p and Los1p suggest that mRNA metabolism and/or protein synthesis are growth rate limiting in rrp6Delta strains. Microarray analyses of gene expression in rrp6Delta strains and a number of suppressor strains support this hypothesis. PMID:17101774

  5. Designing and Operating for Safeguards: Lessons Learned From the Rokkasho Reprocessing Plant (RRP)

    SciTech Connect

    Johnson, Shirley J.; Ehinger, Michael

    2010-08-07

    This paper will address the lessons learned during the implementation of International Atomic Energy Agency (IAEA) safeguards at the Rokkasho Reprocessing Plant (RRP) which are relevant to the issue of ‘safeguards by design’. However, those lessons are a result of a cumulative history of international safeguards experiences starting with the West Valley reprocessing plant in 1969, continuing with the Barnwell plant, and then with the implementation of international safeguards at WAK in Germany and TRP in Japan. The design and implementation of safeguards at RRP in Japan is the latest and most challenging that the IAEA has faced. This paper will discuss the work leading up to the development of a safeguards approach, the design and operating features that were introduced to improve or aid in implementing the safeguards approach, and the resulting recommendations for future facilities. It will provide an overview of how ‘safeguardability’ was introduced into RRP.

  6. Getting a G--RRP on regulated exocytosis in the heart.

    PubMed

    Glembotski, Christopher C

    2007-11-01

    A study by Rybkin et al. (see p. 527) substantially advances our understanding of regulated exocytois by specialized secretory cells, such as atrial myocytes. A second member of the Ras-related protein family, RRP17, was identified and shown to participate in regulating the secretion of the cardiac-derived peptide hormone, atrial natriuretic peptide. In addition to the heart, RRP17 was shown to be expressed in neuronal, pancreatic, and skeletal muscle cells, suggesting a widespread role in regulated secretion for this new protein.

  7. Stability of UV exposed RR-P3BT films by spectroscopic ellipsometry

    SciTech Connect

    Diware, Mangesh S.; Byun, J. S.; Hwang, S. Y.; Kim, T. J.; Kim, Y. D.

    2013-02-05

    Stability of regioregular poly(3-butylthiophene) (RR-P3BT) films under irradiation of ultra-violet (UV) light has been studied by spectroscopic ellipsometry at room temperature. Consistent decrease in dielectric function with UV exposure time showed the degree of degradation of polymer. This work suggests that, protective methods are mandatory to use this kind of material in optical devices.

  8. Stability of UV exposed RR-P3BT films by spectroscopic ellipsometry

    NASA Astrophysics Data System (ADS)

    Diware, Mangesh S.; Byun, J. S.; Hwang, S. Y.; Kim, T. J.; Kim, Y. D.

    2013-02-01

    Stability of regioregular poly(3-butylthiophene) (RR-P3BT) films under irradiation of ultra-violet (UV) light has been studied by spectroscopic ellipsometry at room temperature. Consistent decrease in dielectric function with UV exposure time showed the degree of degradation of polymer. This work suggests that, protective methods are mandatory to use this kind of material in optical devices.

  9. Rrp5 Binding at Multiple Sites Coordinates Pre-rRNA Processing and Assembly

    PubMed Central

    Lebaron, Simon; Segerstolpe, Åsa; French, Sarah L.; Dudnakova, Tatiana; de lima Alves, Flavia; Granneman, Sander; Rappsilber, Juri; Beyer, Ann L.; Wieslander, Lars; Tollervey, David

    2013-01-01

    Summary In vivo UV crosslinking identified numerous preribosomal RNA (pre-rRNA) binding sites for the large, highly conserved ribosome synthesis factor Rrp5. Intramolecular complementation has shown that the C-terminal domain (CTD) of Rrp5 is required for pre-rRNA cleavage at sites A0–A2 on the pathway of 18S rRNA synthesis, whereas the N-terminal domain (NTD) is required for A3 cleavage on the pathway of 5.8S/25S rRNA synthesis. The CTD was crosslinked to sequences flanking A2 and to the snoRNAs U3, U14, snR30, and snR10, which are required for cleavage at A0–A2. The NTD was crosslinked to sequences flanking A3 and to the RNA component of ribonuclease MRP, which cleaves site A3. Rrp5 could also be directly crosslinked to several large structural proteins and nucleoside triphosphatases. A key role in coordinating preribosomal assembly and processing was confirmed by chromatin spreads. Following depletion of Rrp5, cotranscriptional cleavage was lost and preribosome compaction greatly reduced. PMID:24239293

  10. Safety of intralesional cidofovir in patients with recurrent respiratory papillomatosis: an international retrospective study on 635 RRP patients.

    PubMed

    Tjon Pian Gi, R E A; Ilmarinen, T; van den Heuvel, E R; Aaltonen, L M; Andersen, J; Brunings, J W; Chirila, M; Dietz, A; Ferran Vilà, F; Friedrich, G; de Gier, H H W; Golusinski, W; Graupp, M; Hantzakos, A; Horcasitas, R; Jackowska, J; Koelmel, J C; Lawson, G; Lindner, F; Remacle, M; Sittel, C; Weichbold, V; Wierzbicka, M; Dikkers, F G

    2013-05-01

    Intralesional use of cidofovir (Vistide(®)) has been one of the mainstays of adjuvant therapy in patients with recurrent respiratory papillomatosis (RRP) since 1998. In 2011, a communication provided by the producer of cidofovir addressed very serious side effects concerning its off-label use. As this was a general warning, it was inconclusive whether this would account for its use in RRP. The aim of this study is to determine whether nephrotoxic, neutropenic, or oncogenic side effects have occurred after intralesional use of cidofovir in patients with RRP. Update of recent developments in RRP, a multicentre questionnaire and a multicentre retrospective chart review. Sixteen hospitals from eleven countries worldwide submitted records of 635 RRP patients, of whom 275 were treated with cidofovir. RRP patients received a median of three intralesional injections (interquartile range 2-6). There were no statistical differences in occurrence of neutropenia or renal dysfunction before and after cidofovir. There was no statistical difference in occurrence of upper airway and tracheal malignancies between the cidofovir and the non-cidofovir group. In this retrospective patient chart review, no clinical evidence was found for more long-term nephrotoxicity, neutropenia or laryngeal malignancies after the administration of intralesional cidofovir in RRP patients.

  11. Effect of Axial Loading on Quench Performance in Nb3Sn Magnets

    SciTech Connect

    Ambrosio, G.; Bordini, B.; Caspi, S.; Dietderich, D.R.; Felice, H.; Hafalia, A.R.; Hannaford, C.R.; Lizarazo, J.; Lietzke, A.F.; McInturff, A.D.; Sabbi, G.L.; DiMarco, J.D.; Tartaglia, M.; Vedrice, P.; Ferracin, P.

    2008-06-01

    A series of tests has been performed at Lawrence Berkeley National Laboratory (LBNL) and Fermi National Accelerator Laboratory (FNAL) with the goal of assessing the influence of coil axial pre-load on Nb{sub 3}Sn magnet training. The tests involved two subscale Nb{sub 3}Sn magnets: SQ02, a quadrupole magnet fabricated as part of the US LHC Accelerator Research Program (LARP), and SD01, a dipole magnet developed in collaboration between CEA/Saclay and LBNL. Both magnets used similar Nb{sub 3}Sn flat racetrack coils from LBNL Subscale Magnet Program, and implemented an axial support system composed of stainless steel end-plates and aluminum rods. The system was designed to withstand full longitudinal electro-magnetic forces and provide controllable preloads. Quench performances, training, and quench locations have been recorded in various axial loading conditions. Test results are reported.

  12. Test Results of HD1b, an upgraded 16 Tesla Nb3Sn DipoleMagnet

    SciTech Connect

    Lietzke, A.F.; Bartlett, S.E.; Bish, P.; Caspi, S.; Dietderich,D.; Ferracin, P.; Gourlay, S.; Hafalia, A.R.; Hannaford, C.R.; Higley,H.; Lau, W.; Liggins, N.; Mattafirri, S.; Nyman, M.; Sabbi, G.; Scanlan,R.; Swanson, J.

    2005-04-16

    The Superconducting Magnet Group at Lawrence Berkeley National Laboratory has been developing high-field, brittle-superconductor, accelerator magnet technology, in which the conductor's support system can significantly impact conductor performance (as well as magnet training). A recent H-dipole coil test (HD1) achieved a peak bore-field of 16 Tesla, using two, flat-racetrack, double-layer Nb{sub 3}Sn coils. However, its 4.5 K training was slow, with an erratic plateau at {approx}92% of its un-degraded ''short-sample'' expectation ({approx}16.6 T). Quench-origins correlated with regions where low conductor pre-stress had been expected (3-D FEM predictions and variations in 300 K coil-size). The coils were re-assembled with minor coil-support changes and re-tested as ''HD1b'', with a 185 MPa average pre-stress (30 MPa higher than HD1, with a 15-20 MPa pole-turn margin expected at 17 T). Training started higher (15.1 T), and quickly reached a stable, negligibly higher plateau at 16 T. After a thermal cycle, training started at 15.4 T, but peaked at 15.8 T, on the third attempt, before degrading to a 15.7 T plateau. The temperature dependence of this plateau was explored in a sub-atmospheric LHe bath to 3.0 K. Magnet performance data for both thermal cycles is presented and discussed, along with issues for future high-field accelerator magnet development.

  13. Nb3Sn accelerator magnet technology scale up using cos-theta dipole coils

    SciTech Connect

    Nobrega, F.; Andreev, N.; Ambrosio, G.; Barzi, E.; Bossert, R.; Carcagno, R.; Chlachidze, G.; Feher, S.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; /Fermilab

    2007-06-01

    Fermilab is working on the development of Nb{sub 3}Sn accelerator magnets using shell-type dipole coils and the wind-and-react method. As a part of the first phase of technology development, Fermilab built and tested six 1 m long dipole model magnets and several dipole mirror configurations. The last three dipoles and two mirrors reached their design fields of 10-11 T. The technology scale up phase has started by building 2 m and 4 m dipole coils and testing them in a mirror configuration in which one of the two coils is replaced by a half-cylinder made of low carbon steel. This approach allows for shorter fabrication times and extensive instrumentation preserving almost the same level of magnetic field and Lorentz forces in the coils as in a complete dipole model magnet. This paper presents details on the 2 m (HFDM07) and 4 m long (HFDM08) Nb{sub 3}Sn dipole mirror magnet design and fabrication technology, as well as the magnet test results which are compared with 1 m long models.

  14. Fabrication and Test Results of a Nb3Sn Superconducting Racetrack Dipole Magnet

    SciTech Connect

    Chow, K.; Dietderich, D.R.; Gourlay, S.A.; Gupta, R.; Harnden, W.; Lietzke, A. F.; McInturff, A.D.; Millos, G.A.; Morrison, L.; Morrison, M.; Scanlan, R.M.

    2000-02-06

    A 'proof-of-principle' Nb{sub 3}Sn superconducting dual-bore dipole magnet was built from racetrack coils, as a first step in a program to develop an economical, 15 Tesla, accelerator-quality magnet. The mechanical design and magnet fabrication procedures are discussed. No training was required to achieve temperature-dependent plateau currents, despite several thermal cycles that involved partial magnet disassembly and substantial pre-load variations. Subsequent magnets are expected to approach 15 Tesla with substantially improved conductor.

  15. Mechanical analysis of the Nb3Sn dipole magnet HD1

    SciTech Connect

    Ferracin, Paolo; Bartlett, Scott E.; Caspi, Shlomo; Dietderich,Daniel R.; Gourlay, Steve A.; Hannaford, Carles R.; Hafalia, Aurelio R.; Lietzke, Alan F.; Mattafirri, Sara; Sabbi, Gianluca

    2005-04-14

    The Superconducting Magnet Group at Lawrence Berkeley National Laboratory (LBNL) has recently fabricated and tested HD1, a Nb{sub 3}Sn dipole magnet. The magnet reached a 16 T field, and exhibited training quenches in the end regions and in the straight section. After the test, HD1 was disassembled and inspected, and a detailed 3D finite element mechanical analysis was done to investigate for possible quench triggers. The study led to minor modifications to mechanical structure and assembly procedure, which were verified in a second test (HD1b). This paper presents the results of the mechanical analysis, including strain gauge measurements and coil visual inspection. The adjustments implemented in the magnet structure are reported and their effect on magnet training discussed.

  16. Assembly and Tests of SQ02, a Nb3Sn Racetrack Quadrupole Magnet for LARP

    SciTech Connect

    Ferracin, Paolo; Ambrosio, G.; Barzi, E.; Caspi, S.; Dietderich, D.R.; Feher, S.; Gourlay, S.A.; Hafalia, A.R.; Hannaford, C.R.; Lizarazo, J.; Lietzke, A.F.; McInturff, A.D.; Sabbi, G.L.; Zlobin, A.V.

    2007-06-01

    The US LHC Accelerator Research Program (LARP) consists of four US laboratories (BNL, FNAL, LBNL, and SLAC) collaborating with CERN to achieve a successful commissioning of the LHC and to develop the next generation of Interaction Region magnets. In 2004, a large aperture Nb{sub 3}Sn racetrack quadrupole magnet (SQ01) has been fabricated and tested at LBNL. The magnet utilized four subscale racetrack coils and was instrumented with strain gauges on the support structure and directly over the coil's turns. SQ01 exhibited training quenches in two of the four coils and reached a peak field in the conductor of 10.4 T at a current of 10.6 kA. After the test, the magnet was disassembled, inspected with pressure indicating films, and reassembled with minor modifications. A second test (SQ01b) was performed at FNAL and included training studies, strain gauge measurements and magnetic measurements. Magnet inspection, test results, and magnetic measurements are reported and discussed, and a comparison between strain gauge measurements and 3D finite element computations is presented.

  17. Fabrication and test results of a high field, Nb3Sn superconducting racetrack dipole magnet

    SciTech Connect

    Benjegerdes, R.; Bish, P.; Byford, D.; Caspi, S.; Dietderich, D.R.; Gourlay, S.A.; Hafalia, R.; Hannaford, R.; Higley, H.; Jackson, A.; Lietzke, A.; Liggins, N.; McInturff, A.D.; O'Neill, J.; Palmerston, E.; Sabbi, G.; Scanlan, R.M.; Swanson, J.

    2001-06-15

    The LBNL Superconducting Magnet Program is extending accelerator magnet technology to the highest possible fields. A 1 meter long, racetrack dipole magnet, utilizing state-of-the-art Nb{sub 3}Sn superconductor, has been built and tested. A record dipole filed of 14.7 Tesla has been achieved. Relevant features of the final assembly and tested results are discussed.

  18. Development of a single-layer Nb3Sn common coil dipole model

    SciTech Connect

    Igor Novitski et al.

    2002-12-13

    A high-field dipole magnet based on the common coil design was developed at Fermilab for a future Very Large Hadron Collider. A short model of this magnet with a design field of 11 T in two 40-mm apertures is being fabricated using the react-and-wind technique. In order to study and optimize the magnet design two 165-mm long mechanical models were assembled and tested. A technological model consisting of magnet straight section and ends was also fabricated in order to check the tooling and the winding and assembly procedures. This paper describes the design and technology of the common coil dipole magnet and summarizes the status of short model fabrication.The results of the mechanical model tests and comparison with FE mechanical analysis are also presented.

  19. MAGNETIC FIELD MEASUREMENTS OF HD2, A HIgh Nb3Sn DIPOLE MAGNET

    SciTech Connect

    Wang, X.; Caspi, S.; Cheng, D. W.; Felice, H.; Ferracin, P.; Hafalia, R. R.; Joseph, J. M.; Lietzke, A. F.; Lizarazo, J.; McInturff, A. D.; Sabbi, G. L.; Sasaki, K.

    2009-05-04

    The Superconducting Magnet Program at Lawrence Berkeley National Laboratory has designed and tested HD2, a 1 m long Nb{sub 3}Sn accelerator-type dipole based on a simple block-type coil geometry with flared ends. HD2 represents a step toward the development of cost-effective accelerator quality magnets operating in the range of 13-15 T. The design was optimized to minimize geometric harmonics and to address iron saturation and conductor magnetization effects. Field quality was measured during recent cold tests. The measured harmonics are presented and compared to the design values.

  20. LARP NB3SN QUADRUPOLE MAGNETS FOR THE LHC LUMINOSITY UPGRADE

    SciTech Connect

    Ferracin, P.

    2009-06-01

    The US LHC Accelerator Research Program (LARP) is a collaboration between four US laboratories (BNL, FNAL, LBNL, and SLAC) aimed at contributing to the commissioning and operation of the LHC and conducting R&D on its luminosity upgrade. Within LARP, the Magnet Program's main goal is to demonstrate that Nb{sub 3}Sn superconducting magnets are a viable option for a future upgrade of the LHC Interaction Regions. Over the past four years, LARP has successfully fabricated and tested several R&D magnets: (1) the subscale quadrupole magnet SQ, to perform technology studies with 300 mm long racetrack coils, (2) the technology quadrupole TQ, to investigate support structure behavior with 1 m long cos2{theta} coils, and (3) the long racetrack magnet LR, to test 3.6 m long racetrack coils. The next milestone consists in the fabrication and test of the 3.7 m long quadrupole magnet LQ, with the goal of demonstrating that ND{sub 3}Sn technology is mature for use in high energy accelerators. After an overview of design features and test results of the LARP magnets fabricated so far, this paper focuses on the status of the fabrication of LQ: we describe the production of the 3.4 m long cos2{theta} coils, and the qualification of the support structure. Finally, the status of the development of the next 1 m long model HQ, conceived to explore stress and field limits of Nb{sub 3}Sn superconducting magnets, is presented.

  1. Measured strain in Nb3Sn coils during excitation and quence

    SciTech Connect

    Caspi, S.; Barlett, S.E.; Dietderich, D. R.; Ferracin, P.; Gourlay, S. A.; Hannaford, C. R.; Hafalia, A.R.; Lietzke, A.F.; Mattafirri, S.; Nyman, M.; Sabbi, G.

    2005-06-01

    The strain in a high field Nb{sub 3}Sn coil was measured during magnet assembly, cool-down, excitation and spot heater quenches. Strain was measured with a full bridge strain gauge mounted directly over the turns and impregnated with the coil. Two such coils were placed in a 'common coil' fashion capable of reaching 11 T at 4.2 K. The measured steady state strain in the coil is compared with results obtained using the FEM code ANSYS. During quenches, the transient strain (due to temperature rise) was also measured and compared with the calculated mechanical time response to a quench.

  2. Measured Strain of Nb3Sn Coils During Excitation and Quench

    SciTech Connect

    Caspi, S.; Bartlett, S.E.; Dietderich, D.R.; Ferracin, P.; Gourlay, S.A.; Hannaford, C.R.; Hafalia, A.R.; Lietzke, S.; Mattafirri,M.; Nyman, M.; Sabbi, G.

    2005-04-16

    The strain in a high field Nb{sub 3}Sn coil was measured during magnet assembly, cool-down, excitation and spot heater quenches. Strain was measured with a full bridge strain gauge mounted directly over the turns and impregnated with the coil. Two such coils were placed in a ''common coil'' fashion capable of reaching 11T at 4.2K. The measured steady state strain in the coil is compared with results obtained using the FEM code ANSYS. During quenches, the transient strain (due to temperature rise) was also measured and compared with the calculated mechanical time response to a quench.

  3. Field quality measurements of Fermilab Nb(3)Sn common coil dipole model

    SciTech Connect

    Kashikhin, V.S.; Andreev, N.; Dimarco, J.; Feher, S.; Kashikhin, V.V.; Lamm, M.; Novitski, I.; Orris, D.; Schlabach, P.; Sylvester, C.; Tartaglia, M.; Velev, G.; Zlobin, A.V.; Fermilab

    2003-11-01

    A short model of single-layer Nb{sub 3}Sn common coil magnet has been fabricated and is being tested at Fermilab. This paper summarizes results of magnetic measurements in this model. The geometrical harmonics, coil magnetization and iron saturation effects, ramp-rate dependence, field decay and the ''snap-back'' effect at injection are presented.

  4. Test Results for HD1, a 16 Tesla Nb3Sn Dipole Magnet

    SciTech Connect

    Lietzke, A.F.; Bartlett, S.; Bish, P.; Caspi, S.; Chiesa, L.; Dietderich, D.; Ferracin, P.; Gourlay, S.A.; Goli, M.; Hafalia, R.R.; Higley, H.; Hannaford, R.; Lau, W.; Liggens, N.; Mattafirri, S.; McInturff, A.; Nyman, M.; Sabbi, G.; Scanlan, R.; Swanson, J.

    2003-10-01

    The Superconducting Magnet Group at Lawrence Berkeley National Laboratory has been developing the technology for using brittle superconductor in high-field accelerator magnets. HD1, the latest in a series of magnets, contains two, double-layer Nb{sub 3}Sn flat racetrack coils. This single-bore dipole configuration, using the highest performance conductor available, was designed and assembled for a 16 tesla conductor/structure/pre-stress proof-of-principle. With the combination of brittle conductor and high Lorentz stress, considerable care was taken to predict the magnet's mechanical responses to pre-stress, cool-down, and excitation. Subsequent cold testing satisfied expectations: Training started at 13.6 T, 83% of 'short-sample', achieved 90% in 10 quenches, and reached its peak bore field (16 T) after 19 quenches. The average plateau, {approx}92% of 'short-sample', appeared to be limited by 'stick-slip' conductor motions, consistent with the 16.2 T conductor 'lift-off' pre-stress that was chosen for this first test. Some lessons learned and some implications for future conductor and magnet technology development are presented and discussed.

  5. Development and Coil Fabrication for the LARP 3.7-m Long Nb3Sn Quadrupole

    SciTech Connect

    Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bossert, R.; Caspi, S.; Chlachidize, G.; Dietderich, D.; Felice, H.; Ferracin, P.; Ghosh, A.; Hafalia, R.; Hannaford, R.; Jochen, G.; Kashikhin, V.V.; Kovach, P.; Lamm, M.; Lietzke, A.; McInturff, A.; Muratore,, J.; Nobreaga, F.; Novitsky, I.; Peggs, S.; Prestemon, S.; Sabbi, G. L.; Schmalzle, J.; Turrioni, D.; Wanderer, P.; Whitson, G.; Zlobin, A. V.

    2008-08-17

    The U.S. LHC Accelerator Research Program (LARP) has started the fabrication of 3.7-m long Nb{sub 3}Sn quadrupole models. The Long Quadrupoles (LQ) are 'Proof-of-Principle' magnets which are to demonstrate that Nb{sub 3}Sn technology is mature for use in high energy particle accelerators. Their design is based on the LARP Technological Quadrupole (TQ) models, developed at FNAL and LBNL, which have design gradients higher than 200 T/m and an aperture of 90 mm. The plans for the LQ R&D and a design update are presented and discussed in this paper. The challenges of fabricating long accelerator-quality Nb{sub 3}Sn coils are presented together with the solutions adopted for the LQ coils (based on the TQ experience). During the fabrication and inspection of practice coils some problems were found and corrected. The fabrication at BNL and FNAL of the set of coils for the first Long Quadrupole is in progress.

  6. Development of Nb3Sn 11 T single aperture demonstrator dipole for LHC upgrades

    SciTech Connect

    Zlobin, A.V.; Apollinari, G.; Andreev, N.; Barzi, E.; Kashikhin, V.V.; Nobrega, f.; Novitski, I.; Auchmann, B.; Karppinen, M.; Rossi, L.; /CERN

    2011-03-01

    The LHC collimation upgrade foresees additional collimators installed in dispersion suppressor regions. To obtain the necessary space for the collimators, a solution based on the substitution of LHC main dipoles for stronger dipoles is being considered. CERN and FNAL have started a joint program to demonstrate the feasibility of Nb{sub 3}Sn technology for this purpose. The goal of the first phase is the design and construction of a 2-m long single-aperture demonstrator magnet with a nominal field of 11 T at 11.85 kA with 20% margin. This paper describes the magnetic and mechanical design of the demonstrator magnet and summarizes its design parameters.

  7. Development of a Large Aperture Nb3Sn Racetrack Quadrupole Magnet

    SciTech Connect

    Ferracin, Paolo; Bartlett, Scott E.; Caspi, Shlomo; Dietderich, Daniel R.; Gourlay, Steve A.; Hannaford, Charles R.; Hafalia, Aurelio R.; Lietzke, Alan F.; Mattafirri, Sara; McInturff, Alfred D.; Nyman, Mark; Sabbi, Gianluca

    2005-06-01

    The U.S. LHC Accelerator Research Program (LARP), a collaboration between BNL, FNAL, LBNL, and SLAC, has among its major objectives the development of advanced magnet technology for an LHC luminosity upgrade. The LBNL Superconducting Magnet Group supports this program with a broad effort involving design studies, Nb{sub 3}Sn conductor development, mechanical models, and basic prototypes. This paper describes the development of a large aperture Nb{sub 3}Sn racetrack quadrupole magnet using four racetrack coils from the LBNL Subscale Magnet (SM) Program. The magnet provides a gradient of 95 T/m in a 110 mm bore, with a peak field in the conductor of 11.2 T. The coils are pre-stressed by a mechanical structure based on a pre-tensioned aluminum shell, and axially supported with aluminum rods. The mechanical behavior has been monitored with strain gauges and the magnetic field has been measured. Results of the test are reported and analyzed.

  8. Measurement of Fast Voltage Transients in High-Performance Nb3Sn Magnets

    SciTech Connect

    Lietzke, A. F.; Sabbi., G. L.; Ferracin, P.; Caspi, S.; Zimmerman, S.; Joseph, J.; Doering, D.; Lizarazo, J.

    2008-06-01

    The Superconducting Magnet group at Lawrence Berkeley National Laboratory has been developing Nb{sub 3}Sn high-field accelerator magnet technology for the last fifteen years. In order to support the magnet R&D effort, we are developing a diagnostic system that can help identify the causes of performance limiting quenches by recording small flux-changes within the magnet prior to quench-onset. These analysis techniques were applied to the test results from recent Nb{sub 3}Sn magnets. This paper will examine various types of events and their distinguishing characteristics. The present measurement techniques are discussed along with the design of a new data acquisition system that will substantially improve the quality of the recorded signals.

  9. Fabrication and Test Results of a Prototype, Nb3Sn Superconducting Racetrack Dipole Magnet

    SciTech Connect

    Gourlay, S. A.; Chow, K.; Dietderich, D.R.; Gupta, R.; Hannaford, R.; Harnden, W.; Lietzke, A.; McInturff, A.D.; Millos, G.A.; Morrison, L.; Morrison, M.; Scanlan, R.M.

    1998-09-01

    A prototype, Nb{sub 3}Sn superconducting magnet, utilizing a racetrack coil design has been built and tested. This magnet represents the first step in a recently implemented program to develop a high field, accelerator quality magnet. This magnet was constructed with coils wound from conductor developed for the ITER project, limiting the magnet to a field of 6-7 Tesla. Subsequent magnets in the program will utilize improved conductor, culminating in a magnet design capable of producing fields approaching 15 Tesla. The simple geometry is more suitable for the use of brittle superconductors necessary to eventually reach high field levels. In addition, fewer and simpler parts are used in fabricating these coils compared with the more conventional cosine theta cross section coils. The general fabrication steps, mechanical design and quench performance are discussed.

  10. Test Results of a Nb3Sn Wind/React"Stress-Managed" Block Dipole

    SciTech Connect

    McInturff, A.; Blackburn, R.; Diaczenko, N.; Elliott, T.; Henchel, W.; Jaisle, A.; McIntyre, P.; Noyes, P.; Sattarov, A.; Lietzke, A.; Hafalia Jr., R.; Lau, W.; Nyman, M.; Bish, P.

    2007-06-01

    A second phase of a high field dipole technology development has been tested. A Nb{sub 3}Sn block-coil model dipole was fabricated, using magnetic mirror geometry and wind/react coil technology. The primary objective of this phase was to make a first experimental test of the stress-management strategy pioneered at Texas A&M. In this strategy a high-strength support matrix is integrated with the windings to intercept Lorentz stress from the inner winding so that it does not accumulate in the outer winding. The magnet attained a field that was consistent with short sample limit on the first quench; there was no training. The decoupling of Lorentz stress between inner and outer windings was validated. In ramp rate studies the magnet exhibited a remarkable robustness in rapid ramping operation. It reached 85% of short sample(ss) current even while ramping 2-3 T/s. This robustness is attributed to the orientation of the Rutherford cables parallel to the field in the windings, instead of the transverse orientation that characterizes common dipole designs. Test results are presented and the next development phase plans are discussed.

  11. Design and Fabrication of a 14 T, Nb3Sn Superconducting Racetrack Dipole Magnet

    SciTech Connect

    Gourlay, S.A.; Bish, P.; Caspi, S.; Chow, K.; Dietderich, D.R.; Gupta, R.; Hannaford, R.; Harnden, W.; Higley, H.; Lietzke, A.; Liggins, N.; McInturff, A.D.; Millos, G.A.; Morrison, L. Morrison M.; Scanlan, R.M.

    1999-09-01

    Most accelerator magnets for applications in the field range up to 10 T utilize NbTi superconductor and a cosine theta coil design. For fields above 10 T, it is necessary to use Nb{sub 3}Sn or other strain sensitive superconductors land other coil geometries that are more compatible with these materials. This paper describes our recent efforts to design a series of racetrack coil magnets that will provide experimental verification of an alternative magnet design philosophy, with the near-term goal of reaching a field level of approximately 14 T. The conductor and fabrication issues relevant to building high field, racetrack dipoles utilizing Nb{sub 3}Sn superconductor and a wind and react approach will also be discussed.

  12. Investigation of alternative materials for impregnation of Nb3Sn accelerator magnets

    SciTech Connect

    Deepak Reddy Chichili, Jay Hoffman and Alexander Zlobin

    2003-11-17

    Insulation is one of the most important elements of magnet design, which determines the electrical, mechanical, and thermal performance as well as lifetime of the magnet. The exposure to high radiation loads especially for the proposed LHC second-generation interaction region Nb{sub 3}Sn quadrupoles further limits the choices of the insulation materials. Traditionally Nb{sub 3}Sn magnets were impregnated with epoxy to improve both the mechanical and electrical properties. However, the acceptable radiation limit for epoxy is low which reduces the lifetime of the magnet. The paper presents the results of the feasibility study to replace epoxy with high radiation-resistant material during vacuum impregnation. The mechanical, thermal and electrical properties of samples impregnated with Matrimid were measured and compared with epoxy-impregnated samples.

  13. Structure for an LHC 90mm Nb3Sn Quadrupole Magnet

    SciTech Connect

    Hafalia, A.R.; Caspi, S.; Bartlett, S.E.; Dietderich, D.R.; Ferracin, P.; Gourlay, S.A.; Hannaford, C.R.; Higley, H.; Lietzke, A.F.; Lau, B.; Liggins, N.; Mattafirri, S.; McInturff, A.D.; Nyman, M.; Sabbi,G.L.; Scanlan, R.M.; Swanson, J.

    2005-04-16

    A full-scale mechanical model of the LHC Nb{sub 3}Sn quadrupole magnet structure has been designed, built and tested. The structure will support a 90mm bore, 1m long magnet prototype as part of the US LHC Accelerator Research Program (LARP). The structure utilizes Bladder and Key Technology to control and transfer pre-stress from an outer aluminum shell to an inner coil. Axial aluminum rods take care of pre-stress at the ends--ensuring that the coil is fully constrained along all three axes. The outer aluminum shell and an inner ''dummy coil'' (aluminum tube) were extensively instrumented with strain gauges. The gauges were used to monitor and map the effectiveness of the stress relation between the loading structure and a ''dummy'' coil through varying mechanical load conditions --from bladder and key pre-stress at room temperature through cool-down. Test results of the stress distribution in the structure and the in dummy coil is reported and compared with expected results calculated with the structural analysis program ANSYS.

  14. Nb3Sn accelerator magnet technology R&D at Fermilab

    SciTech Connect

    Zlobin, A.V.; Ambrosio, G.; Andreev, N.; Barzi, E.; Bossert, R.; Carcagno, R.; Chlachidze, G.; DiMarco, J.; Feher, S.; Kashikhin, V.S.; Kashikhin, V.V.; /Fermilab

    2007-06-01

    Accelerator magnets based on Nb{sub 3}Sn superconductor are being developed at Fermilab. Six nearly identical 1-m long dipole models and several mirror configurations were built and tested demonstrating magnet performance parameters and their reproducibility. The technology scale up program has started by building and testing long dipole coils. The results of this work are reported in the paper.

  15. Tests of insulation systems for Nb3Sn wind and react coils

    SciTech Connect

    Bossert, R.; Ambrosio, G; Andreev, N.; Whitson, G.; Zlobin, A.; /Fermilab

    2007-07-01

    Tests were performed to assess the viability of several cable insulation systems for use in Nb{sub 3}Sn accelerator magnets. Insulated stacks of cables were subjected to reaction cycles commonly used for Nb{sub 3}Sn coils. After reaction and epoxy impregnation, current leakage between turns was measured at pressures up to 180 MPa and turn-to-turn potentials up to 500V. Systems consisting of S-2 glass, ceramic fiber, and E-glass were tested. Several methods of applying the insulation were incorporated, including sleeves and various spiral wrapped configurations. Methods of sample preparation and testing are described and results are reported.

  16. Nb3Sn superconducting magnets for electron cyclotron resonance ion sources

    SciTech Connect

    Ferracin, P.; Caspi, S.; Felice, H.; Leitner, D.; Lyneis, C. M.; Prestemon, S.; Sabbi, G. L.; Todd, D. S.

    2009-05-04

    Electron cyclotron resonance (ECR) ion sources are an essential component of heavy-ion accelerators. Over the past few decades advances in magnet technology and an improved understanding of the ECR ion source plasma physics have led to remarkable performance improvements of ECR ion sources. Currently third generation high field superconducting ECR ion sources operating at frequencies around 28 GHz are the state of the art ion injectors and several devices are either under commissioning or under design around the world. At the same time, the demand for increased intensities of highly charged heavy ions continues to grow, which makes the development of even higher performance ECR ion sources a necessity. To extend ECR ion sources to frequencies well above 28 GHz, new magnet technology will be needed in order to operate at higher field and force levels. The superconducting magnet program at LBNL has been developing high field superconducting magnets for particle accelerators based on Nb{sub 3}Sn superconducting technology for several years. At the moment, Nb{sub 3}Sn is the only practical conductor capable of operating at the 15 T field level in the relevant configurations. Recent design studies have been focused on the possibility of using Nb{sub 3}Sn in the next generation of ECR ion sources. In the past, LBNL has worked on the VENUS ECR, a 28 GHz source with solenoids and a sextupole made with NbTi operating at fields of 6-7 T. VENUS has now been operating since 2004. We present in this paper the design of a Nb{sub 3}Sn ECR ion source optimized to operate at an rf frequency of 56 GHz with conductor peak fields of 13-15 T. Because of the brittleness and strain sensitivity of Nb{sub 3}Sn- , particular care is required in the design of the magnet support structure, which must be capable of providing support to the coils without overstressing the conductor. In this paper, we present the main features of the support structure, featuring an external aluminum shell pretensioned with water-pressurized bladders, and we analyze the expected coil stresses with a two-dimensional finite element mechanical model.

  17. Design of a Nb3Sn Magnet for a 4th Generation ECR Ion Source

    SciTech Connect

    Prestemon, S,; Trillaud, F.; Caspi, S.; Ferracin, P.; Sabbi, G. L.; Lyneis, C. M.; Leitner, D.; Todd, D. S.; Hafalia, R.

    2008-08-17

    The next generation of Electron Cyclotron Resonant (ECR) ion sources are expected to operate at a heating radio frequency greater than 40 GHz. The existing 3rd generation systems, exemplified by the state of the art system VENUS, operate in the 10-28 GHz range, and use NbTi superconductors for the confinement coils. The magnetic field needed to confine the plasma scales with the rf frequency, resulting in peak fields on the magnets of the 4th generation system in excess of 10 T. High field superconductors such as Nb{sub 3}Sn must therefore be considered. The magnetic design of a 4th. generation ECR ion source operating at an rf frequency of 56 GHz is considered. The analysis considers both internal and external sextupole configurations, assuming commercially available Nb{sub 3}Sn material properties. Preliminary structural design issues are discussed based on the forces and margins associated with the coils in the different configurations, leading to quantitative data for the determination of a final magnet design.

  18. Nb3Sn Quadrupoles in the LHC IR Phase I Upgrade

    SciTech Connect

    Zlobin,A.; Johnstone, J.; Kashikhin, V.; Mokhov, N.; Rakhno, I.; deMaria, R.; Peggs, S.; Robert-Demolaize, F.; Wanderer, P.

    2008-06-23

    After a number of years of operation at nominal parameters, the LHC will be upgraded for higher luminosity. This paper discusses the possibility of using a limited number of Nb{sub 3}Sn quadrupoles for hybrid optics layouts for the LHC Phase I luminosity upgrades with both NbTi and Nb{sub 3}Sn quadrupoles. Magnet parameters and issues related to using Nb{sub 3}Sn quadrupoles including aperture, gradient, magnetic length, field quality, operation margin, et cetera are discussed.

  19. Design Studies of Nb3Sn High-Gradient Quadrupole Models for LARP

    SciTech Connect

    Sabbi, GianLuca; Andreev, Nikolai; Caspi, Shlomo; Dietderich, Daniel; Ferracin, Paolo; Ghosh, Arup; Kashikhin, Vadim; Lietzke, Al; McInturff, Alfred; Novitski, Igor; Zlobin, Alexander

    2007-06-01

    Insertion quadrupoles with large aperture and high gradient are required to achieve the luminosity upgrade goal of 10{sup 35} cm{sup -2} s{sup -1} at the Large Hadron Collider (LHC). In 2004, the US Department of Energy established the LHC Accelerator Research Program (LARP) to develop a technology base for the upgrade. Nb{sub 3}Sn conductor is required in order to operate at high field and with sufficient temperature margin. We report here on the conceptual design studies of a series of 1 m long 'High-gradient Quadrupoles' (HQ) that will explore the magnet performance limits in terms of peak fields, forces and stresses. The HQ design is expected to provide coil peak fields of more than 15 T, corresponding to gradients above 300 T/m in a 90 mm bore. Conductor requirements, magnetic, mechanical and quench protection issues for candidate HQ designs will be presented and discussed.

  20. Nb3Sn quadrupoles in the LHC IR Phase I upgrade

    SciTech Connect

    Zlobin, A.V.; Johnstone, J.A.; Kashikhin, V.V.; Mokhov, N.V.; Rakhno, I.L.; de Maria, R.; Peggs, S.; Robert-Demolaize, G.; Wanderer, P.; /Brookhaven

    2008-06-01

    After a number of years of operation at nominal parameters, the LHC will be upgraded to a higher luminosity. This paper discusses the possibility of using a limited number of Nb{sub 3}Sn quadrupoles for hybrid optics layouts for the LHC Phase I luminosity upgrades with both NbTi and Nb{sub 3}Sn quadrupoles. Magnet parameters and issues related to using Nb{sub 3}Sn quadrupoles including aperture, gradient, magnetic length, field quality, operation margin, et cetera are discussed.

  1. Design of HQ -- a High Field Large Bore Nb3Sn Quadrupole Magnet for LARP

    SciTech Connect

    Felice, H.; Ambrosio, G.; Anerella, M.; Bossert, R.; Caspi, S.; Cheng, D.; Dietderich, D.; Ferracin, P.; Ghosh, A. K.; Hafalia, R.; Hannaford, C. R.; Kashikhin, V.; Schmalze, J.; Prestemon, S.; Sabbi, G. L.; Wanderer, P.; Zlobin, A. V.

    2008-08-17

    In support of the Large Hadron Collider luminosity upgrade, a large bore (120 mm) Nb{sub 3}Sn quadrupole with 15 T peak coil field is being developed within the framework of the US LHC Accelerator Research Program (LARP). The 2-layer design with a 15 mm wide cable is aimed at pre-stress control, alignment and field quality while exploring the magnet performance limits in terms of gradient, forces and stresses. In addition, HQ will determine the magnetic, mechanical, and thermal margins of Nb{sub 3}Sn technology with respect to the requirements of the luminosity upgrade at the LHC.

  2. Recent Test Results of the High Field Nb3Sn Dipole Magnet HD2

    SciTech Connect

    Ferracin, P.; Bingham, B.; Caspi, S.; Cheng, D. W.; Dietderich, D. R.; Felice, H.; Hafalia, A. R.; Hannaford, C. R.; Joseph, J.; Lietzke, A. F.; Lizarazo, J.; Sabbi, G.; Wang, X.

    2009-10-19

    The 1 m long Nb{sub 3}Sn dipole magnet HD2, fabricated and tested at Lawrence Berkeley National Laboratory, represents a step towards the development of block-type accelerator quality magnets operating in the range of 13-15 T. The magnet design features two coil modules composed of two layers wound around a titanium-alloy pole. The layer 1 pole includes a round cutout to provide room for a bore tube with a clear aperture of 36 mm. After a first series of tests where HD2 reached a maximum bore field of 13.8 T, corresponding to an estimated peak field on the conductor of 14.5 T, the magnet was disassembled and reloaded without the bore tube and with a clear aperture increased to 43 mm. We describe in this paper the magnet training observed in two consecutive tests after the removal of the bore tube, with a comparison of the quench performance with respect to the previous tests. An analysis of the voltage signals recorded before and after training quenches is then presented and discussed, and the results of coil visual inspections reported.

  3. Minimization of the hysteresis loss and low-field instability in technical Nb3Al conductors

    NASA Astrophysics Data System (ADS)

    Banno, N.; Takeuchi, T.; Nimori, S.; Tanaka, K.; Nakagawa, K.; Tsuchiya, K.

    2008-11-01

    This paper focuses on the magnetization characteristics of technical Nb3Al conductors, in particular the minimization of their hysteresis loss and low-field instability. Unlike the case of Nb3Sn wire fabrication, the Nb3Al wire is fabricated by a phase transformation process, in which it is believed that the Jc properties of the transformed Nb3Al phase do not depend on the filament size or shape, but rather are principally controlled by the rapid heating and quenching or transformation conditions. However, the rapid heating and quenching process forces us to use high-melting-point metals like niobium as the matrix. The use of Nb strongly affects the magnetization because of its superconductivity in low fields. In this paper, the magnetization properties of several kinds of technical Nb3Al conductors, including Ta matrix wires, were studied. The use of Ta was effective in suppressing low-field instability. In addition, we propose a new process to further minimize the filament diameter by a re-stacking (RS) method, whereby the rapidly quenched strands are re-stacked into a stabilizing material tube and co-drawn. This process leads to a very fine multifilamentary structure with a filament diameter of less than 15 µm, thereby substantially reducing the magnetization, as compared with high-performance Nb3Sn wires, e.g. RRP Nb3Sn wire. The ± 3 T hysteresis loss of the RS Nb3Al conductor was 370 mJ cm-3 and the non-Cu Jc (12 T, 4.2 K) of the conductor was 1350 A mm-2. These values meet the ITER strand specification.

  4. Characteristics of Cu stabilized Nb3Al strands with low Cu ratio

    SciTech Connect

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

    2008-12-01

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

  5. A Novel Plasmid-Based Microarray Screen Identifies Suppressors of rrp6Δ in Saccharomyces cerevisiae▿†

    PubMed Central

    Abruzzi, Katharine; Denome, Sylvia; Olsen, Jens Raabjerg; Assenholt, Jannie; Haaning, Line Lindegaard; Jensen, Torben Heick; Rosbash, Michael

    2007-01-01

    Genetic screens in Saccharomyces cerevisiae provide novel information about interacting genes and pathways. We screened for high-copy-number suppressors of a strain with the gene encoding the nuclear exosome component Rrp6p deleted, with either a traditional plate screen for suppressors of rrp6Δ temperature sensitivity or a novel microarray enhancer/suppressor screening (MES) strategy. MES combines DNA microarray technology with high-copy-number plasmid expression in liquid media. The plate screen and MES identified overlapping, but also different, suppressor genes. Only MES identified the novel mRNP protein Nab6p and the tRNA transporter Los1p, which could not have been identified in a traditional plate screen; both genes are toxic when overexpressed in rrp6Δ strains at 37°C. Nab6p binds poly(A)+ RNA, and the functions of Nab6p and Los1p suggest that mRNA metabolism and/or protein synthesis are growth rate limiting in rrp6Δ strains. Microarray analyses of gene expression in rrp6Δ strains and a number of suppressor strains support this hypothesis. PMID:17101774

  6. Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII.

    PubMed

    Wagschal, Alexandre; Rousset, Emilie; Basavarajaiah, Poornima; Contreras, Xavier; Harwig, Alex; Laurent-Chabalier, Sabine; Nakamura, Mirai; Chen, Xin; Zhang, Ke; Meziane, Oussama; Boyer, Frédéric; Parrinello, Hugues; Berkhout, Ben; Terzian, Christophe; Benkirane, Monsef; Kiernan, Rosemary

    2012-09-14

    Transcription elongation is increasingly recognized as an important mechanism of gene regulation. Here, we show that microprocessor controls gene expression in an RNAi-independent manner. Microprocessor orchestrates the recruitment of termination factors Setx and Xrn2, and the 3'-5' exoribonuclease, Rrp6, to initiate RNAPII pausing and premature termination at the HIV-1 promoter through cleavage of the stem-loop RNA, TAR. Rrp6 further processes the cleavage product, which generates a small RNA that is required to mediate potent transcriptional repression and chromatin remodeling at the HIV-1 promoter. Using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq), we identified cellular gene targets whose transcription is modulated by microprocessor. Our study reveals RNAPII pausing and premature termination mediated by the co-operative activity of ribonucleases, Drosha/Dgcr8, Xrn2, and Rrp6, as a regulatory mechanism of RNAPII-dependent transcription elongation.

  7. Study of the Response Regulator Rrp1 Reveals Its Regulatory Role in Chitobiose Utilization and Virulence of Borrelia burgdorferi

    PubMed Central

    Sze, Ching Wooen; Smith, Alexis; Choi, Young Hee; Yang, Xiuli; Pal, Utpal; Yu, Aiming

    2013-01-01

    Life cycle alternation between arthropod and mammals forces the Lyme disease spirochete, Borrelia burgdorferi, to adapt to different host milieus by utilizing diverse carbohydrates. Glycerol and chitobiose are abundantly present in the Ixodes tick. B. burgdorferi can utilize glycerol as a carbohydrate source for glycolysis and chitobiose to produce N-acetylglucosamine (GlcNAc), a key component of the bacterial cell wall. A recent study reported that Rrp1, a response regulator that synthesizes cyclic diguanylate (c-di-GMP), governs glycerol utilization in B. burgdorferi. In this report, we found that the rrp1 mutant had growth defects and formed membrane blebs that led to cell lysis when GlcNAc was replaced by chitobiose in the growth medium. The gene chbC encodes a key chitobiose transporter of B. burgdorferi. We found that the expression level of chbC was significantly repressed in the mutant and that constitutive expression of chbC in the mutant successfully rescued the growth defect, indicating a regulatory role of Rrp1 in chitobiose uptake. Immunoblotting and transcriptional studies revealed that Rrp1 is required for the activation of bosR and rpoS and that its impact on chbC is most likely mediated by the BosR-RpoS regulatory pathway. Tick-mouse infection studies showed that although the rrp1 mutant failed to establish infection in mice via tick bite, exogenous supplementation of GlcNAc into unfed ticks partially rescued the infection. The finding reported here provides us with new insight into the regulatory role of Rrp1 in carbohydrate utilization and virulence of B. burgdorferi. PMID:23478317

  8. Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: III. The importance of strand surface roughness in long twist pitch conductors

    DOE PAGESBeta

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

    2016-05-31

    As part of the ITER conductor qualification process, 3 m long Cable-in-Conduit Conductors (CICCs) were tested at the SULTAN facility under conditions simulating ITER operation so as to establish the current sharing temperature, Tcs, as a function of multiple full Lorentz force loading cycles. After a comprehensive evaluation of both the Toroidal Field (TF) and the Central Solenoid (CS) conductors, it was found that Tcs degradation was common in long twist pitch TF conductors while short twist pitch CS conductors showed some Tcs increase. However, one kind of TF conductors containing superconducting strand fabricated by the Bochvar Institute of Inorganicmore » Materials (VNIINM) avoided Tcs degradation despite having long twist pitch. In our earlier metallographic autopsies of long and short twist pitch CS conductors, we observed a substantially greater transverse strand movement under Lorentz force loading for long twist pitch conductors, while short twist pitch conductors had negligible transverse movement. With help from the literature, we concluded that the transverse movement was not the source of Tcs degradation but rather an increase of the compressive strain in the Nb3Sn filaments possibly induced by longitudinal movement of the wires. Like all TF conductors this TF VNIINM conductor showed large transverse motions under Lorentz force loading, but Tcs actually increased, as in all short twist pitch CS conductors. We here propose that the high surface roughness of the VNIINM strand may be responsible for the suppression of the compressive strain enhancement (characteristic of long twist pitch conductors). Furthermore, it appears that increasing strand surface roughness could improve the performance of long twist pitch CICCs.« less

  9. Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: III. The importance of strand surface roughness in long twist pitch conductors

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    As part of the ITER conductor qualification process, 3 m long cable-in-conduit conductors (CICCs) were tested at the SULTAN facility under conditions simulating ITER operation so as to establish the current-sharing temperature, T cs, as a function of multiple full Lorentz force loading cycles. After a comprehensive evaluation of both the toroidal field (TF) and the central solenoid (CS) conductors, it was found that T cs degradation was common in long twist pitch TF conductors while short twist pitch CS conductors showed some T cs increase. However, one kind of TF conductors containing superconducting strand fabricated by the Bochvar Institute of Inorganic Materials (VNIINM) avoided T cs degradation despite having long twist pitch. In our earlier metallographic autopsies of long and short twist pitch CS conductors, we observed a substantially greater transverse strand movement under Lorentz force loading for long twist pitch conductors, while short twist pitch conductors had negligible transverse movement. With help from the literature, we concluded that the transverse movement was not the source of T cs degradation but rather an increase of the compressive strain in the Nb3Sn filaments possibly induced by longitudinal movement of the wires. Like all TF conductors this TF VNIINM conductor showed large transverse motions under Lorentz force loading, but T cs actually increased, as in all short twist pitch CS conductors. We here propose that the high surface roughness of the VNIINM strand may be responsible for the suppression of the compressive strain enhancement (characteristic of long twist pitch conductors). It appears that increasing strand surface roughness could improve the performance of long twist pitch CICCs.

  10. Intermittent androgen deprivation (IAD) in patients with biochemical failure after radical retropubic prostatectomy (RRP) for clinically localized prostate cancer.

    PubMed

    Sciarra, A; Di Chiro, C; Di Silverio, F

    2000-12-01

    We report a study in which our objective was to analyze the clinical response during IAD in patients with biochemical failure after RRP for clinically localized prostate cancer. Between February 1994 and May 1996, 34 patients who exhibited a primary postoperative decrease in PSA to below the detection limit after RRP and then showed PSA progression during follow-up were included as group 1 and 17 patients in whom PSA did not decrease after RRP were included as group 2. Patients were offered IAD when PSA progressed over 0.4 ng/ml in group 1 and over 4.0 ng/ml in group 2. Median follow-up is 184 weeks in group 1 and 206 weeks in group 2. The median time "off" therapy increased from 25% (1st cycle) to 68.7% (5th cycle) of the entire cycle in group 1 and from 33.3% to 58.3% in group 2. Nine out of 12 cases with Gleason score > or =8 failed to respond to IAD and all developed metastatic and/or local failure. No case with Gleason score <7 failed to respond to IAD. Our conclusions suggest that IAD may be effective in patients with biochemical progression after RRP. In our experience, Gleason score seems to be an important variable.

  11. RRP5 is required for formation of both 18S and 5.8S rRNA in yeast.

    PubMed Central

    Venema, J; Tollervey, D

    1996-01-01

    Three of the four eukaryotic ribosomal RNA molecules (18S, 5.8S and 25-28S) are synthesized as a single precursor which is subsequently processed into the mature rRNAs by a complex series of cleavage and modification reactions. In the yeast Saccharomyces cerevisiae, the early pre-rRNA cleavages at sites A0, A1 and A2, required for the synthesis of 18S rRNA, are inhibited in strains lacking RNA or protein components of the U3, U14, snR10 and snR30 small nucleolar ribonucleoproteins (snoRNPs). The subsequent cleavage at site A3, required for formation of the major, short form of 5.8S rRNA, is carried out by another ribonucleoprotein, RNase MRP. A screen for mutations showing synthetic lethality with deletion of the non-essential snoRNA, snR10, identified a novel gene, RRP5, which is essential for viability and encodes a 193 kDa nucleolar protein. Genetic depletion of Rrp5p inhibits the synthesis of 18S rRNA and, unexpectedly, also of the major short form of 5.8S rRNA. Pre-rRNA processing is concomitantly impaired at sites A0, A1, A2 and A3. This distinctive phenotype makes Rrp5p the first cellular component simultaneously required for the snoRNP-dependent cleavage at sites A0, A1 and A2 and the RNase MRP-dependent cleavage at A3 and provides evidence for a close interconnection between these processing events. Putative RRP5 homologues from Caenorhabditis elegans and humans were also identified, suggesting that the critical function of Rrp5p is evolutionarily conserved. Images PMID:8896463

  12. RRP41L, a putative core subunit of the exosome, plays an important role in seed germination and early seedling growth in Arabidopsis.

    PubMed

    Yang, Min; Zhang, Bangyue; Jia, Jianheng; Yan, Chunxia; Habaike, Ayijiang; Han, Yuzhen

    2013-01-01

    In prokaryotic and eukaryotic cells, the 3'-5'-exonucleolytic decay and processing of RNAs are essential for RNA metabolism. However, the understanding of the mechanism of 3'-5'-exonucleolytic decay in plants is very limited. Here, we report the characterization of an Arabidopsis (Arabidopsis thaliana) transfer DNA insertional mutant that shows severe growth defects in early seedling growth, including delayed germination and cotyledon expansion, thinner yellow/pale-green leaves, and a slower growth rate. High-efficiency thermal asymmetric interlaced polymerase chain reaction analysis showed that the insertional locus was in the sixth exon of AT4G27490, encoding a predicted 3'-5'-exonuclease, that contained a conserved RNase phosphorolytic domain with high similarity to RRP41, designated RRP41L. Interestingly, we detected highly accumulated messenger RNAs (mRNAs) that encode seed storage protein and abscisic acid (ABA) biosynthesis and signaling pathway-related protein during the early growth stage in rrp41l mutants. The mRNA decay kinetics analysis for seed storage proteins, 9-cis-epoxycarotenoid dioxygenases, and ABA INSENSITIVEs revealed that RRP41L catalyzed the decay of these mRNAs in the cytoplasm. Consistent with these results, the rrp41l mutant was more sensitive to ABA in germination and root growth than wild-type plants, whereas overexpression lines of RRP41L were more resistant to ABA in germination and root growth than wild-type plants. RRP41L was localized to both the cytoplasm and nucleus, and RRP41L was preferentially expressed in seedlings. Altogether, our results showed that RRP41L plays an important role in seed germination and early seedling growth by mediating specific cytoplasmic mRNA decay in Arabidopsis.

  13. Optimization and test of a 120mm LARP Nb3Sn quadrupole coil using magnetic mirror structure

    SciTech Connect

    Bossert, R.; Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Caspi, S.; Cheng, D.; Chlachidze, G.; Dietderich, D.; Felice, H.; Ferracin, P.; /LBL, Berkeley /Brookhaven /LBL, Berkeley /Fermilab /LBL, Berkeley /Brookhaven

    2011-09-01

    The US-LARP collaboration is developing a new generation of large-aperture high-field quadrupoles based on Nb{sub 3}Sn superconductor for the LHC upgrades. The development and implementation of this new technology involves the fabrication and testing of series of model magnets, coils and other components with various design and processing features. New 120-mm HQ coils made of Rutherford cable, one with an interlayer resistive core, and both with optimized reaction processes, were fabricated and tested using a quadrupole mirror structure under operating conditions similar to those in a real magnet. The coils were instrumented with voltage taps and strain gauges to study the mechanical and quench performance. Quench antenna and temperature gauges were installed in the mirror structure to measure the coil temperature and locate quench origins. This paper presents details of the coil design and fabrication procedures, coil assembly and pre-stress in the quadrupole mirror structure, and coil test results.

  14. Fabrication and Test of 90-mm Nb3Sn Quadrupole Model Based on Dipole-type Collar

    SciTech Connect

    Bossert, R.; Andreev, N.; Chlachidze, G.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; Nobrega, F.; Novitski, I.; Tartaglia, M.; Velev, G.; Zlobin, A.V.; /Fermilab

    2010-07-29

    A series of 90-mm TQC quadrupole models with a collar-based mechanical structure has been fabricated and tested within the framework of the US-LHC Accelerator Research Program (LARP) using quadrupole-symmetric stainless steel collar laminations. This paper describes the design features, construction and test of TQC02Eb, the first TQC made with dipole-type collar and collaring techniques. Magnet test includes quench performance and field quality measurements at 4.5 and 1.9 K. Results of model performance for TQC quadrupoles based on dipole-type and quadrupole-type collars are compared and discussed.

  15. Test Results of HD2, A High Field Nb3Sn Dipole with A 36 MM Bore

    SciTech Connect

    Ferracin, Paolo

    2008-05-19

    The Superconducting Magnet Program at Lawrence Berkeley National Laboratory (LBNL) has developed the 1 m long Nb{sub 3}Sn dipole magnet HD2. With tilted (flared) ends to avoid obstructing a 36 mm clear bore, HD2 represents a step towards the use of block-type coils in high-field accelerator magnets. The coil design has been optimized to minimize geometric harmonics and reduce the conductor peak field in the end region, resulting in an expected short sample dipole field of 15 T. The support structure is composed by an external aluminum shell pre-tensioned with pressurized bladders and interference keys, and by two stainless steel end plates compressing the coil ends through four aluminum axial rods. We report on magnet design, assembly, and test results, including training performance, quench locations, and strain gauge measurements.

  16. Assembly and Test of SQ01b, a Nb3Sn Quadrupole Magnet for the LHC Accelerator Research Program

    SciTech Connect

    Ferracin, P.; Ambrosio, G.; Bartlett, S. E.; Bordini, B.; Carcagno, R.H.; Caspi, S.; Dietderich, D.R.; Feher, S.; Gourlay, S.A.; Hafalia, A.R.; Lamm, M.J.; Lietzke, A.F.; Mattafirri, S.; McInturff, A.D.; Orris, D.F.; Pischalnikov, Y.M.; Sabbi, G.L.; Sylvester, C.D.; Tartaglia, M.A.; Velev, G.V.; Zlobin, A.V.; Kashikhin, V.V.

    2006-06-01

    The US LHC Accelerator Research Program (LARP) consists of four US laboratories (BNL, FNAL, LBNL, and SLAC) collaborating with CERN to achieve a successful commissioning of the LHC and to develop the next generation of Interaction Region magnets. In 2004, a large aperture Nb{sub 3}Sn racetrack quadrupole magnet (SQ01) has been fabricated and tested at LBNL. The magnet utilized four subscale racetrack coils and was instrumented with strain gauges on the support structure and directly over the coil's turns. SQ01 exhibited training quenches in two of the four coils and reached a peak field in the conductor of 10.4 T at a current of 10.6 kA. After the test, the magnet was disassembled, inspected with pressure indicating films, and reassembled with minor modifications. A second test (SQ01b) was performed at FNAL and included training studies, strain gauge measurements and magnetic measurements. Magnet inspection, test results, and magnetic measurements are reported and discussed, and a comparison between strain gauge measurements and 3D finite element computations is presented

  17. A Review of the Properties of Nb3Sn and Their Variation with A15Composition, Morphology and Strain State

    SciTech Connect

    Godeke, Arno

    2006-03-27

    Significant efforts can be found throughout the literature to optimize the current carrying capacity of Nb{sub 3}Sn superconducting wires. The achievable transport current density in wires depends on the A15 composition, morphology and strain state. The A15 sections in wires contain, due to compositional inhomogeneities resulting from solid state diffusion A15 formation reactions, a distribution of superconducting properties. The A15 grain size can be different from wire to wire and is also not necessarily homogeneous across the A15 regions. Strain is always present in composite wires, and the strain state changes as a result of thermal contraction differences and Lorentz forces in magnet systems. To optimize the transport properties it is thus required to identify how composition, grain size and strain state influence the superconducting properties. This is not accurately possible in inhomogeneous and spatially complex systems such as wires. This article therefore gives an overview of the available literature on simplified, well defined(quasi--)homogeneous laboratory samples. After more than 50 years of research on superconductivity in Nb{sub 3}Sn, a significant amount of results are available, but these are scattered over a multitude of publications. Two reviews exist on the basic properties of A15 materials in general, but no specific review for Nb{sub 3}Sn is available. This article is intended to provide such an overview. It starts with a basic description of the Niobium--Tin intermetallic. After this it maps the influence of Sn content on the electron--phonon interaction strength and on the field-temperature phase boundary. The literature on the influence of Cu, Ti and Ta additions will then be briefly summarized.This is followed by a review on the effects of grain size and strain. The article is concluded with a summary of the main results.

  18. Steady State Heat Deposits Modeling in the Nb3Sn Quadrupole Magnets for the Upgrade of the LHC Inner Triplet

    SciTech Connect

    Bocian, D.; Ambrosio, G.; Felice, H.; Barzi, E.; Bossert, R.; Caspi, S.; Chlachidze, G.; Dietderich, D.; Feher, S.; Ferracin, P.; Hafalia, R.; /Fermilab /Lawrence Berkeley Lab /Brookhaven

    2011-09-01

    In hadron colliders such as the LHC, the energy deposited in the superconductors by the particles lost from the beams or coming from the collision debris may provoke quenches detrimental to the accelerator operation. In previous papers, a Network Model has been used to study the thermodynamic behavior of magnet coils and to calculate the quench levels in the LHC magnets for expected beam loss profiles. This model was subsequently used for thermal analysis and design optimization of Nb{sub 3}Sn quadrupole magnets, which LARP (US LHC Accelerator Research Program) is developing for possible use in the LHC luminosity upgrade. For these new magnets, the heat transport efficiency from the coil to the helium bath needs to be determined and optimized. In this paper the study of helium cooling channels and the heat evacuation scheme are presented and discussed.

  19. Field Quality Study of the LARP Nb3Sn 3.7m-Long Quadrupole Models of LQ Series

    SciTech Connect

    AMbrosio, G.; Andreev, N.; Bossert, R.; Chlachidze, G.; DiMarco, J.; Kashikhin, V.V.; Lamm, M.J.; Nobrega, F.; Prebys, E.; Sylvester, C.; Tartaglia, M.; /Fermilab /LBL, Berkeley /Brookhaven

    2011-09-01

    After the successful test of the first long Nb{sub 3}Sn quadrupole magnet (LQS01), the US LHC Accelerator Research Program (LARP) has assembled and tested a new 3.7 m-long Nb{sub 3}Sn quadrupole (LQS02). This magnet has four new coils made of the same conductor as LQS01 coils, and it is using the same support structure. LQS02 was tested at the Fermilab Vertical Magnet Test Facility with the main goal to confirm that the long models can achieve field gradient above 200 T/m, LARP target for 90-mm aperture, as well as to measure the field quality. These long models lack some alignment features and it is important to study the field harmonics. Previous field quality measurements of LQS01 showed higher than expected differences between measured and calculated harmonics compared to the short models (TQS) assembled in a similar structure. These differences could be explained by the use of two different impregnation fixtures during coil fabrication. In this paper, we present a comparison of the field quality measurements between LQS01 and LQS02 as well as a comparison with the short TQS models. If the result supports the coil fabrication hypothesis, another LQS assembly with all coils fabricated in the same fixture will be produced for understanding the cause of the discrepancy between short and long models.

  20. Limits of NbTi and Nb3Sn, and development of W& R Bi-2212 High Field Accelerator Magnets

    SciTech Connect

    Cheng, Daniel; Dietderich, Daniel; Ferrracin, Paolo; Prestemon, Soren; Sabbi, GianLuca; Scanlan, Ron; Godeke, A.

    2007-06-01

    NbTi accelerator dipoles are limited to magnetic fields (H) of about 10 T, due to an intrinsic upper critical field (H{sub c2}) limitation of 14 T. To surpass this restriction, prototype Nb{sub 3}Sn magnets are being developed which have reached 16 T. We show that Nb{sub 3}Sn dipole technology is practically limited to 17 to 18 T due to insufficient high field pinning, and intrinsically to 20 to 22 T due to H{sub c2} limitations. Therefore, to obtain magnetic fields approaching 20 T and higher, a material is required with a higher H{sub c2} and sufficient high field pinning capacity. A realistic candidate for this purpose is Bi-2212, which is available in round wires and sufficient lengths for the fabrication of coils based on Rutherford-type cables. We initiated a program to develop the required technology to construct accelerator magnets from 'wind-and-react' (W&R) Bi-2212 coils. We outline the complications that arise through the use of Bi-2212, describe the development paths to address these issues, and conclude with the design of W&R Bi-2212 sub-scale magnets.

  1. Assembly and Test of a Support Structure for 3.5 m Long Nb3Sn Racetrack Coils.

    SciTech Connect

    Ferracin,P.; Ambrosio, G.; Anerella, M.; Caspi, S.; Cheng, D.W.; Felice, H.; Hafalia, A.R.; Hannaford, C.R.; Lietzke, A.F.; Lizarazo, J.; Muratore, J.; Sabbi, G.L.; Schmalzle, J.; Thomas, R.; Wanderer, P.J.

    2007-08-27

    The LHC Accelerator Research Program (LARP) is currently developing 4 m long Nb{sub 3}Sn quadrupole magnets for a possible upgrade of the LHC Interaction Regions (IR). In order to provide a reliable test bed for the fabrication and test of long Nb{sub 3}Sn coils, LARP has started the development of the long racetrack magnet LRS01. The magnet is composed of two 3.6 m long racetrack coils contained in a support structure based on an aluminum shell pre-tensioned with water-pressurized bladders and interference keys. For the phase-one test of the assembly procedure and loading operation, the structure was pre-stressed at room temperature and cooled down to 77 K with instrumented, solid aluminum 'dummy coils'. Mechanical behavior and stress homogeneity were monitored with strain gauges mounted on the shell and the dummy coils. The dummy coils were replaced with reacted and impregnated Nb{sub 3}Sn coils in a second assembly procedure, followed by cool-down to 4.5 K and powered magnet test. This paper reports on the assembly and loading procedures of the support structure as well as the comparison between strain gauge data and 3D model predictions.

  2. Assembly and Test of a Support Structure for 3.6 m Long Nb3Sn Racetrack Coils

    SciTech Connect

    Ambrosio, G.; Anerella, M.; Caspi, S.; Cheng, D.W.; Felice, H.; Hafalia, A.R.; Hannaford, C.R.; Lietzke, A.F.; Lizarazo, J.; Muratore, J.; Sabbi, G.L.; Schmalzle, J.; Thomas, R.; Wanderer, P.J.; Ferracin, P.

    2008-06-01

    The LHC Accelerator Research Program (LARP) is currently developing 4 m long Nb{sub 3}Sn quadrupole magnets for a possible upgrade of the LHC Interaction Regions (IR). In order to provide a reliable test bed for the fabrication and test of long Nb{sub 3}Sn coils, LARP has started the development of the long racetrack magnet LRS01. The magnet is composed of two 3.6 m long racetrack coils contained in a support structure based on an aluminum shell pre-tensioned with water-pressurized bladders and interference keys. For the phase-one test of the assembly procedure and loading operation, the structure was pre-stressed at room temperature and cooled down to 77 K with instrumented, solid aluminum 'dummy coils'. Mechanical behavior and stress homogeneity were monitored with strain gauges mounted on the shell and the dummy coils. The dummy coils were replaced with reacted and impregnated Nb{sub 3}Sn coils in a second assembly procedure, followed by cool-down to 4.5 K and powered magnet test. This paper report on the assembly and loading procedures of the support structure as well as the comparison between strain gauge data and 3D model predictions.

  3. Design and Fabrication of a Supporting Structure for 3.6m Long Nb3Sn Racetrack Coils

    SciTech Connect

    Ambrosio, G.; Anerella, M.; Barzi, E.; Caspi, Shlomo; Cheng, Daniel; Dietderich, Daniel; Gourlay, Steve; Hafalia, A. Ray; Hannaford, Charles; Lietzke, Alan; Nobrega, A.R.; Sabbi, GianLuca; Schmalzle, J.; Wanderer, R. J; Zlobin, A.V.; Ferracin, P.

    2007-06-01

    As part of the LHC Accelerator Research Program (LARP), three US national laboratories (BNL, FNAL, and LBNL) are currently engaged in the development of superconducting magnets for the LHC Interaction Regions (IR) beyond the current design. As a first step towards the development of long Nb{sub 3}Sn quadrupole magnets, a 3.6 m long structure, based on the LBNL Subscale Common-Coil Magnet design, will be fabricated, assembled, and tested with aluminum-plate 'dummy coils'. The structure features an aluminum shell pre-tensioned over iron yokes using pressurized bladders and locking keys (bladder and key technology). Pre-load homogeneity and mechanical responses are monitored with pressure sensitive films and strain gauges mounted on the aluminum shell and the dummy coils. The details of the design and fabrication are presented and discussed, and the expected mechanical behavior is analyzed with finite element models.

  4. Final Development and test preparation of the first 3.7m long Nb3Sn quadrupole by LARP

    SciTech Connect

    Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bingham, B.; Bocian, D.; Bordini, B.; Bossert, R.; Bottura, L.; Caspi, S.; Chlachidize, G.; /Fermilab /Brookhaven /LBL, Berkeley /CERN

    2009-10-01

    The test of the first LARP (LHC Accelerator Research Program) Long Quadrupole is a significant milestone toward the development of Nb{sub 3}Sn quadrupoles for LHC (Large Hadron Collider) Luminosity Upgrades. These 3.7-m long magnets, scaled from the 1-m long Technological Quadrupoles, are used to develop our capabilities to fabricate and assemble Nb{sub 3}Sn coils and structures with lengths comparable to accelerator magnet dimensions. The long quadruples have a target gradient of 200 T/m in a 90-mm aperture. Pre-stress and support are provided by an Al-shell-based structure pre-loaded using bladders and keys. The coils were fabricated at BNL and FNAL, the shell-based structure was designed and assembled at LBNL, the test is performed at FNAL. In this paper we present the final steps of the development of the first model (LQS01), several upgrades to the test facility, the test results of witness cables, and the short sample limit.

  5. Study of the effects of high temperatures during quenches on the performance of a small Nb(3)Sn racetrack magnet

    SciTech Connect

    Linda Imbasciati et al.

    2004-03-23

    Several high field Nb{sub 3}Sn magnets of different design are under development for future particle accelerators. The high levels of stored energy in these magnets and the high current densities in the conductor can cause high peak temperatures during a quench. The thermal gradients generated in the epoxy-impregnated magnet coils during the fast temperature rise can result in high thermo-mechanical stresses. Considering the sensitivity of Nb{sub 3}Sn to strain and epoxy cracks, it is important to define a maximum acceptable temperature in the coils during a quench which does not cause degradation of the magnet performance. A program was launched at Fermilab to study the effects of thermo-mechanical stress in Nb{sub 3}Sn coils, supported by experiments and by analysis. In collaboration with LBNL, a sub-scaled magnet was built and instrumented to measure the effect of the thermo-mechanical shock during magnet quenches. The magnet consisted of two racetrack coils, assembled in a common coil configuration with a small gap in between. During the test, the magnet reached the maximum field of {approx} 11 T at the short sample current of 9100 A. Temperature excursions up to 400 K did not diminish the magnet quench performance; only after temperature excursions over 430 K, the magnet showed detraining effects, which reduced occasionally the quench current of about 6%. Signs of irreversible degradation (reducing the maximum current of about 3%) appeared only after temperature excursions over 550 K.

  6. Measurements of the persistent current decay and snapback effect in Nb3Sn Fermilab-built accelerator prototype magnets

    SciTech Connect

    Velev, G.V.; Chlachidze, G.; DiMarco, J.; Kashikhin, V.V.; /Fermilab

    2012-05-01

    In recent years, Fermilab has been performing an intensive R an D program on Nb{sub 3}Sn accelerator magnets. This program has included dipole and quadrupole magnets for different programs and projects, including LARP and VLHC. A systematic study of the persistent current decay and snapback effect in the fields of these magnets was executed at the Fermilab Magnet Test Facility. The decay and snapback were measured under a range of conditions including variations of the current ramp parameters and flattop and injection plateau durations. This study has mostly focused on the dynamic behavior of the normal sextupole and dodecapole components in dipole and quadrupole magnets respectively. The paper summarizes the recent measurements and presents a comparison with previously measured NbTi magnets.

  7. Use of High Resolution DAQ System to Aid Diagnosis of HD2b, a High Performance Nb3Sn Dipole

    SciTech Connect

    Lizarazo, J.; Doering, D.; Doolittle, L.; Galvin, J.; Caspi, S.; Dietderich, D. R.; Felice, H.; Ferracin, P.; Godeke, A.; Joseph, J.; Lietzke, A. F.; Ratti, A.; Sabbi, G. L.; Trillaud, F.; Wang, X.; Zimmerman, S.

    2008-08-17

    A novel voltage monitoring system to record voltage transients in superconducting magnets is being developed at LBNL. This system has 160 monitoring channels capable of measuring differential voltages of up to 1.5kV with 100kHz bandwidth and 500kS/s digitizing rate. This paper presents analysis results from data taken with a 16 channel prototype system. From that analysis we were able to diagnose a change in the current-temperature margin of the superconducting cable by analyzing Flux-Jump data collected after a magnet energy extraction failure during testing of a high field Nb{sub 3}Sn dipole.

  8. ASSEMBLY AND TEST OF A 120 MM BORE 15 T NB3SN QUADRUPOLE FOR THE LHC UPGRADE

    SciTech Connect

    Felice, H.; Caspi, S.; Cheng, D.; Dietderich, D.; Ferracin, P.; Hafalia, R.; Joseph, J.; Lizarazo, J.; Sabbi, G. L.; Wang, X.; Anerella, M.; Ghosh, A. K.; Schmalzle, J.; Wanderer, P.; Ambrosio, G.; Bossert, R.; Zlobin, A. V.

    2010-05-23

    In support of the Large Hadron Collider (LHC) luminosity upgrade, the US LHC Accelerator Research Program (LARP) has been developing a 1-meter long, 120 mm bore Nb{sub 3}Sn IR quadrupole magnet (HQ). With a design short sample gradient of 219 T/m at 1.9 K and a peak field approaching 15 T, one of the main challenges of this magnet is to provide appropriate mechanical support to the coils. Compared to the previous LARP Technology Quadrupole and Long Quadrupole magnets, the purpose of HQ is also to demonstrate accelerator quality features such as alignment and cooling. So far, 8 HQ coils have been fabricated and 4 of them have been assembled and tested in HQ01a. This paper presents the mechanical assembly and test results of HQ01a.

  9. 2D/3D quench simulation using ANSYS for epoxy impregnated Nb3Sn high field magnets

    SciTech Connect

    Ryuji Yamada et al.

    2002-09-19

    A quench program using ANSYS is developed for the high field collider magnet for three-dimensional analysis. Its computational procedure is explained. The quench program is applied to a one meter Nb{sub 3}Sn high field model magnet, which is epoxy impregnated. The quench simulation program is used to estimate the temperature and mechanical stress inside the coil as well as over the whole magnet. It is concluded that for the one meter magnet with the presented cross section and configuration, the thermal effects due to the quench is tolerable. But we need much more quench study and improvements in the design for longer magnets.

  10. Development of TQC01, a 90mm Nb3Sn model quadrupole for LHC upgrade based on ss collar

    SciTech Connect

    Bossert, R.C.; Ambrosio, G.; Andreev, N.; Barzi, E.; Caspi, S.; Dietderich, D.R.; Ferracin, P.; Ghosh, A.; Gourlay, S.A.; Hafalia, A.R.; Hannaford, C.R.; Kashikhin, V.S.; Kashikhin, V.V.; Lietzke, A.F.; Mattafirri, S.; McInturff, A.D.; Novitski, I.; Sabbi, G.L.; Turrioni, D.; Whitson, G.; Yamada, r.; /Fermilab /LBL, Berkeley /Brookhaven

    2005-10-01

    As a first step toward the development of a large-aperture Nb{sub 3}Sn superconducting quadrupole for the Large Hadron Collider (LHC) luminosity upgrade, two-layer technological quadrupole models (TQS01 at LBNL and TQC01 at Fermilab) are being constructed within the framework of the US LHC Accelerator Research Program (LARP). Both models use the same coil design, but have different coil support structures. This paper describes the TQC01 design, fabrication technology and summarizes its main parameters.

  11. A Nucleolar Protein, Ribosomal RNA Processing 1 Homolog B (RRP1B), Enhances the Recruitment of Cellular mRNA in Influenza Virus Transcription

    PubMed Central

    Su, Wen-Chi; Hsu, Shih-Feng; Lee, Yi-Yuan; Jeng, King-Song

    2015-01-01

    ABSTRACT Influenza A virus (IAV) undergoes RNA transcription by a unique capped-mRNA-dependent transcription, which is carried out by the viral RNA-dependent RNA polymerase (RdRp), consisting of the viral PA, PB1, and PB2 proteins. However, how the viral RdRp utilizes cellular factors for virus transcription is not clear. Previously, we conducted a genome-wide pooled short hairpin RNA (shRNA) screen to identify host factors important for influenza A virus replication. Ribosomal RNA processing 1 homolog B (RRP1B) was identified as one of the candidates. RRP1B is a nucleolar protein involved in ribosomal biogenesis. Upon IAV infection, part of RRP1B was translocated from the nucleolus to the nucleoplasm, where viral RNA synthesis likely takes place. The depletion of RRP1B significantly reduced IAV mRNA transcription in a minireplicon assay and in virus-infected cells. Furthermore, we showed that RRP1B interacted with PB1 and PB2 of the RdRp and formed a coimmunoprecipitable complex with RdRp. The depletion of RRP1B reduced the amount of capped mRNA in the RdRp complex. Taken together, these findings indicate that RRP1B is a host factor essential for IAV transcription and provide a target for new antivirals. IMPORTANCE Influenza virus is an important human pathogen that causes significant morbidity and mortality and threatens the human population with epidemics and pandemics every year. Due to the high mutation rate of the virus, antiviral drugs targeting viral proteins might ultimately lose their effectiveness. An alternative strategy that explores the genetic stability of host factors indispensable for influenza virus replication would thus be desirable. Here, we characterized the rRNA processing 1 homolog B (RRP1B) protein as an important cellular factor for influenza A virus transcription. We showed that silencing RRP1B hampered viral RNA-dependent RNA polymerase (RdRp) activity, which is responsible for virus transcription and replication. Furthermore, we

  12. Intrinsic variability in Pv, RRP size, Ca(2+) channel repertoire, and presynaptic potentiation in individual synaptic boutons.

    PubMed

    Ariel, Pablo; Hoppa, Michael B; Ryan, Timothy A

    2012-01-01

    The strength of individual synaptic contacts is considered a key modulator of information flow across circuits. Presynaptically the strength can be parsed into two key parameters: the size of the readily releasable pool (RRP) and the probability that a vesicle in that pool will undergo exocytosis when an action potential fires (Pv). How these variables are controlled and the degree to which they vary across individual nerve terminals is crucial to understand synaptic plasticity within neural circuits. Here we report robust measurements of these parameters in rat hippocampal neurons and their variability across populations of individual synapses. We explore the diversity of presynaptic Ca(2+) channel repertoires and evaluate their effect on synaptic strength at single boutons. Finally, we study the degree to which synapses can be differentially modified by a known potentiator of presynaptic function, forskolin. Our experiments revealed that both Pv and RRP spanned a large range, even for synapses made by the same axon, demonstrating that presynaptic efficacy is governed locally at the single synapse level. Synapses varied greatly in their dependence on N or P/Q type Ca(2+) channels for neurotransmission, but there was no association between specific channel repertoires and synaptic efficacy. Increasing cAMP concentration using forskolin enhanced synaptic transmission in a Ca(2+)-independent manner that was inversely related with a synapse's initial Pv, and independent of its RRP size. We propose a simple model based on the relationship between Pv and calcium entry that can account for the variable potentiation of synapses based on initial probability of vesicle fusion.

  13. Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis.

    PubMed

    Moriggi, Giulia; Nieto, Blanca; Dosil, Mercedes

    2014-12-01

    During the biogenesis of small ribosomal subunits in eukaryotes, the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm. The mechanisms underlying the nuclear export of these particles and its coordination with other biogenesis steps are mostly unknown. Here we show that yeast Rrp12 is required for the exit of pre-40S particles to the cytoplasm and for proper maturation dynamics of upstream 90S pre-ribosomes. Due to this, in vivo elimination of Rrp12 leads to an accumulation of nucleoplasmic 90S to pre-40S transitional particles, abnormal 35S pre-rRNA processing, delayed elimination of processing byproducts, and no export of intermediate pre-40S complexes. The exportin Crm1 is also required for the same pre-ribosome maturation events that involve Rrp12. Thus, in addition to their implication in nuclear export, Rrp12 and Crm1 participate in earlier biosynthetic steps that take place in the nucleolus. Our results indicate that, in the 40S subunit synthesis pathway, the completion of early pre-40S particle assembly, the initiation of byproduct degradation and the priming for nuclear export occur in an integrated manner in late 90S pre-ribosomes.

  14. Effect of Dual Cathode Buffer Layer on the Charge Carrier Dynamics of rrP3HT:PCBM Based Bulk Heterojunction Solar Cell.

    PubMed

    Singh, Ashish; Dey, Anamika; Das, Dipjyoti; Iyer, Parameswar Krishnan

    2016-05-01

    In bulk heterojunction (BHJ) solar cells, the buffer layer plays a vital role in enhancing the power conversion efficiency (PCE) by improving the charge carrier dynamics. A comprehensive understanding of the contacts is especially essential in order to optimize the performance of organic solar cells (OSCs). Although there are several fundamental reports on this subject, a proper correlation of the physical processes with experimental evidence at the photoactive layer and contact materials is essential. In this work, we incorporated three different additional buffer layers, namely, tris(8-hydroxyquinolinato) aluminum (Alq3), bathophenanthroline (BPhen) or bathocuproine (BCP) with LiF/Al as conventional cathode contact in both rrP3HT:PC61BM and rrP3HT:PC71BM blend BHJ solar cells and their corresponding photovoltaic performances were systematically correlated with their energy level diagram. The device with dual cathode buffer layer having ITO/PEDOT:PSS/blend polymer/BCP/LiF/Al configuration showed the best device performance with PCE, η = 4.96%, Jsc = 13.53 mA/cm(2), Voc = 0.60 V and FF= 61% for rrP3HT:PC71BM and PCE, η = 4.5% with Jsc = 13.3 mA/cm(2), Voc = 0.59 V and FF = 59% for rrP3HT:PC61BM. This drastic improvement in PCE in both the device configurations are due to the combined effects of better hole-blocking capacity of BCP and low work function provided by LiF/Al with the blend polymer. These results successfully explain the role of dual cathode buffer layers and their contribution to the PCE improvement and overall device performance with rrP3HT:PCBM based BHJ solar cell. PMID:27075007

  15. Effect of Dual Cathode Buffer Layer on the Charge Carrier Dynamics of rrP3HT:PCBM Based Bulk Heterojunction Solar Cell.

    PubMed

    Singh, Ashish; Dey, Anamika; Das, Dipjyoti; Iyer, Parameswar Krishnan

    2016-05-01

    In bulk heterojunction (BHJ) solar cells, the buffer layer plays a vital role in enhancing the power conversion efficiency (PCE) by improving the charge carrier dynamics. A comprehensive understanding of the contacts is especially essential in order to optimize the performance of organic solar cells (OSCs). Although there are several fundamental reports on this subject, a proper correlation of the physical processes with experimental evidence at the photoactive layer and contact materials is essential. In this work, we incorporated three different additional buffer layers, namely, tris(8-hydroxyquinolinato) aluminum (Alq3), bathophenanthroline (BPhen) or bathocuproine (BCP) with LiF/Al as conventional cathode contact in both rrP3HT:PC61BM and rrP3HT:PC71BM blend BHJ solar cells and their corresponding photovoltaic performances were systematically correlated with their energy level diagram. The device with dual cathode buffer layer having ITO/PEDOT:PSS/blend polymer/BCP/LiF/Al configuration showed the best device performance with PCE, η = 4.96%, Jsc = 13.53 mA/cm(2), Voc = 0.60 V and FF= 61% for rrP3HT:PC71BM and PCE, η = 4.5% with Jsc = 13.3 mA/cm(2), Voc = 0.59 V and FF = 59% for rrP3HT:PC61BM. This drastic improvement in PCE in both the device configurations are due to the combined effects of better hole-blocking capacity of BCP and low work function provided by LiF/Al with the blend polymer. These results successfully explain the role of dual cathode buffer layers and their contribution to the PCE improvement and overall device performance with rrP3HT:PCBM based BHJ solar cell.

  16. The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation

    PubMed Central

    Khoshnevis, Sohail; Askenasy, Isabel; Dattolo, Maria D.; Young-Erdos, Crystal L.; Stroupe, M. Elizabeth; Karbstein, Katrin

    2016-01-01

    DEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed “helicases,” their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S ribosomes. Interconversion between these two forms by ATP hydrolysis is required for release of Rrp5 from pre-40S ribosomes in vivo, thereby allowing Rrp5 to carry out its role in 60S subunit assembly. Furthermore, our data also strongly suggest that the previously described accumulation of snR30 upon Rok1 inactivation arises because Rrp5 release is blocked and implicate a previously undescribed interaction between Rrp5 and the DEAD-box protein Has1 in mediating snR30 accumulation when Rrp5 release from pre-40S subunits is blocked. PMID:27280440

  17. The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation.

    PubMed

    Khoshnevis, Sohail; Askenasy, Isabel; Johnson, Matthew C; Dattolo, Maria D; Young-Erdos, Crystal L; Stroupe, M Elizabeth; Karbstein, Katrin

    2016-06-01

    DEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S ribosomes. Interconversion between these two forms by ATP hydrolysis is required for release of Rrp5 from pre-40S ribosomes in vivo, thereby allowing Rrp5 to carry out its role in 60S subunit assembly. Furthermore, our data also strongly suggest that the previously described accumulation of snR30 upon Rok1 inactivation arises because Rrp5 release is blocked and implicate a previously undescribed interaction between Rrp5 and the DEAD-box protein Has1 in mediating snR30 accumulation when Rrp5 release from pre-40S subunits is blocked. PMID:27280440

  18. [Mid-term outcomes and survival rates in patients with radical retropubic prostatectomy (RRP) under current Czech healthcare system].

    PubMed

    Safarík, L; Bílek, R; Vísek, J A; Novák, K; Tuíková, J; Pesl, M; Stolz, J; Dvorácek, J

    2009-01-01

    The mid-term results (5 yr) after radical retropubic prostatectomy (RRP) are outlined and compared with pre- and postoperative parameters of patients. While 5 years survival could be expected in as many as 92.4%, relatively higher age (majority over 65) brings a higher risk of complications with it, though fully comparable with international standards. No perioperative mortality was recorded (0%), obstructive symptoms post-operatively developed in 13.4% patients, who were subsequently managed successfully endoscopically. Continence with maximum one pad per 24 hours was recorded in 77.2%, the severe incontinence was only in 3.3%. Spontaneous erection was reported in 4.3%, but except for higher age, the other objective factors were involved.

  19. Characterization of High Current RRP(R) Wires as a Function of Magnetic Field, Temperature and Strain

    SciTech Connect

    Godeke, A.; Mentink, M.G.T.; Dietderich, D. R.; den Ouden, A.

    2009-08-16

    A new instrument for the characterization of superconducting materials as a function of Magnetic Field, Temperature and Strain, was designed, constructed and tested at Lawrence Berkeley National Laboratory (LBNL). A U-shaped bending spring was selected, since that design has proven to enable accurate characterizations of a multitude of superconducting materials for more than a decade. The new device is validated though measurements on very high current Rod Restack Processed (RRP) Internal-Tin (IT) wires, for which we will present initial results, including parameterizations of the superconducting phase boundaries and comparisons with other wire types. Accurate parametrization of modern high magnetic field conductors is important for the analysis of the performance of magnet systems.

  20. tRNA 3′ processing in yeast involves tRNase Z, Rex1, and Rrp6

    PubMed Central

    Skowronek, Ewa; Grzechnik, Pawel; Späth, Bettina; Marchfelder, Anita; Kufel, Joanna

    2014-01-01

    Mature tRNA 3′ ends in the yeast Saccharomyces cerevisiae are generated by two pathways: endonucleolytic and exonucleolytic. Although two exonucleases, Rex1 and Rrp6, have been shown to be responsible for the exonucleolytic trimming, the identity of the endonuclease has been inferred from other systems but not confirmed in vivo. Here, we show that the yeast tRNA 3′ endonuclease tRNase Z, Trz1, is catalyzing endonucleolytic tRNA 3′ processing. The majority of analyzed tRNAs utilize both pathways, with a preference for the endonucleolytic one. However, 3′-end processing of precursors with long 3′ trailers depends to a greater extent on Trz1. In addition to its function in the nucleus, Trz1 processes the 3′ ends of mitochondrial tRNAs, contributing to the general RNA metabolism in this organelle. PMID:24249226

  1. Stressed Kevlar strand test

    SciTech Connect

    Golopol, H.; Clarkson, J.; Moore, R.; Hetherington, N.

    1981-09-10

    Kevlar is a polyaramid fiber used in fiber composites. In order to characterize this material, we determined the effect of time, temperature, and chemical environment on the strength retention of stressed Kevlar strands. In this work, we applied a stress load of 20% of the ultimate tensile strength (UTS). Strands were hung with a suitable weight in a closed container. Each container was then provided with its own heater and chemical environment. No significant loss of strength retention was found on these stressed strands. 4 figures, 5 tables.

  2. Secretome analysis of chickpea reveals dynamic extracellular remodeling and identifies a Bet v1-like protein, CaRRP1 that participates in stress response

    PubMed Central

    Gupta, Sonika; Wardhan, Vijay; Kumar, Amit; Rathi, Divya; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, Niranjan

    2015-01-01

    Secreted proteins maintain cell structure and biogenesis besides acting in signaling events crucial for cellular homeostasis during stress adaptation. To understand the underlying mechanism of stress-responsive secretion, the dehydration-responsive secretome was developed from suspension-cultured cells of chickpea. Cell viability of the suspension culture remained unaltered until 96 h, which gradually declined at later stages of dehydration. Proteomic analysis led to the identification of 215 differentially regulated proteins, involved in a variety of cellular functions that include metabolism, cell defence, and signal transduction suggesting their concerted role in stress adaptation. One-third of the secreted proteins were devoid of N-terminal secretion signals suggesting a non-classical secretory route. Screening of the secretome identified a leaderless Bet v 1-like protein, designated CaRRP1, the export of which was inhibited by brefeldin A. We investigated the gene structure and genomic organization and demonstrated that CaRRP1 may be involved in stress response. Its expression was positively associated with abiotic and biotic stresses. CaRRP1 could complement the aberrant growth phenotype of yeast mutant, deficient in vesicular transport, indicating a partial overlap of protein secretion and stress response. Our study provides the most comprehensive analysis of dehydration-responsive secretome and the complex metabolic network operating in plant extracellular space. PMID:26678784

  3. Distinct 18S rRNA precursors are targets of the exosome complex, the exoribonuclease RRP6L2 and the terminal nucleotidyltransferase TRL in Arabidopsis thaliana.

    PubMed

    Sikorski, Pawel J; Zuber, Hélène; Philippe, Lucas; Sement, François M; Canaday, Jean; Kufel, Joanna; Gagliardi, Dominique; Lange, Heike

    2015-09-01

    The biosynthesis of ribosomal RNA and its incorporation into functional ribosomes is an essential and intricate process that includes production of mature ribosomal RNA from large precursors. Here, we analyse the contribution of the plant exosome and its co-factors to processing and degradation of 18S pre-RNAs in Arabidopsis thaliana. Our data show that, unlike in yeast and humans, an RRP6 homologue, the nucleolar exoribonuclease RRP6L2, and the exosome complex, together with RRP44, function in two distinct steps of pre-18S rRNA processing or degradation in Arabidopsis. In addition, we identify TRL (TRF4/5-like) as the terminal nucleotidyltransferase that is mainly responsible for oligoadenylation of rRNA precursors in Arabidopsis. We show that TRL is required for efficient elimination of the excised 5' external transcribed spacer and of 18S maturation intermediates that escaped 5' processing. Our data also suggest involvement of additional nucleotidyltransferases, including terminal uridylyltransferase(s), in modifying rRNA processing intermediates in plants.

  4. Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger ribonucleoprotein particle (mRNP) in yeast.

    PubMed

    Stuparevic, Igor; Mosrin-Huaman, Christine; Hervouet-Coste, Nadège; Remenaric, Mateja; Rahmouni, A Rachid

    2013-11-01

    The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs.

  5. Cotranscriptional Recruitment of RNA Exosome Cofactors Rrp47p and Mpp6p and Two Distinct Trf-Air-Mtr4 Polyadenylation (TRAMP) Complexes Assists the Exonuclease Rrp6p in the Targeting and Degradation of an Aberrant Messenger Ribonucleoprotein Particle (mRNP) in Yeast*

    PubMed Central

    Stuparevic, Igor; Mosrin-Huaman, Christine; Hervouet-Coste, Nadège; Remenaric, Mateja; Rahmouni, A. Rachid

    2013-01-01

    The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated. Using an experimental approach in which mRNP formation in yeast is disturbed by the action of the bacterial Rho helicase, we have shown previously that the targeting of Rho-induced aberrant mRNPs is mediated by Rrp6p, which is recruited cotranscriptionally in association with Nrd1p following Rho action. Here we investigated the specific involvement in this quality control process of different cofactors associated with the nuclear RNA degradation machinery. We show that, in addition to the main hydrolytic action of the exonuclease Rrp6p, the cofactors Rrp47p, Mpp6p as well as the Trf-Air-Mtr4 polyadenylation (TRAMP) components Trf4p, Trf5p, and Air2p contribute significantly by stimulating the degradation process upon their cotranscriptional recruitment. Trf4p and Trf5p are apparently recruited in two distinct TRAMP complexes that both contain Air2p as component. Surprisingly, Rrp47p appears to play an important role in mutual protein stabilization with Rrp6p, which highlights a close association between the two partners. Together, our results provide an integrated view of how different cofactors of the RNA degradation machinery cooperate to target and eliminate aberrant mRNPs. PMID:24047896

  6. Test Results of LARP 3.6 m Nb3Sn Racetrack Coils Support by Full-length and Segmented Shell Structures

    SciTech Connect

    Muratore, Joseph F.; Ambrosio, Giorgio; Anerella, Michael; Barzi, Emanuela; Bossert, Rodger; Caspi, Shlomo; Cheng, D. W.; Cozzolino, John; Dietderich, Daniel R.; Escallier, John; Feher, Sandor; Felice, Helene; Ferracin, Paolo; Ganetis, George; Ghosh, Arup K.; Gupta, Ramesh C.; Hafalia, A. R.; Hannaford, C. R.; Joshi, Piyush; Kovach, Paul; Lietzke, A. F.; Louie, Wing; Marone, Andrew; McInturff, Al D.; Nobrega, F.; Sabbi, GianLuca; Schmalzle, Jesse; Thomas, Richard; Turrioni, Daniele; Wanderer, Peter

    2008-08-17

    As part of the LHC Accelerator Research Program (LARP) to build a high performance quadrupole magnet with Nb{sub 3}Sn conductor, a pair of 3.6 m-long Nb{sub 3}Sn racetrack coils has been made at Brookhaven National Laboratory (BNL) and installed in two shell-type support structures built by Lawrence Berkeley National Laboratory (LBL). These magnet assemblies have been tested at 4.5 K at BNL to gauge the effect of extended length and prestress on the mechanical performance of the long structure compared to earlier short models. This paper presents the results of quench testing and compares the overall performance of the two versions of the support structure. We also summarize the shell strain measurements and discuss the variation of quench current with ramp rate.

  7. Assembly and Loading of LQS01, a Shell-Based 3.7 m Long Nb3Sn Quadrupole Magnet for LARP

    SciTech Connect

    Ferracin, P.; Ambrosio, G.; Anerella, M.; Bingham, B.; Bossert, R.; Caspi, S.; Cheng, D. W.; Chlachidze, G.; Felice, H.; Hafalia, A. R.; Hannaford, C. R.; Mumper, W.; Nobrega, F.; Prestemon, S.; Sabbi, G. L.; Schmalzle, J.; Sylvester, C.; Tartaglia, M.; Wanderer, P.; Zlobin, A.

    2009-10-19

    The LHC Accelerator Research Program (LARP) has been engaged in the fabrication of the 3.7 m long quadrupole magnet LQS01 in order to demonstrate that Nb{sub 3}Sn magnets are a viable option for future LHC Luminosity upgrades. The LQS01 design, a scale-up of the 1 m long Technology Quadrupole TQS, includes four 3.4 m long cos(theta) coils contained in a support structure based on four 1 m long aluminum shells pre-tensioned with water-pressurized bladders (shell-type structure). In order to verify assembly procedures and loading operations, the structure was pre-stressed around solid aluminum 'dummy coils' and cooled-down to 77 K. Mechanical behavior and stress variations were monitored with strain gauges mounted on the structure and on the dummy coils. The dummy coils were then replaced with Nb{sub 3}Sn coils in a second assembly and loading procedure, in preparation for the cool-down and test. This paper reports on the cool-down test with dummy coils and on the assembly and loading of LQS01, with a comparison between 3D finite element model predictions and strain gauge data.

  8. Fabrication and Test of a 3.7 m Long Support Structure for the LARP Nb3Sn Quadrupole Magnet LQS01

    SciTech Connect

    Ferracin, P.; Ambrosio, G.; Anerella, M.; Bingham, B.; Bossert, R.; Caspi, S.; Cheng, D.W.; Felice, H.; Hafalia, A. R.; Hannaford, C. R.; Nobrega, F.; Prestemon, S.; Sabbi, G. L.; Schmalzle, J.; Trillaud, F.; Wanderer, P.; Zlobin, A. V.

    2008-08-17

    The 3.7 m long quadrupole magnet LQS01 represents a major step of the US LHC Accelerator Research Program (LARP) towards the development of long Nb{sub 3}Sn accelerator quadrupole magnets for a LHC Luminosity upgrade. The magnet support structure is a scale up of the 1 m long Technology Quadrupole TQS design with some modifications suggested by TQS model test results. It includes an aluminum shell pre-tensioned over iron yokes using pressurized bladders and locking keys (bladder and key technology). The axial support is provided by two stainless steel end plates compressed against the coil ends by four stainless steel rods. The structure, instrumented with strain gauges, has been fabricated and assembled around four aluminum 'dummy coils' to determine pre-load homogeneity and mechanical characteristics during cool-down. After presenting the main magnetic and mechanical parameters of LQS01, we report in this paper on the design, assembly, and test of the support structure, with a comparison between strain gauges data and 3D finite element model results.

  9. Design and Analysis of TQS01, a 90 mm Nb3Sn Model Quadrupole for LHC Luminosity Upgrade Based on a Key and Bladder Assembly

    SciTech Connect

    Caspi, S.; Ambrosio, G.; Andreev, N.; Barzi, E.; Bossert, R.C.; Dietderich, D.R.; Ferracin, P.; Ghosh, A.; Gourlay, S.A.; Hafalia, A.R.; Hannaford, C.R.; Kashikhin, V.S.; Kashikhin, V.V.; Lietzke, A.F.; Mattafirri, S.; McInturff, A.D.; Novitsky, I.V.; Sabbi, G.L.; Turrioni, D.; Yamada, R.; Zlobin, A.V.

    2006-06-01

    The US LHC Accelerator Research Program (LARP) is developing Nb{sub 3}Sn accelerator magnet technology for the LHC luminosity upgrade. Two 90 mm 'Technology Quadrupole' models (TQS01, TQC01) are being developed in close collaboration between LBNL and FNAL, using identical coil design, but two different support structures. The TQS01 structure was developed and tested at LBNL. With this approach coils are supported by an outer aluminum shell and assembled using keys and bladders. In contrast, the second model TQC01, utilize stainless steel collars and a thick stainless steel skin. This paper describes the TQS01 model magnet, its 3D ANSYS stress analysis, and anticipated instrumentation and assembly procedure.

  10. Cryptography with DNA binary strands.

    PubMed

    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'.

  11. Report on marine mammal stranding

    NASA Astrophysics Data System (ADS)

    Kumar, Mohi

    2006-06-01

    The U.S. National Oceanic and Atmospheric Administration (NOAA) released a report on 27 April indicating that U.S. Navy sonar transmissions may have played a role in the stranding of more than 150 melon-headed whales on 3 July 2004 off the coast of Kauai, Hawaii. At the time of the stranding, which resulted in one whale death, the Navy was preparing to conduct sonar activities as part of a military exercise. The report notes that six naval surface vessels transiting to the area on the previous night intermittenly transmitted mid-frequency active sonar. That activity is ``a plausible, if not likely, contributing factor'' to the stranding event. There was no significant weather, natural oceanographic event, or known biological factors that would explain the animals' movement into the bay nor the group's continued presence in the bay, according to report lead author Teri Rowles, NOAA marine mammal veterinarian.

  12. Double stranded nucleic acid biochips

    DOEpatents

    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.

  13. Library construction for ancient genomics: single strand or double strand?

    PubMed

    Bennett, E Andrew; Massilani, Diyendo; Lizzo, Giulia; Daligault, Julien; Geigl, Eva-Maria; Grange, Thierry

    2014-06-01

    A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from different library construction methods on a diversity of ancient DNA samples. In addition, the single-stranded method is limited by high cost and lengthy preparation time and is restricted to the Illumina sequencing platform. Here we present in-depth comparisons of the different available library construction methods for DNA purified from 16 ancient and modern faunal and human remains, covering a range of different taphonomic and climatic conditions. We further present a DNA purification method for ancient samples that permits the concentration of a large volume of dissolved extract with minimal manipulation and methodological improvements to the single-stranded method to render it more economical and versatile, in particular to expand its use to both the Illumina and the Ion Torrent sequencing platforms. We show that the single-stranded library construction method improves the relative recovery of endogenous to exogenous DNA for most, but not all, of our ancient extracts.

  14. Library construction for ancient genomics: single strand or double strand?

    PubMed

    Bennett, E Andrew; Massilani, Diyendo; Lizzo, Giulia; Daligault, Julien; Geigl, Eva-Maria; Grange, Thierry

    2014-06-01

    A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from different library construction methods on a diversity of ancient DNA samples. In addition, the single-stranded method is limited by high cost and lengthy preparation time and is restricted to the Illumina sequencing platform. Here we present in-depth comparisons of the different available library construction methods for DNA purified from 16 ancient and modern faunal and human remains, covering a range of different taphonomic and climatic conditions. We further present a DNA purification method for ancient samples that permits the concentration of a large volume of dissolved extract with minimal manipulation and methodological improvements to the single-stranded method to render it more economical and versatile, in particular to expand its use to both the Illumina and the Ion Torrent sequencing platforms. We show that the single-stranded library construction method improves the relative recovery of endogenous to exogenous DNA for most, but not all, of our ancient extracts. PMID:24924389

  15. Heat transfer characteristics of an emergent strand

    NASA Technical Reports Server (NTRS)

    Simon, W. E.; Witte, L. C.; Hedgcoxe, P. G.

    1974-01-01

    A mathematical model was developed to describe the heat transfer characteristics of a hot strand emerging into a surrounding coolant. A stable strand of constant efflux velocity is analyzed, with a constant (average) heat transfer coefficient on the sides and leading surface of the strand. After developing a suitable governing equation to provide an adequate description of the physical system, the dimensionless governing equation is solved with Laplace transform methods. The solution yields the temperature within the strand as a function of axial distance and time. Generalized results for a wide range of parameters are presented, and the relationship of the results and experimental observations is discussed.

  16. Unraveling the strands of Saturn's F ring

    USGS Publications Warehouse

    Murray, C.D.; Gordon, M.K.; Giuliatti, Winter S.M.

    1997-01-01

    Several high-resolution Voyager 2 images of Saturn's F ring show that it is composed of at least four separate, non-intersecting strands extending ~45?? in longitude. Voyager 1 images show that the two brightest strands appear to intersect, giving rise to a "braided" morphology. From a study of all available Voyager images the detectable radial structure is cataloged and reviewed. Previous indications that there is fine material interior to the orbit of the F ring are confirmed. Evidence is presented that a model of four strands with comparable eccentricities and nearly aligned perichrones is consistent with all the Voyager observations. The observed perichrone offset of the two brightest strands suggests a minimum radial separation of ~20 km, which implies intersection of these strands when their finite radial widths are taken into account. The longitude range of such an intersection includes that observed in the Voyager 1 "braid" images. The proximity of these two strands at some longitudes may account for the apparent differences in the ring between the Voyager encounters, as well as provide a source for the short-lived features detected in the Hubble Space Telescope images of the F ring. There is no evidence that the locations of the individual strands are determined by resonant perturbations with known satellites. It is proposed that the radial structure is formed by the localized action of small satellites orbiting within the strand region. ?? 1997 Academic Press.

  17. Magnet design considerations for Fusion Nuclear Science Facility

    DOE PAGESBeta

    Zhai, Yuhu; Kessel, Chuck; El-guebaly, Laila; Titus, Peter

    2016-02-25

    The Fusion Nuclear Science Facility (FNSF) is a nuclear confinement facility to provide a fusion environment with components of the reactor integrated together to bridge the technical gaps of burning plasma and nuclear science between ITER and the demonstration power plant (DEMO). Compared to ITER, the FNSF is smaller in size but generates much higher magnetic field, 30 times higher neutron fluence with 3 orders of magnitude longer plasma operation at higher operating temperatures for structures surrounding the plasma. Input parameters to the magnet design from system code analysis include magnetic field of 7.5 T at the plasma center withmore » plasma major radius of 4.8 m and minor radius of 1.2 m, and a peak field of 15.5 T on the TF coils for FNSF. Both low temperature superconductor (LTS) and high temperature superconductor (HTS) are considered for the FNSF magnet design based on the state-of-the-art fusion magnet technology. The higher magnetic field can be achieved by using the high performance ternary Restack Rod Process (RRP) Nb3Sn strands for toroidal field (TF) magnets. The circular cable-in-conduit conductor (CICC) design similar to ITER magnets and a high aspect ratio rectangular CICC design are evaluated for FNSF magnets but low activation jacket materials may need to be selected. The conductor design concept and TF coil winding pack composition and dimension based on the horizontal maintenance schemes are discussed. Neutron radiation limits for the LTS and HTS superconductors and electrical insulation materials are also reviewed based on the available materials previously tested. As a result, the material radiation limits for FNSF magnets are defined as part of the conceptual design studies for FNSF magnets.« less

  18. Stranded investment and non-utility generation

    SciTech Connect

    Dismukes, D.E. . Center for Energy Studies); Maloney, M.T. )

    1999-06-01

    Stranded cost recovery continues to be a focal point of electricity deregulation. Restructuring has ground to a halt in many places largely due to the contentiousness of the issue, and even where there has been action states have granted substantial stranded cost recovery to utilities, vitiating much of the price reductions that competition is forecast to bring. While a surprisingly large amount of non-utility generation capacity already has been shut down due to obsolescence, this has not choked off capital investment. The example suggests that stranded-cost recovery is neither warranted nor necessary.

  19. Antimicrobials & cholera: are we stranded?

    PubMed

    Ghosh, Amit; Ramamurthy, T

    2011-02-01

    Antimicrobial resistance poses a major threat in the treatment of infectious diseases. Though significant progress in the management of diarrhoeal diseases has been achieved by improved hygiene, development of new antimicrobials and vaccines, the burden remains the same, especially in children below 5 yr of age. In the case of cholera, though oral rehydration treatment is the mainstay, antimicrobial therapy is mandatory at times to reduce the volume of stool and shorten the duration of the disease. Though for many pathogens, antimicrobial resistance emerged soon after the introduction of antibiotics, Vibrio cholerae remained sensitive to most of the antibiotics for quite a long period. However, the scenario changed over the years and today, V. cholerae strains isolated world over are resistant to multiple antibiotics. A myriad number of mechanisms underlie this phenomenon. These include production of extended-spectrum beta-lactamases, enhanced multi-drug efflux pump activity, plasmid-mediated quinolone and fluoroquinolone resistance, and chromosomal mutations. Horizontal transfer of resistance determinants with mobile genetic elements like integrons and the integrating conjugative elements (ICEs), SXTs help in the dissemination of drug resistance. Though all strains isolated are not resistant to all antibiotics and we are not as yet "stranded", expanding spectrum of drug resistance is a definite cause for concern. Pipelines of discovery of new antibiotics are drying up as major pharmaceutical companies are losing interest in investing money in this endeavour, mainly due to the short shelf-life of the antibiotics and also due to the fast emergence of drug resistance. To address this issue, attempts are now being made to discover drugs which are pathogen specific and target their "virulence mechanisms". It is expected that development of resistance against such antibiotics would take much longer. This review briefly focuses on all these issues.

  20. DNA strand displacement system running logic programs.

    PubMed

    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.

  1. DNA strand displacement system running logic programs.

    PubMed

    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. PMID:24211259

  2. Bubbles in live-stranded dolphins.

    PubMed

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

    2012-04-01

    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.

  3. Correlation Between Strand Stability and Magnet Performance

    SciTech Connect

    Dietderich, D.R.; Bartlett, S.E.; Caspi, S.; Ferracin, P.; Gourlay, S.A.; Higley, H.C.; Lietzke, A.F.; Mattafirri, S.; McInturff, A.D.; Sabbi, G.L.; Scanlan, R.M.

    2005-06-01

    Magnet programs at BNL, LBNL and FNAL have observed instabilities in high J{sub c} Nb{sub 3}Sn strands and magnets made from these strands. This paper correlates the strand stability determined from a short sample-strand test to the observed magnet performance. It has been observed that strands that carry high currents at high fields (greater than 10 T) cannot sustain these same currents at low fields (1-3 T) when the sample current is fixed and the magnetic field is ramped. This suggests that the present generation of strand is susceptible to flux jumps (FJ). To prevent flux jumps from limiting stand performance, one must accommodate the energy released during a flux jump. To better understand FJ this work has focused on wire with a given sub-element diameter and shows that one can significantly improve stability by increasing the copper conductivity (higher residual resistivity ratio, RRR, of the Cu). This increased stability significantly improves the conductor performance and permits it to carry more current.

  4. Correlation between Strand Stability and Magnet Performance

    SciTech Connect

    Dietderich, Daniel R.; Bartlett, Scott E.; Caspi, Shlomo; Ferracin, Paolo; G ourlay, Stephen A.; Higley, Hugh C.; Lietzke, Alan F.; Mattafirri, Sara; McInturff, Alfred D.; Sabbi, GianLuca L.; Scanlan,Ronald M.

    2005-04-16

    Magnet programs at BNL, LBNL and FNAL have observed instabilities in high J{sub c} Nb{sub 3}Sn strands and magnets made from these strands. This paper correlates the strand stability determined from a short sample-strand test to the observed magnet performance. It has been observed that strands that carry high currents at high fields (greater than 10T) cannot sustain these same currents at low fields (1-3T) when the sample current is fixed and the magnetic field is ramped. This suggests that the present generation of strand is susceptible to flux jumps (FJ). To prevent flux jumps from limiting stand performance, one must accommodate the energy released during a flux jump. To better understand FJ this work has focused on wire with a given sub-element diameter and shows that one can significantly improve stability by increasing the copper conductivity (higher residual resistivity ratio, RRR, of the Cu). This increased stability significantly improves the conductor performance and permits it to carry more current.

  5. Bubbles in live-stranded dolphins

    PubMed Central

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

    2012-01-01

    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. PMID:21993505

  6. Monitoring steel strands via ultrasonic measurements

    NASA Astrophysics Data System (ADS)

    Rizzo, Piervincenzo; Lanza di Scalea, Francesco

    2002-06-01

    Steel strands are widely used in civil structures as pre- stressing tendons and stay-cables. The structural criticality of strands has led to an increasing interest in developing methods able to monitor applied loads as well as detect potential defects. In this paper ultrasonic guided waves, generated and detected via magnetostrictive sensors, are exploited to address this need. The sensors were developed in collaboration with the US Federal Highway Administration NDE Validation Center. An acousto elastic formulation of the Pochhammer-Chree longitudinal vibrations in cylindrical waveguides is proposed to predict the change of ultrasonic velocity as a function of applied stress. Results from acousto elastic experiments performed on seven- wire strands and on single wires are presented and compared to the theoretical predictions. Ways to enhance the inhernetly-low sensitivity of the acousto elastic measurements are proposed and investigated. The different behavior exhibited by the strand when compared to the single wire suggests the need for widening the theory governing the acousto elastic phenomenon in multi-wire members. The role of the strand anchorages is examined in the context of wave attenuation. The suitability of the guided wave method for the detection of defects is demonstrated including the possibility of inspecting the critical anchored regions.

  7. 5. CABLE STRAND ALARM: Photocopy of December 1966 photograph showing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. CABLE STRAND ALARM: Photocopy of December 1966 photograph showing cable strand alarm located at Beach and Hyde Streets. A strand in the cable (see CA-12-7) forces the fork forward, alerting the powerhouse to the strand by means of an electrical warning device. This strand alarm operates in essentially the same manner as those first used in the 1880s. - San Francisco Cable Railway, Washington & Mason Streets, San Francisco, San Francisco County, CA

  8. Convergent strand array liquid pumping system

    NASA Technical Reports Server (NTRS)

    Collins, Earl R., Jr. (Inventor)

    1989-01-01

    A surface-tension liquid pumping system is provided by one or more arrays of converging solid monofilament fibers or metal wires (strands) spaced apart at an input end to gather liquid, and gathered close together at the opposite end where menisci forms between wetted strands to force liquid in the direction of convergence of the strands. The liquid pumping system is independent of gravity. It is illustrated as being used in a heat pump having a heating box to vaporize the liquid and a condensing chamber. Condensed liquid is returned by the pumping system to the heating box where it is again vaporized. A vapor tube carries the vapor to the condensing chamber. In that way, a closed system pumps heat from the heating box to the evaporating chamber and from there radiated to the atmosphere.

  9. Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids.

    PubMed

    Bohländer, Peggy R; Vilaivan, Tirayut; Wagenknecht, Hans-Achim

    2015-09-21

    The so-called acpcPNA system bears a peptide backbone consisting of 4'-substituted proline units with (2'R,4'R) configuration in an alternating combination with (2S)-amino-cyclopentane-(1S)-carboxylic acids. acpcPNA forms exceptionally stable hybrids with complementary DNA. We demonstrate herein (i) strand displacements by single-stranded DNA from acpcPNA-DNA hybrids, and by acpcPNA strands from DNA duplexes, and (ii) strand invasions by acpcPNA into double-stranded DNA. These processes were studied in vitro using synthetic oligonucleotides and by means of our concept of wavelength-shifting fluorescent nucleic acid probes, including fluorescence lifetime measurements that allow quantifying energy transfer efficiencies. The strand displacements of preannealed 14mer acpcPNA-7mer DNA hybrids consecutively by 10mer and 14mer DNA strands occur with rather slow kinetics but yield high fluorescence color ratios (blue : yellow or blue : red), fluorescence intensity enhancements, and energy transfer efficiencies. Furthermore, 14mer acpcPNA strands are able to invade into 30mer double-stranded DNA, remarkably with quantitative efficiency in all studied cases. These processes can also be quantified by means of fluorescence. This remarkable behavior corroborates the extraordinary versatile properties of acpcPNA. In contrast to conventional PNA systems which require 3 or more equivalents PNA, only 1.5 equivalents acpcPNA are sufficient to get efficient double duplex invasion. Invasions also take place even in the presence of 250 mM NaCl which represents an ionic strength nearly twice as high as the physiological ion concentration. These remarkable results corroborate the extraordinary properties of acpcPNA, and thus acpcPNA represents an eligible tool for biological analytics and antigene applications.

  10. Low-residue euthanasia of stranded mysticetes.

    PubMed

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

    2014-01-01

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

  11. Rescue Your Campus from "Stranded" Costs.

    ERIC Educational Resources Information Center

    Kadamus, David A.

    2003-01-01

    Discusses how to deal with the pressures to defer maintenance on campus buildings, including the issue of accelerated cycles of obsolescence, which "stranded" costs to avoid and to accept, and specific strategies to gain control of the physical asset portfolio. (EV)

  12. Untangling the Strands of the Fourteenth Amendment.

    ERIC Educational Resources Information Center

    Lupu, Ira C.

    1979-01-01

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

  13. Neurobrucellosis in Stranded Dolphins, Costa Rica

    PubMed Central

    Hernández-Mora, Gabriela; González-Barrientos, Rocío; Morales, Juan-Alberto; Chaves-Olarte, Esteban; Guzmán-Verri, Caterina; Baquero-Calvo, Elías; De-Miguel, María-Jesús; Marín, Clara-María; Blasco, José-María

    2008-01-01

    Ten striped dolphins, Stenella coeruleoalba, stranded along the Costa Rican Pacific coast, had meningoencephalitis and antibodies against Brucella spp. Brucella ceti was isolated from cerebrospinal fluid of 6 dolphins and 1 fetus. S. coeruleoalba constitutes a highly susceptible host and a potential reservoir for B. ceti transmission. PMID:18760012

  14. High field superconductor development and understanding project, Final Report

    SciTech Connect

    Larbalestier, David C.; Lee, Peter J.

    2009-07-15

    Over 25 years the Applied Superconductivity Center at the University of Wisconsin-Madison provided a vital technical resource to the High Energy Physics community covering development in superconducting strand for HEP accelerator magnet development. In particular the work of the group has been to develop the next generation of high field superconductors for high field application. Grad students Mike Naus, Chad Fischer, Arno Godeke and Matt Jewell improved our understanding of the microstructure and microchemistry of Nb3Sn and their impact on the physical and mechanical properties. The success of this work has led to the continued funding of this work at the ASC after it moved to the NHMFL and also to direct funding from BNL for some aspects of Nb3Sn cable evaluation.

  15. RNA-catalysed synthesis of complementary-strand RNA

    NASA Astrophysics Data System (ADS)

    Doudna, Jennifer A.; Szostak, Jack W.

    1989-06-01

    The Tetrahymena ribozyme can splice together multiple oligonucleotides aligned on a template strand to yield a fully complementary product strand. This reaction demonstrates the feasibility of RNA-catalysed RNA replications.

  16. Fish stranding in freshwater systems: sources, consequences, and mitigation.

    PubMed

    Nagrodski, Alexander; Raby, Graham D; Hasler, Caleb T; Taylor, Mark K; Cooke, Steven J

    2012-07-30

    Fish can become stranded when water levels decrease, often rapidly, as a result of anthropogenic (e.g., canal drawdown, hydropeaking, vessel wakes) and natural (e.g., floods, drought, winter ice dynamics) events. We summarize existing research on stranding of fish in freshwater, discuss the sources, consequences, and mitigation options for stranding, and report current knowledge gaps. Our literature review revealed that ∼65.5% of relevant peer-reviewed articles were found to focus on stranding associated with hydropower operations and irrigation projects. In fact, anthropogenic sources of fish stranding represented 81.8% of available literature compared to only 19.9% attributed to natural fish stranding events. While fish mortality as a result of stranding is well documented, our analysis revealed that little is known about the sublethal and long-term consequences of stranding on growth and population dynamics. Furthermore, the contribution of stranding to annual mortality rates is poorly understood as are the potential ecosystem-scale impacts. Mitigation strategies available to deal with stranding include fish salvage, ramping rate limitations, and physical habitat works (e.g., to contour substrate to minimize stranding). However, a greater knowledge of the factors that cause fish stranding would promote the development and refinement of mitigation strategies that are economically and ecologically sustainable. PMID:22481278

  17. Analog Computation by DNA Strand Displacement Circuits.

    PubMed

    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. PMID:27363950

  18. Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism

    PubMed Central

    Brown, Timothy A.; Cecconi, Ciro; Tkachuk, Ariana N.; Bustamante, Carlos; Clayton, David A.

    2005-01-01

    The established strand-displacement model for mammalian mitochondrial DNA (mtDNA) replication has recently been questioned in light of new data using two-dimensional (2D) agarose gel electrophoresis. It has been proposed that a synchronous, strand-coupled mode of replication occurs in tissues, thereby casting doubt on the general validity of the “orthodox,” or strand-displacement model. We have examined mtDNA replicative intermediates from mouse liver using atomic force microscopy and 2D agarose gel electrophoresis in order to resolve this issue. The data provide evidence for only the orthodox, strand-displacement mode of replication and reveal the presence of additional, alternative origins of lagging light-strand mtDNA synthesis. The conditions used for 2D agarose gel analysis are favorable for branch migration of asymmetrically replicating nascent strands. These data reconcile the original displacement mode of replication with the data obtained from 2D gel analyses. PMID:16230534

  19. Method and apparatus for testing a forward-moving strand

    DOEpatents

    Ducommun, Joel; Vulliens, Philippe

    1980-01-01

    In a method for testing a continuously forward-moving strand a light beam which passes along a plane that extends approximately perpendicularly to the longitudinal axis of the strand is introduced into the strand. The brightness value is measured on a place of the strand exterior which is distal from the light incidence place by means of at least one photoelectronic element disposed directly on the strand exterior and the measured result is evaluated in a gating circuit which is electrically connected to the photoelectronic element.

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

    DOEpatents

    Gray, J.W.; Pinkel, D.

    1991-07-02

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

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

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel

    1991-01-01

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. Probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations.

  2. The role of aromatic-aromatic interactions in strand-strand stabilization of β-sheets

    PubMed Central

    Budyak, Ivan L.; Zhuravleva, Anastasia; Gierasch, Lila M.

    2013-01-01

    Aromatic-aromatic interactions have long been believed to play key roles in protein structure, folding, and binding functions. Yet we still lack full understanding of the contributions of aromatic-aromatic interactions to protein stability and the timing of their formation during folding. Here, using as a case study an aromatic ladder in the β-barrel protein, cellular retinoic acid binding protein 1 (CRABP1), we find aromatic π stacking plays a greater role in the Phe65-Phe71 cross-strand pair while in another pair, Phe50-Phe65, hydrophobic interactions are dominant. The Phe65/Phe71 pair spans β-strands 4 and 5 in the β-barrel, which lack interstrand hydrogen bonding, and we speculate that it compensates energetically for the absence of strand-strand backbone interactions. Using perturbation analysis, we find that both aromatic-aromatic pairs form after the transition state for folding of CRABP1, thus playing a role in the final stabilization of the β-sheet rather than in its nucleation as had been earlier proposed. The aromatic interaction between strands 4–5 in CRABP1 is highly conserved in the intracellular lipid-binding protein (iLBP) family, and several lines of evidence combine to support a model wherein it acts to maintain barrel structure while allowing the dynamic opening that is necessary for ligand entry. Lastly, we carried out a bioinformatic analysis and found 51 examples of aromatic-aromatic interactions across non-hydrogen-bonded β-strands outside the iLBPs, arguing for the generality of the role played by this structural motif. PMID:23810905

  3. Blocking single-stranded transferred DNA conversion to double-stranded intermediates by overexpression of yeast DNA REPLICATION FACTOR A.

    PubMed

    Dafny-Yelin, Mery; Levy, Avner; Dafny, Raz; Tzfira, Tzvi

    2015-01-01

    Agrobacterium tumefaciens delivers its single-stranded transferred DNA (T-strand) into the host cell nucleus, where it can be converted into double-stranded molecules. Various studies have revealed that double-stranded transfer DNA (T-DNA) intermediates can serve as substrates by as yet uncharacterized integration machinery. Nevertheless, the possibility that T-strands are themselves substrates for integration cannot be ruled out. We attempted to block the conversion of T-strands into double-stranded intermediates prior to integration in order to further investigate the route taken by T-DNA molecules on their way to integration. Transgenic tobacco (Nicotiana benthamiana) plants that overexpress three yeast (Saccharomyces cerevisiae) protein subunits of DNA REPLICATION FACTOR A (RFA) were produced. In yeast, these subunits (RFA1-RFA3) function as a complex that can bind single-stranded DNA molecules, promoting the repair of genomic double strand breaks. Overexpression of the RFA complex in tobacco resulted in decreased T-DNA expression, as determined by infection with A. tumefaciens cells carrying the β-glucuronidase intron reporter gene. Gene expression was not blocked when the reporter gene was delivered by microbombardment. Enhanced green fluorescent protein-assisted localization studies indicated that the three-protein complex was predominantly nuclear, thus indicating its function within the plant cell nucleus, possibly by binding naked T-strands and blocking their conversion into double-stranded intermediates. This notion was further supported by the inhibitory effect of RFA expression on the cell-to-cell movement of Bean dwarf mosaic virus, a single-stranded DNA virus. The observation that RFA complex plants dramatically inhibited the transient expression level of T-DNA and only reduced T-DNA integration by 50% suggests that double-stranded T-DNA intermediates, as well as single-stranded T-DNA, play significant roles in the integration process. PMID:25424309

  4. Flow field studies on yawed, stranded cables

    NASA Astrophysics Data System (ADS)

    Batill, S. M.; Nelson, R. C.; Nebres, J. V.

    A study of the flowfield near yawed, stranded cables was conducted in order to investigate the mechanisms associated with the generation of both steady and unsteady fluid forces on the cables. Rigid cable models and a circular cylinder were tested in a wind tunnel at four different cable angles over a Reynolds number range from 6000 to 14,600 based on the nominal cable diameter. The smoke-wire and the kerosene smoke flow visualization techniques were used to qualitatively evaluate the flowfields associated with each cable geometry.

  5. Method for producing labeled single-stranded nucleic acid probes

    DOEpatents

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  6. Why double-stranded RNA resists condensation.

    PubMed

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

    2014-01-01

    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes--internal and external--distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.

  7. Repair of DNA Double-Strand Breaks

    NASA Astrophysics Data System (ADS)

    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.

  8. Euler-Poincaré equations for G-Strands

    NASA Astrophysics Data System (ADS)

    Holm, Darryl D.; Ivanov, Rossen I.

    2014-03-01

    The G-strand equations for a map Bbb R × Bbb R into a Lie group G are associated to a G-invariant Lagrangian. The Lie group manifold is also the configuration space for the Lagrangian. The G-strand itself is the map g(t, s) : Bbb R × Bbb R → G, where t and s are the independent variables of the G-strand equations. The Euler-Poincaré reduction of the variational principle leads to a formulation where the dependent variables of the G-strand equations take values in the corresponding Lie algebra and its co-algebra, * with respect to the pairing provided by the variational derivatives of the Lagrangian. We review examples of different G-strand constructions, including matrix Lie groups and diffeomorphism group. In some cases the G-strand equations are completely integrable 1+1 Hamiltonian systems that admit soliton solutions.

  9. Translocation of double strand DNA into a biological nanopore

    NASA Astrophysics Data System (ADS)

    Chatkaew, Sunita; Mlayeh, Lamia; Leonetti, Marc; Homble, Fabrice

    2009-03-01

    Translocation of double strand DNA across a unique mitochondrial biological nanopore (VDAC) is observed by an electrophysiological method. Characteristics of opened and sub-conductance states of VDAC are studied. When the applied electric potential is beyond ± 20 mV, VDAC transits to a sub-conductance state. Plasmids (circular double strand DNA) with a diameter greater than that of the channel shows the current reduction into the channel during the interaction but the state with zero-current is not observed. On the contrary, the interaction of linear double strand DNA with the channel shows the current reduction along with the zero-current state. These show the passages of linear double strand DNA across the channel and the electrostatic effect due to the surface charges of double strand DNA and channel for circular and linear double strand DNA.

  10. New progress of ITER-PF strand production in WST

    NASA Astrophysics Data System (ADS)

    Li, J. F.; Liu, W. T.; Yan, L. X.; H, J.; Gao, H. X.; Liu, J. W.; Du, S. J.; Liu, X. H.; Feng, Y.; Zhang, P. X.; Liu, S.; Li, H. W.; Niu, E. W.

    2014-05-01

    ITER Poloidal Field (PF) systems consist of 6 independent coils with different dimensions and require NbTi superconductor and copper strands. Western Superconducting Technologies Co.,Ltd.(WST) will supply PF2-5 NbTi strand for ITER, and over 14,000 km of NbTi strands have been produced in the past two years. Main performance of NbTi strands, including critical current, n value, wire diameter, Cu/non-Cu ratio, hysteresis loss and RRR are reported and analysed in this paper.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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

  13. Why double-stranded RNA resists condensation

    SciTech Connect

    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.

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

    PubMed

    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 <3% endogenous 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.

  15. Double strand binding – single strand incision mechanism for human flap endonuclease: implications for the superfamily

    PubMed Central

    Tsutakawa, Susan E.; Tainer, John A.

    2012-01-01

    Detailed structural, mutational, and biochemical analyses of human FEN1/DNA complexes have revealed the mechanism for recognition of 5′ flaps formed during lagging strand replication and DNA repair. FEN1 processes 5′ flaps through a previously unknown, but structurally elegant double-stranded (ds) recognition/single stranded (ss) incision mechanism that both selects for 5′ flaps and selects against ss DNA or RNA, intact dsDNA, and 3′ flaps. Two major DNA binding interfaces, including a K+ bridge between the DNA and the H2TH motif, are spaced one helical turn apart and together select for substrates with dsDNA. A conserved helical gateway and a helical cap protects the two-metal active site and selects for ss flaps with free termini. Structures of substrate and product reveal an unusual step between binding substrate and incision that involves a double base unpairing with incision occurring in the resulting unpaired DNA or RNA. Ordering of the active site requires a disorder-to-order transition induced by binding of an unpaired 3′ flap, which ensures that the product is ligatable. Comparison with FEN superfamily members, including XPG, EXO1, and GEN1, identifies superfamily motifs such as the helical gateway that select for ss-dsDNA junctions and provides key biological insights into nuclease specificity and regulation. PMID:22244820

  16. Saliva of Lygus lineolaris digests double stranded ribonucleic acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The prospects for development of highly specific pesticides based on double stranded ribonucleic acid have been a recent focus of scientific research. Creative applications have been proposed and demonstrated. However, not all insects are sensitive to double stranded RNA (dsRNA) gene knockdown effec...

  17. Progress in the Long $${\\rm Nb}_{3}{\\rm Sn}$$ Quadrupole R&D by LARP

    DOE PAGESBeta

    Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bocian, D.; Bossert, R.; Buehler, M.; Caspi, S.; Chlachidze, G.; Dietderich, D.; et al

    2011-11-14

    After the successful test of the first long Nb3Sn quadrupole (LQS01) the US LHC Accelerator Research Program (LARP, a collaboration of BNL, FNAL, LBNL and SLAC) is assessing training memory, reproducibility, and other accelerator quality features of long Nb3Sn quadrupole magnets. LQS01b (a reassembly of LQS01 with more uniform and higher pre-stress) was subjected to a full thermal cycle and reached the previous plateau of 222 T/m at 4.5 K in two quenches. A new set of four coils, made of the same type of conductor used in LQS01 (RRP 54/61 by Oxford Superconducting Technology), was assembled in the LQS01more » structure and tested at 4.5 K and lower temperatures. The new magnet (LQS02) reached the target gradient (200 T/m) only at 2.6 K and lower temperatures, at intermediate ramp rates. The preliminary test analysis, here reported, showed a higher instability in the limiting coil than in the other coils of LQS01 and LQS02.« less

  18. Relationship between marine mammal stranding events and offshore earthquakes

    NASA Astrophysics Data System (ADS)

    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.

  19. Computing in mammalian cells with nucleic acid strand exchange

    NASA Astrophysics Data System (ADS)

    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.

  20. Computing in mammalian cells with nucleic acid strand exchange

    PubMed Central

    Pochekailov, Sergii; Kirschman, Jonathan L.; Santangelo, Philip J.; Seelig, Georg

    2015-01-01

    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. PMID:26689378

  1. Quantitative cooling histories from stranded diffusion profiles

    NASA Astrophysics Data System (ADS)

    Watson, E. B.; Cherniak, D. J.

    2015-06-01

    Stranded elemental or isotopic diffusion profiles in geological materials have the potential to reveal information on the thermal history of the host sample. In the specific case of a concentration step that is established at high temperature, the extent of diffusive relaxation during cooling depends on the details of the cooling path and the Arrhenius diffusion law of the species of interest: In principle, a measured profile in a sample can provide quantitative information on the nature of the cooling path if the diffusion law is known. Using a combination of mathematics and numerical simulations, we derive a simple relationship describing the extent of profile relaxation (as gauged by the slope S 0 of a diffusion profile) as a function of the initial temperature ( T i) and cooling rate () of the system and the activation energy ( E a) and pre-exponential factor ( D 0) for diffusion: The initial temperature T i is expressed in K, is in °/s, D 0 is in m2/s, and E a is in kJ/mol. The slope of the profile of interest can be estimated either at the midpoint of an interdiffusion profile or at a crystal margin. In the former case, concentrations are normalized to a difference of 100 between the upper (=100) and lower (=0) initial concentration plateaus. For profiles at crystal margins, the normalization range is 0 to 50. The equation above applies equally well to linear and exponential cooling paths because the extent of relaxation indicated by S 0 is essentially the same for a given linear cooling path and an exponential one characterized by the same initial cooling rate. Cooling from the top of parabolic T- t "dome" results in more extensive profile relaxation; this is also well described by the above equation if the leading constant 2.504 is changed to 2.165. If S 0 of a stranded profile has been characterized in the laboratory, and if the Arrhenius law of the diffusant is known, the above equation can be solved uniquely for one of the cooling path parameters ( T i

  2. Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall.

    PubMed

    Yu, Chuanhe; Gan, Haiyun; Han, Junhong; Zhou, Zhi-Xiong; Jia, Shaodong; Chabes, Andrei; Farrugia, Gianrico; Ordog, Tamas; Zhang, Zhiguo

    2014-11-20

    In eukaryotic cells, DNA replication proceeds with continuous synthesis of leading-strand DNA and discontinuous synthesis of lagging-strand DNA. Here we describe a method, eSPAN (enrichment and sequencing of protein-associated nascent DNA), which reveals the genome-wide association of proteins with leading and lagging strands of DNA replication forks. Using this approach in budding yeast, we confirm the strand specificities of DNA polymerases delta and epsilon and show that the PCNA clamp is enriched at lagging strands compared with leading-strand replication. Surprisingly, at stalled forks, PCNA is unloaded specifically from lagging strands. PCNA unloading depends on the Elg1-containing alternative RFC complex, ubiquitination of PCNA, and the checkpoint kinases Mec1 and Rad53. Cells deficient in PCNA unloading exhibit increased chromosome breaks. Our studies provide a tool for studying replication-related processes and reveal a mechanism whereby checkpoint kinases regulate strand-specific unloading of PCNA from stalled replication forks to maintain genome stability.

  3. Recombination in Eukaryotic Single Stranded DNA Viruses

    PubMed Central

    Martin, Darren P.; Biagini, Philippe; Lefeuvre, Pierre; Golden, Michael; Roumagnac, Philippe; Varsani, Arvind

    2011-01-01

    Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution. PMID:21994803

  4. A double-stranded DNA rotaxane

    NASA Astrophysics Data System (ADS)

    Ackermann, Damian; Schmidt, Thorsten L.; Hannam, Jeffrey S.; Purohit, Chandra S.; Heckel, Alexander; Famulok, Michael

    2010-06-01

    Mechanically interlocked molecules such as rotaxanes and catenanes have potential as components of molecular machinery. Rotaxanes consist of a dumb-bell-shaped molecule encircled by a macrocycle that can move unhindered along the axle, trapped by bulky stoppers. Previously, rotaxanes have been made from a variety of molecules, but not from DNA. Here, we report the design, assembly and characterization of rotaxanes in which both the dumb-bell-shaped molecule and the macrocycle are made of double-stranded DNA, and in which the axle of the dumb-bell is threaded through the macrocycle by base pairing. The assembly involves the formation of pseudorotaxanes, in which the macrocycle and the axle are locked together by hybridization. Ligation of stopper modules to the axle leads to the characteristic dumb-bell topology. When an oligonucleotide is added to release the macrocycle from the axle, the pseudorotaxanes are either converted to mechanically stable rotaxanes, or they disassemble by means of a slippage mechanism to yield a dumb-bell and a free macrocycle. Our DNA rotaxanes allow the fields of mechanically interlocked molecules and DNA nanotechnology to be combined, thus opening new possibilities for research into molecular machines and synthetic biology.

  5. Fluid mechanics of DNA double-strand filter elution.

    PubMed Central

    Rudinger, George; Blazek, Ed Robert

    2002-01-01

    Measurement of infrequent DNA double-strand breaks (DSB) in mammalian cells is essential for the understanding of cell damage by ionizing radiation and many DNA-reactive drugs. One of the most important assays for measuring DSB in cellular DNA is filter elution. This study is an attempt to determine whether standard concepts of fluid mechanics can yield a self-consistent model of this process. Major assumptions of the analysis are reptation through a channel formed by surrounding strands, with only strand ends captured by filter pores. Both viscosity and entanglement with surrounding strands are considered to determine the resistance to this motion. One important result is that the average elution time of a strand depends not only on its length, but also on the size distribution of the surrounding strands. This model is consistent with experimental observations, such as the dependence of elution kinetics upon radiation dose, but independence from the size of the DNA sample up to a critical filter loading, and possible overlap of elution times for strands of different length. It indicates how the dependence of elution time on the flow rate could reveal the relative importance of viscous and entanglement resistance, and also predicts the consequences of using different filters. PMID:11751292

  6. Recurrent Respiratory Papillomatosis (RRP)-Juvenile Onset.

    PubMed

    Dyrstad, Sara W; Rao, Krishna A

    2008-01-01

    In this article, we describe the treatment of long standing juvenile-onset recurrent respiratory papillomatosis (JORRP) with eventual transformation to carcinoma in a patient who lived to the age of 73. Treatment modalities consisted of bronchoscopy and local excision initially. Later, YAG and CO2 laser debulking were used. Radiotherapy, chemotherapy with carboplatin (300 mg/m2) and 5-FU (600 mg/m2), oral methotrexate (5-7.5 mg/week), pegylated Interferon, indole-3-carbamide, and intralesional cidofovir were also utilized in the treatment of this patient. Except for methotrexate, each of the treatment regimens used in this patient, initially decreased growth of the papillomas and improved symptoms experienced by the patient. Interestingly, we found that this patient's long standing JORRP initially responded to a chemotherapy regimen of 4 cycles of carboplatin (300 mg/m2) and 5-FU (600 mg/m2) as well. Ultimately, the disease became resistant to all forms of treatment and progressed. The patient eventually succumbed to the disease after an approximate 77 year course.

  7. Hairpin-dimer equilibrium of a parallel-stranded DNA hairpin: formation of a four-stranded complex.

    PubMed Central

    Dornberger, U; Behlke, J; Birch-Hirschfeld, E; Fritzsche, H

    1997-01-01

    The 24mer deoxyoligonucleotide 3'-d(T)10-5'-5'-d(C)4- d(A)10-3'(psC4) with an uncommon 5'-p-5'phosphodiester linkage was designed to enable the formation of a hairpin structure with unusual parallel-stranded stem. As reference hairpin structure with an antiparallel-stranded stem, the 24mer 5'-d(T)10-d(C)4-d(A)10-3'(apsC4) was chosen. The behaviour of these oligonucleotides at different temperatures, DNA and salt concentrations was characterised by a combination of UV melting, CD, CD melting, infrared and Raman spectroscopy, infrared melting and analytical ultracentrifugation. The parallel-stranded hairpin structure was found to be formed by psC4 only under conditions of low DNA concentration and low salt concentration. Increase of the NaCl concentration beyond the physiological level or high DNA concentration supports the formation of intermolecular multi-stranded structures. The experimental data are in agreement with a four-stranded complex formed by two molecules of psC4. The base pairing model of this asymmetric four-stranded complex is based on the pyrimidine motif of a triple helix with two bifurcated hydrogen bonds at the O4 of the thymine each directed towards one of the amino protons of both adenines. In contrast, the reference oligonucleotide apsC4 forms only an antiparallel-stranded hairpin under all experimental conditions. PMID:9016633

  8. Hairpin-dimer equilibrium of a parallel-stranded DNA hairpin: formation of a four-stranded complex.

    PubMed

    Dornberger, U; Behlke, J; Birch-Hirschfeld, E; Fritzsche, H

    1997-02-15

    The 24mer deoxyoligonucleotide 3'-d(T)10-5'-5'-d(C)4- d(A)10-3'(psC4) with an uncommon 5'-p-5'phosphodiester linkage was designed to enable the formation of a hairpin structure with unusual parallel-stranded stem. As reference hairpin structure with an antiparallel-stranded stem, the 24mer 5'-d(T)10-d(C)4-d(A)10-3'(apsC4) was chosen. The behaviour of these oligonucleotides at different temperatures, DNA and salt concentrations was characterised by a combination of UV melting, CD, CD melting, infrared and Raman spectroscopy, infrared melting and analytical ultracentrifugation. The parallel-stranded hairpin structure was found to be formed by psC4 only under conditions of low DNA concentration and low salt concentration. Increase of the NaCl concentration beyond the physiological level or high DNA concentration supports the formation of intermolecular multi-stranded structures. The experimental data are in agreement with a four-stranded complex formed by two molecules of psC4. The base pairing model of this asymmetric four-stranded complex is based on the pyrimidine motif of a triple helix with two bifurcated hydrogen bonds at the O4 of the thymine each directed towards one of the amino protons of both adenines. In contrast, the reference oligonucleotide apsC4 forms only an antiparallel-stranded hairpin under all experimental conditions.

  9. OVERVIEW OF AMERICAN BRASS BUFFALO PLANT FROM ROOF OF STRAND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    OVERVIEW OF AMERICAN BRASS BUFFALO PLANT FROM ROOF OF STRAND ANNEALING TOWER, INCLUDING ORIGINAL BRASS MILL (1906-7,1911) TUBE MILL (1915), COPPER MILL (1921). - American Brass Foundry, 70 Sayre Street, Buffalo, Erie County, NY

  10. OVERVIEW OF AMERICAN BRASS BUFFALO PLANT FROM ROOF OF STRAND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    OVERVIEW OF AMERICAN BRASS BUFFALO PLANT FROM ROOF OF STRAND ANNEALING TOWER, INCLUDING CASTING SHOP AND BAG HOUSE (CENTER-LEFT) AND PORTION OF REROLL BAY (R). VIEW LOOKING SOUTHWEST. - American Brass Foundry, 70 Sayre Street, Buffalo, Erie County, NY

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

    PubMed

    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.

  12. DNA nanotechnology. Programming colloidal phase transitions with DNA strand displacement.

    PubMed

    Rogers, W Benjamin; Manoharan, Vinothan N

    2015-02-01

    DNA-grafted nanoparticles have been called "programmable atom-equivalents": Like atoms, they form three-dimensional crystals, but unlike atoms, the particles themselves carry information (the sequences of the grafted strands) that can be used to "program" the equilibrium crystal structures. We show that the programmability of these colloids can be generalized to the full temperature-dependent phase diagram, not just the crystal structures themselves. We add information to the buffer in the form of soluble DNA strands designed to compete with the grafted strands through strand displacement. Using only two displacement reactions, we program phase behavior not found in atomic systems or other DNA-grafted colloids, including arbitrarily wide gas-solid coexistence, reentrant melting, and even reversible transitions between distinct crystal phases. PMID:25657244

  13. Equilibrious Strand Exchange Promoted by DNA Conformational Switching

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  14. Background meeting and technology demonstration: Chromium electroplating of superconductor strand

    SciTech Connect

    1995-05-01

    A meeting concerned with electroplating copper onto superconducting wires was held. Topics of discussion were concerned with the market, strand cleanliness, and an improved rinsing system for the process.

  15. DNA nanotechnology. Programming colloidal phase transitions with DNA strand displacement.

    PubMed

    Rogers, W Benjamin; Manoharan, Vinothan N

    2015-02-01

    DNA-grafted nanoparticles have been called "programmable atom-equivalents": Like atoms, they form three-dimensional crystals, but unlike atoms, the particles themselves carry information (the sequences of the grafted strands) that can be used to "program" the equilibrium crystal structures. We show that the programmability of these colloids can be generalized to the full temperature-dependent phase diagram, not just the crystal structures themselves. We add information to the buffer in the form of soluble DNA strands designed to compete with the grafted strands through strand displacement. Using only two displacement reactions, we program phase behavior not found in atomic systems or other DNA-grafted colloids, including arbitrarily wide gas-solid coexistence, reentrant melting, and even reversible transitions between distinct crystal phases.

  16. 215. Dennis Hill, Photographer May 1998 DETAIL VIEW OF STRAND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    215. Dennis Hill, Photographer May 1998 DETAIL VIEW OF STRAND SHOES AND STORM CABLE EYE BARS IN YERBA BUENA ANCHORAGE, FACING EAST. - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  17. Molecular architecture of tailed double-stranded DNA phages

    PubMed Central

    Fokine, Andrei; Rossmann, Michael G

    2014-01-01

    The tailed double-stranded DNA bacteriophages, or Caudovirales, constitute ~96% of all the known phages. Although these phages come in a great variety of sizes and morphology, their virions are mainly constructed of similar molecular building blocks via similar assembly pathways. Here we review the structure of tailed double-stranded DNA bacteriophages at a molecular level, emphasizing the structural similarity and common evolutionary origin of proteins that constitute these virions. PMID:24616838

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

    SciTech Connect

    Pozo-Yauner, Luis del; Wall, Jonathan S.; González Andrade, Martín; Sánchez-López, Rosana; Rodríguez-Ambriz, Sandra L.; Pérez Carreón, Julio I.; 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.

  19. Test and Analysis of 4 Technology Quadrupole Shell (TQS) models for LARP

    SciTech Connect

    Caspi, S.; Ambrosio, G.; Andreev, A.N.; Barzi, E.; Bossert, R.; Dietderich, D. R.; Felice, H.; Ferracin, P.; Ghosh, A.; Hafalia, A. R.; Lietzke, A. F.; Novitski, I.; Sabbi, G.L.; Zlobin, A.V.

    2008-06-01

    Test results are reported on TQS02a, a second model in support of the development of a large-aperture Nb{sub 3}Sn superconducting quadrupole for the US LHC Accelerator Research Program (LARP). The magnet uses key and bladder technology with supporting iron yoke and an aluminum shell. Changes from the previous first model (tested in 2006) include: (1) Titanium island poles; (2) no axial island gaps during reaction; and (3) RRP Nb3Sn conductor. Design changes resulted from previous tests with three different magnet assemblies (TQS01a, TQS01b and TQS01c) using coils with bronze segmented islands, with gaps and MJR conductor The paper summarizes the assembly, cool-down and performance of TQS01a, TQS01b, TQS01c, and TQS02 and compares measurements with design expectations.

  20. Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand*

    PubMed Central

    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

  1. Hearing loss in stranded odontocete dolphins and whales.

    PubMed

    Mann, David; Hill-Cook, Mandy; Manire, Charles; Greenhow, Danielle; Montie, Eric; Powell, Jessica; Wells, Randall; Bauer, Gordon; Cunningham-Smith, Petra; Lingenfelser, Robert; DiGiovanni, Robert; Stone, Abigale; Brodsky, Micah; Stevens, Robert; Kieffer, George; Hoetjes, Paul

    2010-01-01

    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. PMID:21072206

  2. Characterization of strand exchange activity of yeast Rad51 protein.

    PubMed Central

    Namsaraev, E; Berg, P

    1997-01-01

    The Saccharomyces cerevisiae RAD51 gene product takes part in genetic recombination and repair of DNA double strand breaks. Rad51, like Escherichia coli RecA, catalyzes strand exchange between homologous circular single-stranded DNA (ssDNA) and linear double-stranded DNA (dsDNA) in the presence of ATP and ssDNA-binding protein. The formation of joint molecules between circular ssDNA and linear dsDNA is initiated at either the 5' or the 3' overhanging end of the complementary strand; joint molecules are formed only if the length of the overhanging end is more than 1 nucleotide. Linear dsDNAs with recessed complementary or blunt ends are not utilized. The polarity of strand exchange depends upon which end is used to initiate the formation of joint molecules. Joint molecules formed via the 5' end are processed by branch migration in the 3'-to-5' direction with respect to ssDNA, and joint molecules formed with a 3' end are processed in the opposite direction. PMID:9271413

  3. Elongation of discotic liquid crystal strands and lubricant effects.

    PubMed

    Bhattacharyya, Surjya Sarathi; Galerne, Yves

    2014-05-19

    After a short review on the physics of pulled threads and their mechanical properties, the paper reports and discusses the strand elongation of disordered columnar phases, hexagonal or lamella-columnar, of small molecules or polymers. The mechanical properties appear to be relevant to the length of the columns of molecules compared to the thread length, instead of the usual correlation length. If, taking the entanglement effect into account, the column length is short, the strand exhibits rather fluid-like properties that may even look nematic-like at the macroscopic scale. The Plateau-Rayleigh instability breaks the thread shortly thereafter. However, because the hydrodynamic objects are the columns instead of the molecules, the viscosity is anomalously large. The observations show that the strands in the columnar phases are made of filaments, or fibrils, which are bundles of columns of molecules. This explains the grooves and rings, which are observed on the antenna or bamboo-like strand profiles. On pulling a strand, the elongation stress eventually exceeds the plasticity threshold, thus breaking the columns and the filaments. As a result, cracks, more exactly, giant dislocations are formed. These change the strand thickness by steps of different birefringence colors. Interestingly, the addition of a solute may drastically change the effective viscosity of the columnar phase and its mechanical properties. Some solutes, such as alkanes, exhibit lubricant and detangling properties, whereas others such as triphenylene, are antilubricant. PMID:24302445

  4. A model capturing novel strand symmetries in bacterial DNA

    SciTech Connect

    Sobottka, Marcelo; Hart, Andrew G.

    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.

  5. Red Tide Strands South African Rock Lobsters

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Although some red tides form a healthy part of phytoplankton production, recurrent harmful or toxic blooms also occur, with results depending upon the type of plankton and on atmospheric and oceanic conditions. At Elands Bay in South Africa's Western Cape province, about 1000 tons of rock lobsters beached themselves during February 2002, when the decay of dense blooms of phytoplankton caused a rapid reduction in the oxygen concentration of nearshore waters. The lobsters (or crayfish, as they are known locally) moved toward the breaking surf in search of oxygen, but were stranded by the retreating tide.

    The Multi-angle Imaging SpectroRadiometer's nadir camera acquired these red, green, blue composites on February 2 and 18, 2002, during Terra orbits 11315 and 11548. The colors have been accentuated to highlight the bloom, and land and water have been enhanced separately. The two views show the shoreward migration of the algal bloom. Each image represents an area of about 205 kilometers x 330 kilometers. Elands Bay is situated near the mouth of the Doring River, about 75 kilometers northeast of the jutting Cape Columbine.

    The term 'red tide' is used to refer to a number of different types of phytoplankton blooms of various hues. The wine color of certain parts of this bloom are consistent with the ciliate species Mesodinium rubrum, which has been associated with recurring harmful algal blooms along the Western Cape coast. Under these conditions, the lobsters are not poisoned. During the recent event, government and military staff transported as many of the living lobsters as possible to areas that were less affected by the red tide. At the same time, people came from across South Africa to gather the undersized creatures for food. The effects of the losses on the maritime economy are expected to be felt over the next few years.

    MISR was built and is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Office of Earth Science, Washington

  6. Red Tide Strands South African Rock Lobsters

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Although some red tides form a healthy part of phytoplankton production, recurrent harmful or toxic blooms also occur, with results depending upon the type of plankton and on atmospheric and oceanic conditions. At Elands Bay in South Africa's Western Cape province, about 1000 tons of rock lobsters beached themselves during February 2002, when the decay of dense blooms of phytoplankton caused a rapid reduction in the oxygen concentration of nearshore waters. The lobsters (or crayfish, as they are known locally) moved toward the breaking surf in search of oxygen, but were stranded by the retreating tide. The Multi-angle Imaging SpectroRadiometer's nadir camera acquired these red, green, blue composites on February 2 and 18, 2002, during Terra orbits 11315 and 11548. The colors have been accentuated to highlight the bloom, and land and water have been enhanced separately. The two views show the shoreward migration of the algal bloom. Each image represents an area of about 205 kilometers x 330 kilometers. Elands Bay is situated near the mouth of the Doring River, about 75 kilometers northeast of the jutting Cape Columbine. The term 'red tide' is used to refer to a number of different types of phytoplankton blooms of various hues. The wine color of certain parts of this bloom are consistent with the ciliate species Mesodinium rubrum, which has been associated with recurring harmful algal blooms along the Western Cape coast. Under these conditions, the lobsters are not poisoned. During the recent event, government and military staff transported as many of the living lobsters as possible to areas that were less affected by the red tide. At the same time, people came from across South Africa to gather the undersized creatures for food. The effects of the losses on the maritime economy are expected to be felt over the next few years. MISR was built and is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Office of Earth Science, Washington, DC. The Terra

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

    SciTech Connect

    Poeschla, Eric

    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.

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

    PubMed

    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. PMID:26730951

  9. Role of stranded gas in increasing global gas supplies

    USGS Publications Warehouse

    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.

  10. New Views on Strand Asymmetry in Insect Mitochondrial Genomes

    PubMed Central

    Wei, Shu-Jun; Shi, Min; Chen, Xue-Xin; Sharkey, Michael J.; van Achterberg, Cornelis; Ye, Gong-Yin; He, Jun-Hua

    2010-01-01

    Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera), Aleyrodidae (Hemiptera) and Braconidae (Hymenoptera); the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew) was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms. PMID:20856815

  11. Stranding Events of Kogia Whales along the Brazilian Coast

    PubMed Central

    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. PMID:26730951

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

    PubMed

    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.

  13. DNA-directed mutations. Leading and lagging strand specificity

    NASA Technical Reports Server (NTRS)

    Sinden, R. R.; Hashem, V. I.; Rosche, W. A.

    1999-01-01

    The fidelity of replication has evolved to reproduce B-form DNA accurately, while allowing a low frequency of mutation. The fidelity of replication can be compromised, however, by defined order sequence DNA (dosDNA) that can adopt unusual or non B-DNA conformations. These alternative DNA conformations, including hairpins, cruciforms, triplex DNAs, and slipped-strand structures, may affect enzyme-template interactions that potentially lead to mutations. To analyze the effect of dosDNA elements on spontaneous mutagenesis, various mutational inserts containing inverted repeats or direct repeats were cloned in a plasmid containing a unidirectional origin of replication and a selectable marker for the mutation. This system allows for analysis of mutational events that are specific for the leading or lagging strands during DNA replication in Escherichia coli. Deletions between direct repeats, involving misalignment stabilized by DNA secondary structure, occurred preferentially on the lagging strand. Intermolecular strand switch events, correcting quasipalindromes to perfect inverted repeats, occurred preferentially during replication of the leading strand.

  14. An intercalation-locked parallel-stranded DNA tetraplex

    SciTech Connect

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.

  15. An intercalation-locked parallel-stranded DNA tetraplex

    DOE PAGESBeta

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs betweenmore » adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

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

    NASA Astrophysics Data System (ADS)

    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.

  17. An intercalation-locked parallel-stranded DNA tetraplex

    PubMed Central

    Tripathi, Shailesh; Zhang, Daoning; Paukstelis, Paul J.

    2015-01-01

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5′-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures. PMID:25628357

  18. Proceedings of a Workshop on Antarctic Meteorite Stranding Surfaces

    NASA Technical Reports Server (NTRS)

    Cassidy, W. A. (Editor); Whillans, I. M. (Editor)

    1990-01-01

    The discovery of large numbers of meteorites on the Antarctic Ice Sheet is one of the most exciting developments in polar science in recent years. The meteorites are found on areas of ice called stranding surfaces. Because of the sudden availability of hundreds, and then thousands, of new meteorite specimens at these sites, the significance of the discovery of meteorite stranding surfaces in Antarctica had an immediate and profound impact on planetary science, but there is also in this discovery an enormous, largely unrealized potential to glaciology for records of climatic and ice sheet changes. The glaciological interest derives from the antiquity of the ice in meteorite stranding surfaces. This exposed ice covers a range of ages, probably between zero and more than 500,000 years. The Workshop on Antarctic Meteorite Stranding Surfaces was convened to explore this potential and to devise a course of action that could be recommended to granting agencies. The workshop recognized three prime functions of meteorite stranding surfaces. They provide: (1) A proxy record of climatic change (i.e., a long record of climatic change is probably preserved in the exposed ice stratigraphy); (2) A proxy record of ice volume change; and (3) A source of unique nonterrestrial material.

  19. Mass stranding of wedge-tailed shearwater chicks in Hawaii

    USGS Publications Warehouse

    Work, T.M.; Rameyer, R.A.

    1999-01-01

    Unusual numbers of wedge-tailed shearwater (Puffinus pacificus) chicks stranded on Oahu (Hawaii, USA) in 1994. Compared to healthy wedge-tailed shearwater (WTSW) chicks, stranded chicks were underweight, dehydrated, leukopenic, lymphopenic, eosinopenic, and heterophilic; some birds were toxemic and septic. Stranded chicks also were hypoglycemic and had elevated aspartate amino transferase levels. Most chicks apparently died from emaciation, dehydration, or bacteremia. Because many birds with bacteremia also had severe necrosis of the gastrointestinal (GI) mucosa associated with bacteria, we suspect the GI tract to be the source of disseminated bacterial infection. The identity of the bacteria was not confirmed. The daily number of chicks stranded was significantly related to average wind speeds, and the mortality coincided with the fledging period for WTSW. Strong southeasterly winds were a distinguishing meteorologic factor in 1994 and contributed to the distribution of stranded chicks on Oahu. More objective data on WTSW demographics would enhance future efforts to determine predisposing causes of WTSW wrecks and their effects on seabird colonies.

  20. Proceedings of a Workshop on Antarctic Meteorite Stranding Surfaces

    SciTech Connect

    Cassidy, W.A.; Whillans, I.M.

    1990-08-01

    The discovery of large numbers of meteorites on the Antarctic Ice Sheet is one of the most exciting developments in polar science in recent years. The meteorites are found on areas of ice called stranding surfaces. Because of the sudden availability of hundreds, and then thousands, of new meteorite specimens at these sites, the significance of the discovery of meteorite stranding surfaces in Antarctica had an immediate and profound impact on planetary science, but there is also in this discovery an enormous, largely unrealized potential to glaciology for records of climatic and ice sheet changes. The glaciological interest derives from the antiquity of the ice in meteorite stranding surfaces. This exposed ice covers a range of ages, probably between zero and more than 500,000 years. The Workshop on Antarctic Meteorite Stranding Surfaces was convened to explore this potential and to devise a course of action that could be recommended to granting agencies. The workshop recognized three prime functions of meteorite stranding surfaces. They provide: (1) A proxy record of climatic change (i.e., a long record of climatic change is probably preserved in the exposed ice stratigraphy); (2) A proxy record of ice volume change; and (3) A source of unique nonterrestrial material.

  1. Persistence and breakdown of strand symmetry in the human genome.

    PubMed

    Zhang, Shang-Hong

    2015-04-01

    Afreixo, V., Bastos, C.A.C., Garcia, S.P., Rodrigues, J.M.O.S., Pinho, A.J., Ferreira, P.J.S.G., 2013. The breakdown of the word symmetry in the human genome. J. Theor. Biol. 335, 153-159 analyzed the word symmetry (strand symmetry or the second parity rule) in the human genome. They concluded that strand symmetry holds for oligonucleotides up to 6 nt and is no longer statistically significant for oligonucleotides of higher orders. However, although they provided some new results for the issue, their interpretation would not be fully justified. Also, their conclusion needs to be further evaluated. Further analysis of their results, especially those of equivalence tests and word symmetry distance, shows that strand symmetry would persist for higher-order oligonucleotides up to 9 nt in the human genome, at least for its overall frequency framework (oligonucleotide frequency pattern). PMID:25576243

  2. Error-Prone Repair of DNA Double-Strand Breaks.

    PubMed

    Rodgers, Kasey; McVey, Mitch

    2016-01-01

    Preserving the integrity of the DNA double helix is crucial for the maintenance of genomic stability. Therefore, DNA double-strand breaks represent a serious threat to cells. In this review, we describe the two major strategies used to repair double strand breaks: non-homologous end joining and homologous recombination, emphasizing the mutagenic aspects of each. We focus on emerging evidence that homologous recombination, long thought to be an error-free repair process, can in fact be highly mutagenic, particularly in contexts requiring large amounts of DNA synthesis. Recent investigations have begun to illuminate the molecular mechanisms by which error-prone double-strand break repair can create major genomic changes, such as translocations and complex chromosome rearrangements. We highlight these studies and discuss proposed models that may explain some of the more extreme genetic changes observed in human cancers and congenital disorders.

  3. Double-strand break-induced targeted mutagenesis in plants.

    PubMed

    Lyznik, L Alexander; Djukanovic, Vesna; Yang, Meizhu; Jones, Spencer

    2012-01-01

    Double-strand breaks are very potent inducers of DNA recombination. There is no recombination between DNA molecules unless one or two DNA strands are broken. It has become feasible to introduce double-strand breaks at specific chromosomal loci by using dedicated, redesigned endonucleases with altered DNA-binding specificities. Such breaks are mainly repaired by error-prone nonhomologous recombination pathways in somatic cells, thus frequently producing mutations at the preselected chromosomal sites. Although the art and science of reengineering protein properties have been advancing quickly, an empirical validation of new endonucleases in a particular experimental environment is essential for successful targeted mutagenesis experiments. This chapter presents methods that were developed for a comprehensive evaluation of the DNA-binding and DNA-cutting activities of homing endonucleases in maize cells; however, they can be adopted for similar evaluation studies of other endonucleases and other plant species that are amenable for Agrobacterium-mediated transformation. PMID:22351025

  4. Evidence that filament fracture occurs in an ITER toroidal field conductor after cyclic Lorentz force loading in SULTAN

    NASA Astrophysics Data System (ADS)

    Sanabria, Carlos; Lee, Peter J.; Starch, William; Pong, Ian; Vostner, Alexander; Jewell, Matthew C.; Devred, Arnaud; Larbalestier, David C.

    2012-07-01

    We analyzed the ITER TFEU5 cable-in-conduit conductor (CICC) after the full SULTAN conductor qualification test in order to explore whether Lorentz force induced strand movement inside the CICC produces any fracture of the brittle Nb3Sn filaments. Metallographic image analysis was used to quantify the change in void fraction of each sub-cable (petal); strands move in the direction of the Lorentz force, increasing the void space on the low force side of the CICC and producing a densification on the high force side. Adjacent strand counting shows that local increases in void space result in lower local strand-strand support. Extensive metallographic sampling unambiguously confirms that Nb3Sn filament fracture occurred in the TFEU5 CICC, but the filament fracture was highly localized to strand sections with high local curvature (likely produced during cabling, where strands are pivoted around each other). More than 95% of the straighter strand sections were free of filament cracks, while less than 60% of the bent strand sections were crack free. The high concentration of filament fractures on the tensile side of the strand-strand pivot points indicates that these pivot points are responsible for the vast majority of filament fracture. Much lower crack densities were observed in CICC sections extracted from a lower, gradient-field region of the SULTAN-tested cable. We conclude that localized filament fracture is induced by high Lorentz forces during SULTAN testing of this prototype toroidal field CICC and that the strand sections with the most damage are located at the petal corners of the high field zone.

  5. Apparatus and method for fabricating multi-strand superconducting cable

    DOEpatents

    Borden, Albert R.

    1986-01-01

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet is fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  6. Method for fabricating multi-strand superconducting cable

    DOEpatents

    Borden, A.R.

    1985-04-01

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet are fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  7. Electrodeless dielectrophoresis of single- and double-stranded DNA.

    PubMed Central

    Chou, Chia-Fu; Tegenfeldt, Jonas O; Bakajin, Olgica; Chan, Shirley S; Cox, Edward C; Darnton, Nicholas; Duke, Thomas; Austin, Robert H

    2002-01-01

    Dielectrophoretic trapping of molecules is typically carried out using metal electrodes to provide high field gradients. In this paper we demonstrate dielectrophoretic trapping using insulating constrictions at far lower frequencies than are feasible with metallic trapping structures because of water electrolysis. We demonstrate that electrodeless dielectrophoresis (EDEP) can be used for concentration and patterning of both single-strand and double-strand DNA. A possible mechanism for DNA polarization in ionic solution is discussed based on the frequency, viscosity, and field dependence of the observed trapping force. PMID:12324434

  8. Assembly of highly aligned DNA strands onto Si chips.

    PubMed

    Zhang, Jianming; Ma, Yufeng; Stachura, Sylwia; He, Huixin

    2005-04-26

    This paper reports a robust and efficient approach to assemble highly aligned DNA strands onto Si chips. The method combines advantages from molecular combing and microcontact printing to realize controlling both the density and direction of DNA strands on the Si chip. In addition, it also can be utilized to prepare stretched DNA structures on solid surfaces. Compared to approaches that use molecular combing directly on silanated surfaces, the stretched single-chain DNA structures are straighter. Furthermore, by exploiting the hydrophobic property of the intrinsic poly(dimethylsiloxane) stamp, this study also describes a simple way to produce straight bundled DNA arrays on Si and other substrates.

  9. Correlation between strand asymmetry and phylogeny in mitochondrial DNA.

    PubMed

    Barral P, J; Cantini, L; Hasmy, A; Jiménez, J; Marcano, A

    2005-10-21

    An evolutionary distance is introduced in order to propose an efficient and feasible procedure for phylogeny studies. Our analysis are based on the strand asymmetry property of mitochondrial DNA, but can be applied to other genomes. Comparison of our results with those reported in conventional phylogenetic trees, gives confidence about our approximation. Our findings support the hypotheses about the origin of the skew and its dependence upon evolutionary pressures, and improves previous efforts on using the strand asymmetry property of genomes for phylogeny inference. For the evolutionary distance introduced here, we observe that the more adequate technique for tree reconstructions correspond to an average link method which employs a sequential clustering algorithm.

  10. Crystal structure of four-stranded Oxytricha telomeric DNA

    NASA Technical Reports Server (NTRS)

    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.

  11. Three dimensional FEM quench simulations of superconducting strands

    SciTech Connect

    Yamada, Ryuji; Wake, Masayoshi; /KEK, Tsukuba

    2005-09-01

    The detailed phenomena in quench starting of Nb{sub 3}Sn strands are simulated in 3-D and in time using ANSYS and FEMLAB programs. The current sharing between the superconductor and copper stabilizer in strands at the beginning of a quench was studied and displayed in time. The differences in copper configuration and RRR value of copper were found to have large effect to the stability and quench propagation velocity. The MPZ theory was found to be effective for 3D multifilament situation.

  12. Industry participation workshop: Chromium electroplating of superconductor strand. Proceedings

    SciTech Connect

    1994-12-13

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

  13. Double-strand breaks from a radical commonly produced by DNA-damaging agents.

    PubMed

    Taverna Porro, Marisa L; Greenberg, Marc M

    2015-04-20

    Double-strand breaks are widely accepted to be the most toxic form of DNA damage. Molecules that produce double-strand breaks via a single chemical event are typically very cytotoxic and far less common than those that form single-strand breaks. It was recently reported that a commonly formed C4'-radical produces double-strand breaks under aerobic conditions. Experiments described herein indicate that a peroxyl radical initiates strand damage on the complementary strand via C4'-hydrogen atom abstraction. Inferential evidence suggests that a C3'-peroxyl radical induces complementary strand damage more efficiently than does a C4'-peroxyl radical. Complementary strand hydrogen atom abstraction by the peroxyl radical is efficiently quenched by thiols. This mechanism could contribute to the higher than expected yield of double-strand breaks produced by ionizing radiation.

  14. Blocking Single-Stranded Transferred DNA Conversion to Double-Stranded Intermediates by Overexpression of Yeast DNA REPLICATION FACTOR A1

    PubMed Central

    Levy, Avner; Dafny, Raz; Tzfira, Tzvi

    2015-01-01

    Agrobacterium tumefaciens delivers its single-stranded transferred DNA (T-strand) into the host cell nucleus, where it can be converted into double-stranded molecules. Various studies have revealed that double-stranded transfer DNA (T-DNA) intermediates can serve as substrates by as yet uncharacterized integration machinery. Nevertheless, the possibility that T-strands are themselves substrates for integration cannot be ruled out. We attempted to block the conversion of T-strands into double-stranded intermediates prior to integration in order to further investigate the route taken by T-DNA molecules on their way to integration. Transgenic tobacco (Nicotiana benthamiana) plants that overexpress three yeast (Saccharomyces cerevisiae) protein subunits of DNA REPLICATION FACTOR A (RFA) were produced. In yeast, these subunits (RFA1–RFA3) function as a complex that can bind single-stranded DNA molecules, promoting the repair of genomic double strand breaks. Overexpression of the RFA complex in tobacco resulted in decreased T-DNA expression, as determined by infection with A. tumefaciens cells carrying the β-glucuronidase intron reporter gene. Gene expression was not blocked when the reporter gene was delivered by microbombardment. Enhanced green fluorescent protein-assisted localization studies indicated that the three-protein complex was predominantly nuclear, thus indicating its function within the plant cell nucleus, possibly by binding naked T-strands and blocking their conversion into double-stranded intermediates. This notion was further supported by the inhibitory effect of RFA expression on the cell-to-cell movement of Bean dwarf mosaic virus, a single-stranded DNA virus. The observation that RFA complex plants dramatically inhibited the transient expression level of T-DNA and only reduced T-DNA integration by 50% suggests that double-stranded T-DNA intermediates, as well as single-stranded T-DNA, play significant roles in the integration process. PMID

  15. Purification and characterization of a protein from Saccharomyces cerevisiae that binds tightly to single-stranded DNA and stimulates a cognate strand exchange protein.

    PubMed

    Heyer, W D; Kolodner, R D

    1989-04-01

    A single-stranded DNA binding protein (yeast SSB protein) was purified to near-homogeneity from mitotic Saccharomyces cerevisiae cells. The Mr 34,000 protein specifically eluted at high salt (approximately 1200 mM NaCl) during chromatography on a single-stranded DNA-cellulose column. The protein formed stable complexes with single-stranded DNA in an apparent cooperative fashion. As judged from titration and competition experiments, the affinity of the protein was much higher for single-stranded DNA than for double-stranded DNA or single-stranded RNA. The SSB protein also was found to stimulate the strand exchange reaction between linear M13mp19 RF DNA and circular M13mp19 viral DNA as catalyzed by a yeast strand exchange protein previously purified in this laboratory [Kolodner, R., Evans, D. H., & Morrison, P. T. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 5660-5664]. Titration experiments showed maximum stimulation of joint molecule formation at a stoichiometry of about 1 Mr 34,000 monomer yeast SSB per 18 nucleotides of single-stranded DNA. Kinetic experiments demonstrated at least an 18-fold increase in the rate of strand exchange due to the presence of the SSB in reactions where the amount of strand exchange protein was limiting. The yeast SSB protein stimulated the Escherichia coli RecA protein in the strand exchange reaction involving linear M13mp19 RF DNA and circular M13mp19 viral DNA as efficiently as E. coli SSB. However, the E. coli SSB protein did not substitute for the yeast SSB protein in reactions with the yeast strand exchange protein. This suggests that the stimulation of the yeast strand exchange protein by the yeast SSB may involve specific protein/protein interactions.

  16. TOP OF STRAND ANNEALING TOWER, ONE OF FIVE SUCH STRUCTURES ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    TOP OF STRAND ANNEALING TOWER, ONE OF FIVE SUCH STRUCTURES THE BUFFALO PLANT OF AMERICAN BRASS. HEAVIER-GAUGE STRIP IS CONTINUOUSLY ANNEALED TO GIVE THE PRODUCT A MORE UNIFORM GRAIN SIZE AND RENDER IT MORE DUCTILE. - American Brass Foundry, 70 Sayre Street, Buffalo, Erie County, NY

  17. Polarity, continuity, and alignment in plant vascular strands.

    PubMed

    Sawchuk, Megan G; Scarpella, Enrico

    2013-09-01

    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.

  18. On the Distinction between Preposition Stranding and Orphan Prepositions

    ERIC Educational Resources Information Center

    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…

  19. Short interfering RNA guide strand modifiers from computational screening.

    PubMed

    Onizuka, Kazumitsu; Harrison, Jason G; Ball-Jones, Alexi A; Ibarra-Soza, José M; Zheng, Yuxuan; Ly, Diana; Lam, Walter; Mac, Stephanie; Tantillo, Dean J; Beal, Peter A

    2013-11-13

    Short interfering RNAs (siRNAs) are promising drug candidates for a wide range of targets including those previously considered "undruggable". However, properties associated with the native RNA structure limit drug development, and chemical modifications are necessary. Here we describe the structure-guided discovery of functional modifications for the guide strand 5'-end using computational screening with the high-resolution structure of human Ago2, the key nuclease on the RNA interference pathway. Our results indicate the guide strand 5'-end nucleotide need not engage in Watson-Crick (W/C) H-bonding but must fit the general shape of the 5'-end binding site in MID/PIWI domains of hAgo2 for efficient knockdown. 1,2,3-Triazol-4-yl bases formed from the CuAAC reaction of azides and 1-ethynylribose, which is readily incorporated into RNA via the phosphoramidite, perform well at the guide strand 5'-end. In contrast, purine derivatives with modified Hoogsteen faces or N2 substituents are poor choices for 5'-end modifications. Finally, we identified a 1,2,3-triazol-4-yl base incapable of W/C H-bonding that performs well at guide strand position 12, where base pairing to target was expected to be important. This work expands the repertoire of functional nucleotide analogues for siRNAs. PMID:24152142

  20. Unused and useless: The strange economics of stranded investment

    SciTech Connect

    Michaels, R.J.

    1994-10-01

    Stranded investment cost claims are the last gasp of cost-of-service ratemaking in the face of competition. Even if compensation were theoretically sound, efficient implementation is so problematic that the world would be better off without it. The author discusses this issue which is being raised by some electric utilities in the face of impending competition in the marketplace.

  1. Solid phase sequencing of double-stranded nucleic acids

    DOEpatents

    Fu, Dong-Jing; Cantor, Charles R.; Koster, Hubert; Smith, Cassandra L.

    2002-01-01

    This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

  2. Antiparallel Triple-strand Architecture for Prefibrillar Aβ42 Oligomers*

    PubMed Central

    Gu, Lei; Liu, Cong; Stroud, James C.; Ngo, Sam; Jiang, Lin; Guo, Zhefeng

    2014-01-01

    Aβ42 oligomers play key roles in the pathogenesis of Alzheimer disease, but their structures remain elusive partly due to their transient nature. Here, we show that Aβ42 in a fusion construct can be trapped in a stable oligomer state, which recapitulates characteristics of prefibrillar Aβ42 oligomers and enables us to establish their detailed structures. Site-directed spin labeling and electron paramagnetic resonance studies provide structural restraints in terms of side chain mobility and intermolecular distances at all 42 residue positions. Using these restraints and other biophysical data, we present a novel atomic-level oligomer model. In our model, each Aβ42 protein forms a single β-sheet with three β-strands in an antiparallel arrangement. Each β-sheet consists of four Aβ42 molecules in a head-to-tail arrangement. Four β-sheets are packed together in a face-to-back fashion. The stacking of identical segments between different β-sheets within an oligomer suggests that prefibrillar oligomers may interconvert with fibrils via strand rotation, wherein β-strands undergo an ∼90° rotation along the strand direction. This work provides insights into rational design of therapeutics targeting the process of interconversion between toxic oligomers and non-toxic fibrils. PMID:25118290

  3. 75 FR 4104 - Prestressed Concrete Steel Wire Strand From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-26

    ... Harmonized Tariff Schedule of the United States (``HTSUS'').'' 74 FR 30536, December 23, 2009. For further... FR 68036 (November 8, 2002). Even where electronic filing of a document is permitted, certain... COMMISSION Prestressed Concrete Steel Wire Strand From China AGENCY: United States International...

  4. 75 FR 8113 - Prestressed Concrete Steel Wire Strand From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ... subject investigations (75 FR 4104, January 26, 2010). On January 28, 2010, the Commission was notified by... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Prestressed Concrete Steel Wire Strand From China AGENCY: United States International...

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

    PubMed

    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 (<41 base pairs) resisted this force and remained straight; longer strands became bent, a phenomenon called '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.

  6. Isolating single stranded DNA using a microfluidic dialysis device

    PubMed Central

    Sheng, Yixiao

    2013-01-01

    Isolating a particular strand of DNA from a double stranded DNA duplex is an important step in aptamer generation as well as many other biotechnology applications. Here we describe a microfluidic, flow-through, dialysis device for isolating single-stranded DNA (ssDNA) from double-stranded DNA (dsDNA). The device consists of two channels fabricated in polydimethylsiloxane (PDMS) separated by a track etched polycarbonate membrane (800 nm pore size). To isolate ssDNA, dual-biotin labelled dsDNA was immobilized onto streptavidin-coated polystyrene beads. Alkaline treatment was used to denature dsDNA, releasing the non-biotinylated ssDNA. In the flow-through dialysis device the liberated ssDNA was able to cross the membrane and was collected in an outlet channel. The complementary sequence bound to the bead was unable to cross the membrane and was directed to a waste channel. The effect of NaOH concentration and flow rate on purity and yield were compared. >95% ssDNA purity was achieved at 25mM NaOH. However, lower flow rates were necessary to achieve ssDNA yields approaching the 50% theoretical maximum of the concurrent-flow device. Under optimized conditions the microfluidic isolation achieved even higher purity ssDNA than analogous manual procedures. PMID:24213273

  7. Enzymatic Synthesis of Single-Stranded Clonal Pure Oligonucleotides.

    PubMed

    Ducani, Cosimo; Högberg, Björn

    2017-01-01

    Single-stranded oligonucleotides, or oligodeoxyribonucleotides (ODNs), are very important in several fields of science such as molecular biology, diagnostics, nanotechnology, and gene therapy. They are usually chemically synthesized. Here we describe an enzymatic method which enables us to synthesize pure oligonucleotides which can be up to several hundred long bases. PMID:27671934

  8. The Extra Strand of the Maori Science Curriculum

    ERIC Educational Resources Information Center

    Stewart, Georgina

    2011-01-01

    This paper comments on the process of re-development of the Maori-medium Science (Putaiao) curriculum, as part of overall curriculum development in Aotearoa New Zealand. A significant difference from the English Science curriculum was the addition of an "extra strand" covering the history and philosophy of science. It is recommended that this…

  9. A method for assessing strand breaks in DNA.

    PubMed

    Peng, L; Brisco, M J; Morley, A A

    1998-08-15

    A simple method has been developed to assess strand breaks in extracted DNA. The method uses the enzyme terminal deoxynucleotidyl transferase (TDT) to incorporate labeled deoxycytidine triphosphate (dCTP) in the presence of dideoxy-CTP (ddCTP) which is added to ensure that the reaction goes to completion. Following development of the method, the extent of DNA degradation in 21 blood or bone marrow samples, which had varying degrees of DNA degradation, was measured by the TDT assay, by gel electrophoresis, or by a laborious PCR-based method which quantifies the number of amplifiable N-ras targets in a sample. The TDT assay was more sensitive at detecting strand breaks than electrophoresis and there was good correlation between the results of the TDT assay and the N-ras assay. The TDT assay was also used to demonstrate the development of strand breaks during induced apoptosis. The TDT assay is thus a simple and semiquantitative method to study strand breaks produced by DNA damage.

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

    PubMed

    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.

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

    PubMed Central

    Wierer, Sebastian; Daldrop, Peter; Ud Din Ahmad, Misbha; Boos, Winfried; Drescher, Malte; Welte, Wolfram; Seidel, Ralf

    2016-01-01

    In many hyperthermophilic archaea the DNA binding protein TrmBL2 or one of its homologues is abundantly expressed. TrmBL2 is thought to play a significant role in modulating the chromatin architecture in combination with the archaeal histone proteins and Alba. However, its precise physiological role is poorly understood. It has been previously shown that upon binding TrmBL2 covers double-stranded DNA, which leads to the formation of a thick and fibrous filament. Here we investigated the filament formation process as well as the stabilization of DNA by TrmBL2 from Pyroccocus furiosus in detail. We used magnetic tweezers that allow to monitor changes of the DNA mechanical properties upon TrmBL2 binding on the single-molecule level. Extended filaments formed in a cooperative manner and were considerably stiffer than bare double-stranded DNA. Unlike Alba, TrmBL2 did not form DNA cross-bridges. The protein was found to bind double- and single-stranded DNA with similar affinities. In mechanical disruption experiments of DNA hairpins this led to stabilization of both, the double- (before disruption) and the single-stranded (after disruption) DNA forms. Combined, these findings suggest that the biological function of TrmBL2 is not limited to modulating genome architecture and acting as a global repressor but that the protein acts additionally as a stabilizer of DNA secondary structure. PMID:27214207

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

    PubMed Central

    Beyersdoerfer, Sascha Tobias; Vollmar, Brigitte; Mittlmeier, Thomas; Gierer, Philip

    2016-01-01

    Introduction. This study was designed to investigate the influence of the amount of suture material on the formation of peritendinous adhesions of intrasynovial flexor tendon repairs. Materials and Methods. In 14 rabbits, the flexor tendons of the third and the fourth digit of the right hind leg were cut and repaired using a 2- or 4-strand core suture technique. The repaired tendons were harvested after three and eight weeks. The range of motion of the affected toes was measured and the tendons were processed histologically. The distance between the transected tendon ends, the changes in the peritendinous space, and cellular and extracellular inflammatory reaction were quantified by different staining. Results. A 4-strand core suture resulted in significantly less gap formation. The 2-strand core suture showed a tendency to less adhesion formation. Doubling of the intratendinous suture material was accompanied by an initial increase in leukocyte infiltration and showed a greater amount of formation of myofibroblasts. From the third to the eighth week after flexor tendon repair, both the cellular and the extracellular inflammation decreased significantly. Conclusion. A 4-strand core suture repair leads to a significantly better tendon healing process with less diastasis between the sutured tendon ends despite initially pronounced inflammatory response. PMID:27446949

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

    PubMed

    Wierer, Sebastian; Daldrop, Peter; Ud Din Ahmad, Misbha; Boos, Winfried; Drescher, Malte; Welte, Wolfram; Seidel, Ralf

    2016-01-01

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

  14. The Importance of becoming double-stranded: innate immunity and the kinetic model of HIV-1 central plus strand synthesis

    PubMed Central

    Poeschla, Eric

    2013-01-01

    Central initiation of plus strand synthesis is a conserved feature of lentiviruses and certain other retroelements. This complication of the standard reverse transcription mechanism produces a transient “central DNA flap” in the viral cDNA, which has been proposed to mediate its subsequent nuclear import. This model has assumed that the important feature is the flapped DNA structure itself rather than the process that produces it. Recently, an alternative kinetic model was proposed. It posits that central plus strand synthesis functions to accelerate conversion to the double-stranded state, thereby helping HIV-1 to evade single-strand DNA-targeting antiviral restrictions such as APOBEC3 proteins, and perhaps to avoid innate immune sensor mechanisms. The model is consistent with evidence that lentiviruses must often synthesize their cDNAs when dNTP concentrations are limiting and with data linking reverse transcription and uncoating. There may be additional kinetic advantages for the artificial genomes of lentiviral gene therapy vectors. PMID:23561461

  15. 78 FR 54867 - Proposed Information Collection; Comment Request; Marine Mammal Health and Stranding Response...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration Proposed Information Collection; Comment Request; Marine Mammal Health and Stranding Response Program, Level A Stranding and Rehabilitation Disposition Data...

  16. 75 FR 62820 - Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-13

    ...- Stranded DNA AGENCY: Department of Health and Human Services, Office of the Secretary. ACTION: Notice... provides a framework for screening synthetic double-stranded DNA (dsDNA). This document, the Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA (the Guidance), sets forth...

  17. 75 FR 36678 - Prestressed Concrete Steel Wire Strand From China; Determinations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-28

    ... publishing the notice in the Federal Register of February 23, 2010 (75 FR 8113). The hearing was held in... COMMISSION Prestressed Concrete Steel Wire Strand From China; Determinations On the basis of the record \\1... of prestressed concrete steel wire strand (PC strand), provided for in subheading 7312.10.30 of...

  18. Molecular aptamer beacon tuned DNA strand displacement to transform small molecules into DNA logic outputs.

    PubMed

    Zhu, Jinbo; Zhang, Libing; Zhou, Zhixue; Dong, Shaojun; Wang, Erkang

    2014-03-28

    A molecular aptamer beacon tuned DNA strand displacement reaction was introduced in this work. This strand displacement mode can be used to transform the adenosine triphosphate (ATP) input into a DNA strand output signal for the downstream gates to process. A simple logic circuit was built on the basis of this mechanism.

  19. Cold plasma activation of continuously moving fiber glass strand

    SciTech Connect

    Das, B.

    1992-03-01

    A few selectively activated products were made using 13.6 MHz radio frequency cold plasma induced gases; such as, argon, oxygen, ammonia, Freon{trademark}, and the 30:70 mixture of Freon{trademark} and oxygen. Surface wetting force measurements of random filaments drawn from the activated strands were made using a Wilhelmy Balance. These measurements indicated that chemical modifications of filaments had indeed occurred on all the filaments drawn either from the interior or the surface of the activated strand bundle. In some cases, Ion Scattering Spectrometry was used at Pennsylvania State University to confirm that surface modification of the fiber glass surface had, in fact, taken place during cold plasma activation. While argon and ammonia induced plasma activation did not cause any strength degradation of Emery or organic size coated fibers, the oxygen and Freon{trademark} induced activation did. 16 refs., 7 figs., 3 tabs.

  20. Cardiomyopathy in stranded pygmy and dwarf sperm whales.

    PubMed

    Bossart, G D; Odell, D K; Altman, N H

    1985-12-01

    Necropsy and histologic examinations were performed in 23 pygmy sperm whales (Kogia breviceps) and 6 dwarf sperm whales (Kogia simus) that had been stranded singly or in cow-calf pairs along the southeastern coastline of the United States. At necropsy, the gross findings in the adult whales included pale, flabby right ventricles. Microscopically, lesions in the hearts of the whales were characterized by moderate to extensive myocellular degeneration, atrophy, and fibrosis. Similar changes were not seen in 5 of 6 sexually immature whales or in the whale calves. Hepatic changes were consistent with heart failure. The cause of the myocardial lesions was not determined. The systemic effects of failing myocardium probably were a major reason for the stranding of the adult whales.

  1. Single-strand stacking free energy from DNA beacon kinetics.

    PubMed

    Aalberts, Daniel P; Parman, John M; Goddard, Noel L

    2003-05-01

    DNA beacons are short single-stranded chains which can form closed hairpin shapes through complementary base pairing at their ends. Contrary to the common polymer theory assumption that only their loop length matters, experiments show that their closing kinetics depend on the loop composition. We have modeled the closing kinetics and in so doing have obtained stacking enthalpies and entropies for single-stranded nucleic acids. The resulting change of persistence length with temperature effects the dynamics. With a Monte Carlo study, we answer another polymer question of how the closing time scales with chain length, finding tau approximately N(2.44+/-0.02). There is a significant crossover for shorter chains, bringing the effective exponent into good agreement with experiment.

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Neural network computation with DNA strand displacement cascades.

    PubMed

    Qian, Lulu; Winfree, Erik; Bruck, Jehoshua

    2011-07-21

    The impressive capabilities of the mammalian brain--ranging from perception, pattern recognition and memory formation to decision making and motor activity control--have inspired their re-creation in a wide range of artificial intelligence systems for applications such as face recognition, anomaly detection, medical diagnosis and robotic vehicle control. Yet before neuron-based brains evolved, complex biomolecular circuits provided individual cells with the 'intelligent' behaviour required for survival. However, the study of how molecules can 'think' has not produced an equal variety of computational models and applications of artificial chemical systems. Although biomolecular systems have been hypothesized to carry out neural-network-like computations in vivo and the synthesis of artificial chemical analogues has been proposed theoretically, experimental work has so far fallen short of fully implementing even a single neuron. Here, building on the richness of DNA computing and strand displacement circuitry, we show how molecular systems can exhibit autonomous brain-like behaviours. Using a simple DNA gate architecture that allows experimental scale-up of multilayer digital circuits, we systematically transform arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades that function as small neural networks. Our approach even allows us to implement a Hopfield associative memory with four fully connected artificial neurons that, after training in silico, remembers four single-stranded DNA patterns and recalls the most similar one when presented with an incomplete pattern. Our results suggest that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment. PMID:21776082

  4. Double-Stranded Water on Stepped Platinum Surfaces

    NASA Astrophysics Data System (ADS)

    Kolb, Manuel J.; Farber, Rachael G.; Derouin, Jonathan; Badan, Cansin; Calle-Vallejo, Federico; Juurlink, Ludo B. F.; Killelea, Daniel R.; Koper, Marc T. M.

    2016-04-01

    The interaction of platinum with water plays a key role in (electro)catalysis. Herein, we describe a combined theoretical and experimental study that resolves the preferred adsorption structure of water wetting the Pt(111)-step type with adjacent (111) terraces. Double stranded lines wet the step edge forming water tetragons with dissimilar hydrogen bonds within and between the lines. Our results qualitatively explain experimental observations of water desorption and impact our thinking of solvation at the Pt electrochemical interface.

  5. Repair of DNA double strand breaks: in vivo biochemistry.

    PubMed

    Sugawara, Neal; Haber, James E

    2006-01-01

    Double strand breaks (DSBs) can cause damage to the genomic integrity of a cell as well as initiate genetic recombination processes. The HO and I-SceI endonucleases from budding yeast have provided a way to study these events by inducing a unique DSB in vivo under the control of a galactose-inducible promoter. The GAL::HO construct has been used extensively to study processes such as nonhomologous end joining, intra- and interchromosomal gene conversion, single strand annealing and break-induced recombination. Synchronously induced DSBs have also been important in the study of the DNA damage checkpoint, adaptation, and recovery pathways of yeast. This chapter describes methods of using GAL::HO to physically monitor the progression of events following a DSB, specifically the events leading to the switching of mating type by gene conversion of MAT using the silent donors at HML and HMR. Southern blot analysis can be used to follow the overall events in this process such as the formation of the DSB and product. Denaturing alkaline gels and slot blot techniques can be employed to follow the 5' to 3' resection of DNA starting at the DSB. After resection, the 3' tail initiates a homology search and then strand invades its homologous sequence at the donor cassette. Polymerase chain reaction is an important means to assay strand invasion and the priming of new DNA synthesis as well as the completion of gene conversion. Methods such as chromatin immunoprecipitation have provided a means to study many proteins that associate with a DSB, including not only recombination proteins, but also proteins involved in nonhomologous end joining, cell cycle arrest, chromatin remodeling, cohesin function, and mismatch repair.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Commercial possibilities for stranded conventional gas from Alaska's North Slope

    USGS Publications Warehouse

    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.

  8. Single strand transposition at the host replication fork

    PubMed Central

    Lavatine, Laure; He, Susu; Caumont-Sarcos, Anne; Guynet, Catherine; Marty, Brigitte; Chandler, Mick; Ton-Hoang, Bao

    2016-01-01

    Members of the IS200/IS605 insertion sequence family differ fundamentally from classical IS essentially by their specific single-strand (ss) transposition mechanism, orchestrated by the Y1 transposase, TnpA, a small HuH enzyme which recognizes and processes ss DNA substrates. Transposition occurs by the ‘peel and paste’ pathway composed of two steps: precise excision of the top strand as a circular ss DNA intermediate; and subsequent integration into a specific ssDNA target. Transposition of family members was experimentally shown or suggested by in silico high-throughput analysis to be intimately coupled to the lagging strand template of the replication fork. In this study, we investigated factors involved in replication fork targeting and analysed DNA-binding properties of the transposase which can assist localization of ss DNA substrates on the replication fork. We showed that TnpA interacts with the β sliding clamp, DnaN and recognizes DNA which mimics replication fork structures. We also showed that dsDNA can facilitate TnpA targeting ssDNA substrates. We analysed the effect of Ssb and RecA proteins on TnpA activity in vitro and showed that while RecA does not show a notable effect, Ssb inhibits integration. Finally we discuss the way(s) in which integration may be directed into ssDNA at the replication fork. PMID:27466393

  9. Carbon Fiber Strand Tensile Failure Dynamic Event Characterization

    NASA Technical Reports Server (NTRS)

    Johnson, Kenneth L.; Reeder, James

    2016-01-01

    There are few if any clear, visual, and detailed images of carbon fiber strand failures under tension useful for determining mechanisms, sequences of events, different types of failure modes, etc. available to researchers. This makes discussion of physics of failure difficult. It was also desired to find out whether the test article-to-test rig interface (grip) played a part in some failures. These failures have nothing to do with stress rupture failure, thus representing a source of waste for the larger 13-00912 investigation into that specific failure type. Being able to identify or mitigate any competing failure modes would improve the value of the 13-00912 test data. The beginnings of the solution to these problems lay in obtaining images of strand failures useful for understanding physics of failure and the events leading up to failure. Necessary steps include identifying imaging techniques that result in useful data, using those techniques to home in on where in a strand and when in the sequence of events one should obtain imaging data.

  10. Force-Driven Separation of Short Double-Stranded DNA

    PubMed Central

    Ho, Dominik; Zimmermann, Julia L.; Dehmelt, Florian A.; Steinbach, Uta; Erdmann, Matthias; Severin, Philip; Falter, Katja; Gaub, Hermann E.

    2009-01-01

    Abstract Short double-stranded DNA is used in a variety of nanotechnological applications, and for many of them, it is important to know for which forces and which force loading rates the DNA duplex remains stable. In this work, we develop a theoretical model that describes the force-dependent dissociation rate for DNA duplexes tens of basepairs long under tension along their axes (“shear geometry”). Explicitly, we set up a three-state equilibrium model and apply the canonical transition state theory to calculate the kinetic rates for strand unpairing and the rupture-force distribution as a function of the separation velocity of the end-to-end distance. Theory is in excellent agreement with actual single-molecule force spectroscopy results and even allows for the prediction of the rupture-force distribution for a given DNA duplex sequence and separation velocity. We further show that for describing double-stranded DNA separation kinetics, our model is a significant refinement of the conventionally used Bell-Evans model. PMID:20006953

  11. Yields of single-strand breaks in double-stranded calf thymus DNA irradiated in aqueous solution in the presence of oxygen and scavengers

    SciTech Connect

    Udovicic, Lj.; Mark, F.; Bothe, E.

    1994-11-01

    Yields of radiation-induced single-strand breaks in double-stranded calf thymus DNA have been measured as a function of OH scavenger concentration in N{sub 2}O/O{sub 2}-saturated aqueous solution. The experimental data are well represented by a theoretical model based on non-homogeneous reaction kinetics, without the need to adjust any parameter. The good agreement between experimental and theoretical data is taken as evidence that, in the presence of oxygen, the main effect of added scavengers with respect to the formation of single-strand breaks in double-stranded DNA is OH radical scavenging. 30 refs., 3 figs., 1 tab.

  12. Carbohydrate radicals: from ethylene glycol to DNA strand breakage.

    PubMed

    von Sonntag, Clemens

    2014-06-01

    Radiation-induced DNA strand breakage results from the reactions of radicals formed at the sugar moiety of DNA. In order to elucidate the mechanism of this reaction investigations were first performed on low molecular weight model systems. Results from studies on deoxygenated aqueous solutions of ethylene glycol, 2-deoxy-d-ribose and other carbohydrates and, more relevantly, of d-ribose-5-phosphate have shown that substituents can be eliminated from the β-position of the radical site either proton and base-assisted (as in the case of the OH substituent), or spontaneously (as in the case of the phosphate substituent). In DNA the C(4') radical undergoes strand breakage via this type of reaction. In the presence of oxygen the carbon-centred radicals are rapidly converted into the corresponding peroxyl radicals. Again, low molecular weights models have been investigated to elucidate the key reactions. A typical reaction of DNA peroxyl radicals is the fragmentation of the C(4')-C(S') bond, a reaction not observed in the absence of oxygen. Although OH radicals may be the important direct precursors of the sugar radicals of DNA, results obtained with poly(U) indicate that base radicals may well be of even greater importance. The base radicals, formed by addition of the water radicals (H and OH) to the bases would in their turn attack the sugar moiety to produce sugar radicals which then give rise to strand breakage and base release. For a better understanding of strand break formation it is therefore necessary to investigate in more detail the reactions of the base radicals. For a start, the radiolysis of uracil in oxygenated solutions has been reinvestigated, and it has been shown that the major peroxyl radical in this system undergoes base-catalysed elimination of [Formula: see text], a reaction that involves the proton at N(l). In the nucleic acids the pyrimidines are bound at N(l) to the sugar moiety and this type of reaction can no longer occur. Therefore, with

  13. Sequence selective double strand DNA cleavage by peptide nucleic acid (PNA) targeting using nuclease S1.

    PubMed Central

    Demidov, V; Frank-Kamenetskii, M D; Egholm, M; Buchardt, O; Nielsen, P E

    1993-01-01

    A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand cleavage at an occupied PNA strand displacement binding site, and under optimized conditions complete cleavage can be obtained. The efficiency of this cleavage is more than 10 fold enhanced when a tandem PNA site is targeted, and additionally enhanced if this site is in trans rather than in cis orientation. Thus in effect, the PNA targeting makes the single strand specific nuclease S1 behave like a pseudo restriction endonuclease. Images PMID:8502550

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

    PubMed

    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).

  15. Analysis of BRCA1 Variants in Double-Strand Break Repair by Homologous Recombination and Single-Strand Annealing

    PubMed Central

    Towler, William I.; Zhang, Jie; Ransburgh, Derek J. R.; Toland, Amanda E.; Ishioka, Chikashi; Chiba, Natsuko; Parvin, Jeffrey D.

    2014-01-01

    Missense substitutions of uncertain clinical significance in the BRCA1 gene are a vexing problem in genetic counseling for women who have a family history of breast cancer. In this study, we evaluated the functions of 29 missense substitutions of BRCA1 in two DNA repair pathways. Repair of double-strand breaks by homology-directed recombination (HDR) had been previously analyzed for 16 of these BRCA1 variants, and 13 more variants were analyzed in this study. All 29 variants were also analyzed for function in double-strand break repair by the single-strand annealing (SSA) pathway. We found that among the pathogenic mutations in BRCA1, all were defective for DNA repair by either pathway. The HDR assay was accurate because all pathogenic mutants were defective for HDR, and all nonpathogenic variants were fully functional for HDR. Repair by SSA accurately identified pathogenic mutants, but several nonpathogenic variants were scored as defective or partially defective. These results indicated that specific amino acid residues of the BRCA1 protein have different effects in the two related DNA repair pathways, and these results validate the HDR assay as highly correlative with BRCA1-associated breast cancer. PMID:23161852

  16. Relationships among the positive strand and double-strand RNA viruses as viewed through their RNA-dependent RNA polymerases.

    PubMed

    Bruenn, J A

    1991-01-25

    The sequences of 50 RNA-dependent RNA polymerases (RDRPs) from 43 positive strand and 7 double strand RNA (dsRNA) viruses have been compared. The alignment permitted calculation of distances among the 50 viruses and a resultant dendrogram based on every amino acid, rather than just those amino acids in the conserved motifs. Remarkably, a large subgroup of these viruses, including vertebrate, plant, and insect viruses, forms a single cluster whose only common characteristic is exploitation of insect hosts or vectors. This similarity may be due to molecular constraints associated with a present and/or past ability to infect insects and/or to common descent from insect viruses. If common descent is important, as it appears to be, all the positive strand RNA viruses of eucaryotes except for the picornaviruses may have evolved from an ancestral dsRNA virus. Viral RDRPs appear to be inherited as modules rather than as portions of single RNA segments, implying that RNA recombination has played an important role in their dissemination.

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

    PubMed

    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). PMID:26803414

  18. Adenovirus-associated virus multiplication. VI. Base compostion of the deoxyribonucleic acid strand species and strand-specific in vivo transcription.

    PubMed

    Rose, J A; Koczot, F

    1971-11-01

    The two complementary strand species of 5-bromodeoxyuridine-substituted, adenovirus-associated virus type 2 (AAV-2) deoxyribonucleic acid were preparatively separated in CsCl density gradients and further purified by sedimentation through 5 to 20% sucrose. The base composition of each strand species was determined, and it was found that the species banding at a greater density in CsCl (heavy strands) had an expected higher thymidine content (26.5%) than that 21.7%) of the less dense species (light strands). Furthermore, the base composition of in vivo-synthesized, AAV-specific ribonucleic acid was similar to that of light-strand deoxyribonucleic acid, and this ribonucleic acid apparently hybridized only with heavy strands. These observations indicate that the heavy-strand species alone serves as the transcriptional template in vivo. This study represents the first instance in which the base composition and specificity of in vivo transcription have been determined for each of the complementary strands of an animal virus deoxyribonucleic acid.

  19. Prostate brachytherapy postimplant dosimetry: Automatic plan reconstruction of stranded implants

    SciTech Connect

    Chng, N.; Spadinger, I.; Morris, W. J.; Usmani, N.; Salcudean, S.

    2011-01-15

    Purpose: Plan reconstruction for permanent implant prostate brachytherapy is the process of determining the correspondence between planned and implanted seeds in postimplant analysis. Plan reconstruction informs many areas of brachytherapy quality assurance, including the verification of seed segmentation, misplacement and migration assessment, implant simulations, and the dosimetry of mixed-activity or mixed-species implants. Methods: An algorithm has been developed for stranded implants which uses the interseed spacing constraints imposed by the suture to improve the accuracy of reconstruction. Seventy randomly selected clinical cases with a mean of 23.6 (range 18-30) needles and mean density of 2.0 (range 1.6-2.6) 2.0 (range 1.6-2.6) seeds/cm{sup 3} were automatically reconstructed and the accuracy compared to manual reconstructions performed using a custom 3D graphical interface. Results: Using the automatic algorithm, the mean accuracy of the assignment relative to manual reconstruction was found to be 97.7{+-}0.5%. Fifty-two of the 70 cases (74%) were error-free; of seeds in the remaining cases, 96.7{+-}0.3% were found to be attributed to the correct strand and 97.0{+-}0.3% were correctly connected to their neighbors. Any necessary manual correction using the interface is usually straightforward. For the clinical data set tested, neither the number of seeds or needles, average density, nor the presence of clusters was found to have an effect on reconstruction accuracy using this method. Conclusions: Routine plan reconstruction of stranded implants can be performed with a high degree of accuracy to support postimplant dosimetry and quality analyses.

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

    PubMed Central

    Morales, Maria E.; Derbes, Rebecca S.; Ade, Catherine M.; Ortego, Jonathan C.; Stark, Jeremy; Deininger, Prescott L.; Roy-Engel, Astrid M.

    2016-01-01

    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. PMID:26966913

  1. Replication of murine coronavirus defective interfering RNA from negative-strand transcripts.

    PubMed

    Joo, M; Banerjee, S; Makino, S

    1996-09-01

    The positive-strand defective interfering (DI) RNA of the murine coronavirus mouse hepatitis virus (MHV), when introduced into MHV-infected cells, results in DI RNA replication and accumulation. We studied whether the introduction of negative-strand transcripts of MHV DI RNA would also result in replication. At a location downstream of the T7 promoter and upstream of the human hepatitis delta virus ribozyme domain, we inserted a complete cDNA clone of MHV DI RNA in reverse orientation; in vitro-synthesized RNA from this plasmid yielded a negative-strand RNA copy of the MHV DI RNA. When the negative-strand transcripts of the DI RNA were expressed in MHV-infected cells by a vaccinia virus T7 expression system, positive-strand DI RNAs accumulated in the plasmid-transfected cells. DI RNA replication depended on the expression of T7 polymerase and on the presence of the T7 promoter. Transfection of in vitro-synthesized negative-strand transcripts into MHV-infected cells and serial passage of virus samples from RNA-transfected cells also resulted in accumulation of the DI RNA. Positive-strand DI RNA transcripts were undetectable in sample preparations of the in vitro-synthesized negative-strand DI RNA transcripts, and DI RNA did not accumulate after cotransfection of a small amount of positive-strand DI RNA and truncated-replication-disabled negative-strand transcripts; clearly, the DI RNA replicated from the transfected negative-strand transcripts and not from minute amounts of positive-strand DI RNAs that might be envisioned as artifacts of T7 transcription. Sequence analysis of positive-strand DI RNAs in the cells transfected with negative-strand transcripts showed that DI RNAs maintained the DI-specific unique sequences introduced within the leader sequence. These data indicated that positive-strand DI RNA synthesis occurred from introduced negative-strand transcripts in the MHV-infected cells; this demonstration, using MHV, of DI RNA replication from transfected

  2. Bluegill virus is a ribovirus of positive-strand polarity.

    PubMed

    Robin, J; Larivière-Durand, C

    1983-01-01

    RNA was extracted from purified Bluegill virus (BGV) and fractionated onto a poly (U)-Sepharose-4 B column. More than 70 per cent of this RNA became bound and could be subsequently eluted from the column. By polynucleotide phosphorylase digestion, the poly (A) sequences were located at the 3'-terminus of the RNA. This RNA and purified BGV RNA were infectious as shown by plaque assay titration of the virus produced. Furthermore, we were unable to detect RNA polymerase activity in preparations of BGV. These results indicate that the genome in the BGV particle is a positive-strand RNA.

  3. The growing problem of stranded used nuclear fuel.

    PubMed

    Alley, William M; Alley, Rosemarie

    2014-02-18

    By 2050, almost all U.S. nuclear reactors will have reached their 60 year maximum expected life. Many will shut down sooner. With no assurance that the current approach for finding a geologic repository or interim storage sites will succeed, used nuclear fuel could be stranded indefinitely at more than 70 sites in 35 states. Societal discussions about the future of nuclear waste should be framed in terms of the relative risks of all alternatives. We review and compare onsite storage, interim storage, and a geologic repository, as well as how these alternatives are presented to the public.

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

    PubMed

    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.

  5. Double strand breaks: hurdles for RNA polymerase II transcription?

    PubMed

    Pankotai, Tibor; Soutoglou, Evi

    2013-01-01

    DNA lesions pose a physical obstacle to DNA-dependent cellular transactions such as replication and transcription. A great deal is known regarding RNA polymerase II (RNAP II) transcription stalling in the presence of lesions induced by UV, but recent studies have uncovered previously uncharacterized behavior of the RNAP II machinery in the presence of double strand breaks (DSBs). These new data, although contradictory, contribute to our understanding of a vital cellular mechanism that defends against the production of aberrant transcripts and protects cell viability.

  6. Herpetic keratoconjunctivitis: Therapy with synthetic double-stranded RNA

    USGS Publications Warehouse

    Friedman, I.; Evans, C.; Meighan, C.W.; Foote, L.J.; Aiello, P.V.; Park, J.H.; Baron, S.

    1968-01-01

    A study was undertaken in rabbits to determine how late in the course of keratoconjunctivitis caused by herpes simplex recovery could be effected by an inducer of interferon. Interferon was induced by means of synthetic double-stranded RNA copolymer formed with polynosinic acid : polycytidilic acid RNA. Therapy promotes recovery from severe and fully established keratoconjunctivitis for which treatment was begun as late as 3 days after virus inoculation. No drug toxicity was observed in the therapeutic dose range. These findings further support the proposed role of the interferon mechanism in the natural recovery of already established viral infection. They also suggest the usefulness of interferon inducers in viral infections of man.

  7. Mechanical Separation of the Complementary Strands of DNA

    NASA Astrophysics Data System (ADS)

    Essevaz-Roulet, B.; Bockelmann, U.; Heslot, F.

    1997-10-01

    We describe the mechanical separation of the two complementary strands of a single molecule of bacteriophage λ DNA. The 3' and 5' extremities on one end of the molecule are pulled progressively apart, and this leads to the opening of the double helix. The typical forces along the opening are in the range of 10-15 pN. The separation force signal is shown to be related to the local GC vs. AT content along the molecule. Variations of this content on a typical scale of 100-500 bases are presently detected.

  8. The growing problem of stranded used nuclear fuel.

    PubMed

    Alley, William M; Alley, Rosemarie

    2014-02-18

    By 2050, almost all U.S. nuclear reactors will have reached their 60 year maximum expected life. Many will shut down sooner. With no assurance that the current approach for finding a geologic repository or interim storage sites will succeed, used nuclear fuel could be stranded indefinitely at more than 70 sites in 35 states. Societal discussions about the future of nuclear waste should be framed in terms of the relative risks of all alternatives. We review and compare onsite storage, interim storage, and a geologic repository, as well as how these alternatives are presented to the public. PMID:24437358

  9. Adenosine triphosphatases of thermophilic archaeal double-stranded DNA viruses

    PubMed Central

    2014-01-01

    Adenosine triphosphatases (ATPases) of double-stranded (ds) DNA archaeal viruses are structurally related to the AAA+ hexameric helicases and translocases. These ATPases have been implicated in viral life cycle functions such as DNA entry into the host, and viral genome packaging into preformed procapsids. We summarize bioinformatical analyses of a wide range of archaeal ATPases, and review the biochemical and structural properties of those archaeal ATPases that have measurable ATPase activity. We discuss their potential roles in genome delivery into the host, virus assembly and genome packaging in comparison to hexameric helicases and packaging motors from bacteriophages. PMID:25105011

  10. Silence of the strands: RNA interference in eukaryotic pathogens.

    PubMed

    Cottrell, Tricia R; Doering, Tamara L

    2003-01-01

    Double-stranded (ds) RNA interference (RNAi) is a recent technological advance that enables researchers to reduce gene expression at the post-transcriptional level. This form of RNA silencing is initiated by dsRNA, expressed in or introduced into a cell of interest, which triggers homology-dependent degradation of the corresponding mRNA. This versatile technique has remarkable promise as a tool for the study of eukaryotic pathogens. Protozoan parasites and pathogenic fungi often resist manipulation using standard molecular genetic approaches. Researchers studying these organisms need flexible molecular tools, particularly to exploit newly sequenced genomes; this review offers a practical guide to establishing RNAi in pathogenic eukaryotes.

  11. Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets.

    PubMed

    Kuhn, Heiko; Demidov, Vadim V; Coull, James M; Fiandaca, Mark J; Gildea, Brian D; Frank-Kamenetskii, Maxim D

    2002-02-13

    Molecular beacons are sensitive fluorescent probes hybridizing selectively to designated DNA and RNA targets. They have recently become practical tools for quantitative real-time monitoring of single-stranded nucleic acids. Here, we comparatively study the performance of a variety of such probes, stemless and stem-containing DNA and PNA (peptide nucleic acid) beacons, in Tris-buffer solutions containing various concentrations of NaCl and MgCl(2). We demonstrate that different molecular beacons respond differently to the change of salt concentration, which could be attributed to the differences in their backbones and constructions. We have found that the stemless PNA beacon hybridizes rapidly to the complementary oligodeoxynucleotide and is less sensitive than the DNA beacons to the change of salt thus allowing effective detection of nucleic acid targets under various conditions. Though we found stemless DNA beacons improper for diagnostic purposes due to high background fluorescence, we believe that use of these DNA and similar RNA constructs in molecular-biophysical studies may be helpful for analysis of conformational flexibility of single-stranded nucleic acids. With the aid of PNA "openers", molecular beacons were employed for the detection of a chosen target sequence directly in double-stranded DNA (dsDNA). Conditions are found where the stemless PNA beacon strongly discriminates the complementary versus mismatched dsDNA targets. Together with the insensitivity of PNA beacons to the presence of salt and DNA-binding/processing proteins, the latter results demonstrate the potential of these probes as robust tools for recognition of specific sequences within dsDNA without denaturation and deproteinization of duplex DNA.

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

    NASA Astrophysics Data System (ADS)

    Fields, Alexander; Axelrod, Kevin; Cohen, Adam

    2012-02-01

    Bare double-stranded DNA is a stiff biopolymer with a persistence length of roughly 53 nm under physiological conditions. Cells and viruses employ extensive protein machinery to overcome this stiffness and bend, twist, and loop DNA to accomplish tasks such as packaging, recombination, gene regulation, and repair. The mechanical properties of DNA are of fundamental importance to the mechanism and thermodynamics of these processes, but physiologically relevant curvature has been difficult to access experimentally. We designed and synthesized a DNA hairpin construct in which base-pairing interactions generated a compressive force on a short segment of duplex DNA, inducing Euler buckling followed by bending to thermally inaccessible radii of curvature. The efficiency of F"orster resonance energy transfer (FRET) between two fluorophores covalently linked to the hairpin indicated the degree of buckling. Bulk and single-molecule measurements yielded distinctly different force-compression curves for intact DNA and for strands with single nicks, base pair mismatches, and damage sites. These results suggest that changes in local mechanical properties may play a significant role in the recognition of these features by DNA-binding proteins.

  13. Single-Stranded Tile Stoppers for Interlocked DNA Architectures.

    PubMed

    Valero, Julián; Lohmann, Finn; Keppner, Daniel; Famulok, Michael

    2016-06-16

    Interlocked DNA architectures are useful for DNA nanotechnology because of their mechanically bonded components, which can move relative to one another without disassembling. We describe the design, synthesis, and characterization of novel single-stranded tile (SST) stoppers for the assembly of interlocked DNA architectures. SST stoppers are shown to self-assemble into a square-shaped rigid structure upon mixing 97 oligodeoxynucleotide (ODN) strands. The structures are equipped with a sticky end that is designed for hybridization with the sticky ends of a dsDNA axle of a DNA rotaxane. Because the diameter of the macrocycle threaded onto the axle is 14 nm, the dimension of the square-shaped stopper was designed to be bulky enough to prevent the dethreading of the macrocycle. An asymmetric rotaxane with a SST- and a ring-shaped stopper featuring two stations for hybridization of the macrocycle to the axle was assembled. The macrocycle can be directed towards one or the other station upon triggering with fuel ODNs.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Entropy in DNA Double-Strand Break, Detection and Signaling

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Schindler, Christina; Heermann, Dieter

    2014-03-01

    In biology, the term entropy is often understood as a measure of disorder - a restrictive interpretation that can even be misleading. Recently it has become clearer and clearer that entropy, contrary to conventional wisdom, can help to order and guide biological processes in living cells. DNA double-strand breaks (DSBs) are among the most dangerous lesions and efficient damage detection and repair is essential for organism viability. However, what remains unknown is the precise mechanism of targeting the site of damage within billions of intact nucleotides and a crowded nuclear environment, a process which is often referred to as recruitment or signaling. Here we show that the change in entropy associated with inflicting a DSB facilitates the recruitment of damage sensor proteins. By means of computational modeling we found that higher mobility and local chromatin structure accelerate protein association at DSB ends. We compared the effect of different chromatin architectures on protein dynamics and concentrations in the vicinity of DSBs, and related these results to experiments on repair in heterochromatin. Our results demonstrate how entropy contributes to a more efficient damage detection. We identify entropy as the physical basis for DNA double-strand break signaling.

  16. Single-Stranded Tile Stoppers for Interlocked DNA Architectures.

    PubMed

    Valero, Julián; Lohmann, Finn; Keppner, Daniel; Famulok, Michael

    2016-06-16

    Interlocked DNA architectures are useful for DNA nanotechnology because of their mechanically bonded components, which can move relative to one another without disassembling. We describe the design, synthesis, and characterization of novel single-stranded tile (SST) stoppers for the assembly of interlocked DNA architectures. SST stoppers are shown to self-assemble into a square-shaped rigid structure upon mixing 97 oligodeoxynucleotide (ODN) strands. The structures are equipped with a sticky end that is designed for hybridization with the sticky ends of a dsDNA axle of a DNA rotaxane. Because the diameter of the macrocycle threaded onto the axle is 14 nm, the dimension of the square-shaped stopper was designed to be bulky enough to prevent the dethreading of the macrocycle. An asymmetric rotaxane with a SST- and a ring-shaped stopper featuring two stations for hybridization of the macrocycle to the axle was assembled. The macrocycle can be directed towards one or the other station upon triggering with fuel ODNs. PMID:26972112

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

    SciTech Connect

    Ortín, Juan; Martín-Benito, Jaime

    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.

  18. Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data

    PubMed Central

    Ye, Yuzhen; Zhang, Quan

    2016-01-01

    CRISPR–Cas systems are bacterial adaptive immune systems, each typically composed of a locus of cas genes and a CRISPR array of spacers flanked by repeats. Processed transcripts of CRISPR arrays (crRNAs) play important roles in the interference process mediated by these systems, guiding targeted immunity. Here we developed computational approaches that allow us to characterize the expression of many CRISPRs in their natural environments, using community RNA-seq (metatranscriptomic) data. By exploiting public human gut metatranscriptomic data sets, we studied the expression of 56 repeat-sequence types of CRISPRs, revealing that most CRISPRs are transcribed in one direction (producing crRNAs). In rarer cases, including a type II system associated with Bacteroides fragilis, CRISPRs are transcribed in both directions. Type III CRISPR–Cas systems were found in the microbiomes, but metatranscriptomic reads were barely found for their CRISPRs. We observed individual-level variation of the crRNA transcription, and an even greater transcription of a CRISPR from the antisense strand than the crRNA strand in one sample. The orientations of CRISPR expression implicated by metatranscriptomic data are largely in agreement with prior predictions for CRISPRs, with exceptions. Our study shows the promise of exploiting community RNA-seq data for investigating the transcription of CRISPR–Cas systems. PMID:27190232

  19. Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation

    SciTech Connect

    Railsback, Justin; Singh, Abhishek; Pearce, Ryan; McKnight, Timothy E; Collazo, Ramon; Sitar, Zlatko; Yingling, Yaroslava; Melechko, Anatoli Vasilievich

    2012-01-01

    The understanding of interactions between double stranded (ds) DNA and charged nanoparticles will have a broad bearing on many important applications from drug delivery [ 1 4 ] to DNAtemplated metallization. [ 5 , 6 ] Cationic nanoparticles (NPs) can bind to DNA, a negatively charged molecule, through a combination of electrostatic attraction, groove binding, and intercalation. Such binding events induce changes in the conformation of a DNA strand. In nature, DNA wraps around a cylindrical protein assembly (diameter and height of 6 nm) [ 7 ] with an 220 positive charge, [ 8 ] creating the complex known as chromatin. Wrapping and bending of DNA has also been achieved in the laboratory through the binding of highly charged species such as molecular assemblies, [ 9 , 10 ] cationic dendrimers, [ 11 , 12 ] and nanoparticles. [ 13 15 ] The charge of a nanoparticle plays a crucial role in its ability to induce DNA structural changes. If a nanoparticle has a highly positive surface charge density, the DNA is likely to wrap and bend upon binding to the nanoparticle [ 13 ] (as in the case of chromatin). On the other hand, if a nanoparticle is weakly charged it will not induce dsDNA compaction. [ 9 , 10 , 15 ] Consequently, there is a transition zone from extended to compact DNA conformations which depends on the chemical nature of the nanoparticle and occurs for polycations with charges between 5 and 10. [ 9 ] While the interactions between highly charged NPs and DNA have been extensively studied, the processes that occur within the transition zone are less explored.

  20. Nucleolar responses to DNA double-strand breaks.

    PubMed

    Larsen, Dorthe Helena; Stucki, Manuel

    2016-01-29

    Maintenance of cellular homeostasis is key to prevent transformation and disease. The cellular response to DNA double-strand breaks, primarily orchestrated by the ATM/ATR kinases is one of many mechanisms that serve to uphold genome stability and homeostasis. Upon detection of double-strand breaks (DSBs), several signaling cascades are activated to halt cell cycle progression and initiate repair. Furthermore, the DNA damage response (DDR) controls cellular processes such as transcription, splicing and metabolism. Recent studies have uncovered aspects of how the DDR operates within nucleoli. It appears that the DDR controls transcription in the nucleoli, not only when DNA breaks occur in the rDNA repeats, but also when a nuclear DDR is activated. In addition, we have gained first insights into how repair of DSBs is organized in the nucleolus. Collectively, these recent studies provide a more comprehensive picture of how the DDR regulates basic cellular functions to maintain cellular homeostasis. In this review we will summarize recent findings and discuss their implications for our understanding of how the DDR regulates transcription and repair in the nucleolus.

  1. Dynamic control of strand excision during human DNA mismatch repair.

    PubMed

    Jeon, Yongmoon; Kim, Daehyung; Martín-López, Juana V; Lee, Ryanggeun; Oh, Jungsic; Hanne, Jeungphill; Fishel, Richard; Lee, Jong-Bong

    2016-03-22

    Mismatch repair (MMR) is activated by evolutionarily conserved MutS homologs (MSH) and MutL homologs (MLH/PMS). MSH recognizes mismatched nucleotides and form extremely stable sliding clamps that may be bound by MLH/PMS to ultimately authorize strand-specific excision starting at a distant 3'- or 5'-DNA scission. The mechanical processes associated with a complete MMR reaction remain enigmatic. The purified human (Homo sapien or Hs) 5'-MMR excision reaction requires the HsMSH2-HsMSH6 heterodimer, the 5' → 3' exonuclease HsEXOI, and the single-stranded binding heterotrimer HsRPA. The HsMLH1-HsPMS2 heterodimer substantially influences 5'-MMR excision in cell extracts but is not required in the purified system. Using real-time single-molecule imaging, we show that HsRPA or Escherichia coli EcSSB restricts HsEXOI excision activity on nicked or gapped DNA. HsMSH2-HsMSH6 activates HsEXOI by overcoming HsRPA/EcSSB inhibition and exploits multiple dynamic sliding clamps to increase tract length. Conversely, HsMLH1-HsPMS2 regulates tract length by controlling the number of excision complexes, providing a link to 5' MMR.

  2. Nucleolar responses to DNA double-strand breaks

    PubMed Central

    Larsen, Dorthe Helena; Stucki, Manuel

    2016-01-01

    Maintenance of cellular homeostasis is key to prevent transformation and disease. The cellular response to DNA double-strand breaks, primarily orchestrated by the ATM/ATR kinases is one of many mechanisms that serve to uphold genome stability and homeostasis. Upon detection of double-strand breaks (DSBs), several signaling cascades are activated to halt cell cycle progression and initiate repair. Furthermore, the DNA damage response (DDR) controls cellular processes such as transcription, splicing and metabolism. Recent studies have uncovered aspects of how the DDR operates within nucleoli. It appears that the DDR controls transcription in the nucleoli, not only when DNA breaks occur in the rDNA repeats, but also when a nuclear DDR is activated. In addition, we have gained first insights into how repair of DSBs is organized in the nucleolus. Collectively, these recent studies provide a more comprehensive picture of how the DDR regulates basic cellular functions to maintain cellular homeostasis. In this review we will summarize recent findings and discuss their implications for our understanding of how the DDR regulates transcription and repair in the nucleolus. PMID:26615196

  3. Chromatin modifications and DNA repair: beyond double-strand breaks

    PubMed Central

    House, Nealia C. M.; Koch, Melissa R.; Freudenreich, Catherine H.

    2014-01-01

    DNA repair must take place in the context of chromatin, and chromatin modifications and DNA repair are intimately linked. The study of double-strand break repair has revealed numerous histone modifications that occur after induction of a DSB, and modification of the repair factors themselves can also occur. In some cases the function of the modification is at least partially understood, but in many cases it is not yet clear. Although DSB repair is a crucial activity for cell survival, DSBs account for only a small percentage of the DNA lesions that occur over the lifetime of a cell. Repair of single-strand gaps, nicks, stalled forks, alternative DNA structures, and base lesions must also occur in a chromatin context. There is increasing evidence that these repair pathways are also regulated by histone modifications and chromatin remodeling. In this review, we will summarize the current state of knowledge of chromatin modifications that occur during non-DSB repair, highlighting similarities and differences to DSB repair as well as remaining questions. PMID:25250043

  4. Wheeling and stranded investment-is there a better way

    SciTech Connect

    Ferrar, T.

    1994-03-25

    Under current franchise law, retail wheeling must be addressed on a state-by-state basis, and (therefore) it will not sweep the electric power industry as deregulation has been visited upon the telecommunications, airline, natural gas and other industries. Nevertheless, many industry observers remain concerned that retail competition will create a significant stranded investment problem. That is, broadened competition among power generators for customers will result in the market value of some existing (previously market-protected) generation assets falling below book value. The significance of such asset revaluations, and the time required for adjustment, increases with the capital intensity of the industry; this is the reason for the heightened concern regarding the introduction of retail wheeling into the electric power industry. One policy direction that may be worthy of further debate and losses during the power market's transition to a more competitive equilibrium - i.e., until regulation-induced differentials between market and book values are mitigated. A two-part policy proposal is offered for consideration. First, the use of intra-pool transfer payments; second, if stranded investment continues to exist, a temporary uniform pool-wide wheeling surcharge.

  5. Vacuum-ultraviolet circular dichroism reveals DNA duplex formation between short strands of adenine and thymine.

    PubMed

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

    2012-11-21

    Absorbance spectroscopy is used extensively to tell when two DNA single strands come together and form a double strand. Here we show that circular dichroism in the vacuum ultraviolet region provides an even stronger indication for duplex formation in the case of short strands of adenine and thymine (4 to 16 bases in each strand). Indeed, our results show that a strong positive CD band appears at 179 nm when double strands are formed. Melting experiments were done in aqueous solution with and without added Na(+) counter ions. With additional salt present a huge increase in the 179 nm CD band was observed when lowering the temperature. A 179 nm CD marker band for duplex formation can be used to measure the kinetics for the association of two single strands. Such experiments rely on large changes at one particular wavelength since it is too time-consuming to record a full-wavelength spectrum.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26083230

  7. A comprehensive classification of nucleic acid structural families based on strand direction and base pairing.

    PubMed Central

    Lavery, R; Zakrzewska, K; Sun, J S; Harvey, S C

    1992-01-01

    We propose a classification of DNA structures formed from 1 to 4 strands, based only on relative strand directions, base to strand orientation and base pairing geometries. This classification and its associated notation enable all nucleic acids to be grouped into structural families and bring to light possible structures which have not yet been observed experimentally. It also helps in understanding transitions between families and can assist in the design of multistrand structures. PMID:1383936

  8. Edwardsiella tarda sepsis in a live-stranded sperm whale (Physeter macrocephalus).

    PubMed

    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.

  9. Interpreting the spatio-temporal patterns of sea turtle strandings: Going with the flow

    USGS Publications Warehouse

    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 (< two weeks). Our findings suggest that marine turtle 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

  10. Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA

    PubMed Central

    Lipfert, Jan; Skinner, Gary M.; Keegstra, Johannes M.; Hensgens, Toivo; Jager, Tessa; Dulin, David; Köber, Mariana; Yu, Zhongbo; Donkers, Serge P.; Chou, Fang-Chieh; Das, Rhiju; Dekker, Nynke H.

    2014-01-01

    RNA plays myriad roles in the transmission and regulation of genetic information that are fundamentally constrained by its mechanical properties, including the elasticity and conformational transitions of the double-stranded (dsRNA) form. Although double-stranded DNA (dsDNA) mechanics have been dissected with exquisite precision, much less is known about dsRNA. Here we present a comprehensive characterization of dsRNA under external forces and torques using magnetic tweezers. We find that dsRNA has a force–torque phase diagram similar to that of dsDNA, including plectoneme formation, melting of the double helix induced by torque, a highly overwound state termed “P-RNA,” and a highly underwound, left-handed state denoted “L-RNA.” Beyond these similarities, our experiments reveal two unexpected behaviors of dsRNA: Unlike dsDNA, dsRNA shortens upon overwinding, and its characteristic transition rate at the plectonemic buckling transition is two orders of magnitude slower than for dsDNA. Our results challenge current models of nucleic acid mechanics, provide a baseline for modeling RNAs in biological contexts, and pave the way for new classes of magnetic tweezers experiments to dissect the role of twist and torque for RNA–protein interactions at the single-molecule level. PMID:25313077

  11. DNA ligase III acts as a DNA strand break sensor in the cellular orchestration of DNA strand break repair

    PubMed Central

    Abdou, Ismail; Poirier, Guy G.; Hendzel, Michael J.; Weinfeld, Michael

    2015-01-01

    In the current model of DNA SSBR, PARP1 is regarded as the sensor of single-strand breaks (SSBs). However, biochemical studies have implicated LIG3 as another possible SSB sensor. Using a laser micro-irradiation protocol that predominantly generates SSBs, we were able to demonstrate that PARP1 is dispensable for the accumulation of different single-strand break repair (SSBR) proteins at sites of DNA damage in live cells. Furthermore, we show in live cells for the first time that LIG3 plays a role in mediating the accumulation of the SSBR proteins XRCC1 and PNKP at sites of DNA damage. Importantly, the accumulation of LIG3 at sites of DNA damage did not require the BRCT domain-mediated interaction with XRCC1. We were able to show that the N-terminal ZnF domain of LIG3 plays a key role in the enzyme's SSB sensing function. Finally, we provide cellular evidence that LIG3 and not PARP1 acts as the sensor for DNA damage caused by the topoisomerase I inhibitor, irinotecan. Our results support the existence of a second damage-sensing mechanism in SSBR involving the detection of nicks in the genome by LIG3. PMID:25539916

  12. A design principle for a single-stranded RNA genome that replicates with less double-strand formation.

    PubMed

    Usui, Kimihito; Ichihashi, Norikazu; Yomo, Tetsuya

    2015-09-18

    Single-stranded RNA (ssRNA) is the simplest form of genetic molecule and constitutes the genome in some viruses and presumably in primitive life-forms. However, an innate and unsolved problem regarding the ssRNA genome is formation of inactive double-stranded RNA (dsRNA) during replication. Here, we addressed this problem by focusing on the secondary structure. We systematically designed RNAs with various structures and observed dsRNA formation during replication using an RNA replicase (Qβ replicase). From the results, we extracted a simple rule regarding ssRNA genome replication with less dsRNA formation (less GC number in loops) and then designed an artificial RNA that encodes a domain of the β-galactosidase gene based on this rule. We also obtained evidence that this rule governs the natural genomes of all bacterial and most fungal viruses presently known. This study revealed one of the structural design principles of an ssRNA genome that replicates continuously with less dsRNA formation.

  13. Single-stranded DNA used as an efficient new vehicle for transformation of plant protoplasts.

    PubMed

    Rodenburg, K W; de Groot, M J; Schilperoort, R A; Hooykaas, P J

    1989-12-01

    In relation to the question which DNA form (single- or double-stranded) is transferred by Agrobacterium tumefaciens to plant cells, we studied the behaviour of single-stranded DNA, as compared to double-stranded DNA, when it is introduced into plant protoplasts by electroporation. To this end, we cloned a construct with a plant NPTII gene as well as a CAT gene in the M13 vectors tg130 and tg131. We found that both complementary single-stranded molecules gave rise to substantial CAT activity in plant protoplasts, suggesting that single-stranded DNA is converted into double-stranded DNA by the plant cell replication machinery. Unexpectedly, we found that single-stranded DNA leads to a 3-10-fold higher frequency of stable transformation (selection for kanamycin resistance) than double-stranded DNA. These results indicate that the use of single-stranded DNA might be considered in experiments in which optimal transformation frequencies are needed, e.g. with protoplasts from recalcitrant plant species.

  14. Transport AC loss characteristics of a nine strand YBCO Roebel cable

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    Li, Xin; Wang, Xun; Song, Tao; Lu, Wei; Chen, Zhihua; Shi, Xiaolong

    2015-01-01

    DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement. PMID:26491602

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

    PubMed

    Li, Xin; Wang, Xun; Song, Tao; Lu, Wei; Chen, Zhihua; Shi, Xiaolong

    2015-01-01

    DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement. PMID:26491602

  17. Workshop on effects of chromium coating on Nb{sub 3}Sn superconductor strand: Proceedings

    SciTech Connect

    Not Available

    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.

  18. Electromagnetic fields and the induction of DNA strand breaks.

    PubMed

    Ruiz-Gómez, Miguel J; Martínez-Morillo, Manuel

    2009-01-01

    The International Agency for Research on Cancer (IARC) has classified the extremely low-frequency (ELF) electromagnetic fields (EMF) as "possible carcinogenic" based on the reported effects. The purpose of this work is to review and compare the recent findings related to the induction of DNA strand breaks (DNA-SB) by magnetic field (MF) exposure. We found 29 studies (genotoxic and epigenetic) about the induction of DNA-SB by MF. 50% showed effect of MF and 50% showed no DNA-SB. Nevertheless, considering only genotoxic or only epigenetic studies, 37.5% and 69.2% found induction of DNA-SB by MF, respectively. In relation to these data it seems that MF could act as a co-inductor of DNA damage rather than as a genotoxic agent per se. Nevertheless, the published results, in some cases conflicting with negative findings, do not facilitate to obtain a common consensus about MF effects and biophysical interaction mechanisms.

  19. DNA double-strand break repair pathway choice and cancer

    PubMed Central

    Aparicio, Tomas; Baer, Richard

    2014-01-01

    Summary Since DNA double-strand breaks (DSBs) contribute to the genomic instability that drives cancer development, DSB repair pathways serve as important mechanisms for tumor suppression. Thus, genetic lesions, such as BRCA1 and BRCA2 mutations, that disrupt DSB repair are often associated with cancer susceptibility. In addition, recent evidence suggests that DSB “mis-repair”, in which DSBs are resolved by an inappropriate repair pathway, can also promote genomic instability and presumably tumorigenesis. This notion has gained currency from recent cancer genome sequencing studies which have uncovered numerous chromosomal rearrangements harboring pathological DNA repair signatures. In this perspective, we discuss the factors that regulate DSB repair pathway choice and their consequences for genome stability and cancer. PMID:24746645

  20. Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors.

    PubMed

    Jauker, Mario; Griesser, Helmut; Richert, Clemens

    2015-11-23

    How the biochemical machinery evolved from simple precursors is an open question. Here we show that ribonucleotides and amino acids condense to peptidyl RNAs in the absence of enzymes under conditions established for genetic copying. Untemplated formation of RNA strands that can encode genetic information, formation of peptidyl chains linked to RNA, and formation of the cofactors NAD(+), FAD, and ATP all occur under the same conditions. In the peptidyl RNAs, the peptide chains are phosphoramidate-linked to a ribonucleotide. Peptidyl RNAs with long peptide chains were selected from an initial pool when a lipophilic phase simulating the interior of membranes was offered, and free peptides were released upon acidification. Our results show that key molecules of genetics, catalysis, and metabolism can emerge under the same conditions, without a mineral surface, without an enzyme, and without the need for chemical pre-activation.

  1. Developments in Plant Negative-Strand RNA Virus Reverse Genetics.

    PubMed

    Jackson, Andrew O; Li, Zhenghe

    2016-08-01

    Twenty years ago, breakthroughs for reverse genetics analyses of negative-strand RNA (NSR) viruses were achieved by devising conditions for generation of infectious viruses in susceptible cells. Recombinant strategies have subsequently been engineered for members of all vertebrate NSR virus families, and research arising from these advances has profoundly increased understanding of infection cycles, pathogenesis, and complexities of host interactions of animal NSR viruses. These strategies also permitted development of many applications, including attenuated vaccines and delivery vehicles for therapeutic and biotechnology proteins. However, for a variety of reasons, it was difficult to devise procedures for reverse genetics analyses of plant NSR viruses. In this review, we discuss advances that have circumvented these problems and resulted in construction of a recombinant system for Sonchus yellow net nucleorhabdovirus. We also discuss possible extensions to other plant NSR viruses as well as the applications that may emanate from recombinant analyses of these pathogens. PMID:27359368

  2. Using both strands: The fundamental nature of antisense transcription.

    PubMed

    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.

  3. Hepatic lesions in cetaceans stranded in the Canary Islands.

    PubMed

    Jaber, J R; Pérez, J; Arbelo, M; Andrada, M; Hidalgo, M; Gómez-Villamandos, J C; Van Den Ingh, T; Fernández, A

    2004-03-01

    This article describes the gross, histopathologic, and ultrastructural findings of the livers of cetaceans stranded on the coast of the Canary Islands between 1992 and 2000. A total of 135 cetaceans were included in the study, among which 25 were common dolphins (Delphinus delphis), 23 Atlantic spotted dolphins (Stenella frontalis), 19 striped dolphins (Stenella coeruleoalba), and 15 other species of dolphins and whales. The most common lesion observed in these animals was a nonspecific chronic reactive hepatitis (47/135), followed by hyaline intracytoplasmic inclusions in hepatocytes (33/135). Parasitic cholangitis was detected in 8/135 animals, whereas hepatic lipidosis was presented in 7/135 animals. The ultrastructure of hyaline hepatocytic cytoplasmic inclusions is described, and possible causes of these inclusions are discussed. PMID:15017028

  4. Enzymatic Production of Monoclonal Stoichiometric Single-Stranded DNA Oligonucleotides

    PubMed Central

    Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M.; Högberg, Björn

    2013-01-01

    Single-stranded oligonucleotides are important as research tools as probes for diagnostics and gene therapy. Today, production of oligonucleotides is done via solid-phase synthesis. However, the capabilities of current polymer chemistry are limited in comparison to what can be produced in biological systems. The errors in synthetic DNA increases with oligonucleotide length, and sequence diversity can often be a problem. Here, we present the Monoclonal Stoichiometric (MOSIC) method for enzymatic DNA oligonucleotide production. Using this method, we amplify oligonucleotides from clonal templates followed by digestion of a cutter-hairpin, resulting in pools of monoclonal oligonucleotides with precisely controlled relative stoichiometric ratios. We present data where MOSIC oligonucleotides, 14–378 nt long, were prepared either by in vitro rolling-circle amplification, or by amplification in Escherichia coli in the form of phagemid DNA. The formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides. PMID:23727986

  5. Disentangling DNA during replication: a tale of two strands.

    PubMed

    Hardy, Christine D; Crisona, Nancy J; Stone, Michael D; Cozzarelli, Nicholas R

    2004-01-29

    The seminal papers by Watson and Crick in 1953 on the structure and function of DNA clearly enunciated the challenge their model presented of how the intertwined strands of DNA are unwound and separated for replication to occur. We first give a historical overview of the major discoveries in the past 50 years that address this challenge. We then describe in more detail the cellular mechanisms responsible for the unlinking of DNA. No single strategy on its own accounts for the complete unlinking of chromosomes required for DNA segregation to proceed. Rather, it is the combined effects of topoisomerase action, chromosome organization and DNA-condensing proteins that allow the successful partitioning of chromosomes into dividing cells. Finally, we propose a model of chromosome structure, consistent with recent findings, that explains how the problem of unlinking is alleviated by the division of chromosomal DNA into manageably sized domains.

  6. Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites

    PubMed Central

    Minko, Irina G.; Jacobs, Aaron C.; de Leon, Arnie R.; Gruppi, Francesca; Donley, Nathan; Harris, Thomas M.; Rizzo, Carmelo J.; McCullough, Amanda K.; Lloyd, R. Stephen

    2016-01-01

    Apurinic/apyrimidinic (AP) sites are constantly formed in cellular DNA due to instability of the glycosidic bond, particularly at purines and various oxidized, alkylated, or otherwise damaged nucleobases. AP sites are also generated by DNA glycosylases that initiate DNA base excision repair. These lesions represent a significant block to DNA replication and are extremely mutagenic. Some DNA glycosylases possess AP lyase activities that nick the DNA strand at the deoxyribose moiety via a β- or β,δ-elimination reaction. Various amines can incise AP sites via a similar mechanism, but this non-enzymatic cleavage typically requires high reagent concentrations. Herein, we describe a new class of small molecules that function at low micromolar concentrations as both β- and β,δ-elimination catalysts at AP sites. Structure-activity relationships have established several characteristics that appear to be necessary for the formation of an iminium ion intermediate that self-catalyzes the elimination at the deoxyribose ring. PMID:27363485

  7. Stranded Whole Transcriptome RNA-Seq for All RNA Types

    PubMed Central

    Yan, Pearlly X.; Fang, Fang; Buechlein, Aaron; Ford, James B.; Tang, Haixu; Huang, Tim H.; Burow, Matthew E.; Liu, Yunlong; Rusch, Douglas B.

    2015-01-01

    Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA) and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libraries for multiplexing on the Illumina platform are generated with this approach but it can be applied to other platforms with a few modifications. PMID:25599667

  8. Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors

    PubMed Central

    Jauker, Mario; Griesser, Helmut; Richert, Clemens

    2015-01-01

    How the biochemical machinery evolved from simple precursors is an open question. Here we show that ribonucleotides and amino acids condense to peptidyl RNAs in the absence of enzymes under conditions established for genetic copying. Untemplated formation of RNA strands that can encode genetic information, formation of peptidyl chains linked to RNA, and formation of the cofactors NAD+, FAD, and ATP all occur under the same conditions. In the peptidyl RNAs, the peptide chains are phosphoramidate-linked to a ribonucleotide. Peptidyl RNAs with long peptide chains were selected from an initial pool when a lipophilic phase simulating the interior of membranes was offered, and free peptides were released upon acidification. Our results show that key molecules of genetics, catalysis, and metabolism can emerge under the same conditions, without a mineral surface, without an enzyme, and without the need for chemical pre-activation. PMID:26435376

  9. Stranded Whole Transcriptome RNA-Seq for All RNA Types.

    PubMed

    Miller, David F B; Yan, Pearlly X; Fang, Fang; Buechlein, Aaron; Ford, James B; Tang, Haixu; Huang, Tim H; Burow, Matthew E; Liu, Yunlong; Rusch, Douglas B; Nephew, Kenneth P

    2015-01-20

    Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA), and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libraries for multiplexing on the Illumina platform are generated with this approach but it can be applied to other platforms with a few modifications.

  10. RNA-directed repair of DNA double-strand breaks.

    PubMed

    Yang, Yun-Gui; Qi, Yijun

    2015-08-01

    DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, which if unrepaired or repaired incorrectly can cause cell death or genome instability that may lead to cancer. To counteract these adverse consequences, eukaryotes have evolved a highly orchestrated mechanism to repair DSBs, namely DNA-damage-response (DDR). DDR, as defined specifically in relation to DSBs, consists of multi-layered regulatory modes including DNA damage sensors, transducers and effectors, through which DSBs are sensed and then repaired via DNAprotein interactions. Unexpectedly, recent studies have revealed a direct role of RNA in the repair of DSBs, including DSB-induced small RNA (diRNA)-directed and RNA-templated DNA repair. Here, we summarize the recent discoveries of RNA-mediated regulation of DSB repair and discuss the potential impact of these novel RNA components of the DSB repair pathway on genomic stability and plasticity.

  11. Nuclear Proteins Hijacked by Mammalian Cytoplasmic Plus Strand RNA Viruses

    PubMed Central

    Lloyd, Richard E.

    2015-01-01

    Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. PMID:25818028

  12. UV-Induced Proton Transfer between DNA Strands.

    PubMed

    Zhang, Yuyuan; de La Harpe, Kimberly; Beckstead, Ashley A; Improta, Roberto; Kohler, Bern

    2015-06-10

    UV radiation creates excited states in DNA that lead to mutagenic photoproducts. Photoexcitation of single-stranded DNA can transfer an electron between stacked bases, but the fate of excited states in the double helix has been intensely debated. Here, photoinduced interstrand proton transfer (PT) triggered by intrastrand electron transfer (ET) is detected for the first time by time-resolved vibrational spectroscopy and quantum mechanical calculations. Long-lived excited states are shown to be oppositely charged base pair radical ions. In two of the duplexes, the base pair radical anions are present as tautomers formed by interstrand PT. Charge recombination occurs on the picosecond time scale preventing the accumulation of damaging radicals or mutagenic tautomers. PMID:26005794

  13. Do DNA Double-Strand Breaks Drive Aging?

    PubMed

    White, Ryan R; Vijg, Jan

    2016-09-01

    DNA double-strand breaks (DSBs) are rare, but highly toxic, lesions requiring orchestrated and conserved machinery to prevent adverse consequences, such as cell death and cancer-causing genome structural mutations. DSBs trigger the DNA damage response (DDR) that directs a cell to repair the break, undergo apoptosis, or become senescent. There is increasing evidence that the various endpoints of DSB processing by different cells and tissues are part of the aging phenotype, with each stage of the DDR associated with specific aging pathologies. In this Perspective, we discuss the possibility that DSBs are major drivers of intrinsic aging, highlighting the dynamics of spontaneous DSBs in relation to aging, the distinct age-related pathologies induced by DSBs, and the segmental progeroid phenotypes in humans and mice with genetic defects in DSB repair. A model is presented as to how DSBs could drive some of the basic mechanisms underlying age-related functional decline and death. PMID:27588601

  14. RNA-directed repair of DNA double-strand breaks.

    PubMed

    Yang, Yun-Gui; Qi, Yijun

    2015-08-01

    DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, which if unrepaired or repaired incorrectly can cause cell death or genome instability that may lead to cancer. To counteract these adverse consequences, eukaryotes have evolved a highly orchestrated mechanism to repair DSBs, namely DNA-damage-response (DDR). DDR, as defined specifically in relation to DSBs, consists of multi-layered regulatory modes including DNA damage sensors, transducers and effectors, through which DSBs are sensed and then repaired via DNAprotein interactions. Unexpectedly, recent studies have revealed a direct role of RNA in the repair of DSBs, including DSB-induced small RNA (diRNA)-directed and RNA-templated DNA repair. Here, we summarize the recent discoveries of RNA-mediated regulation of DSB repair and discuss the potential impact of these novel RNA components of the DSB repair pathway on genomic stability and plasticity. PMID:25960340

  15. Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites.

    PubMed

    Minko, Irina G; Jacobs, Aaron C; de Leon, Arnie R; Gruppi, Francesca; Donley, Nathan; Harris, Thomas M; Rizzo, Carmelo J; McCullough, Amanda K; Lloyd, R Stephen

    2016-01-01

    Apurinic/apyrimidinic (AP) sites are constantly formed in cellular DNA due to instability of the glycosidic bond, particularly at purines and various oxidized, alkylated, or otherwise damaged nucleobases. AP sites are also generated by DNA glycosylases that initiate DNA base excision repair. These lesions represent a significant block to DNA replication and are extremely mutagenic. Some DNA glycosylases possess AP lyase activities that nick the DNA strand at the deoxyribose moiety via a β- or β,δ-elimination reaction. Various amines can incise AP sites via a similar mechanism, but this non-enzymatic cleavage typically requires high reagent concentrations. Herein, we describe a new class of small molecules that function at low micromolar concentrations as both β- and β,δ-elimination catalysts at AP sites. Structure-activity relationships have established several characteristics that appear to be necessary for the formation of an iminium ion intermediate that self-catalyzes the elimination at the deoxyribose ring. PMID:27363485

  16. Optimization of CFETR CSMC cabling based on numerical modeling and experiments

    NASA Astrophysics Data System (ADS)

    Qin, Jinggang; Dai, Chao; Liu, Bo; Wu, Yu; Liu, Fang; Liao, Guojun; Xue, Tianjun; Wei, Zhourong; Nijhuis, Arend; Zhou, Chao; Devred, Arnaud

    2015-12-01

    The China Fusion Engineering Test Reactor (CFETR) is a new tokamak device, whose magnet system includes toroidal field (TF), central solenoid (CS) and poloidal field (PF) coils. The main goal is to build a fusion engineering tokamak reactor with 50-200 MW fusion power and self-sufficiency by blanket, which means that the deuterium-tritium reaction in the plasma produces neutrons and alpha particles, and the neutrons react with the lithium-containing blanket surrounding the plasma, breeding the tritium by lithium-neutron reaction. To develop the manufacturing technique for the full-size CS coil, the Central Solenoid Model Coil (CSMC) project for CFETR was launched first. A Nb3Sn conductor is to be used in the CFETR CSMC, whose design refers to the ITER CS conductor with the same short-twist-pitch cable pattern. Due to the short twist pitch and relatively low void fraction, a high compaction ratio is required during cabling and the risk of strand damage is increased significantly. Although it is impossible to avoid strand deformation for this design, it is crucial to find a way to reduce strand damage as much as possible. A numerical model was used to analyze the causes of strand damage, including variation in twist pitch length as well as different mechanical properties for copper and Nb3Sn strands. Several experiments have been performed to verify the numerical results, including cabling trials for different conditions and critical current (I c) tests on strands with/without deformation. The results show that the numerical analysis is consistent with the experiments and provides the optimal cabling conditions for the CFETR CSMC.

  17. Non-Specific Blocking of miR-17-5p Guide Strand in Triple Negative Breast Cancer Cells by Amplifying Passenger Strand Activity

    PubMed Central

    Jin, Yuan-Yuan; Andrade, Jade; Wickstrom, Eric

    2015-01-01

    Conventional wisdom holds that only one of the two strands in a micro ribonucleic acid (miRNA) precursor duplex is selected as the active miRNA guide strand. The complementary miRNA passenger strand, however, is thought to be inactive. High levels of the oncogenic miRNA (oncomiR) guide strand called miR-17-5p is overexpressed in triple negative breast cancer (TNBC) and can inhibit ribosomal translation of tumor suppressor gene mRNAs, such as programmed cell death 4 (PDCD4) or phosphatase and tensin homolog (PTEN). We hypothesized that knocking down the oncogenic microRNA (oncomiR) miR-17-5p might restore the expression levels of PDCD4 and PTEN tumor suppressor proteins, illustrating a route to oligonucleotide therapy of TNBC. Contrary to conventional wisdom, antisense knockdown of oncomiR miR-17-5p guide strand reduced PDCD4 and PTEN proteins by 1.8±0.3 fold in human TNBC cells instead of raising them. Bioinformatics analysis and folding energy calculations revealed that mRNA targets of miR-17-5p guide strand, such as PDCD4 and PTEN, could also be regulated by miR-17-3p passenger strand. Due to high sequence homology between the antisense molecules and miR-17-3p passenger strand, as well as the excess binding sites for the passenger strand on the 3’UTR of PDCD4 and PTEN mRNAs, introducing a miR-17-3p DNA-LNA mimic to knock down miR-17-5p reduced PDCD4 and PTEN protein expression instead of raising them. Our results imply that therapeutic antisense sequences against miRNAs should be designed to target the miRNA strand with the greatest number of putative binding sites in the target mRNAs, while minimizing affinity for the minor strand. PMID:26629823

  18. Replication of simian virus 40 DNA after UV irradiation: evidence of growing fork blockage and single-stranded gaps in daughter strands

    SciTech Connect

    Mezzina, M.; Menck, C.F.M.; Courtin, P.; Sarasin, A.

    1988-11-01

    The molecular mechanisms of in vivo inhibition of mammalian DNA replication by exposure to UV light (at 254 nm) was studied in monkey and human cells infected with simian virus 40. Analysis of viral DNA by electron microscopy and sucrose gradients confirmed that the presence of UV-induced lesions severely blocks DNA synthesis, and thus the conversion of replicative intermediates (RIs) into fully replicated form I DNA is inhibited by UV irradiation. These blocked RI molecules present several special features when visualized by electron microscopy. In excision repair-proficient monkey and human cells they are composed of a double-stranded circular DNA with a double-stranded tail whose size corresponds to the average interpyrimidine dimer distance, as determined by the dimer-specific T4 endonuclease V. In excision repair-deficient human cells from patients with xeroderma pigmentosum, UV-irradiated RIs present a Carins-like structure similar to that observed for replicating molecules obtained from unirradiated infected cells. Single-stranded gaps are visualized in the replicated portions of UV-irradiated RI molecules; such regions are detected and clearly distinguishable from double-stranded DNA when probed by a specific single-stranded DNA-binding protein such as the bacteriophage T4 gene 32 product. Consistent with the presence of gaps in UV-irradiated RI molecules, single-strand-specific S1 nuclease digestion causes a shift in their sedimentation properties when analyzed in neutral sucrose gradients compared with undamaged molecules.

  19. A sensitive method for the quantification of virion-sense and complementary-sense DNA strands of circular single-stranded DNA viruses.

    PubMed

    Rodríguez-Negrete, Edgar A; Sánchez-Campos, Sonia; Cañizares, M Carmen; Navas-Castillo, Jesús; Moriones, Enrique; Bejarano, Eduardo R; Grande-Pérez, Ana

    2014-01-01

    Circular single-stranded DNA (ssDNA) viruses are the smallest viruses known to infect eukaryotes. High recombination and mutation rates have conferred these viruses with an evolutionary potential that has facilitated their emergence. Their damaging effects on livestock (circoviruses) and crops (geminiviruses and nanoviruses), and the ubiquity of anelloviruses in human populations and other mammalian species, have resulted in increased interest in better understanding their epidemiology and infection mechanisms. Circular ssDNA viral replication involves the synthesis of dsDNA intermediates containing complementary-sense (CS) and virion-sense (VS) strands. Precise quantification of VS and CS accumulation during viral infections can provide insights into the molecular mechanisms underlying viral replication and the host invasion process. Although qPCR protocols for quantifying viral molecules exist, none of them discriminate VS and CS strands. Here, using a two-step qPCR protocol we have quantified VS and CS molecule accumulation during the infection process of Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) (genus Begomovirus, family Geminiviridae). Our results show that the VS/CS strand ratio and overall dsDNA amounts vary throughout the infection process. Moreover, we show that these values depend on the virus-host combination, and that most CS strands are present as double-stranded molecules. PMID:25241765

  20. Acid-induced molten globule state of a prion protein: crucial role of Strand 1-Helix 1-Strand 2 segment.

    PubMed

    Honda, Ryo P; Yamaguchi, Kei-ichi; Kuwata, Kazuo

    2014-10-31

    The conversion of a cellular prion protein (PrP(C)) to its pathogenic isoform (PrP(Sc)) is a critical event in the pathogenesis of prion diseases. Pathogenic conversion is usually associated with the oligomerization process; therefore, the conformational characteristics of the pre-oligomer state may provide insights into the conversion process. Previous studies indicate that PrP(C) is prone to oligomer formation at low pH, but the conformation of the pre-oligomer state remains unknown. In this study, we systematically analyzed the acid-induced conformational changes of PrP(C) and discovered a unique acid-induced molten globule state at pH 2.0 termed the "A-state." We characterized the structure of the A-state using far/near-UV CD, 1-anilino-8-naphthalene sulfonate fluorescence, size exclusion chromatography, and NMR. Deuterium exchange experiments with NMR detection revealed its first unique structure ever reported thus far; i.e. the Strand 1-Helix 1-Strand 2 segment at the N terminus was preferentially unfolded, whereas the Helix 2-Helix 3 segment at the C terminus remained marginally stable. This conformational change could be triggered by the protonation of Asp(144), Asp(147), and Glu(196), followed by disruption of key salt bridges in PrP(C). Moreover, the initial population of the A-state at low pH (pH 2.0-5.0) was well correlated with the rate of the β-rich oligomer formation, suggesting that the A-state is the pre-oligomer state. Thus, the specific conformation of the A-state would provide crucial insights into the mechanisms of oligomerization and further pathogenic conversion as well as facilitating the design of novel medical chaperones for treating prion diseases. PMID:25217639

  1. Equal Sensitivity of the Two Strands of øX174 Replicative DNA to Breakage by Ionizing Radiation

    PubMed Central

    Achey, Phillip M.; Courtney, Deborah G.

    1973-01-01

    The supertwisted, double-stranded, replicative intermediate of øX174 DNA (RFI) has been used to determine whether one of the two strands of the double helix is uniquely sensitive to induction of single-strand breaks by ionizing radiation. This could result from a particularly sensitive base sequence or a transfer of energy to a specific location of the DNA molecule. The results indicate that both strands of the double helix are equally broken, even though their base compositions are significantly different. If there are “hot spots” in the strands, then they are present in equal amounts in each strand. PMID:4575520

  2. Tracking Cryptosporidium parvum by sequence analysis of small double-stranded RNA.

    PubMed Central

    Xiao, L.; Limor, J.; Bern, C.; Lal, A. A.

    2001-01-01

    We sequenced a 173-nucleotide fragment of the small double-stranded viruslike RNA of Cryptosporidium parvum isolates from 23 calves and 38 humans. Sequence diversity was detected at 17 sites. Isolates from the same outbreak had identical double-stranded RNA sequences, suggesting that this technique may be useful for tracking Cryptosporidium infection sources. PMID:11266306

  3. Oligonucleotides containing a lysine residue as 3'-3' junction for alternate strand triple helix formation.

    PubMed

    Barone, G; De Napoli, L; Di Fabio, G; Giancola, C; Messere, A; Montesarchio, D; Petraccone, L; Piccialli, G

    2001-11-01

    Oligonucleotides with a 3'-3' inversion of polarity site assured by one lysine residue have been synthesized, characterized and used as third strands in alternate strand triple helix formation. UV melting studies and molecular mechanics calculations have been carried out to investigate the stability and the geometry of these new triplexes.

  4. Stability of triple helices containing RNA and DNA strands: experimental and molecular modeling studies.

    PubMed Central

    Escudé, C; François, J C; Sun, J S; Ott, G; Sprinzl, M; Garestier, T; Hélène, C

    1993-01-01

    UV-absorption spectrophotometry and molecular modeling have been used to study the influence of the chemical nature of sugars (ribose or deoxyribose) on triple helix stability. For the Pyrimidine.purine* Pyrimidine motif, all eight combinations were tested with each of the three strands composed of either DNA or RNA. The chemical nature of sugars has a dramatic influence on triple helix stability. For each double helix composition, a more stable triple helix was formed when the third strand was RNA rather than DNA. No stable triple helix was detected when the polypurine sequence was made of RNA with a third strand made of DNA. Energy minimization studies using the JUMNA program suggested that interactions between the 2'-hydroxyl group of the third strand and the phosphates of the polypurine strand play an important role in determining the relative stabilities of triple-helical structures in which the polypyrimidine third strand is oriented parallel to the polypurine sequence. These interactions are not allowed when the third strand adopts an antiparallel orientation with respect to the target polypurine sequence, as observed when the third strand contains G and A or G and T/U. We show by footprinting and gel retardation experiments that an oligoribonucleotide containing G and A or G and U fails to bind double helical DNA, while the corresponding DNA oligomers form stable triple-helical complexes. Images PMID:7506827

  5. The Cross-Case Analyses of Elementary Students' Engagement in the Strands of Science Proficiency

    ERIC Educational Resources Information Center

    Minogue, James; Madden, Lauren; Bedward, John; Wiebe, Eric; Carter, Mike

    2010-01-01

    Recent reports have begun to lay the foundation for a re-visioned K-8 science curriculum which includes four strands that could be used to define and assess science proficiency for all students. Using these strands as an analytic lens, this pre-post multiple-case case study explores elementary school science teachers' practices and their students'…

  6. Hairpin DNA Sequences Bound Strongly by Bleomycin Exhibit Enhanced Double-Strand Cleavage

    PubMed Central

    2014-01-01

    Clinically used bleomycin A5 has been employed in a study of double-strand cleavage of a library of 10 hairpin DNAs originally selected on the basis of their strong binding to bleomycin. Each of the DNAs underwent double-strand cleavage at more than one site, and all of the cleavage sites were within, or in close proximity to, an eight-base-pair region of the duplex that had been randomized to create the original library. A total of 31 double-strand cleavage sites were identified on the 10 DNAs, and 14 of these sites were found to represent coupled cleavage sites, that is, events in which one of the two strands was always cleaved first, followed by the associated site on the opposite strand. Most of these coupled sites underwent cleavage by a mechanism described previously by the Povirk laboratory and afforded cleavage patterns entirely analogous to those reported. However, at least one coupled cleavage event was noted that did not conform to the pattern of those described previously. More surprisingly, 17 double-strand cleavages were found not to result from coupled double-strand cleavage, and we posit that these cleavages resulted from a new mechanism not previously described. Enhanced double-strand cleavages at these sites appear to be a consequence of the dynamic nature of the interaction of Fe·BLM A5 with the strongly bound hairpin DNAs. PMID:24548300

  7. Antibiotic efficacy in eliminating leptospiruria in California sea lions (Zalophus californianus) stranding with leptospirosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. Extrachromosomal DNA of pea (Pisum sativum) root-tip cells replicates by strand displacement

    SciTech Connect

    Krimer, D.B.; Van't Hof, J.

    1983-04-01

    In cultured pea roots there is extrachromosomal DNA associated with cells that differentiate from the G/sub 2/ phase of the cell cycle that is absent from those that differentiate from the G/sub 1/ phase. The authors examined this extrachromosomal DNA by electron microscopy and found that it consisted of three types: (i) double-stranded linear molecules with single-stranded branches (74%), (ii) double-stranded molecules without branches (26%), and (iii) free single-stranded molecules. The double-stranded molecules with or without branches were similar in length, having a modal length of 10-15 ..mu..m. The free single-stranded molecules were shorter and had a mean length of 3.8 ..mu..m. The length of the branches attached to the duplex molecules was only slightly less than that of the free form. The duplex molecules with branches were interpreted as configurations reflecting an ongoing strand-displacement process that results in free single-stranded molecules. Finally, measurements on duplex molecules with multiple branches suggested that the extrachromosomal DNA may exist in the form of tandemly repeated sequences. 8 references, 8 figures.

  9. Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5'-flaps.

    PubMed

    Koc, Katrina N; Stodola, Joseph L; Burgers, Peter M; Galletto, Roberto

    2015-04-30

    The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in vitro the basic biochemical properties that allow Pol δ-exo(-) to carry out strand displacement synthesis and discovered that it is regulated by the 5'-flaps in the DNA strand to be displaced. Under conditions where Pol δ carries out strand displacement synthesis, the presence of long 5'-flaps or addition in trans of ssDNA suppress this activity. This suggests the presence of a secondary DNA binding site on the enzyme that is responsible for modulation of strand displacement activity. The inhibitory effect of a long 5'-flap can be suppressed by its interaction with single-stranded DNA binding proteins. However, this relief of flap-inhibition does not simply originate from binding of Replication Protein A to the flap and sequestering it. Interaction of Pol δ with PCNA eliminates flap-mediated inhibition of strand displacement synthesis by masking the secondary DNA site on the polymerase. These data suggest that in addition to enhancing the processivity of the polymerase PCNA is an allosteric modulator of other Pol δ activities.

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

    PubMed

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

    2016-03-01

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

  11. 77 FR 2958 - Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-20

    ...; Opportunity To Request Administrative Review, 77 FR 83 (January 3, 2012). Subsequent to this publication, we... 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...

  12. Characteristics of round and extracted strands of Nb3Al Rutherford cable

    SciTech Connect

    Kikuchi, A.; Yamada, R.; Ambrosio, G.; Andreev, N.; Barzi, E.; Cooper, C.; Iijima, Y.; Kobayashi, M.; Kitaguchi, H.; Nimori, S.; Lamm, M.; Tagawa, K.; Takeuchi, T.; Tsuchiya, K.; Turrioni, D.; Wake, M.; Zlobin, A.V.; /NIMC, Tsukuba /Fermilab /KEK, Tsukuba

    2006-08-01

    Long Nb{sub 3}Al strands with copper stabilizer are promising for future high field accelerator magnets. A 1.2 kilometer Nb{sub 3}Al strand with Cu stabilizer was fabricated at the National Institute for Materials Science in Japan. Using this strand a 30 meter Cu stabilized Nb{sub 3}Al Rutherford cable was made for the first time by a collaboration of NIMS and Fermilab. The Nb{sub 3}Al strands extracted from cable with a relatively low packing factor showed almost no J{sub c} degradation. But the extracted strands from the highly compacted cable showed some degradation in both J{sub c} and n value, which may be caused by local separation of the copper stabilizer. Still, its J{sub c} degradation is lower than that of typical Nb{sub 3}Sn strands. The current limit due to magnetic instability in low field is about 500 A at 4.2 K. The magnetization of the strands, which was measured with balanced coils at 4.2 K, showed large flux jumps, usually around 1.5 T. This value is much larger than the B{sub c2} (4.2 K) of the Nb matrix, which is around 0.4 Tesla. The magnetic instability of the Nb{sub 3}Al strand at low field is not completely understood, but it might be explained by the superconducting coupling current through the Nb matrix.

  13. Collision-induced dissociation of intact duplex and single-stranded siRNA anions.

    PubMed

    Huang, Teng-Yi; Liu, Jian; Liang, Xiaorong; Hodges, Brittany D M; McLuckey, Scott A

    2008-11-15

    A tandem mass spectrometry approach is demonstrated for complete sequencing of a model small interfering RNA (siRNA) based on ion trap collisional activation of intact single-stranded anions. Various charge states of the siRNA duplex and the individual strands were generated by nanoelectrospray (nano-ESI). The siRNA duplex anions were predominantly dissociated into the sense and antisense strands by collisional activation. The characteristic fragment ions (c/y- and a-B/w-ion series) from both strands were observed when higher activation amplitude was applied and when beam-type collisional activation was examined; however, the coexistence of fragment ions from both strands complicated spectral interpretation. The effect of precursor ion charge state on the dissociation of the individual sense and antisense strand siRNA anions was studied using ion trap collision-induced dissociation under various activation amplitudes. Through the activation of relatively low charge state precursor ions at relatively low excitation energy, selective backbone dissociation predominantly via the c/y channels was achieved. By applying relatively high excitation energy, the a-B/w channels also became prominent; however, the increase in spectral complexity made complete peak assignment difficult. In order to simplify the product ion spectra, proton-transfer reactions were applied, and complete sequencing of each strand was achieved. The application of tandem mass spectrometry to intact single-stranded anions demonstrated in this study can be adapted for the rapid identification of other noncoding RNAs in RNomics studies.

  14. Invasive reaction assisted strand-displacement signal amplification for sensitive DNA detection.

    PubMed

    Zou, Bingjie; Song, Qinxin; Wang, Jianping; Liu, Yunlong; Zhou, Guohua

    2014-11-18

    A novel DNA detection assay was proposed by invasive reaction coupled with molecular beacon assisted strand-displacement signal amplification (IRASA). Target DNAs are firstly hybridized to two probes to initiate invasive reaction to produce amplified flaps. Then these flaps are further amplified by strand-displacement signal amplification. The detection limit was around 0.2 pM.

  15. 18 CFR 35.26 - Recovery of stranded costs by public utilities and transmitting utilities.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... POWER ACT FILING OF RATE SCHEDULES AND TARIFFS Other Filing Requirements § 35.26 Recovery of stranded... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Recovery of stranded... means any wholesale requirements contract executed on or before July 11, 1994. (c) Recovery of...

  16. 18 CFR 35.26 - Recovery of stranded costs by public utilities and transmitting utilities.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... POWER ACT FILING OF RATE SCHEDULES AND TARIFFS Other Filing Requirements § 35.26 Recovery of stranded... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Recovery of stranded... means any wholesale requirements contract executed on or before July 11, 1994. (c) Recovery of...

  17. 18 CFR 35.26 - Recovery of stranded costs by public utilities and transmitting utilities.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... POWER ACT FILING OF RATE SCHEDULES AND TARIFFS Other Filing Requirements § 35.26 Recovery of stranded... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Recovery of stranded... means any wholesale requirements contract executed on or before July 11, 1994. (c) Recovery of...

  18. A NEW ROLE FOR HIV NUCLEOCAPSID PROTEIN IN MODULATING THE SPECIFICITY OF PLUS STRAND PRIMING

    PubMed Central

    Jacob, Deena T.; DeStefano, Jeffrey J.

    2008-01-01

    The current study indicates a new role for HIV nucleocapsid protein (NC) in modulating the specificity of plus strand priming. RNase H cleavage by reverse transcriptase (RT) during minus strand synthesis gives rise to RNA fragments that could potentially be used as primers for synthesis of the plus strand, leading to the initiation of priming from multiple points as has been observed for other retroviruses. For HIV, the central and 3′ polypurine tracts (PPTs) are the major sites of plus strand initiation. Using reconstituted in vitro assays, results showed that NC greatly reduced the efficiency of extension of non-PPT RNA primers, but not PPT. Experiments mimicking HIV replication showed that RT generated and used both PPT and non-PPT RNAs to initiate “plus strand” synthesis, but non-PPT usage was strongly inhibited by NC. The results support a role for NC in specifying primer usage during plus strand synthesis. PMID:18632127

  19. DNA strand breaks (comet assay) in blood lymphocytes from wild bottlenose dolphins.

    PubMed

    Lee, Richard F; Bulski, Karrie; Adams, Jeffrey D; Peden-Adams, Margie; Bossart, Gregory D; King, Lydia; Fair, Patricia A

    2013-12-15

    The comet assay was carried out on blood lymphocytes from a large number of wild dolphins (71 from Indian River Lagoon, FL, USA; 51 from Charleston Harbor, SC, USA) and provides a baseline study of DNA strand breaks in wild dolphin populations. There were no significant differences in the comet assay (% DNA in tail) results between the different age and sex categories. Significant difference in DNA strand breaks were found between Charleston Harbor dolphins (median--17.4% DNA in tail) and Indian River Lagoon dolphins (median--14.0% DNA in tail). A strong correlation found between T-cell proliferation and DNA strand breaks in dolphin lymphocytes suggests that dolphins with a high numbers of DNA strand breaks have a decreased ability to respond to infection. Higher concentrations of genotoxic agents in Charleston Harbor compared with Indian River lagoon may have been one of the causes of higher DNA strand breaks in these dolphins.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  1. Electronic transport in DNA sequences: The role of correlations and inter-strand coupling

    NASA Astrophysics Data System (ADS)

    Albuquerque, E. L.; Lyra, M. L.; de Moura, F. A. B. F.

    2006-10-01

    We investigate the electronic properties in sequences of single and double-strand DNA molecules made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. Using a tight-binding formulation we solve the time-dependent Schrödinger equation to compute the spread of initially localized wave packets. We also compute the localization length in finite segments by employing a Green's function recursion method. We compare the results for the genomic DNA sequence with those of two artificial sequences, namely the quasiperiodic Rudin-Shapiro one, which has long-range correlations, and a intra-strand pair correlated DNA sequence. We found that the short-range character of the intra-strand correlations suffices for a quantitative description of the one-electron wave-packet dynamics in the double-strand real DNA sequences. Further, the inter-strand coupling promotes electronic transport over a longer segment.

  2. Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation.

    PubMed

    Rand, Tim A; Petersen, Sean; Du, Fenghe; Wang, Xiaodong

    2005-11-18

    The mRNA-cleavage step of RNA interference is mediated by an endonuclease, Argonaute2 (Ago2), within the RNA-induced silencing complex (RISC). Ago2 uses one strand of the small interfering (si) RNA duplex as a guide to find messenger RNAs containing complementary sequences and cleaves the phosphodiester backbone at a specific site measured from the guide strand's 5' end. Here, we show that both strands of siRNA get loaded onto Ago2 protein in Drosophila S2 cell extracts. The anti-guide strand behaves as a RISC substrate and is cleaved by Ago2. This cleavage event is important for the removal of the anti-guide strand from Ago2 protein and activation of RISC.

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

    PubMed

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

    2015-01-01

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

  4. Factors affecting stranding of juvenile salmonids by wakes from ship passage in the Lower Columbia River

    SciTech Connect

    Pearson, Walter H.; Skalski, John R.

    2011-09-01

    The effects of deep-draft vessel traffic in confined riverine channels on shorelines and fish are of widespread concern. In the Pacific Northwest of the United States, wakes and subsequent beach run-up from ships transiting the Lower Columbia River have been observed to strand juvenile salmon and other fish. As part of a before-and-after study to assess stranding effects that may be associated with channel deepening, we measured 19 co-variables from observations of 126 vessel passages at three low-slope beaches and used multiple logistic regression to discern the significant factors influencing the frequency of stranding. Subyearling Chinook salmon were 82% of the fish stranded over all sites and seasons. Given a low-slope beach, stranding frequencies for juvenile salmon were significantly related to river location, salmon density in the shallows, a proxy for ship kinetic energy, tidal height, and two interactions. The beach types selected for our study do not include all the beach types along the Lower Columbia River so that the stranding probabilities described here cannot be extrapolated river-wide. A more sophisticated modeling effort, informed by additional field data, is needed to assess salmon losses by stranding for the entire lower river. Such modeling needs to include river-scale factors such as beach type, berms, proximity to navigation channel, and perhaps, proximity to tributaries that act as sources of out-migrating juvenile salmon. At both river and beach scales, no one factor produces stranding; rather interactions among several conditions produce a stranding event and give stranding its episodic nature.

  5. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    SciTech Connect

    sumption, Mike; Majoros, Milan; Collings, E. W.; Van der Laan, D. C.

    2014-11-07

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software. Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.

  6. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    SciTech Connect

    Majoros, M.; Sumption, M. D.; Collings, E. W.; Long, N. J.

    2015-04-08

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software. Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.

  7. Materials, Strands, and Cables for Superconducting Accelerator Magnets. Final Report

    SciTech Connect

    Sumption, Mike D.; Collings, Edward W.

    2014-09-19

    This report focuses on Materials, Strands and Cables for High Energy Physics Particle accelerators. In the materials area, work has included studies of basic reactions, diffusion, transformations, and phase assemblage of Nb3Sn. These materials science aspects have been married to results, in the form of flux pinning, Bc2, Birr, and transport Jc, with an emphasis on obtaining the needed Jc for HEP needs. Attention has also been paid to the “intermediate-temperature superconductor”, magnesium diboride emphasis being placed on (i) irreversibility field enhancement, (ii) critical current density and flux pinning, and (iii) connectivity. We also report on studies of Bi-2212. The second area of the program has been in the area of “Strands” in which, aside from the materials aspect of the conductor, its physical properties and their influence on performance have been studied. Much of this work has been in the area of magnetization estimation and flux jump calculation and control. One of the areas of this work was strand instabilities in high-performance Nb3Sn conductors due to combined fields and currents. Additionally, we investigated quench and thermal propagation in YBCO coated conductors at low temperatures and high fields. The last section, “Cables”, focussed on interstrand contact resistance, ICR, it origins, control, and implications. Following on from earlier work in NbTi, the present work in Nb3Sn has aimed to make ICR intermediate between the two extremes of too little contact (no current sharing) and too much (large and unacceptable magnetization and associated beam de-focussing). Interstrand contact and current sharing measurements are being made on YBCO based Roebel cables using transport current methods. Finally, quench was investigated for YBCO cables and the magnets wound from them, presently with a focus on 50 T solenoids for muon collider applications.

  8. High resolution atomic force microscopy of double-stranded RNA

    NASA Astrophysics Data System (ADS)

    Ares, Pablo; Fuentes-Perez, Maria Eugenia; Herrero-Galán, Elías; Valpuesta, José M.; Gil, Adriana; Gomez-Herrero, Julio; Moreno-Herrero, Fernando

    2016-06-01

    Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to

  9. Holocene geologic slip rate for Mission Creek strand of the southern San Andreas Fault

    NASA Astrophysics Data System (ADS)

    Fryer, R.; Behr, W. M.; Sharp, W. D.; Gold, P. O.

    2015-12-01

    The San Andreas Fault (SAF) is the primary structure accommodating motion between the Pacific and North American plates. The Coachella Valley segment of the southern SAF has not ruptured historically, and is considered overdue for an earthquake because it has exceeded its average recurrence interval. In the northwestern Coachella Valley, this fault splits into three additional fault strands: the Mission Creek strand, which strikes northwest in the San Bernardino Mountains, and the Banning and Garnet Hill strands, which continue west, transferring slip into San Gorgonio Pass. Determining how slip is partitioned between these faults is critical for southern California seismic hazard models. Recent work near the southern end of the Mission Creek strand at Biskra Palms yielded a slip rate of ~14-17 mm/yr since 50 ka, and new measurements from Pushawalla Canyon suggest a possible rate of ~20 mm/yr since 2.5 ka and 70 ka. Slip appears to transfer away from the Mission Creek strand and to the Banning and Garnet Hill strands within the Indio Hills, but the slip rate for the Garnet Hill strand is unknown and the 4-5 mm/yr slip rate for the Banning strand is applicable only since the mid Holocene. Additional constraints on the Holocene slip rate for the Mission Creek strand are critical for resolving the total slip rate for the southern SAF, and also for comparing slip rates on all three fault strands in the northern Coachella Valley over similar time scales. We have identified a new slip rate site at the southern end of the Mission Creek strand between Pushawalla and Biskra Palms. At this site, (the Three Palms Site), three alluvial fans sourced from three distinct catchments have been displaced approximately 80 meters by the Mission Creek Strand. Initial observations from an exploratory pit excavated into the central fan show soil development consistent with Holocene fan deposition and no evidence of soil profile disruption. To more precisely constrain the minimum

  10. How a short double-stranded DNA bends

    NASA Astrophysics Data System (ADS)

    Shin, Jaeoh; Lee, O.-Chul; Sung, Wokyung

    2015-04-01

    A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 102-106 than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment.

  11. Prion search and cellular prion protein expression in stranded dolphins.

    PubMed

    Di Guardo, G; Cocumelli, C; Meoli, R; Barbaro, K; Terracciano, G; Di Francesco, C E; Mazzariol, S; Eleni, C

    2012-01-01

    The recent description of a prion disease (PD) case in a free-ranging bottlenose dolphin (Tursiops truncatus) prompted us to carry out an extensive search for the disease-associated isoform (PrPSc) of the cellular prion protein (PrPC) in the brain and in a range of lymphoid tissues from 23 striped dolphins (Stenella coeruleoalba), 5 bottlenose dolphins and 2 Risso s dolphins (Grampus griseus) found stranded between 2007 and 2012 along the Italian coastline. Three striped dolphins and one bottlenose dolphin showed microscopic lesions of encephalitis, with no evidence of spongiform brain lesions being detected in any of the 30 free-ranging cetaceans investigated herein. Nevertheless, we could still observe a prominent PrPC immunoreactivity in the brain as well as in lymphoid tissues from these dolphins. Although immunohistochemical and Western blot investigations yielded negative results for PrPSc deposition in all tissues from the dolphins under study, the reported occurrence of a spontaneous PD case in a wild dolphin is an intriguing issue and a matter of concern for both prion biology and intra/inter-species transmissibility, as well as for cetacean conservation medicine. PMID:23034277

  12. Architecture and regulation of negative-strand viral enzymatic machinery

    PubMed Central

    Kranzusch, Philip J.; Whelan, Sean P.J.

    2012-01-01

    Negative-strand (NS) RNA viruses initiate infection with a unique polymerase complex that mediates both mRNA transcription and subsequent genomic RNA replication. For nearly all NS RNA viruses, distinct enzymatic domains catalyzing RNA polymerization and multiple steps of 5′ mRNA cap formation are contained within a single large polymerase protein (L). While NS RNA viruses include a variety of emerging human and agricultural pathogens, the enzymatic machinery driving viral replication and gene expression remains poorly understood. Recent insights with Machupo virus and vesicular stomatitis virus have provided the first structural information of viral L proteins, and revealed how the various enzymatic domains are arranged into a conserved architecture shared by both segmented and nonsegmented NS RNA viruses. In vitro systems reconstituting RNA synthesis from purified components provide new tools to understand the viral replicative machinery, and demonstrate the arenavirus matrix protein regulates RNA synthesis by locking a polymerase–template complex. Inhibition of gene expression by the viral matrix protein is a distinctive feature also shared with influenza A virus and nonsegmented NS RNA viruses, possibly illuminating a conserved mechanism for coordination of viral transcription and polymerase packaging PMID:22767259

  13. Protein lysine methylation by seven-β-strand methyltransferases.

    PubMed

    Falnes, Pål Ø; Jakobsson, Magnus E; Davydova, Erna; Ho, Angela; Małecki, Jędrzej

    2016-07-15

    Methylation of biomolecules is a frequent biochemical reaction within the cell, and a plethora of highly specific methyltransferases (MTases) catalyse the transfer of a methyl group from S-adenosylmethionine (AdoMet) to various substrates. The posttranslational methylation of lysine residues, catalysed by numerous lysine (K)-specific protein MTases (KMTs), is a very common and important protein modification, which recently has been subject to intense studies, particularly in the case of histone proteins. The majority of KMTs belong to a class of MTases that share a defining 'SET domain', and these enzymes mostly target lysines in the flexible tails of histones. However, the so-called seven-β-strand (7BS) MTases, characterized by a twisted beta-sheet structure and certain conserved sequence motifs, represent the largest MTase class, and these enzymes methylate a wide range of substrates, including small metabolites, lipids, nucleic acids and proteins. Until recently, the histone-specific Dot1/DOT1L was the only identified eukaryotic 7BS KMT. However, a number of novel 7BS KMTs have now been discovered, and, in particular, several recently characterized human and yeast members of MTase family 16 (MTF16) have been found to methylate lysines in non-histone proteins. Here, we review the status and recent progress on the 7BS KMTs, and discuss these enzymes at the levels of sequence/structure, catalytic mechanism, substrate recognition and biological significance. PMID:27407169

  14. ATM controls meiotic double-strand break formation

    PubMed Central

    Lange, Julian; Pan, Jing; Cole, Francesca; Thelen, Michael P.; Jasin, Maria; Keeney, Scott

    2011-01-01

    In many organisms, developmentally programmed double-strand breaks (DSBs) formed by the SPO11 transesterase initiate meiotic recombination, which promotes pairing and segregation of homologous chromosomes1. Because every chromosome must receive a minimum number of DSBs, attention has focused on factors that support DSB formation2. However, improperly repaired DSBs can cause meiotic arrest or mutation3,4, thus having too many DSBs is likely as deleterious as having too few. Only a small fraction of SPO11 protein ever makes a DSB in yeast or mouse5, and SPO11 and its accessory factors remain abundant long after most DSB formation ceases1, implying the existence of mechanisms that restrain SPO11 activity to limit DSB numbers. Here we report that the number of meiotic DSBs in mouse is controlled by ATM, a kinase activated by DNA damage to trigger checkpoint signaling and promote DSB repair. Levels of SPO11-oligonucleotide complexes, by-products of meiotic DSB formation, are elevated at least ten-fold in spermatocytes lacking ATM. Moreover, Atm mutation renders SPO11-oligonucleotide levels sensitive to genetic manipulations that modulate SPO11 protein levels. We propose that ATM restrains SPO11 via a negative feedback loop in which kinase activation by DSBs suppresses further DSB formation. Our findings explain previously puzzling phenotypes of Atm-null mice and provide a molecular basis for the gonadal dysgenesis observed in ataxia telangiectasia, the human syndrome caused by ATM deficiency. PMID:22002603

  15. Patterns of evolution of research strands in the hydrologic sciences

    NASA Astrophysics Data System (ADS)

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  16. A Spinach molecular beacon triggered by strand displacement.

    PubMed

    Bhadra, Sanchita; Ellington, Andrew D

    2014-08-01

    We have re-engineered the fluorescent RNA aptamer Spinach to be activated in a sequence-dependent manner. The original Spinach aptamer was extended at its 5'- and 3'-ends to create Spinach.ST, which is predicted to fold into an inactive conformation and thus prevent association with the small molecule fluorophore DFHBI. Hybridization of a specific trigger oligonucleotide to a designed toehold leads to toehold-initiated strand displacement and refolds Spinach into the active, fluorophore-binding conformation. Spinach.ST not only specifically detects its target oligonucleotide but can discriminate readily against single-nucleotide mismatches. RNA amplicons produced during nucleic acid sequence-based amplification (NASBA) of DNA or RNA targets could be specifically detected and reported in real-time by conformational activation of Spinach.ST generated by in vitro transcription. In order to adapt any target sequence to detection by a Spinach reporter we used a primer design technique that brings together otherwise distal toehold sequences via hairpin formation. The same techniques could potentially be used to adapt common Spinach reporters to non-nucleic acid analytes, rather than by making fusions between aptamers and Spinach.

  17. Herpesvirus infection in stranded Pacific harbor seals of coastal California.

    PubMed

    Gulland, F M; Lowenstine, L J; Lapointe, J M; Spraker, T; King, D P

    1997-07-01

    Histopathological examination revealed multifocal acute to chronic adrenal necrosis in 74 of 162 (45%) Pacific harbor seal pups (Phoca vitulina richardsi) dying during rehabilitation following live stranding along the coast of central and northern California (USA). Necrotic adrenal cells contained amphophilic, smudgy intranuclear inclusion bodies that were stained positive for DNA. Fifty of these seals also had lesions typical of sepsis, bacterial omphalophlebitis, pneumonia or gastroenteritis. Twenty four seals had no lesions other than thymic atrophy and occasional multifocal hepatic necrosis. Prior to death, affected seals had a marked lymphopenia. Electron microscopy revealed unenveloped intranuclear hexagonal to round viral particles approximately 100 nm in diameter, and cytoplasmic enveloped virions approximately 160 nm in diameter. These were morphologically consistent with herpesvirus. Inoculation of phocine adrenal and kidney cell lines with an adrenal tissue homogenate from affected animals produced a cytopathic effect in 5 days. Electron microscopy of cell cultures showing this cytopathic effect revealed similar viral particles to those observed in affected adrenal glands. Cases with characteristic inclusion bodies were observed in 42 of 95 (44%) male and 32 of 67 (47%) female seals. Affected animals had been in rehabilitation 0 to 63 days and were below average birth weight for this species. PMID:9249689

  18. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

    SciTech Connect

    Lloyd, Richard E.

    2015-05-15

    Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.

  19. Patterns of evolution of research strands in the hydrologic sciences

    NASA Astrophysics Data System (ADS)

    Schwartz, F. W.; Fang, Y. C.; Parthasarathy, S.

    2005-03-01

    This paper examines issues of impact and innovation in groundwater research by using bibliometric data and citation analysis.The analysis is based on 3120 papers from the journal Water Resources Research with full contents and their citation data from the ISI Web of Science. The research is designed to develop a better understanding of the way citation numbers can be interpreted by scientists. Not surprisingly, the most highly cited papers appear to be pioneers in the field with papers departing significantly from what has come before and to be effective in creating similar, follow-on papers. Papers that are early contributions to a new research strand that is highly influential will be on average highly cited. However, the importance of a research strand as measured by citations seems to fall with time. The citation patterns of some classic papers show that the activity in the topical area and impact of follow-on papers gradually decline with time, which has similarities with Kuhn's ideas of revolutionary and normal science. The results of this study reinforce the importance of being a pioneer in a research strand, strategically shifting research strands, adopting strategies that can facilitate really major research breakthroughs. L'article examine les problèmes d'impact et d'innovation dans la recherche des eaux souterraines en utilisant les données bibliométriques et l'analyse des citations. L'analyse a été faite sur 3120 articles parus dans Water Resources Research en tenant compte de leur texte complet et de toutes citations parues dans l' ISI Web de la Science. Le but de la recherche a été de mieux comprendre comment le nombre des citations peut être interprété par les scientifiques. Ce n'est pas une surprise que les plus cités articles soient les articles-pionniers dans leurs domaines, qui s'écartent d'une manière significative de ce qui a été écrit auparavant et qui ont été suivi par des nouveaux articles. Les articles qui présentent une

  20. [Double-stranded DNA microarray: principal, techniques and applications].

    PubMed

    Pan, Yan; Wang, Jin-Ke

    2013-03-01

    Double-stranded DNA (dsDNA) microarray, also known as protein binding microarray (PBM), is an important technique that can be used to assay the interaction of DNA-binding protein (such as transcription factor, TF) with vast amount of DNA molecules in high-throughput format. This technique immobilizes large amount of various dsDNA molecules on the surface of a solid support (such as glass slide) for detecting the binding interaction of a DNA-binding protein with all of the immobilized dsDNA molecules, and thus determining the DNA-binding affinity, specificity and preference of TFs. In recent years, this technique has demonstrated its valuable applications in several aspects, including rapidly characterizing DNA-binding specificity of large number of TFs, building DNA-binding profiles of TFs, identifying DNA-binding sites and target genes of TFs, discriminating the subtle DNA-binding preferences of members and their dimmers of a TF family, and examining the effects of a cofactor on the DNA-binding specificity of TFs. This paper reviews the principal, techniques, and applications of dsDNA microarray.