Iso-nuclear tungsten dielectronic recombination rates for use in magnetically-confined fusion plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Duck-Hee; Lee, Wonwook; Preval, Simon

Under the auspices of the IAEA Atomic and Molecular Data Center and the Korean Atomic Energy Research Institute, our assembled group of authors has reviewed the current state of dielectronic recombination (DR) rate coefficients for various ion stages of tungsten (W). Subsequent recommendations were based upon available experimental data, first-principle calculations carried out in support of this paper and from available recombination data within existing atomic databases. If a recommendation was possible, data were compiled, evaluated and fitted to a functional form with associated uncertainty information retained, where available. In conclusion, this paper also considers the variation of the Wmore » fractional abundance due to the underlying atomic data when employing different data sets.« less

Dielectronic and Trielectronic Recombination Rate Coefficients of Be-like Ar14+

NASA Astrophysics Data System (ADS)

Huang, Z. K.; Wen, W. Q.; Xu, X.; Mahmood, S.; Wang, S. X.; Wang, H. B.; Dou, L. J.; Khan, N.; Badnell, N. R.; Preval, S. P.; Schippers, S.; Xu, T. H.; Yang, Y.; Yao, K.; Xu, W. Q.; Chuai, X. Y.; Zhu, X. L.; Zhao, D. M.; Mao, L. J.; Ma, X. M.; Li, J.; Mao, R. S.; Yuan, Y. J.; Wu, B.; Sheng, L. N.; Yang, J. C.; Xu, H. S.; Zhu, L. F.; Ma, X.

2018-03-01

Electron–ion recombination of Be-like 40Ar14+ has been measured by employing the electron–ion merged-beams method at the cooler storage ring CSRm. The measured absolute recombination rate coefficients for collision energies from 0 to 60 eV are presented, covering all dielectronic recombination (DR) resonances associated with 2s 2 → 2s2p core transitions. In addition, strong trielectronic recombination (TR) resonances associated with 2s 2 → 2p 2 core transitions were observed. Both DR and TR processes lead to series of peaks in the measured recombination spectrum, which have been identified by the Rydberg formula. Theoretical calculations of recombination rate coefficients were performed using the state-of-the-art multi-configuration Breit–Pauli atomic structure code AUTOSTRUCTURE to compare with the experimental results. The plasma rate coefficients for DR+TR of Ar14+ were deduced from the measured electron–ion recombination rate coefficients in the temperature range from 103 to 107 K, and compared with calculated data from the literature. The experimentally derived plasma rate coefficients are 60% larger and 30% lower than the previously recommended atomic data for the temperature ranges of photoionized plasmas and collisionally ionized plasmas, respectively. However, good agreement was found between experimental results and the calculations by Gu and Colgan et al. The plasma rate coefficients deduced from experiment and calculated by the current AUTOSTRUCTURE code show agreement that is better than 30% from 104 to 107 K. The present results constitute a set of benchmark data for use in astrophysical modeling.

Theoretical study of the dielectronic recombination process of Li-like Xe51+ ions

NASA Astrophysics Data System (ADS)

Dou, Lijun; Xie, Luyou; Zhang, Denghong; Dong, Chenzhong; Wen, Weiqiang; Huang, Zhongkui; Ma, Xinwen

2017-05-01

The dielectronic recombination of Li-like Xe51+ (2s) ions was studied using the flexible atomic code based on the relativistic configuration interaction method. The resonance energies, radiative and autoionization rates, and resonance strengths were calculated systematically for the doubly excited states (2p1/2nlj)J(n = 18-32) and (2p3/2n'lj)J(n' = 9-27) of Be-like Xe50+ ions. For the higher Rydberg resonance states with n ≥ 33 and n' ≥ 28, the resonance energies and strengths were obtained by extrapolation based on quantum defect theory. The theoretical rate coefficients, covering the center-of-mass energy range 0-505 eV, are in a better agreement with the experimental results measured at the heavy-ion storage ring ESR than the Multi-Configuration Dirac-Fock calculations, especially at the resonance energy range close to the series limits. Contribution to the Topical Issue: "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, Grzegorz Karwasz.

High Rydberg resonances in dielectronic recombination of pb(79+).

PubMed

Brandau, C; Bartsch, T; Hoffknecht, A; Knopp, H; Schippers, S; Shi, W; Müller, A; Grün, N; Scheid, W; Steih, T; Bosch, F; Franzke, B; Kozhuharov, C; Mokler, P H; Nolden, F; Steck, M; Stöhlker, T; Stachura, Z

2002-07-29

Dielectronic recombination resonances of Pb (79+) associated with 2s(1/2)-->2p(1/2) excitations were measured at the heavy-ion storage ring ESR at GSI. The fine structure of the energetically lowest resonance manifold Pb (78+)(1s(2)2p(1/2)20l(j)) at around 18 eV could partially be resolved, and rate coefficients on an absolute scale were obtained. A comparison of the experimental data with results of a fully relativistic theoretical approach shows that high-angular-momentum components up to j=31/2 significantly contribute to the total resonance strength demonstrating the necessity to revise the widespread notion of negligible high-angular-momentum contributions at least for very highly charged ions.

A search for evidence of below threshold dielectronic recombination in low temperature plasmas

NASA Astrophysics Data System (ADS)

Nemer, Ahmad; Loch, Stuart; Sterling, Nicholas C.; Raymond, John C.

2018-06-01

There are two main types of photoionized gaseous nebulae that exist in the universe, H II regions and Planetary Nebulae (PNe), that mark the endpoints of stellar evolution, and understanding their composition will lead to better understanding of stellar evolution processes, and galactic chemical nucleosynthesis. Determination of heavy elements’ abundances is essential in the analysis of these nebulae. In addition, lines emitted from these heavy elements are typically used for nebular condition deduction. There has been a long-standing problem regarding discrepancy of temperatures and abundances resolved from optical recombination lines and collisionally excited lines. One of the reasons suggested to explain the discrepancy is Dielectronic Recombination (DR). DR is thought to necessarily occur through continuum states overlapping with autoionizing states that are above the ionization threshold. Robicheaux et al. (2010) proposed that DR to below threshold states is possible through ‘negative’ energy electrons recombining to below threshold doubly excited states. The spectral lines emitted from this process could provide an efficient mechanism to cool off plasma in addition to having satellite lines blended with collisionally excited lines related to plasma diagnostics. Furthermore, this phenomenon would occur significantly in low temperature plasmas which makes it challenging to prepare an experiment for testing it in a lab. In this research we present a spectroscopic study into this process through observed optical spectra from seven PNe that suffer from abundance discrepancy problem. A code was developed that produces a synthetic spectrum for 2 cases; namely, C IV recombining to C III and C III to C II. There is faint emission in the optical for these cases. Other possible mechismas to activiate these lines were included in the model and found insignificant. The Auger rates were calculated using the atomic physics code AUTOSTRUCTURE, and the lines were synthesized using a collisional-radiative model.

Photoionization and Recombination

NASA Technical Reports Server (NTRS)

Nahar, Sultana N.

2000-01-01

Theoretically self-consistent calculations for photoionization and (e + ion) recombination are described. The same eigenfunction expansion for the ion is employed in coupled channel calculations for both processes, thus ensuring consistency between cross sections and rates. The theoretical treatment of (e + ion) recombination subsumes both the non-resonant recombination ("radiative recombination"), and the resonant recombination ("di-electronic recombination") processes in a unified scheme. In addition to the total, unified recombination rates, level-specific recombination rates and photoionization cross sections are obtained for a large number of atomic levels. Both relativistic Breit-Pauli, and non-relativistic LS coupling, calculations are carried out in the close coupling approximation using the R-matrix method. Although the calculations are computationally intensive, they yield nearly all photoionization and recombination parameters needed for astrophysical photoionization models with higher precision than hitherto possible, estimated at about 10-20% from comparison with experimentally available data (including experimentally derived DR rates). Results are electronically available for over 40 atoms and ions. Photoionization and recombination of He-, and Li-like C and Fe are described for X-ray modeling. The unified method yields total and complete (e+ion) recombination rate coefficients, that can not otherwise be obtained theoretically or experimentally.

Dielectronic Satellite Spectra of Na-like Mo Ions Benchmarked by LLNL EBIT with Application to HED Plasmas

NASA Astrophysics Data System (ADS)

Stafford, A.; Safronova, A. S.; Kantsyrev, V. L.; Safronova, U. I.; Petkov, E. E.; Shlyaptseva, V. V.; Childers, R.; Shrestha, I.; Beiersdorfer, P.; Hell, H.; Brown, G. V.

2017-10-01

Dielectronic recombination (DR) is an important process for astrophysical and laboratory high energy density (HED) plasmas and the associated satellite lines are frequently used for plasma diagnostics. In particular, K-shell DR satellite lines were studied in detail in low-Z plasmas. L-shell Na-like spectral features from Mo X-pinches considered here represent the blend of DR and inner shell satellites and motivated the detailed study of DR at the EBIT-1 electron beam ion trap at LLNL. In these experiments the beam energy was swept between 0.6 - 2.4 keV to produce resonances at certain electron beam energies. The advantages of using an electron beam ion trap to better understand atomic processes with highly ionized ions in HED Mo plasma are highlighted. This work was supported by NNSA under DOE Grant DE-NA0002954. Work at LLNL was performed under the auspices of the U.S. DOE under Contract No. DE-AC52-07NA27344.

Dielectronic recombination of lowly charged tungsten ions Wq+(q = 5 - 10)

NASA Astrophysics Data System (ADS)

Kwon, Duck-Hee

2018-03-01

Dielectronic recombination (DR) rate coefficients for the ground levels of low ionization state Wq+ (q = 5 - 10) ions have been obtained by an ab-inito level-by-level calculation using the flexible atomic code (FAC) based on relativistic jj coupling scheme and independent process, isolated resonance, distorted wave approximation. The radiative transition calculation in the original FAC has been adapted into parallel programming for time effective dealing with so many resonance levels of the complex open 4f, 5p, or 5d-shell structure ion. Core excitations Δnc = 0 , 1 of 4f, 5p, and 5d (W5+), Δnc = 2 of 4f, and Δnc = 0 of 4d (W7+), and 5s (W8+) are included to the total DR rate coefficient. The core excitations Δnc = 0 , 5p → 5l and Δnc = 1 , 4f → 5l mainly contribute to the total DR rate coefficients. The strong resonances involved in the DR are analyzed and the total DR rate coefficients are compared with available previous ab-initio predictions and with ADAS data by a simple semiempirical formula.

Strong higher-order resonant contributions to x-ray line polarization in hot plasmas

NASA Astrophysics Data System (ADS)

Shah, Chintan; Amaro, Pedro; Steinbrügge, Rene; Beilmann, Christian; Bernitt, Sven; Fritzsche, Stephan; Surzhykov, Andrey; Crespo López-Urrutia, José R.; Tashenov, Stanislav

2016-06-01

We studied angular distributions of x rays emitted in resonant recombination of highly charged iron and krypton ions, resolving dielectronic, trielectronic, and quadruelectronic channels. A tunable electron beam drove these processes, inducing x rays registered by two detectors mounted along and perpendicular to the beam axis. The measured emission asymmetries comprehensively benchmarked full-order atomic calculations. We conclude that accurate polarization diagnostics of hot plasmas can only be obtained under the premise of inclusion of higher-order processes that were neglected in earlier work.

Dielectronic recombination experiments at the storage rings: From the present CSR to the future HIAF

NASA Astrophysics Data System (ADS)

Huang, Z. K.; Wen, W. Q.; Xu, X.; Wang, H. B.; Dou, L. J.; Chuai, X. Y.; Zhu, X. L.; Zhao, D. M.; Li, J.; Ma, X. M.; Mao, L. J.; Yang, J. C.; Yuan, Y. J.; Xu, W. Q.; Xie, L. Y.; Xu, T. H.; Yao, K.; Dong, C. Z.; Zhu, L. F.; Ma, X.

2017-10-01

Dielectronic recombination (DR) experiments of highly charged ions at the storage rings have been developed as a precision spectroscopic tool to investigate the atomic structure as well as nuclear properties of stable and unstable nuclei. The DR experiment on lithium-like argon ions was successfully performed at main Cooler Storage Ring (CSRm) at Heavy Ion Research Facility in Lanzhou (HIRFL) accelerator complex. The DR experiments on heavy highly charged ions and even radioactive ions are currently under preparation at the experimental Cooler Storage Ring (CSRe) at HIRFL. The current status of DR experiments at the CSRm and the preparation of the DR experiments at the CSRe are presented. In addition, an overview of DR experiments by employing an electron cooler and a separated ultra-cold electron target at the upcoming High Intensity heavy ion Accelerator Facility (HIAF) will be given.

Ion Storage Ring Measurements of Low Temperature Dielectronic Recombination Rate Coefficients for Modeling X-Ray Photoionized Cosmic Plasmas

NASA Technical Reports Server (NTRS)

Savin, D. W.; Gwinner, G.; Schwalm, D.; Wolf, A.; Mueller, A.; Schippers, S.

2002-01-01

Low temperature dielectronic recombination (DR) is the dominant recombination mechanism for most ions in X-ray photoionized cosmic plasmas. Reliably modeling and interpreting spectra from these plasmas requires accurate low temperature DR rate Coefficients. Of particular importance are the DR rate coefficients for the iron L-shell ions (Fe XVII-Fe XXIV). These ions are predicted to play an important role in determining the thermal structure and line emission of X-ray photoionized plasmas, which form in the media surrounding accretion powered sources such as X-ray binaries (XRBs), active galactic nuclei (AGN), and cataclysmic variables (Savin et al., 2000). The need for reliable DR data of iron L-shell ions has become particularly urgent after the launches of Chandra and XMM-Newton. These satellites are now providing high-resolution X-ray spectra from a wide range of X-ray photoionized sources. Interpreting the spectra from these sources requires reliable DR rate coefficients. However, at the temperatures relevant, for X-ray photoionized plasmas, existing theoretical DR rate coefficients can differ from one another by factors of two to orders of magnitudes.

Laboratory Measurements of the Dielectronic Recombination Satellite Transitions of He-Like FE XXV and H-Like FE XXVI

NASA Technical Reports Server (NTRS)

Gu, M. F.; Beiersdorfer, P.; Brown, G. V.; Graf, A.; Kelley, R. I.; Kilbourne, C. A.; Porter, F. S.; Kahn, S. M,

2012-01-01

We present laboratory spectra of dielectronic recombination (DR) satellite transitions attached to the He-like and H-like iron resonance lines obtained with the NASA Goddard Space Flight Center X-ray calorimeter and produced by a thermal plasma simu1ation technique on the EBIT-I electron beam ion trap at the Lawrence Livermore National Laboratory. We demonstrate that the calorimeter has sufficient spectral resolution in the 6-9 keV range to provide reliable measurements not only of standard DR satellite to resonance line intensities but also of DR satellite to DR satellite ratios that can be used to diagnose nonthermal electron distributions. Electron temperatures derived from the measured line intensities are consistent with the temperature of the simulated plasma. Temperature measurements based on DR satellite transitions have significant advantages over those based on collisional ionization equilibrium or continuum shape. Thus, successful demonstration of this method with the X-ray calorimeter is an important step fur its application in X-ray astronomy.

Dielectronic Recombination In Active Galactic Nuclei

NASA Technical Reports Server (NTRS)

Lukic, D. V.; Schnell, M.; Savin, D. W.; Altun, Z.; Badnell, N.; Brandau, C.; Schmidt, E. W.; Mueller, A.; Schippers, S.; Sprenger, F.;

KLL dielectronic recombination resonant strengths of He-like up to O-like xenon ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, K.; Geng, Z.; Xiao, J.

2010-02-15

In this work, the KLL dielectronic recombination (DR) resonant strengths of He- through to O-like Xe ions were studied, both through experiment and calculation. The experiments were done using a fast electron beam-energy scanning technique at the Shanghai electron beam ion trap. The calculations were done by using the flexible atomic code (FAC), in which the relativistic configuration interaction (RCI) method was employed. For the total resonant strengths, the present experimental and theoretical results for He-, Be-, B-, C-, N-, and O-like Xe ions agree within experimental uncertainties (about 9%). But the experimental result for Li-like Xe is 14% highermore » than the calculation. The present FAC calculations of the total DR strengths were compared with the available previous calculations, using RCI or multiconfiguration Dirac-Fock (MCDF) methods, and the agreement was very good. In this work, some intermediate-state resolved KLL DR strengths were also obtained and compared with theoretical results, and more discrepancies were revealed.« less

Spectroscopy of berylliumlike xenon ions using dielectronic recombination

NASA Astrophysics Data System (ADS)

Bernhardt, D.; Brandau, C.; Harman, Z.; Kozhuharov, C.; Böhm, S.; Bosch, F.; Fritzsche, S.; Jacobi, J.; Kieslich, S.; Knopp, H.; Nolden, F.; Shi, W.; Stachura, Z.; Steck, M.; Stöhlker, Th; Schippers, S.; Müller, A.

2015-07-01

Be-like 136X{{e}50+} ions have been investigated employing the resonant electron-ion collision process of dielectronic recombination (DR) as a spectroscopic tool. The experiments were performed at the experimental storage ring in Darmstadt, Germany, using its electron cooler as a target for free electrons. DR Rydberg resonance series 2{{s}2}+{{e}-}\\to 2s2{{p}{{j\\prime }}}n{{l}j} for the associated intra-L-shell transitions 2{{s}2}{{ }1}{{S}0}-2s2{{p}1/2}{{ }3}{{P}1},2{{s}2}{{ }1}{{S}0}-2s2{{p}3/2}{{ }3}{{P}2} and 2{{s}2}{{ }1}{{S}0}-2s2{{p}3/2}{{ }1}{{P}1} were observed with high resolution. In addition to these excitations from the ground state we determined resonances associated with excitations 2s2{{p}1/2}{{ }3}{{P}0}\\to 2{{p}1/2}2{{p}3/2}{{ }3}{{P}1} of ions initially in the metastable 2s2{{p}1/2}{{ }3}{{P}0} state. The corresponding excitation energies were determined to be E{{(}1}{{S}0}\\to {{ }3}{{P}1})=127.269(46) eV, E{{(}1}{{S}0}\\to {{ }3}{{P}2})=469.474(81) eV and E{{(}1}{{S}0}\\to {{ }1}{{P}1})=532.801(16) eV, and E{{(}3}{{P}0}\\to 2{{p}1/2}2{{p}3/2}{{ }3}{{P}1})=533.733(22) eV. These excitation energies are compared with previous measurements and with recent state-of-the-art atomic structure calculations.

Low energy range dielectronic recombination of Fluorine-like Fe17+ at the CSRm

NASA Astrophysics Data System (ADS)

Khan, Nadir; Huang, Zhong-Kui; Wen, Wei-Qiang; Mahmood, Sultan; Dou, Li-Jun; Wang, Shu-Xing; Xu, Xin; Wang, Han-Bing; Chen, Chong-Yang; Chuai, Xiao-Ya; Zhu, Xiao-Long; Zhao, Dong-Mei; Mao, Li-Jun; Li, Jie; Yin, Da-Yu; Yang, Jian-Cheng; Yuan, You-Jin; Zhu, Lin-Fan; Ma, Xin-Wen

2018-05-01

The accuracy of dielectronic recombination (DR) data for astrophysics related ions plays a key role in astrophysical plasma modeling. The absolute DR rate coefficient of Fe17+ ions was measured at the main cooler storage ring at the Institute of Modern Physics, Lanzhou, China. The experimental electron-ion collision energy range covers the first Rydberg series up to n = 24 for the DR resonances associated with the {}2P1/2\\to {}2P3/2{{Δ }}n=0 core excitations. A theoretical calculation was performed by using FAC code and compared with the measured DR rate coefficient. Overall reasonable agreement was found between the experimental results and calculations. Moreover, the plasma rate coefficient was deduced from the experimental DR rate coefficient and compared with the available results from the literature. At the low energy range, significant discrepancies were found, and the measured resonances challenge state-of-the-art theory at low collision energies. Supported by the National Key R&D Program of China (2017YFA0402300), the National Natural Science Foundation of China through (11320101003, U1732133, 11611530684) and Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SLH006)

Self-consistent ab initio Calculations for Photoionization and Electron-Ion Recombination Using the R-Matrix Method

NASA Astrophysics Data System (ADS)

Nahar, S. N.

2003-01-01

Most astrophysical plasmas entail a balance between ionization and recombination. We present new results from a unified method for self-consistent and ab initio calculations for the inverse processes of photoionization and (e + ion) recombination. The treatment for (e + ion) recombination subsumes the non-resonant radiative recombination and the resonant dielectronic recombination processes in a unified scheme (S.N. Nahar and A.K. Pradhan, Phys. Rev. A 49, 1816 (1994);H.L. Zhang, S.N. Nahar, and A.K. Pradhan, J.Phys.B, 32,1459 (1999)). Calculations are carried out using the R-matrix method in the close coupling approximation using an identical wavefunction expansion for both processes to ensure self-consistency. The results for photoionization and recombination cross sections may also be compared with state-of-the-art experiments on synchrotron radiation sources for photoionization, and on heavy ion storage rings for recombination. The new experiments display heretofore unprecedented detail in terms of resonances and background cross sections and thereby calibrate the theoretical data precisely. We find a level of agreement between theory and experiment at about 10% for not only the ground state but also the metastable states. The recent experiments therefore verify the estimated accuracy of the vast amount of photoionization data computed under the OP, IP and related works. features. Present work also reports photoionization cross sections including relativistic effects in the Breit-Pauli R-matrix (BPRM) approximation. Detailed features in the calculated cross sections exhibit the missing resonances due to fine structure. Self-consistent datasets for photoionization and recombination have so far been computed for approximately 45 atoms and ions. These are being reported in a continuing series of publications in Astrophysical J. Supplements (e.g. references below). These data will also be available from the electronic database TIPTOPBASE (http://heasarc.gsfc.nasa.gov)

Anomalous Abundances in Gaseous Nebulae From Recombination and Collisional Lines: Improved Photoionization and Recombination Studies

NASA Astrophysics Data System (ADS)

Pradhan, Anil Kumar; Nahar, S. N.; Eissner, W. B.; Montenegro, M.

2011-01-01

A perplexing anomaly arises in the determination of abundances of common elements in gaseous nebulae, as derived from collisionally excited lines (CEL) as opposed to those from Recombination Lines (RCL). The "abundance discrepancy factors" can range from a factor of 2 to an order of magnitude or more. That has led to quite different interpretation of the physical structure and processes in gaseous nebulae, such as temperature fluctuations across the object, or metal-rich concentrations leading to a dual-abundnace scenario. We show that the problem may lie in inaccuracies in photoionization and recombination models neglecting low-energy resonance phenomena due to fine structure. Whereas the atomic physics of electron impact excitation of forbidden lines is well understood, and accurate collision strengths have long been available, that is not generally the case for electron-ion recombination cross sections. A major problem is the inclusion of relativisitic effects as it pertains to the existence of very low-energy fine structure resonances in photoionization cross sections. We carry out new relativistic calculations for photoionization and recombination cross sections using a recently extended version of the Breit-Pauli R-matrix codes, and the unified electron-ion recombination method that subsumes both the radiative and the dielectronic recombination (RR and DR) processes in an ab initio and self-consistent manner. We find that near-thresold resonances manifest themselves within fine structure levels of the ground state of ions, enhancing low-temperature recombination rate coefficients at 1000-10,000 K. The resulting enahncement in level-specific and total recombination rate coefficients should therefore lead to reduced abundances derived from RCL, and in accordance with those from CEL. We present results for photoionization of O II into, and recombination from, O III. Theoretical cross sections are benchmarked against high-resolution measurements from synchrotron based light sources. Work on other atomic species is in progress.

Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

NASA Astrophysics Data System (ADS)

Sterling, Nicholas C.; Kerlin, Austin B.

2016-01-01

We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

Atomic Calculations and Laboratory Measurements Relevant to X-ray Warm Absorbers

NASA Technical Reports Server (NTRS)

Kallman, Tim; Bautista, M.; Palmeri, P.

2007-01-01

This viewgraph document reviews the atomic calculations and the measurements from the laboratory that are relevant to our understanding of X-Ray Warm Absorbers. Included is a brief discussion of the theoretical and the experimental tools. Also included is a discussion of the challenges, and calculations relevant to dielectronic recombination, photoionization cross sections, and collisional ionization. A review of the models is included, and the sequence that the models were applied.

Improved Simulations of Astrophysical Plasmas: Computation of New Atomic Data

NASA Technical Reports Server (NTRS)

Gorczyca, Thomas W.; Korista, Kirk T.

2005-01-01

Our research program is designed to carry out state-of-the-art atomic physics calculations crucial to advancing our understanding of fundamental astrophysical problems. We redress the present inadequacies in the atomic data base along two important areas: dielectronic recombination and inner-shell photoionization and multiple electron ejection/Auger fluorescence therefrom. All of these data are disseminated to the astrophysical community in the proper format for implementation in spectral simulation code.

Dielectronic satellite spectra of hydrogen-like titanium (Ti XXII)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bitter, M.; von Goeler, S.; Cohen, S.

High resolution spectra of the Ly ..cap alpha../sub 1/ and Ly ..cap alpha../sub 2/ lines of hydrogenlike titanium, TiXXII, and the associated dielectronic satellites which are due to transitions 1snl-2pnl with n greater than or equal to 2, have been observed from tokamak discharges with auxiliary ion cyclotron heating (ICRH) with central electron temperatures of 2 keV and central electron densities of 8 x 10/sup 13/ cm/sup -3/ on the Princeton Large Torus (PLT). The data have been used for a detailed comparison with theoretical predictions based on the Z - expansion method and Hartree - Fock calculations. The resultsmore » obtained with the Z - expansion method are in excellent agreement with the observed spectral data except for minor discrepancies between the theoretical and experimental wavelengths of 0.0003 A for the n = 2 satellites and of 0.0001 A for the separation of the Ly ..cap alpha../sub 1/ and Ly ..cap alpha../sub 2/ lines. Very good agreement with the experimental data is also obtained for the results from the Hartree - Fock calculations though somewhat larger discrepancies (approx. = 0.0009 A) exist between experimental and theoretical wavelengths which are systematically too small. The observed spectra are used for diagnosis of the central ion and electron temperatures of the PLT discharges and for a measurement of the dielectronic recombination rate coefficient of TiXXII.« less

A New Temperature Determination Using the Fe XVII Emission of Capella

NASA Astrophysics Data System (ADS)

Beiersdorfer, P.; Gu, M. F.; Lepson, J.; Desai, P.

2011-12-01

Typically, the most reliable way to spectroscopically determine the electron temperature is to measure the strength of dielectronic recombination (DR) satellite lines relative to the associated resonance line, IDR/ Ir, as this ratio varies steeply with temperature and does not require assumptions associated with the calculations of ionization equilibria. We have applied this method to the Fe XVII lines, which are very bright in the spectrum of Capella observed with high resolution with Chandra's High Energy Transmission Grating Spectrometer. In particular, we have determined the intensity of the dielectronic satellite lines next to the Fe XVII 2p-3d resonance line, commonly denoted 3C. The atomic data needed to do this are supplied by the Flexible Atomic Code. The temperature, TDR, we have derived from this method is somewhat lower than TDEM, derived from the differential emission measure for Fe XVII. We show that the precision of this method is very high, and we discuss the its limitations.

Excitation energies, radiative and autoionization rates, dielectronic satellite lines, and dielectronic recombination rates for excited states of Rb-like W from Kr-like W [Relativistic atomic data for Rb-like tungsten

DOE PAGES

Safronova, U. I.; Safronova, A. S.; Beiersdorfer, P.

2016-11-02

Energy levels, radiative transition probabilities, and autoionization rates for [Ni]more » $$4{s}^{2}4{p}^{6}{nl}$$, [Ni]$$4{s}^{2}4{p}^{5}4l^{\\prime} {nl}$$ ($$l^{\\prime} =d,f,n$$ = 4–7), [Ni]$$4s4{p}^{6}4l^{\\prime} {nl}$$, ($$l^{\\prime} =d,f,n$$ = 4–7), [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} {nl}$$ (n = 5–7), and [Ni]$$4s4{p}^{6}6l^{\\prime} {nl}$$ (n = 6–7) states in Rb-like tungsten (W37+) are calculated using the relativistic many-body perturbation theory method (RMBPT code) and the Hartree–Fock-relativistic method (COWAN code). Autoionizing levels above the [Ni]$$4{s}^{2}4{p}^{6}$$ threshold are considered. It is found that configuration mixing among [Ni]$$4{s}^{2}4{p}^{5}4l^{\\prime} {nl}$$ and [Ni]$$4s4{p}^{6}4l^{\\prime} {nl}$$ plays an important role for all atomic characteristics. Branching ratios relative to the first threshold and intensity factors are calculated for satellite lines, and dielectronic recombination (DR) rate coefficients are determined for the [Ni]$$4{s}^{2}4{p}^{6}{nl}$$ (n = 4–7) singly excited states, as well as the [Ni]$$4{s}^{2}4{p}^{5}4{dnl}$$, [Ni]$$4{s}^{2}4{p}^{5}4{fnl}$$, [Ni]$$4s4{p}^{6}4{dnl}$$, [Ni]$$4{s}^{2}4{p}^{6}4{fnl}$$, (n = 4–6), and [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} 5l$$ doubly excited nonautoionizing states in Rb-like W37+ ion. Contributions from the [Ni]$$4s24{p}^{6}4{fnl}$$ (n = 6–7), [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} {nl}$$ (n = 5–6), and [Ni]$$4{s}^{2}4{p}^{5}6l^{\\prime} {nl}$$ (n = 6–7) doubly excited autoionizing states are evaluated numerically. The high-n state (with n up to 500) contributions are very important for high temperatures. These contributions are determined by using a scaling procedure. Synthetic dielectronic satellite spectra from Rb-like W are simulated in a broad spectral range from 8 to 70 Å. Here, these calculations provide highly accurate values for a number of W 37+ properties useful for a variety of applications including for fusion applications.« less

Astronomy-inspired Atomic and Molecular Physics

NASA Astrophysics Data System (ADS)

Rau, A. R. P.

2002-02-01

Aimed at senior undergraduate and first-year graduate students in departments of physics and astronomy, this textbook gives a systematic treatment of atomic and molecular structure and spectra, together with the effect of weak and strong external electromagnetic fields. Topics chosen are those of interest in astronomy and indeed many were inspired by specific astronomical contexts. Examples include the negative ion of hydrogen and the effects of strong magnetic fields such as those occurring on certain white dwarfs and neutron stars. Adiabatic and non-adiabatic handling of electron correlations and application to processes such as dielectronic recombination are included. Astronomical examples are provided throughout as well as end-of-the chapter problems and exercises. Over seventy illustrative diagrams complete this unique and comprehensive volume. Link: http://www.wkap.nl/prod/b/1-4020-0467-2

The OI 989-A tropical nightglow

NASA Technical Reports Server (NTRS)

Abreu, V. J.; Solomon, S. C.; Dalgarno, A.; Yee, J. H.; Chakrabarti, S.

1984-01-01

Attention is given to the morphology and origin of the OI 989 A emission in the tropical nightglow. Dielectronic recombination of O(+) is suggested as the mechanism responsible for populating the 3s' 3D0 state of this 2p4 3P 3s' 3D0 emission. The spectrometer used is that aboard the STP 78-1 satellite, which is in sun-synchronous orbit. The emission morphology is characterized by tropical arcs on each side of the dip equator.

X-Ray Spectroscopic Laboratory Experiments in Support of the X-Ray Astronomy Program

NASA Technical Reports Server (NTRS)

Kahn, Steven M.

1997-01-01

Our program is to perform a series of laboratory investigations designed to resolved significant atomic physics uncertainties that limit the interpretation of cosmic X-ray spectra. Specific goals include a quantitative characterization of Fe L-shell spectra; the development of new techniques to simulate Maxwellian plasmas using an Electron Beam Ion Trap (EBIT); and the measurement of dielectronic recombination rates for photoionized gas. New atomic calculations have also been carried out in parallel with the laboratory investigations.

Laboratory Studies in UV and EUV Solar Physics

NASA Technical Reports Server (NTRS)

Parkinson, W. H.; Wagner, William J. (Technical Monitor)

2002-01-01

The Ion Beam Experiment at the Center for Astrophysics is dedicated to the study of ion-electron collision processes of importance in solar physics. The analysis of measurements of Electron Impact Excitation (EIE) from the 3s3p(exp 3)P(exp o) metastable state to the 3s3p(exp 1)P state of Si(2+) was completed during the past year and a paper describing the results is available as a preprint. Our current program is directed at measuring absolute cross sections for dielectronic recombination (DR) and EIE in Si(3+), one of the primary ions used for probing the solar transition region. Our study of DR is particularly concerned with the effects of electric and magnetic fields on the recombination rates. Measurements of silicon ions with charge greater than n=2 have necessitated upgrading the experiment with a new ion source. The new source is also suitable for producing C(2+) beams to be used for measurements of EIE and DR for that system. The source is expected to be capable of producing beams of more highly charged systems as well.

Low-frequency Carbon Radio Recombination Lines. I. Calculations of Departure Coefficients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salgado, F.; Morabito, L. K.; Oonk, J. B. R.

In the first paper of this series, we study the level population problem of recombining carbon ions. We focus our study on high quantum numbers, anticipating observations of carbon radio recombination lines to be carried out by the Low Frequency Array. We solve the level population equation including angular momentum levels with updated collision rates up to high principal quantum numbers. We derive departure coefficients by solving the level population equation in the hydrogenic approximation and including low-temperature dielectronic capture effects. Our results in the hydrogenic approximation agree well with those of previous works. When comparing our results including dielectronicmore » capture, we find differences that we ascribe to updates in the atomic physics (e.g., collision rates) and to the approximate solution method of the statistical equilibrium equations adopted in previous studies. A comparison with observations is discussed in an accompanying article, as radiative transfer effects need to be considered.« less

An abundance study of IC 418 using high-resolution, signal-to-noise emission spectra

NASA Astrophysics Data System (ADS)

Sharpee, Brian David

2003-11-01

An on-going problem in astrophysics involves the large and varying disagreement between abundances measurements made in planetary nebulae (PNe), determined from the strengths of emission lines arising from the same source ion, but excited by differing mechanisms (recombination and collisional excitation) in planetary nebulae (PNe). We investigate the extent of this problem in IC 418, a PN chosen for its great surface brightness and perceived visually uncomplicated geometry, through the use of high resolution (R ≈ 30000 = 10 km sec-1 at 6500Å) echelle emission spectroscopy in the optical regime (3500 9850Å). These observations allow us to construct the most detailed list of atomic emission lines ever compiled for IC 418, and among the most detailed from among all PNe. Ionic abundances are calculated from the fluxes of numerous weak (1 × 10-5 Hβ) atomic emission lines from the ions of C,N,O, and Ne, using the most recent and accurate atomic transition information presently available. The high resolution of these spectra provides well-defined line profiles, which, coupled with the perceived simplicity of the object's expansion velocity distribution, allows us to better determine where in the nebula lines are formed, and where the ions that produce them are concentrated. Evidence for “non-conventional” line excitation mechanisms, such as continuum fluorescence from the ground state or enhanced dielectronic recombination, is sought in the profile morphologies and relative line strengths. Non-conventional excitation processes may influence the strengths of lines enough to significantly alter abundances calculated from them. Our calculations show that recombination line-derived abundances exceed those derived from collisionally excited lines, for those ions for which we observed lines of both types: O+, O+2, and Ne +2 by real and varying amounts. We find that both continuum fluorescence and dielectronic recombination excites numerous lines in IC 418, but that there is no evidence in our data that either process is responsible for the observed overabundances in all recombination lines as opposed to their collisionally excited counterparts. The calculated levels of temperature fluctuations in the zones in which these ion reside are dubious, and significantly exceed model predicted values. In summary, no satisfactory, single universally applicable answer to the abundance discrepancy problem shown to exist by us in IC 418, is revealed by our observations. We developed several new techniques to analyze these data. Of particular interest is EMILI (Emission Line Identifier), a public-domain program that utilizes a comprehensive atomic transition list and a set of simple tests and criteria, to quickly provide its user with a list of rank ordered IDs for unidentified emission lines found in deep, high resolution spectra. Presented here are the results of applying EMILI to the identification of weak emission lines in the spectra of IC 418 and other PNe.

The origin of N III lambda 990 and C III lambda 977 emission in AGN narrow-line region gas

NASA Technical Reports Server (NTRS)

Ferguson, J. W.; Ferland, G. J.; Pradhan, A. K.

1995-01-01

We discuss implications of Hopkins Ultraviolet Telescope (HUT) detections of C III lambda 977 and N III lambda 990 emission from the narrow-line region of the Seyfert 2 galaxy NGC 1068. In their discovery paper Kriss et al. showed that the unexpectedly great strength of these lines implies that the emitting gas must be shock-heated if the lines are collisionally excited. Here we investigate other processes which excite these lines in photoionization equilibrium. Recombination, mainly dielectronic, and continuum fluorescence are strong contributors to the line. The resulting intensities are sensitive to the velocity field of the emitting gas and require that the turbulence be of the same order of magnitude as the observed line width. We propose optical observations that will decide whether the gas is collisionally or radiatively heated.

The Origin of NIII λ990 and CIII λ977 Emission in NGC 1068

NASA Astrophysics Data System (ADS)

Ferguson, Jason W.; Ferland, Gary J.

1994-12-01

We discuss implications of HUT detections of C III λ977 and N III λ990 emission from the Narrow Lined Region (NLR) of the Seyfert 2 galaxy NGC 1068. In their discovery paper Kriss et al. (1992, ApJ, 394, L37) showed that unexpectedly great strength of these lines implies that the emitting gas must be shock heated if the lines are collisionally excited. Here we investigate other processes which excite these lines in photoionization equilibrium. Recombination, mainly dielectronic, and continuum fluorescence, are strong contributors to the line. The resulting intensities are sensitive to the velocity field of the emitting gas, and require that the turbulence be the same order of magnitude as the observed line width. We propose optical observations that will decide whether the gas is collisionally or radiatively heated.

Excitation energies, radiative and autoionization rates, dielectronic satellite lines, and dielectronic recombination rates for excited states of Na-like W from Ne-like W

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safronova, U.I.; Safronova, A.S.; Beiersdorfer, P.

Energy levels, radiative transition probabilities, and autoionization rates for 1s{sup 2}2s{sup 2}2p{sup 5}3l{sup '}nl,1s{sup 2}2s2p{sup 6}3l{sup '}nl(n=3-7,l{<=}n-1) and 1s{sup 2}2s{sup 2}2p{sup 5}4l{sup '}nl,1s{sup 2}2s2p{sup 6}4l{sup '}nl(n=4-6,l{<=}n-1) states in Na-like tungsten (W{sup 63+}) are calculated. Cowan's relativistic Hartree-Fock method, the relativistic multiconfiguration method implemented in the Hebrew University Lawrence Livermore Atomic Code, and the relativistic many-body perturbation theory method, are used. Autoionizing levels above the threshold 1s{sup 2}2s{sup 2}2p{sup 6} are considered. It is found that configuration mixing [3sns+3pnp+3dnd],[3snp+3pns+3pnd+3dnp] plays an important role for all atomic characteristics. Also strong mixing between states with 2s and 2p holes (1s{sup 2}2s{sup 2}2p{sup 5}3l{submore » 1}nl{sub 2}+1s{sup 2}2s2p{sup 6}3l{sub 3}nl{sub 4}) occurs. Branching ratios relative to the first threshold and intensity factors are calculated for satellite lines, and dielectronic recombination (DR) rate coefficients are determined for the excited 1s{sup 2}2s{sup 2}2p{sup 6}nl(n=3-7,l{<=}n-1) states. It is shown that the contribution of the highly excited states is very important for calculation of total DR rates. Contributions from the autoionizing states 1s{sup 2}2s{sup 2}2p{sup 5}3l{sup '}nl,1s{sup 2}2s2p{sup 6}3l{sup '}nl(n{>=}8) and 1s{sup 2}2s{sup 2}2p{sup 5}4l{sup '}nl,1s{sup 2}2s2p{sup 6}4l{sup '}nl(n{>=}7) to the DR rate coefficients are estimated by extrapolation of all atomic parameters. The orbital angular momentum (l) distribution of the rate coefficients shows a peak at l=2. The total DR rate coefficient is derived as a function of electron temperature. The dielectronic satellite spectra of W{sup 63+} are important for L-shell diagnostics of very high-temperature laboratory plasmas such as future ITER fusion plasmas.« less

Measurement of dielectron continuum in p + p at sqrt(s) = 200 GeV as a baseline study for chiral symmetry restoration

NASA Astrophysics Data System (ADS)

Rolnick, Sky Deva

Dielectrons are a very important probe used for studying the properties of hot dense nuclear matter created in heavy ion collisions. Since dielectrons are color neutral and produced during all stages of the collision, they provide access to an abundance of information not readily available from other sources. These include thermal sources, vector meson resonances, heavy charm and bottom decay, and Drell-Yan processes. Previous measurements of the dielectron continuum in PHENIX have indicated an unexpectedly large enhancement in Au+Au collisions in the low mass region (0.3 - 0.8GeV/c2), a possible signal of chiral symmetry restoration, but these measurements were limited by large systematic uncertainties primarily from a poor signal to background ratio. In 2009 the PHENIX experiment was upgraded with the addition of the Hadron Blind Detector which improves the background rejection by detecting partially reconstructed Dalitz decays and gamma conversion pairs. In this thesis, I will review the status of electromagnetic probes measured from the collision of heavy nuclei and present and compare the results obtained from 2009 data in p + p at 200 GeV using the HBD which will serve as a baseline for Au+Au results obtained in 2010.

Absolute Measurements of Field Enhanced Dielectronic Recombination and Electron Impact Excitation

NASA Astrophysics Data System (ADS)

Savin, Daniel Wolf

Absolute measurements have been made of the dielectronic recombination (DR) rate coefficient for C^ {3+}, via the 2s-2p core -excitation, in an external electric field of 11.4 +/- 0.9(1sigma) V cm ^{-1}; and of the electron impact excitation (EIE) rate coefficient for C ^{3+}(2s-2p) at energies near threshold. The ion-rest-frame FWHM of the electron energy spread was 1.74 +/- 0.22(1sigma) eV. The measured DR rate, at a mean electron energy of 8.26 +/- 0.07(1sigma ) eV, was (2.76+/- 0.75)times 10^{-10} cm^{3 } s^{-1}. The uncertainty quoted for the DR rate is the total experimental uncertainty at a 1sigma<=vel. The present DR result appears to agree with an intermediate coupling calculation which uses the isolated-resonance, single-configuration approximation. In comparing with theory, a semi-classical formula was used to determine which recombined ions were field-ionized by the 4.65 kV cm^{-1} fields in the final-charge-state analyzer and not detected. A more precise treatment of field-ionization, which includes the lifetime of the high Rydberg C^{2+} ions in the external field and the time evolution and rotation of the fields experienced by the recombined ions, is needed before a definitive comparison between experiment and theory can be made. For the EIE results, at an ion-rest-frame energy of 10.10 eV, the measured rate coefficient was (7.79+/- 2.10)times 10^{ -8} cm^3 s^ {-1}. The measured cross section was (4.15+/- 1.12)times 10^{ -16} cm^2. The uncertainties quoted here represent the total experimental uncertainty at a 90 percent confidence level. Good agreement is found with other measurements. Agreement is not good with Coulomb -Born with exchange and two-state close-coupling calculations which fall outside the 90-percent-confidence uncertainty limits. Agreement is better with a nine-state close-coupling calculation which lies at the extreme of the uncertainty limits. Taking into account previous measurements in C ^{3+} and also a measurement of EIE in Be^+ which lies 19 percent below close-coupling calculations, there is a suggestion that the C^{3+}(2s-2p) EIE rate coefficient may fall slightly below presently accepted values.

Dielectron Azimuthal Anisotropy at mid-rapidity in Au+Au collisions at root s=200GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adamczyk, L.

We report on the first measurement of the azimuthal anisotropy (v₂) of dielectrons (e⁺e⁻ pairs) at mid-rapidity from √( sNN)=200 GeV Au + Au collisions with the STAR detector at the Relativistic Heavy Ion Collider (RHIC), presented as a function of transverse momentum (p T) for different invariant-mass regions. In the mass region Mee<1.1 GeV/c² the dielectron v₂ measurements are found to be consistent with expectations from π⁰,η,ω, and Φ decay contributions. In the mass region 1.1ee<2.9GeV/c², the measured dielectron v₂ is consistent, within experimental uncertainties, with that from the cc¯ contributions.

Dielectron Azimuthal Anisotropy at mid-rapidity in Au+Au collisions at root s=200GeV

DOE PAGES

Adamczyk, L.

2014-12-11

We report on the first measurement of the azimuthal anisotropy (v₂) of dielectrons (e⁺e⁻ pairs) at mid-rapidity from √( sNN)=200 GeV Au + Au collisions with the STAR detector at the Relativistic Heavy Ion Collider (RHIC), presented as a function of transverse momentum (p T) for different invariant-mass regions. In the mass region Mee<1.1 GeV/c² the dielectron v₂ measurements are found to be consistent with expectations from π⁰,η,ω, and Φ decay contributions. In the mass region 1.1ee<2.9GeV/c², the measured dielectron v₂ is consistent, within experimental uncertainties, with that from the cc¯ contributions.

Atomic Data for Neutron-capture Elements I. Photoionization and Recombination Properties of Low-charge Selenium Ions

NASA Technical Reports Server (NTRS)

Sterling, N. C.; Witthoeft, Michael

2011-01-01

We present multi-configuration Breit-Pauli AUTOSTRUCTURE calculations of distorted-wave photoionization (PI) cross sections. and total and partial final-state resolved radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for the first six ions of the trans-iron element Se. These calculations were motivated by the recent detection of Se emission lines in a large number of planetary nebulae. Se is a potentially useful tracer of neutron-capture nucleosynthesis. but accurate determinations of its abundance in photoionized nebulae have been hindered by the lack of atomic data governing its ionization balance. Our calculations were carried out in intermediate coupling with semi re1ativistic radial wavefunctions. PI and recombination data were determined for levels within the ground configuration of each ion, and experimental PI cross-section measurements were used to benchmark our results. For DR, we allowed (Delta)n = 0 core excitations, which are important at photoionized plasma temperatures. We find that DR is the dominant recombination process for each of these Se ions at temperatures representative of photoionized nebulae (approx.10(exp 4) K). In order to estimate the uncertainties of these data, we compared results from three different configuration-interaction expansions for each ion, and also tested the sensitivity of the results to the radial scaling factors in the structure calculations. We find that the internal uncertainties are typically 30-50% for the direct PI cross sections and approx.10% for the computed RR rate coefficients, while those for low-temperature DR can be considerably larger (from 15-30% up to two orders of magnitude) due to the unknown energies of near-threshold autoionization resonances. These data are available at the CDS, and fitting coefficients to the total RR and DR rate coefficients are presented. The results are suitable for incorporation into photoionization codes used to numerically simulate astrophysical nebulae, and will enable robust determinations of nebular Se abundances.

Low-mass dielectrons in pp, p-Pb and Pb-Pb collisions measured by the ALICE Experiment

NASA Astrophysics Data System (ADS)

Vorobyev, Ivan

2018-02-01

Dielectrons produced in ultra-relativistic heavy-ion collisions at the LHC provide a unique probe of the system evolution as they are unperturbed by final-state interactions. The dielectron continuum is extremely rich in physics sources: on top of ordinary Dalitz and resonance decays of pseudoscalar and vector mesons, thermal black-body radiation is of particular interest as it carries information about the temperature of the hot and dense system created in such collisions. The dielectron invariant-mass distribution is furthermore sensitive to medium modifications of the spectral function of short-lived vector mesons that are linked to the potential restoration of chiral symmetry at high temperatures. Correlated electron pairs from semi-leptonic charm and beauty decays provide complementary information about the heavy-quark energy loss.

Collisional Ionization Equilibrium for Optically Thin Plasmas

NASA Technical Reports Server (NTRS)

Bryans, P.; Mitthumsiri, W.; Savin, D. W.; Badnell, N. R.; Gorczyca, T. W.; Laming, J. M.

2006-01-01

Reliably interpreting spectra from electron-ionized cosmic plasmas requires accurate ionization balance calculations for the plasma in question. However, much of the atomic data needed for these calculations have not been generated using modern theoretical methods and their reliability are often highly suspect. We have utilized state-of-the-art calculations of dielectronic recombination (DR) rate coefficients for the hydrogenic through Na-like ions of all elements from He to Zn. We have also utilized state-of-the-art radiative recombination (RR) rate coefficient calculations for the bare through Na-like ions of all elements from H to Zn. Using our data and the recommended electron impact ionization data of Mazzotta et al. (1998), we have calculated improved collisional ionization equilibrium calculations. We compare our calculated fractional ionic abundances using these data with those presented by Mazzotta et al. (1998) for all elements from H to Ni, and with the fractional abundances derived from the modern DR and RR calculations of Gu (2003a,b, 2004) for Mg, Si, S, Ar, Ca, Fe, and Ni.

Electron-ion collision spectroscopy: Lithium-like xenon ions

NASA Astrophysics Data System (ADS)

Bernhardt, D.; Brandau, C.; Harman, Z.; Kozhuharov, C.; Böhm, S.; Bosch, F.; Fritzsche, S.; Jacobi, J.; Kieslich, S.; Knopp, H.; Nolden, F.; Shi, W.; Stachura, Z.; Steck, M.; Stöhlker, Th.; Schippers, S.; Müller, A.

2015-01-01

The resonant process of dielectronic recombination (DR) has been applied as a spectroscopic tool to investigate intra-L -shell excitations 2 s -2 pj in Li-like 136Xe51+ . The experiments were carried out at the electron cooler of the Experimental Storage Ring of the GSI-Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany. The observed center-of-mass energy range (0-505 eV) covers all resonances associated with the 2 s +e-→(2p1/2n lj) J and (2p3/2n lj) J DR processes. Energies and strengths of isolated 2 p1 /2n and 2 p3 /2n DR-resonance groups were obtained for principal quantum numbers n up to 43 and 36, respectively. The 2 s -2 p1 /2 and 2 s -2 p3 /2 excitation energies were deduced to be 119.816(42) eV and 492.174(52) eV. The excitation energies are compared with previous measurements of other groups and with recent QED calculations. In addition, the experimental spectra and extracted resonance strengths are compared with multiconfiguration Dirac-Fock calculations. Measurements and theory are found to be in good agreement with each other.

THE ABUNDANCES OF LIGHT NEUTRON-CAPTURE ELEMENTS IN PLANETARY NEBULAE. III. THE IMPACT OF NEW ATOMIC DATA ON NEBULAR SELENIUM AND KRYPTON ABUNDANCE DETERMINATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sterling, N. C.; Porter, R. L.; Dinerstein, Harriet L., E-mail: nsterlin@westga.edu, E-mail: ryanlporter@gmail.com, E-mail: harriet@astro.as.utexas.edu

The detection of neutron(n)-capture elements in several planetary nebulae (PNe) has provided a new means of investigating s-process nucleosynthesis in low-mass stars. However, a lack of atomic data has inhibited accurate trans-iron element abundance determinations in astrophysical nebulae. Recently, photoionization (PI) and recombination data were determined for Se and Kr, the two most widely detected n-capture elements in nebular spectra. We have incorporated these new data into the photoionization code Cloudy. To test the atomic data, numerical models were computed for 15 PNe that exhibit emission lines from multiple Kr ions. We found systematic discrepancies between the predicted and observedmore » emission lines that are most likely caused by inaccurate PI and recombination data. These discrepancies were removed by adjusting the Kr{sup +}–Kr{sup 3+} PI cross sections within their cited uncertainties and the dielectronic recombination rate coefficients by slightly larger amounts. From grids of models spanning the physical conditions encountered in PNe, we derive new, broadly applicable ionization correction factor (ICF) formulae for calculating Se and Kr elemental abundances. The ICFs were applied to our previous survey of near-infrared [Kr iii] and [Se iv] emission lines in 120 PNe. The revised Se and Kr abundances are 0.1–0.3 dex lower than former estimates, with average values of [Se/(O, Ar)] = 0.12 ± 0.27 and [Kr/(O, Ar)] = 0.82 ± 0.29, but correlations previously found between their abundances and other nebular and stellar properties are unaffected. We also find a tendency for high-velocity PNe that can be associated with the Galactic thick disk to exhibit larger s-process enrichments than low-velocity PNe belonging to the thin-disk population.« less

Dielectron azimuthal anisotropy at mid-rapidity in Au + Au collisions at s N N = 200 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.

We report on the first measurement of the azimuthal anisotropy (v2) of dielectrons (e+e- pairs) at mid-rapidity from √sNN=200 GeV Au + Au collisions with the STAR detector at the Relativistic Heavy Ion Collider (RHIC), presented as a function of transverse momentum (pT) for different invariant-mass regions. In the mass region Mee<1.1 GeV/c2 the dielectron v2 measurements are found to be consistent with expectations from π0,η,ω, and Φ decay contributions. In the mass region 1.1

Dissociative Recombination of FeO(+) with Electrons: Implications for Plasma Layers in the Ionosphere.

PubMed

Bones, D L; Plane, J M C; Feng, W

2016-03-10

The dissociative recombination (DR) of FeO(+) ions with electrons has been studied in a flowing afterglow reactor. FeO(+) was generated by the pulsed laser ablation of a solid Fe target, and then entrained in an Ar(+) ion/electron plasma where the absolute electron density was measured using a Langmuir probe. A kinetic model describing gas-phase chemistry and diffusion to the reactor walls was fitted to the experimental data, yielding a DR rate coefficient at 298 K of k(FeO(+) + e(-)) = (5.5 ± 1.0) × 10(-7) cm(3) molecule(-1) s(-1), where the quoted uncertainty is at the 2σ level. Fe(+) ions in the lower thermosphere are oxidized by O3 to FeO(+), and this DR reaction is shown to provide a more important route for neutralizing Fe(+) below 110 km than the radiative/dielectronic recombination of Fe(+) with electrons. The experimental system was first validated by measuring two other DR reaction rate coefficients: k(O2(+) + e(-)) = (2.0 ± 0.4) × 10(-7) and k(N2O(+) + e(-)) = (3.3 ± 0.8) × 10(-7) cm(3) molecule(-1) s(-1), which are in good agreement with the recent literature.

Non local-thermodynamical-equilibrium effects in the simulation of laser-produced plasmas

NASA Astrophysics Data System (ADS)

Klapisch, M.; Bar-Shalom, A.; Oreg, J.; Colombant, D.

1998-05-01

Local thermodynamic equilibrium (LTE) breaks down in directly or indirectly driven laser plasmas because of sharp gradients, energy deposition, etc. For modeling non-LTE effects in hydrodynamical simulations, Busquet's model [Phys. Fluids B 5, 4191 (1993)] is very convenient and efficient. It uses off-line generated LTE opacities and equation of states via an effective, radiation-dependent ionization temperature Tz. An overview of the model is given. The results are compared with an elaborate collisional radiative model based on superconfigurations. The agreements for average charge Z* and opacities are surprisingly good, even more so when the plasma is immersed in a radiation field. Some remaining discrepancy at low density is attributed to dielectronic recombination. Improvement appears possible, especially for emissivities, because the concept of ionization temperature seems to be validated.

Analyzing non-LTE Kr plasmas produced in high energy density experiments: from the Z machine to the National Ignition Facility

NASA Astrophysics Data System (ADS)

Dasgupta, Arati

2015-11-01

Designing high fluence photon sources above 10 keV are a challenge for High Energy Density plasmas. This has motivated radiation source development investigations of Kr with K-shell energies around 13 keV. Recent pulsed power driven gas-puff experiments on the refurbished Z machine at Sandia have produced intense X-rays in the multi-keV photon energy range. K-shell radiative yields and efficiencies are very high for Ar, but rapidly decrease for higher atomic number (ZA) elements such as Kr. It has been suggested that an optimum exists corresponding to a trade-off between the increase of photon energy for higher ZA elements and the corresponding fall off in radiative power. However the conversion efficiency on NIF, where the drive, energy deposition process, and target dynamics are different, does not fall off with higher ZA as rapidly as on Z. We have developed detailed atomic structure and collisional data for the full K-, L- and partial M-shell of Kr using the Flexible Atomic Code (FAC). Our non-LTE atomic model includes all collisional and recombination processes, including state-specific dielectronic recombination (DR), that significantly affect ionization balance and spectra of Kr plasmas at the temperatures and densities of concern. The model couples ionization physics, radiation production and transport, and magnetohydrodynamics. In this talk, I will give a detailed description of the model and discuss 1D Kr simulations employing a multifrequency radiation transport scheme. Synthetic K- and L-shell spectra will be compared with available experimental data. This talk will analyze experimental data indicative of the differences between Z and NIF experimental data and discuss how they affect the K-shell radiative output of Kr plasma. Work supported by DOE/NNSA.

Dielectron widths of the Gamma(1S,2S,3S) resonances.

PubMed

Rosner, J L; Adam, N E; Alexander, J P; Berkelman, K; Cassel, D G; Duboscq, J E; Ecklund, K M; Ehrlich, R; Fields, L; Galik, R S; Gibbons, L; Gray, R; Gray, S W; Hartill, D L; Heltsley, B K; Hertz, D; Jones, C D; Kandaswamy, J; Kreinick, D L; Kuznetsov, V E; Mahlke-Krüger, H; Meyer, T O; Onyisi, P U E; Patterson, J R; Peterson, D; Phillips, E A; Pivarski, J; Riley, D; Ryd, A; Sadoff, A J; Schwarthoff, H; Shi, X; Stroiney, S; Sun, W M; Wilksen, T; Weinberger, M; Athar, S B; Avery, P; Breva-Newell, L; Patel, R; Potlia, V; Stoeck, H; Yelton, J; Rubin, P; Cawlfield, C; Eisenstein, B I; Karliner, I; Kim, D; Lowrey, N; Naik, P; Sedlack, C; Selen, M; White, E J; Wiss, J; Shepherd, M R; Besson, D; Pedlar, T K; Cronin-Hennessy, D; Gao, K Y; Gong, D T; Hietala, J; Kubota, Y; Klein, T; Lang, B W; Poling, R; Scott, A W; Smith, A; Dobbs, S; Metreveli, Z; Seth, K K; Tomaradze, A; Zweber, P; Ernst, J; Arms, K; Severini, H; Dytman, S A; Love, W; Mehrabyan, S; Savinov, V; Aquines, O; Li, Z; Lopez, A; Mendez, H; Ramirez, J; Huang, G S; Miller, D H; Pavlunin, V; Sanghi, B; Shipsey, I P J; Xin, B; Adams, G S; Anderson, M; Cummings, J P; Danko, I; Napolitano, J; He, Q; Insler, J; Muramatsu, H; Park, C S; Thorndike, E H; Coan, T E; Gao, Y S; Liu, F; Stroynowski, R; Artuso, M; Blusk, S; Butt, J; Li, J; Menaa, N; Mountain, R; Nisar, S; Randrianarivony, K; Redjimi, R; Sia, R; Skwarnicki, T; Stone, S; Wang, J C; Zhang, K; Csorna, S E; Bonvicini, G; Cinabro, D; Dubrovin, M; Lincoln, A; Asner, D M; Edwards, K W; Briere, R A; Chen, J; Ferguson, T; Tatishvili, G; Vogel, H; Watkins, M E

2006-03-10

We determine the dielectron widths of the Gamma(1S), Gamma(2S), and Gamma(3S) resonances with better than 2% precision by integrating the cross section of e+e- -->Gamma over the e+e- center-of-mass energy. Using e+e- energy scans of the Gamma resonances at the Cornell Electron Storage Ring and measuring Gamma production with the CLEO detector, we find dielectron widths of 1.252+/-0.004(sigma(stat))+/-0.019(sigma(syst)) keV, 0.581+/-0.004+/-0.009 keV, and 0.413+/-0.004+/-0.006 keV for the Gamma(1S), Gamma(2S), and Gamma(3S), respectively.

Measurements of the dielectron continuum in pp, p-Pb and Pb-Pb collisions with ALICE at the LHC

NASA Astrophysics Data System (ADS)

Vázquez Doce, O.; Alice Collaboration

2017-11-01

Dielectrons produced in ultra-relativistic heavy-ion collisions provide a unique probe of the whole system evolution as they are unperturbed by final-state interactions. The dielectron continuum is extremely rich in physics sources: thermal radiation is of particular interest as it carries information about the temperature of the hot and dense system created in such collisions. The dielectron invariant mass distribution is sensitive to medium modifications of the spectral function of vector mesons that are linked to the potential restoration of chiral symmetry. Correlated electron pairs from semi-leptonic charm and beauty decays provide information about the heavy-quark energy loss. A summary of the LHC Run-1 preliminary results in all three collisions systems (pp, p-Pb and Pb-Pb) is presented. Furthermore, the status of the ongoing Run-2 analyses is discussed with a focus on pp collisions collected with a high charged-particle multiplicity trigger, on new analysis methods to separate prompt from non-prompt sources, and on the usage of machine learning methods for background rejection.

Silicon X-ray line emission from solar flares and active regions

NASA Technical Reports Server (NTRS)

Parkinson, J. H.; Wolff, R. S.; Kestenbaum, H. L.; Ku, W. H.-M.; Lemen, J. R.; Long, K. S.; Novick, R.; Suozzo, R. J.; Weisskopf, M. C.

1978-01-01

New observations of solar flare and active region X-ray spectra obtained with the Columbia University instrument on OSO-8 are presented and discussed. The high sensitivity of the graphite crystal panel has allowed both line and continuum spectra to be served with moderate spectral resolution. Observations with higher spectral resolution have been made with a panel of pentaerythritol crystals. Twenty-nine lines between 1.5 and 7.0 A have been resolved and identified, including several dielectronic recombination satellite lines to Si XIV and Si XIII lines which have been observed for the first time. It has been found that thermal continuum models specified by single values of temperature and emission measure have fitted the data adequately, there being good agreement with the values of these parameters derived from line intensity ratios.

Measurement of Dielectron Spectra with the Hadron Blind Detector in PHENIX

NASA Astrophysics Data System (ADS)

Sun, Jiayin

2013-04-01

Dielectrons are an important color neutral probe for studying the evolution of the hot dense medium created by heavy ion collisions at RHIC. At low mass region, dielectron spectra consists mainly of direct photons and light vector mesons, and give insight on the earliest stages of the collisions and thus constrain theoretical models on thermalization and chiral symmetry restoration in heavy ion collisions. At intermediate and high mass region, there are significant contributions from charm and bottom. The region was utilized to measure cross sections of open charm and open bottom, as well as quarkonium suppression. The measurement of the dielectron spectra, however, suffers from an unfavorable signal to background ratio. Random combination of electron positron pairs from unrelated sources, mostly Dalitz decay of π0 and external conversion of decay photon to electrons, are the main contributor to the background. The Hadron Blind Detector, a windowless proximity focusing Cerenkov detector, is designed to reduce this background by identifying electron tracks from photon conversions and π0 Dalitz decays. The detector has been installed and operated in PHENIX in 2009 and 2010, where Au+Au and reference p+p data sets were taken. Results from these data sets will be presented.

Recombination Line versus Forbidden Line Abundances in Planetary Nebulae

NASA Astrophysics Data System (ADS)

Robertson-Tessi, Mark; Garnett, Donald R.

2005-04-01

Recombination lines (RLs) of C II, N II, and O II in planetary nebulae (PNs) have been found to give abundances that are much larger in some cases than abundances from collisionally excited forbidden lines (CELs). The origins of this abundance discrepancy are highly debated. We present new spectroscopic observations of O II and C II recombination lines for six planetary nebulae. With these data we compare the abundances derived from the optical recombination lines with those determined from collisionally excited lines. Combining our new data with published results on RLs in other PNs, we examine the discrepancy in abundances derived from RLs and CELs. We find that there is a wide range in the measured abundance discrepancy Δ(O+2)=logO+2(RL)-logO+2(CEL), ranging from approximately 0.1 dex (within the 1 σ measurement errors) up to 1.4 dex. This tends to rule out errors in the recombination coefficients as a source of the discrepancy. Most RLs yield similar abundances, with the notable exception of O II multiplet V15, known to arise primarily from dielectronic recombination, which gives abundances averaging 0.6 dex higher than other O II RLs. We compare Δ(O+2) against a variety of physical properties of the PNs to look for clues as to the mechanism responsible for the abundance discrepancy. The strongest correlations are found with the nebula diameter and the Balmer surface brightness; high surface brightness, compact PNs show small values of Δ(O+2), while large low surface brightness PNs show the largest discrepancies. An inverse correlation of Δ(O+2) with nebular density is also seen. A marginal correlation of Δ(O+2) is found with expansion velocity. No correlations are seen with electron temperature, He+2/He+, central star effective temperature and luminosity, stellar mass-loss rate, or nebular morphology. Similar results are found for carbon in comparing C II RL abundances with ultraviolet measurements of C III].

Theoretical Study of Radiation from a Broad Range of Impurity Ions for Magnetic Fusion Diagnostics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safronova, Alla

Spectroscopy of radiation emitted by impurities plays an important role in the study of magnetically confined fusion plasmas. The measurements of these impurities are crucial for the control of the general machine conditions, for the monitoring of the impurity levels, and for the detection of various possible fault conditions. Low-Z impurities, typically present in concentrations of 1%, are lithium, beryllium, boron, carbon, and oxygen. Some of the common medium-Z impurities are metals such as iron, nickel, and copper, and high-Z impurities, such as tungsten, are present in smaller concentrations of 0.1% or less. Despite the relatively small concentration numbers, themore » aforementioned impurities might make a substantial contribution to radiated power, and also influence both plasma conditions and instruments. A detailed theoretical study of line radiation from impurities that covers a very broad spectral range from less than 1 Å to more than 1000 Å has been accomplished and the results were applied to the LLNL Electron Beam Ion Trap (EBIT) and the Sustained Spheromak Physics Experiment (SSPX) and to the National Spherical Torus Experiment (NSTX) at Princeton. Though low- and medium-Z impurities were also studied, the main emphasis was made on the comprehensive theoretical study of radiation from tungsten using different state-of-the-art atomic structure codes such as Relativistic Many-Body Perturbation Theory (RMBPT). The important component of this research was a comparison of the results from the RMBPT code with other codes such as the Multiconfigurational Hartree–Fock developed by Cowan (COWAN code) and the Multiconfiguration Relativistic Hebrew University Lawrence Atomic Code (HULLAC code), and estimation of accuracy of calculations. We also have studied dielectronic recombination, an important recombination process for fusion plasma, for variety of highly and low charged tungsten ions using COWAN and HULLAC codes. Accurate DR rate coefficients are needed for describing the ionization balance of plasmas, which in turn determines the lines contributing to the spectral emission and the radiative power loss. In particular, we have calculated relativistic atomic data and corresponding dielectronic satellite spectra of highly ionized W ions, such as, for example, Li-like W (with the shortest wavelength of x-ray radiation of about 0.2 Å) that might exist in ITER core plasmas at very high temperatures of 30-40 keV. In addition, we have completed relativistic calculations of low ionized W ions from Lu-like (W3+) to Er-like (W6+) and for Sm-like(W12+) and Pm-like (W13+) that cover a spectral range from few hundred to thousand Å and are more relevant to the edge plasma diagnostics in tokamak.« less

Energy dependence of acceptance-corrected dielectron excess mass spectrum at mid-rapidity in Au +Au collisions at √{sNN} = 19.6 and 200 GeV

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Alford, J.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Averichev, G. S.; Banerjee, A.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandin, A. V.; Bunzarov, I.; Burton, T. P.; Butterworth, J.; Caines, H.; Calder'on de la Barca S'anchez, M.; Campbell, J. M.; Cebra, D.; Cervantes, M. C.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chattopadhyay, S.; Chen, J. H.; Chen, X.; Cheng, J.; Cherney, M.; Christie, W.; Codrington, M. J. M.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; di Ruzza, B.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Engelage, J.; Eppley, G.; Esha, R.; Evdokimov, O.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Fedorisin, J.; Feng; Filip, P.; Fisyak, Y.; Flores, C. E.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Greiner, L.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, S.; Gupta, A.; Guryn, W.; Hamad, A.; Hamed, A.; Haque, R.; Harris, J. W.; He, L.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Hofman, D. J.; Horvat, S.; Huang, H. Z.; Huang, X.; Huang, B.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jang, H.; Jiang, K.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z. H.; Kikola, D. P.; Kisel, I.; Kisiel, A.; Klein, S. R.; Koetke, D. D.; Kollegger, T.; Kosarzewski, L. K.; Kotchenda, L.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kulakov, I.; Kumar, L.; Kycia, R. A.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, X.; Li, X.; Li, W.; Li, Z. M.; Li, Y.; Li, C.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, X.; Ma, L.; Ma, R.; Ma, G. L.; Ma, Y. G.; Magdy, N.; Majka, R.; Manion, A.; Margetis, S.; Markert, C.; Masui, H.; Matis, H. S.; McDonald, D.; Meehan, K.; Minaev, N. G.; Mioduszewski, S.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Mustafa, M. K.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nigmatkulov, G.; Nogach, L. V.; Noh, S. Y.; Novak, J.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V.; Olvitt, D. L.; Page, B. S.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlak, T.; Pawlik, B.; Pei, H.; Perkins, C.; Peterson, A.; Pile, P.; Planinic, M.; Pluta, J.; Poljak, N.; Poniatowska, K.; Porter, J.; Posik, M.; Poskanzer, A. M.; Pruthi, N. K.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Raniwala, R.; Raniwala, S.; Ray, R. L.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Roy, A.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandacz, A.; Sandweiss, J.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, M. K.; Sharma, B.; Shen, W. Q.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Skoby, M. J.; Smirnov, N.; Smirnov, D.; Solanki, D.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stock, R.; Strikhanov, M.; Stringfellow, B.; Sumbera, M.; Summa, B. J.; Sun, Y.; Sun, Z.; Sun, X. M.; Sun, X.; Surrow, B.; Svirida, D. N.; Szelezniak, M. A.; Takahashi, J.; Tang, A. H.; Tang, Z.; Tarnowsky, T.; Tawfik, A. N.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Trzeciak, B. A.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vandenbroucke, M.; Varma, R.; Vasiliev, A. N.; Vertesi, R.; Videbaek, F.; Viyogi, Y. P.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, Y.; Wang, F.; Wang, H.; Wang, J. S.; Wang, G.; Wang, Y.; Webb, J. C.; Webb, G.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y. F.; Xiao, Z.; Xie, W.; Xin, K.; Xu, Z.; Xu, Q. H.; Xu, N.; Xu, H.; Xu, Y. F.; Yang, Y.; Yang, C.; Yang, S.; Yang, Q.; Yang, Y.; Ye, Z.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, J. B.; Zhang, X. P.; Zhang, S.; Zhang, J.; Zhang, Z.; Zhang, Y.; Zhang, J. L.; Zhao, F.; Zhao, J.; Zhong, C.; Zhou, L.; Zhu, X.; Zoulkarneeva, Y.; Zyzak, M.

2015-11-01

The acceptance-corrected dielectron excess mass spectra, where the known hadronic sources have been subtracted from the inclusive dielectron mass spectra, are reported for the first time at mid-rapidity |yee | < 1 in minimum-bias Au +Au collisions at √{sNN} = 19.6 and 200 GeV. The excess mass spectra are consistently described by a model calculation with a broadened ρ spectral function for Mee < 1.1 GeV /c2. The integrated dielectron excess yield at √{sNN} = 19.6 GeV for 0.4

Stellar Astrophysics with Arcus

NASA Astrophysics Data System (ADS)

Brickhouse, Nancy S.; Huenemoerder, David P.; Wolk, Scott; Schulz, Norbert; Foster, Adam; Brenneman, Laura; Poppenhaeger, Katja; Arcus Team

2018-01-01

The Arcus mission is now in Phase A of the NASA Medium-Class Explorer competition. We present here the Arcus science case for stellar astrophysics. With spectral resolving power of at least 2500 and effective area greater than 400 cm^2, Arcus will measure new diagnostic lines, e.g. for H- and He-like ions of oxygen and other elements. Weak dielectronic recombination lines will provide sensitive measurements of temperature to test stellar coronal heating models. Arcus will also resolve the coronal and accretion line components in young accreting stars, allowing detailed studies of accretion shocks and their post-shock behavior. Arcus can resolve line shapes and variability in hot star winds to study inhomogeneities and dynamics of wind structure. Such profiles will provide an independent measure of mass loss rates, for which theoretical and observational discrepancies can reach an order of magnitude. Arcus will also study exoplanet atmospheres through X-ray absorption, determing their extent and composition.

Accurate Wavelength Measurements and Modeling of Fe XV to Fe XIX Spectra Recorded in High-Density Plasmas between 13.5 and 17 Å

NASA Astrophysics Data System (ADS)

May, M. J.; Beiersdorfer, P.; Dunn, J.; Jordan, N.; Hansen, S. B.; Osterheld, A. L.; Faenov, A. Ya.; Pikuz, T. A.; Skobelev, I. Yu.; Flora, F.; Bollanti, S.; Di Lazzaro, P.; Murra, D.; Reale, A.; Reale, L.; Tomassetti, G.; Ritucci, A.; Francucci, M.; Martellucci, S.; Petrocelli, G.

2005-06-01

Iron spectra have been recorded from plasmas created at three different laser plasma facilities: the Tor Vergata University laser in Rome (Italy), the Hercules laser at ENEA in Frascati (Italy), and the Compact Multipulse Terawatt (COMET) laser at LLNL in California (USA). The measurements provide a means of identifying dielectronic satellite lines from Fe XVI and Fe XV in the vicinity of the strong 2p-->3d transitions of Fe XVII. About 80 Δn>=1 lines of Fe XV (Mg-like) to Fe XIX (O-like) were recorded between 13.8 and 17.1 Å with a high spectral resolution (λ/Δλ~4000) about 30 of these lines are from Fe XVI and Fe XV. The laser-produced plasmas had electron temperatures between 100 and 500 eV and electron densities between 1020 and 1022 cm-3. The Hebrew University Lawrence Livermore Atomic Code (HULLAC) was used to calculate the atomic structure and atomic rates for Fe XV-XIX. HULLAC was used to calculate synthetic line intensities at Te=200 eV and ne=1021 cm-3 for three different conditions to illustrate the role of opacity: optically thin plasmas with no excitation-autoionization/dielectronic recombination (EA/DR) contributions to the line intensities, optically thin plasmas that included EA/DR contributions to the line intensities, and optically thick plasmas (optical depth ~200 μm) that included EA/DR contributions to the line intensities. The optically thick simulation best reproduced the recorded spectrum from the Hercules laser. However, some discrepancies between the modeling and the recorded spectra remain.

Accurate wavelength measurements and modeling of FeXV to FeXIX spectra recorded in high density plasmas between 13.5 to 17 A.

DOE Office of Scientific and Technical Information (OSTI.GOV)

May, M; Beiersdorfer, P; Dunn, J

Iron spectra have been recorded from plasmas created at three different laser plasma facilities, the Tor Vergata University laser in Rome (Italy), the Hercules laser at ENEA in Frascati (Italy), and the Compact Multipulse Terawatt (COMET) laser at LLNL in California (USA). The measurements provide a means of identifying dielectronic satellite lines from FeXVI and FeXV in the vicinity of the strong 2p {yields} 3d transitions of FeXVII. About 80 {Delta}n {ge} 1 lines of FeXV (Mg-like) to FeXIX (O-like) were recorded between 13.8 to 17.1 {angstrom} with a high spectral resolution ({lambda}/{Delta}{lambda} {approx} 4000), about thirty of these linesmore » are from FeXVI and FeXV. The laser produced plasmas had electron temperatures between 100 to 500 eV and electron densities between 10{sup 20} to 10{sup 22} cm{sup -3}. The Hebrew University Lawrence Livermore Atomic Code (HULLAC) was used to calculate the atomic structure and atomic rates for FeXV to FeXIX. HULLAC was used to calculate synthetic line intensities at T{sub e} = 200 eV and n{sub e} = 10{sup 21}cm{sup -3} for three different conditions to illustrate the role of opacity: optically thin plasmas with no excitation-autoionization/dielectronic recombination (EA/DR) contributions to the line intensities, optically thin plasmas that included EA/DR contributions to the line intensities, and optically thick plasmas (optical depth {approx} 200 {micro}m) that included EA/DR contributions to the line intensities. The optically thick simulation best reproduced the recorded spectrum from the Hercules laser. However some discrepancies between the modeling and the recorded spectra remain.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozminski, Joseph Francis

The first measurement of the top-antitop production cross section in proton-antiproton collisions at √s = 1.96 TeV using 243 pb -1 of data collected with the D0 detector at Fermilab is presented. In this analysis, only the dielectron final state is considered. Five events are observed, and 0.93 background events are expected. The measured cross section, after accounting for the expected branching ratio to the dielectron channel, is σ tmore » $$\\bar{t}$$ = 14.9$$+9.4\\atop{-7.0}$$(stat)$$+2.5\\atop{-1.8}$${sup +2.5}(syst) ± 1.0 (lumi) pb, which agrees with the predicted cross section for top quarks with a mass of 175 GeV. In addition, a first-pass at a measurement of the top mass using the neutrino-weighting method is presented. This measurement is also performed in the dielectron channel using the five events observed in the cross section measurement.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waitz, M.; Metz, D.; Lower, J.

Here, wWe investigate the photodouble ionization of H 2 molecules with 400 eV photons. We find that the emitted electrons do not show any sign of two-center interference fringes in their angular emission distributions if considered separately. Conversely, the quasiparticle consisting of both electrons (i.e., the "dielectron") does. The work highlights the fact that nonlocal effects are embedded everywhere in nature where many-particle processes are involved.

Laboratory studies in ultraviolet solar physics

NASA Technical Reports Server (NTRS)

Parkinson, W. H.; Kohl, J. L.; Gardner, L. D.; Raymond, J. C.; Smith, P. L.

1991-01-01

The research activity comprised the measurement of basic atomic processes and parameters which relate directly to the interpretation of solar ultraviolet observations and to the development of comprehensive models of the component structures of the solar atmosphere. The research was specifically directed towards providing the relevant atomic data needed to perform and to improve solar diagnostic techniques which probe active and quiet portions of the solar chromosphere, the transition zone, the inner corona, and the solar wind acceleration regions of the extended corona. The accuracy with which the physical conditions in these structures can be determined depends directly on the accuracy and completeness of the atomic and molecular data. These laboratory data are used to support the analysis programs of past and current solar observations (e.g., the Orbiting solar Observatories, the Solar Maximum Mission, the Skylab Apollo Telescope Mount, and the Naval Research Laboratory's rocket-borne High Resolution Telescope and Spectrograph). In addition, we attempted to anticipate the needs of future space-borne solar studies such as from the joint ESA/NASA Solar and Heliospheric Observatory (SOHO) spacecraft. Our laboratory activities stressed two categories of study: (1) the measurement of absolute rate coefficients for dielectronic recombination and electron impact excitation; and (2) the measurement of atomic transition probabilities for solar density diagnostics. A brief summary of the research activity is provided.

Spectroscopic Non-LTE Modeling of Highly Charged Gold Plasma

NASA Astrophysics Data System (ADS)

Dasgupta, A.; Ouart, N. D.; Giuliani, J. L.; Obenschain, S. P.; Clark, R. W.; Aglitskiy, Y.

2013-10-01

An X-ray spectrometer is under development at the Naval Research Laboratory (NRL) to investigate emissions from gold targets irradiated by the NIKE KrF facility. This effort is in support of the indirect drive campaign on the National Ignition Facility (NIF). To analyze and interpret the NIKE experimental spectra, we are theoretically exploring line emissions from a gold plasma in the M-band, i.e., 1.5 to 3.5 keV. We employ a detailed Non-LTE atomic model for ions near Ni-like gold by including an adequate number of configurations to obtain spectroscopic details in this range. The atomic states are coupled both collisionally and radiatively, including all dominant atomic processes that have significant contributions to the ionization and emitted synthetic spectra. In particular, we will investigate the effect of dielectronic recombination, which can have a dominant effect on level populations for highly ionized high Z plasmas. Since the radiation field can affect level populations through photoionization and photoexcitation, our collisional-radiative model will include non-local radiation transport. The line shapes of the strong overlapping lines will be resolved by a multifrequency radiation transport method. Synthetic spectra with radiation transport, including resonant photo-pumping, will be generated for realistic densities and temperatures to compare with the NIKE data. Work supported by DOE/NNSA.

Variations in iron and calcium abundances during solar flares

NASA Astrophysics Data System (ADS)

Antonucci, E.; Martin, R.

1995-07-01

Evidence for variations in iron and calcium abundances during the impulsive phase of solar flares has been obtained by analyzing the Ca XIX and Fe XXV spectra, detected with the Bent Crystal Spectrometer of the Solar Maximum Mission. The plasma thermal conditions have been investigated by considering different temperature indicators: namely, the temperatures TCa and TFe, derived from the intensity ratios of the dielectronic recombination satellites to the resonance line, and the temperature TCaFe, calculated from the ratio of the resonance lines of Ca XIX and Fe XXV, which is also depending on the Fe/Ca abundance ratio. The observed values of TCa and TFe can be ascribed to the specific characteristics of the plasma therma distribution, the corresponding values of TCaFe can be explained by allowing also for variations in the Fe/Ca abundance ratio relative to the photospheric ratio by a factor within 0.2 and 2.4. According to the observed abundance variations, the events analyzed can be divided in Ca-rich and Fe-rich flares.

Absolute brightness modeling for improved measurement of electron temperature from soft x-rays on MST

NASA Astrophysics Data System (ADS)

Reusch, L. M.; Franz, P.; Goetz, J. A.; den Hartog, D. J.; Nornberg, M. D.; van Meter, P.

2017-10-01

The two-color soft x-ray tomography (SXT) diagnostic on MST is now capable of Te measurement down to 500 eV. The previous lower limit was 1 keV, due to the presence of SXR emission lines from Al sputtered from the MST wall. The two-color technique uses two filters of different thickness to form a coarse spectrometer to estimate the slope of the continuum x-ray spectrum, which depends on Te. The 1.6 - 2.0 keV Al emission lines were previously filtered out by using thick Be filters (400 µm and 800 µm), thus restricting the range of the SXT diagnostic to Te >= 1 keV. Absolute brightness modeling explicitly includes several sources of radiation in the analysis model, enabling the use of thinner filters and measurement of much lower Te. Models based on the atomic database and analysis structure (ADAS) agree very well with our experimental SXR measurements. We used ADAS to assess the effect of bremsstrahlung, recombination, dielectronic recombination, and line emission on the inferred Te. This assessment informed the choice of the optimum filter pair to extend the Te range of the SXT diagnostic. This material is based upon work supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Sciences program under Award Numbers DE-FC02-05ER54814 and DE-SC0015474.

Two-Particle Interference of Electron Pairs on a Molecular Level

DOE PAGES

Waitz, M.; Metz, D.; Lower, J.; ...

2016-08-15

Here, wWe investigate the photodouble ionization of H 2 molecules with 400 eV photons. We find that the emitted electrons do not show any sign of two-center interference fringes in their angular emission distributions if considered separately. Conversely, the quasiparticle consisting of both electrons (i.e., the "dielectron") does. The work highlights the fact that nonlocal effects are embedded everywhere in nature where many-particle processes are involved.

Study of Z production in PbPb and pp collisions at TeV in the dimuon and dielectron decay channels

NASA Astrophysics Data System (ADS)

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, M.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Luyckx, S.; Ochesanu, S.; Roland, B.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Pol, M. E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Du, R.; Jiang, C. H.; Liang, D.; Liang, S.; Plestina, R.; Tao, J.; Wang, X.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Guo, Y.; Li, Q.; Li, W.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Zhang, L.; Zou, W.; Avila, C.; Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Ellithi Kamel, A.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Paganini, P.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Bagaturia, I.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Olschewski, M.; Padeken, K.; Papacz, P.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Weber, M.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Lingemann, J.; Nowack, A.; Nugent, I. M.; Perchalla, L.; Pooth, O.; Stahl, A.; Asin, I.; Bartosik, N.; Behr, J.; Behrenhoff, W.; Behrens, U.; Bell, A. J.; Bergholz, M.; Bethani, A.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Garay Garcia, J.; Geiser, A.; Gunnellini, P.; Hauk, J.; Hempel, M.; Horton, D.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Krücker, D.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Lutz, B.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Novgorodova, O.; Nowak, F.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Ron, E.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schmidt, R.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Vargas Trevino, A. D. R.; Walsh, R.; Wissing, C.; Aldaya Martin, M.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Erfle, J.; Garutti, E.; Goebel, K.; Görner, M.; Haller, J.; Hoffmann, M.; Höing, R. S.; Kirschenmann, H.; Klanner, R.; Kogler, R.; Lange, J.; Lapsien, T.; Lenz, T.; Marchesini, I.; Ott, J.; Peiffer, T.; Pietsch, N.; Poehlsen, J.; Rathjens, D.; Sander, C.; Schettler, H.; Schleper, P.; Schlieckau, E.; Schmidt, A.; Seidel, M.; Sola, V.; Stadie, H.; Steinbrück, G.; Troendle, D.; Usai, E.; Vanelderen, L.; Barth, C.; Baus, C.; Berger, J.; Böser, C.; Butz, E.; Chwalek, T.; De Boer, W.; Descroix, A.; Dierlamm, A.; Feindt, M.; Frensch, F.; Giffels, M.; Hartmann, F.; Hauth, T.; Husemann, U.; Katkov, I.; Kornmayer, A.; Kuznetsova, E.; Lobelle Pardo, P.; Mozer, M. U.; Müller, Th.; Nürnberg, A.; Quast, G.; Rabbertz, K.; Ratnikov, F.; Röcker, S.; Simonis, H. J.; Stober, F. M.; Ulrich, R.; Wagner-Kuhr, J.; Wayand, S.; Weiler, T.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. 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M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Primavera, F.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Travaglini, R.; Albergo, S.; Cappello, G.; Chiorboli, M.; Costa, S.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Ciulli, V.; Civinini, C.; D'Alessandro, R.; Focardi, E.; Gallo, E.; Gonzi, S.; Gori, V.; Lenzi, P.; Meschini, M.; Paoletti, S.; Sguazzoni, G.; Tropiano, A.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Ferro, F.; Lo Vetere, M.; Robutti, E.; Tosi, S.; Dinardo, M. E.; Fiorendi, S.; Gennai, S.; Gerosa, R.; Ghezzi, A.; Govoni, P.; Lucchini, M. T.; Malvezzi, S.; Manzoni, R. A.; Martelli, A.; Marzocchi, B.; Menasce, D.; Moroni, L.; Paganoni, M.; Pedrini, D.; Ragazzi, S.; Redaelli, N.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; Di Guida, S.; Fabozzi, F.; Iorio, A. O. M.; Lista, L.; Meola, S.; Merola, M.; Paolucci, P.; Azzi, P.; Bacchetta, N.; Bisello, D.; Branca, A.; Carlin, R.; Checchia, P.; Dall'Osso, M.; Dorigo, T.; Galanti, M.; Gasparini, F.; Gasparini, U.; Giubilato, P.; Gozzelino, A.; Kanishchev, K.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Passaseo, M.; Pazzini, J.; Pegoraro, M.; Pozzobon, N.; Ronchese, P.; Torassa, E.; Tosi, M.; Zotto, P.; Zucchetta, A.; Zumerle, G.; Gabusi, M.; Ratti, S. P.; Riccardi, C.; Salvini, P.; Vitulo, P.; Biasini, M.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Mantovani, G.; Menichelli, M.; Romeo, F.; Saha, A.; Santocchia, A.; Spiezia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fiori, F.; Foà, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Moon, C. S.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Serban, A. 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J.; Lee, S.; Oh, Y. D.; Park, H.; Sakharov, A.; Son, D. C.; Kim, T. J.; Kim, J. Y.; Song, S.; Choi, S.; Gyun, D.; Hong, B.; Jo, M.; Kim, H.; Kim, Y.; Lee, B.; Lee, K. S.; Park, S. K.; Roh, Y.; Choi, M.; Kim, J. H.; Park, I. C.; Park, S.; Ryu, G.; Ryu, M. S.; Choi, Y.; Choi, Y. K.; Goh, J.; Kim, D.; Kwon, E.; Lee, J.; Seo, H.; Yu, I.; Juodagalvis, A.; Komaragiri, J. R.; Ali, M. A. B. Md; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-de La Cruz, I.; Lopez-Fernandez, R.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Vazquez Valencia, F.; Pedraza, I.; Salazar Ibarguen, H. A.; Casimiro Linares, E.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Reucroft, S.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khalid, S.; Khan, W. A.; Khurshid, T.; Shah, M. 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V.; Moisenz, P.; Palichik, V.; Perelygin, V.; Shmatov, S.; Skatchkov, N.; Smirnov, V.; Tikhonenko, E.; Zarubin, A.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Levchenko, P.; Murzin, V.; Oreshkin, V.; Smirnov, I.; Sulimov, V.; Uvarov, L.; Vavilov, S.; Vorobyev, A.; Vorobyev, An.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Safronov, G.; Semenov, S.; Spiridonov, A.; Stolin, V.; Vlasov, E.; Zhokin, A.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Mesyats, G.; Rusakov, S. V.; Vinogradov, A.; Belyaev, A.; Boos, E.; Ershov, A.; Gribushin, A.; Kaminskiy, A.; Kodolova, O.; Korotkikh, V.; Lokhtin, I.; Obraztsov, S.; Petrushanko, S.; Savrin, V.; Snigirev, A.; Vardanyan, I.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Tourtchanovitch, L.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Ekmedzic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Battilana, C.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Domínguez Vázquez, D.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Merino, G.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; Albajar, C.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Brun, H.; Cuevas, J.; Fernandez Menendez, J.; Folgueras, S.; Gonzalez Caballero, I.; Lloret Iglesias, L.; Brochero Cifuentes, J. A.; Cabrillo, I. J.; Calderon, A.; Duarte Campderros, J.; Fernandez, M.; Gomez, G.; Graziano, A.; Lopez Virto, A.; Marco, J.; Marco, R.; Martinez Rivero, C.; Matorras, F.; Munoz Sanchez, F. J.; Piedra Gomez, J.; Rodrigo, T.; Rodríguez-Marrero, A. Y.; Ruiz-Jimeno, A.; Scodellaro, L.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Benaglia, A.; Bendavid, J.; Benhabib, L.; Benitez, J. F.; Bernet, C.; Bianchi, G.; Bloch, P.; Bocci, A.; Bonato, A.; Bondu, O.; Botta, C.; Breuker, H.; Camporesi, T.; Cerminara, G.; Colafranceschi, S.; D'Alfonso, M.; d'Enterria, D.; Dabrowski, A.; David, A.; De Guio, F.; De Roeck, A.; De Visscher, S.; Dobson, M.; Dordevic, M.; Dupont-Sagorin, N.; Elliott-Peisert, A.; Eugster, J.; Franzoni, G.; Funk, W.; Gigi, D.; Gill, K.; Giordano, D.; Girone, M.; Glege, F.; Guida, R.; Gundacker, S.; Guthoff, M.; Hammer, J.; Hansen, M.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kousouris, K.; Krajczar, K.; Lecoq, P.; Lourenço, C.; Magini, N.; Malgeri, L.; Mannelli, M.; Marrouche, J.; Masetti, L.; Meijers, F.; Mersi, S.; Meschi, E.; Moortgat, F.; Morovic, S.; Mulders, M.; Musella, P.; Orsini, L.; Pape, L.; Perez, E.; Perrozzi, L.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Pimiä, M.; Piparo, D.; Plagge, M.; Racz, A.; Rolandi, G.; Rovere, M.; Sakulin, H.; Schäfer, C.; Schwick, C.; Sharma, A.; Siegrist, P.; Silva, P.; Simon, M.; Sphicas, P.; Spiga, D.; Steggemann, J.; Stieger, B.; Stoye, M.; Treille, D.; Tsirou, A.; Veres, G. I.; Vlimant, J. R.; Wardle, N.; Wöhri, H. K.; Wollny, H.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; König, S.; Kotlinski, D.; Langenegger, U.; Renker, D.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Bortignon, P.; Buchmann, M. A.; Casal, B.; Chanon, N.; Deisher, A.; Dissertori, G.; Dittmar, M.; Donegà, M.; Dünser, M.; Eller, P.; Grab, C.; Hits, D.; Lustermann, W.; Mangano, B.; Marini, A. C.; Martinez Ruiz del Arbol, P.; Meister, D.; Mohr, N.; Nägeli, C.; Nessi-Tedaldi, F.; Pandolfi, F.; Pauss, F.; Peruzzi, M.; Quittnat, M.; Rebane, L.; Rossini, M.; Starodumov, A.; Takahashi, M.; Theofilatos, K.; Wallny, R.; Weber, H. A.; Amsler, C.; Canelli, M. F.; Chiochia, V.; De Cosa, A.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Millan Mejias, B.; Ngadiuba, J.; Robmann, P.; Ronga, F. J.; Taroni, S.; Verzetti, M.; Yang, Y.; Cardaci, M.; Chen, K. H.; Ferro, C.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Volpe, R.; Yu, S. S.; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Grundler, U.; Hou, W.-S.; Kao, K. Y.; Lei, Y. J.; Liu, Y. F.; Lu, R.-S.; Majumder, D.; Petrakou, E.; Tzeng, Y. M.; Wilken, R.; Asavapibhop, B.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Bakirci, M. N.; Cerci, S.; Dozen, C.; Dumanoglu, I.; Eskut, E.; Girgis, S.; Gokbulut, G.; Gurpinar, E.; Hos, I.; Kangal, E. E.; Kayis Topaksu, A.; Onengut, G.; Ozdemir, K.; Ozturk, S.; Polatoz, A.; Sogut, K.; Sunar Cerci, D.; Tali, B.; Topakli, H.; Vergili, M.; Akin, I. V.; Bilin, B.; Bilmis, S.; Gamsizkan, H.; Karapinar, G.; Ocalan, K.; Sekmen, S.; Surat, U. E.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Isildak, B.; Kaya, M.; Kaya, O.; Bahtiyar, H.; Barlas, E.; Cankocak, K.; Vardarlı, F. I.; Yücel, M.; Levchuk, L.; Sorokin, P.; Brooke, J. J.; Clement, E.; Cussans, D.; Flacher, H.; Frazier, R.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Meng, Z.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Senkin, S.; Smith, V. J.; Williams, T.; Belyaev, A.; Brew, C.; Brown, R. M.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Womersley, W. J.; Worm, S. D.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Burton, D.; Colling, D.; Cripps, N.; Cutajar, M.; Dauncey, P.; Davies, G.; Della Negra, M.; Dunne, P.; Ferguson, W.; Fulcher, J.; Futyan, D.; Gilbert, A.; Hall, G.; Iles, G.; Jarvis, M.; Karapostoli, G.; Kenzie, M.; Lane, R.; Lucas, R.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mathias, B.; Nash, J.; Nikitenko, A.; Pela, J.; Pesaresi, M.; Petridis, K.; Raymond, D. M.; Rogerson, S.; Rose, A.; Seez, C.; Sharp, P.; Tapper, A.; Vazquez Acosta, M.; Virdee, T.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leggat, D.; Leslie, D.; Martin, W.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Dittmann, J.; Hatakeyama, K.; Kasmi, A.; Liu, H.; Scarborough, T.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; Avetisyan, A.; Bose, T.; Fantasia, C.; Heister, A.; Lawson, P.; Richardson, C.; Rohlf, J.; Sperka, D.; St. John, J.; Sulak, L.; Alimena, J.; Berry, E.; Bhattacharya, S.; Christopher, G.; Cutts, D.; Demiragli, Z.; Ferapontov, A.; Garabedian, A.; Heintz, U.; Kukartsev, G.; Laird, E.; Landsberg, G.; Luk, M.; Narain, M.; Segala, M.; Sinthuprasith, T.; Speer, T.; Swanson, J.; Breedon, R.; Breto, G.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Gardner, M.; Ko, W.; Lander, R.; Miceli, T.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Searle, M.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Farrell, C.; Hauser, J.; Ignatenko, M.; Rakness, G.; Takasugi, E.; Valuev, V.; Weber, M.; Babb, J.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Ivova Rikova, M.; Jandir, P.; Kennedy, E.; Lacroix, F.; Liu, H.; Long, O. R.; Luthra, A.; Malberti, M.; Nguyen, H.; Olmedo Negrete, M.; Shrinivas, A.; Sumowidagdo, S.; Wimpenny, S.; Andrews, W.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; D'Agnolo, R. T.; Evans, D.; Holzner, A.; Kelley, R.; Klein, D.; Lebourgeois, M.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Palmer, C.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Sudano, E.; Tadel, M.; Tu, Y.; Vartak, A.; Welke, C.; Würthwein, F.; Yagil, A.; Yoo, J.; Barge, D.; Bradmiller-Feld, J.; Campagnari, C.; Danielson, T.; Dishaw, A.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Incandela, J.; Justus, C.; Mccoll, N.; Richman, J.; Stuart, D.; To, W.; West, C.; Apresyan, A.; Bornheim, A.; Bunn, J.; Chen, Y.; Di Marco, E.; Duarte, J.; Mott, A.; Newman, H. B.; Pena, C.; Rogan, C.; Spiropulu, M.; Timciuc, V.; Wilkinson, R.; Xie, S.; Zhu, R. Y.; Azzolini, V.; Calamba, A.; Ferguson, T.; Iiyama, Y.; Paulini, M.; Russ, J.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Gaz, A.; Luiggi Lopez, E.; Nauenberg, U.; Smith, J. G.; Stenson, K.; Ulmer, K. A.; Wagner, S. R.; Alexander, J.; Chatterjee, A.; Chu, J.; Dittmer, S.; Eggert, N.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Ryd, A.; Salvati, E.; Skinnari, L.; Sun, W.; Teo, W. D.; Thom, J.; Thompson, J.; Tucker, J.; Weng, Y.; Winstrom, L.; Wittich, P.; Winn, D.; Abdullin, S.; Albrow, M.; Anderson, J.; Apollinari, G.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gao, Y.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hanlon, J.; Hare, D.; Harris, R. M.; Hirschauer, J.; Hooberman, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Kaadze, K.; Klima, B.; Kreis, B.; Kwan, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lykken, J.; Maeshima, K.; Marraffino, J. M.; Martinez Outschoorn, V. I.; Maruyama, S.; Mason, D.; McBride, P.; Mishra, K.; Mrenna, S.; Musienko, Y.; Nahn, S.; Newman-Holmes, C.; O'Dell, V.; Prokofyev, O.; Sexton-Kennedy, E.; Sharma, S.; Soha, A.; Spalding, W. J.; Spiegel, L.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vidal, R.; Whitbeck, A.; Whitmore, J.; Yang, F.; Acosta, D.; Avery, P.; Bourilkov, D.; Carver, M.; Cheng, T.; Curry, D.; Das, S.; De Gruttola, M.; Di Giovanni, G. P.; Field, R. D.; Fisher, M.; Furic, I. K.; Hugon, J.; Konigsberg, J.; Korytov, A.; Kypreos, T.; Low, J. F.; Matchev, K.; Milenovic, P.; Mitselmakher, G.; Muniz, L.; Rinkevicius, A.; Shchutska, L.; Skhirtladze, N.; Snowball, M.; Yelton, J.; Zakaria, M.; Hewamanage, S.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Adams, T.; Askew, A.; Bochenek, J.; Diamond, B.; Haas, J.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Prosper, H.; Veeraraghavan, V.; Weinberg, M.; Baarmand, M. M.; Hohlmann, M.; Kalakhety, H.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Bazterra, V. E.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Khalatyan, S.; Kurt, P.; Moon, D. H.; O'Brien, C.; Silkworth, C.; Turner, P.; Varelas, N.; Albayrak, E. A.; Bilki, B.; Clarida, W.; Dilsiz, K.; Duru, F.; Haytmyradov, M.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Rahmat, R.; Sen, S.; Tan, P.; Tiras, E.; Wetzel, J.; Yetkin, T.; Yi, K.; Barnett, B. A.; Blumenfeld, B.; Bolognesi, S.; Fehling, D.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Swartz, M.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Gray, J.; Kenny, R. P.; Malek, M.; Murray, M.; Noonan, D.; Sanders, S.; Sekaric, J.; Stringer, R.; Wang, Q.; Wood, J. S.; Barfuss, A. F.; Chakaberia, I.; Ivanov, A.; Khalil, S.; Makouski, M.; Maravin, Y.; Saini, L. K.; Shrestha, S.; Svintradze, I.; Gronberg, J.; Lange, D.; Rebassoo, F.; Wright, D.; Baden, A.; Belloni, A.; Calvert, B.; Eno, S. C.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kolberg, T.; Lu, Y.; Marionneau, M.; Mignerey, A. C.; Pedro, K.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Bauer, G.; Busza, W.; Cali, I. A.; Chan, M.; Di Matteo, L.; Dutta, V.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Ma, T.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Stöckli, F.; Sumorok, K.; Velicanu, D.; Veverka, J.; Wyslouch, B.; Yang, M.; Zanetti, M.; Zhukova, V.; Dahmes, B.; Gude, A.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Pastika, N.; Rusack, R.; Singovsky, A.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Gonzalez Suarez, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Malik, S.; Meier, F.; Snow, G. R.; Dolen, J.; Godshalk, A.; Iashvili, I.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Haley, J.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Trocino, D.; Wang, R.-J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Velasco, M.; Won, S.; Brinkerhoff, A.; Chan, K. M.; Drozdetskiy, A.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Luo, W.; Lynch, S.; Marinelli, N.; Pearson, T.; Planer, M.; Ruchti, R.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Puigh, D.; Rodenburg, M.; Smith, G.; Vuosalo, C.; Winer, B. L.; Wolfe, H.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zenz, S. C.; Zuranski, A.; Brownson, E.; Mendez, H.; Ramirez Vargas, J. E.; Alagoz, E.; Barnes, V. E.; Benedetti, D.; Bolla, G.; Bortoletto, D.; De Mattia, M.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Lopes Pegna, D.; Maroussov, V.; Merkel, P.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Yoo, H. D.; Zablocki, J.; Zheng, Y.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. M.; Geurts, F. J. M.; Li, W.; Michlin, B.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Khukhunaishvili, A.; Petrillo, G.; Vishnevskiy, D.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Lungu, G.; Mesropian, C.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Lath, A.; Panwalkar, S.; Park, M.; Patel, R.; Salur, S.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Khotilovich, V.; Krutelyov, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Sakuma, T.; Suarez, I.; Tatarinov, A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kovitanggoon, K.; Kunori, S.; Lee, S. W.; Libeiro, T.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sharma, M.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Woods, N.

2015-03-01

The production of Z bosons is studied in the dimuon and dielectron decay channels in PbPb and pp collisions at TeV, using data collected by the CMS experiment at the LHC. The PbPb data sample corresponds to an integrated luminosity of about 166 μb-1, while the pp data sample collected in 2013 at the same nucleon-nucleon centre-of-mass energy has an integrated luminosity of 5.4 pb-1. The Z boson yield is measured as a function of rapidity, transverse momentum, and collision centrality. The ratio of PbPb to pp yields, scaled by the number of inelastic nucleon-nucleon collisions, is found to be 1.06 ± 0.05 (stat) ± 0.08 (syst) in the dimuon channel and 1.02 ± 0.08 (stat) ± 0.15 (syst) in the dielectron channel, for centrality-integrated Z boson production. This binary collision scaling is seen to hold in the entire kinematic region studied, as expected for a colourless probe that is unaffected by the hot and dense QCD medium produced in heavy ion collisions. [Figure not available: see fulltext.

Effects of relativity of RTEX in collisions of U sup q+ with light targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Mau Hsiung.

1990-11-07

We have calculated the resonant transfer and excitation cross sections in collisions of U{sup q+} (q = 82, 89, 90) ion with H{sub 2}, He and C in impulse approximation using the multi-configuration Dirac-Fock method. The calculations were carried out in intermediate coupling with configuration interaction. The quantum electrodynamic and finite nuclear size corrections were included in the calculations of transition energies. The Auger rates were calculated including the contributions from Coulomb as well as the transverse Breit interactions. For U{sup 89+} and U{sup 90+}, effects of relatively not only shift the peak positions but also change the peak structure.more » The total dielectronic recombination strength has been found to increase by 50% due to the effects of relativity. The present theoretical RTEX cross sections for U{sup 90+} in hydrogen agree well with experiment. For U{sup 82+}, Breit interaction had been found to have little effect on the RTEX cross sections involving L-shell excitation. However, the spin-orbit interaction can still make significant change in the peak structure. 24 refs., 4 figs.« less

Proceedings of the 3rd US-Japan Workshop on Plasma Polarization Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beiersdorfer, P; Flyimoto, T

The third US-Japan Workshop on Plasma Polarization Spectroscopy was held at the Lawrence Livermore National Laboratory in Livermore, California, on June 18-21, 2001. The talks presented at this workshop are summarized in these proceedings. The papers cover both experimental investigation and applications of plasma polarization spectroscopy as well as the theoretical foundation and formalisms to understand and describe the polarization phenomena. The papers give an overview of the history of plasma polarization spectroscopy, derive the formal aspects of polarization spectroscopy, including the effects of electric and magnetic fields, discuss spectra perturbed by intense microwave fields, charge exchange, and dielectronic recombination,more » and present calculations of various collisional excitation and ionization cross sections and the modeling of plasma polarization spectroscopy phenomena. Experimental results are given from the WT-3 tokamak, the MST reverse field pinch, the Large Helical Device, the GAMMA 10 mirror machine, the Nevada Terrawatt Facility, the Livermore EBIT-II electron beam ion trap, and beam-foil spectroscopy. In addition, results were presented from studies of several laser-produced plasma experiments and new instrumental techniques were demonstrated.« less

Study of Z production in PbPb and pp collisions at $$ \\sqrt{s_{\\mathrm{NN}}}=2.76 $$ TeV in the dimuon and dielectron decay channels

DOE PAGES

Chatrchyan, Serguei

2015-03-04

We found that the production of Z bosons is studied in the dimuon and dielectron decay channels in PbPb and pp collisions at √s NN=2.76 TeV, using data collected by the CMS experiment at the LHC. The PbPb data sample corresponds to an integrated luminosity of about 166 μb -1, while the pp data sample collected in 2013 at the same nucleon-nucleon centre-of-mass energy has an integrated luminosity of 5.4 pb -1. The Z boson yield is measured as a function of rapidity, transverse momentum, and collision centrality. The ratio of PbPb to pp yields, scaled by the number ofmore » inelastic nucleon-nucleon collisions, is found to be 1.06 ± 0.05 (stat) ± 0.08 (syst) in the dimuon channel and 1.02 ± 0.08 (stat) ± 0.15 (syst) in the dielectron channel, for centrality-integrated Z boson production. Finally, this binary collision scaling is seen to hold in the entire kinematic region studied, as expected for a colourless probe that is unaffected by the hot and dense QCD medium produced in heavy ion collisions.« less

Measurement of the differential and double-differential Drell-Yan cross sections in proton-proton collisions at sqrt{s} = 7 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatrchyan, Serguei; et al.,

2013-12-01

Measurements of the differential and double-differential Drell-Yan cross sections are presented using an integrated luminosity of 4.5(4.8) inverse femtobarns in the dimuon (dielectron) channel of proton-proton collision data recorded with the CMS detector at the LHC at sqrt{s} = 7 TeV. The measured inclusive cross section in the Z-peak region (60-120 GeV) is \\sigma(\\ell \\ell) = 986.4 +/- 0.6 (stat.) +/- 5.9 (exp. syst.) +/- 21.7 (th. syst.) +/- 21.7 (lum.) pb for the combination of the dimuon and dielectron channels. Differential cross sectionsmore » $$d\\sigma/dm$$ for the dimuon, dielectron, and combined channels are measured in the mass range 15 to 1500 GeV and corrected to the full phase space. Results are also presented for the measurement of the double-differential cross section d^2\\sigma/dm d |y| in the dimuon channel over the mass range 20 to 1500 GeV and absolute dimuon rapidity from 0 to 2.4. These measurements are compared to the predictions of perturbative QCD calculations at next-to-leading and next-to-next-to-leading orders using various sets of parton distribution functions.« less

Investigation of the Contribution of Lower Charger State Ar Ions to the Unknown Faint X-Ray Feature Found in the Stacked Spectrum of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Gall, Amy

Driven by the recent detection of an unidentified emission line previously reported at 3.55-3.57 keV in a stacked spectrum of galaxy clusters, in this work we investigated the resonant dielectronic recombination (DR) process in Li-like Ar as a possible source of, or contributor to, the emission line. The Li-like transition 1s22l-1s2l3l' was suggested to produce a 3.62 keV photon [1] near the unidentified line at 3.57 keV and was the primary focus of our study. The Electron Beam Ion Trap at NIST was used to produce and trap the highly-charged ions of argon. The energy of the quasi-monoenergetic electron beam was incremented in steps of 15 eV to scan over all of the Li-like Ar DR resonances. A Johann-type crystal spectrometer and a solid-state germanium detector were used to take x-ray measurements perpendicular to the electron beam. Our broadband results allowed us to identify the processes that produced specific spectral features, while our high-resolution spectra allowed the experimental separation of features that are less than 2 eV apart. We have used the collisional radiative model NOMAD [2] aided by atomic data calculations by FAC [3] to interpret our observations and account for corrections. Experimental results were compared to the atomic database AtomDB, used to fit the galaxy cluster spectra. We found a number of measured features due to DR in lower charge state Ar ions not included in the database, close in energy to the identified line at 3.57 keV, and suggest their inclusion for improved interpretation and diagnosis of other astrophysical spectra.

A non-LTE analysis of high energy density Kr plasmas on Z and NIF

NASA Astrophysics Data System (ADS)

Dasgupta, A.; Clark, R. W.; Ouart, N.; Giuliani, J.; Velikovich, A.; Ampleford, D. J.; Hansen, S. B.; Jennings, C.; Harvey-Thompson, A. J.; Jones, B.; Flanagan, T. M.; Bell, K. S.; Apruzese, J. P.; Fournier, K. B.; Scott, H. A.; May, M. J.; Barrios, M. A.; Colvin, J. D.; Kemp, G. E.

2016-10-01

Multi-keV X-ray radiation sources have a wide range of applications, from biomedical studies and research on thermonuclear fusion to materials science and astrophysics. The refurbished Z pulsed power machine at the Sandia National Laboratories produces intense multi-keV X-rays from argon Z-pinches, but for a krypton Z-pinch, the yield decreases much faster with atomic number ZA than similar sources on the National Ignition Facility (NIF) laser at the Lawrence Livermore National Laboratory. To investigate whether fundamental energy deposition differences between pulsed power and lasers could account for the yield differences, we consider the Kr plasma on the two machines. The analysis assumes the plasma not in local thermodynamic equilibrium, with a detailed coupling between the hydrodynamics, the radiation field, and the ionization physics. While for the plasma parameters of interest the details of krypton's M-shell are not crucial, both the L-shell and the K-shell must be modeled in reasonable detail, including the state-specific dielectronic recombination processes that significantly affect Kr's ionization balance and the resulting X-ray spectrum. We present a detailed description of the atomic model, provide synthetic K- and L-shell spectra, and compare these with the available experimental data from the Z-machine and from NIF to show that the K-shell yield behavior versus ZA is indeed related to the energy input characteristics. This work aims at understanding the probable causes that might explain the differences in the X-ray conversion efficiencies of several radiation sources on Z and NIF.

Lineshape measurements of He- β spectra on the ORION laser facility

DOE PAGES

Beiersdorfer, P.; Brown, G. V.; Shepherd, R.; ...

2016-10-25

Here, we have utilized a newly developed high-resolution X-ray spectrometer to measure the shapes of spectral lines produced from laser-irradiated targets on the Orion laser facility in the United Kingdom. We present measurements of the He-β spectra of chlorine and chromium from targets irradiated by either a long-pulse or a short-pulse laser beam. The experimental conditions provide a spread in plasma density ranging from about 10 19 to about 10 24 cm –3. We present spectral calculations that show that the relative intensities of the Li-like satellite lines can be used to infer the density in the lower range, especiallymore » if the lithiumlike satellite lines are well resolved. In addition, we use the Stark-broadened width of the He-β line to infer densities above about 10 22 cm –3. In the case of a short-pulse irradiated chromium foil, we find that the He-like chromium is produced at a density of almost 8 g/cm 3, i.e., solid density. In addition, we can infer the electron temperature from the observation of dielectronic recombination satellite lines.« less

Photoionization Models of Bromine, Rubidium, and Xenon in Planetary Nebulae

NASA Astrophysics Data System (ADS)

Sterling, Nicholas C.; Porter, Ryan; Spencer, Courteney; Sherrard, Cameroun G.

2017-06-01

We present numerical simulations of the Br, Rb, and Xe ionization balance in five planetary nebulae (PNe). These neutron-capture elements (atomic number Z > 30) can be enriched by s-process nucleosynthesis during the asymptotic giant branch (AGB) evolutionary stage of PN progenitor stars. Recent calculations of photoionization cross sections and rate coefficients for radiative recombination, dielectronic recombination, and charge transfer (Kerlin et al. 2017, in preparation; Sterling & Kerlin 2016, 227th AAS, #238.02; Sterling & Stancil 2011, A&A, 535, A117) allow the Br, Rb, and Xe ionization equilibria to be modeled in PNe for the first time. We have added these elements and their atomic data to Cloudy (Ferland et al. 2013, RMxA&A, 49, 137). We model the PNe IC 418, IC 2501, IC 4191, NGC 2440, and NGC 7027, all of which exhibit emission from multiple Xe ions in the optical data of Sharpee et al. (2007, ApJ, 659, 1265). Multiple Br and Rb ions were also detected in NGC 7027. The model central star temperatures and luminosities, and nebular densities, outer radii, and abundances were optimized to best reproduce the observed intensities of Sharpee et al. We find that IC 418 and NGC 7027 are enriched in Br, Rb, and Xe, in accordance with results for Se and Kr (Sterling et al. 2015, ApJS, 218, 25). Given the small sample size and the weakness of the lines involved, it is not clear whether discrepancies between modeled and observed intensities are due to observational, model, or atomic data uncertainties. This sample will be expanded to include other PNe, such as those in our optical survey (Sherrard et al. poster, this session), which will allow us to test the veracity of the new atomic data for Xe and, for a smaller number of PNe, Br and Rb. Following the methods of Sterling et al. (2015), grids of Cloudy models will be computed to derive ionization correction factors for Br, Rb, and Xe for the first time, allowing their abundances to be determined with higher accuracy than previously possible. We acknowledge support from NSF grant AST-1412928.

Polarization of resonantly excited X-ray lines

NASA Astrophysics Data System (ADS)

Shah, Chintan; Amaro, Pedro; Steinbrügge, René; Bernitt, Sven; Fritzsche, Stephan; Surzhykov, Andrey; Crespo Lopez-Urrutia, José R.; Tashenov, Stanislav

2017-08-01

For a wide range of temperatures, resonantly captured electrons with energies below the excitation threshold are the strongest source of X-ray line excitation in hot plasmas containing highly charged Fe ions. The angular distribution and polarization of X-rays emitted due to these processes were experimentally studied using an electron beam ion trap. The electron-ion collision energy was scanned over the KLL dielectronic, trielectronic, and quadruelectronic recombination resonances of Fe18+..24+ and Kr28+..34+ with an exemplary resolution of ~6 eV. The angular distribution of induced X-ray fluorescence was measured along and perpendicular to the electron beam propagation direction [1]. Subsequently, the polarization of X-ray fluorescence was also measured using a novel Compton polarimeter [2, 3].The experimental data reveal the alignment of the populated excited states and exhibit a high sensitivity to the relativistic Breit interaction [2, 4]. We observed that most of the transitions lead to polarization, including hitherto-neglected trielectronic and quadruelectronic recombination channels. Furthermore, these channels dominate the polarization of the prominent Kα X-rays emitted by hot anisotropic plasmas in a wide temperature range. The present experimental results comprehensively benchmark full-order atomic calculations carried out with the FAC [5] and RATIP [6] codes. We conclude that accurate polarization diagnostics of hot anisotropic plasmas, e.~g., of solar flares and active galactic nuclei, and laboratory fusion plasmas of tokamaks can only be obtained under the premise of careful inclusion of relativistic effects and higher-order resonances which were often neglected in previous works [1]. The present experiments also demonstrate the suitability of the applied technique for accurate directional diagnostics of electron or ion beams in hot plasmas [7].[1] C. Shah et al., Phys. Rev. E 93, 061201 (R) (2016)[2] C. Shah et al., Phys. Rev. A 92, 042702 (2015)[3] S. Weber et al., Rev. Sci. Instr. 86, 093110 (2015)[4] P. Amaro et al., Phys. Rev. A 95, 022712 (2017)[5] M. F. Gu, Can. Phys. J 86, 675 (2008)[6] S. Fritzsche, Comput. Phys. Commu. 183, 1525-1559 (2012)[7] C. Shah et al., submitted (2017)

Review of the 9th NLTE code comparison workshop

DOE PAGES

Piron, Robin; Gilleron, Franck; Aglitskiy, Yefim; ...

2017-02-24

Here, we review the 9th NLTE code comparison workshop, which was held in the Jussieu campus, Paris, from November 30th to December 4th, 2015. This time, the workshop was mainly focused on a systematic investigation of iron NLTE steady-state kinetics and emissivity, over a broad range of temperature and density. Through these comparisons, topics such as modeling of the dielectronic processes, density effects or the effect of an external radiation field were addressed. The K-shell spectroscopy of iron plasmas was also addressed, notably through the interpretation of tokamak and laser experimental spectra.

Review of the 9th NLTE code comparison workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piron, Robin; Gilleron, Franck; Aglitskiy, Yefim

Here, we review the 9th NLTE code comparison workshop, which was held in the Jussieu campus, Paris, from November 30th to December 4th, 2015. This time, the workshop was mainly focused on a systematic investigation of iron NLTE steady-state kinetics and emissivity, over a broad range of temperature and density. Through these comparisons, topics such as modeling of the dielectronic processes, density effects or the effect of an external radiation field were addressed. The K-shell spectroscopy of iron plasmas was also addressed, notably through the interpretation of tokamak and laser experimental spectra.

Review of the 9th NLTE code comparison workshop

NASA Astrophysics Data System (ADS)

Piron, R.; Gilleron, F.; Aglitskiy, Y.; Chung, H.-K.; Fontes, C. J.; Hansen, S. B.; Marchuk, O.; Scott, H. A.; Stambulchik, E.; Ralchenko, Yu.

2017-06-01

We review the 9th NLTE code comparison workshop, which was held in the Jussieu campus, Paris, from November 30th to December 4th, 2015. This time, the workshop was mainly focused on a systematic investigation of iron NLTE steady-state kinetics and emissivity, over a broad range of temperature and density. Through these comparisons, topics such as modeling of the dielectronic processes, density effects or the effect of an external radiation field were addressed. The K-shell spectroscopy of iron plasmas was also addressed, notably through the interpretation of tokamak and laser experimental spectra.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safronova, U. I.; Safronova, A. S.; Beiersdorfer, P.

Energy levels, radiative transition probabilities, and autoionization rates for [Ni]more » $$4{s}^{2}4{p}^{6}{nl}$$, [Ni]$$4{s}^{2}4{p}^{5}4l^{\\prime} {nl}$$ ($$l^{\\prime} =d,f,n$$ = 4–7), [Ni]$$4s4{p}^{6}4l^{\\prime} {nl}$$, ($$l^{\\prime} =d,f,n$$ = 4–7), [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} {nl}$$ (n = 5–7), and [Ni]$$4s4{p}^{6}6l^{\\prime} {nl}$$ (n = 6–7) states in Rb-like tungsten (W37+) are calculated using the relativistic many-body perturbation theory method (RMBPT code) and the Hartree–Fock-relativistic method (COWAN code). Autoionizing levels above the [Ni]$$4{s}^{2}4{p}^{6}$$ threshold are considered. It is found that configuration mixing among [Ni]$$4{s}^{2}4{p}^{5}4l^{\\prime} {nl}$$ and [Ni]$$4s4{p}^{6}4l^{\\prime} {nl}$$ plays an important role for all atomic characteristics. Branching ratios relative to the first threshold and intensity factors are calculated for satellite lines, and dielectronic recombination (DR) rate coefficients are determined for the [Ni]$$4{s}^{2}4{p}^{6}{nl}$$ (n = 4–7) singly excited states, as well as the [Ni]$$4{s}^{2}4{p}^{5}4{dnl}$$, [Ni]$$4{s}^{2}4{p}^{5}4{fnl}$$, [Ni]$$4s4{p}^{6}4{dnl}$$, [Ni]$$4{s}^{2}4{p}^{6}4{fnl}$$, (n = 4–6), and [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} 5l$$ doubly excited nonautoionizing states in Rb-like W37+ ion. Contributions from the [Ni]$$4s24{p}^{6}4{fnl}$$ (n = 6–7), [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} {nl}$$ (n = 5–6), and [Ni]$$4{s}^{2}4{p}^{5}6l^{\\prime} {nl}$$ (n = 6–7) doubly excited autoionizing states are evaluated numerically. The high-n state (with n up to 500) contributions are very important for high temperatures. These contributions are determined by using a scaling procedure. Synthetic dielectronic satellite spectra from Rb-like W are simulated in a broad spectral range from 8 to 70 Å. Here, these calculations provide highly accurate values for a number of W 37+ properties useful for a variety of applications including for fusion applications.« less

A non-LTE analysis of high energy density Kr plasmas on Z and NIF

DOE PAGES

Dasgupta, A.; Clark, R. W.; Ouart, N.; ...

2016-10-20

We report that multi-keV X-ray radiation sources have a wide range of applications, from biomedical studies and research on thermonuclear fusion to materials science and astrophysics. The refurbished Z pulsed power machine at the Sandia National Laboratories produces intense multi-keV X-rays from argon Z-pinches, but for a krypton Z-pinch, the yield decreases much faster with atomic number Z A than similar sources on the National Ignition Facility (NIF) laser at the Lawrence Livermore National Laboratory. To investigate whether fundamental energy deposition differences between pulsed power and lasers could account for the yield differences, we consider the Kr plasma on themore » two machines. The analysis assumes the plasma not in local thermodynamic equilibrium, with a detailed coupling between the hydrodynamics, the radiation field, and the ionization physics. While for the plasma parameters of interest the details of krypton’s M-shell are not crucial, both the L-shell and the K-shell must be modeled in reasonable detail, including the state-specific dielectronic recombination processes that significantly affect Kr’s ionization balance and the resulting X-ray spectrum. We present a detailed description of the atomic model, provide synthetic K- and L-shell spectra, and compare these with the available experimental data from the Z-machine and from NIF to show that the K-shell yield behavior versus Z A is indeed related to the energy input characteristics. In conclusion, this work aims at understanding the probable causes that might explain the differences in the X-ray conversion efficiencies of several radiation sources on Z and« less

A non-LTE analysis of high energy density Kr plasmas on Z and NIF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dasgupta, A.; Clark, R. W.; Ouart, N.

We report that multi-keV X-ray radiation sources have a wide range of applications, from biomedical studies and research on thermonuclear fusion to materials science and astrophysics. The refurbished Z pulsed power machine at the Sandia National Laboratories produces intense multi-keV X-rays from argon Z-pinches, but for a krypton Z-pinch, the yield decreases much faster with atomic number Z A than similar sources on the National Ignition Facility (NIF) laser at the Lawrence Livermore National Laboratory. To investigate whether fundamental energy deposition differences between pulsed power and lasers could account for the yield differences, we consider the Kr plasma on themore » two machines. The analysis assumes the plasma not in local thermodynamic equilibrium, with a detailed coupling between the hydrodynamics, the radiation field, and the ionization physics. While for the plasma parameters of interest the details of krypton’s M-shell are not crucial, both the L-shell and the K-shell must be modeled in reasonable detail, including the state-specific dielectronic recombination processes that significantly affect Kr’s ionization balance and the resulting X-ray spectrum. We present a detailed description of the atomic model, provide synthetic K- and L-shell spectra, and compare these with the available experimental data from the Z-machine and from NIF to show that the K-shell yield behavior versus Z A is indeed related to the energy input characteristics. In conclusion, this work aims at understanding the probable causes that might explain the differences in the X-ray conversion efficiencies of several radiation sources on Z and« less

Atomic data and spectral modeling constraints from high-resolution X-ray observations of the Perseus cluster with Hitomi

NASA Astrophysics Data System (ADS)

Hitomi Collaboration; Aharonian, Felix; Akamatsu, Hiroki; Akimoto, Fumie; Allen, Steven W.; Angelini, Lorella; Audard, Marc; Awaki, Hisamitsu; Axelsson, Magnus; Bamba, Aya; Bautz, Marshall W.; Blandford, Roger; Brenneman, Laura W.; Brown, Gregory V.; Bulbul, Esra; Cackett, Edward M.; Chernyakova, Maria; Chiao, Meng P.; Coppi, Paolo S.; Costantini, Elisa; de Plaa, Jelle; de Vries, Cor P.; den Herder, Jan-Willem; Done, Chris; Dotani, Tadayasu; Ebisawa, Ken; Eckart, Megan E.; Enoto, Teruaki; Ezoe, Yuichiro; Fabian, Andrew C.; Ferrigno, Carlo; Foster, Adam R.; Fujimoto, Ryuichi; Fukazawa, Yasushi; Furuzawa, Akihiro; Galeazzi, Massimiliano; Gallo, Luigi C.; Gandhi, Poshak; Giustini, Margherita; Goldwurm, Andrea; Gu, Liyi; Guainazzi, Matteo; Haba, Yoshito; Hagino, Kouichi; Hamaguchi, Kenji; Harrus, Ilana M.; Hatsukade, Isamu; Hayashi, Katsuhiro; Hayashi, Takayuki; Hayashida, Kiyoshi; Hell, Natalie; Hiraga, Junko S.; Hornschemeier, Ann; Hoshino, Akio; Hughes, John P.; Ichinohe, Yuto; Iizuka, Ryo; Inoue, Hajime; Inoue, Yoshiyuki; Ishida, Manabu; Ishikawa, Kumi; Ishisaki, Yoshitaka; Iwai, Masachika; Kaastra, Jelle; Kallman, Tim; Kamae, Tsuneyoshi; Kataoka, Jun; Katsuda, Satoru; Kawai, Nobuyuki; Kelley, Richard L.; Kilbourne, Caroline A.; Kitaguchi, Takao; Kitamoto, Shunji; Kitayama, Tetsu; Kohmura, Takayoshi; Kokubun, Motohide; Koyama, Katsuji; Koyama, Shu; Kretschmar, Peter; Krimm, Hans A.; Kubota, Aya; Kunieda, Hideyo; Laurent, Philippe; Lee, Shiu-Hang; Leutenegger, Maurice A.; Limousin, Olivier; Loewenstein, Michael; Long, Knox S.; Lumb, David; Madejski, Greg; Maeda, Yoshitomo; Maier, Daniel; Makishima, Kazuo; Markevitch, Maxim; Matsumoto, Hironori; Matsushita, Kyoko; McCammon, Dan; McNamara, Brian R.; Mehdipour, Missagh; Miller, Eric D.; Miller, Jon M.; Mineshige, Shin; Mitsuda, Kazuhisa; Mitsuishi, Ikuyuki; Miyazawa, Takuya; Mizuno, Tsunefumi; Mori, Hideyuki; Mori, Koji; Mukai, Koji; Murakami, Hiroshi; Mushotzky, Richard F.; Nakagawa, Takao; Nakajima, Hiroshi; Nakamori, Takeshi; Nakashima, Shinya; Nakazawa, Kazuhiro; Nobukawa, Kumiko K.; Nobukawa, Masayoshi; Noda, Hirofumi; Odaka, Hirokazu; Ohashi, Takaya; Ohno, Masanori; Okajima, Takashi; Ota, Naomi; Ozaki, Masanobu; Paerels, Frits; Paltani, Stéphane; Petre, Robert; Pinto, Ciro; Porter, Frederick S.; Pottschmidt, Katja; Reynolds, Christopher S.; Safi-Harb, Samar; Saito, Shinya; Sakai, Kazuhiro; Sasaki, Toru; Sato, Goro; Sato, Kosuke; Sato, Rie; Sawada, Makoto; Schartel, Norbert; Serlemtsos, Peter J.; Seta, Hiromi; Shidatsu, Megumi; Simionescu, Aurora; Smith, Randall K.; Soong, Yang; Stawarz, Łukasz; Sugawara, Yasuharu; Sugita, Satoshi; Szymkowiak, Andrew; Tajima, Hiroyasu; Takahashi, Hiromitsu; Takahashi, Tadayuki; Takeda, Shin'ichiro; Takei, Yoh; Tamagawa, Toru; Tamura, Takayuki; Tanaka, Takaaki; Tanaka, Yasuo; Tanaka, Yasuyuki T.; Tashiro, Makoto S.; Tawara, Yuzuru; Terada, Yukikatsu; Terashima, Yuichi; Tombesi, Francesco; Tomida, Hiroshi; Tsuboi, Yohko; Tsujimoto, Masahiro; Tsunemi, Hiroshi; Tsuru, Takeshi Go; Uchida, Hiroyuki; Uchiyama, Hideki; Uchiyama, Yasunobu; Ueda, Shutaro; Ueda, Yoshihiro; Uno, Shin'ichiro; Urry, C. Megan; Ursino, Eugenio; Watanabe, Shin; Werner, Norbert; Wilkins, Dan R.; Williams, Brian J.; Yamada, Shinya; Yamaguchi, Hiroya; Yamaoka, Kazutaka; Yamasaki, Noriko Y.; Yamauchi, Makoto; Yamauchi, Shigeo; Yaqoob, Tahir; Yatsu, Yoichi; Yonetoku, Daisuke; Zhuravleva, Irina; Zoghbi, Abderahmen; Raassen, A. J. J.

2018-03-01

The Hitomi Soft X-ray Spectrometer spectrum of the Perseus cluster, with ˜5 eV resolution in the 2-9 keV band, offers an unprecedented benchmark of the atomic modeling and database for hot collisional plasmas. It reveals both successes and challenges of the current atomic data and models. The latest versions of AtomDB/APEC (3.0.8), SPEX (3.03.00), and CHIANTI (8.0) all provide reasonable fits to the broad-band spectrum, and are in close agreement on best-fit temperature, emission measure, and abundances of a few elements such as Ni. For the Fe abundance, the APEC and SPEX measurements differ by 16%, which is 17 times higher than the statistical uncertainty. This is mostly attributed to the differences in adopted collisional excitation and dielectronic recombination rates of the strongest emission lines. We further investigate and compare the sensitivity of the derived physical parameters to the astrophysical source modeling and instrumental effects. The Hitomi results show that accurate atomic data and models are as important as the astrophysical modeling and instrumental calibration aspects. Substantial updates of atomic databases and targeted laboratory measurements are needed to get the current data and models ready for the data from the next Hitomi-level mission.

The Heidelberg compact electron beam ion traps

NASA Astrophysics Data System (ADS)

Micke, P.; Kühn, S.; Buchauer, L.; Harries, J. R.; Bücking, T. M.; Blaum, K.; Cieluch, A.; Egl, A.; Hollain, D.; Kraemer, S.; Pfeifer, T.; Schmidt, P. O.; Schüssler, R. X.; Schweiger, Ch.; Stöhlker, T.; Sturm, S.; Wolf, R. N.; Bernitt, S.; Crespo López-Urrutia, J. R.

2018-06-01

Electron beam ion traps (EBITs) are ideal tools for both production and study of highly charged ions (HCIs). In order to reduce their construction, maintenance, and operation costs, we have developed a novel, compact, room-temperature design, the Heidelberg Compact EBIT (HC-EBIT). Four already commissioned devices operate at the strongest fields (up to 0.86 T) reported for such EBITs using permanent magnets, run electron beam currents up to 80 mA, and energies up to 10 keV. They demonstrate HCI production, trapping, and extraction of pulsed Ar16+ bunches and continuous 100 pA ion beams of highly charged Xe up to charge state 29+, already with a 4 mA, 2 keV electron beam. Moreover, HC-EBITs offer large solid-angle ports and thus high photon count rates, e.g., in x-ray spectroscopy of dielectronic recombination in HCIs up to Fe24+, achieving an electron-energy resolving power of E/ΔE > 1500 at 5 keV. Besides traditional on-axis electron guns, we have also implemented a novel off-axis gun for laser, synchrotron, and free-electron laser applications, offering clear optical access along the trap axis. We report on its first operation at a synchrotron radiation facility demonstrating the resonant photoexcitation of highly charged oxygen.

A Si IV/O IV Electron Density Diagnostic for the Analysis of IRIS Solar Spectra

NASA Astrophysics Data System (ADS)

Young, P. R.; Keenan, F. P.; Milligan, R. O.; Peter, H.

2018-04-01

Solar spectra of ultraviolet bursts and flare ribbons from the Interface Region Imaging Spectrograph (IRIS) have suggested high electron densities of > {10}12 cm‑3 at transition region temperatures of 0.1 MK, based on large intensity ratios of Si IV λ1402.77 to O IV λ1401.16. In this work, a rare observation of the weak O IV λ1343.51 line is reported from an X-class flare that peaked at 21:41 UT on 2014 October 24. This line is used to develop a theoretical prediction of the Si IV λ1402.77 to O IV λ1401.16 ratio as a function of density that is recommended to be used in the high-density regime. The method makes use of new pressure-dependent ionization fractions that take account of the suppression of dielectronic recombination at high densities. It is applied to two sequences of flare kernel observations from the October 24 flare. The first shows densities that vary between 3× {10}12 and 3× {10}13 cm‑3 over a seven-minute period, while the second location shows stable density values of around 2× {10}12 cm‑3 over a three-minute period.

Search for physics beyond the standard model in dilepton mass spectra in proton-proton collisions at TeV

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, M.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Luyckx, S.; Ochesanu, S.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Zenoni, F.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Dos Reis Martins, T.; Mora Herrera, C.; Pol, M. E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Tao, J.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Zou, W.; Avila, C.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Elgammal, S.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Paganini, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Bouvier, E.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Pook, T.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Weber, M.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Heister, A.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Künsken, A.; Lingemann, J.; Nowack, A.; Nugent, I. M.; Perchalla, L.; Pooth, O.; Stahl, A.; Asin, I.; Bartosik, N.; Behr, J.; Behrenhoff, W.; Behrens, U.; Bell, A. J.; Bergholz, M.; Bethani, A.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Garay Garcia, J.; Geiser, A.; Gunnellini, P.; Hauk, J.; Hempel, M.; Horton, D.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Krücker, D.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Lutz, B.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Novgorodova, O.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Roland, B.; Ron, E.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schmidt, R.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Vargas Trevino, A. D. R.; Walsh, R.; Wissing, C.; Aldaya Martin, M.; Blobel, V.; Centis Vignali, M.; Draeger, A. 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T.; Spagnolo, P.; Squillacioti, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Vernieri, C.; Barone, L.; Cavallari, F.; D'imperio, G.; Del Re, D.; Diemoz, M.; Grassi, M.; Jorda, C.; Longo, E.; Margaroli, F.; Meridiani, P.; Micheli, F.; Nourbakhsh, S.; Organtini, G.; Paramatti, R.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Soffi, L.; Traczyk, P.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bellan, R.; Biino, C.; Cartiglia, N.; Casasso, S.; Costa, M.; Degano, A.; Demaria, N.; Finco, L.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Musich, M.; Obertino, M. M.; Ortona, G.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Potenza, A.; Romero, A.; Ruspa, M.; Sacchi, R.; Solano, A.; Staiano, A.; Tamponi, U.; Belforte, S.; Candelise, V.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Gobbo, B.; La Licata, C.; Marone, M.; Schizzi, A.; Umer, T.; Zanetti, A.; Chang, S.; Kropivnitskaya, A.; Nam, S. K.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Kong, D. J.; Lee, S.; Oh, Y. D.; Park, H.; Sakharov, A.; Son, D. C.; Kim, T. J.; Kim, J. Y.; Song, S.; Choi, S.; Gyun, D.; Hong, B.; Jo, M.; Kim, H.; Kim, Y.; Lee, B.; Lee, K. S.; Park, S. K.; Roh, Y.; Yoo, H. D.; Choi, M.; Kim, J. H.; Park, I. C.; Ryu, G.; Ryu, M. S.; Choi, Y.; Choi, Y. K.; Goh, J.; Kim, D.; Kwon, E.; Lee, J.; Seo, H.; Yu, I.; Juodagalvis, A.; Komaragiri, J. R.; Ali, M. A. B. Md; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-de La Cruz, I.; Hernandez-Almada, A.; Lopez-Fernandez, R.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Vazquez Valencia, F.; Pedraza, I.; Salazar Ibarguen, H. A.; Casimiro Linares, E.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Reucroft, S.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khalid, S.; Khan, W. A.; Khurshid, T.; Shah, M. A.; Shoaib, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Brona, G.; Bunkowski, K.; Cwiok, M.; Dominik, W.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Wolszczak, W.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Lloret Iglesias, L.; Nguyen, F.; Rodrigues Antunes, J.; Seixas, J.; Varela, J.; Vischia, P.; Golutvin, I.; Gorbunov, I.; Kamenev, A.; Karjavin, V.; Konoplyanikov, V.; Kozlov, G.; Lanev, A.; Malakhov, A.; Matveev, V.; Moisenz, P.; Palichik, V.; Perelygin, V.; Savina, M.; Shmatov, S.; Shulha, S.; Skatchkov, N.; Smirnov, V.; Zarubin, A.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Levchenko, P.; Murzin, V.; Oreshkin, V.; Smirnov, I.; Sulimov, V.; Uvarov, L.; Vavilov, S.; Vorobyev, A.; Vorobyev, An.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Safronov, G.; Semenov, S.; Spiridonov, A.; Stolin, V.; Vlasov, E.; Zhokin, A.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Mesyats, G.; Rusakov, S. V.; Vinogradov, A.; Belyaev, A.; Boos, E.; Bunichev, V.; Dubinin, M.; Dudko, L.; Gribushin, A.; Klyukhin, V.; Kodolova, O.; Lokhtin, I.; Obraztsov, S.; Perfilov, M.; Savrin, V.; Snigirev, A.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Tourtchanovitch, L.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Ekmedzic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Battilana, C.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Domínguez Vázquez, D.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; Albajar, C.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Brun, H.; Cuevas, J.; Fernandez Menendez, J.; Folgueras, S.; Gonzalez Caballero, I.; Brochero Cifuentes, J. A.; Cabrillo, I. J.; Calderon, A.; Duarte Campderros, J.; Fernandez, M.; Gomez, G.; Graziano, A.; Lopez Virto, A.; Marco, J.; Marco, R.; Martinez Rivero, C.; Matorras, F.; Munoz Sanchez, F. J.; Piedra Gomez, J.; Rodrigo, T.; Rodríguez-Marrero, A. Y.; Ruiz-Jimeno, A.; Scodellaro, L.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Benaglia, A.; Bendavid, J.; Benhabib, L.; Benitez, J. F.; Bernet, C.; Bloch, P.; Bocci, A.; Bonato, A.; Bondu, O.; Botta, C.; Breuker, H.; Camporesi, T.; Cerminara, G.; Colafranceschi, S.; D'Alfonso, M.; d'Enterria, D.; Dabrowski, A.; David, A.; De Guio, F.; De Roeck, A.; De Visscher, S.; Di Marco, E.; Dobson, M.; Dordevic, M.; Dorney, B.; Dupont-Sagorin, N.; Elliott-Peisert, A.; Eugster, J.; Franzoni, G.; Funk, W.; Gigi, D.; Gill, K.; Giordano, D.; Girone, M.; Glege, F.; Guida, R.; Gundacker, S.; Guthoff, M.; Hammer, J.; Hansen, M.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kousouris, K.; Krajczar, K.; Lecoq, P.; Lourenço, C.; Magini, N.; Malgeri, L.; Mannelli, M.; Marrouche, J.; Masetti, L.; Meijers, F.; Mersi, S.; Meschi, E.; Moortgat, F.; Morovic, S.; Mulders, M.; Musella, P.; Orsini, L.; Pape, L.; Perez, E.; Perrozzi, L.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Pimiä, M.; Piparo, D.; Plagge, M.; Racz, A.; Rolandi, G.; Rovere, M.; Sakulin, H.; Schäfer, C.; Schwick, C.; Sharma, A.; Siegrist, P.; Silva, P.; Simon, M.; Sphicas, P.; Spiga, D.; Steggemann, J.; Stieger, B.; Stoye, M.; Takahashi, Y.; Treille, D.; Tsirou, A.; Veres, G. I.; Wardle, N.; Wöhri, H. K.; Wollny, H.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Renker, D.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Buchmann, M. A.; Casal, B.; Chanon, N.; Dissertori, G.; Dittmar, M.; Donegà, M.; Dünser, M.; Eller, P.; Grab, C.; Hits, D.; Hoss, J.; Lustermann, W.; Mangano, B.; Marini, A. C.; Martinez Ruiz del Arbol, P.; Masciovecchio, M.; Meister, D.; Mohr, N.; Nägeli, C.; Nessi-Tedaldi, F.; Pandolfi, F.; Pauss, F.; Peruzzi, M.; Quittnat, M.; Rebane, L.; Rossini, M.; Starodumov, A.; Takahashi, M.; Theofilatos, K.; Wallny, R.; Weber, H. A.; Amsler, C.; Canelli, M. F.; Chiochia, V.; De Cosa, A.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Lange, C.; Millan Mejias, B.; Ngadiuba, J.; Robmann, P.; Ronga, F. J.; Taroni, S.; Verzetti, M.; Yang, Y.; Cardaci, M.; Chen, K. H.; Ferro, C.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Volpe, R.; Yu, S. S.; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Grundler, U.; Hou, W.-S.; Kao, K. Y.; Lei, Y. J.; Liu, Y. F.; Lu, R.-S.; Majumder, D.; Petrakou, E.; Tzeng, Y. M.; Wilken, R.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Bakirci, M. N.; Cerci, S.; Dozen, C.; Dumanoglu, I.; Eskut, E.; Girgis, S.; Gokbulut, G.; Gurpinar, E.; Hos, I.; Kangal, E. E.; Kayis Topaksu, A.; Onengut, G.; Ozdemir, K.; Ozturk, S.; Polatoz, A.; Sunar Cerci, D.; Tali, B.; Topakli, H.; Vergili, M.; Akin, I. V.; Bilin, B.; Bilmis, S.; Gamsizkan, H.; Karapinar, G.; Ocalan, K.; Sekmen, S.; Surat, U. E.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Isildak, B.; Kaya, M.; Kaya, O.; Cankocak, K.; Vardarlı, F. I.; Levchuk, L.; Sorokin, P.; Brooke, J. J.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Meng, Z.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Senkin, S.; Smith, V. J.; Williams, T.; Bell, K. 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A.; Blumenfeld, B.; Bolognesi, S.; Fehling, D.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Swartz, M.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Kenny, R. P.; Malek, M.; Murray, M.; Noonan, D.; Sanders, S.; Sekaric, J.; Stringer, R.; Wang, Q.; Wood, J. S.; Chakaberia, I.; Ivanov, A.; Khalil, S.; Makouski, M.; Maravin, Y.; Saini, L. K.; Shrestha, S.; Skhirtladze, N.; Svintradze, I.; Gronberg, J.; Lange, D.; Rebassoo, F.; Wright, D.; Baden, A.; Belloni, A.; Calvert, B.; Eno, S. C.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kolberg, T.; Lu, Y.; Marionneau, M.; Mignerey, A. C.; Pedro, K.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Bauer, G.; Busza, W.; Cali, I. A.; Chan, M.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Ma, T.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Stöckli, F.; Sumorok, K.; Velicanu, D.; Veverka, J.; Wyslouch, B.; Yang, M.; Zanetti, M.; Zhukova, V.; Dahmes, B.; Gude, A.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Pastika, N.; Rusack, R.; Singovsky, A.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Gonzalez Suarez, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Malik, S.; Meier, F.; Snow, G. R.; Zvada, M.; Dolen, J.; Godshalk, A.; Iashvili, I.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Haley, J.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Trocino, D.; Wang, R.-J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Velasco, M.; Won, S.; Brinkerhoff, A.; Chan, K. M.; Drozdetskiy, A.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Luo, W.; Lynch, S.; Marinelli, N.; Pearson, T.; Planer, M.; Ruchti, R.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hart, A.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Puigh, D.; Rodenburg, M.; Smith, G.; Winer, B. L.; Wolfe, H.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Brownson, E.; Mendez, H.; Ramirez Vargas, J. E.; Barnes, V. E.; Benedetti, D.; Bortoletto, D.; De Mattia, M.; Gutay, L.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Lopes Pegna, D.; Maroussov, V.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Zablocki, J.; Zheng, Y.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. 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W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Clarke, C.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Dodd, L.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Taylor, D.; Verwilligen, P.; Vuosalo, C.; Woods, N.

2015-04-01

Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb-1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z{SSM/'} resonance lighter than 2.90 TeV, a superstring-inspired Z{/ψ '} lighter than 2.57 TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Similarly, lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel. [Figure not available: see fulltext.

Search for narrow resonances in dilepton mass spectra in proton-proton collisions at √{ s} = 13 TeV and combination with 8 TeV data

NASA Astrophysics Data System (ADS)

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A.; Kyriakis, A.; Loukas, D.; Topsis-Giotis, I.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Tziaferi, E.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Loukas, N.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Filipovic, N.; Bencze, G.; Hajdu, C.; Hidas, P.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Makovec, A.; Molnar, J.; Szillasi, Z.; Bartók, M.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Bahinipati, S.; Choudhury, S.; Mal, P.; Mandal, K.; Nayak, A.; Sahoo, D. K.; Sahoo, N.; Swain, S. K.; Bansal, S.; Beri, S. B.; Bhatnagar, V.; Chawla, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, A.; Kaur, M.; Kumar, R.; Mehta, A.; Mittal, M.; Singh, J. B.; Walia, G.; Kumar, Ashok; Bhardwaj, A.; Choudhary, B. C.; Garg, R. 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M.; Fahim, A.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Calabria, C.; Caputo, C.; Colaleo, A.; Creanza, D.; Cristella, L.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; Miniello, G.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Ranieri, A.; Selvaggi, G.; Silvestris, L.; Venditti, R.; Verwilligen, P.; Abbiendi, G.; Battilana, C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Chhibra, S. S.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Rovelli, T.; Siroli, G. 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M.; Lanza, G.; Lista, L.; Meola, S.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Bacchetta, N.; Benato, L.; Bisello, D.; Boletti, A.; Carlin, R.; Carvalho Antunes De Oliveira, A.; Checchia, P.; Dall'Osso, M.; De Castro Manzano, P.; Dorigo, T.; Dosselli, U.; Gasparini, F.; Gasparini, U.; Gozzelino, A.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Torassa, E.; Zanetti, M.; Zotto, P.; Zucchetta, A.; Zumerle, G.; Braghieri, A.; Magnani, A.; Montagna, P.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Alunni Solestizi, L.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Leonardi, R.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fedi, G.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Cipriani, M.; D'imperio, G.; Del Re, D.; Diemoz, M.; Gelli, S.; Longo, E.; Margaroli, F.; Meridiani, P.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bartosik, N.; Bellan, R.; Biino, C.; Cartiglia, N.; Costa, M.; Cotto, G.; Covarelli, R.; Degano, A.; Demaria, N.; Finco, L.; Kiani, B.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Monteil, E.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Ravera, F.; Romero, A.; Rotondo, F.; Ruspa, M.; Sacchi, R.; Sola, V.; Solano, A.; Staiano, A.; Traczyk, P.; Belforte, S.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; La Licata, C.; Schizzi, A.; Zanetti, A.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Lee, S.; Lee, S. W.; Oh, Y. 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A.; Uribe Estrada, C.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khan, W. A.; Shah, M. A.; Shoaib, M.; Waqas, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Bunkowski, K.; Byszuk, A.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Walczak, M.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Di Francesco, A.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Hollar, J.; Leonardo, N.; Lloret Iglesias, L.; Nemallapudi, M. V.; Rodrigues Antunes, J.; Seixas, J.; Toldaiev, O.; Vadruccio, D.; Varela, J.; Vischia, P.; Belotelov, I.; Bunin, P.; Gavrilenko, M.; Golutvin, I.; Gorbunov, I.; Kamenev, A.; Karjavin, V.; Lanev, A.; Malakhov, A.; Matveev, V.; Moisenz, P.; Palichik, V.; Perelygin, V.; Savina, M.; Shmatov, S.; Shulha, S.; Smirnov, V.; Voytishin, N.; Zarubin, A.; Chtchipounov, L.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Kuznetsova, E.; Murzin, V.; Oreshkin, V.; Sulimov, V.; Vorobyev, A.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Karneyeu, A.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Pozdnyakov, I.; Safronov, G.; Spiridonov, A.; Toms, M.; Vlasov, E.; Zhokin, A.; Bylinkin, A.; Chadeeva, M.; Popova, E.; Tarkovskii, E.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Rusakov, S. V.; Terkulov, A.; Baskakov, A.; Belyaev, A.; Boos, E.; Dubinin, M.; Dudko, L.; Ershov, A.; Gribushin, A.; Klyukhin, V.; Kodolova, O.; Lokhtin, I.; Miagkov, I.; Obraztsov, S.; Petrushanko, S.; Savrin, V.; Snigirev, A.; Blinov, V.; Skovpen, Y.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Elumakhov, D.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Cirkovic, P.; Devetak, D.; Dordevic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Barrio Luna, M.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Cuevas, J.; Fernandez Menendez, J.; Gonzalez Caballero, I.; González Fernández, J. R.; Palencia Cortezon, E.; Sanchez Cruz, S.; Suárez Andrés, I.; Vizan Garcia, J. M.; Cabrillo, I. J.; Calderon, A.; Castiñeiras De Saa, J. R.; Curras, E.; Fernandez, M.; Garcia-Ferrero, J.; Gomez, G.; Lopez Virto, A.; Marco, J.; Martinez Rivero, C.; Matorras, F.; Piedra Gomez, J.; Rodrigo, T.; Ruiz-Jimeno, A.; Scodellaro, L.; Trevisani, N.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Bloch, P.; Bocci, A.; Bonato, A.; Botta, C.; Camporesi, T.; Castello, R.; Cepeda, M.; Cerminara, G.; D'Alfonso, M.; d'Enterria, D.; Dabrowski, A.; Daponte, V.; David, A.; De Gruttola, M.; De Roeck, A.; Di Marco, E.; Dobson, M.; Dorney, B.; du Pree, T.; Duggan, D.; Dünser, M.; Dupont, N.; Elliott-Peisert, A.; Fartoukh, S.; Franzoni, G.; Fulcher, J.; Funk, W.; Gigi, D.; Gill, K.; Girone, M.; Glege, F.; Gulhan, D.; Gundacker, S.; Guthoff, M.; Hammer, J.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kieseler, J.; Kirschenmann, H.; Knünz, V.; Kornmayer, A.; Kortelainen, M. J.; Kousouris, K.; Krammer, M.; Lange, C.; Lecoq, P.; Lourenço, C.; Lucchini, M. T.; Malgeri, L.; Mannelli, M.; Martelli, A.; Meijers, F.; Merlin, J. A.; Mersi, S.; Meschi, E.; Moortgat, F.; Morovic, S.; Mulders, M.; Neugebauer, H.; Orfanelli, S.; Orsini, L.; Pape, L.; Perez, E.; Peruzzi, M.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Racz, A.; Reis, T.; Rolandi, G.; Rovere, M.; Ruan, M.; Sakulin, H.; Sauvan, J. B.; Schäfer, C.; Schwick, C.; Seidel, M.; Sharma, A.; Silva, P.; Sphicas, P.; Steggemann, J.; Stoye, M.; Takahashi, Y.; Tosi, M.; Treille, D.; Triossi, A.; Tsirou, A.; Veckalns, V.; Veres, G. I.; Wardle, N.; Zagozdzinska, A.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Casal, B.; Dissertori, G.; Dittmar, M.; Donegà, M.; Eller, P.; Grab, C.; Heidegger, C.; Hits, D.; Hoss, J.; Kasieczka, G.; Lecomte, P.; Lustermann, W.; Mangano, B.; Marionneau, M.; Martinez Ruiz del Arbol, P.; Masciovecchio, M.; Meinhard, M. T.; Meister, D.; Micheli, F.; Musella, P.; Nessi-Tedaldi, F.; Pandolfi, F.; Pata, J.; Pauss, F.; Perrin, G.; Perrozzi, L.; Quittnat, M.; Rossini, M.; Schönenberger, M.; Starodumov, A.; Tavolaro, V. R.; Theofilatos, K.; Wallny, R.; Aarrestad, T. K.; Amsler, C.; Caminada, L.; Canelli, M. F.; De Cosa, A.; Galloni, C.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Ngadiuba, J.; Pinna, D.; Rauco, G.; Robmann, P.; Salerno, D.; Yang, Y.; Candelise, V.; Doan, T. H.; Jain, Sh.; Khurana, R.; Konyushikhin, M.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Pozdnyakov, A.; Yu, S. S.; Kumar, Arun; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Fiori, F.; Hou, W.-S.; Hsiung, Y.; Liu, Y. F.; Lu, R.-S.; Miñano Moya, M.; Paganis, E.; Psallidas, A.; Tsai, J. f.; Tzeng, Y. M.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Bakirci, M. N.; Cerci, S.; Damarseckin, S.; Demiroglu, Z. S.; Dozen, C.; Dumanoglu, I.; Girgis, S.; Gokbulut, G.; Guler, Y.; Gurpinar, E.; Hos, I.; Kangal, E. E.; Kara, O.; Kayis Topaksu, A.; Kiminsu, U.; Oglakci, M.; Onengut, G.; Ozdemir, K.; Tali, B.; Turkcapar, S.; Zorbakir, I. S.; Zorbilmez, C.; Bilin, B.; Bilmis, S.; Isildak, B.; Karapinar, G.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Kaya, M.; Kaya, O.; Yetkin, E. A.; Yetkin, T.; Cakir, A.; Cankocak, K.; Sen, S.; Grynyov, B.; Levchuk, L.; Sorokin, P.; Aggleton, R.; Ball, F.; Beck, L.; Brooke, J. J.; Burns, D.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Sakuma, T.; Seif El Nasr-storey, S.; Smith, D.; Smith, V. J.; Barducci, D.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Calligaris, L.; Cieri, D.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Williams, T.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Bundock, A.; Burton, D.; Casasso, S.; Citron, M.; Colling, D.; Corpe, L.; Dauncey, P.; Davies, G.; De Wit, A.; Della Negra, M.; Di Maria, R.; Dunne, P.; Elwood, A.; Futyan, D.; Haddad, Y.; Hall, G.; Iles, G.; James, T.; Lane, R.; Laner, C.; Lucas, R.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mastrolorenzo, L.; Nash, J.; Nikitenko, A.; Pela, J.; Penning, B.; Pesaresi, M.; Raymond, D. M.; Richards, A.; Rose, A.; Seez, C.; Summers, S.; Tapper, A.; Uchida, K.; Vazquez Acosta, M.; Virdee, T.; Wright, J.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leslie, D.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Liu, H.; Pastika, N.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; West, C.; Arcaro, D.; Avetisyan, A.; Bose, T.; Gastler, D.; Rankin, D.; Richardson, C.; Rohlf, J.; Sulak, L.; Zou, D.; Benelli, G.; Berry, E.; Cutts, D.; Garabedian, A.; Hakala, J.; Heintz, U.; Hogan, J. M.; Jesus, O.; Laird, E.; Landsberg, G.; Mao, Z.; Narain, M.; Piperov, S.; Sagir, S.; Spencer, E.; Syarif, R.; Breedon, R.; Breto, G.; Burns, D.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Flores, C.; Funk, G.; Gardner, M.; Ko, W.; Lander, R.; Mclean, C.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Florent, A.; Hauser, J.; Ignatenko, M.; Saltzberg, D.; Schnaible, C.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Olmedo Negrete, M.; Paneva, M. I.; Shrinivas, A.; Si, W.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; Derdzinski, M.; Gerosa, R.; Holzner, A.; Klein, D.; Krutelyov, V.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Welke, C.; Wood, J.; Würthwein, F.; Yagil, A.; Zevi Della Porta, G.; Bhandari, R.; Bradmiller-Feld, J.; Campagnari, C.; Dishaw, A.; Dutta, V.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Gran, J.; Heller, R.; Incandela, J.; Mccoll, N.; Mullin, S. D.; Ovcharova, A.; Richman, J.; Stuart, D.; Suarez, I.; Yoo, J.; Anderson, D.; Apresyan, A.; Bendavid, J.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Lawhorn, J. M.; Mott, A.; Newman, H. B.; Pena, C.; Spiropulu, M.; Vlimant, J. R.; Xie, S.; Zhu, R. Y.; Andrews, M. B.; Azzolini, V.; Ferguson, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Jensen, F.; Johnson, A.; Krohn, M.; Mulholland, T.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chaves, J.; Chu, J.; Dittmer, S.; Mcdermott, K.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Soffi, L.; Tan, S. M.; Tao, Z.; Thom, J.; Tucker, J.; Wittich, P.; Zientek, M.; Winn, D.; Abdullin, S.; Albrow, M.; Apollinari, G.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Cremonesi, M.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hare, D.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jayatilaka, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Klima, B.; Kreis, B.; Lammel, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lopes De Sá, R.; Lykken, J.; Maeshima, K.; Magini, N.; Marraffino, J. M.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mrenna, S.; Nahn, S.; Newman-Holmes, C.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Ristori, L.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Stoynev, S.; Strobbe, N.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Wang, M.; Weber, H. A.; Whitbeck, A.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Brinkerhoff, A.; Carnes, A.; Carver, M.; Curry, D.; Das, S.; Field, R. D.; Furic, I. K.; Konigsberg, J.; Korytov, A.; Ma, P.; Matchev, K.; Mei, H.; Milenovic, P.; Mitselmakher, G.; Rank, D.; Shchutska, L.; Sperka, D.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Ackert, A.; Adams, J. R.; Adams, T.; Askew, A.; Bein, S.; Diamond, B.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Khatiwada, A.; Prosper, H.; Santra, A.; Weinberg, M.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Kurt, P.; O'Brien, C.; Sandoval Gonzalez, I. D.; Turner, P.; Varelas, N.; Wang, H.; Wu, Z.; Zakaria, M.; Zhang, J.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tiras, E.; Wetzel, J.; Yi, K.; Anderson, I.; Blumenfeld, B.; Cocoros, A.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Osherson, M.; Roskes, J.; Sarica, U.; Swartz, M.; Xiao, M.; Xin, Y.; You, C.; Al-bataineh, A.; Baringer, P.; Bean, A.; Boren, S.; Bowen, J.; Bruner, C.; Castle, J.; Forthomme, L.; Kenny, R. P., III; Kropivnitskaya, A.; Majumder, D.; Mcbrayer, W.; Murray, M.; Sanders, S.; Stringer, R.; Tapia Takaki, J. D.; Wang, Q.; Ivanov, A.; Kaadze, K.; Khalil, S.; Makouski, M.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Toda, S.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Gomez, J. A.; Hadley, N. J.; Jabeen, S.; Kellogg, R. G.; Kolberg, T.; Kunkle, J.; Lu, Y.; Mignerey, A. C.; Shin, Y. H.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Abercrombie, D.; Allen, B.; Apyan, A.; Barbieri, R.; Baty, A.; Bi, R.; Bierwagen, K.; Brandt, S.; Busza, W.; Cali, I. A.; Demiragli, Z.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Hsu, D.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Krajczar, K.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Sumorok, K.; Tatar, K.; Varma, M.; Velicanu, D.; Veverka, J.; Wang, J.; Wang, T. W.; Wyslouch, B.; Yang, M.; Zhukova, V.; Benvenuti, A. C.; Chatterjee, R. M.; Evans, A.; Finkel, A.; Gude, A.; Hansen, P.; Kalafut, S.; Kao, S. C.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bartek, R.; Bloom, K.; Claes, D. R.; Dominguez, A.; Fangmeier, C.; Gonzalez Suarez, R.; Kamalieddin, R.; Kravchenko, I.; Malta Rodrigues, A.; Meier, F.; Monroy, J.; Siado, J. E.; Snow, G. R.; Stieger, B.; Alyari, M.; Dolen, J.; George, J.; Godshalk, A.; Harrington, C.; Iashvili, I.; Kaisen, J.; Kharchilava, A.; Kumar, A.; Parker, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Baumgartel, D.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Teixeira De Lima, R.; Trocino, D.; Wang, R.-J.; Wood, D.; Bhattacharya, S.; Hahn, K. A.; Kubik, A.; Kumar, A.; Low, J. F.; Mucia, N.; Odell, N.; Pollack, B.; Schmitt, M. H.; Sung, K.; Trovato, M.; Velasco, M.; Dev, N.; Hildreth, M.; Hurtado Anampa, K.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Smith, G.; Taroni, S.; Wayne, M.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Hughes, R.; Ji, W.; Liu, B.; Luo, W.; Puigh, D.; Winer, B. L.; Wulsin, H. W.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Lange, D.; Luo, J.; Marlow, D.; Medvedeva, T.; Mei, K.; Mooney, M.; Olsen, J.; Palmer, C.; Piroué, P.; Stickland, D.; Tully, C.; Zuranski, A.; Malik, S.; Barker, A.; Barnes, V. E.; Folgueras, S.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, A. W.; Jung, K.; Miller, D. H.; Neumeister, N.; Shi, X.; Sun, J.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Redjimi, R.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Betchart, B.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Agapitos, A.; Chou, J. P.; Contreras-Campana, E.; Gershtein, Y.; Gómez Espinosa, T. A.; Halkiadakis, E.; Heindl, M.; Hidas, D.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Kyriacou, S.; Lath, A.; Nash, K.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Foerster, M.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Juska, E.; Kamon, T.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Rose, A.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; De Guio, F.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Peltola, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Sun, X.; Wang, Y.; Wolfe, E.; Xia, F.; Clarke, C.; Harr, R.; Karchin, P. E.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Ojalvo, I.; Perry, T.; Polese, G.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.; CMS Collaboration

2017-05-01

A search for narrow resonances in dielectron and dimuon invariant mass spectra has been performed using data obtained from proton-proton collisions at √{ s} = 13 TeV collected with the CMS detector. The integrated luminosity for the dielectron sample is 2.7 fb-1 and for the dimuon sample 2.9 fb-1. The sensitivity of the search is increased by combining these data with a previously analyzed set of data obtained at √{ s} = 8 TeV and corresponding to a luminosity of 20 fb-1. No evidence for non-standard-model physics is found, either in the 13 TeV data set alone, or in the combined data set. Upper limits on the product of production cross section and branching fraction have also been calculated in a model-independent manner to enable interpretation in models predicting a narrow dielectron or dimuon resonance structure. Limits are set on the masses of hypothetical particles that could appear in new-physics scenarios. For the ZSSM‧ particle, which arises in the sequential standard model, and for the superstring inspired Zψ‧ particle, 95% confidence level lower mass limits for the combined data sets and combined channels are found to be 3.37 and 2.82 TeV, respectively. The corresponding limits for the lightest Kaluza-Klein graviton arising in the Randall-Sundrum model of extra dimensions with coupling parameters 0.01 and 0.10 are 1.46 and 3.11 TeV, respectively. These results significantly exceed the limits based on the 8 TeV LHC data.

Measurements of dielectron production in Au + Au collisions at s N N = 200 GeV from the STAR experiment

DOE PAGES

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; ...

2015-08-24

We report on measurements of dielectron (e⁺e⁻) production in Au+Au collisions at a center-of-mass energy of 200 GeV per nucleon-nucleon pair using the STAR detector at RHIC. Systematic measurements of the dielectron yield as a function of transverse momentum (p T) and collision centrality show an enhancement compared to a cocktail simulation of hadronic sources in the low invariant-mass region (M ee < 1GeV/c 2). This enhancement cannot be reproduced by the ρ-meson vacuum spectral function. In minimum-bias collisions, in the invariant-mass range of 0.30 – 0.76GeV/c², integrated over the full p T acceptance, the enhancement factor is 1.76±0.06(stat.)±0.26(sys.)±0.29(cocktail). Themore » enhancement factor exhibits weak centrality and p T dependence in STAR's accessible kinematic regions, while the excess yield in this invariant-mass region as a function of the number of participating nucleons follows a power-law shape with a power of 1.44±0.10. Models that assume an in-medium broadening of the ρ-meson spectral function consistently describe the observed excess in these measurements. In addition, we report on measurements of ω- and Φ-meson production through their e⁺e⁻ decay channel. These measurements show good agreement with Tsallis blast-wave model predictions, as well as, in the case of the Φ meson, results through its K⁺K⁻ decay channel. In the intermediate invariant-mass region (1.1 < M ee < 3GeV/c²), we investigate the spectral shapes from different collision centralities. Physics implications for possible in-medium modification of charmed hadron production and other physics sources are discussed.« less

Search for physics beyond the standard model in dilepton mass spectra in proton-proton collisions at √s = 8 TeV

DOE PAGES

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; ...

2015-04-07

Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb –1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z SSM ' resonance lighter than 2.90 TeV, a superstring-inspired Z ψ ' lighter thanmore » 2.57 TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Thus lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel.« less

Search for narrow resonances in dilepton mass spectra in proton-proton collisions at $$\\sqrt{s}$$ = 13 TeV and combination with 8 TeV data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khachatryan, Vardan

A search for narrow resonances in dielectron and dimuon invariant mass spectra has been performed using data obtained from proton-proton collisions atmore » $$ \\sqrt{s} = $$ 13 TeV collected with the CMS detector. The integrated luminosity for the dielectron sample is 2.7 fb$$^{-1}$$ and for the dimuon sample 2.9 fb$$^{-1}$$. The sensitivity of the search is increased by combining these data with a previously analysed set of data obtained at $$ \\sqrt{s} = $$ 8 TeV and corresponding to a luminosity of 20 fb$$^{-1}$$. No evidence for non-standard-model physics is found, either in the 13 TeV data set alone, or in the combined data set. Upper limits on the product of production cross section and branching fraction have also been calculated in a model-independent manner to enable interpretation in models predicting a narrow dielectron or dimuon resonance structure. Limits are set on the masses of hypothetical particles that could appear in new-physics scenarios. For the $$\\mathrm{Z}'_{\\text{SSM}}$$ particle, which arises in the sequential standard model, and for the superstring inspired $$\\mathrm{Z}'_{\\psi}$$ particle, 95% confidence level lower mass limits for the combined data sets and combined channels are found to be 3.37 and 2.82 TeV, respectively. The corresponding limits for Kaluza-Klein gravitons arising in the Randall-Sundrum model of extra dimensions with coupling parameters 0.01 and 0.10 are 1.46 and 3.11 TeV, respectively. Lastly, these results significantly extend previous limits.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.

Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb –1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z SSM ' resonance lighter than 2.90 TeV, a superstring-inspired Z ψ ' lighter thanmore » 2.57 TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Thus lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel.« less

Search for narrow resonances in dilepton mass spectra in proton-proton collisions at $$\\sqrt{s}$$ = 13 TeV and combination with 8 TeV data

DOE PAGES

Khachatryan, Vardan

2017-02-14

A search for narrow resonances in dielectron and dimuon invariant mass spectra has been performed using data obtained from proton-proton collisions atmore » $$ \\sqrt{s} = $$ 13 TeV collected with the CMS detector. The integrated luminosity for the dielectron sample is 2.7 fb$$^{-1}$$ and for the dimuon sample 2.9 fb$$^{-1}$$. The sensitivity of the search is increased by combining these data with a previously analysed set of data obtained at $$ \\sqrt{s} = $$ 8 TeV and corresponding to a luminosity of 20 fb$$^{-1}$$. No evidence for non-standard-model physics is found, either in the 13 TeV data set alone, or in the combined data set. Upper limits on the product of production cross section and branching fraction have also been calculated in a model-independent manner to enable interpretation in models predicting a narrow dielectron or dimuon resonance structure. Limits are set on the masses of hypothetical particles that could appear in new-physics scenarios. For the $$\\mathrm{Z}'_{\\text{SSM}}$$ particle, which arises in the sequential standard model, and for the superstring inspired $$\\mathrm{Z}'_{\\psi}$$ particle, 95% confidence level lower mass limits for the combined data sets and combined channels are found to be 3.37 and 2.82 TeV, respectively. The corresponding limits for Kaluza-Klein gravitons arising in the Randall-Sundrum model of extra dimensions with coupling parameters 0.01 and 0.10 are 1.46 and 3.11 TeV, respectively. Lastly, these results significantly extend previous limits.« less

Search for high-mass dilepton resonances in p p collisions at s = 8 TeV with the ATLAS detector

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2014-09-19

Here, the ATLAS detector at the Large Hadron Collider is used to search for high-mass resonances decaying to dielectron or dimuon final states. Results are presented from an analysis of proton-proton (pp) collisions at a center-of-mass energy of 8 TeV corresponding to an integrated luminosity of 20.3 fb –1 in the dimuon channel. A narrow resonance with Standard Model Z couplings to fermions is excluded at 95% confidence level for masses less than 2.79 TeV in the dielectron channel, 2.53 TeV in the dimuon channel, and 2.90 TeV in the two channels combined. Limits on other model interpretations are alsomore » presented, including a grand-unification model based on the E 6 gauge group, Z* bosons, minimal Z' models, a spin-2 graviton excitation from Randall-Sundrum models, quantum black holes, and a minimal walking technicolor model with a composite Higgs boson.« less

Identification of the 1s2s2p 4P5/2-->1s22s 2S1/2 magnetic quadrupole inner-shell satellite line in the Ar16+ K-shell x-ray spectrum

NASA Astrophysics Data System (ADS)

Beiersdorfer, P.; Bitter, M.; Hey, D.; Reed, K. J.

2002-09-01

We have identified the dipole-forbidden 1s2s2p 4P5/2-->1s22s 2S1/2 transition in lithiumlike Ar15+ in high-resolution K-shell x-ray emission spectra recorded at the Livermore EBIT-II electron-beam ion trap and the Princeton National Spherical Tokamak Experiment. Unlike other Ar15+ satellite lines, which can be excited by dielectronic recombination, the line is exclusively excited by electron-impact excitation. Its predicted radiative rate is comparable to that of the well-known 1s2p 3P1-->1s2 1S0 magnetic quadrupole transition in heliumlike Ar16+. As a result, it can also only be observed in low-density plasma. We present calculations of the electron-impact excitation cross sections of the innershell excited Ar15+ satellite lines, including the magnetic sublevels needed for calculating the linear line polarization. We compare these calculations to the relative magnitudes of the observed 1s2s2p-->1s22s transitions and find good agreement, confirming the identification of the lithiumlike 1s2s2p 4P5/2-->1s22s 2S1/2 magnetic quadrupole line.

Measurement of the production cross-section of pair of top quarks in a final state with di-electrons in the data collected by D0 experiment in Run-IIa (in French)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin Dit Latour, Bertrand

2008-09-29

The top quark has been discovered in 1995 by CDF and D0 collaborations in proton-antiproton collisions at the Tevatron. The amount of data recorded by both experiments makes it possible to accurately measure the properties of this very massive quark. This thesis is devoted to the measurement of the top pair production cross-section via the strong interaction, in a final state composed of two electrons, two particle jets and missing transverse energy. It is based on a 1 fb -1 data set collected by the D0 experiment between 2002 and 2006. The reconstruction and identification of electrons and jets ismore » of major importance in this analysis, and have been studied in events where a Z boson is produced together with one or more jets. The Z+jets process is indeed the dominant physics background to top pair production in the dielectron final state. The primary goal of this cross-section measurement is to verify Standard Model predictions. In this document, this result is also interpreted to indirectly extract the top quark mass. Moreover, the cross-section measurement is sensitive to new physics such as the existence of a charged Higgs boson. The selection established for the cross-section analysis has been used to search for a H + boson lighter than the top quark, where the latter can decay into a W + or H + boson and a b quark. The model that has been studied makes the assumption that the H + boson can only decay into a tau lepton and a neutrino.« less

Measurement of the weak mixing angle using the forward-backward asymmetry of Drell-Yan events in pp collisions at 8 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirunyan, Albert M; et al.

A measurement is presented of the effective leptonic weak mixing angle (more » $$\\sin^2\\theta^{\\ell}_{\\text{eff}}$$) using the forward-backward asymmetry of Drell-Yan lepton pairs ($$\\mu\\mu$$ and ee) produced in proton-proton collisions at $$\\sqrt{s}=$$ 8 TeV at the CMS experiment of the LHC. The data correspond to integrated luminosities of 18.8 and 19.6 fb$$^{-1}$$ in the dimuon and dielectron channels, respectively, containing 8.2 million dimuon and 4.9 million dielectron events. With more events and new analysis techniques, including constraints obtained on the parton distribution functions from the measured forward-backward asymmetry, the statistical and systematic uncertainties are significantly reduced relative to previous CMS measurements. The extracted value of $$\\sin^2\\theta^{\\ell}_{\\text{eff}}$$ from the combined dilepton data is $$\\sin^2\\theta^{\\ell}_{\\text{eff}}=$$0.23101 $$\\pm$$ 0.00036 (stat) $$\\pm$$ 0.00018 (syst) $$\\pm$$ 0.00016 (theo) $$\\pm$$ 0.00031 (parton distributions in proton) =0.23101 $$\\pm$$ 0.00053.« less

Measurement of Dielectron Invariant Mass Spectra in Au + Au Collisions at p sNN = 200GeV with HBD in PHENIX

NASA Astrophysics Data System (ADS)

Sun, Jiayin

Dileptons are emitted throughout the entire space-time evolution of heavy ion collisions. Being colorless, these electromagnetic probes do not participate in the final-state strong interactions during the passage through the hot medium, and retain the information on the conditions of their creation. This characteristic renders them valuable tools for studying the properties of the Quark Gluon Plasma created during ultra-relativistic heavy ion collisions. The invariant mass spectra of dileptons contain a wealth of information on every stage of the evolution of heavy ion collisions. At low mass, dilepton spectra consist mainly of light meson decays. The medium modification of the light vector mesons gives insight on the chiral symmetry restoration in heavy ion collisions. At intermediate and high mass, there are significant contributions from charm and bottom, with a minor contribution from QGP thermal radiation. The region was utilized to measure cross sections of open charm and open bottom, as well as quarkonium suppression as demonstrated by PHENIX. An earlier PHENIX measurement of dielectron spectra in heavy ion collisions, using data taken in 2004, shows significant deviations from the hadronic decay expectations. The measurement, however, suffered from an unfavorable signal to background ratio. Random combination of electron-positron pairs from unrelated sources, mostly Dalitz decay of pi0 and external conversion of decay photon to electrons, is the main contributor to the background. Mis-identified hadrons are another major background source. To improve the situation, the Hadron Blind Detector (HBD), a windowless proximity focusing Cerenkov detector, is designed to reduce this background by identifying electron tracks from photon conversions and pi. 0 Dalitzdecays. The detector has been installed and operated in PHENIX in 2009 and 2010, where reference p+p and Au+Au data sets were successfully taken. We will present the dielectron results from the analysis of the Au+Au collisions, and compare the measured mass spectra to theoretical expectations.

Recombination in Enteroviruses Is a Biphasic Replicative Process Involving the Generation of Greater-than Genome Length ‘Imprecise’ Intermediates

PubMed Central

Lowry, Kym; Woodman, Andrew; Cook, Jonathan; Evans, David J.

2014-01-01

Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of ‘evolution by duplication’ in the positive-strand RNA viruses. PMID:24945141

Non-Radiative Carrier Recombination Enhanced by Two-Level Process: A First-Principles Study

NASA Astrophysics Data System (ADS)

Yang, Ji-Hui; Shi, Lin; Wang, Lin-Wang; Wei, Su-Huai

2016-02-01

Non-radiative recombination plays an important role in the performance of optoelectronic semiconductor devices such as solar cells and light-emitting diodes. Most textbook examples assume that the recombination process occurs through a single defect level, where one electron and one hole are captured and recombined. Based on this simple picture, conventional wisdom is that only defect levels near the center of the bandgap can be effective recombination centers. Here, we present a new two-level recombination mechanism: first, one type of carrier is captured through a defect level forming a metastable state; then the local defect configuration rapidly changes to a stable state, where the other type of carrier is captured and recombined through another defect level. This novel mechanism is applied to the recombination center in CdTe. We show that this two-level process can significantly increase the recombination rate (by three orders of magnitude) in agreement with experiments. We expect that this two-level recombination process can exist in a wide range of semiconductors, so its effect should be carefully examined in characterizing optoelectronic materials.

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

PubMed Central

Feulner, Philine G. D.; Johnston, Susan E.; Santure, Anna W.; Smadja, Carole M.

2017-01-01

Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109219

Statistical equilibrium calculations for silicon in early-type model stellar atmospheres

NASA Technical Reports Server (NTRS)

Kamp, L. W.

1976-01-01

Line profiles of 36 multiplets of silicon (Si) II, III, and IV were computed for a grid of model atmospheres covering the range from 15,000 to 35,000 K in effective temperature and 2.5 to 4.5 in log (gravity). The computations involved simultaneous solution of the steady-state statistical equilibrium equations for the populations and of the equation of radiative transfer in the lines. The variables were linearized, and successive corrections were computed until a minimal accuracy of 1/1000 in the line intensities was reached. The common assumption of local thermodynamic equilibrium (LTE) was dropped. The model atmospheres used also were computed by non-LTE methods. Some effects that were incorporated into the calculations were the depression of the continuum by free electrons, hydrogen and ionized helium line blocking, and auto-ionization and dielectronic recombination, which later were found to be insignificant. Use of radiation damping and detailed electron (quadratic Stark) damping constants had small but significant effects on the strong resonance lines of Si III and IV. For weak and intermediate-strength lines, large differences with respect to LTE computations, the results of which are also presented, were found in line shapes and strengths. For the strong lines the differences are generally small, except for the models at the hot, low-gravity extreme of our range. These computations should be useful in the interpretation of the spectra of stars in the spectral range B0-B5, luminosity classes III, IV, and V.

The XMM-Newton View of Stellar Coronae: High-Resolution X-Ray Spectroscopy of Capella

NASA Technical Reports Server (NTRS)

Audard, M.; Behar, E.; Guedel, M.; Raassen, A. J. J.; Porquet, D.; Mewe, R.; Foley, C. A.; Bromage, G. E.

2000-01-01

We present the high-resolution RGS spectrum of the bright stellar binary Capella observed by the XMM-Newton satellite. A multi-thermal approach has been applied to fit the data and derive elemental abundances. The differential emission measure distribution is reconstructed using a Chebychev polynomial fit. The DEM shape is found to display a sharp peak around 7 MK, consistent with previous EUVE and ASCA results. A small but significant amount of emission measure is required around 1.8 MK in order to explain the O VII He-like triplet and the C VI Ly(alpha) line. Using the sensitivity to temperature of dielectronic recombination lines from O VI around 22 A, we confirm that the cool plasma temperature needs to be higher than 1.2 MK. In the approximation of a cool plasma described by one temperature, we used line ratios from the forbidden, intercombination, and resonance lines of the O VII triplet and derived an average density for the cool coronal plasma at the low density limit. A tentative study of line ratios from the M XI triplet gives an average temperature close to the sharp peak in emission measure and an average density of the order of 10(exp 12)cu cm, three orders of magnitude higher than for O VII. Implications for the coronal physics of Capella are discussed. We complement this paper with a discussion of the importance of the atomic code uncertainties on the spectral fitting procedure.

Non-radiative carrier recombination enhanced by two-level process: A first-principles study

DOE PAGES

Yang, Ji -Hui; Shi, Lin; Wang, Lin -Wang; ...

2016-02-16

In this study, non-radiative recombination plays an important role in the performance of optoelectronic semiconductor devices such as solar cells and light-emitting diodes. Most textbook examples assume that the recombination process occurs through a single defect level, where one electron and one hole are captured and recombined. Based on this simple picture, conventional wisdom is that only defect levels near the center of the bandgap can be effective recombination centers. Here, we present a new two-level recombination mechanism: first, one type of carrier is captured through a defect level forming a metastable state; then the local defect configuration rapidly changesmore » to a stable state, where the other type of carrier is captured and recombined through another defect level. This novel mechanism is applied to the recombination center Te 2+ cd in CdTe. We show that this two-level process can significantly increase the recombination rate (by three orders of magnitude) in agreement with experiments. We expect that this two-level recombination process can exist in a wide range of semiconductors, so its effect should be carefully examined in characterizing optoelectronic materials.« less

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution.

PubMed

Mostowy, Rafal; Croucher, Nicholas J; Hanage, William P; Harris, Simon R; Bentley, Stephen; Fraser, Christophe

2014-05-01

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes.

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

PubMed Central

Hanage, William P.; Harris, Simon R.; Bentley, Stephen; Fraser, Christophe

2014-01-01

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes. PMID:24786281

Centrality and transverse momentum dependence of J/ψ production in Pb-Pb collisions at √SNN = 5.02 TeV at mid-rapidity with ALICE

NASA Astrophysics Data System (ADS)

Weiser, Dennis

2018-02-01

We present new results for the nuclear modification factor RAA of J/ψ mesons as a function of centrality and transverse momentum at mid-rapidity. The measurement is carried out with the ALICE central barrel detectors in the acceptance range |y| < 0.9 and pT > 0 in the dielectron decay channel.

The Accuracy of Molecular Processes

NASA Astrophysics Data System (ADS)

Stavans, Joel

Recombination is arguably one of the most fundamental mechanisms driving genetic diversity during evolution. Recombination takes place in one way or another from viruses such as HIV and polio, to bacteria, and finally to man. In both prokaryotes and eukaryotes, homologous recombination is assisted by enzymes, recombinases, that promote the exchange of strands between two segments of DNA, thereby creating new genetic combinations. In bacteria, homologous recombination takes place as a pathway for the repair of DNA lesions and also during horizontal or lateral gene transfer processes, in which cells take in exogenous pieces of DNA. This allows bacteria to evolve rapidly by acquiring large sequences of DNA, a process which would take too long by gene duplications and single mutations. I will survey recent results on the fidelity of homologous recombination as catalyzed by the bacterial recombinase RecA. These results show discrimination up to the level of single base mismatches, during the initial stages of the recombination process. A cascaded kinetic proofreading process is proposed to explain this high discrimination. Kinetic proofreading ideas are also reviewed.

Recombination, Pairing, and Synapsis of Homologs during Meiosis

PubMed Central

Zickler, Denise; Kleckner, Nancy

2015-01-01

Recombination is a prominent feature of meiosis in which it plays an important role in increasing genetic diversity during inheritance. Additionally, in most organisms, recombination also plays mechanical roles in chromosomal processes, most notably to mediate pairing of homologous chromosomes during prophase and, ultimately, to ensure regular segregation of homologous chromosomes when they separate at the first meiotic division. Recombinational interactions are also subject to important spatial patterning at both early and late stages. Recombination-mediated processes occur in physical and functional linkage with meiotic axial chromosome structure, with interplay in both directions, before, during, and after formation and dissolution of the synaptonemal complex (SC), a highly conserved meiosis-specific structure that links homolog axes along their lengths. These diverse processes also are integrated with recombination-independent interactions between homologous chromosomes, nonhomology-based chromosome couplings/clusterings, and diverse types of chromosome movement. This review provides an overview of these diverse processes and their interrelationships. PMID:25986558

Limit on the production of a low-mass vector boson in e+e- → Uγ, U →e+e- with the KLOE experiment

NASA Astrophysics Data System (ADS)

Anastasi, A.; Babusci, D.; Bencivenni, G.; Berlowski, M.; Bloise, C.; Bossi, F.; Branchini, P.; Budano, A.; Caldeira Balkeståhl, L.; Cao, B.; Ceradini, F.; Ciambrone, P.; Curciarello, F.; Czerwiński, E.; D'Agostini, G.; Danè, E.; De Leo, V.; De Lucia, E.; De Santis, A.; De Simone, P.; Di Cicco, A.; Di Domenico, A.; Di Salvo, R.; Domenici, D.; D'Uffizi, A.; Fantini, A.; Felici, G.; Fiore, S.; Gajos, A.; Gauzzi, P.; Giardina, G.; Giovannella, S.; Graziani, E.; Happacher, F.; Heijkenskjöld, L.; Ikegami Andersson, W.; Johansson, T.; Kamińska, D.; Krzemien, W.; Kupsc, A.; Loffredo, S.; Mandaglio, G.; Martini, M.; Mascolo, M.; Messi, R.; Miscetti, S.; Morello, G.; Moricciani, D.; Moskal, P.; Palladino, A.; Papenbrock, M.; Passeri, A.; Patera, V.; Perez del Rio, E.; Ranieri, A.; Santangelo, P.; Sarra, I.; Schioppa, M.; Silarski, M.; Sirghi, F.; Tortora, L.; Venanzoni, G.; Wiślicki, W.; Wolke, M.

2015-11-01

The existence of a new force beyond the Standard Model is compelling because it could explain several striking astrophysical observations which fail standard interpretations. We searched for the light vector mediator of this dark force, the U boson, with the KLOE detector at the DAΦNE e+e- collider. Using an integrated luminosity of 1.54 fb-1, we studied the process e+e- → Uγ, with U →e+e-, using radiative return to search for a resonant peak in the dielectron invariant-mass distribution. We did not find evidence for a signal, and set a 90% CL upper limit on the mixing strength between the Standard Model photon and the dark photon, ɛ2, at 10-6-10-4 in the 5- 520 MeV /c2 mass range.

Search for RS-gravitons at CDF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strologas, John; /New Mexico U.

2011-09-01

We present a search for Randall-Sundrum (RS) gravitons decaying to diphotons or dielectrons or dimuons, performed with the CDF II detector and using up to 5.7 fb{sup -1} of integrated luminosity. The respective mass spectra are consistent with the ones expected by the standard model. For the RS-model parameter k/{bar M}{sub Pl} = 0.1, RS-gravitons with mass less than 1111 GeV/c{sup 2} are excluded at 95% CL.

Measurement of forward-backward asymmetry A{sub FB} and of the weak mixing angle in processes of dilepton production in proton-proton collisions at {radical} s = 7 TeV in the CMS experiment at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorbunov, I. N., E-mail: Ilya.Gorbunov@cern.ch; Shmatov, S. V., E-mail: shmatov@cern.ch

2013-09-15

The results obtained by measuring the forward-backward asymmetry (A{sub FB}) of Drell-Yan lepton pairs in proton-proton collisions at {radical} s = 7 TeV at the LHC are presented. This asymmetry is measured as a function of the dilepton mass and rapidity in the dielectron and dimuon channels. The values of A{sub FB} were found for invariant masses of dileptons in the range of 40 Less-Than-Or-Slanted-Equal-To M{sub ll} Less-Than-Or-Slanted-Equal-To 600 GeV. The results for the effective weak mixing angle that were deduced from data on dimuon production in Drell-Yan processes are also presented. The respective data sample was collected by usingmore » the Compact Muon Solenoid (CMS) detector over the period spanning the years 2010 and 2011. The measured asymmetry and the effective weak mixing are consistent with the respective Standard Model predictions.« less

25th anniversary article: charge transport and recombination in polymer light-emitting diodes.

PubMed

Kuik, Martijn; Wetzelaer, Gert-Jan A H; Nicolai, Herman T; Craciun, N Irina; De Leeuw, Dago M; Blom, Paul W M

2014-01-01

This article reviews the basic physical processes of charge transport and recombination in organic semiconductors. As a workhorse, LEDs based on a single layer of poly(p-phenylene vinylene) (PPV) derivatives are used. The hole transport in these PPV derivatives is governed by trap-free space-charge-limited conduction, with the mobility depending on the electric field and charge-carrier density. These dependencies are generally described in the framework of hopping transport in a Gaussian density of states distribution. The electron transport on the other hand is orders of magnitude lower than the hole transport. The reason is that electron transport is hindered by the presence of a universal electron trap, located at 3.6 eV below vacuum with a typical density of ca. 3 × 10¹⁷ cm⁻³. The trapped electrons recombine with free holes via a non-radiative trap-assisted recombination process, which is a competing loss process with respect to the emissive bimolecular Langevin recombination. The trap-assisted recombination in disordered organic semiconductors is governed by the diffusion of the free carrier (hole) towards the trapped carrier (electron), similar to the Langevin recombination of free carriers where both carriers are mobile. As a result, with the charge-carrier mobilities and amount of trapping centers known from charge-transport measurements, the radiative recombination as well as loss processes in disordered organic semiconductors can be fully predicted. Evidently, future work should focus on the identification and removing of electron traps. This will not only eliminate the non-radiative trap-assisted recombination, but, in addition, will shift the recombination zone towards the center of the device, leading to an efficiency improvement of more than a factor of two in single-layer polymer LEDs. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

RPA homologs and ssDNA processing during meiotic recombination.

PubMed

Ribeiro, Jonathan; Abby, Emilie; Livera, Gabriel; Martini, Emmanuelle

2016-06-01

Meiotic homologous recombination is a specialized process that involves homologous chromosome pairing and strand exchange to guarantee proper chromosome segregation and genetic diversity. The formation and repair of DNA double-strand breaks (DSBs) during meiotic recombination differs from those during mitotic recombination in that the homologous chromosome rather than the sister chromatid is the preferred repair template. The processing of single-stranded DNA (ssDNA) formed on intermediate recombination structures is central to driving the specific outcomes of DSB repair during meiosis. Replication protein A (RPA) is the main ssDNA-binding protein complex involved in DNA metabolism. However, the existence of RPA orthologs in plants and the recent discovery of meiosis specific with OB domains (MEIOB), a widely conserved meiosis-specific RPA1 paralog, strongly suggest that multiple RPA complexes evolved and specialized to subdivide their roles during DNA metabolism. Here we review ssDNA formation and maturation during mitotic and meiotic recombination underlying the meiotic specific features. We describe and discuss the existence and properties of MEIOB and multiple RPA subunits in plants and highlight how they can provide meiosis-specific fates to ssDNA processing during homologous recombination. Understanding the functions of these RPA homologs and how they interact with the canonical RPA subunits is of major interest in the fields of meiosis and DNA repair.

Effect of sex, age, and breed on genetic recombination features in cattle

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is a fundamental biological process which generates genetic diversity, affects fertility, and influences evolvability. Here we investigate the roles of sex, age, and breed in cattle recombination features, including recombination rate, location and crossover interference. Usin...

Anomalous charge storage exponents of organic bulk heterojunction solar cells.

NASA Astrophysics Data System (ADS)

Nair, Pradeep; Dwivedi, Raaz; Kumar, Goutam; Dept of Electrical Engineering, IIT Bombay Team

2013-03-01

Organic bulk heterojunction (BHJ) devices are increasingly being researched for low cost solar energy conversion. The efficiency of such solar cells is dictated by various recombination processes involved. While it is well known that the ideality factor and hence the charge storage exponents of conventional PN junction diodes are influenced by the recombination processes, the same aspects are not so well understood for organic solar cells. While dark currents of such devices typically show an ideality factor of 1 (after correcting for shunt resistance effects, if any), surprisingly, a wide range of charge storage exponents for such devices are reported in literature alluding to apparent concentration dependence for bi-molecular recombination rates. In this manuscript we critically analyze the role of bi-molecular recombination processes on charge storage exponents of organic solar cells. Our results indicate that the charge storage exponents are fundamentally influenced by the electrostatics and recombination processes and can be correlated to the dark current ideality factors. We believe that our findings are novel, and advance the state-of the art understanding on various recombination processes that dictate the performance limits of organic solar cells. The authors would like to thank the Centre of Excellence in Nanoelectronics (CEN) and the National Centre for Photovoltaic Research and Education (NCPRE), IIT Bombay for computational and financial support

Recombinant protein production and insect cell culture and process

NASA Technical Reports Server (NTRS)

Spaulding, Glenn (Inventor); Prewett, Tacey (Inventor); Goodwin, Thomas (Inventor); Francis, Karen (Inventor); Andrews, Angela (Inventor); Oconnor, Kim (Inventor)

1993-01-01

A process has been developed for recombinant production of selected polypeptides using transformed insect cells cultured in a horizontally rotating culture vessel modulated to create low shear conditions. A metabolically transformed insect cell line is produced using the culture procedure regardless of genetic transformation. The recombinant polypeptide can be produced by an alternative process using the cultured insect cells as host for a virus encoding the described polypeptide such as baculovirus. The insect cells can also be a host for viral production.

Recombinant Protein Production and Insect Cell Culture and Process

NASA Technical Reports Server (NTRS)

Spaulding, Glenn F. (Inventor); Goodwin, Thomas J. (Inventor); OConnor, Kim C. (Inventor); Francis, Karen M. (Inventor); Andrews, Angela D. (Inventor); Prewett, Tracey L. (Inventor)

1997-01-01

A process has been developed for recombinant production of selected polypeptides using transformed insect cells cultured in a horizontally rotating culture vessel modulated to create low shear conditions. A metabolically transformed insect cell line is produced using the culture procedure regardless of genetic transformation. The recombinant polypeptide can be produced by an alternative process using virtually infected or stably transformed insect cells containing a gene encoding the described polypeptide. The insect cells can also be a host for viral production.

Recombinant microorganisms for increased production of organic acids

DOEpatents

Yi, Jian [East Lansing, MI; Kleff, Susanne [East Lansing, MI; Guettler, Michael V [Holt, MI

2012-02-21

Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

Recombinant microorganisms for increased production of organic acids

DOEpatents

Yi, Jian; Kleff, Susanne; Guettler, Michael V

2013-04-30

Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

Break-induced replication and recombinational telomere elongation in yeast.

PubMed

McEachern, Michael J; Haber, James E

2006-01-01

When a telomere becomes unprotected or if only one end of a chromosomal double-strand break succeeds in recombining with a template sequence, DNA can be repaired by a recombination-dependent DNA replication process termed break-induced replication (BIR). In budding yeasts, there are two BIR pathways, one dependent on the Rad51 recombinase protein and one Rad51 independent; these two repair processes lead to different types of survivors in cells lacking the telomerase enzyme that is required for normal telomere maintenance. Recombination at telomeres is triggered by either excessive telomere shortening or disruptions in the function of telomere-binding proteins. Telomere elongation by BIR appears to often occur through a "roll and spread" mechanism. In this process, a telomeric circle produced by recombination at a dysfunctional telomere acts as a template for a rolling circle BIR event to form an elongated telomere. Additional BIR events can then copy the elongated sequence to all other telomeres.

Detection of an unidentified emission line in the stacked X-ray spectrum of galaxy clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bulbul, Esra; Foster, Adam; Smith, Randall K.

2014-07-01

We detect a weak unidentified emission line at E = (3.55-3.57) ± 0.03 keV in a stacked XMM-Newton spectrum of 73 galaxy clusters spanning a redshift range 0.01-0.35. When the full sample is divided into three subsamples (Perseus, Centaurus+Ophiuchus+Coma, and all others), the line is seen at >3σ statistical significance in all three independent MOS spectra and the PN 'all others' spectrum. It is also detected in the Chandra spectra of the Perseus Cluster. However, it is very weak and located within 50-110 eV of several known lines. The detection is at the limit of the current instrument capabilities. Wemore » argue that there should be no atomic transitions in thermal plasma at this energy. An intriguing possibility is the decay of sterile neutrino, a long-sought dark matter particle candidate. Assuming that all dark matter is in sterile neutrinos with m{sub s} = 2E = 7.1 keV, our detection corresponds to a neutrino decay rate consistent with previous upper limits. However, based on the cluster masses and distances, the line in Perseus is much brighter than expected in this model, significantly deviating from other subsamples. This appears to be because of an anomalously bright line at E = 3.62 keV in Perseus, which could be an Ar XVII dielectronic recombination line, although its emissivity would have to be 30 times the expected value and physically difficult to understand. Another alternative is the above anomaly in the Ar line combined with the nearby 3.51 keV K line also exceeding expectation by a factor of 10-20. Confirmation with Astro-H will be critical to determine the nature of this new line.« less

Progressive Recombination Suppression and Differentiation in Recently Evolved Neo-sex Chromosomes

PubMed Central

Natri, Heini M.; Shikano, Takahito; Merilä, Juha

2013-01-01

Recombination suppression leads to the structural and functional differentiation of sex chromosomes and is thus a crucial step in the process of sex chromosome evolution. Despite extensive theoretical work, the exact processes and mechanisms of recombination suppression and differentiation are not well understood. In threespine sticklebacks (Gasterosteus aculeatus), a different sex chromosome system has recently evolved by a fusion between the Y chromosome and an autosome in the Japan Sea lineage, which diverged from the ancestor of other lineages approximately 2 Ma. We investigated the evolutionary dynamics and differentiation processes of sex chromosomes based on comparative analyses of these divergent lineages using 63 microsatellite loci. Both chromosome-wide differentiation patterns and phylogenetic inferences with X and Y alleles indicated that the ancestral sex chromosomes were extensively differentiated before the divergence of these lineages. In contrast, genetic differentiation appeared to have proceeded only in a small region of the neo-sex chromosomes. The recombination maps constructed for the Japan Sea lineage indicated that recombination has been suppressed or reduced over a large region spanning the ancestral and neo-sex chromosomes. Chromosomal regions exhibiting genetic differentiation and suppressed or reduced recombination were detected continuously and sequentially in the neo-sex chromosomes, suggesting that differentiation has gradually spread from the fusion point following the extension of recombination suppression. Our study illustrates an ongoing process of sex chromosome differentiation, providing empirical support for the theoretical model postulating that recombination suppression and differentiation proceed in a gradual manner in the very early stage of sex chromosome evolution. PMID:23436913

Search for Excited or Exotic Electron Production Using the Dielectron + Photon Signature at CDF in Run II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerberich, Heather Kay

The author presents a search for excited or exotic electrons decaying to an electron and a photon with high transverse momentum. An oppositely charged electron is produced in association with the excited electron, yielding a final state dielectron + photon signature. The discovery of excited electrons would be a first indication of lepton compositeness. They use ~ 202 pb -1 of data collected in pmore » $$\\bar{p}$$ collisions at √s = 1.96 TeV with the Collider Detector at Fermilab during March 2001 through September 2003. The data are consistent with standard model expectations. Upper limits are set on the experimental cross-section σ($$\\bar{p}$$p → ee* → eeγ) at the 95% confidence level in a contact-interaction model and a gauge-mediated interaction model. Limits are also presented as exclusion regions in the parameter space of the excited electron mass (M e*) and the compositeness energy scale (Λ). In the contact-interaction model, for which there are no previously published limits, they find M e* < 906 GeV is excluded for M e* = Λ. In the gauge-mediated model, the exclusion region in the M e* versus the phenomenological coupling f/Λ parameter space is extended to M{sub e*} < 430 GeV for f/Λ ~ 10 -2 GeV -1. In comparison, other experiments have excluded M e* < 280 GeV for f/Λ ~ 10 -2 GeV -1.« less

Properties of laser-produced GaAs plasmas measured from highly resolved X-ray line shapes and ratios

NASA Astrophysics Data System (ADS)

Seely, J. F.; Fein, J.; Manuel, M.; Keiter, P.; Drake, P.; Kuranz, C.; Belancourt, Patrick; Ralchenko, Yu.; Hudson, L.; Feldman, U.

2018-03-01

The properties of hot, dense plasmas generated by the irradiation of GaAs targets by the Titan laser at Lawrence Livermore National Laboratory were determined by the analysis of high resolution K shell spectra in the 9 keV to 11 keV range. The laser parameters, such as relatively long pulse duration and large focal spot, were chosen to produce a steady-state plasma with minimal edge gradients, and the time-integrated spectra were compared to non-LTE steady state spectrum simulations using the FLYCHK and NOMAD codes. The bulk plasma streaming velocity was measured from the energy shifts of the Ga He-like transitions and Li-like dielectronic satellites. The electron density and the electron energy distribution, both the thermal and the hot non-thermal components, were determined from the spectral line ratios. After accounting for the spectral line broadening contributions, the plasma turbulent motion was measured from the residual line widths. The ionization balance was determined from the ratios of the He-like through F-like spectral features. The detailed comparison of the experimental Ga spectrum and the spectrum simulated by the FLYCHK code indicates two significant discrepancies, the transition energy of a Li-like dielectronic satellite (designated t) and the calculated intensity of a He-like line (x), that should lead to improvements in the kinetics codes used to simulate the X-ray spectra from highly-charged ions.

Better understanding of homologous recombination through a 12-week laboratory course for undergraduates majoring in biotechnology.

PubMed

Li, Ming; Shen, Xiaodong; Zhao, Yan; Hu, Xiaomei; Hu, Fuquan; Rao, Xiancai

2017-07-08

Homologous recombination, a central concept in biology, is defined as the exchange of DNA strands between two similar or identical nucleotide sequences. Unfortunately, undergraduate students majoring in biotechnology often experience difficulties in understanding the molecular basis of homologous recombination. In this study, we developed and implemented a 12-week laboratory course for biotechnology undergraduates in which gene targeting in Streptococcus suis was used to facilitate their understanding of the basic concept and process of homologous recombination. Students worked in teams of two to select a gene of interest to create a knockout mutant using methods that relied on homologous recombination. By integrating abstract knowledge and practice in the process of scientific research, students gained hands-on experience in molecular biology techniques while learning about the principle and process of homologous recombination. The learning outcomes and survey-based assessment demonstrated that students substantially enhanced their understanding of how homologous recombination could be used to study gene function. Overall, the course was very effective for helping biotechnology undergraduates learn the theory and application of homologous recombination, while also yielding positive effects in developing confidence and scientific skills for future work in research. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):329-335, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Homologous Recombination—Experimental Systems, Analysis and Significance

PubMed Central

Kuzminov, Andrei

2014-01-01

Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in E. coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange) and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role, and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy. PMID:26442506

Recombination Processes on Low Bandgap Antimonides for Thermophotovoltaic Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saroop, Sudesh

1999-09-01

Recombination processes in antimonide-based (TPV) devices have been investigated using a technique, in which a Nd-YAG pulsed laser is materials for thermophotovoltaic radio-frequency (RF) photoreflectance used to excite excess carriers and the short-pulse response and photoconductivity decay are monitored with an inductively-coupled non-contacting RF probe. The system has been used to characterize surface and bulk recombination mechanisms in Sb-based materials.

Exciton-dominant Electroluminescence from a Diode of Monolayer MoS2

DTIC Science & Technology

2014-05-14

caused by a phonon-assisted nonradiative process, as the two peaks display different current dependencies. We pro- pose this is a different effect...monolayer MoS2. The Auger process opens up a nonradiative recombination channel for electron-hole pair recombination. If the Auger process is

The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis

PubMed Central

Hong, Ye; Sonneville, Remi; Agostinho, Ana; Meier, Bettina; Wang, Bin; Blow, J. Julian; Gartner, Anton

2016-01-01

Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis. PMID:27010650

The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis.

PubMed

Hong, Ye; Sonneville, Remi; Agostinho, Ana; Meier, Bettina; Wang, Bin; Blow, J Julian; Gartner, Anton

2016-03-01

Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.

Search for large extra dimensions in dielectron and diphoton production.

PubMed

Abbott, B; Abolins, M; Abramov, V; Acharya, B S; Adams, D L; Adams, M; Alves, G A; Amos, N; Anderson, E W; Baarmand, M M; Babintsev, V V; Babukhadia, L; Baden, A; Baldin, B; Balm, P W; Banerjee, S; Bantly, J; Barberis, E; Baringer, P; Bartlett, J F; Bassler, U; Bean, A; Begel, M; Belyaev, A; Beri, S B; Bernardi, G; Bertram, I; Besson, A; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Bhattacharjee, M; Blazey, G; Blessing, S; Boehnlein, A; Bojko, N I; Borcherding, F; Brandt, A; Breedon, R; Briskin, G; Brock, R; Brooijmans, G; Bross, A; Buchholz, D; Buehler, M; Buescher, V; Burtovoi, V S; Butler, J M; Canelli, F; Carvalho, W; Casey, D; Casilum, Z; Castilla-Valdez, H; Chakraborty, D; Chan, K M; Chekulaev, S V; Cho, D K; Choi, S; Chopra, S; Christenson, J H; Chung, M; Claes, D; Clark, A R; Cochran, J; Coney, L; Connolly, B; Cooper, W E; Coppage, D; Cummings, M A; Cutts, D; Dahl, O I; Davis, G A; Davis, K; De, K; Del Signore, K; Demarteau, M; Demina, R; Demine, P; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Di Loreto, G; Doulas, S; Draper, P; Ducros, Y; Dudko, L V; Duensing, S; Dugad, S R; Dyshkant, A; Edmunds, D; Ellison, J; Elvira, V D; Engelmann, R; Eno, S; Eppley, G; Ermolov, P; Eroshin, O V; Estrada, J; Evans, H; Evdokimov, V N; Fahland, T; Feher, S; Fein, D; Ferbel, T; Fisk, H E; Fisyak, Y; Flattum, E; Fleuret, F; Fortner, M; Frame, K C; Fuess, S; Gallas, E; Galyaev, A N; Gartung, P; Gavrilov, V; Genik, R J; Genser, K; Gerber, C E; Gershtein, Y; Gibbard, B; Gilmartin, R; Ginther, G; Gómez, B; Gómez, G; Goncharov, P I; González Solís, J L; Gordon, H; Goss, L T; Gounder, K; Goussiou, A; Graf, N; Graham, G; Grannis, P D; Green, J A; Greenlee, H; Grinstein, S; Groer, L; Grudberg, P; Grünendahl, S; Gupta, A; Gurzhiev, S N; Gutierrez, G; Gutierrez, P; Hadley, N J; Haggerty, H; Hagopian, S; Hagopian, V; Hahn, K S; Hall, R E; Hanlet, P; Hansen, S; Hauptman, J M; Hays, C; Hebert, C; Hedin, D; Heinson, A P; Heintz, U; Heuring, T; Hirosky, R; Hobbs, J D; Hoeneisen, B; Hoftun, J S; Hou, S; Huang, Y; Ito, A S; Jerger, S A; Jesik, R; Johns, K; Johnson, M; Jonckheere, A; Jones, M; Jöstlein, H; Juste, A; Kahn, S; Kajfasz, E; Karmanov, D; Karmgard, D; Kehoe, R; Kim, S K; Klima, B; Klopfenstein, C; Knuteson, B; Ko, W; Kohli, J M; Kostritskiy, A V; Kotcher, J; Kotwal, A V; Kozelov, A V; Kozlovsky, E A; Krane, J; Krishnaswamy, M R; Krzywdzinski, S; Kubantsev, M; Kuleshov, S; Kulik, Y; Kunori, S; Kuznetsov, V E; Landsberg, G; Leflat, A; Lehner, F; Li, J; Li, Q Z; Lima, J G; Lincoln, D; Linn, S L; Linnemann, J; Lipton, R; Lucotte, A; Lueking, L; Lundstedt, C; Maciel, A K; Madaras, R J; Manankov, V; Mao, H S; Marshall, T; Martin, M I; Martin, R D; Mauritz, K M; May, B; Mayorov, A A; McCarthy, R; McDonald, J; McMahon, T; Melanson, H L; Meng, X C; Merkin, M; Merritt, K W; Miao, C; Miettinen, H; Mihalcea, D; Mincer, A; Mishra, C S; Mokhov, N; Mondal, N K; Montgomery, H E; Moore, R W; Mostafa, M; da Motta, H; Nagy, E; Nang, F; Narain, M; Narasimham, V S; Neal, H A; Negret, J P; Negroni, S; Norman, D; Oesch, L; Oguri, V; Olivier, B; Oshima, N; Padley, P; Pan, L J; Para, A; Parashar, N; Partridge, R; Parua, N; Paterno, M; Patwa, A; Pawlik, B; Perkins, J; Peters, M; Peters, O; Piegaia, R; Piekarz, H; Pope, B G; Popkov, E; Prosper, H B; Protopopescu, S; Qian, J; Quintas, P Z; Raja, R; Rajagopalan, S; Ramberg, E; Rapidis, P A; Reay, N W; Reucroft, S; Rha, J; Rijssenbeek, M; Rockwell, T; Roco, M; Rubinov, P; Ruchti, R; Rutherfoord, J; Santoro, A; Sawyer, L; Schamberger, R D; Schellman, H; Schwartzman, A; Sculli, J; Sen, N; Shabalina, E; Shankar, H C; Shivpuri, R K; Shpakov, D; Shupe, M; Sidwell, R A; Simak, V; Singh, H; Singh, J B; Sirotenko, V; Slattery, P; Smith, E; Smith, R P; Snihur, R; Snow, G R; Snow, J; Snyder, S; Solomon, J; Sorín, V; Sosebee, M; Sotnikova, N; Soustruznik, K; Souza, M; Stanton, N R; Steinbrück, G; Stephens, R W; Stevenson, M L; Stichelbaut, F; Stoker, D; Stolin, V; Stoyanova, D A; Strauss, M; Streets, K; Strovink, M; Stutte, L; Sznajder, A; Taylor, W; Tentindo-Repond, S; Thompson, J; Toback, D; Tripathi, S M; Trippe, T G; Turcot, A S; Tuts, P M; van Gemmeren, P; Vaniev, V; Van Kooten, R; Varelas, N; Volkov, A A; Vorobiev, A P; Wahl, H D; Wang, H; Wang, Z; Warchol, J; Watts, G; Wayne, M; Weerts, H; White, A; White, J T; Whiteson, D; Wightman, J A; Wijngaarden, D A; Willis, S; Wimpenny, S J; Wirjawan, J V; Womersley, J; Wood, D R; Yamada, R; Yamin, P; Yasuda, T; Yip, K; Youssef, S; Yu, J; Yu, Z; Zanabria, M; Zheng, H; Zhou, Z; Zhu, Z H; Zielinski, M; Zieminska, D; Zieminski, A; Zutshi, V; Zverev, E G; Zylberstejn, A

2001-02-12

We report a search for effects of large extra spatial dimensions in pp collisions at a center-of-mass energy of 1.8 TeV with the D0 detector, using events containing a pair of electrons or photons. The data are in good agreement with the expected background and do not exhibit evidence for large extra dimensions. We set the most restrictive lower limits to date, at the 95% C.L. on the effective Planck scale between 1.0 and 1.4 TeV for several formalisms and numbers of extra dimensions.

Evaluation of the effectiveness and safety of the thermo-treatment process to dispose of recombinant DNA waste from biological research laboratories.

PubMed

Li, Meng-Nan; Zheng, Guang-Hong; Wang, Lei; Xiao, Wei; Fu, Xiao-Hua; Le, Yi-Quan; Ren, Da-Ming

2009-01-01

The discharge of recombinant DNA waste from biological laboratories into the eco-system may be one of the pathways resulting in horizontal gene transfer or "gene pollution". Heating at 100 degrees C for 5-10 min is a common method for treating recombinant DNA waste in biological research laboratories in China. In this study, we evaluated the effectiveness and the safety of the thermo-treatment method in the disposal of recombinant DNA waste. Quantitative PCR, plasmid transformation and electrophoresis technology were used to evaluate the decay/denaturation efficiency during the thermo-treatment process of recombinant plasmid, pET-28b. Results showed that prolonging thermo-treatment time could improve decay efficiency of the plasmid, and its decay half-life was 2.7-4.0 min during the thermo-treatment at 100 degrees C. However, after 30 min of thermo-treatment some transforming activity remained. Higher ionic strength could protect recombinant plasmid from decay during the treatment process. These results indicate that thermo-treatment at 100 degrees C cannot decay and inactivate pET-28b completely. In addition, preliminary results showed that thermo-treated recombinant plasmids were not degraded completely in a short period when they were discharged into an aquatic environment. This implies that when thermo-treated recombinant DNAs are discharged into the eco-system, they may have enough time to re-nature and transform, thus resulting in gene diffusion.

Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination.

PubMed

Woodman, Andrew; Arnold, Jamie J; Cameron, Craig E; Evans, David J

2016-08-19

Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3' non-coding region we have further developed a cell-based assay (the 3'CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genetic recombination of the hepatitis C virus: clinical implications.

PubMed

Morel, V; Fournier, C; François, C; Brochot, E; Helle, F; Duverlie, G; Castelain, S

2011-02-01

Genetic recombination is a well-known feature of RNA viruses that plays a significant role in their evolution. Although recombination is well documented for Flaviviridae family viruses, the first natural recombinant strain of hepatitis C virus (HCV) was identified as recently as 2002. Since then, a few other natural inter-genotypic, intra-genotypic and intra-subtype recombinant HCV strains have been described. However, the frequency of recombination may have been underestimated because not all known HCV recombinants are screened for in routine practice. Furthermore, the choice of treatment regimen and its predictive outcome remain problematic as the therapeutic strategy for HCV infection is genotype dependent. HCV recombination also raises many questions concerning its mechanisms and effects on the epidemiological and physiopathological features of the virus. This review provides an update on recombinant HCV strains, the process that gives rise to recombinants and clinical implications of recombination. © 2010 Blackwell Publishing Ltd.

The Development of Novel Recombinant Human Gelatins as Replacements for Animal-Derived Gelatin in Pharmaceutical Applications

NASA Astrophysics Data System (ADS)

Olsen, David; Chang, Robert; Williams, Kim E.; Polarek, James W.

We have developed a recombinant expression system to produce a series of novel recombinant human gelatins that can substitute for animal sourced gelatin preparations currently used in pharmaceutical and nutraceutical applications. This system allows the production of human sequence gelatins, or, if desired, gelatins from any other species depending on the availability of the cloned gene. The gelatins produced with this recombinant system are of defined molecular weight, unlike the animal-sourced gelatins, which consist of numerous polypeptides of varying size. The fermentation and purification process used to prepare these recombinant gelatins does not use any human- or animal-derived components and thus this recombinant material should be free from viruses and agents that cause transmissible spongiform encephalopathies. The recombinant gelatins exhibit lot-to-lot reproducibility and we have performed extensive analytical testing on them. We have demonstrated the utility of these novel gelatins as biological stabilizers and plasma expanders, and we have shown they possess qualities that are important in applications where gel formation is critical. Finally, we provide examples of how our system allows the engineering of these recombinant gelatins to optimize the production process.

Photocharge accumulation and recombination in perovskite solar cells regarding device performance and stability

NASA Astrophysics Data System (ADS)

Li, Yusheng; Li, Yiming; Shi, Jiangjian; Li, Hongshi; Zhang, Huiyin; Wu, Jionghua; Li, Dongmei; Luo, Yanhong; Wu, Huijue; Meng, Qingbo

2018-01-01

Photocharge accumulation and recombination in perovskite solar cells have been systematically investigated in this paper by electrochemical spectroscopy and transient photocurrent/photovoltage methods. It is found that the non-equilibrium photocharges stored in the selective charge transport layers follow a backward recombination mechanism. That is, the photocharges are first captured by the interface defects corresponding to the fast photovoltage decay, while the bulk charge recombination instead of the diffusion process dominates the slow photovoltage decay process. Further investigation reveals that the device degradation preferentially takes place at the interface under working conditions, which thus can confirm the importance of interface engineering to enhance the device stability.

DNA polymorphism in recombining and non-recombing mating-type-specific loci of the smut fungus Microbotryum

PubMed Central

Votintseva, A A; Filatov, D A

2011-01-01

The population-genetic processes leading to the genetic degeneration of non-recombining regions have mainly been studied in animal and plant sex chromosomes. Here, we report population genetic analysis of the processes in the non-recombining mating-type-specific regions of the smut fungus Microbotryum violaceum. M. violaceum has A1 and A2 mating types, determined by mating-type-specific ‘sex chromosomes' that contain 1–2 Mb long non-recombining regions. If genetic degeneration were occurring, then one would expect reduced DNA polymorphism in the non-recombining regions of this fungus. The analysis of DNA diversity among 19 M. violaceum strains, collected across Europe from Silene latifolia flowers, revealed that (i) DNA polymorphism is relatively low in all 20 studied loci (π∼0.15%), (ii) it is not significantly different between the two mating-type-specific chromosomes nor between the non-recombining and recombining regions, (iii) there is substantial population structure in M. violaceum populations, which resembles that of its host species, S. latifolia, and (iv) there is significant linkage disequilibrium, suggesting that widespread selfing in this species results in a reduction of the effective recombination rate across the genome. We hypothesise that selfing-related reduction of recombination across the M. violaceum genome negates the difference in the level of DNA polymorphism between the recombining and non-recombining regions, and may possibly lead to similar levels of genetic degeneration in the mating-type-specific regions of the non-recombining ‘sex chromosomes' and elsewhere in the genome. PMID:21081967

A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

PubMed Central

Fritsch, Emilie S.; Chabbert, Christophe D.; Klaus, Bernd; Steinmetz, Lars M.

2014-01-01

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome maintenance. PMID:25081569

A genome-wide map of mitochondrial DNA recombination in yeast.

PubMed

Fritsch, Emilie S; Chabbert, Christophe D; Klaus, Bernd; Steinmetz, Lars M

2014-10-01

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome maintenance. Copyright © 2014 by the Genetics Society of America.

Novel strategy for phenyllactic acid biosynthesis from phenylalanine by whole cell recombinant Escherichia coli coexpressing L-phenylalanine oxidase and L-lactate dehydrogenase.

PubMed

Zhang, Jianzhi; Li, Xi

2018-01-01

To enhance the efficiency of phenyllactic acid (PLA) production from L-phenylalanine (L-Phe) by introducing a novel artificial pathway into Escherichia coli RESULTS: The production of PLA from L-Phe by recombinant E. coli (ldh-lpox) coexpressing L-phenylalanine oxidase and L-lactate dehydrogenase was studied. The new PLA synthesis pathway was confirmed to be efficient in recombinant E. coli. Subsequently, two different biocatalyst processes were carried out and optimized for PLA production. In the whole cell biosynthesis process at high cell density using collected recombinant cells as catalyst, at optimal conditions (L-Phe 6 g/l, pH 7.5, 35 °C, CDW 24.5 g/l and 200 rpm), the recombinant E. coli (ldh-lpox) produced 1.62 g PLA/l with a conversion of 28% from L-Phe. Similarly, during the two-temperature-stage fermentation process in flasks using IPTG-induced cells, the temperature in the second stage was increased to 35 °C to benefit the biocatalyst process, and comparable phenyllactic acid production of 1.47 g/l was obtained from 12 g L-Phe/l. Recombinant E. coli (ldh-lpox) was efficient in PLA production realizing a high titer of several folds compared with studies using L-Phe as substrate.

Mitochondrial genetics in Bakers' yeast: a molecular mechanism for recombinational polarity and suppressiveness.

PubMed

Perlman, P S; Birky, C W

1974-11-01

Recombinational polarity and suppressiveness are two well-known but puzzling cytoplasmic genetic phenomena in bakers' yeast, Saccharomyces cerevisiae. Little progress has been made in characterizing the underlying molecular mechanisms of these phenomena. In this paper we describe a molecular model for recombinational polarity that is compatible with the available genetic evidence. The model stresses the role of small deletions and excision/repair processes in otherwise canonical recombinational events. According to the model, both phenomena require recombination and may share mechanistic elements.

An active recombinant cocoonase from the silkworm Bombyx mori: bleaching, degumming and sericin degrading activities.

PubMed

Unajak, Sasimanas; Aroonluke, Suradet; Promboon, Amornrat

2015-04-01

Cocoonase is a serine protease produced by silk moths and used for softening the cocoons so that they can escape. Degumming is one of the important steps in silk processing. This research aimed to produce an active recombinant Bombyx mori cocoonase (BmCoc) for the silk degumming process. A recombinant BmCoc was successfully expressed in a Pichia pastoris system. The purified enzyme showed specific activity of 227 U mg(-1) protein, 2.4-fold purification, 95% yield and a molecular weight of 26 kDa. The enzyme exhibited optimal temperature at 40 °C and optimal pH at 8, and showed thermal stability at 25-45 °C and pH stability at 5-9. The recombinant enzyme exhibited sericin degumming ability and color bleaching characteristics, and did not affect the fibroin fiber. The enzyme also degraded sericin substrate with a product size about 30-70 kDa. In this study, we successfully produced the active recombinant BmCoc in P. pastoris with promising functions for the Thai silk degumming process, which includes degumming, sericin degrading and color bleaching activities. Our data clearly indicated that the recombinant enzyme had proteolytic activity on sericin but not on fibroin proteins. The recombinant BmCoc has proven to be suitable for numerous applications in the silk industry. © 2014 Society of Chemical Industry.

Biochemistry of homologous recombination in Escherichia coli.

PubMed Central

Kowalczykowski, S C; Dixon, D A; Eggleston, A K; Lauder, S D; Rehrauer, W M

1994-01-01

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination. Images PMID:7968921

Recombination phenomena in high efficiency silicon solar cells

NASA Technical Reports Server (NTRS)

Sah, C. T.

1985-01-01

The dominant recombination phenomena which limit the highest efficiency attainable in silicon solar cells under terrestrial sunlight are reviewed. The ultimate achievable efficiency is limited by the two intrinsic recombination mechanisms, the interband Auger recombination and interband Radiative recombination, both of which occur in the entire cell body but principally in the base layer. It is suggested that an optimum (26%) cell design is one with lowly doped 50 to 100 micron thick base, a perfect BSF, and zero extrinsic recombination such as the thermal mechanism at recombination centers the Shockley-Read-Hall process (SRH) in the bulk, on the surface and at the interfaces. The importance of recombination at the interfaces of a high-efficiency cell is demonstrated by the ohmic contact on the back surface whose interface recombination velocity is infinite. The importance of surface and interface recombination is demonstrated by representing the auger and radiative recombination losses by effective recombination velocities. It is demonstrated that the three highest efficiency cells may all be limited by the SRH recombination losses at recombination centers in the base layer.

Gene and process level modulation to overcome the bottlenecks of recombinant proteins expression in Pichia pastoris.

PubMed

Prabhu, Ashish A; Boro, Bibari; Bharali, Biju; Chakraborty, Shuchishloka; Dasu, Veeranki V

2017-01-01

Process development involving system metabolic engineering and bioprocess engineering has become one of the major thrust for the development of therapeutic proteins or enzymes. Pichia pastoris has emerged as a prominent host for the production of therapeutic protein or enzymes. Regardless of producing high protein titers, various cellular and process level bottlenecks restrict the expression of recombinant proteins in P. pastoris. In the present review, we have summarized the recent developments in the expression of foreign proteins in P. pastoris. Further, we have discussed various cellular engineering strategies which include codon optimization, pathway engineering, signal peptide processing, development of protease deficient strain and glyco-engineered strains for the high yield protein secretion of recombinant protein. Bioprocess development of recombinant proteins in large-scale bioreactor including medium optimization, optimum feeding strategy and co-substrate feeding in fed-batch as well as continuous cultivation have been described. The recent advances in system and synthetic biology studies including metabolic flux analysis in understanding the phenotypic characteristics of recombinant Pichia and genome editing with CRISPR-CAS system have also been summarized. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Large-scale chromatin remodeling at the immunoglobulin heavy chain locus: a paradigm for multigene regulation.

PubMed

Bolland, Daniel J; Wood, Andrew L; Corcoran, Anne E

2009-01-01

V(D)J recombination in lymphocytes is the cutting and pasting together of antigen receptor genes in cis to generate the enormous variety of coding sequences required to produce diverse antigen receptor proteins. It is the key role of the adaptive immune response, which must potentially combat millions of different foreign antigens. Most antigen receptor loci have evolved to be extremely large and contain multiple individual V, D and J genes. The immunoglobulin heavy chain (Igh) and immunoglobulin kappa light chain (Igk) loci are the largest multigene loci in the mammalian genome and V(D)J recombination is one of the most complicated genetic processes in the nucleus. The challenge for the appropriate lymphocyte is one of macro-management-to make all of the antigen receptor genes in a particular locus available for recombination at the appropriate developmental time-point. Conversely, these large loci must be kept closed in lymphocytes in which they do not normally recombine, to guard against genomic instability generated by the DNA double strand breaks inherent to the V(D)J recombination process. To manage all of these demanding criteria, V(D)J recombination is regulated at numerous levels. It is restricted to lymphocytes since the Rag genes which control the DNA double-strand break step of recombination are only expressed in these cells. Within the lymphocyte lineage, immunoglobulin recombination is restricted to B-lymphocytes and TCR recombination to T-lymphocytes by regulation of locus accessibility, which occurs at multiple levels. Accessibility of recombination signal sequences (RSSs) flanking individual V, D and J genes at the nucleosomal level is the key micro-management mechanism, which is discussed in greater detail in other chapters. This chapter will explore how the antigen receptor loci are regulated as a whole, focussing on the Igh locus as a paradigm for the mechanisms involved. Numerous recent studies have begun to unravel the complex and complementary processes involved in this large-scale locus organisation. We will examine the structure of the Igh locus and the large-scale and higher-order chromatin remodelling processes associated with V(D)J recombination, at the level of the locus itself, its conformational changes and its dynamic localisation within the nucleus.

Recombination Promoted by DNA Viruses: Phage λ to Herpes Simplex Virus

PubMed Central

Weller, Sandra K.; Sawitzke, James A.

2015-01-01

The purpose of this review is to explore recombination strategies in DNA viruses. Homologous recombination is a universal genetic process that plays multiple roles in the biology of all organisms, including viruses. Recombination and DNA replication are interconnected, with recombination being essential for repairing DNA damage and supporting replication of the viral genome. Recombination also creates genetic diversity, and viral recombination mechanisms have important implications for understanding viral origins as well as the dynamic nature of viral-host interactions. Both bacteriophage λ and herpes simplex virus (HSV) display high rates of recombination, both utilizing their own proteins and commandeering cellular proteins to promote recombination reactions. We focus primarily on λ and HSV, as they have proven amenable to both genetic and biochemical analysis and have recently been shown to exhibit some surprising similarities that will guide future studies. PMID:25002096

Detecting and Analyzing Genetic Recombination Using RDP4.

PubMed

Martin, Darren P; Murrell, Ben; Khoosal, Arjun; Muhire, Brejnev

2017-01-01

Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. The evolutionary value of recombination has been widely debated and so too has its influence on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. When nucleic acids recombine, the evolution of the daughter or recombinant molecule cannot be accurately described by a single phylogeny. This simple fact can seriously undermine the accuracy of any phylogenetics-based analytical approach which assumes that the evolutionary history of a set of recombining sequences can be adequately described by a single phylogenetic tree. There are presently a large number of available methods and associated computer programs for analyzing and characterizing recombination in various classes of nucleotide sequence datasets. Here we examine the use of some of these methods to derive and test recombination hypotheses using multiple sequence alignments.

Measurements of differential and double-differential Drell–Yan cross sections in proton–proton collisions at √s = 8 TeV

DOE PAGES

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; ...

2015-04-09

Measurements of the differential and double-differential Drell–Yan cross sections in the dielectron and dimuon channels are presented. They are based on proton–proton collision data at √s = 8TeV recorded with the CMS detector at the LHC and corresponding to an integrated luminosity of 19.7fb –1. The measured inclusive cross section in the Z peak region (60–120GeV), obtained from the combination of the dielectron and dimuon channels, is 1138 ± 8 (exp) ± 25 (theo) ± 30 (lumi)\\,pb, where the statistical uncertainty is negligible. The differential cross section dσ/dm in the dilepton mass range 15–2000GeV is measured and corrected to themore » full phase space. The double-differential cross section d 2σ/dmd|y| is also measured over the mass range 20 to 1500GeV and absolute dilepton rapidity from 0 to 2.4. In addition, the ratios of the normalized differential cross sections measured at √s = 7 and 8TeV are presented. These measurements are compared to the predictions of perturbative QCD at next-to-leading and next-to-next-to-leading (NNLO) orders using various sets of parton distribution functions (PDFs). The results agree with the NNLO theoretical predictions computed with FEWZ 3.1 using the CT10 NNLO and NNPDF2.1 NNLO PDFs. Furthermore, the measured double-differential cross section and ratio of normalized differential cross sections are sufficiently precise to constrain the proton PDFs.« less

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

NASA Astrophysics Data System (ADS)

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

2015-08-01

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in irradiated materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1.0a0 to 3.3a0 have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomic level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a0 by taking the average of the recombination distances from 80 simulation cases. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.

Recombination Processes and Nonlinear Markov Chains.

PubMed

Pirogov, Sergey; Rybko, Alexander; Kalinina, Anastasia; Gelfand, Mikhail

2016-09-01

Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.

Mechanisms and Factors that Influence High Frequency Retroviral Recombination

PubMed Central

Delviks-Frankenberry, Krista; Galli, Andrea; Nikolaitchik, Olga; Mens, Helene; Pathak, Vinay K.; Hu, Wei-Shau

2011-01-01

With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development. PMID:21994801

Heparin-binding peptide as a novel affinity tag for purification of recombinant proteins.

PubMed

Morris, Jacqueline; Jayanthi, Srinivas; Langston, Rebekah; Daily, Anna; Kight, Alicia; McNabb, David S; Henry, Ralph; Kumar, Thallapuranam Krishnaswamy Suresh

2016-10-01

Purification of recombinant proteins constitutes a significant part of the downstream processing in biopharmaceutical industries. Major costs involved in the production of bio-therapeutics mainly depend on the number of purification steps used during the downstream process. Affinity chromatography is a widely used method for the purification of recombinant proteins expressed in different expression host platforms. Recombinant protein purification is achieved by fusing appropriate affinity tags to either N- or C- terminus of the target recombinant proteins. Currently available protein/peptide affinity tags have proved quite useful in the purification of recombinant proteins. However, these affinity tags suffer from specific limitations in their use under different conditions of purification. In this study, we have designed a novel 34-amino acid heparin-binding affinity tag (HB-tag) for the purification of recombinant proteins expressed in Escherichia coli (E. coli) cells. HB-tag fused recombinant proteins were overexpressed in E. coli in high yields. A one-step heparin-Sepharose-based affinity chromatography protocol was developed to purify HB-fused recombinant proteins to homogeneity using a simple sodium chloride step gradient elution. The HB-tag has also been shown to facilitate the purification of target recombinant proteins from their 8 M urea denatured state(s). The HB-tag has been demonstrated to be successfully released from the fusion protein by an appropriate protease treatment to obtain the recombinant target protein(s) in high yields. Results of the two-dimensional NMR spectroscopy experiments indicate that the purified recombinant target protein(s) exist in the native conformation. Polyclonal antibodies raised against the HB-peptide sequence, exhibited high binding specificity and sensitivity to the HB-fused recombinant proteins (∼10 ng) in different crude cell extracts obtained from diverse expression hosts. In our opinion, the HB-tag provides a cost-effective, rapid, and reliable avenue for the purification of recombinant proteins in heterologous hosts. Copyright © 2016 Elsevier Inc. All rights reserved.

Ultrafast dynamics of defect-assisted electron-hole recombination in monolayer MoS2.

PubMed

Wang, Haining; Zhang, Changjian; Rana, Farhan

2015-01-14

In this Letter, we present nondegenerate ultrafast optical pump-probe studies of the carrier recombination dynamics in MoS2 monolayers. By tuning the probe to wavelengths much longer than the exciton line, we make the probe transmission sensitive to the total population of photoexcited electrons and holes. Our measurement reveals two distinct time scales over which the photoexcited electrons and holes recombine; a fast time scale that lasts ∼ 2 ps and a slow time scale that lasts longer than ∼ 100 ps. The temperature and the pump fluence dependence of the observed carrier dynamics are consistent with defect-assisted recombination as being the dominant mechanism for electron-hole recombination in which the electrons and holes are captured by defects via Auger processes. Strong Coulomb interactions in two-dimensional atomic materials, together with strong electron and hole correlations in two-dimensional metal dichalcogenides, make Auger processes particularly effective for carrier capture by defects. We present a model for carrier recombination dynamics that quantitatively explains all features of our data for different temperatures and pump fluences. The theoretical estimates for the rate constants for Auger carrier capture are in good agreement with the experimentally determined values. Our results underscore the important role played by Auger processes in two-dimensional atomic materials.

Flexible Retrieval: When True Inferences Produce False Memories

ERIC Educational Resources Information Center

Carpenter, Alexis C.; Schacter, Daniel L.

2017-01-01

Episodic memory involves flexible retrieval processes that allow us to link together distinct episodes, make novel inferences across overlapping events, and recombine elements of past experiences when imagining future events. However, the same flexible retrieval and recombination processes that underpin these adaptive functions may also leave…

Quantitative X-ray - UV Line and Continuum Spectroscopy with Application to AGN: State-Specific Hydrogenic Recombination Cooling Coefficients for a Wide Range of Conditions

NASA Technical Reports Server (NTRS)

LaMothe, J.; Ferland, Gary J.

2002-01-01

Recombination cooling, in which a free electron emits light while being captured to an ion, is an important cooling process in photoionized clouds that are optically thick or have low metallicity. State specific rather than total recombination cooling rates are needed since the hydrogen atom tends to become optically thick in high-density regimes such as Active Galactic Nuclei. This paper builds upon previous work to derive the cooling rate over the full temperature range where the process can be a significant contributor in a photoionized plasma. We exploit the fact that the recombination and cooling rates are given by intrinsically similar formulae to express the cooling rate in terms of the closely related radiative recombination rate. We give an especially simple but accurate approximation that works for any high hydrogenic level and can be conveniently employed in large-scale numerical simulations.

Effect of interface roughness on Auger recombination in semiconductor quantum wells

NASA Astrophysics Data System (ADS)

Tan, Chee-Keong; Sun, Wei; Wierer, Jonathan J.; Tansu, Nelson

2017-03-01

Auger recombination in a semiconductor is a three-carrier process, wherein the energy from the recombination of an electron and hole pair promotes a third carrier to a higher energy state. In semiconductor quantum wells with increased carrier densities, the Auger recombination becomes an appreciable fraction of the total recombination rate and degrades luminescence efficiency. Gaining insight into the variables that influence Auger recombination in semiconductor quantum wells could lead to further advances in optoelectronic and electronic devices. Here we demonstrate the important role that interface roughness has on Auger recombination within quantum wells. Our computational studies find that as the ratio of interface roughness to quantum well thickness is increased, Auger recombination is significantly enhanced. Specifically, when considering a realistic interface roughness for an InGaN quantum well, the enhancement in Auger recombination rate over a quantum well with perfect heterointerfaces can be approximately four orders of magnitude.

Sordaria, a model system to uncover links between meiotic pairing and recombination

PubMed Central

Zickler, Denise; Espagne, Eric

2017-01-01

The mycelial fungus Sordaria macrospora was first used as experimental system for meiotic recombination. This review shows that it provides also a powerful cytological system for dissecting chromosome dynamics in wild-type and mutant meioses. Fundamental cytogenetic findings include: (1) The identification of presynaptic alignment as a key step in pairing of homologous chromosomes. (2) The discovery that biochemical complexes that mediate recombination at the DNA level concomitantly mediate pairing of homologs. (3) This pairing process involves not only resolution but also avoidance of chromosomal entanglements and the resolution system includes dissolution of constraining DNA recombination interactions, achieved by a unique role of Mlh1. (4) Discovery that the central components of the synaptonemal complex directly mediate the re-localization of the recombination proteins from on-axis to in-between homologue axis positions. (5) Identification of putative STUbL protein Hei10 as a structure-based signal transduction molecule that coordinates progression and differentiation of recombinational interactions at multiple stages. (6) Discovery that a single interference process mediates both nucleation of the SC and designation of crossover sites, thereby ensuring even spacing of both features. (7) Discovery of local modulation of sister-chromatid cohesion at sites of crossover recombination. PMID:26877138

Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast

PubMed Central

Muto, Machiko; Henry, Ryan E; Mayfield, Stephen P

2009-01-01

Background Expression of recombinant proteins in green algal chloroplast holds substantial promise as a platform for the production of human therapeutic proteins. A number of proteins have been expressed in the chloroplast of Chlamydomonas reinhardtii, including complex mammalian proteins, but many of these proteins accumulate to significantly lower levels than do endogenous chloroplast proteins. We examined if recombinant protein accumulation could be enhanced by genetically fusing the recombinant reporter protein, luciferase, to the carboxy-terminal end of an abundant endogenous protein, the large subunit of ribulose bisphosphate carboxylase (Rubisco LSU). Additionally, as recombinant proteins fused to endogenous proteins are of little clinical or commercial value, we explored the possibility of engineering our recombinant protein to be cleavable from the endogenous protein in vivo. This strategy would obviate the need for further in vitro processing steps in order to produce the desired recombinant protein. To achieve this, a native protein-processing site from preferredoxin (preFd) was placed between the Rubisco LSU and luciferase coding regions in the fusion protein construct. Results The luciferase from the fusion protein accumulated to significantly higher levels than luciferase expressed alone. By eliminating the endogenous Rubisco large subunit gene (rbcL), we achieved a further increase in luciferase accumulation with respect to luciferase expression in the WT background. Importantly, near-wild type levels of functional Rubisco holoenzyme were generated following the proteolytic removal of the fused luciferase, while luciferase activity for the fusion protein was almost ~33 times greater than luciferase expressed alone. These data demonstrate the utility of using fusion proteins to enhance recombinant protein accumulation in algal chloroplasts, and also show that engineered proteolytic processing sites can be used to liberate the exogenous protein from the endogenous fusion partner, allowing for the purification of the intended mature protein. Conclusion These results demonstrate the utility of fusion proteins in algal chloroplast as a method to increase accumulation of recombinant proteins that are difficult to express. Since Rubisco is ubiquitous to land plants and green algae, this strategy may also be applied to higher plant transgenic expression systems. PMID:19323825

Atmospheric NLTE models for the spectroscopic analysis of blue stars with winds. III. X-ray emission from wind-embedded shocks

NASA Astrophysics Data System (ADS)

Carneiro, L. P.; Puls, J.; Sundqvist, J. O.; Hoffmann, T. L.

2016-05-01

Context. Extreme ultraviolet (EUV) and X-ray radiation emitted from wind-embedded shocks in hot, massive stars can affect the ionization balance in their outer atmospheres and can be the mechanism responsible for producing highly ionized atomic species detected in stellar wind UV spectra. Aims: To allow for these processes in the context of spectral analysis, we have implemented the emission from wind-embedded shocks and related physics into our unified, NLTE model atmosphere/spectrum synthesis code FASTWIND. Methods: The shock structure and corresponding emission is calculated as a function of user-supplied parameters (volume filling factor, radial stratification of shock strength, and radial onset of emission). We account for a temperature and density stratification inside the postshock cooling zones, calculated for radiative and adiabatic cooling in the inner and outer wind, respectively. The high-energy absorption of the cool wind is considered by adding important K-shell opacities, and corresponding Auger ionization rates have been included in the NLTE network. To test our implementation and to check the resulting effects, we calculated a comprehensive model grid with a variety of X-ray emission parameters. Results: We tested and verified our implementation carefully against corresponding results from various alternative model atmosphere codes, and studied the effects from shock emission for important ions from He, C, N, O, Si, and P. Surprisingly, dielectronic recombination turned out to play an essential role for the ionization balance of O iv/O v (particularly in dwarfs with Teff~ 45 000 K). Finally, we investigated the frequency dependence and radial behavior of the mass absorption coefficient, κν(r), which is important in the context of X-ray line formation in massive star winds. Conclusions: In almost all of the cases considered, direct ionization is of major influence because of the enhanced EUV radiation field, and Auger ionization only affects N vi and O vi significantly. The approximation of a radially constant κν is justified for r ≳ 1.2 R∗ and λ ≲ 18 Å and also for many models at longer wavelengths. To estimate the actual value of this quantity, however, the He II opacities need to be calculated from detailed NLTE modeling, at least for wavelengths longer than 18 to 20 Å, and information on the individual CNO abundances has to be present.

The remarkable frequency of human immunodeficiency virus type 1 genetic recombination.

PubMed

Onafuwa-Nuga, Adewunmi; Telesnitsky, Alice

2009-09-01

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) results from a combination of point mutations and genetic recombination, and rates of both processes are unusually high. This review focuses on the mechanisms and outcomes of HIV-1 genetic recombination and on the parameters that make recombination so remarkably frequent. Experimental work has demonstrated that the process that leads to recombination--a copy choice mechanism involving the migration of reverse transcriptase between viral RNA templates--occurs several times on average during every round of HIV-1 DNA synthesis. Key biological factors that lead to high recombination rates for all retroviruses are the recombination-prone nature of their reverse transcription machinery and their pseudodiploid RNA genomes. However, HIV-1 genes recombine even more frequently than do those of many other retroviruses. This reflects the way in which HIV-1 selects genomic RNAs for coencapsidation as well as cell-to-cell transmission properties that lead to unusually frequent associations between distinct viral genotypes. HIV-1 faces strong and changeable selective conditions during replication within patients. The mode of HIV-1 persistence as integrated proviruses and strong selection for defective proviruses in vivo provide conditions for archiving alleles, which can be resuscitated years after initial provirus establishment. Recombination can facilitate drug resistance and may allow superinfecting HIV-1 strains to evade preexisting immune responses, thus adding to challenges in vaccine development. These properties converge to provide HIV-1 with the means, motive, and opportunity to recombine its genetic material at an unprecedented high rate and to allow genetic recombination to serve as one of the highest barriers to HIV-1 eradication.

Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates.

PubMed

Spring-Pearson, Senanu M; Stone, Joshua K; Doyle, Adina; Allender, Christopher J; Okinaka, Richard T; Mayo, Mark; Broomall, Stacey M; Hill, Jessica M; Karavis, Mark A; Hubbard, Kyle S; Insalaco, Joseph M; McNew, Lauren A; Rosenzweig, C Nicole; Gibbons, Henry S; Currie, Bart J; Wagner, David M; Keim, Paul; Tuanyok, Apichai

2015-01-01

The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is 'open', with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.

Search for rare and forbidden decays D+ --> h+/- e+/- e+.

PubMed

He, Q; Muramatsu, H; Park, C S; Thorndike, E H; Coan, T E; Gao, Y S; Liu, F; Artuso, M; Boulahouache, C; Blusk, S; Butt, J; Dorjkhaidav, O; Li, J; Menaa, N; Mountain, R; Nandakumar, R; Randrianarivony, K; Redjimi, R; Sia, R; Skwarnicki, T; Stone, S; Wang, J C; Zhang, K; Csorna, S E; Bonvicini, G; Cinabro, D; Dubrovin, M; Briere, R A; Chen, G P; Chen, J; Ferguson, T; Tatishvili, G; Vogel, H; Watkins, M E; Rosner, J L; Adam, N E; Alexander, J P; Berkelman, K; Cassel, D G; Crede, V; Duboscq, J E; Ecklund, K M; Ehrlich, R; Fields, L; Galik, R S; Gibbons, L; Gittelman, B; Gray, R; Gray, S W; Hartill, D L; Heltsley, B K; Hertz, D; Jones, C D; Kandaswamy, J; Kreinick, D L; Kuznetsov, V E; Mahlke-Krüger, H; Meyer, T O; Onyisi, P U E; Patterson, J R; Peterson, D; Phillips, E A; Pivarski, J; Riley, D; Ryd, A; Sadoff, A J; Schwarthoff, H; Shi, X; Shepherd, M R; Stroiney, S; Sun, W M; Urner, D; Wilksen, T; Weaver, K M; Weinberger, M; Athar, S B; Avery, P; Breva-Newell, L; Patel, R; Potlia, V; Stoeck, H; Yelton, J; Rubin, P; Cawlfield, C; Eisenstein, B I; Gollin, G D; Karliner, I; Kim, D; Lowrey, N; Naik, P; Sedlack, C; Selen, M; White, E J; Williams, J; Wiss, J; Asner, D M; Edwards, K W; Besson, D; Pedlar, T K; Cronin-Hennessy, D; Gao, K Y; Gong, D T; Hietala, J; Kubota, Y; Klein, T; Lang, B W; Li, S Z; Poling, R; Scott, A W; Smith, A; Dobbs, S; Metreveli, Z; Seth, K K; Tomaradze, A; Zweber, P; Ernst, J; Severini, H; Dytman, S A; Love, W; Mehrabyan, S; Mueller, J A; Savinov, V; Li, Z; Lopez, A; Mendez, H; Ramirez, J; Huang, G S; Miller, D H; Pavlunin, V; Sanghi, B; Shipsey, I P J; Adams, G S; Cravey, M; Cummings, J P; Danko, I; Napolitano, J

2005-11-25

Using 0.8 x 10(6) D+ D- pairs collected with the CLEO-c detector at the psi(3770) resonance, we have searched for flavor-changing neutral current and lepton-number-violating decays of D+ mesons to final states with dielectrons. We find no indication of either, obtaining 90% confidence level upper limits of B(D+ --> pi+ e+ e-) < 7.4 x 10(-6), B(D+ --> pi- e+ d+) < 3.6 x 10(-6), B(D+ --> K+ e+ e-) < 6.2 x 10(-6), and B(D+ --> K- e+ e+) < 4.5 x 10(-6).

Collisional-radiative nonequilibrium in partially ionized atomic nitrogen

NASA Technical Reports Server (NTRS)

Kunc, J. A.; Soon, W. H.

1989-01-01

A nonlinear collisional-radiative model for determination of nonequilibrium production of electrons, excited atoms, and bound-bound, dielectronic and continuum line intensities in stationary partially ionized atomic nitrogen is presented. Populations of 14 atomic levels and line intensities are calculated in plasma with T(e) = 8000-15,000 K and N(t) = 10 to the 12th - 10 to the 18th/cu cm. Transport of radiation is included by coupling the rate equations of production of the electrons and excited atoms with the radiation escape factors, which are not constant but depend on plasma conditions.

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in neutron irradiated nuclear materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1:0a₀ to 3:3a₀ have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomicmore » level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a₀ by taking the average of the recombination distances from 80 simulation cases. This value agrees well with the experimental estimate. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.« less

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

DOE PAGES

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

2015-08-04

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in neutron irradiated nuclear materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1:0a₀ to 3:3a₀ have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomicmore » level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a₀ by taking the average of the recombination distances from 80 simulation cases. This value agrees well with the experimental estimate. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.« less

Signals from the epoch of cosmological recombination (Karl Schwarzschild Award Lecture 2008)

NASA Astrophysics Data System (ADS)

Sunyaev, R. A.; Chluba, J.

2009-07-01

The physical ingredients to describe the epoch of cosmological recombination are amazingly simple and well-understood. This fact allows us to take into account a very large variety of physical processes, still finding potentially measurable consequences for the energy spectrum and temperature anisotropies of the Cosmic Microwave Background (CMB). In this contribution we provide a short historical overview in connection with the cosmological recombination epoch and its connection to the CMB. Also we highlight some of the detailed physics that were studied over the past few years in the context of the cosmological recombination of hydrogen and helium. The impact of these considerations is two-fold: The associated release of photons during this epoch leads to interesting and unique deviations of the Cosmic Microwave Background (CMB) energy spectrum from a perfect blackbody, which, in particular at decimeter wavelength and the Wien part of the CMB spectrum, may become observable in the near future. Despite the fact that the abundance of helium is rather small, it still contributes a sizeable amount of photons to the full recombination spectrum, leading to additional distinct spectral features. Observing the spectral distortions from the epochs of hydrogen and helium recombination, in principle would provide an additional way to determine some of the key parameters of the Universe (e.g. the specific entropy, the CMB monopole temperature and the pre-stellar abundance of helium). Also it permits us to confront our detailed understanding of the recombination process with direct observational evidence. In this contribution we illustrate how the theoretical spectral template of the cosmological recombination spectrum may be utilized for this purpose. We also show that because hydrogen and helium recombine at very different epochs it is possible to address questions related to the thermal history of our Universe. In particular the cosmological recombination radiation may allow us to distinguish between Compton y-distortions that were created by energy release before or after the recombination of the Universe finished. With the advent of high precision CMB data, e.g. as will be available using the PLANCK Surveyor or CMBPOL, a very accurate theoretical understanding of the ionization history of the Universe becomes necessary for the interpretation of the CMB temperature and polarization anisotropies. Here we show that the uncertainty in the ionization history due to several processes, which until now were not taken in to account in the standard recombination code RECFAST, reaches the percent level. In particular He II->He I recombination occurs significantly faster because of the presence of a tiny fraction of neutral hydrogen at {z⪉ 2400}. Also recently it was demonstrated that in the case of H I Lyman α photons the time-dependence of the emission process and the asymmetry between the emission and absorption profile cannot be ignored. However, it is indeed surprising how inert the cosmological recombination history is even at percent-level accuracy. Observing the cosmological recombination spectrum should in principle allow us to directly check this conclusion, which until now is purely theoretical. Also it may allow to reconstruct the ionization history using observational data.

Requirements for high-efficiency solar cells

NASA Technical Reports Server (NTRS)

Sah, C. T.

1986-01-01

Minimum recombination and low injection level are essential for high efficiency. Twenty percent AM1 efficiency requires a dark recombination current density of 2 x 10 to the minus 13th power A/sq cm and a recombination center density of less than 10 to the 10th power /cu cm. Recombination mechanisms at thirteen locations in a conventional single crystalline silicon cell design are reviewed. Three additional recombination locations are described at grain boundaries in polycrystalline cells. Material perfection and fabrication process optimization requirements for high efficiency are outlined. Innovative device designs to reduce recombination in the bulk and interfaces of single crystalline cells and in the grain boundary of polycrystalline cells are reviewed.

SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY

PubMed Central

WILLIAMS, PAUL D.; POLLOCK, DAVID D.

2010-01-01

Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population. PMID:25473139

Selective Advantage of Recombination in Evolving Protein Populations:. a Lattice Model Study

NASA Astrophysics Data System (ADS)

Williams, Paul D.; Pollock, David D.; Goldstein, Richard A.

Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population.

Extraction and purification methods in downstream processing of plant-based recombinant proteins.

PubMed

Łojewska, Ewelina; Kowalczyk, Tomasz; Olejniczak, Szymon; Sakowicz, Tomasz

2016-04-01

During the last two decades, the production of recombinant proteins in plant systems has been receiving increased attention. Currently, proteins are considered as the most important biopharmaceuticals. However, high costs and problems with scaling up the purification and isolation processes make the production of plant-based recombinant proteins a challenging task. This paper presents a summary of the information regarding the downstream processing in plant systems and provides a comprehensible overview of its key steps, such as extraction and purification. To highlight the recent progress, mainly new developments in the downstream technology have been chosen. Furthermore, besides most popular techniques, alternative methods have been described. Copyright © 2015 Elsevier Inc. All rights reserved.

Tritium waste package

DOEpatents

Rossmassler, Rich; Ciebiera, Lloyd; Tulipano, Francis J.; Vinson, Sylvester; Walters, R. Thomas

1995-01-01

A containment and waste package system for processing and shipping tritium xide waste received from a process gas includes an outer drum and an inner drum containing a disposable molecular sieve bed (DMSB) seated within outer drum. The DMSB includes an inlet diffuser assembly, an outlet diffuser assembly, and a hydrogen catalytic recombiner. The DMSB absorbs tritium oxide from the process gas and converts it to a solid form so that the tritium is contained during shipment to a disposal site. The DMSB is filled with type 4A molecular sieve pellets capable of adsorbing up to 1000 curies of tritium. The recombiner contains a sufficient amount of catalyst to cause any hydrogen add oxygen present in the process gas to recombine to form water vapor, which is then adsorbed onto the DMSB.

Tritium waste package

DOEpatents

Rossmassler, R.; Ciebiera, L.; Tulipano, F.J.; Vinson, S.; Walters, R.T.

1995-11-07

A containment and waste package system for processing and shipping tritium oxide waste received from a process gas includes an outer drum and an inner drum containing a disposable molecular sieve bed (DMSB) seated within the outer drum. The DMSB includes an inlet diffuser assembly, an outlet diffuser assembly, and a hydrogen catalytic recombiner. The DMSB absorbs tritium oxide from the process gas and converts it to a solid form so that the tritium is contained during shipment to a disposal site. The DMSB is filled with type 4A molecular sieve pellets capable of adsorbing up to 1000 curies of tritium. The recombiner contains a sufficient amount of catalyst to cause any hydrogen and oxygen present in the process gas to recombine to form water vapor, which is then adsorbed onto the DMSB. 1 fig.

Biotechnological advances towards an enhanced peroxidase production in Pichia pastoris.

PubMed

Krainer, Florian W; Gerstmann, Michaela A; Darnhofer, Barbara; Birner-Gruenberger, Ruth; Glieder, Anton

2016-09-10

Horseradish peroxidase (HRP) is a high-demand enzyme for applications in diagnostics, bioremediation, biocatalysis and medicine. Current HRP preparations are isolated from horseradish roots as mixtures of biochemically diverse isoenzymes. Thus, there is a strong need for a recombinant production process enabling a steady supply with enzyme preparations of consistent high quality. However, most current recombinant production systems are limited at titers in the low mg/L range. In this study, we used the well-known yeast Pichia pastoris as host for recombinant HRP production. To enhance recombinant enzyme titers we systematically evaluated engineering approaches on the secretion process, coproduction of helper proteins, and compared expression from the strong methanol-inducible PAOX1 promoter, the strong constitutive PGAP promoter, and a novel bidirectional promoter PHTX1. Ultimately, coproduction of HRP and active Hac1 under PHTX1 control yielded a recombinant HRP titer of 132mg/L after 56h of cultivation in a methanol-independent and easy-to-do bioreactor cultivation process. With regard to the many versatile applications for HRP, the establishment of a microbial host system suitable for efficient recombinant HRP production was highly overdue. The novel HRP production platform in P. pastoris presented in this study sets a new benchmark for this medically relevant enzyme. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Sordaria, a model system to uncover links between meiotic pairing and recombination.

PubMed

Zickler, Denise; Espagne, Eric

2016-06-01

The mycelial fungus Sordaria macrospora was first used as experimental system for meiotic recombination. This review shows that it provides also a powerful cytological system for dissecting chromosome dynamics in wild-type and mutant meioses. Fundamental cytogenetic findings include: (1) the identification of presynaptic alignment as a key step in pairing of homologous chromosomes. (2) The discovery that biochemical complexes that mediate recombination at the DNA level concomitantly mediate pairing of homologs. (3) This pairing process involves not only resolution but also avoidance of chromosomal entanglements and the resolution system includes dissolution of constraining DNA recombination interactions, achieved by a unique role of Mlh1. (4) Discovery that the central components of the synaptonemal complex directly mediate the re-localization of the recombination proteins from on-axis to in-between homologue axis positions. (5) Identification of putative STUbL protein Hei10 as a structure-based signal transduction molecule that coordinates progression and differentiation of recombinational interactions at multiple stages. (6) Discovery that a single interference process mediates both nucleation of the SC and designation of crossover sites, thereby ensuring even spacing of both features. (7) Discovery of local modulation of sister-chromatid cohesion at sites of crossover recombination. Copyright © 2016 Elsevier Ltd. All rights reserved.

RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence.

PubMed

Xiao, Yinghong; Rouzine, Igor M; Bianco, Simone; Acevedo, Ashley; Goldstein, Elizabeth Faul; Farkov, Mikhail; Brodsky, Leonid; Andino, Raul

2016-04-13

Mutation and recombination are central processes driving microbial evolution. A high mutation rate fuels adaptation but also generates deleterious mutations. Recombination between two different genomes may resolve this paradox, alleviating effects of clonal interference and purging deleterious mutations. Here we demonstrate that recombination significantly accelerates adaptation and evolution during acute virus infection. We identified a poliovirus recombination determinant within the virus polymerase, mutation of which reduces recombination rates without altering replication fidelity. By generating a panel of variants with distinct mutation rates and recombination ability, we demonstrate that recombination is essential to enrich the population in beneficial mutations and purge it from deleterious mutations. The concerted activities of mutation and recombination are key to virus spread and virulence in infected animals. These findings inform a mathematical model to demonstrate that poliovirus adapts most rapidly at an optimal mutation rate determined by the trade-off between selection and accumulation of detrimental mutations. Copyright © 2016 Elsevier Inc. All rights reserved.

Mechanism of biphasic charge recombination and accumulation in TiO2 mesoporous structured perovskite solar cells.

PubMed

Wang, Hao-Yi; Wang, Yi; Yu, Man; Han, Jun; Guo, Zhi-Xin; Ai, Xi-Cheng; Zhang, Jian-Ping; Qin, Yujun

2016-04-28

Organic-inorganic halide perovskite solar cells are becoming the next big thing in the photovoltaic field owing to their rapidly developing photoelectric conversion performance. Herein, mesoporous structured perovskite devices with various perovskite grain sizes are fabricated by a sequential dropping method, and the charge recombination dynamics is investigated by transient optical-electric measurements. All devices exhibit an overall power conversion efficiency around 15%. More importantly, a biphasic trap-limited charge recombination process is proposed and interpreted by taking into account the specific charge accumulation mechanism in perovskite solar cells. At low Fermi levels, photo-generated electrons predominately populate in the perovskite phase, while at high Fermi levels, most electrons occupy traps in mesoporous TiO2. As a result, the dynamics of charge recombination is, respectively, dominated by the perovskite phase and mesoporous TiO2 in these two cases. The present work would give a new perspective on the charge recombination process in meso-structured perovskite solar cells.

Optical determination of Shockley-Read-Hall and interface recombination currents in hybrid perovskites

PubMed Central

Sarritzu, Valerio; Sestu, Nicola; Marongiu, Daniela; Chang, Xueqing; Masi, Sofia; Rizzo, Aurora; Colella, Silvia; Quochi, Francesco; Saba, Michele; Mura, Andrea; Bongiovanni, Giovanni

2017-01-01

Metal-halide perovskite solar cells rival the best inorganic solar cells in power conversion efficiency, providing the outlook for efficient, cheap devices. In order for the technology to mature and approach the ideal Shockley-Queissier efficiency, experimental tools are needed to diagnose what processes limit performances, beyond simply measuring electrical characteristics often affected by parasitic effects and difficult to interpret. Here we study the microscopic origin of recombination currents causing photoconversion losses with an all-optical technique, measuring the electron-hole free energy as a function of the exciting light intensity. Our method allows assessing the ideality factor and breaks down the electron-hole recombination current into bulk defect and interface contributions, providing an estimate of the limit photoconversion efficiency, without any real charge current flowing through the device. We identify Shockley-Read-Hall recombination as the main decay process in insulated perovskite layers and quantify the additional performance degradation due to interface recombination in heterojunctions. PMID:28317883

Solvation suppression of ion recombination in gas discharge afterglow

NASA Astrophysics Data System (ADS)

Amirov, R. Kh.; Lankin, A. V.; Norman, G. E.

2018-03-01

An effect which suppresses recombination in ion plasmas is considered both theoretically and experimentally. Experimental results are presented for the ion recombination rate in fluorine plasma, which are obtained from data for the gas discharge afterglow. To interpret them, a suppression factor is considered: ion solvation in weakly ionized plasma. It is shown that the recombination process has a two-stage character with the formation of intermediate metastable ion pairs. The pairs consist of negative and positive ion-molecular clusters. A theoretical explanation is given for the slowing down of the ion recombination with the increase of the Coulomb coupling compared to the ion recombination rate calculated in the ideal plasma approximation. The approximate similarity of the recombination rate of the ion temperature and concentration and reasons for the slight deviation from the similarity are elucidated.

PCR-mediated recombination in amplification products derived from polyploid cotton.

Treesearch

Richard C. Cronn; M. Cedroni; T. Haselkorn; C. Grover; Jonathan F. Wendel

2002-01-01

PCR recombination describes a process of in vitro chimera formation from non-identical templates. The key requirements of this process is the inclusion of two partially homologous templates in one reaction, a condition met when amplifying any locus from polyploid organisms and members of multigene families from diploid organisms. Because polyploids possess two or more...

Recombinant organisms for production of industrial products

PubMed Central

Adrio, Jose-Luis

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. PMID:21326937

Study of ND3-enhanced MAR processes in D2-N2 plasmas to induce plasma detachment

NASA Astrophysics Data System (ADS)

Abe, Shota; Chakraborty Thakur, Saikat; Doerner, Russ; Tynan, George

2017-10-01

The Molecular Assisted Recombination (MAR) process is thought to be a main channel of volumetric recombination to induce the plasma detachment operation. Authors have focused on a new plasma recombination process supported by ammonia molecules, which will be formed by impurity seeding of N2 for controlling divertor plasma temperature and heat loads in ITER. This ammonia-enhanced MAR process would occur throughout two steps. In this study, the first step of the new MAR process is investigated in low density plasmas (Ne 1016 m-3, Te 4 eV) fueled by D2 and N2. Ion and neutral densities are measured by a calibrated Electrostatic Quadrupole Plasma (EQP) analyzer, combination of an ion energy analyzer and mass spectrometer. The EQP shows formation of ND3 during discharges. Ion densities calculated by a rate equation model are compared with experimental results. We find that the model can reproduce the observed ion densities in the plasma. The model calculation shows that the dominant neutralization channel of Dx+(x =1-3) ions in the volume is the formation of NDy+(y =3 or 4) throughout charge/D+ exchange reactions with ND3. Furthermore, high density plasmas (Ne 1016 m-3) have been achieved to investigate electron-impact dissociative recombination processes of formed NDy+,which is the second step of this MAR process.

A study of trap and recombination centers in MAPbI3 perovskites.

PubMed

Gordillo, G; Otálora, C A; Ramirez, A A

2016-12-07

Trapping and recombination processes in thin films of CH 3 NH 3 PbI 3 (MAPbI 3 ) were studied by means of transient photoconductivity measurements and theoretical simulations of the relaxation curves resulting from the photocurrent measurements; in particular, the influence of temperature as well as of the sample temperature and intensity of illumination and pressure inside the measurement system on the photoconductivity response, were studied. The experimental curves of photocurrent were analyzed using the real part of the Fourier transform. The study revealed that the photocurrent of the MAPbI 3 films, measured at atmospheric pressure, is mainly governed by surface related processes induced by chemisorption and desorption of oxygen, whereas the photocurrent resulting from measurements performed in a vacuum is mainly governed by bulk related processes. It was found that, in general, the photocurrent response is affected by both trap assisted fast recombination processes and traps whose activation process is delayed, with the contribution in the intensity of the photocurrent of the first process being greater that of the second one. Evidence that the MAPbI 3 film exhibits a deep trap state at around 459 meV attributed to trap assisted recombination was found; furthermore, the MAPbI 3 films present shallow trap states at 129 and 24 meV that correspond to trap states whose activation process is delayed.

Spinning of Fibers from Aqueous Solutions

DTIC Science & Technology

2003-08-01

recombinant silk product BioSteel . Publications, patents and presentations 1. Arcidiacono, S., et al., Purification and characterization of recombinant...ABSTRACT Previous funding supporting this research focused primarily on development of the aqueous-based method for processing silk into spin solutions. Much...of this effort consisted of production of recombinant silk protein in bacterial and yeast expression systems. In spite of the small quantities

The Role of Trap-assisted Recombination in Luminescent Properties of Organometal Halide CH3NH3PbBr3 Perovskite Films and Quantum Dots

NASA Astrophysics Data System (ADS)

Zhang, Zhen-Yu; Wang, Hai-Yu; Zhang, Yan-Xia; Hao, Ya-Wei; Sun, Chun; Zhang, Yu; Gao, Bing-Rong; Chen, Qi-Dai; Sun, Hong-Bo

2016-06-01

Hybrid metal halide perovskites have been paid enormous attentions in photophysics research, whose excellent performances were attributed to their intriguing charge carriers proprieties. However, it still remains far from satisfaction in the comprehensive understanding of perovskite charge-transport properities, especially about trap-assisted recombination process. In this Letter, through time-resolved transient absorption (TA) and photoluminescence (PL) measurements, we provided a relative comprehensive investigation on the charge carriers recombination dynamics of CH3NH3PbBr3 (MAPbBr3) perovskite films and quantum dots (QDs), especially about trap-assisted recombination. It was found that the integral recombination mode of MAPbBr3 films was highly sensitive to the density distribution of generated charge carriers and trap states. Additional, Trap effects would be gradually weakened with elevated carrier densities. Furthermore, the trap-assisted recombination can be removed from MAPbBr3 QDs through its own surface passivation mechanism and this specialty may render the QDs as a new material in illuminating research. This work provides deeper physical insights into the dynamics processes of MAPbBr3 materials and paves a way toward more light-harvesting applications in future.

Multiple exciton generation and recombination in carbon nanotubes and nanocrystals.

PubMed

Kanemitsu, Yoshihiko

2013-06-18

Semiconducting nanomaterials such as single-walled carbon nanotubes (SWCNTs) and nanocrystals (NCs) exhibit unique size-dependent quantum properties. They have therefore attracted considerable attention from the viewpoints of fundamental physics and functional device applications. SWCNTs and NCs also provide an excellent new stage for experimental studies of many-body effects of electrons and excitons on optical processes in nanomaterials. In this Account, we discuss multiple exciton generation and recombination in SWCNTs and NCs for next-generation photovoltaics. Strongly correlated ensembles of conduction-band electrons and valence-band holes in semiconductors are complex quantum systems that exhibit unique optical phenomena. In bulk crystals, the carrier recombination dynamics can be described by a simple model, which includes the nonradiative single-carrier trapping rate, the radiative two-carrier recombination rate, and the nonradiative three-carrier Auger recombination rate. The nonradiative Auger recombination rate determines the carrier recombination dynamics at high carrier density and depends on the spatial localization of carriers in two-dimensional quantum wells. The Auger recombination and multiple exciton generation rates can be advantageously manipulated by nanomaterials with designated energy structures. In addition, SWCNTs and NCs show quantized recombination dynamics of multiple excitons and carriers. In one-dimensional SWCNTs, excitons have large binding energies and are very stable at room temperature. The extremely rapid Auger recombination between excitons determines the photoluminescence (PL) intensity, the PL linewidth, and the PL lifetime. SWCNTs can undergo multiple exciton generation, while strong exciton-exciton interactions and complicated exciton structures affect the quantized Auger rate and the multiple exciton generation efficiency. Interestingly, in zero-dimensional NC quantum dots, quantized Auger recombination causes unique optical phenomena. The breakdown of the k-conversion rule and strong Coulomb interactions between carriers in NCs enhance Auger recombination rate and decrease the energy threshold for multiple exciton generation. We discuss this impact of the k-conservation rule on two-carrier radiative recombination and the three-carrier Auger recombination processes in indirect-gap semiconductor Si NCs. In NCs and SWCNTs, multiple exciton generation competes with Auger recombination, surface trapping of excitons, and cooling of hot electrons or excitons. In addition, we explore heterostructured NCs and impurity-doped NCs in the context of the optimization of charge carrier extraction from excitons in NCs.

The chromatography-free release, isolation and purification of recombinant peptide for fibril self-assembly.

PubMed

Hartmann, B M; Kaar, W; Yoo, I K; Lua, L H L; Falconer, R J; Middelberg, A P J

2009-12-01

One of the major expenses associated with recombinant peptide production is the use of chromatography in the isolation and purification stages of a bioprocess. Here we report a chromatography-free isolation and purification process for recombinant peptide expressed in Escherichia coli (E. coli). Initial peptide release is by homogenization and then by enzymatic cleavage of the peptide-containing fusion protein, directly in the E. coli homogenate. Release is followed by selective solvent precipitation (SSP) to isolate and purify the peptide away from larger cell contaminants. Specifically, we expressed in E. coli the self-assembling beta-sheet forming peptide P(11)-2 in fusion to thioredoxin. Homogenate was heat treated (55 degrees C, 15 min) and then incubated with tobacco etch virus protease (TEVp) to release P(11)-2 having a native N-terminus. SSP with ethanol at room temperature then removed contaminating proteins in an integrated isolation-purification step; it proved necessary to add 250 mM NaCl to homogenate to prevent P(11)-2 from partitioning to the precipitate. This process structure gave recombinant P(11)-2 peptide at 97% polypeptide purity and 40% overall yield, without a single chromatography step. Following buffer-exchange of the 97% pure product by bind-elute chromatography into defined chemical conditions, the resulting peptide was shown to be functionally active and able to form self-assembled fibrils. To the best of our knowledge, this manuscript reports the first published process for chromatography-free recombinant peptide release, isolation and purification. The process proved able to deliver functional recombinant peptide at high purity and potentially low cost, opening cost-sensitive materials applications for peptide-based materials.

Recombination activity of grain boundaries in high-performance multicrystalline Si during solar cell processing

NASA Astrophysics Data System (ADS)

Adamczyk, Krzysztof; Søndenâ, Rune; Stokkan, Gaute; Looney, Erin; Jensen, Mallory; Lai, Barry; Rinio, Markus; Di Sabatino, Marisa

2018-02-01

In this work, we applied internal quantum efficiency mapping to study the recombination activity of grain boundaries in High Performance Multicrystalline Silicon under different processing conditions. Wafers were divided into groups and underwent different thermal processing, consisting of phosphorus diffusion gettering and surface passivation with hydrogen rich layers. After these thermal treatments, wafers were processed into heterojunction with intrinsic thin layer solar cells. Light Beam Induced Current and Electron Backscatter Diffraction were applied to analyse the influence of thermal treatment during standard solar cell processing on different types of grain boundaries. The results show that after cell processing, most random-angle grain boundaries in the material are well passivated, but small-angle grain boundaries are not well passivated. Special cases of coincidence site lattice grain boundaries with high recombination activity are also found. Based on micro-X-ray fluorescence measurements, a change in the contamination level is suggested as the reason behind their increased activity.

Development of a fed-batch process for a recombinant Pichia pastoris Δoch1 strain expressing a plant peroxidase.

PubMed

Gmeiner, Christoph; Saadati, Amirhossein; Maresch, Daniel; Krasteva, Stanimira; Frank, Manuela; Altmann, Friedrich; Herwig, Christoph; Spadiut, Oliver

2015-01-08

Pichia pastoris is a prominent host for recombinant protein production, amongst other things due to its capability of glycosylation. However, N-linked glycans on recombinant proteins get hypermannosylated, causing problems in subsequent unit operations and medical applications. Hypermannosylation is triggered by an α-1,6-mannosyltransferase called OCH1. In a recent study, we knocked out OCH1 in a recombinant P. pastoris CBS7435 Mut(S) strain (Δoch1) expressing the biopharmaceutically relevant enzyme horseradish peroxidase. We characterized the strain in the controlled environment of a bioreactor in dynamic batch cultivations and identified the strain to be physiologically impaired. We faced cell cluster formation, cell lysis and uncontrollable foam formation.In the present study, we investigated the effects of the 3 process parameters temperature, pH and dissolved oxygen concentration on 1) cell physiology, 2) cell morphology, 3) cell lysis, 4) productivity and 5) product purity of the recombinant Δoch1 strain in a multivariate manner. Cultivation at 30°C resulted in low specific methanol uptake during adaptation and the risk of methanol accumulation during cultivation. Cell cluster formation was a function of the C-source rather than process parameters and went along with cell lysis. In terms of productivity and product purity a temperature of 20°C was highly beneficial. In summary, we determined cultivation conditions for a recombinant P. pastoris Δoch1 strain allowing high productivity and product purity.

Trap-assisted and Langevin-type recombination in organic light-emitting diodes

NASA Astrophysics Data System (ADS)

Wetzelaer, G. A. H.; Kuik, M.; Nicolai, H. T.; Blom, P. W. M.

2011-04-01

Trapping of charges is known to play an important role in the charge transport of organic semiconductors, but the role of traps in the recombination process has not been addressed. Here we show that the ideality factor of the current of organic light-emitting diodes (OLEDs) in the diffusion-dominated regime has a temperature-independent value of 2, which reveals that nonradiative trap-assisted recombination dominates the current. In contrast, the ideality factor of the light output approaches unity, demonstrating that luminance is governed by recombination of the bimolecular Langevin type. This apparent contradiction can be resolved by measuring the current and luminance ideality factor for a white-emitting polymer, where both free and trapped charge carriers recombine radiatively. With increasing bias voltage, Langevin recombination becomes dominant over trap-assisted recombination due to its stronger dependence on carrier density, leading to an enhancement in OLED efficiency.

Heterologously expressed Aspergillus aculeatus β-glucosidase in Saccharomyces cerevisiae is a cost-effective alternative to commercial supplementation of β-glucosidase in industrial ethanol production using Trichoderma reesei cellulases.

PubMed

Treebupachatsakul, Treesukon; Nakazawa, Hikaru; Shinbo, Hideaki; Fujikawa, Hiroki; Nagaiwa, Asami; Ochiai, Nobuhiro; Kawaguchi, Takashi; Nikaido, Mitsuru; Totani, Kazuhide; Shioya, Koki; Shida, Yosuke; Morikawa, Yasushi; Ogasawara, Wataru; Okada, Hirofumi

2016-01-01

Trichoderma reesei is a filamentous organism that secretes enzymes capable of degrading cellulose to cellobiose. The culture supernatant of T. reesei, however, lacks sufficient activity to convert cellobiose to glucose using β-glucosidase (BGL1). In this study, we identified a BGL (Cel3B) from T. reesei (TrCel3B) and compared it with the active β-glucosidases from Aspergillus aculeatus (AaBGL1). AaBGL1 showed higher stability and conversion of sugars to ethanol compared to TrCel3B, and therefore we chose to express this recombinant protein for use in fermentation processes. We expressed the recombinant protein in the yeast Saccharomyces cerevisiae, combined it with the superb T. reesei cellulase machinery and used the combination in a simultaneous saccharification and fermentation (SSF) process, with the hope that the recombinant would supplement the BGL activity. As the sugars were processed, the yeast immediately converted them to ethanol, thereby eliminating the problem posed by end product inhibition. Recombinant AaBGL1 activity was compared with Novozyme 188, a commercially available supplement for BGL activity. Our results show that the recombinant protein is as effective as the commercial supplement and can process sugars with equal efficiency. Expression of AaBGL1 in S. cerevisiae increased ethanol production effectively. Thus, heterologous expression of AaBGL1 in S. cerevisiae is a cost-effective and efficient process for the bioconversion of ethanol from lignocellulosic biomass. Copyright © 2015. Published by Elsevier B.V.

Auger recombination in sodium iodide

NASA Astrophysics Data System (ADS)

McAllister, Andrew; Kioupakis, Emmanouil; Åberg, Daniel; Schleife, André

2014-03-01

Scintillators are an important tool used to detect high energy radiation - both in the interest of national security and in medicine. However, scintillator detectors currently suffer from lower energy resolutions than expected from basic counting statistics. This has been attributed to non-proportional light yield compared to incoming radiation, but the specific mechanism for this non-proportionality has not been identified. Auger recombination is a non-radiative process that could be contributing to the non-proportionality of scintillating materials. Auger recombination comes in two types - direct and phonon-assisted. We have used first-principles calculations to study Auger recombination in sodium iodide, a well characterized scintillating material. Our findings indicate that phonon-assisted Auger recombination is stronger in sodium iodide than direct Auger recombination. Computational resources provided by LLNL and NERSC. Funding provided by NA-22.

Variation block-based genomics method for crop plants.

PubMed

Kim, Yul Ho; Park, Hyang Mi; Hwang, Tae-Young; Lee, Seuk Ki; Choi, Man Soo; Jho, Sungwoong; Hwang, Seungwoo; Kim, Hak-Min; Lee, Dongwoo; Kim, Byoung-Chul; Hong, Chang Pyo; Cho, Yun Sung; Kim, Hyunmin; Jeong, Kwang Ho; Seo, Min Jung; Yun, Hong Tai; Kim, Sun Lim; Kwon, Young-Up; Kim, Wook Han; Chun, Hye Kyung; Lim, Sang Jong; Shin, Young-Ah; Choi, Ik-Young; Kim, Young Sun; Yoon, Ho-Sung; Lee, Suk-Ha; Lee, Sunghoon

2014-06-15

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.

The core structure and recombination energy of a copper screw dislocation: a Peierls study

NASA Astrophysics Data System (ADS)

Szajewski, B. A.; Hunter, A.; Beyerlein, I. J.

2017-09-01

The recombination process of dislocations is central to cross-slip, and transmission through ?3 grain boundaries among other fundamental plastic deformation processes. Despite its importance, a detailed mechanistic understanding remains lacking. We apply a continuous dislocation model, inspired by Peierls and Nabarro, complete with an ab-initio computed ?-surface and continuous units of infinitesimal dislocation slip, towards computing the stress-dependent recombination path of both an isotropic and anisotropic Cu screw dislocation. Under no applied stress, our model reproduces the stacking fault width between Shockley partial dislocations as predicted by discrete linear elasticity. Upon application of a compressive Escaig stress, the two partial dislocations coalesce to a separation of ??. Upon increased loading the edge components of each partial dislocation recede, leaving behind a spread Peierls screw dislocation, indicating the recombined state. We demonstrate that the critical stress required to achieve the recombined state is independent of the shear modulus. Rather the critical recombination stress depends on an energy difference between an unstable fault energy (?) and the intrinsic stacking fault energy (?-?). We report recombination energies of ?W = 0.168 eV/Å and ?W = 0.084 eV/Å, respectively, for the Cu screw dislocation within isotropic and anisotropic media. We develop an analytic model which provides insight into our simulation results which compare favourably with other (similar) models.

Trends in recombinant protein use in animal production.

PubMed

Gifre, Laia; Arís, Anna; Bach, Àlex; Garcia-Fruitós, Elena

2017-03-04

Recombinant technologies have made possible the production of a broad catalogue of proteins of interest, including those used for animal production. The most widely studied proteins for the animal sector are those with an important role in reproduction, feed efficiency, and health. Nowadays, mammalian cells and fungi are the preferred choice for recombinant production of hormones for reproductive purposes and fibrolytic enzymes to enhance animal performance, respectively. However, the development of low-cost products is a priority, particularly in livestock. The study of cell factories such as yeast and bacteria has notably increased in the last decades to make the new developed reproductive hormones and fibrolytic enzymes a real alternative to the marketed ones. Important efforts have also been invested to developing new recombinant strategies for prevention and therapy, including passive immunization and modulation of the immune system. This offers the possibility to reduce the use of antibiotics by controlling physiological processes and improve the efficacy of preventing infections. Thus, nowadays different recombinant fibrolytic enzymes, hormones, and therapeutic molecules with optimized properties have been successfully produced through cost-effective processes using microbial cell factories. However, despite the important achievements for reducing protein production expenses, alternative strategies to further reduce these costs are still required. In this context, it is necessary to make a giant leap towards the use of novel strategies, such as nanotechnology, that combined with recombinant technology would make recombinant molecules affordable for animal industry.

General features of the dissociative recombination of polyatomic molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pratt, S. T.; Jungen, Ch.; Schneider, I. F.

We discuss some aspects of a simple expression for the low-energy dissociative recombination cross section that applies when the recombination process is dominated by the indirect mechanism. In most previous applications, this expression has been applied to capture into vibrationally excited Rydberg states with the assumption that capture is always followed by prompt dissociation. Here we consider the dissociative recombination of larger polyatomic ions and electrons. More specifically, we consider capture into electronically core-excited Rydberg states, and begin to assess its potential importance for larger systems.

Dissociative recombination in aeronomy

NASA Technical Reports Server (NTRS)

Fox, J. L.

1989-01-01

The importance of dissociative recombination in planetary aeronomy is summarized, and two examples are discussed. The first is the role of dissociative recombination of N2(+) in the escape of nitrogen from Mars. A previous model is updated to reflect new experimental data on the electronic states of N produced in this process. Second, the intensity of the atomic oxygen green line on the nightside of Venus is modeled. Use is made of theoretical rate coefficients for production of O (1S) in dissociative recombination from different vibrational levels of O2(+).

General features of the dissociative recombination of polyatomic molecules

DOE PAGES

Pratt, S. T.; Jungen, Ch.; Schneider, I. F.; ...

2015-01-29

We discuss some aspects of a simple expression for the low-energy dissociative recombination cross section that applies when the recombination process is dominated by the indirect mechanism. In most previous applications, this expression has been applied to capture into vibrationally excited Rydberg states with the assumption that capture is always followed by prompt dissociation. Here we consider the dissociative recombination of larger polyatomic ions and electrons. More specifically, we consider capture into electronically core-excited Rydberg states, and begin to assess its potential importance for larger systems.

Feline immunodeficiency virus (FIV) env recombinants are common in natural infections.

PubMed

Bęczkowski, Paweł M; Hughes, Joseph; Biek, Roman; Litster, Annette; Willett, Brian J; Hosie, Margaret J

2014-09-17

Recombination is a common feature of retroviral biology and one of the most important factors responsible for generating viral diversity at both the intra-host and the population levels. However, relatively little is known about rates and molecular processes of recombination for retroviruses other than HIV, including important model viruses such as feline immunodeficiency virus (FIV). We investigated recombination in complete FIV env gene sequences (n = 355) isolated from 43 naturally infected cats. We demonstrated that recombination is abundant in natural FIV infection, with over 41% of the cats being infected with viruses containing recombinant env genes. In addition, we identified shared recombination breakpoints; the most significant hotspot occurred between the leader/signal fragment and the remainder of env. Our results have identified the leader/signal fragment of env as an important site for recombination and highlight potential limitations of the current phylogenetic classification of FIV based on partial env sequences. Furthermore, the presence of abundant recombinant FIV in the USA poses a significant challenge for commercial diagnostic tests and should inform the development of the next generation of FIV vaccines.

Analysis of magnesium XI line profiles from solar active regions

NASA Technical Reports Server (NTRS)

Blake, R. L.; Cowan, R. D.; Felthauser, H.; Fenimore, E. E.; Hockaday, M. P.; Bely-Dubau, F.; Faucher, P.; Steenman-Clark, L.

1984-01-01

High-resolution solar spectra of the Mg XI 1s2 1S0-1s2p 1P1 resonance line at 9.169 A and the associated nearby satellite lines obtained from two rocket-borne crystal spectrometer measurements are presented. Comparisons with two independent sets of theoretical calculations for the 1s2nl-1s2pnl dielectronic satellite lines with n = 3-7 indicate electron temperatures of 4-4.5 million K. Measured line widths indicate either that the ion temperature exceeds the electron temperature by about a million K or that about 28 km/s of turbulence is present.

Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast.

PubMed

Wu, Min; Kwoh, Chee-Keong; Li, Xiaoli; Zheng, Jie

2014-09-11

The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, cancer research, etc. Recombination events cluster into short genomic regions called "recombination hotspots". Recently, a zinc finger protein PRDM9 was reported to regulate recombination hotspots in human and mouse genomes. In addition, a 13-mer motif contained in the binding sites of PRDM9 is found to be enriched in human hotspots. However, this 13-mer motif only covers a fraction of hotspots, indicating that PRDM9 is not the only regulator of recombination hotspots. Therefore, the challenge of discovering other regulators of recombination hotspots becomes significant. Furthermore, recombination is a complex process. Hence, multiple proteins acting as machinery, rather than individual proteins, are more likely to carry out this process in a precise and stable manner. Therefore, the extension of the prediction of individual trans-regulators to protein complexes is also highly desired. In this paper, we introduce a pipeline to identify genes and protein complexes associated with recombination hotspots. First, we prioritize proteins associated with hotspots based on their preference of binding to hotspots and coldspots. Second, using the above identified genes as seeds, we apply the Random Walk with Restart algorithm (RWR) to propagate their influences to other proteins in protein-protein interaction (PPI) networks. Hence, many proteins without DNA-binding information will also be assigned a score to implicate their roles in recombination hotspots. Third, we construct sub-PPI networks induced by top genes ranked by RWR for various species (e.g., yeast, human and mouse) and detect protein complexes in those sub-PPI networks. The GO term analysis show that our prioritizing methods and the RWR algorithm are capable of identifying novel genes associated with recombination hotspots. The trans-regulators predicted by our pipeline are enriched with epigenetic functions (e.g., histone modifications), demonstrating the epigenetic regulatory mechanisms of recombination hotspots. The identified protein complexes also provide us with candidates to further investigate the molecular machineries for recombination hotspots. Moreover, the experimental data and results are available on our web site http://www.ntu.edu.sg/home/zhengjie/data/RecombinationHotspot/NetPipe/.

X-ray And EUV Spectroscopy Of Highly Charged Tungsten Ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Biedermann, Christoph; Radtke, Rainer

2009-09-10

The Berlin EBIT has been established by the Max-Planck-Institut fuer Plasmaphysik to generate atomic physics data in support of research in the field of controlled nuclear fusion, by measuring the radiation from highly charged ions in the x-ray, extreme ultraviolet and visible spectral ranges and providing valuable diagnostics for high temperature plasmas. In future fusion devices, for example ITER, currently being constructed at Cadarache, France, the plasma facing components will be armored with high-Z materials, most likely tungsten, due to the favorable properties of this element. At the same time the tremendous radiation cooling of these high-Z materials represents amore » threat to fusion and obliges one to monitor carefully the radiation. With EBIT a selected ensemble of ions in specific charge states can be produced, stored and excited for spectroscopic investigations. Employing this technique, we have for example resolved the wide structure observed around 5 nm at the ASDEX Upgrade tokamak as originating from E1-transitions into the open 4d shell of tungsten ions in charge states 25+ to 37+ producing a band-like emission pattern. Further, these ions emit well-separated M1 lines in the EUV range around 65 nm suitable for plasma diagnostics. Kr-like to Cr-like tungsten ions (38+ to 50+) show strong soft-x-ray lines in the range 0.5 to 2 and 5 to 15 nm. Lines of even higher charged tungsten ions, up to Ne-like W{sup 64+}, abundant in the core plasma of present and future fusion test devices, have been investigated with high resolution Bragg-crystal spectroscopy at 0.13 nm. Recently, x-ray spectroscopic measurements of the dielectronic recombination LMn resonances of W{sup 60+} to W{sup 67+} ions have been preformed and compare well with atomic structure calculations.« less

Recombinant organisms for production of industrial products.

PubMed

Adrio, Jose-Luis; Demain, Arnold L

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. © 2010 Landes Bioscience

Sex in a test tube: testing the benefits of in vitro recombination.

PubMed

Pesce, Diego; Lehman, Niles; de Visser, J Arjan G M

2016-10-19

The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes. As this approach allows extreme control over evolutionary conditions and parameters, it also facilitates the detection of small or position-specific recombination benefits and benefits associated with recombination between highly divergent genotypes. Yet, in vitro approaches have been largely exploratory and motivated by obtaining improved end products rather than testing hypotheses of recombination benefits. Here, we review the various experimental systems and approaches used by in vitro studies of recombination, discuss what they say about the evolutionary role of recombination, and sketch their potential for addressing extant questions about the evolutionary role of sex and recombination, in particular on complex fitness landscapes. We also review recent insights into the role of 'extracellular recombination' during the origin of life.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

A Critical Review of the Concept of Transgenic Plants: Insights into Pharmaceutical Biotechnology and Molecular Farming.

PubMed

Abiri, Rambod; Valdiani, Alireza; Maziah, Mahmood; Shaharuddin, Noor Azmi; Sahebi, Mahbod; Yusof, Zetty Norhana Balia; Atabaki, Narges; Talei, Daryush

2016-01-01

Using transgenic plants for the production of high-value recombinant proteins for industrial and clinical applications has become a promising alternative to using conventional bioproduction systems, such as bacteria, yeast, and cultured insect and animal cells. This novel system offers several advantages over conventional systems in terms of safety, scale, cost-effectiveness, and the ease of distribution and storage. Currently, plant systems are being utilised as recombinant bio-factories for the expression of various proteins, including potential vaccines and pharmaceuticals, through employing several adaptations of recombinant processes and utilizing the most suitable tools and strategies. The level of protein expression is a critical factor in plant molecular farming, and this level fluctuates according to the plant species and the organs involved. The production of recombinant native and engineered proteins is a complicated procedure that requires an inter- and multi-disciplinary effort involving a wide variety of scientific and technological disciplines, ranging from basic biotechnology, biochemistry, and cell biology to advanced production systems. This review considers important plant resources, affecting factors, and the recombinant-protein expression techniques relevant to the plant molecular farming process.

Evolution of meiotic recombination genes in maize and teosinte.

PubMed

Sidhu, Gaganpreet K; Warzecha, Tomasz; Pawlowski, Wojciech P

2017-01-25

Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathway itself. Although the recombination pathway is fundamentally conserved across different species, genetic variation in recombination components and outcomes has been observed. Theoretical predictions and empirical studies suggest that changes in the recombination pathway are likely to provide adaptive abilities to populations experiencing directional or strong selection pressures, such as those occurring during species domestication. We hypothesized that adaptive changes in recombination may be associated with adaptive evolution patterns of genes involved in meiotic recombination. To examine how maize evolution and domestication affected meiotic recombination genes, we studied patterns of sequence polymorphism and divergence in eleven genes controlling key steps in the meiotic recombination pathway in a diverse set of maize inbred lines and several accessions of teosinte, the wild ancestor of maize. We discovered that, even though the recombination genes generally exhibited high sequence conservation expected in a pathway controlling a key cellular process, they showed substantial levels and diverse patterns of sequence polymorphism. Among others, we found differences in sequence polymorphism patterns between tropical and temperate maize germplasms. Several recombination genes displayed patterns of polymorphism indicative of adaptive evolution. Despite their ancient origin and overall sequence conservation, meiotic recombination genes can exhibit extensive and complex patterns of molecular evolution. Changes in these genes could affect the functioning of the recombination pathway, and may have contributed to the successful domestication of maize and its expansion to new cultivation areas.

Parallel steady state studies on a milliliter scale accelerate fed-batch bioprocess design for recombinant protein production with Escherichia coli.

PubMed

Schmideder, Andreas; Cremer, Johannes H; Weuster-Botz, Dirk

2016-11-01

In general, fed-batch processes are applied for recombinant protein production with Escherichia coli (E. coli). However, state of the art methods for identifying suitable reaction conditions suffer from severe drawbacks, i.e. direct transfer of process information from parallel batch studies is often defective and sequential fed-batch studies are time-consuming and cost-intensive. In this study, continuously operated stirred-tank reactors on a milliliter scale were applied to identify suitable reaction conditions for fed-batch processes. Isopropyl β-d-1-thiogalactopyranoside (IPTG) induction strategies were varied in parallel-operated stirred-tank bioreactors to study the effects on the continuous production of the recombinant protein photoactivatable mCherry (PAmCherry) with E. coli. Best-performing induction strategies were transferred from the continuous processes on a milliliter scale to liter scale fed-batch processes. Inducing recombinant protein expression by dynamically increasing the IPTG concentration to 100 µM led to an increase in the product concentration of 21% (8.4 g L -1 ) compared to an implemented high-performance production process with the most frequently applied induction strategy by a single addition of 1000 µM IPGT. Thus, identifying feasible reaction conditions for fed-batch processes in parallel continuous studies on a milliliter scale was shown to be a powerful, novel method to accelerate bioprocess design in a cost-reducing manner. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1426-1435, 2016. © 2016 American Institute of Chemical Engineers.

Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies

PubMed Central

Yamaguchi, Hiroshi; Miyazaki, Masaya

2015-01-01

Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies. PMID:25531187

Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies.

PubMed

Yamaguchi, Hiroshi; Miyazaki, Masaya

2015-01-01

Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies.

Exciton-dissociation and charge-recombination processes in pentacene/C60 solar cells: theoretical insight into the impact of interface geometry.

PubMed

Yi, Yuanping; Coropceanu, Veaceslav; Brédas, Jean-Luc

2009-11-04

The exciton-dissociation and charge-recombination processes in organic solar cells based on pentacene/C(60) heterojunctions are investigated by means of quantum-mechanical calculations. The electronic couplings and the rates of exciton dissociation and charge recombination have been evaluated for several geometrical configurations of the pentacene/C(60) complex, which are relevant to bilayer and bulk heterojunctions. The results suggest that, irrespective of the actual pentacene-fullerene orientation, both pentacene-based and C(60)-based excitons are able to dissociate efficiently. Also, in the case of parallel configurations of the molecules at the pentacene/C(60) interface, the decay of the lowest charge-transfer state to the ground state is calculated to be very fast; as a result, it can compete with the dissociation process into mobile charge carriers. Since parallel configurations are expected to be found more frequently in bulk heterojunctions than in bilayer heterojunctions, the performance of pentacene/C(60) bulk-heterojunction solar cells is likely to be more affected by charge recombination than that of bilayer devices.

Recombinant spider silk from aqueous solutions via a bio-inspired microfluidic chip

NASA Astrophysics Data System (ADS)

Peng, Qingfa; Zhang, Yaopeng; Lu, Li; Shao, Huili; Qin, Kankan; Hu, Xuechao; Xia, Xiaoxia

2016-11-01

Spiders achieve superior silk fibres by controlling the molecular assembly of silk proteins and the hierarchical structure of fibres. However, current wet-spinning process for recombinant spidroins oversimplifies the natural spinning process. Here, water-soluble recombinant spider dragline silk protein (with a low molecular weight of 47 kDa) was adopted to prepare aqueous spinning dope. Artificial spider silks were spun via microfluidic wet-spinning, using a continuous post-spin drawing process (WS-PSD). By mimicking the natural spinning apparatus, shearing and elongational sections were integrated in the microfluidic spinning chip to induce assembly, orientation of spidroins, and fibril structure formation. The additional post-spin drawing process following the wet-spinning section partially mimics the spinning process of natural spider silk and substantially contributes to the compact aggregation of microfibrils. Subsequent post-stretching further improves the hierarchical structure of the fibres, including the crystalline structure, orientation, and fibril melting. The tensile strength and elongation of post-treated fibres reached up to 510 MPa and 15%, respectively.

The effect of recombination under short-circuit conditions on the determination of charge transport properties in nanostructured photoelectrodes.

PubMed

Villanueva-Cab, J; Anta, J A; Oskam, G

2016-01-28

We report on the commonly unaccounted for process of recombination under short-circuit conditions in nanostructured photoelectrodes with special attention to the charge collection efficiency. It is observed that when recombination under short circuit conditions is significant, small perturbation methods overestimate the charge-collection efficiency, which is related to the inaccurate determination of the electron diffusion coefficient and diffusion length.

Methods and materials for the production of L-lactic acid in yeast

DOEpatents

Hause, Ben [Jordan, MN; Rajgarhia, Vineet [Minnetonka, MN; Suominen, Pirkko [Maple Grove, MN

2009-05-19

Recombinant yeast are provided having, in one aspect, multiple exogenous LDH genes integrated into the genome, while leaving native PDC genes intact. In a second aspect, recombinant yeast are provided having an exogenous LDH gene integrated into its genome at the locus of a native PDC gene, with deletion of the native PDC gene. The recombinant yeast are useful in fermentation process for producing lactic acid.

Electron-Beam Recombination Lasers

NASA Astrophysics Data System (ADS)

Rhoades, Robert Lewis

1992-01-01

The first known instance of electron-beam pumping of the 546.1 nm mercury laser is reported. This has been achieved using high-energy electrons to create intense ionization in a coaxial diode chamber containing a mixture of noble gases with a small amount of mercury vapor. Also reported are the results of a study of the 585.3 nm neon laser in He:Ne:Ar mixtures under similar experimental conditions. Both of these lasers are believed to be predominantly pumped by recombination. For the mercury laser, kinetic processes in the partially ionized plasma following the excitation pulse of high-energy electrons should favor the production of atomic mercury ions and molecular ions containing mercury. Subsequent recombination with electrons heavily favors the production of the 7^3S and 6^3 D states of Hg, of which 7^3S is the upper level of the reported laser. For the neon laser, the dominant recombining ion has been previously shown to be Ne_2^{+}. One of the dominant roles of helium in recombination lasers is inferred from the data for the neon laser at low helium concentrations. Helium appears to be necessary for the rapid relaxation of the electron energy which then increases the reaction rates for all known recombination processes thus increasing the pump rate into the upper state.

The core structure and recombination energy of a copper screw dislocation: a Peierls study

DOE PAGES

Szajewski, B. A.; Hunter, A.; Beyerlein, I. J.

2017-05-19

The recombination process of dislocations is central to cross-slip, and transmission through Σ3 grain boundaries among other fundamental plastic deformation processes. Despite its importance, a detailed mechanistic understanding remains lacking. In this paper, we apply a continuous dislocation model, inspired by Peierls and Nabarro, complete with an ab-initio computed -surface and continuous units of infinitesimal dislocation slip, towards computing the stress-dependent recombination path of both an isotropic and anisotropic Cu screw dislocation. Under no applied stress, our model reproduces the stacking fault width between Shockley partial dislocations as predicted by discrete linear elasticity. Upon application of a compressive Escaig stress,more » the two partial dislocations coalesce to a separation of ~|b|. Upon increased loading the edge components of each partial dislocation recede, leaving behind a spread Peierls screw dislocation, indicating the recombined state. We demonstrate that the critical stress required to achieve the recombined state is independent of the shear modulus. Rather the critical recombination stress depends on an energy difference between an unstable fault energy (γτ) and the intrinsic stacking fault energy (γτ-γisf). We report recombination energies of ΔW = 0.168 eV/Å and ΔW = 0.084 eV/Å, respectively, for the Cu screw dislocation within isotropic and anisotropic media. Finally, we develop an analytic model which provides insight into our simulation results which compare favourably with other (similar) models.« less

The core structure and recombination energy of a copper screw dislocation: a Peierls study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szajewski, B. A.; Hunter, A.; Beyerlein, I. J.

The recombination process of dislocations is central to cross-slip, and transmission through Σ3 grain boundaries among other fundamental plastic deformation processes. Despite its importance, a detailed mechanistic understanding remains lacking. In this paper, we apply a continuous dislocation model, inspired by Peierls and Nabarro, complete with an ab-initio computed -surface and continuous units of infinitesimal dislocation slip, towards computing the stress-dependent recombination path of both an isotropic and anisotropic Cu screw dislocation. Under no applied stress, our model reproduces the stacking fault width between Shockley partial dislocations as predicted by discrete linear elasticity. Upon application of a compressive Escaig stress,more » the two partial dislocations coalesce to a separation of ~|b|. Upon increased loading the edge components of each partial dislocation recede, leaving behind a spread Peierls screw dislocation, indicating the recombined state. We demonstrate that the critical stress required to achieve the recombined state is independent of the shear modulus. Rather the critical recombination stress depends on an energy difference between an unstable fault energy (γτ) and the intrinsic stacking fault energy (γτ-γisf). We report recombination energies of ΔW = 0.168 eV/Å and ΔW = 0.084 eV/Å, respectively, for the Cu screw dislocation within isotropic and anisotropic media. Finally, we develop an analytic model which provides insight into our simulation results which compare favourably with other (similar) models.« less

Horizontal transmissible protection against myxomatosis and rabbit hemorrhagic disease by using a recombinant myxoma virus.

PubMed

Bárcena, J; Morales, M; Vázquez, B; Boga, J A; Parra, F; Lucientes, J; Pagès-Manté, A; Sánchez-Vizcaíno, J M; Blasco, R; Torres, J M

2000-02-01

We have developed a new strategy for immunization of wild rabbit populations against myxomatosis and rabbit hemorrhagic disease (RHD) that uses recombinant viruses based on a naturally attenuated field strain of myxoma virus (MV). The recombinant viruses expressed the RHDV major capsid protein (VP60) including a linear epitope tag from the transmissible gastroenteritis virus (TGEV) nucleoprotein. Following inoculation, the recombinant viruses induced specific antibody responses against MV, RHDV, and the TGEV tag. Immunization of wild rabbits by the subcutaneous and oral routes conferred protection against virulent RHDV and MV challenges. The recombinant viruses showed a limited horizontal transmission capacity, either by direct contact or in a flea-mediated process, promoting immunization of contact uninoculated animals.

Horizontal Transmissible Protection against Myxomatosis and Rabbit Hemorrhagic Disease by Using a Recombinant Myxoma Virus

PubMed Central

Bárcena, Juan; Morales, Mónica; Vázquez, Belén; Boga, José A.; Parra, Francisco; Lucientes, Javier; Pagès-Manté, Albert; Sánchez-Vizcaíno, José M.; Blasco, Rafael; Torres, Juan M.

2000-01-01

We have developed a new strategy for immunization of wild rabbit populations against myxomatosis and rabbit hemorrhagic disease (RHD) that uses recombinant viruses based on a naturally attenuated field strain of myxoma virus (MV). The recombinant viruses expressed the RHDV major capsid protein (VP60) including a linear epitope tag from the transmissible gastroenteritis virus (TGEV) nucleoprotein. Following inoculation, the recombinant viruses induced specific antibody responses against MV, RHDV, and the TGEV tag. Immunization of wild rabbits by the subcutaneous and oral routes conferred protection against virulent RHDV and MV challenges. The recombinant viruses showed a limited horizontal transmission capacity, either by direct contact or in a flea-mediated process, promoting immunization of contact uninoculated animals. PMID:10627521

Compartmentalization of the yeast meiotic nucleus revealed by analysis of ectopic recombination.

PubMed

Schlecht, Hélène B; Lichten, Michael; Goldman, Alastair S H

2004-11-01

As yeast cells enter meiosis, chromosomes move from a centromere-clustered (Rabl) to a telomere-clustered (bouquet) configuration and then to states of progressive homolog pairing where telomeres are more dispersed. It is uncertain at which stage of this process sequences commit to recombine with each other. Previous analyses using recombination between dispersed homologous sequences (ectopic recombination) support the view that, on average, homologs are aligned end to end by the time of commitment to recombination. We have undertaken further analyses incorporating new inserts, chromosome rearrangements, an alternate mode of recombination initiation, and mutants that disrupt nuclear structure or telomere metabolism. Our findings support previous conclusions and reveal that distance from the nearest telomere is an important parameter influencing recombination between dispersed sequences. In general, the farther dispersed sequences are from their nearest telomere, the less likely they are to engage in ectopic recombination. Neither the mode of initiating recombination nor the formation of the bouquet appears to affect this relationship. We suggest that aspects of telomere localization and behavior influence the organization and mobility of chromosomes along their entire length, during a critical period of meiosis I prophase that encompasses the homology search.

Exciton localization in solution-processed organolead trihalide perovskites

PubMed Central

He, Haiping; Yu, Qianqian; Li, Hui; Li, Jing; Si, Junjie; Jin, Yizheng; Wang, Nana; Wang, Jianpu; He, Jingwen; Wang, Xinke; Zhang, Yan; Ye, Zhizhen

2016-01-01

Organolead trihalide perovskites have attracted great attention due to the stunning advances in both photovoltaic and light-emitting devices. However, the photophysical properties, especially the recombination dynamics of photogenerated carriers, of this class of materials are controversial. Here we report that under an excitation level close to the working regime of solar cells, the recombination of photogenerated carriers in solution-processed methylammonium–lead–halide films is dominated by excitons weakly localized in band tail states. This scenario is evidenced by experiments of spectral-dependent luminescence decay, excitation density-dependent luminescence and frequency-dependent terahertz photoconductivity. The exciton localization effect is found to be general for several solution-processed hybrid perovskite films prepared by different methods. Our results provide insights into the charge transport and recombination mechanism in perovskite films and help to unravel their potential for high-performance optoelectronic devices. PMID:26996605

Development of a scaled-down aerobic fermentation model for scale-up in recombinant protein vaccine manufacturing.

PubMed

Farrell, Patrick; Sun, Jacob; Gao, Meg; Sun, Hong; Pattara, Ben; Zeiser, Arno; D'Amore, Tony

2012-08-17

A simple approach to the development of an aerobic scaled-down fermentation model is presented to obtain more consistent process performance during the scale-up of recombinant protein manufacture. Using a constant volumetric oxygen mass transfer coefficient (k(L)a) for the criterion of a scale-down process, the scaled-down model can be "tuned" to match the k(L)a of any larger-scale target by varying the impeller rotational speed. This approach is demonstrated for a protein vaccine candidate expressed in recombinant Escherichia coli, where process performance is shown to be consistent among 2-L, 20-L, and 200-L scales. An empirical correlation for k(L)a has also been employed to extrapolate to larger manufacturing scales. Copyright © 2012 Elsevier Ltd. All rights reserved.

Analysis of Recombinant Proteins in Transgenic Rice Seeds: Identity, Localization, Tolerance to Digestion, and Plant Stress Response.

PubMed

Wakasa, Yuhya; Takaiwa, Fumio

2016-01-01

Rice seeds are an ideal production platform for high-value recombinant proteins in terms of economy, scalability, safety, and stability. Strategies for the expression of large amounts of recombinant proteins in rice seeds have been established in the past decade and transgenic rice seeds that accumulate recombinant products such as bioactive peptides and proteins, which promote the health and quality of life of humans, have been generated in many laboratories worldwide. One of the most important advantages is the potential for direct oral delivery of transgenic rice seeds without the need for recombinant protein purification (downstream processing), which has been attributed to the high expression levels of recombinant products. Transgenic rice will be beneficial as a delivery system for pharmaceuticals and nutraceuticals in the future. This chapter introduces the strategy for producing recombinant protein in the edible part (endosperm) of the rice grain and describes methods for the analysis of transgenic rice seeds in detail.

Ethanol production by recombinant hosts

DOEpatents

Fowler, David E.; Horton, Philip G.; Ben-Bassat, Arie

1996-01-01

Novel plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase are described. Also described are recombinant hosts which have been transformed with genes coding for alcohol dehydrogenase and pyruvate. By virtue of their transformation with these genes, the recombinant hosts are capable of producing significant amounts of ethanol as a fermentation product. Also disclosed are methods for increasing the growth of recombinant hosts and methods for reducing the accumulation of undesirable metabolic products in the growth medium of these hosts. Also disclosed are recombinant host capable of producing significant amounts of ethanol as a fermentation product of oligosaccharides and plasmids comprising genes encoding polysaccharases, in addition to the genes described above which code for the alcohol dehydrogenase and pyruvate decarboxylase. Further, methods are described for producing ethanol from oligomeric feedstock using the recombinant hosts described above. Also provided is a method for enhancing the production of functional proteins in a recombinant host comprising overexpressing an adhB gene in the host. Further provided are process designs for fermenting oligosaccharide-containing biomass to ethanol.

Ethanol production by recombinant hosts

DOEpatents

Ingram, Lonnie O.; Beall, David S.; Burchhardt, Gerhard F. H.; Guimaraes, Walter V.; Ohta, Kazuyoshi; Wood, Brent E.; Shanmugam, Keelnatham T.

1995-01-01

Novel plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase are described. Also described are recombinant hosts which have been transformed with genes coding for alcohol dehydrogenase and pyruvate. By virtue of their transformation with these genes, the recombinant hosts are capable of producing significant amounts of ethanol as a fermentation product. Also disclosed are methods for increasing the growth of recombinant hosts and methods for reducing the accumulation of undesirable metabolic products in the growth medium of these hosts. Also disclosed are recombinant host capable of producing significant amounts of ethanol as a fermentation product of oligosaccharides and plasmids comprising genes encoding polysaccharases, in addition to the genes described above which code for the alcohol dehydrogenase and pyruvate decarboxylase. Further, methods are described for producing ethanol from oligomeric feedstock using the recombinant hosts described above. Also provided is a method for enhancing the production of functional proteins in a recombinant host comprising overexpressing an adhB gene in the host. Further provided are process designs for fermenting oligosaccharide-containing biomass to ethanol.

Ethanol precipitation for purification of recombinant antibodies.

PubMed

Tscheliessnig, Anne; Satzer, Peter; Hammerschmidt, Nikolaus; Schulz, Henk; Helk, Bernhard; Jungbauer, Alois

2014-10-20

Currently, the golden standard for the purification of recombinant humanized antibodies (rhAbs) from CHO cell culture is protein A chromatography. However, due to increasing rhAbs titers alternative methods have come into focus. A new strategy for purification of recombinant human antibodies from CHO cell culture supernatant based on cold ethanol precipitation (CEP) and CaCl2 precipitation has been developed. This method is based on the cold ethanol precipitation, the process used for purification of antibodies and other components from blood plasma. We proof the applicability of the developed process for four different antibodies resulting in similar yield and purity as a protein A chromatography based process. This process can be further improved using an anion-exchange chromatography in flowthrough mode e.g. a monolith as last step so that residual host cell protein is reduced to a minimum. Beside the ethanol based process, our data also suggest that ethanol could be replaced with methanol or isopropanol. The process is suited for continuous operation. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Investigation of chromatography and polymer/salt aqueous two-phase processes for downstream processing development of recombinant phenylalanine dehydrogenase.

PubMed

Omidinia, Eskandar; Shahbaz Mohamadi, Hamid; Dinarvand, Rassoul; Taherkhani, Heshmat-Allah

2010-03-01

This work presents a comprehensive study between the polymer/salt aqueous two-phase systems (ATPS) and chromatography process for downstream processing of recombinant Bacillus badius phenylalanine dehydrogenase (PheDH). First, the partitioning behavior of recombinant PheDH in polyethylene glycol (PEG)/K2HPO4 ATPS was examined. For comparative purpose, a classical chromatographic protocol was performed as well. Investigation of chromatography and ATPS procedures revealed that the ATPS comprising of 9% (w/w) PEG-6000, 16% (w/w) K2HPO4 and 16% (w/w) KCl with pH of 8.0, volume ratio (V ( R )) of 0.25, temperature of 25 degrees C and 40% (w/w) cell lysate ensured the most favorable approach for PheDH downstream process. A specific activity of 4,231.4 U/mg, a yield of 96.7% and a recovery of 162.0% were obtained. Furthermore, the shorter process time (4 vs. 48 h) and the lower total cost (4 vs. 20 euro) were additionally features that confirmed the suitability of proposed technique.

Requirement of mismatch repair genes MSH2 and MSH3 in the RAD1-RAD10 pathway of mitotic recombination in Saccharomyces cerevisiae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saparbaev, M.; Prakash, L.; Prakash, S.

1996-03-01

The RAD1 and RAD10 genes of Saccharomyces cerevisiae are required for nucleotide excision repair and they also act in mitotic recombination. The Rad1-Rad10 complex has a single-stranded DNA endonuclease activity. Here, we show that the mismatch repair genes MSH2 and MSH3 function in mitotic recombination. For both his3 and his4 duplications, and for homologous integration of a linear DNA fragment into the genome, the msh3-A mutation has an effect on recombination similar to that of the rad1{Delta} and rad10{Delta} mutations. The msh2{Delta} mutation also reduces the rate of recombination of the his3 duplication and lowers the incidence of homologous integrationmore » of a linear DNA fragment. Epistasis analyses indicate that MSH2 and MSH3 function in the RAD1-RAD10 recombination pathway, and studies presented here suggest an involvement of the RAM-RAD10 pathway in reciprocal recombination. The possible roles of Msh2, Msh3, Rad1, and Rad10 proteins in genetic recombination are discussed. Coupling of mismatch binding proteins with the recombinational machinery could be important for ensuring genetic fidelity in the recombination process. 59 refs., 2 figs., 7 tabs.« less

Requirement of mismatch repair genes MSH2 and MSH3 in the RAD1-RAD10 pathway of mitotic recombination in Saccharomyces cerevisiae.

PubMed

Saparbaev, M; Prakash, L; Prakash, S

1996-03-01

The RAD1 and RAD10 genes of Saccharomyces cerevisiae are required for nucleotide excision repair and they also act in mitotic recombination. The Rad1-Rad10 complex has a single-stranded DNA endonuclease activity. Here, we show that the mismatch repair genes MSH2 and MSH3 function in mitotic recombination. For both his3 and his4 duplications, and for homologous integration of a linear DNA fragment into the genome, the msh3 delta mutation has an effect on recombination similar to that of the rad1 delta and rad10 delta mutations. The msh2 delta mutation also reduces the rate of recombination of the his3 duplication and lowers the incidence of homologous integration of a linear DNA fragment. Epistasis analyses indicate that MSH2 and MSH3 function in the RAD1-RAD10 recombination pathway, and studies presented here suggest an involvement of the RAD1-RAD10 pathway in reciprocal recombination. The possible roles of Msh2, Msh3, Rad1, and Rad10 proteins in genetic recombination are discussed. Coupling of mismatch binding proteins with the recombinational machinery could be important for ensuring genetic fidelity in the recombination process.

The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data.

PubMed

Booker, Tom R; Ness, Rob W; Keightley, Peter D

2017-09-01

Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies. In this study, we constructed fine-scale recombination rate maps for a natural population of the Eastern house mouse, Mus musculus castaneus We performed simulations to assess the accuracy of recombination rate inference in the presence of phase errors, and we used a novel approach to quantify phase error. The spatial distribution of recombination events is strongly positively correlated between our castaneus map, and a map constructed using inbred lines derived predominantly from M. m. domesticus Recombination hotspots in wild castaneus show little overlap, however, with the locations of double-strand breaks in wild-derived house mouse strains. Finally, we also find that genetic diversity in M. m. castaneus is positively correlated with the rate of recombination, consistent with pervasive natural selection operating in the genome. Our study suggests that recombination rate variation is conserved at broad scales between house mouse subspecies, but it is not strongly conserved at fine scales. Copyright © 2017 by the Genetics Society of America.

RECOMBINATION PROCESSES AND NATURE OF THE TAIL AND GAP STATES IN a-Si:H and a-Si:H/a-SiNx:H MULTILAYERS

NASA Astrophysics Data System (ADS)

Morigaki, K.

We discuss recombination processes and nature of the tail and gap states in a-Si:H and a-Si:H/a-SiNx:H multilayers on the basis of our ODMR, luminescence, photoinduced absorption and ENDOR measurements. We present other results relevant to this subject and attempt to interpret them in terms of our model.

[Recombinant granulocyte-colony stimulating factor (filgrastim): optimization of conditions of isolation and purification from inclusion body].

PubMed

Kononova, N V; Iakovlev, A V; Zhuravko, A M; Pankeev, N N; Minaev, S V; Bobruskin, A I; Mart'ianov, V A

2014-01-01

We developed a unified process platform for two recombinant human GCSF medicines--one with the non-prolonged and the other with prolonged action. This unified technology led to a simpler and cheaper production while introduction of the additional pegylation stage to the technological line eased obtaining of the medicines with different action and allowed to standardize technological process documenting according to GMP requirements.

Theoretical prediction of the impact of Auger recombination on charge collection from an ion track

NASA Technical Reports Server (NTRS)

Edmonds, Larry D.

1991-01-01

A recombination mechanism that significantly reduces charge collection from very dense ion tracks in silicon devices was postulated by Zoutendyk et al. The theoretical analysis presented here concludes that Auger recombination is such a mechanism and is of marginal importance for higher density tracks produced by 270-MeV krypton, but of major importance for higher density tracks. The analysis shows that recombination loss is profoundly affected by track diffusion. As the track diffuses, the density and recombination rate decrease so fast that the linear density (number of electron-hole pairs per unit length) approaches a non-zero limiting value as t yields infinity. Furthermore, the linear density is very nearly equal to this limiting value in a few picoseconds or less. When Auger recombination accompanies charge transport processes that have much longer time scales, it can be simulated by assigning a reduced linear energy transfer to the ion.

Putative recombination events and evolutionary history of five economically important viruses of fruit trees based on coat protein-encoding gene sequence analysis.

PubMed

Boulila, Moncef

2010-06-01

To enhance the knowledge of recombination as an evolutionary process, 267 accessions retrieved from GenBank were investigated, all belonging to five economically important viruses infecting fruit crops (Plum pox, Apple chlorotic leaf spot, Apple mosaic, Prune dwarf, and Prunus necrotic ringspot viruses). Putative recombinational events were detected in the coat protein (CP)-encoding gene using RECCO and RDP version 3.31beta algorithms. Based on RECCO results, all five viruses were shown to contain potential recombination signals in the CP gene. Reconstructed trees with modified topologies were proposed. Furthermore, RECCO performed better than the RDP package in detecting recombination events and exhibiting their evolution rate along the sequences of the five viruses. RDP, however, provided the possible major and minor parents of the recombinants. Thus, the two methods should be considered complementary.

Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee, Apis mellifera

PubMed Central

Wallberg, Andreas; Glémin, Sylvain; Webster, Matthew T.

2015-01-01

Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 – 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution. PMID:25902173

Processing of human cytomegalovirus glycoprotein B in recombinant adenovirus-infected cells.

PubMed

Marshall, G S; Fenger, D P; Stout, G G; Knights, M E; Hunt, L A

1996-07-01

Intracellular processing of human cytomegalovirus (HCMV) glycoprotein B (gB; gpUL55) expressed by a recombinant adenovirus (Ad-gB) was studied in human A549 cells as processing events could affect immunogenicity when such viruses are used as live-recombinant vaccines. Cleavage of [35S]methionine-labelled gp13O into gp93 and gp55 reached a maximum after a 3 h chase. Cleavage was completely inhibited by brefeldin A, suggesting that processing normally occurs as a late Golgi or post-Golgi event. Uncleaved gp 130 remained completely sensitive to endo-beta-N-acetylglucosaminidase H (Endo-H) in untreated cells following long chase periods, indicating high-mannose oligosaccharides at all of the 18 N-linked glycosylation sites (Asn-X-Ser/Thr) and retention in the endoplasmic reticulum. Endo-H analysis of gp55 from swainsonine-treated and untreated cells was consistent with glycosylation at all three potential sites, with two oligosaccharides remaining sensitive to Endo-H and one being processed to Endo-H resistance. The heavily glycosylated N-terminal gp93 subunit was not detected by [35S]methionine-labelling but was easily detected along with gp55 after labelling with [3H]mannose. No cleavage of gp 130 was observed in analogous pulse-chase radiolabelling of Ad-gB-infected human fibroblasts, even though these cells are permissive for HCMV replication and can process the native gB molecule. Processing of gB in recombinant adenovirus-infected A549 cells was generally similar to that previously reported for native gB in HCMV-infected fibroblasts.

Use of a protein engineering strategy to overcome limitations in the production of "Difficult to Express" recombinant proteins.

PubMed

Hussain, Hirra; Fisher, David I; Abbott, W Mark; Roth, Robert G; Dickson, Alan J

2017-10-01

Certain recombinant proteins are deemed "difficult to express" in mammalian expression systems requiring significant cell and/or process engineering to abrogate expression bottlenecks. With increasing demand for the production of recombinant proteins in mammalian cells, low protein yields can have significant consequences for industrial processes. To investigate the molecular mechanisms that restrict expression of recombinant proteins, naturally secreted model proteins were analyzed from the tissue inhibitors of metalloproteinase (TIMP) protein family. In particular, TIMP-2 and TIMP-3 were subjected to detailed study. TIMP proteins share significant sequence homology (∼50% identity and ∼70% similarity in amino acid sequence). However, they show marked differences in secretion in mammalian expression systems despite this extensive sequence homology. Using these two proteins as models, this study characterized the molecular mechanisms responsible for poor recombinant protein production. Our results reveal that both TIMP-2 and TIMP-3 are detectable at mRNA and protein level within the cell but only TIMP-2 is secreted effectively into the extracellular medium. Analysis of protein localization and the nature of intracellular protein suggest TIMP-3 is severely limited in its post-translational processing. To overcome this challenge, modification of the TIMP-3 sequence to include a furin protease-cleavable pro-sequence resulted in secretion of the modified TIMP-3 protein, however, incomplete processing was observed. Based on the TIMP-3 data, the protein engineering approach was optimized and successfully applied in combination with cell engineering, the overexpression of furin, to another member of the TIMP protein family (the poorly expressed TIMP-4). Use of the described protein engineering strategy resulted in successful secretion of poorly (TIMP-4) and non-secreted (TIMP-3) targets, and presents a novel strategy to enhance the production of "difficult" recombinant targets. Biotechnol. Bioeng. 2017;114: 2348-2359. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing.

PubMed

Cartwright, Joseph F; Anderson, Karin; Longworth, Joseph; Lobb, Philip; James, David C

2018-06-01

High-fidelity replication of biologic-encoding recombinant DNA sequences by engineered mammalian cell cultures is an essential pre-requisite for the development of stable cell lines for the production of biotherapeutics. However, immortalized mammalian cells characteristically exhibit an increased point mutation frequency compared to mammalian cells in vivo, both across their genomes and at specific loci (hotspots). Thus unforeseen mutations in recombinant DNA sequences can arise and be maintained within producer cell populations. These may affect both the stability of recombinant gene expression and give rise to protein sequence variants with variable bioactivity and immunogenicity. Rigorous quantitative assessment of recombinant DNA integrity should therefore form part of the cell line development process and be an essential quality assurance metric for instances where synthetic/multi-component assemblies are utilized to engineer mammalian cells, such as the assessment of recombinant DNA fidelity or the mutability of single-site integration target loci. Based on Pacific Biosciences (Menlo Park, CA) single molecule real-time (SMRT™) circular consensus sequencing (CCS) technology we developed a rDNA sequence analysis tool to process the multi-parallel sequencing of ∼40,000 single recombinant DNA molecules. After statistical filtering of raw sequencing data, we show that this analytical method is capable of detecting single point mutations in rDNA to a minimum single mutation frequency of 0.0042% (<1/24,000 bases). Using a stable CHO transfectant pool harboring a randomly integrated 5 kB plasmid construct encoding GFP we found that 28% of recombinant plasmid copies contained at least one low frequency (<0.3%) point mutation. These mutations were predominantly found in GC base pairs (85%) and that there was no positional bias in mutation across the plasmid sequence. There was no discernable difference between the mutation frequencies of coding and non-coding DNA. The putative ratio of non-synonymous and synonymous changes within the open reading frames (ORFs) in the plasmid sequence indicates that natural selection does not impact upon the prevalence of these mutations. Here we have demonstrated the abundance of mutations that fall outside of the reported range of detection of next generation sequencing (NGS) and second generation sequencing (SGS) platforms, providing a methodology capable of being utilized in cell line development platforms to identify the fidelity of recombinant genes throughout the production process. © 2018 Wiley Periodicals, Inc.

Vibroacoustic processes and structural variations in muscular tissue

NASA Astrophysics Data System (ADS)

Antonets, V. A.; Klochkov, B. N.; Kovaleva, E. P.

1995-03-01

This paper reviews the problems and results obtained in the course of experimental and theoretical investigations of the vibroacoustic activity of contracting muscles. Two types of such processes are examined: (1) acoustic vibrations due to the macromolecular recombinations of muscle proteins, which are responsible for the muscle contraction, and (2) acoustic vibrations associated with the finite accuracy and speed of the receptor-effector system that controls the muscle contraction. By investigating the acoustic vibrations, we examine structural recombinations (conformation variations) in macromolecules during mechanochemical reactions. Since chemical reactions of macromolecules are always accompanied by conformational recombinations, the generation mechanism, which is responsible for the contraction processes in a muscular tissue, can also be extended to other macromolecular media. Investigation of infrasound vibrations makes it possible to explore the quality and error of control for the processes in the muscle under different types of loading. Since a living body is controlled via perceptions, the latter can be quantitatively estimated by the parametess of infrasound vibrations.

Solid methane in neutron radiation: Cryogenic moderators and cometary cryo volcanism

NASA Astrophysics Data System (ADS)

Kirichek, O.; Lawson, C. R.; Jenkins, D. M.; Ridley, C. J. T.; Haynes, D. J.

2017-12-01

The effect of ionizing radiation on solid methane has previously been an area of interest in the astrophysics community. In the late 1980s this interest was further boosted by the possibility of using solid methane as a moderating medium in spallation neutron sources. Here we present test results of solid methane moderators commissioned at the ISIS neutron source, and compare them with a model based on the theory of thermal explosion. Good agreement between the moderator test data and our model suggests that the process of radiolysis defect recombination happens at two different temperature ranges: the ;lower temperature; recombination process occurs at around 20 K, with the ;higher temperature; process taking place between 50 and 60 K. We discuss consequences of this mechanism for the designing and operation of solid methane moderators used in advanced neutron sources. We also discuss the possible role of radiolysis defect recombination processes in cryo-volcanism on comets, and suggest an application based on this phenomenon.

Rhizomucor miehei triglyceride lipase is processed and secreted from transformed Aspergillus oryzae.

PubMed

Huge-Jensen, B; Andreasen, F; Christensen, T; Christensen, M; Thim, L; Boel, E

1989-09-01

The cDNA encoding the precursor of the Rhizomucor miehei triglyceride lipase was inserted in an Aspergillus oryzae expression vector. In this vector the expression of the lipase cDNA is under control of the Aspergillus oryzae alpha-amylase gene promoter and the Aspergillus niger glucoamylase gene terminator. The recombinant plasmid was introduced into Aspergillus oryzae, and transformed colonies were selected and screened for lipase expression. Lipase-positive transformants were grown in a small fermentor, and recombinant triglyceride lipase was purified from the culture broth. The purified enzymatically active recombinant lipase (rRML) secreted from A. oryzae was shown to have the same characteristics with respect to mobility on reducing SDS-gels and amino acid composition as the native enzyme. N-terminal amino acid sequencing indicated that approximately 70% of the secreted rRML had the same N-terminal sequence as the native Rhizomucor miehei enzyme, whereas 30% of the secreted rRML was one amino acid residue shorter in the N-terminal. The recombinant lipase precursor, which has a 70 amino acid propeptide, is thus processed in and secreted from Aspergillus oryzae. We have hereby demonstrated the utility of this organism as a host for the production of recombinant triglyceride lipases.

Joint Molecule Resolution Requires the Redundant Activities of MUS-81 and XPF-1 during Caenorhabditis elegans Meiosis

PubMed Central

O'Neil, Nigel J.; Martin, Julie S.; Youds, Jillian L.; Ward, Jordan D.; Petalcorin, Mark I. R.; Rose, Anne M.; Boulton, Simon J.

2013-01-01

The generation and resolution of joint molecule recombination intermediates is required to ensure bipolar chromosome segregation during meiosis. During wild type meiosis in Caenorhabditis elegans, SPO-11-generated double stranded breaks are resolved to generate a single crossover per bivalent and the remaining recombination intermediates are resolved as noncrossovers. We discovered that early recombination intermediates are limited by the C. elegans BLM ortholog, HIM-6, and in the absence of HIM-6 by the structure specific endonuclease MUS-81. In the absence of both MUS-81 and HIM-6, recombination intermediates persist, leading to chromosome breakage at diakinesis and inviable embryos. MUS-81 has an additional role in resolving late recombination intermediates in C. elegans. mus-81 mutants exhibited reduced crossover recombination frequencies suggesting that MUS-81 is required to generate a subset of meiotic crossovers. Similarly, the Mus81-related endonuclease XPF-1 is also required for a subset of meiotic crossovers. Although C. elegans gen-1 mutants have no detectable meiotic defect either alone or in combination with him-6, mus-81 or xpf-1 mutations, mus-81;xpf-1 double mutants are synthetic lethal. While mus-81;xpf-1 double mutants are proficient for the processing of early recombination intermediates, they exhibit defects in the post-pachytene chromosome reorganization and the asymmetric disassembly of the synaptonemal complex, presumably triggered by crossovers or crossover precursors. Consistent with a defect in resolving late recombination intermediates, mus-81; xpf-1 diakinetic bivalents are aberrant with fine DNA bridges visible between two distinct DAPI staining bodies. We were able to suppress the aberrant bivalent phenotype by microinjection of activated human GEN1 protein, which can cleave Holliday junctions, suggesting that the DNA bridges in mus-81; xpf-1 diakinetic oocytes are unresolved Holliday junctions. We propose that the MUS-81 and XPF-1 endonucleases act redundantly to process late recombination intermediates to form crossovers during C. elegans meiosis. PMID:23874209

Development of a silicon limitation inducible expression system for recombinant protein production in the centric diatoms Thalassiosira pseudonana and Cyclotella cryptica

DOE PAGES

Shrestha, Roshan P.; Hildebrand, Mark

2017-08-17

An inducible promoter for recombinant protein expression provides substantial benefits because under induction conditions cellular energy and metabolic capability can be directed into protein synthesis. The most widely used inducible promoter for diatoms is for nitrate reductase, however, nitrogen metabolism is tied into diverse aspects of cellular function, and the induction response is not necessarily robust. Silicon limitation offers a means to eliminate energy and metabolic flux into cell division processes, with little other detrimental effect on cellular function, and a protein expression system that works under those conditions could be advantageous. In this study, we evaluate a number ofmore » promoters for recombinant protein expression induced by silicon limitation and repressed by the presence of silicon in the diatoms Thalassiosira pseudonana and Cyclotella cryptica. In addition to silicon limitation, we describe additional strategies to elevate recombinant protein expression level, including inclusion of the 5' fragment of the coding region of the native gene and reducing carbon flow into ancillary processes of pigment synthesis and formation of photosynthetic storage products. We achieved yields of eGFP to 1.8% of total soluble protein in C. cryptica, which is about 3.6-fold higher than that obtained with chloroplast expression and ninefold higher than nuclear expression in another well-established algal system. Our studies demonstrate that the combination of inducible promoter and other strategies can result in robust expression of recombinant protein in a nuclear-based expression system in diatoms under silicon limited conditions, separating the protein expression regime from growth processes and improving overall recombinant protein yields.« less

Development of a silicon limitation inducible expression system for recombinant protein production in the centric diatoms Thalassiosira pseudonana and Cyclotella cryptica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shrestha, Roshan P.; Hildebrand, Mark

An inducible promoter for recombinant protein expression provides substantial benefits because under induction conditions cellular energy and metabolic capability can be directed into protein synthesis. The most widely used inducible promoter for diatoms is for nitrate reductase, however, nitrogen metabolism is tied into diverse aspects of cellular function, and the induction response is not necessarily robust. Silicon limitation offers a means to eliminate energy and metabolic flux into cell division processes, with little other detrimental effect on cellular function, and a protein expression system that works under those conditions could be advantageous. In this study, we evaluate a number ofmore » promoters for recombinant protein expression induced by silicon limitation and repressed by the presence of silicon in the diatoms Thalassiosira pseudonana and Cyclotella cryptica. In addition to silicon limitation, we describe additional strategies to elevate recombinant protein expression level, including inclusion of the 5' fragment of the coding region of the native gene and reducing carbon flow into ancillary processes of pigment synthesis and formation of photosynthetic storage products. We achieved yields of eGFP to 1.8% of total soluble protein in C. cryptica, which is about 3.6-fold higher than that obtained with chloroplast expression and ninefold higher than nuclear expression in another well-established algal system. Our studies demonstrate that the combination of inducible promoter and other strategies can result in robust expression of recombinant protein in a nuclear-based expression system in diatoms under silicon limited conditions, separating the protein expression regime from growth processes and improving overall recombinant protein yields.« less

Optimization of Ammonium Sulfate Concentration for Purification of Colorectal Cancer Vaccine Candidate Recombinant Protein GA733-FcK Isolated from Plants.

PubMed

Park, Se-Ra; Lim, Chae-Yeon; Kim, Deuk-Su; Ko, Kisung

2015-01-01

A protein purification procedure is required to obtain high-value recombinant injectable vaccine proteins produced in plants as a bioreactor. However, existing purification procedures for plant-derived recombinant proteins are often not optimized and are inefficient, with low recovery rates. In our previous study, we used 25-30% ammonium sulfate to precipitate total soluble proteins (TSPs) in purification process for recombinant proteins from plant leaf biomass which has not been optimized. Thus, the objective in this study is to optimize the conditions for plant-derived protein purification procedures. Various ammonium sulfate concentrations (15-80%) were compared to determine their effects on TSPs yield. With 50% ammonium sulfate, the yield of precipitated TSP was the highest, and that of the plant-derived colorectal cancer-specific surface glycoprotein GA733 fused to the Fc fragment of human IgG tagged with endoplasmic reticulum retention signal KDEL (GA733(P)-FcK) protein significantly increased 1.8-fold. SDS-PAGE analysis showed that the purity of GA733(P)-FcK protein band appeared to be similar to that of an equal dose of mammalian-derived GA733-Fc (GA733(M)-Fc). The binding activity of purified GA733(P)-FcK to anti-GA733 mAb was as efficient as the native GA733(M)-Fc. Thus, the purification process was effectively optimized for obtaining a high yield of plant-derived antigenic protein with good quality. In conclusion, the purification recovery rate of large quantities of recombinant protein from plant expression systems can be enhanced via optimization of ammonium sulfate concentration during downstream processes, thereby offering a promising solution for production of recombinant GA733-Fc protein in plants.

Search for Randall-Sundrum gravitons in the dielectron and diphoton final states with 5.4  fb(-1) of data from pp collisions at square root(s) = 1.96  TeV.

PubMed

Abazov, V M; Abbott, B; Abolins, M; Acharya, B S; Adams, M; Adams, T; Aguilo, E; Alexeev, G D; Alkhazov, G; Alton, A; Alverson, G; Alves, G A; Ancu, L S; Aoki, M; Arnoud, Y; Arov, M; Askew, A; Asman, B; Atramentov, O; Avila, C; Backus Mayes, J; Badaud, F; Bagby, L; Baldin, B; Bandurin, D V; Banerjee, S; Barberis, E; Barfuss, A-F; Baringer, P; Barreto, J; Bartlett, J F; Bassler, U; Beale, S; Bean, A; Begalli, M; Begel, M; Belanger-Champagne, C; Bellantoni, L; Benitez, J A; Beri, S B; Bernardi, G; Bernhard, R; Bertram, I; Besançon, M; Beuselinck, R; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Blazey, G; Blessing, S; Bloom, K; Boehnlein, A; Boline, D; Bolton, T A; Boos, E E; Borissov, G; Bose, T; Brandt, A; Brock, R; Brooijmans, G; Bross, A; Brown, D; Bu, X B; Buchholz, D; Buehler, M; Buescher, V; Bunichev, V; Burdin, S; Burnett, T H; Buszello, C P; Calfayan, P; Calpas, B; Calvet, S; Camacho-Pérez, E; Cammin, J; Carrasco-Lizarraga, M A; Carrera, E; Casey, B C K; Castilla-Valdez, H; Chakrabarti, S; Chakraborty, D; Chan, K M; Chandra, A; Chen, G; Chevalier-Théry, S; Cho, D K; Cho, S W; Choi, S; Choudhary, B; Christoudias, T; Cihangir, S; Claes, D; Clutter, J; Cooke, M S; Cooke, M; Cooper, W E; Corcoran, M; Couderc, F; Cousinou, M-C; Croc, A; Cutts, D; Cwiok, M; Das, A; Davies, G; De, K; de Jong, S J; De la Cruz-Burelo, E; DeVaughan, K; Déliot, F; Demarteau, M; Demina, R; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Dominguez, A; Dorland, T; Dubey, A; Dudko, L V; Duggan, D; Duperrin, A; Dutt, S; Dyshkant, A; Eads, M; Edmunds, D; Ellison, J; Elvira, V D; Enari, Y; Eno, S; Evans, H; Evdokimov, A; Evdokimov, V N; Facini, G; Ferapontov, A V; Ferbel, T; Fiedler, F; Filthaut, F; Fisher, W; Fisk, H E; Fortner, M; Fox, H; Fuess, S; Gadfort, T; Garcia-Bellido, A; Gavrilov, V; Gay, P; Geist, W; Geng, W; Gerbaudo, D; Gerber, C E; Gershtein, Y; Gillberg, D; Ginther, G; Golovanov, G; Goussiou, A; Grannis, P D; Greder, S; Greenlee, H; Greenwood, Z D; Gregores, E M; Grenier, G; Gris, Ph; Grivaz, J-F; Grohsjean, A; Grünendahl, S; Grünewald, M W; Guo, F; Guo, J; Gutierrez, G; Gutierrez, P; Haas, A; Haefner, P; Hagopian, S; Haley, J; Hall, I; Han, L; Harder, K; Harel, A; Hauptman, J M; Hays, J; Hebbeker, T; Hedin, D; Heinson, A P; Heintz, U; Hensel, C; Heredia-De la Cruz, I; Herner, K; Hesketh, G; Hildreth, M D; Hirosky, R; Hoang, T; Hobbs, J D; Hoeneisen, B; Hohlfeld, M; Hossain, S; Houben, P; Hu, Y; Hubacek, Z; Huske, N; Hynek, V; Iashvili, I; Illingworth, R; Ito, A S; Jabeen, S; Jaffré, M; Jain, S; Jamin, D; Jesik, R; Johns, K; Johnson, C; Johnson, M; Johnston, D; Jonckheere, A; Jonsson, P; Juste, A; Kaadze, K; Kajfasz, E; Karmanov, D; Kasper, P A; Katsanos, I; Kehoe, R; Kermiche, S; Khalatyan, N; Khanov, A; Kharchilava, A; Kharzheev, Y N; Khatidze, D; Kirby, M H; Kirsch, M; Kohli, J M; Kozelov, A V; Kraus, J; Kumar, A; Kupco, A; Kurca, T; Kuzmin, V A; Kvita, J; Lammers, S; Landsberg, G; Lebrun, P; Lee, H S; Lee, W M; Lellouch, J; Li, L; Li, Q Z; Lietti, S M; Lim, J K; Lincoln, D; Linnemann, J; Lipaev, V V; Lipton, R; Liu, Y; Liu, Z; Lobodenko, A; Lokajicek, M; Love, P; Lubatti, H J; Luna-Garcia, R; Lyon, A L; Maciel, A K A; Mackin, D; Madar, R; Magaña-Villalba, R; Mal, P K; Malik, S; Malyshev, V L; Maravin, Y; Martínez-Ortega, J; McCarthy, R; McGivern, C L; Meijer, M M; Melnitchouk, A; Menezes, D; Mercadante, P G; Merkin, M; Meyer, A; Meyer, J; Mondal, N K; Moulik, T; Muanza, G S; Mulhearn, M; Nagy, E; Naimuddin, M; Narain, M; Nayyar, R; Neal, H A; Negret, J P; Neustroev, P; Nilsen, H; Novaes, S F; Nunnemann, T; Obrant, G; Onoprienko, D; Orduna, J; Osman, N; Osta, J; Otero y Garzón, G J; Owen, M; Padilla, M; Pangilinan, M; Parashar, N; Parihar, V; Park, S-J; Park, S K; Parsons, J; Partridge, R; Parua, N; Patwa, A; Penning, B; Perfilov, M; Peters, K; Peters, Y; Petrillo, G; Pétroff, P; Piegaia, R; Piper, J; Pleier, M-A; Podesta-Lerma, P L M; Podstavkov, V M; Pol, M-E; Polozov, P; Popov, A V; Prewitt, M; Price, D; Protopopescu, S; Qian, J; Quadt, A; Quinn, B; Rangel, M S; Ranjan, K; Ratoff, P N; Razumov, I; Renkel, P; Rich, P; Rijssenbeek, M; Ripp-Baudot, I; Rizatdinova, F; Rominsky, M; Royon, C; Rubinov, P; Ruchti, R; Safronov, G; Sajot, G; Sánchez-Hernández, A; Sanders, M P; Sanghi, B; Savage, G; Sawyer, L; Scanlon, T; Schaile, D; Schamberger, R D; Scheglov, Y; Schellman, H; Schliephake, T; Schlobohm, S; Schwanenberger, C; Schwienhorst, R; Sekaric, J; Severini, H; Shabalina, E; Shary, V; Shchukin, A A; Shivpuri, R K; Simak, V; Sirotenko, V; Skubic, P; Slattery, P; Smirnov, D; Snow, G R; Snow, J; Snyder, S; Söldner-Rembold, S; Sonnenschein, L; Sopczak, A; Sosebee, M; Soustruznik, K; Spurlock, B; Stark, J; Stolin, V; Stoyanova, D A; Strang, M A; Strauss, E; Strauss, M; Ströhmer, R; Strom, D; Stutte, L; Svoisky, P; Takahashi, M; Tanasijczuk, A; Taylor, W; Tiller, B; Titov, M; Tokmenin, V V; Tsybychev, D; Tuchming, B; Tully, C; Tuts, P M; Unalan, R; Uvarov, L; Uvarov, S; Uzunyan, S; Van Kooten, R; van Leeuwen, W M; Varelas, N; Varnes, E W; Vasilyev, I A; Verdier, P; Vertogradov, L S; Verzocchi, M; Vesterinen, M; Vilanova, D; Vint, P; Vokac, P; Wahl, H D; Wang, M H L S; Warchol, J; Watts, G; Wayne, M; Weber, G; Weber, M; Wetstein, M; White, A; Wicke, D; Williams, M R J; Wilson, G W; Wimpenny, S J; Wobisch, M; Wood, D R; Wyatt, T R; Xie, Y; Xu, C; Yacoob, S; Yamada, R; Yang, W-C; Yasuda, T; Yatsunenko, Y A; Ye, Z; Yin, H; Yip, K; Yoo, H D; Youn, S W; Yu, J; Zelitch, S; Zhao, T; Zhou, B; Zhou, N; Zhu, J; Zielinski, M; Zieminska, D; Zivkovic, L

2010-06-18

Using 5.4  fb(-1) of integrated luminosity from pp collisions at square root(s)=1.96  TeV collected by the D0 detector at the Fermilab Tevatron Collider, we search for decays of the lightest Kaluza-Klein mode of the graviton in the Randall-Sundrum model to ee and γγ. We set 95% C.L. lower limits on the mass of the lightest graviton between 560 and 1050 GeV for values of the coupling k/M(Pl) between 0.01 and 0.1.

Improvements to the RADIOM non-LTE model

NASA Astrophysics Data System (ADS)

Busquet, M.; Colombant, D.; Klapisch, M.; Fyfe, D.; Gardner, J.

2009-12-01

In 1993, we proposed the RADIOM model [M. Busquet, Phys. Fluids 85 (1993) 4191] where an ionization temperature T z is used to derive non-LTE properties from LTE data. T z is obtained from an "extended Saha equation" where unbalanced transitions, like radiative decay, give the non-LTE behavior. Since then, major improvements have been made. T z has been shown to be more than a heuristic value, but describes the actual distribution of excited and ionized states and can be understood as an "effective temperature". Therefore we complement the extended Saha equation by introducing explicitly the auto-ionization/dielectronic capture. Also we use the SCROLL model to benchmark the computed values of T z.

Cross section for b b ¯ production via dielectrons in d + Au collisions at √{sN N}=200 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Al-Bataineh, H.; Alexander, J.; Angerami, A.; Aoki, K.; Apadula, N.; Aramaki, Y.; Atomssa, E. T.; Averbeck, R.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Baksay, G.; Baksay, L.; Barish, K. N.; Bassalleck, B.; Basye, A. T.; Bathe, S.; Baublis, V.; Baumann, C.; Bazilevsky, A.; Belikov, S.; Belmont, R.; Bennett, R.; Bhom, J. H.; Blau, D. S.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Buesching, H.; Bumazhnov, V.; Bunce, G.; Butsyk, S.; Campbell, S.; Caringi, A.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choudhury, R. K.; Christiansen, P.; Chujo, T.; Chung, P.; Chvala, O.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Conesa Del Valle, Z.; Connors, M.; Csanád, M.; Csörgő, T.; Dahms, T.; Dairaku, S.; Danchev, I.; Das, K.; Datta, A.; David, G.; Dayananda, M. K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Dharmawardane, K. V.; Dietzsch, O.; Dion, A.; Donadelli, M.; Drapier, O.; Drees, A.; Drees, K. A.; Durham, J. M.; Durum, A.; Dutta, D.; D'Orazio, L.; Edwards, S.; Efremenko, Y. V.; Ellinghaus, F.; Engelmore, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Fadem, B.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Fraenkel, Z.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fujiwara, K.; Fukao, Y.; Fusayasu, T.; Garishvili, I.; Glenn, A.; Gong, H.; Gonin, M.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grim, G.; Grosse Perdekamp, M.; Gunji, T.; Gustafsson, H.-Å.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamblen, J.; Han, R.; Hanks, J.; Haslum, E.; Hayano, R.; He, X.; Heffner, M.; Hemmick, T. K.; Hester, T.; Hill, J. C.; Hohlmann, M.; Holzmann, W.; Homma, K.; Hong, B.; Horaguchi, T.; Hornback, D.; Huang, S.; Ichihara, T.; Ichimiya, R.; Ikeda, Y.; Imai, K.; Inaba, M.; Isenhower, D.; Ishihara, M.; Issah, M.; Ivanischev, D.; Iwanaga, Y.; Jacak, B. V.; Jia, J.; Jiang, X.; Jin, J.; Johnson, B. M.; Jones, T.; Joo, K. S.; Jouan, D.; Jumper, D. S.; Kajihara, F.; Kamin, J.; Kang, J. H.; Kapustinsky, J.; Karatsu, K.; Kasai, M.; Kawall, D.; Kawashima, M.; Kazantsev, A. V.; Kempel, T.; Khanzadeev, A.; Kijima, K. M.; Kikuchi, J.; Kim, A.; Kim, B. I.; Kim, D. J.; Kim, E.-J.; Kim, Y.-J.; Kinney, E.; Kiss, Á.; Kistenev, E.; Kleinjan, D.; Kochenda, L.; Komkov, B.; Konno, M.; Koster, J.; Král, A.; Kravitz, A.; Kunde, G. J.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Kyle, G. S.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lebedev, A.; Lee, D. M.; Lee, J.; Lee, K. B.; Lee, K. S.; Leitch, M. J.; Leite, M. A. L.; Li, X.; Lichtenwalner, P.; Liebing, P.; Linden Levy, L. A.; Liška, T.; Liu, H.; Liu, M. X.; Love, B.; Lynch, D.; Maguire, C. F.; Makdisi, Y. I.; Malik, M. D.; Manko, V. I.; Mannel, E.; Mao, Y.; Masui, H.; Matathias, F.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; Means, N.; Meredith, B.; Miake, Y.; Mibe, T.; Mignerey, A. C.; Miki, K.; Milov, A.; Mitchell, J. T.; Mohanty, A. K.; Moon, H. J.; Morino, Y.; Morreale, A.; Morrison, D. P.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Nagamiya, S.; Nagle, J. L.; Naglis, M.; Nagy, M. I.; Nakagawa, I.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Nam, S.; Newby, J.; Nguyen, M.; Nihashi, M.; Nouicer, R.; Nyanin, A. S.; Oakley, C.; O'Brien, E.; Oda, S. X.; Ogilvie, C. A.; Oka, M.; Okada, K.; Onuki, Y.; Oskarsson, A.; Ouchida, M.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, I. H.; Park, S. K.; Park, W. J.; Pate, S. F.; Pei, H.; Peng, J.-C.; Pereira, H.; Peressounko, D. Yu.; Petti, R.; Pinkenburg, C.; Pisani, R. P.; Proissl, M.; Purschke, M. L.; Qu, H.; Rak, J.; Ravinovich, I.; Read, K. F.; Rembeczki, S.; Reygers, K.; Riabov, V.; Riabov, Y.; Richardson, E.; Roach, D.; Roche, G.; Rolnick, S. D.; Rosati, M.; Rosen, C. A.; Rosendahl, S. S. E.; Ružička, P.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sakashita, K.; Samsonov, V.; Sano, S.; Sato, T.; Sawada, S.; Sedgwick, K.; Seele, J.; Seidl, R.; Seto, R.; Sharma, D.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Silvestre, C.; Sim, K. S.; Singh, B. K.; Singh, C. P.; Singh, V.; Slunečka, M.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Stenlund, E.; Stoll, S. P.; Sugitate, T.; Sukhanov, A.; Sziklai, J.; Takagui, E. M.; Taketani, A.; Tanabe, R.; Tanaka, Y.; Taneja, S.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Themann, H.; Thomas, D.; Thomas, T. L.; Togawa, M.; Toia, A.; Tomášek, L.; Torii, H.; Towell, R. S.; Tserruya, I.; Tsuchimoto, Y.; Vale, C.; Valle, H.; van Hecke, H. W.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Virius, M.; Vrba, V.; Vznuzdaev, E.; Wang, X. R.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Wei, F.; Wei, R.; Wessels, J.; White, S. N.; Winter, D.; Woody, C. L.; Wright, R. M.; Wysocki, M.; Yamaguchi, Y. L.; Yamaura, K.; Yang, R.; Yanovich, A.; Ying, J.; Yokkaichi, S.; You, Z.; Young, G. R.; Younus, I.; Yushmanov, I. E.; Zajc, W. A.; Zhou, S.; Phenix Collaboration

2015-01-01

We report a measurement of e+e- pairs from semileptonic heavy-flavor decays in d +Au collisions at √{sNN}=200 GeV. By exploring the mass and transverse-momentum dependence of the yield, the bottom decay contribution can be isolated from charm, and quantified by comparison to pythia and mc@nlo simulations. The resulting b b ¯ -production cross section is σbb ¯ d Au=1.37 ±0.28 (stat ) ±0.46 (syst ) mb, which is equivalent to a nucleon-nucleon cross section of σbb N N=3.4 ±0.8 (stat ) ±1.1 (syst ) μ b .

Simplified model to describe the dissociative recombination of linear polyatomic ions of astrophysical interest

NASA Astrophysics Data System (ADS)

Douguet, N.; Fonseca dos Santos, S.; Kokoouline, V.; Orel, A. E.

2015-01-01

We present results of a theoretical study on dissociative recombination of the HCNH+, HCO+ and N2H+ linear polyatomic ions at low energies using a simple theoretical model. In the present study, the indirect mechanism for recombination proceeds through the capture of the incoming electron in excited vibrational Rydberg states attached to the degenerate transverse modes of the linear ions. The strength of the non-adiabatic coupling responsible for dissociative recombination is determined directly from the near-threshold scattering matrix obtained numerically using the complex Kohn variational method. The final cross sections for the process are compared with available experimental data. It is demonstrated that at low collision energies, the major contribution to the dissociative recombination cross section is due to the indirect mechanism.

Effects of high optical injection levels in polycrystalline Si wafers on carrier transport

NASA Astrophysics Data System (ADS)

Steele, Doneisha; Semichaevsky, Andrey

High levels of carrier injection in polycrystalline Si may arise, for example, in solar cells under concentrated sunlight. Mechanisms for non-radiative carrier recombination include trap-mediated SRH and higher-order processes, e.g., Auger recombination. In this paper we present our experimental results for intensity-dependent carrier lifetimes and conduction currents in polycrystalline Si wafers illuminated with pulses of up to 50 Sun intensity. We also use a computational model for carrier transport that includes both SRH and Auger recombination mechanisms, in order to explain our experiments. The model allows quantifying recombination rate dependence on carrier concentration. Our goal is to relate the recombination rates to Si microstructure and defect densities that are revealed by IR PL images. We acknowledge the NSF support through Grant 1505377.

Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA.

PubMed

Chen, Xin Jie

2013-09-01

Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.

Mechanism of Homologous Recombination and Implications for Aging-Related Deletions in Mitochondrial DNA

PubMed Central

2013-01-01

SUMMARY Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells. PMID:24006472

Two mechanisms of constructive recollection: Perceptual recombination and conceptual fluency.

PubMed

Doss, Manoj K; Bluestone, Maximilian R; Gallo, David A

2016-11-01

Recollection is constructive and prone to distortion, but the mechanisms through which recollections can become embellished with rich yet illusory details are still debated. According to the conceptual fluency hypothesis, abstract semantic or conceptual activation increases the familiarity of a nonstudied event, causing one to falsely attribute imagined features to actual perception. In contrast, according to the perceptual recombination hypothesis, details from actually perceived events are partially recollected and become erroneously bound to a nonstudied event, again causing a detailed yet false recollection. Here, we report the first experiments aimed at disentangling these 2 mechanisms. Participants imagined pictures of common objects, and then they saw an actual picture of some of the imagined objects. We next presented misinformation associated with these studied items, designed to increase conceptual fluency (i.e., semantically related words) or perceptual recombination (i.e., perceptually similar picture fragments). Finally, we tested recollection for the originally seen pictures using verbal labels as retrieval cues. Consistent with conceptual fluency, processing-related words increased false recollection of pictures that were never seen, and consistent with perceptual recombination, processing picture fragments further increased false recollection. We also found that conceptual fluency was more short-lived than perceptual recombination, further dissociating these 2 mechanisms. These experiments provide strong evidence that conceptual fluency and perceptual recombination independently contribute to the constructive aspects of recollection. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

The Kinetics of Oxygen Atom Recombination in the Presence of Carbon Dioxide

NASA Astrophysics Data System (ADS)

Jamieson, C. S.; Garcia, R. M.; Pejakovic, D.; Kalogerakis, K.

2009-12-01

Understanding processes involving atomic oxygen is crucial for the study and modeling of composition, energy transfer, airglow, and transport dynamics in planetary atmospheres. Significant gaps and uncertainties exist in the understanding of these processes and often the relevant input from laboratory measurements is missing or outdated. We are conducting laboratory experiments to measure the rate coefficient for O + O + CO2 recombination and investigating the O2 excited states produced following the recombination. These measurements will provide key input for a quantitative understanding and reliable modeling of the atmospheres of the CO2 planets and their airglow. An excimer laser providing pulsed output at either 193 nm or 248 nm is employed to produce O atoms by dissociating carbon dioxide, nitrous oxide, or ozone. In an ambient-pressure background of CO2, O atoms recombine in a time scale of a few milliseconds. Detection of laser-induced fluorescence at 845 nm following two-photon excitation near 226 nm monitors the decay of the oxygen atom population. From the temporal evolution of the signal the recombination rate coefficient is extracted. Fluorescence spectroscopy is used to detect the products of O-atom recombination and subsequent relaxation in CO2. This work is supported by the US National Science Foundation’s (NSF) Planetary Astronomy Program. Rosanne Garcia’s participation was funded by the NSF Research Experiences for Undergraduates (REU) Program.

Dissociative recombination in interstellar clouds

NASA Technical Reports Server (NTRS)

Black, John H.; Van Dishoeck, Ewine F.

1989-01-01

Molecular ions play a significant role in the chemistry and evolution of interstellar molecular clouds, even though these regions are overwhelmingly neutral. The dissociative recombination (DR) process governs the abundances of many of these ions and of related neutral species. The gas-phase ion-molecule chemistry of the simplest species is summarized, with emphasis on those problems which are most sensitive to uncertain rates or product branching ratios of DR processes. Examples of the kinds of information needed about DR processes are presented. The importance of the H3(+) ion and prospects for its direct observation are discussed.

Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria

PubMed Central

Cahoon, Laty A.; Seifert, H. Steven

2011-01-01

Summary Some pathogenic microbes utilize homologous recombination to generate antigenic variability in targets of immune surveillance. These specialized systems rely on the cellular recombination machinery to catalyze dedicated, high-frequency reactions that provide extensive diversity in the genes encoding surface antigens. A description of the specific mechanisms that allow unusually high rates of recombination without deleterious effects on the genome in the well characterized pilin antigenic variation systems of Neisseria gonorrhoeae and Neisseria meningitidis is presented. We will also draw parallels to selected bacterial and eukaryotic antigenic variation systems, and suggest the most pressing unanswered questions related to understanding these important processes. PMID:21812841

DNA recombination protein-dependent mechanism of homoplasmy and its proposed functions.

PubMed

Shibata, Takehiko; Ling, Feng

2007-01-01

Homoplasmy is a basic genetic state of mitochondria, in which all of the hundreds to thousands of mitochondrial (mt)DNA copies within a cell or an individual have the same nucleotide-sequence. It was recently found that "vegetative segregation" to generate homoplasmic cells is an active process under genetic control. In the yeast Saccharomyces cerevisiae, the Mhr1 protein which catalyzes a key reaction in mtDNA homologous recombination, plays a pivotal role in vegetative segregation. Conversely, within the nuclear genome, homologous DNA recombination causes genetic diversity. Considering these contradictory roles of this key reaction in DNA recombination, possible functions of homoplasmy are discussed.

Advanced control of dissolved oxygen concentration in fed batch cultures during recombinant protein production.

PubMed

Kuprijanov, A; Gnoth, S; Simutis, R; Lübbert, A

2009-02-01

Design and experimental validation of advanced pO(2) controllers for fermentation processes operated in the fed-batch mode are described. In most situations, the presented controllers are able to keep the pO(2) in fermentations for recombinant protein productions exactly on the desired value. The controllers are based on the gain-scheduling approach to parameter-adaptive proportional-integral controllers. In order to cope with the most often appearing distortions, the basic gain-scheduling feedback controller was complemented with a feedforward control component. This feedforward/feedback controller significantly improved pO(2) control. By means of numerical simulations, the controller behavior was tested and its parameters were determined. Validation runs were performed with three Escherichia coli strains producing different recombinant proteins. It is finally shown that the new controller leads to significant improvements in the signal-to-noise ratio of other key process variables and, thus, to a higher process quality.

DNA Strand Exchange and RecA Homologs in Meiosis

PubMed Central

Brown, M. Scott; Bishop, Douglas K.

2015-01-01

Homology search and DNA strand–exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand–exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand–exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved. PMID:25475089

Monitoring Recombination During Meiosis in Budding Yeast.

PubMed

Owens, Shannon; Tang, Shangming; Hunter, Neil

2018-01-01

Homologous recombination is fundamental to sexual reproduction, facilitating accurate segregation of homologous chromosomes at the first division of meiosis, and creating novel allele combinations that fuel evolution. Following initiation of meiotic recombination by programmed DNA double-strand breaks (DSBs), homologous pairing and DNA strand exchange form joint molecule (JM) intermediates that are ultimately resolved into crossover and noncrossover repair products. Physical monitoring of the DNA steps of meiotic recombination in Saccharomyces cerevisiae (budding yeast) cultures undergoing synchronous meiosis has provided seminal insights into the molecular basis of meiotic recombination and affords a powerful tool for dissecting the molecular roles of recombination factors. This chapter describes a suit of electrophoretic and Southern hybridization techniques used to detect and quantify the DNA intermediates of meiotic recombination at recombination hotspots in budding yeast. DSBs and recombination products (crossovers and noncrossovers) are resolved using one-dimensional electrophoresis and distinguished by restriction site polymorphisms between the parental chromosomes. Psoralen cross-linking is used to stabilize branched JMs, which are resolved from linear species by native/native two-dimensional electrophoresis. Native/denaturing two-dimensional electrophoresis is employed to determine the component DNA strands of JMs and to measure the processing of DSBs. These techniques are generally applicable to any locus where the frequency of recombination is high enough to detect intermediates by Southern hybridization. © 2018 Elsevier Inc. All rights reserved.

Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations

PubMed Central

Petit, Morgane; Astruc, Jean-Michel; Sarry, Julien; Drouilhet, Laurence; Fabre, Stéphane; Moreno, Carole R.; Servin, Bertrand

2017-01-01

Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. PMID:28978774

Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations.

PubMed

Petit, Morgane; Astruc, Jean-Michel; Sarry, Julien; Drouilhet, Laurence; Fabre, Stéphane; Moreno, Carole R; Servin, Bertrand

2017-10-01

Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. Copyright © 2017 by the Genetics Society of America.

Frequency and genetic characterization of V(DD)J recombinants in the human peripheral blood antibody repertoire.

PubMed

Briney, Bryan S; Willis, Jordan R; Hicar, Mark D; Thomas, James W; Crowe, James E

2012-09-01

Antibody heavy-chain recombination that results in the incorporation of multiple diversity (D) genes, although uncommon, contributes substantially to the diversity of the human antibody repertoire. Such recombination allows the generation of heavy chain complementarity determining region 3 (HCDR3) regions of extreme length and enables junctional regions that, because of the nucleotide bias of N-addition regions, are difficult to produce through normal V(D)J recombination. Although this non-classical recombination process has been observed infrequently, comprehensive analysis of the frequency and genetic characteristics of such events in the human peripheral blood antibody repertoire has not been possible because of the rarity of such recombinants and the limitations of traditional sequencing technologies. Here, through the use of high-throughput sequencing of the normal human peripheral blood antibody repertoire, we analysed the frequency and genetic characteristics of V(DD)J recombinants. We found that these recombinations were present in approximately 1 in 800 circulating B cells, and that the frequency was severely reduced in memory cell subsets. We also found that V(DD)J recombination can occur across the spectrum of diversity genes, indicating that virtually all recombination signal sequences that flank diversity genes are amenable to V(DD)J recombination. Finally, we observed a repertoire bias in the diversity gene repertoire at the upstream (5') position, and discovered that this bias was primarily attributable to the order of diversity genes in the genomic locus. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

Strong Artificial Selection in Domestic Mammals Did Not Result in an Increased Recombination Rate

PubMed Central

Muñoz-Fuentes, Violeta; Marcet-Ortega, Marina; Alkorta-Aranburu, Gorka; Linde Forsberg, Catharina; Morrell, Jane M.; Manzano-Piedras, Esperanza; Söderberg, Arne; Daniel, Katrin; Villalba, Adrian; Toth, Attila; Di Rienzo, Anna; Roig, Ignasi; Vilà, Carles

2015-01-01

Recombination rates vary in intensity and location at the species, individual, sex and chromosome levels. Despite the fundamental biological importance of this process, the selective forces that operate to shape recombination rate and patterns are unclear. Domestication offers a unique opportunity to study the interplay between recombination and selection. In domesticates, intense selection for particular traits is imposed on small populations over many generations, resulting in organisms that differ, sometimes dramatically, in morphology and physiology from their wild ancestor. Although earlier studies suggested increased recombination rate in domesticates, a formal comparison of recombination rates between domestic mammals and their wild congeners was missing. In order to determine broad-scale recombination rate, we used immunolabeling detection of MLH1 foci as crossover markers in spermatocytes in three pairs of closely related wild and domestic species (dog and wolf, goat and ibex, and sheep and mouflon). In the three pairs, and contrary to previous suggestions, our data show that contemporary recombination rate is higher in the wild species. Subsequently, we inferred recombination breakpoints in sequence data for 16 genomic regions in dogs and wolves, each containing a locus associated with a dog phenotype potentially under selection during domestication. No difference in the number and distribution of recombination breakpoints was found between dogs and wolves. We conclude that our data indicate that strong directional selection did not result in changes in recombination in domestic mammals, and that both upper and lower bounds for crossover rates may be tightly regulated. PMID:25414125

Atomic Data Needs for X-Ray Astronomy

NASA Technical Reports Server (NTRS)

Kallman, Timothy; White, Nicholas E. (Technical Monitor)

1999-01-01

This publication contains written versions of most of the invited talks presented at the workshop on Atomic Data Needs for X-ray Astronomy which was held at NASA's Goddard Space Flight Center on December 16-1 7 1999. The idea of hosting such a workshop emerged from an imminent need to update and complete current atomic datasets in anticipation of a new era of high quality X-ray spectra starting with the launching of Chandra and XMM-Newton observatories. At first, our vision of the workshop was of a short and limited attendance event, given the specialization of the topic. But it, was soon realized, from the response to the first workshop announcement, that the topic was of much interest, to researchers working in X-ray spectra (physicists and astronomers). As a result, the workshop grew to approximately 120 participants from several countries. The kind of atomic data that interests us are those parameters needed for analysis and modeling of spectra shortward of about about 100 A and relevant to ionic species of astronomical interest. The physical mechanisms of interest in the formation of spectra include photoionization. collisional ionization, recombination (radiative and dielectronic). collisional excitation (by electrons and protons). and radiative deexcitation. Unique to X-ray spectroscopy are the ionization and excitation processes from inner-closed shells. in addition to the challenges in interpret,ing the medium resolution (epsilon/delta epsilon is about 0.05 - 0.1) data obtained by current X-ray astronomy experiments. Line wavelengths are of interest too, particularly owing to the high resolution spectra from the new experiments. The workshop was divided into five major areas: Observational Spectroscopy, Theoretical Calculations of Atomic Data, Laboratory Measurements of Atomic Parameters. Spectra Modeling, and Atomic Databases. One comforting finding from the work shop is that the enthusiasm felt by X-ray astronomers about the new observational missions seems to be shared by theoretical and experimental physicists. Talks were presented about several exciting new projects and experimental and theoretical techniques devoted to X-ray spectroscopy. Simultaneously, several new tools for spectral analysis and modeling have recently been developed, together with improved atomic databases. These proceeding are expected to be of interests to producers and users of atomic data. Moreover. the contributions presented here have been written in a way that can be used by a general audience of scientists and graduate students in X-ray astronomy, modelling, and in computational and experimental atomic physics.

Process for Assembly and Transformation into Saccharomyces cerevisiae of a Synthetic Yeast Artificial Chromosome Containing a Multigene Cassette to Express Enzymes That Enhance Xylose Utilization Designed for an Automated Platform.

PubMed

Hughes, Stephen R; Cox, Elby J; Bang, Sookie S; Pinkelman, Rebecca J; López-Núñez, Juan Carlos; Saha, Badal C; Qureshi, Nasib; Gibbons, William R; Fry, Michelle R; Moser, Bryan R; Bischoff, Kenneth M; Liu, Siqing; Sterner, David E; Butt, Tauseef R; Riedmuller, Steven B; Jones, Marjorie A; Riaño-Herrera, Néstor M

2015-12-01

A yeast artificial chromosome (YAC) containing a multigene cassette for expression of enzymes that enhance xylose utilization (xylose isomerase [XI] and xylulokinase [XKS]) was constructed and transformed into Saccharomyces cerevisiae to demonstrate feasibility as a stable protein expression system in yeast and to design an assembly process suitable for an automated platform. Expression of XI and XKS from the YAC was confirmed by Western blot and PCR analyses. The recombinant and wild-type strains showed similar growth on plates containing hexose sugars, but only recombinant grew on D-xylose and L-arabinose plates. In glucose fermentation, doubling time (4.6 h) and ethanol yield (0.44 g ethanol/g glucose) of recombinant were comparable to wild type (4.9 h and 0.44 g/g). In whole-corn hydrolysate, ethanol yield (0.55 g ethanol/g [glucose + xylose]) and xylose utilization (38%) for recombinant were higher than for wild type (0.47 g/g and 12%). In hydrolysate from spent coffee grounds, yield was 0.46 g ethanol/g (glucose + xylose), and xylose utilization was 93% for recombinant. These results indicate introducing a YAC expressing XI and XKS enhanced xylose utilization without affecting integrity of the host strain, and the process provides a potential platform for automated synthesis of a YAC for expression of multiple optimized genes to improve yeast strains. © 2015 Society for Laboratory Automation and Screening.

Modulating Excitonic Recombination Effects through One-Step Synthesis of Perovskite Nanoparticles for Light-Emitting Diodes.

PubMed

Kulkarni, Sneha A; Muduli, Subas; Xing, Guichuan; Yantara, Natalia; Li, Mingjie; Chen, Shi; Sum, Tze Chien; Mathews, Nripan; White, Tim J; Mhaisalkar, Subodh G

2017-10-09

The primary advantages of halide perovskites for light-emitting diodes (LEDs) are solution processability, direct band gap, good charge-carrier diffusion lengths, low trap density, and reasonable carrier mobility. The luminescence in 3 D halide perovskite thin films originates from free electron-hole bimolecular recombination. However, the slow bimolecular recombination rate is a fundamental performance limitation. Perovskite nanoparticles could result in improved performance but processability and cumbersome synthetic procedures remain challenges. Herein, these constraints are overcome by tailoring the 3 D perovskite as a near monodisperse nanoparticle film prepared through a one-step in situ deposition method. Replacing methyl ammonium bromide (CH 3 NH 3 Br, MABr) partially by octyl ammonium bromide [CH 3 (CH 2 ) 7 NH 3 Br, OABr] in defined mole ratios in the perovskite precursor proved crucial for the nanoparticle formation. Films consisting of the in situ formed nanoparticles displayed signatures associated with excitonic recombination, rather than that of bimolecular recombination associated with 3 D perovskites. This transition was accompanied by enhanced photoluminescence quantum yield (PLQY≈20.5 % vs. 3.40 %). Perovskite LEDs fabricated from the nanoparticle films exhibit a one order of magnitude improvement in current efficiency and doubling in luminance efficiency. The material processing systematics derived from this study provides the means to control perovskite morphologies through the selection and mixing of appropriate additives. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recombinant levels of Escherichia coli K-12 mutants deficient in various replication, recombination, or repair genes.

PubMed Central

Zieg, J; Maples, V F; Kushner, S R

1978-01-01

Escherichia coli strains containing mutations in lexA, rep, uvrA, uvrD, uvrE, lig, polA, dam, or xthA were constructed and tested for conjugation and transduction proficiencies and ability to form Lac+ recombinants in an assay system utilizing a nontandem duplication of two partially deleted lactose operons (lacMS286phi80dIIlacBK1). lexA and rep mutants were as deficient (20% of wild type) as recB and recC strains in their ability to produce Lac+ progeny. All the other strains exhibited increased frequencies of Lac+ recombinant formation, compared with wild type, ranging from 2- to 13-fold. Some strains showed markedly increased conjugation proficiency (dam uvrD) compared to wild type, while others appeared deficient (polA107). Some differences in transduction proficiency were also observed. Analysis of the Lac+ recombinants formed by the various mutants indicated that they were identical to the recombinants formed by a wild-type strain. The results indicate that genetic recombination in E. coli is a highly regulated process involving multiple gene products. PMID:350859

Marker-Dependent Recombination in T4 Bacteriophage. IV. Recombinational Effects of Antimutator T4 DNA Polymerase

PubMed Central

Shcherbakov, V. P.; Plugina, L. A.; Kudryashova, E. A.

1995-01-01

Recombinational effects of the antimutator allele tsL42 of gene 43 of phage T4, encoding DNA polymerase, were studied in crosses between rIIB mutants. Recombination under tsL42-restricted conditions differed from the normal one in several respects: (1) basic recombination was enhanced, especially within very short distances; (2) mismatch repair tracts were shortened, while the contribution of mismatch repair to recombination was not changed; (3) marker interference at very short distances was augmented. We infer that the T4 DNA polymerase is directly involved in mismatch repair, performing both excision of a nonmatched single strand (by its 3' -> 5' exonuclease) and filling the resulting gap. A pathway for the mismatch repair was substantiated; it includes sequential action of endo VII (gp49) -> 3'->5' exonuclease (gp43) -> DNA polymerase (gp43) -> DNA ligase (gp30). It is argued that the marker interference at very short distances may result from the same sequence of events during the final processing of recombinational intermediates. PMID:7635281

An overview on the strategies to exploit rice endosperm as production platform for biopharmaceuticals.

PubMed

Takaiwa, Fumio; Wakasa, Yuhya; Hayashi, Shimpei; Kawakatsu, Taiji

2017-10-01

Cereal seed has been utilized as production platform for high-value biopharmaceutical proteins. Especially, protein bodies (PBs) in seeds are not only natural specialized storage organs of seed storage proteins (SSPs), but also suitable intracellular deposition compartment for recombinant proteins. When various recombinant proteins were produced as secretory proteins by attaching N terminal ER signal peptide and C terminal KDEL endoplasmic reticulum (ER) retention signal or as fusion proteins with SSPs, high amounts of recombinant proteins can be predominantly accumulated in the PBs. Recombinant proteins bioencapsulated in PBs exhibit high resistance to digestive enzymes in gastrointestinal tract than other intracellular compartments and are highly stable at ambient temperature, thus allowing oral administration of PBs containing recombinant proteins as oral drugs or functional nutrients in cost-effective minimum processed formulation. In this review, we would like to address key factors determining accumulation levels of recombinant proteins in PBs. Understanding of bottle neck parts and improvement of specific deposition to PBs result in much higher levels of production of high quality recombinant proteins. Copyright © 2017. Published by Elsevier B.V.

LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.

PubMed

Guo, Jing; Chen, Hao; Yang, Peng; Lee, Yew Ti; Wu, Min; Przytycka, Teresa M; Kwoh, Chee Keong; Zheng, Jie

2018-04-20

Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. DATABASE URL: http://histone.scse.ntu.edu.sg/LDSplitDB.

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.

PubMed

Ma, Li; O'Connell, Jeffrey R; VanRaden, Paul M; Shen, Botong; Padhi, Abinash; Sun, Chuanyu; Bickhart, Derek M; Cole, John B; Null, Daniel J; Liu, George E; Da, Yang; Wiggans, George R

2015-11-01

Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

PubMed Central

Ma, Li; O'Connell, Jeffrey R.; VanRaden, Paul M.; Shen, Botong; Padhi, Abinash; Sun, Chuanyu; Bickhart, Derek M.; Cole, John B.; Null, Daniel J.; Liu, George E.; Da, Yang; Wiggans, George R.

2015-01-01

Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination. PMID:26540184

Growth and Optimization of 2 Micrometers InGaSb/AlGaSb Quantum-Well-Based VECSELs on GaAs/AlGaAs DBRs

DTIC Science & Technology

2013-08-01

overwhelming nonradiative recombination losses in the antimonide active region. Furthermore, if the growth of the antimonide active region is done on a GaAs...This is important as threading dislocations would introduce a strong nonradiative recombination process in the QWs and relaxation that is not 100...These defects can act as nonradiative recombination centers. Thus, the source of the threading dislocations and their density in the active region

Screw dislocation-induced growth spirals as emissive exciton localization centers in Al-rich AlGaN/AlN quantum wells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Funato, Mitsuru, E-mail: funato@kuee.kyoto-u.ac.jp; Banal, Ryan G.; Kawakami, Yoichi

2015-11-15

Screw dislocations in Al-rich AlGaN/AlN quantum wells cause growth spirals with an enhanced Ga incorporation, which create potential minima. Although screw dislocations and their surrounding potential minima suggest non-radiative recombination processes within growth spirals, in reality, screw dislocations are not major non-radiative sinks for carriers. Consequently, carriers localized within growth spirals recombine radiatively without being captured by non-radiative recombination centers, resulting in intense emissions from growth spirals.

Graph Model of Coalescence with Recombinations

NASA Astrophysics Data System (ADS)

Parida, Laxmi

One of the primary genetic events shaping an autosomal chromosome is recombination. This is a process that occurs during meiosis, in eukaryotes, that results in the offsprings having different combinations of (homologous) genes, or chromosomal segments, of the two parents. The presence of these recombination events in the evolutionary history of each chromosome complicates the genetic landscape of a population, and understanding the manifestations of these genetic exchanges in the chromosome sequences has been a subject of intense curiosity (see [Hud83, Gri99, HSW05] and citations therein).

Cattle sex-specific recombination and genetic control from a very large pedigree

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is an essential biological process that generates novel genetic variants and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified ov...

Cooper-pair and Bose-Einstein condensations in two dimensions: A critical analysis based on the Nozieres and Schmitt-Rink formalism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tokumitu, A.; Miyake, K.; Yamada, K.

1993-05-01

The crossover between the Cooper-pair condensation and the Bose-Einstein condensation of di-electronic'' molecules in two-dimensional superconductors is investigated in detail on the basis of the Nozieres and Schmitt-Rink formalism. It is shown that temperature dependence of the chemical potential [mu] so calculated is classified into two classes as decreasing temperatures; i.e., class (a) where [mu] approaches the point of Bose-Einstein condensation of two-dimensional ideal Bose gas of di-electronic'' molecules, and class (b) where [mu] diverges positively along the line of BCS-type mean-field pair condensation. This feature is rather universal irrespective of strength [ital V] of the attractive interaction of themore » [ital s]-wave type. While the former class (a) has been found by Schmitt-Rink, Varma, and Ruckenstein, existence of the latter class (b) is recognized here. In the case where [ital V] is fixed, class (a) is realized for electron number density [ital N] smaller than [ital N][sub cr], which is an increasing function of [ital V], and class (b) is realized for [ital N] larger than [ital N][sub cr]. If [ital N][much gt][ital N][sub cr] in particular, there exists a regime, where the Fermi-liquid-like description is valid, between the BCS-type mean-field transition temperature and the Fermi temperature. In the situation where [ital V] is changed with [ital N] being fixed, low-temperature states for the strong-coupling case belong to class (a) while those for the weak-coupling case belong to class (b). Therefore, with decreasing [ital V], the chemical potential [mu]([ital T]), at temperatures far below the Fermi temperature, shows a discontinuous jump at [ital V]=[ital V][sub cr]([ital N]) corresponding to the transition from class (a) to (b).« less

Induction of potential protective immunity against enterotoxemia in calves by single or multiple recombinant Clostridium perfringens toxoids.

PubMed

Jiang, Zhigang; De, Yanyan; Chang, Jitao; Wang, Fang; Yu, Li

2014-11-01

Cattle enterotoxemia caused by Clostridium perfringens toxins is a noncontagious, sporadic, and fatal disease characterized by sudden death. Strategies for controlling and preventing cattle enterotoxemia are based on systematic vaccination of herds with toxoids. Because the process of producing conventional clostridial vaccines is dangerous, expensive, and time-consuming, the prospect of recombinant toxoid vaccines against diseases caused by C. perfringens toxins is promising. In this study, nontoxic recombinant toxoids derived from α-, β- and ε-toxins of C. perfringens, namely, rCPA247-370 , rCPB and rEtxHP, respectively, were expressed in Escherichia coli. High levels of specific IgG antibodies and neutralizing antibodies against the toxins were detected in sera from calves vaccinated with either a single recombinant toxoid or a mixed cocktail of all three recombinant toxoids, indicating the potential of these recombinant toxoids to provide calves with protective immunity against enterotoxemia caused by C. perfringens. © 2014 The Societies and Wiley Publishing Asia Pty Ltd.

The BCL11A Transcription Factor Directly Activates RAG Gene Expression and V(D)J Recombination

PubMed Central

Lee, Baeck-seung; Dekker, Joseph D.; Lee, Bum-kyu; Iyer, Vishwanath R.; Sleckman, Barry P.; Shaffer, Arthur L.; Ippolito, Gregory C.

2013-01-01

Recombination-activating gene 1 protein (RAG1) and RAG2 are critical enzymes for initiating variable-diversity-joining (VDJ) segment recombination, an essential process for antigen receptor expression and lymphocyte development. The transcription factor BCL11A is required for B cell development, but its molecular function(s) in B cell fate specification and commitment is unknown. We show here that the major B cell isoform, BCL11A-XL, binds the RAG1 promoter and Erag enhancer to activate RAG1 and RAG2 transcription in pre-B cells. We employed BCL11A overexpression with recombination substrates in a cultured pre-B cell line as well as Cre recombinase-mediated Bcl11alox/lox deletion in explanted murine pre-B cells to demonstrate direct consequences of BCL11A/RAG modulation on V(D)J recombination. We conclude that BCL11A is a critical component of a transcriptional network that regulates B cell fate by controlling V(D)J recombination. PMID:23438597

Electron-temperature dependence of dissociative recombination of electrons with N2/+/.N2 dimer ions

NASA Technical Reports Server (NTRS)

Whitaker, M.; Biondi, M. A.; Johnsen, R.

1981-01-01

The variation with electron temperature of the dissociative recombination of electrons with N2(+).N2 dimer ions is investigated in light of the importance of such ions in the lower ionosphere and in laser plasmas. Dissociative recombination coefficients were determined by means of a microwave afterglow mass spectrometer technique for electron temperatures from 300-5600 K and an ion and neutral temperature of 300 K. The recombination coefficient is found to be proportional to the -0.41 power of the electron temperature in this range, similar to that observed for the CO(+).CO dimer ion and consistent with the expected energy dependence for a fast dissociative process.

21 CFR 514.8 - Supplements and other changes to an approved application.

Code of Federal Regulations, 2013 CFR

2013-04-01

... method(s) or an addition, deletion, or substitution of steps in an aseptic processing operation; (D... solely affecting a natural product, a recombinant DNA-derived protein/polypeptide, or a complex or...) or references to previously approved documentation; (H) For a natural product, a recombinant DNA...

21 CFR 514.8 - Supplements and other changes to an approved application.

Code of Federal Regulations, 2014 CFR

2014-04-01

... method(s) or an addition, deletion, or substitution of steps in an aseptic processing operation; (D... solely affecting a natural product, a recombinant DNA-derived protein/polypeptide, or a complex or...) or references to previously approved documentation; (H) For a natural product, a recombinant DNA...

21 CFR 514.8 - Supplements and other changes to an approved application.

Code of Federal Regulations, 2012 CFR

2012-04-01

... method(s) or an addition, deletion, or substitution of steps in an aseptic processing operation; (D... solely affecting a natural product, a recombinant DNA-derived protein/polypeptide, or a complex or...) or references to previously approved documentation; (H) For a natural product, a recombinant DNA...

Recombinant DNA for Teachers.

ERIC Educational Resources Information Center

Duvall, James G., III

1992-01-01

A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

Airbreathing Pulse Detonation Engine Performance

NASA Technical Reports Server (NTRS)

Povinelli, Louis A.; Yungster, Shaye

2002-01-01

This paper presents performance results for pulse detonation engines taking into account the effects of dissociation and recombination. The amount of sensible heat recovered through recombination in the PDE chamber and exhaust process was found to be significant. These results have an impact on the specific thrust, impulse and fuel consumption of the PDE.

Expression of three Trichoderma reesei cellulase genes in Saccharomyces pastorianus for the development of a two-step process of hydrolysis and fermentation of cellulose.

PubMed

Fitzpatrick, J; Kricka, W; James, T C; Bond, U

2014-07-01

To compare the production of recombinant cellulase enzymes in two Saccharomyces species so as to ascertain the most suitable heterologous host for the degradation of cellulose-based biomass and its conversion into bioethanol. cDNA copies of genes representing the three major classes of cellulases (Endoglucanases, Cellobiohydrolases and β-glucosidases) from Trichoderma reesei were expressed in Saccharomyces pastorianus and Saccharomyces cerevisiae. The recombinant enzymes were secreted by the yeast hosts into the medium and were shown to act in synergy to hydrolyse cellulose. The conditions required to achieve maximum release of glucose from cellulose by the recombinant enzymes were defined and the activity of the recombinant enzymes was compared to a commercial cocktail of T. reesei cellulases. We demonstrate that significantly higher levels of cellulase activity were achieved by expression of the genes in S. pastorianus compared to S. cerevisiae. Hydrolysis of cellulose by the combined activity of the recombinant enzymes was significantly better at 50°C than at 30°C, the temperature used for mesophilic yeast fermentations, reflecting the known temperature profiles of the native enzymes. The results demonstrate that host choice is important for the heterologous production of cellulases. On the basis of the low activity of the T. reesei recombinant enzymes at fermentation temperatures, we propose a two-step process for the hydrolysis of cellulose and its fermentation into alcohol using cellulases produced in situ. © 2014 The Society for Applied Microbiology.

Size and Temperature Dependence of Electron Transfer between CdSe Quantum Dots and a TiO 2 Nanobelt

DOE PAGES

Tafen, De Nyago; Prezhdo, Oleg V.

2015-02-24

Understanding charge transfer reactions between quantum dots (QD) and metal oxides is fundamental for improving photocatalytic, photovoltaic and electronic devices. The complexity of these processes makes it difficult to find an optimum QD size with rapid charge injection and low recombination. We combine time-domain density functional theory with nonadiabatic molecular dynamics to investigate the size and temperature dependence of the experimentally studied electron transfer and charge recombination at CdSe QD-TiO 2 nanobelt (NB) interfaces. The electron injection rate shows strong dependence on the QD size, increasing for small QDs. The rate exhibits Arrhenius temperature dependence, with the activation energy ofmore » the order of millielectronvolts. The charge recombination process occurs due to coupling of the electronic subsystem to vibrational modes of the TiO 2 NB. Inelastic electron-phonon scattering happens on a picosecond time scale, with strong dependence on the QD size. Our simulations demonstrate that the electron-hole recombination rate decreases significantly as the QD size increases, in excellent agreement with experiments. The temperature dependence of the charge recombination rates can be successfully modeled within the framework of the Marcus theory through optimization of the electronic coupling and the reorganization energy. Our simulations indicate that by varying the QD size, one can modulate the photoinduced charge separation and charge recombination, fundamental aspects of the design principles for high efficiency devices.« less

Charge Separation and Recombination at Polymer-Fullerene Heterojunctions: Delocalization and Hybridization Effects.

PubMed

D'Avino, Gabriele; Muccioli, Luca; Olivier, Yoann; Beljonne, David

2016-02-04

We address charge separation and recombination in polymer/fullerene solar cells with a multiscale modeling built from accurate atomistic inputs and accounting for disorder, interface electrostatics and genuine quantum effects on equal footings. Our results show that bound localized charge transfer states at the interface coexist with a large majority of thermally accessible delocalized space-separated states that can be also reached by direct photoexcitation, thanks to their strong hybridization with singlet polymer excitons. These findings reconcile the recent experimental reports of ultrafast exciton separation ("hot" process) with the evidence that high quantum yields do not require excess electronic or vibrational energy ("cold" process), and show that delocalization, by shifting the density of charge transfer states toward larger effective electron-hole radii, may reduce energy losses through charge recombination.

Engineer Medium and Feed for Modulating N-Glycosylation of Recombinant Protein Production in CHO Cell Culture.

PubMed

Fan, Yuzhou; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

2017-01-01

Chinese hamster ovary (CHO) cells have become the primary expression system for the production of complex recombinant proteins due to their long-term success in industrial scale production and generating appropriate protein N-glycans similar to that of humans. Control and optimization of protein N-glycosylation is crucial, as the structure of N-glycans can largely influence both biological and physicochemical properties of recombinant proteins. Protein N-glycosylation in CHO cell culture can be controlled and tuned by engineering medium, feed, culture process, as well as genetic elements of the cell. In this chapter, we will focus on how to carry out experiments for N-glycosylation modulation through medium and feed optimization. The workflow and typical methods involved in the experiment process will be presented.

Dissociative recombination of N2/+/ in the ionosphere

NASA Technical Reports Server (NTRS)

Torr, M. R.; Torr, D. G.

1979-01-01

N2(+) ion measurements are examined which were made with the Atmospheric Explorer-C satellite during a phase of solar activity in 1978 that was significantly higher than near the earlier minimum. It is found that the major source of N2(+) is photoionization, rather than charge exchange with O(+) (2D), and that the major loss process above 300 km is dissociative recombination with electrons. A data sample for which the electron temperature (T sub e) covered the range from 1000 to 3400 K is used to evaluate the rate constant, alpha, for the dissociative-recombination process. The results show good agreement with laboratory measurements given by the expression: alpha = 1.8 x 10 to the -7th (T sub e/300) to the -0.39th cu cm/sec.

Recombinatorial biases and convergent recombination determine interindividual TCRβ sharing in murine thymocytes.

PubMed

Li, Hanjie; Ye, Congting; Ji, Guoli; Wu, Xiaohui; Xiang, Zhe; Li, Yuanyue; Cao, Yonghao; Liu, Xiaolong; Douek, Daniel C; Price, David A; Han, Jiahuai

2012-09-01

Overlap of TCR repertoires among individuals provides the molecular basis for public T cell responses. By deep-sequencing the TCRβ repertoires of CD4+CD8+ thymocytes from three individual mice, we observed that a substantial degree of TCRβ overlap, comprising ∼10-15% of all unique amino acid sequences and ∼5-10% of all unique nucleotide sequences across any two individuals, is already present at this early stage of T cell development. The majority of TCRβ sharing between individual thymocyte repertoires could be attributed to the process of convergent recombination, with additional contributions likely arising from recombinatorial biases; the role of selection during intrathymic development was negligible. These results indicate that the process of TCR gene recombination is the major determinant of clonotype sharing between individuals.

Improved photovoltaic performance and stability of quantum dot sensitized solar cells using Mn-ZnSe shell structure with enhanced light absorption and recombination control.

PubMed

Gopi, Chandu V V M; Venkata-Haritha, M; Kim, Soo-Kyoung; Kim, Hee-Je

2015-08-07

To make quantum-dot-sensitized solar cells (QDSSCs) competitive, photovoltaic parameters comparable to those of other emerging solar cell technologies are necessary. In the present study, ZnSe was used as an alternative to ZnS, one of the most widely used passivation materials in QDSSCs. ZnSe was deposited on a TiO2-CdS-CdSe photoanode to form a core-shell structure, which was more efficient in terms of reducing the electron recombination in QDSSCs. The development of an efficient passivation layer is a requirement for preventing recombination processes in order to attain high-performance and stable QDSSCs. A layer of inorganic Mn-ZnSe was applied to a QD-sensitized photoanode to enhance the adsorption and strongly inhibit interfacial recombination processes in QDSSCs, which greatly improved the power conversion efficiency. Impedance spectroscopy revealed that the combined Mn doping with ZnSe treatment reduces interfacial recombination and increases charge collection efficiency compared with Mn-ZnS, ZnS, and ZnSe. A solar cell based on the CdS-CdSe-Mn-ZnSe photoanode yielded excellent performance with a solar power conversion efficiency of 5.67%, Voc of 0.584 V, and Jsc of 17.59 mA cm(-2). Enhanced electron transport and reduced electron recombination are responsible for the improved Jsc and Voc of the QDSSCs. The effective electron lifetime of the device with Mn-ZnSe was higher than those with Mn-ZnS, ZnSe, and ZnS, leading to more efficient electron-hole separation and slower electron recombination.

Selective binding of meiosis-specific yeast Hop1 protein to the holliday junctions distorts the DNA structure and its implications for junction migration and resolution.

PubMed

Tripathi, Pankaj; Anuradha, S; Ghosal, Gargi; Muniyappa, K

2006-12-08

Saccharomyces cerevisiae HOP1, which encodes a component of synaptonemal complex (SC), plays an important role in both gene conversion and crossing over between homologs, as well as enforces meiotic recombination checkpoint control over the progression of recombination intermediates. In hop1Delta mutants, meiosis-specific double-strand breaks (DSBs) are reduced to 10% of the wild-type level, and at aberrantly late times, these DSBs are processed into inter-sister recombination intermediates. However, the underlying mechanism by which Hop1 protein regulates these nuclear events remains obscure. Here we show that Hop1 protein interacts selectively with the Holliday junction, changes its global conformation and blocks the dissolution of the junction by a RecQ helicase. The Holliday junction-Hop1 protein complexes are significantly more stable at higher ionic strengths and molar excess of unlabeled competitor DNA than complexes containing other recombination intermediates. Structural analysis of the Holliday junction using 2-aminopurine fluorescence emission, DNase I footprinting and KMnO4 probing provide compelling evidence that Hop1 protein binding induces significant distortion at the center of the Holliday junction. We propose that Hop1 protein might coordinate the physical monitoring of meiotic recombination intermediates with the process of branch migration of Holliday junction.

Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing.

PubMed

Valdés-Alemán, Javier; Téllez-Sosa, Juan; Ovilla-Muñoz, Marbella; Godoy-Lozano, Elizabeth; Velázquez-Ramírez, Daniel; Valdovinos-Torres, Humberto; Gómez-Barreto, Rosa E; Martinez-Barnetche, Jesús

2014-01-01

High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.

Diffusion controlled initial recombination

NASA Astrophysics Data System (ADS)

Christen, T.; Büttiker, M.

1998-08-01

This work addresses nucleation rates in systems with strong initial recombination. Initial (or ``geminate'') recombination is a process where a dissociated structure (anion, vortex, kink, etc.) recombines with its twin brother (cation, antivortex, antikink) generated in the same nucleation event. Initial recombination is important if there is an asymptotically vanishing interaction force instead of a generic saddle-type activation barrier. At low temperatures, initial recombination strongly dominates homogeneous recombination. In a first part, we discuss the effect in one-, two-, and three-dimensional diffusion controlled systems with spherical symmetry. Since there is no well-defined saddle, we introduce a threshold which is to some extent arbitrary but which is restricted by physically reasonable conditions. We show that the dependence of the nucleation rate on the specific choice of this threshold is strongest for one-dimensional systems and decreases in higher dimensions. We also discuss the influence of a weak driving force, and show that the transport current is directly determined by the imbalance of the activation rate in the direction of the field and the rate against this direction. In a second part, we apply the results to the overdamped sine-Gordon system at equilibrium. It turns out that diffusive initial recombination is the essential mechanism which governs the equilibrium kink nucleation rate. We emphasize analogies between the single particle problem with initial recombination and the multidimensional kink-antikink nucleation problem.

Nanobodies and recombinant binders in cell biology

PubMed Central

Helma, Jonas; Cardoso, M. Cristina; Muyldermans, Serge

2015-01-01

Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes. PMID:26056137

Reduced genetic distance and high replication levels increase the RNA recombination rate of hepatitis delta virus.

PubMed

Lin, Chia-Chi; Yang, Zhi-Wei; Iang, Shan-Bei; Chao, Mei

2015-01-02

Hepatitis delta virus (HDV) replication is carried out by host RNA polymerases. Since homologous inter-genotypic RNA recombination is known to occur in HDV, possibly via a replication-dependent process, we hypothesized that the degree of sequence homology and the replication level should be related to the recombination frequency in cells co-expressing two HDV sequences. To confirm this, we separately co-transfected cells with three different pairs of HDV genomic RNAs and analyzed the obtained recombinants by RT-PCR followed by restriction fragment length polymorphism and sequencing analyses. The sequence divergence between the clones ranged from 24% to less than 0.1%, and the difference in replication levels was as high as 100-fold. As expected, significant differences were observed in the recombination frequencies, which ranged from 0.5% to 47.5%. Furthermore, varying the relative amounts of parental RNA altered the dominant recombinant species produced, suggesting that template switching occurs frequently during the synthesis of genomic HDV RNA. Taken together, these data suggest that during the host RNA polymerase-driven RNA recombination of HDV, both inter- and intra-genotypic recombination events are important in shaping the genetic diversity of HDV. Copyright © 2014 Elsevier B.V. All rights reserved.

Spin-dependent recombination probed through the dielectric polarizability

PubMed Central

Bayliss, Sam L.; Greenham, Neil C.; Friend, Richard H.; Bouchiat, Hélène; Chepelianskii, Alexei D

2015-01-01

Despite residing in an energetically and structurally disordered landscape, the spin degree of freedom remains a robust quantity in organic semiconductor materials due to the weak coupling of spin and orbital states. This enforces spin-selectivity in recombination processes which plays a crucial role in optoelectronic devices, for example, in the spin-dependent recombination of weakly bound electron-hole pairs, or charge-transfer states, which form in a photovoltaic blend. Here, we implement a detection scheme to probe the spin-selective recombination of these states through changes in their dielectric polarizability under magnetic resonance. Using this technique, we access a regime in which the usual mixing of spin-singlet and spin-triplet states due to hyperfine fields is suppressed by microwave driving. We present a quantitative model for this behaviour which allows us to estimate the spin-dependent recombination rate, and draw parallels with the Majorana–Brossel resonances observed in atomic physics experiments. PMID:26439933

Recombination of ions of a dense ion plasma in a fluorine atmosphere

NASA Astrophysics Data System (ADS)

Lankin, A. V.

2016-08-01

A new effect leading to the slowing of recombination in a weakly nonideal ion plasma is considered. The solvation of ions is included in the explanation of the results from studying a gas discharge afterglow in a fluorine atmosphere. It is shown that recombination in such a system is slowed in comparison to the standard relationships for ideal plasma. The formation and composition of cluster ions in such a medium are considered. The relationship between the variation in the kinetics of recombination and the course of the process according to a complicated mechanism with the intermediate formation of metastable cluster pairs is established. A quantitative model is built and a formula allowing us to describe the recombination rate over a wide range of parameters of the medium is obtained. It is shown that the proposed model is in good agreement with the experimental data.

Genetic variation of the Borrelia burgdorferi gene vlsE involves cassette-specific, segmental gene conversion.

PubMed

Zhang, J R; Norris, S J

1998-08-01

The Lyme disease spirochete Borrelia burgdorferi possesses 15 silent vls cassettes and a vls expression site (vlsE) encoding a surface-exposed lipoprotein. Segments of the silent vls cassettes have been shown to recombine with the vlsE cassette region in the mammalian host, resulting in combinatorial antigenic variation. Despite promiscuous recombination within the vlsE cassette region, the 5' and 3' coding sequences of vlsE that flank the cassette region are not subject to sequence variation during these recombination events. The segments of the silent vls cassettes recombine in the vlsE cassette region through a unidirectional process such that the sequence and organization of the silent vls loci are not affected. As a result of recombination, the previously expressed segments are replaced by incoming segments and apparently degraded. These results provide evidence for a gene conversion mechanism in VlsE antigenic variation.

Utilization of Multi-Immunization and Multiple Selection Strategies for Isolation of Hapten-Specific Antibodies from Recombinant Antibody Phage Display Libraries.

PubMed

Tullila, Antti; Nevanen, Tarja K

2017-05-31

Phage display technology provides a powerful tool for the development of novel recombinant antibodies. In this work, we optimized and streamlined the recombinant antibody discovery process for haptens as an example. A multi-immunization approach was used in order to avoid the need for construction of multiple antibody libraries. Selection methods were developed to utilize the full potential of the recombinant antibody library by applying four different elution conditions simultaneously. High-throughput immunoassays were used to analyse the binding properties of the individual antibody clones. Different carrier proteins were used in the immunization, selection, and screening phases to avoid enrichment of the antibodies for the carrier protein epitopes. Novel recombinant antibodies against mycophenolic acid and ochratoxin A, with affinities up to 39 nM and 34 nM, respectively, were isolated from a multi-immunized fragment antigen-binding (Fab) library.

Characterization of recombinant human HBP/CAP37/azurocidin, a pleiotropic mediator of inflammation-enhancing LPS-induced cytokine release from monocytes.

PubMed

Rasmussen, P B; Bjørn, S; Hastrup, S; Nielsen, P F; Norris, K; Thim, L; Wiberg, F C; Flodgaard, H

1996-07-15

Neutrophil-derived heparin-binding protein (HBP) is a strong chemoattractant for monocytes. We report here for the first time the expression of recombinant HBP. A baculovirus containing the human HBP cDNA mediated in insect cells the secretion of a 7-residue N-terminally extended HBP form (pro-HBP). Deletion of the pro-peptide-encoding cDNA sequence resulted in correctly processed HBP at the N-terminus. Electrospray mass spectrum analysis of recombinant HBP yielded a molecular weight of 27.237 +/- 3 amu. Consistent with this mass is a HBP form of 225 amino acids (mature part +3 amino acid C-terminal extension). The biological activity of recombinant HBP was confirmed by its chemotactic action towards monocytes. Furthermore, we have shown that recombinant HBP stimulates in a dose-dependent manner the lipopolysaccharide (LPS)-induced cytokine release from human monocytes.

Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae

PubMed Central

Chaguza, Chrispin; Cornick, Jennifer E.; Everett, Dean B.

2015-01-01

Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus. PMID:25904996

Genetic recombination as a major cause of mutagenesis in the human globin gene clusters.

PubMed

Borg, Joseph; Georgitsi, Marianthi; Aleporou-Marinou, Vassiliki; Kollia, Panagoula; Patrinos, George P

2009-12-01

Homologous recombination is a frequent phenomenon in multigene families and as such it occurs several times in both the alpha- and beta-like globin gene families. In numerous occasions, genetic recombination has been previously implicated as a major mechanism that drives mutagenesis in the human globin gene clusters, either in the form of unequal crossover or gene conversion. Unequal crossover results in the increase or decrease of the human globin gene copies, accompanied in the majority of cases with minor phenotypic consequences, while gene conversion contributes either to maintaining sequence homogeneity or generating sequence diversity. The role of genetic recombination, particularly gene conversion in the evolution of the human globin gene families has been discussed elsewhere. Here, we summarize our current knowledge and review existing experimental evidence outlining the role of genetic recombination in the mutagenic process in the human globin gene families.

Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae.

PubMed

Chaguza, Chrispin; Cornick, Jennifer E; Everett, Dean B

2015-01-01

Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus.

Utilization of Multi-Immunization and Multiple Selection Strategies for Isolation of Hapten-Specific Antibodies from Recombinant Antibody Phage Display Libraries

PubMed Central

Tullila, Antti; Nevanen, Tarja K.

2017-01-01

Phage display technology provides a powerful tool for the development of novel recombinant antibodies. In this work, we optimized and streamlined the recombinant antibody discovery process for haptens as an example. A multi-immunization approach was used in order to avoid the need for construction of multiple antibody libraries. Selection methods were developed to utilize the full potential of the recombinant antibody library by applying four different elution conditions simultaneously. High-throughput immunoassays were used to analyse the binding properties of the individual antibody clones. Different carrier proteins were used in the immunization, selection, and screening phases to avoid enrichment of the antibodies for the carrier protein epitopes. Novel recombinant antibodies against mycophenolic acid and ochratoxin A, with affinities up to 39 nM and 34 nM, respectively, were isolated from a multi-immunized fragment antigen-binding (Fab) library. PMID:28561803

Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination

PubMed Central

Kim, Taejin; Chitteni-Pattu, Sindhu; Cox, Benjamin L.; Wood, Elizabeth A.; Sandler, Steven J.; Cox, Michael M.

2015-01-01

The recombination activity of Escherichia coli (E. coli) RecA protein reflects an evolutionary balance between the positive and potentially deleterious effects of recombination. We have perturbed that balance, generating RecA variants exhibiting improved recombination functionality via random mutagenesis followed by directed evolution for enhanced function in conjugation. A recA gene segment encoding a 59 residue segment of the protein (Val79-Ala137), encompassing an extensive subunit-subunit interface region, was subjected to degenerate oligonucleotide-mediated mutagenesis. An iterative selection process generated at least 18 recA gene variants capable of producing a higher yield of transconjugants. Three of the variant proteins, RecA I102L, RecA V79L and RecA E86G/C90G were characterized based on their prominence. Relative to wild type RecA, the selected RecA variants exhibited faster rates of ATP hydrolysis, more rapid displacement of SSB, decreased inhibition by the RecX regulator protein, and in general displayed a greater persistence on DNA. The enhancement in conjugational function comes at the price of a measurable RecA-mediated cellular growth deficiency. Persistent DNA binding represents a barrier to other processes of DNA metabolism in vivo. The growth deficiency is alleviated by expression of the functionally robust RecX protein from Neisseria gonorrhoeae. RecA filaments can be a barrier to processes like replication and transcription. RecA regulation by RecX protein is important in maintaining an optimal balance between recombination and other aspects of DNA metabolism. PMID:26047498

Charging of a conducting sphere in a weakly ionized collisional plasma: Temporal dynamics and stationary state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grach, V. S., E-mail: vsgrach@app.sci-nnov.ru; Garasev, M. A.

2015-07-15

We consider the interaction of a isolated conducting sphere with a collisional weakly ionized plasma in an external field. We assume that the plasma consists of two species of ions neglecting of electrons. We take into account charging of the sphere due to sedimentation of plasma ions on it, the field of the sphere charge and the space charge, as well as recombination and molecular diffusion. The nonstationary problem of interaction of the sphere with the surrounding plasma is solved numerically. The temporal dynamics of the sphere charge and plasma perturbations is analyzed, as well as the properties of themore » stationary state. It is shown that the duration of transient period is determined by the recombination time and by the reverse conductivity of ions. The temporal dynamics of the sphere charge and plasma perturbations is determined by the intensity of recombination processes relative to the influence of the space charge field and diffusion. The stationary absolute value of the sphere charge increases linearly with the external electric field, decreases with the relative intensity of recombination processes and increases in the presence of substantial diffusion. The scales of the perturbed region in the plasma are determined by the radius of the sphere, the external field, the effect of diffusion, and the relative intensity of recombination processes. In the limiting case of the absence of molecular diffusion and a strong external field, the properties of the stationary state coincide with those obtained earlier as a result of approximate solution.« less

Enhanced Production of a Recombinant Multidomain Thermostable GH9 Processive Endo-1,4-β-Glucanase (CenC) from Ruminiclostridium thermocellum in a Mesophilic Host Through Various Cultivation and Induction Strategies.

PubMed

Haq, Ikram Ul; Akram, Fatima

2017-09-01

Commonly, unintentional induction and inadvertently preparing medium for engineered Escherichia coli BL21 CodonPlus (DE3)-RIPL, give poor or variable yields of heterologous proteins. Therefore, to enhance the activity and production of an industrially relevant recombinant processive endo-1,4-β-glucanase (CenC) propagated in Escherichia coli BL21 CodonPlus(DE3)-RIPL through various cultivation and induction strategies. Investigation of various growth media and induction parameters revealed that high-cell-density and optimal CenC expression were obtained in ZYBM9 medium induced either with 0.5 mM IPTG/150 mM lactose, after 6 h induction at 37 °C; and before induction, bacterial cells were given heat shock (42 °C) for 1 h when culture density (OD 600nm ) reached at 0.6. Intracellular enzyme activity was enhanced by 6.67 and 3.20-fold in ZYBM9 and 3×ZYBM9 medium, respectively, under optimal conditions. Using YNG auto-induction medium, activity was 2.5-fold increased after 10 h incubation at 37 °C. Approximately similar results were obtained by transferring the optimized process at the bioreactor level. Results showed that the effective process strategy is essential to enhance recombinant bacterial cell mass and enzyme production from small to large-scale. To the best of our knowledge, this is the first ever report on enhanced production of thermostable processive endo-1,4-β-glucanase cloned from Ruminiclostridium thermocellum, which is a suitable candidate for industrial applications. Graphical Abstract Flow Chart Summary of Enhanced Production of a Recombinant Multidomain Thermostable GH9 Processive Endo-1,4-β-glucanase from Ruminiclostridium thermocellum.

Calculation of the rate constant for state-selected recombination of H+O2(v) as a function of temperature and pressure

NASA Astrophysics Data System (ADS)

Teitelbaum, Heshel; Caridade, Pedro J. S. B.; Varandas, António J. C.

2004-06-01

Classical trajectory calculations using the MERCURY/VENUS code have been carried out on the H+O2 reactive system using the DMBE-IV potential energy surface. The vibrational quantum number and the temperature were selected over the ranges v=0 to 15, and T=300 to 10 000 K, respectively. All other variables were averaged. Rate constants were determined for the energy transfer process, H+O2(v)-->H+O2(v''), for the bimolecular exchange process, H+O2(v)-->OH(v')+O, and for the dissociative process, H+O2(v)-->H+O+O. The dissociative process appears to be a mere extension of the process of transferring large amounts of energy. State-to-state rate constants are given for the exchange reaction, and they are in reasonable agreement with previous results, while the energy transfer and dissociative rate constants have never been reported previously. The lifetime distributions of the HO2 complex, calculated as a function of v and temperature, were used as a basis for determining the relative contributions of various vibrational states of O2 to the thermal rate coefficients for recombination at various pressures. This novel approach, based on the complex's ability to survive until it collides in a secondary process with an inert gas, is used here for the first time. Complete falloff curves for the recombination of H+O2 are also calculated over a wide range of temperatures and pressures. The combination of the two separate studies results in pressure- and temperature-dependent rate constants for H+O2(v)(+Ar)⇄HO2(+Ar). It is found that, unlike the exchange reaction, vibrational and rotational-translational energy are liabilities in promoting recombination.

Airbreathing Pulse Detonation Engine Performance

NASA Technical Reports Server (NTRS)

Povinelli, Louis A.; Yungster, Shaye

2002-01-01

This paper presents performance results for pulse detonation engines (PDE) taking into account the effects of dissociation and recombination. The amount of sensible heat recovered through recombination in the PDE chamber and exhaust process was found to be significant. These results have an impact on the specific thrust, impulse and fuel consumption of the PDE.

Costs and benefits of natural transformation in Acinetobacter baylyi.

PubMed

Hülter, Nils; Sørum, Vidar; Borch-Pedersen, Kristina; Liljegren, Mikkel M; Utnes, Ane L G; Primicerio, Raul; Harms, Klaus; Johnsen, Pål J

2017-02-15

Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells. We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions. In head-to-head competition experiments between DNA uptake-proficient and -deficient strains, we observed a fitness benefit of DNA uptake independent of UV stress. This benefit was found with both homologous and heterologous DNA and was independent of recombination. Recombination with taken-up DNA reduced survival of transformed cells with increasing levels of UV-stress through interference with nucleotide excision repair, suggesting that DNA strand breaks occur during recombination attempts with taken-up DNA. Consistent with this, we show that absence of RecBCD and RecFOR recombinational DNA repair pathways strongly decrease natural transformation. Our data show a physiological benefit of DNA uptake unrelated to recombination. In contrast, recombination during transformation is a strand break inducing process that represents a previously unrecognized cost of natural transformation.

Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes

PubMed Central

Dreissig, Steven; Fuchs, Jörg; Himmelbach, Axel; Mascher, Martin; Houben, Andreas

2017-01-01

Meiotic recombination is a fundamental mechanism to generate novel allelic combinations which can be harnessed by breeders to achieve crop improvement. The recombination landscape of many crop species, including the major crop barley, is characterized by a dearth of recombination in 65% of the genome. In addition, segregation distortion caused by selection on genetically linked loci is a frequent and undesirable phenomenon in double haploid populations which hampers genetic mapping and breeding. Here, we present an approach to directly investigate recombination at the DNA sequence level by combining flow-sorting of haploid pollen nuclei of barley with single-cell genome sequencing. We confirm the skewed distribution of recombination events toward distal chromosomal regions at megabase resolution and show that segregation distortion is almost absent if directly measured in pollen. Furthermore, we show a bimodal distribution of inter-crossover distances, which supports the existence of two classes of crossovers which are sensitive or less sensitive to physical interference. We conclude that single pollen nuclei sequencing is an approach capable of revealing recombination patterns in the absence of segregation distortion. PMID:29018459

Mgm101 is a Rad52-related protein required for mitochondrial DNA recombination.

PubMed

Mbantenkhu, MacMillan; Wang, Xiaowen; Nardozzi, Jonathan D; Wilkens, Stephan; Hoffman, Elizabeth; Patel, Anamika; Cosgrove, Michael S; Chen, Xin Jie

2011-12-09

Homologous recombination is a conserved molecular process that has primarily evolved for the repair of double-stranded DNA breaks and stalled replication forks. However, the recombination machinery in mitochondria is poorly understood. Here, we show that the yeast mitochondrial nucleoid protein, Mgm101, is related to the Rad52-type recombination proteins that are widespread in organisms from bacteriophage to humans. Mgm101 is required for repeat-mediated recombination and suppression of mtDNA fragmentation in vivo. It preferentially binds to single-stranded DNA and catalyzes the annealing of ssDNA precomplexed with the mitochondrial ssDNA-binding protein, Rim1. Transmission electron microscopy showed that Mgm101 forms large oligomeric rings of ∼14-fold symmetry and highly compressed helical filaments. Specific mutations affecting ring formation reduce protein stability in vitro. The data suggest that the ring structure may provide a scaffold for stabilization of Mgm101 by preventing the aggregation of the otherwise unstable monomeric conformation. Upon binding to ssDNA, Mgm101 is remobilized from the rings to form distinct nucleoprotein filaments. These studies reveal a recombination protein of likely bacteriophage origin in mitochondria and support the notion that recombination is indispensable for mtDNA integrity.

Recombinant drugs-on-a-chip: The usage of capillary electrophoresis and trends in miniaturized systems - A review.

PubMed

Morbioli, Giorgio Gianini; Mazzu-Nascimento, Thiago; Aquino, Adriano; Cervantes, Cesar; Carrilho, Emanuel

2016-09-07

We present here a critical review covering conventional analytical tools of recombinant drug analysis and discuss their evolution towards miniaturized systems foreseeing a possible unique recombinant drug-on-a-chip device. Recombinant protein drugs and/or pro-drug analysis require sensitive and reproducible analytical techniques for quality control to ensure safety and efficacy of drugs according to regulatory agencies. The versatility of miniaturized systems combined with their low-cost could become a major trend in recombinant drugs and bioprocess analysis. Miniaturized systems are capable of performing conventional analytical and proteomic tasks, allowing for interfaces with other powerful techniques, such as mass spectrometry. Microdevices can be applied during the different stages of recombinant drug processing, such as gene isolation, DNA amplification, cell culture, protein expression, protein separation, and analysis. In addition, organs-on-chips have appeared as a viable alternative to testing biodrug pharmacokinetics and pharmacodynamics, demonstrating the capabilities of the miniaturized systems. The integration of individual established microfluidic operations and analytical tools in a single device is a challenge to be overcome to achieve a unique recombinant drug-on-a-chip device. Copyright © 2016 Elsevier B.V. All rights reserved.

Guidelines to reach high-quality purified recombinant proteins.

PubMed

Oliveira, Carla; Domingues, Lucília

2018-01-01

The final goal in recombinant protein production is to obtain high-quality pure protein samples. Indeed, the successful downstream application of a recombinant protein depends on its quality. Besides production, which is conditioned by the host, the quality of a recombinant protein product relies mainly on the purification procedure. Thus, the purification strategy must be carefully designed from the molecular level. On the other hand, the quality control of a protein sample must be performed to ensure its purity, homogeneity and structural conformity, in order to validate the recombinant production and purification process. Therefore, this review aims at providing succinct information on the rational purification design of recombinant proteins produced in Escherichia coli, specifically the tagging purification, as well as on accessible tools for evaluating and optimizing protein quality. The classical techniques for structural protein characterization-denaturing protein gel electrophoresis (SDS-PAGE), size exclusion chromatography (SEC), dynamic light scattering (DLS) and circular dichroism (CD)-are revisited with focus on the protein and their main advantages and disadvantages. Furthermore, methods for determining protein concentration and protein storage are also presented. The guidelines compiled herein will aid preparing pure, soluble and homogeneous functional recombinant proteins from the very beginning of the molecular cloning design.

Interdependence between transcription and mRNP processing and export, and its impact on genetic stability.

PubMed

Luna, Rosa; Jimeno, Sonia; Marín, Mercedes; Huertas, Pablo; García-Rubio, María; Aguilera, Andrés

2005-06-10

The conserved eukaryotic THO-TREX complex acts at the interface between transcription and mRNA export and affects transcription-associated recombination. To investigate the interdependence of nuclear mRNA processes and their impact on genomic integrity, we analyzed transcript accumulation and recombination of 40 selected mutants covering representative steps of the biogenesis and export of the messenger ribonucleoprotein particle (mRNP). None of the mutants analyzed shared the strong transcript-accumulation defect and hyperrecombination of THO mutants. Nevertheless, mutants in 3' end cleavage/polyadenylation, nuclear exosome, and mRNA export showed a weak but significant effect on recombination and transcript accumulation. Mutants of the nuclear exosome (rrp6) and 3' end processing factors (rna14 and rna15) showed inefficient transcription elongation and genetic interactions with THO. The results suggest a tight interdependence among mRNP biogenesis steps and transcription and an unexpected effect of the nuclear exosome and the cleavage/polyadenylation factors on transcription elongation and genetic integrity.

High-level recombinant protein expression in transgenic plants by using a double-inducible viral vector

PubMed Central

Werner, Stefan; Breus, Oksana; Symonenko, Yuri; Marillonnet, Sylvestre; Gleba, Yuri

2011-01-01

We describe here a unique ethanol-inducible process for expression of recombinant proteins in transgenic plants. The process is based on inducible release of viral RNA replicons from stably integrated DNA proreplicons. A simple treatment with ethanol releases the replicon leading to RNA amplification and high-level protein production. To achieve tight control of replicon activation and spread in the uninduced state, the viral vector has been deconstructed, and its two components, the replicon and the cell-to-cell movement protein, have each been placed separately under the control of an inducible promoter. Transgenic Nicotiana benthamiana plants incorporating this double-inducible system demonstrate negligible background expression, high (over 0.5 × 104-fold) induction multiples, and high absolute levels of protein expression upon induction (up to 4.3 mg/g fresh biomass). The process can be easily scaled up, supports expression of practically important recombinant proteins, and thus can be directly used for industrial manufacturing. PMID:21825158

Controlling the influence of Auger recombination on the performance of quantum-dot light-emitting diodes

PubMed Central

Bae, Wan Ki; Park, Young-Shin; Lim, Jaehoon; Lee, Donggu; Padilha, Lazaro A.; McDaniel, Hunter; Robel, Istvan; Lee, Changhee; Pietryga, Jeffrey M.; Klimov, Victor I.

2013-01-01

Development of light-emitting diodes (LEDs) based on colloidal quantum dots is driven by attractive properties of these fluorophores such as spectrally narrow, tunable emission and facile processibility via solution-based methods. A current obstacle towards improved LED performance is an incomplete understanding of the roles of extrinsic factors, such as non-radiative recombination at surface defects, versus intrinsic processes, such as multicarrier Auger recombination or electron-hole separation due to applied electric field. Here we address this problem with studies that correlate the excited state dynamics of structurally engineered quantum dots with their emissive performance within LEDs. We find that because of significant charging of quantum dots with extra electrons, Auger recombination greatly impacts both LED efficiency and the onset of efficiency roll-off at high currents. Further, we demonstrate two specific approaches for mitigating this problem using heterostructured quantum dots, either by suppressing Auger decay through the introduction of an intermediate alloyed layer, or by using an additional shell that impedes electron transfer into the quantum dot to help balance electron and hole injection. PMID:24157692

The future of recombinant growth factors in wound healing.

PubMed

Robson, M C; Mustoe, T A; Hunt, T K

1998-08-01

For more than a decade, clinical trials have been conducted of the application of topical exogenous recombinant growth factors in attempts to accelerate the healing of chronic wounds. Although the results of some of these trials have been encouraging, overall the results have been somewhat discouraging. Much of the difficulty lies in the paucity of carefully controlled clinical trials of wound healing. Since wound healing is a complex process that can be influenced, both positively and negatively, by many factors, designing these trials has proved difficult. To date, only a single recombinant growth factor-recombinant human platelet-derived growth factor-BB (rhPDGF-BB)- has been approved by the US Food and Drug Administration; and that only for use in diabetic foot ulcers. It is unlikely, however, that a single growth factor will be able to resolve all issues of repair or strengthen all vulnerabilities of chronic wounds. Our expectation, therefore, is that growth factors, cytokines, and other biologic agents will be used more specifically in the future, for example, by targeting growth factor therapy at those specific components or processes that a given wound uses to heal.

Internuclear Genetic Transfer in Dikaryons of SCHIZOPHYLLUM COMMUNE. II. Direct Recovery and Analysis of Recombinant Nuclei

PubMed Central

Leonard, Thomas J.; Gaber, Richard F.; Dick, Stanley

1978-01-01

The recessive gene, mound (mnd), allows the appearance of globose masses of compacted hyphae. Dikaryons of Schizophyllum commune that are heteroallelic for mnd [(mosaic dikaryons: (mnd + mnd+)] have been successfully dedikaryotized in cholate-containing medium in order to recover the component nuclear types directly. The relative proportion of the two recovered monokaryotic types shows in all cases a marked deviation from 1:1. Hyphae from nonmound mycelial regions yield monokaryotic types identical to those originally used to form the dikaryons. In hyphae from mound-forming regions, however, homoallelism of the mnd allele has been demonstrated; the nuclear type that formerly contained the mnd+ allele acquired a mnd allele.—The process of internuclear transfer or recombination is unaccompanied by the simultaneous alteration of any additional genetic markers carried by the recipient nucleus. The newly acquired mnd allele segregates in Mendelian fashion in subsequent outcrosses and appears to be chromosomally located. A novel process of somatic recombination, with several features distinct from classical parasexual mitotic recombination, appears to be in operation. PMID:17248847

The HADES-RICH upgrade using Hamamatsu H12700 MAPMTs with DiRICH FEE + Readout

NASA Astrophysics Data System (ADS)

Patel, V.; Traxler, M.

2018-03-01

The High Acceptance Di-Electron Spectrometer (HADES) is operational since the year 2000 and uses a hadron blind RICH detector for electron identification. The RICH photon detector is currently replaced by Hamamatsu H12700 MAPMTs with a readout system based on the DiRICH front-end module. The electronic readout chain is being developed as a joint effort of the HADES-, CBM- and PANDA collaborations and will also be used in the photon detectors for the upcoming Compressed Baryonic Matter (CBM) and PANDA experiments at FAIR . This article gives a brief overview on the photomultipliers and their quality assurance test measurements, as well as first measurements of the new DiRICH front-end module in final configurations.

Ionization balance for iron XXV, XXIV and XXIII derived from solar flare X-ray spectra

NASA Astrophysics Data System (ADS)

Antonucci, E.; Dodero, M. A.; Gabriel, A. H.; Tanaka, K.; Dubau, J.

1987-06-01

An analysis has been carried out using over 300 spectra of solar flares from both the XRP instrument on SMM and the SOX instrument on Hinotori. The helium-like iron and associated dielectronic satellite spectra were used in order to derive a revised ionization balance for Fe XXIV/Fe XXV. This is found to lie between the theoretical curves based upon ECIP ionization rates, and those using Lotz formalism, with a tendency to be closer to the former. An extension of the analysis to include Fe XXIII is subject to a somewhat larger uncertainty in the interpretation. However it indicates a similar effect for this ion. Using all three ions, a revised ionization balance for iron is presented.

Measurement of the relative prompt production rate of χ c2 and χ c1 in pp collisions at $$\\sqrt{s} = 7\\ \\mathrm{TeV}$$

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.

A measurement is presented of the relative prompt production rate of chi(c2) and chi(c1) with 4.6 inverse femtobarns of data collected by the CMS experiment at the LHC in pp collisions at sqrt(s) = 7 TeV. The two states are measured via their radiative decays chi(c) to J/psi + gamma, with the photon converting into a dielectron pair for J/psi rapidity abs(y(J/psi)) < 1.0 and photon transverse momentum pt(gamma) > 0.5 GeV. The measurement is given for six intervals of pt(J/psi) between 7 and 25 GeV. The results are compared to theoretical predictions.

Optimization and revision of the production process of the Necator americanus glutathione S-transferase 1 (Na-GST-1), the lead hookworm vaccine recombinant protein candidate

PubMed Central

Curti, Elena; Seid, Christopher A; Hudspeth, Elissa; Center, Lori; Rezende, Wanderson; Pollet, Jeroen; Kwityn, Cliff; Hammond, Molly; Matsunami, Rise K; Engler, David A; Hotez, Peter J; Elena Bottazzi, Maria

2014-01-01

Infection by the human hookworm Necator americanus is a leading cause of anemia and disability in the developing countries of Africa, Asia, and the Americas. In order to prevent childhood hookworm disease in resource poor settings, a recombinant vaccine is under development by the Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, a Product Development Partnership (PDP). Previously, we reported on the expression and purification of a highly promising hookworm vaccine candidate, Na-GST-1, an N. americanus glutathione s-transferase expressed in Pichia pastoris (yeast), which led to production of 1.5 g of 95% pure recombinant protein at a 20L scale.1, 2, 3 This yield and purity of Na-GST-1 was sufficient for early pilot manufacturing and initial phase 1 clinical testing. However, based on the number of doses which would be required to allow mass vaccination and a potential goal to deliver a vaccine as inexpensively as possible, a higher yield of expression of the recombinant antigen at the lowest possible cost is highly desirable. Here we report on modifications to the fermentation (upstream process) of the antigen expressed in P. pastoris, and to the purification (downstream process) of the recombinant protein that allowed for a 2–3-fold improvement in the final yield of Na-GST-1 purified protein. The major improvements included upstream process changes such as the addition of a sorbitol pulse and co-feed during methanol induction as well as an extension of the induction stage to approximately 96 hours; downstream process changes included modifying the UFDF to flat sheet with a 10 kDa Molecular Weight cut-off (MWCO), adjusting the capacity of an ion-exchange chromatography step utilizing a gradient elution as opposed to the original step elution, and altering the hydrophobic interaction chromatography conditions. The full process, as well as the purity and stability profiles of the target Na-GST-1, and its formulation on Alhydrogel®, is described. PMID:25424799

Factors controlling charge recombination under dark and light conditions in dye sensitised solar cells.

PubMed

Barnes, Piers R F; Anderson, Assaf Y; Juozapavicius, Mindaugas; Liu, Lingxuan; Li, Xiaoe; Palomares, Emilio; Forneli, Amparo; O'Regan, Brian C

2011-02-28

A simple and powerful approach for assessing the recombination losses in dye sensitised solar cells (DSSCs) across the current voltage curve (j-V) as a function of TiO(2) electron concentration (n) is demonstrated. The total flux of electrons recombining with iodine species in the electrolyte and oxidised dye molecules can be thought of as a recombination current density, defined as j(rec) = j(inj)-j where j(inj) is the current of electrons injected from optically excited dye states and j is the current density collected at cell voltage (V). The electron concentration at any given operating conditions is determined by charge extraction. This allows comparison of factors influencing electron recombination rates at matched n. We show that j(rec) is typically 2-3 times higher under 1 sun equivalent illumination (j(inj) > 0) relative to dark (j(inj) = 0) conditions. This difference was increased by increasing light intensity, electrolyte iodine concentration and electrolyte solvent viscosity. The difference was reduced by increasing the electrolyte iodide concentration and increasing the temperature. These results allowed us to verify a numerical model of complete operational cells (Barnes et al., Phys. Chem. Chem. Phys., DOI: 10.1039/c0cp01554g) and to relate the differences in j(rec) to physical processes in the devices. The difference between j(rec) in the light and dark can be explained by two factors: (1) an increase in the concentration of electron acceptor species (I(3)(-) and/or I(2)) when current is flowing under illumination relative to dark conditions where the current is flowing in the opposite direction, and (2) a non-trivial contribution from electron recombination to oxidised dye molecules under light conditions. More generally, the technique helps to assign the observed relationship between the components, processing and performance of DSSCs to more fundamental physical processes.

Blocking the proliferation of human tumor cell lines by peptidase inhibitors from Bauhinia seeds.

PubMed

Nakahata, Adriana Miti; Mayer, Barbara; Neth, Peter; Hansen, Daiane; Sampaio, Misako Uemura; Oliva, Maria Luiza Vilela

2013-03-01

In cancer tumors, growth, invasion, and formation of metastasis at a secondary site play a pivotal role, participating in diverse processes in the development of the pathology, such as degradation of extracellular matrix. Bauhinia seeds contain relatively large quantities of peptidase inhibitors, and two Bauhinia inhibitors were obtained in a recombinant form from the Bauhinia bauhinioides species, B. bauhinoides cruzipain inhibitor, which is a cysteine and serine peptidase inhibitor, and B. bauhinioides kallikrein inhibitor, which is a serine peptidase inhibitor. While recombinant B. bauhinoides cruzipain inhibitor inhibits human neutrophil elastase cathepsin G and the cysteine proteinase cathepsin L, recombinant B. bauhinioides kallikrein inhibitor inhibits plasma kallikrein and plasmin. The effects of recombinant B. bauhinoides cruzipain inhibitor and recombinant B. bauhinioides kallikrein inhibitor on the viability of tumor cell lines with a distinct potential of growth from the same tissue were compared to those of the clinical cytotoxic drug 5-fluorouracil. At 12.5 µM concentration, recombinant B. bauhinoides cruzipain inhibitor and recombinant B. bauhinioides kallikrein inhibitor were more efficient than 5-fluorouracil in inhibiting MKN-28 and Hs746T (gastric), HCT116 and HT29 (colorectal), SkBr-3 and MCF-7 (breast), and THP-1 and K562 (leukemia) cell lines. Additionally, recombinant B. bauhinoides cruzipain inhibitor inhibited 40 % of the migration of Hs746T, the most invasive gastric cell line, while recombinant B. bauhinioides kallikrein inhibitor did not affect cell migration. Recombinant B. bauhinioides kallikrein inhibitor and recombinant B. bauhinoides cruzipain inhibitor, even at high doses, did not affect hMSC proliferation while 5-fluorouracil greatly reduced the proliferation rates of hMSCs. Therefore, both recombinant B. bauhinoides cruzipain inhibitor and recombinant B. bauhinioides kallikrein inhibitor might be considered for further studies to block peptidase activities in order to target specific peptidase-mediated growth and invasion characteristics of individual tumors, mainly in patients resistant to 5-fluorouracil chemotherapy. Georg Thieme Verlag KG Stuttgart · New York.

Investigation of Exciton Recombination Zone in Quantum Dot Light-Emitting Diodes Using a Fluorescent Probe.

PubMed

Huang, Xiaoyu; Zhang, Heng; Xu, Dingxin; Wen, Feng; Chen, Shuming

2017-08-23

Exciton recombination zone, where the photons are generated, can greatly affect the performance, such as the efficiency and color purity, of the quantum dot (QD) light-emitting diodes (QLEDs). To probe the exciton recombination zone, 4-(dicyanomethylene)-2-t-butyl-6(1,1,7,7-tetramethyljulolidyl-9-enyl)-4H-pyran (DCJTB) is doped into the charge transport layer as a fluorescent sensor; by monitoring the Förster resonant energy transfer (FRET) between QD and DCJTB, the location of the recombination zone can be determined. It is found that the electron transport layer (ETL) has a great impact on the recombination zone. For example, in QLEDs with ZnMgO ETL, the recombination zone is near the interface of the QD/hole transport layer (HTL) and is shifted to the interface of the QD/ETL as the driving voltage is increased, whereas in devices with 1,3,5-tris(2-N-phenylbenzimidazolyl) benzene (TPBi) ETL, the recombination zone is close to the interface of the QD/ETL and moved to the interface of the QD/HTL with the increase in the driving voltage. Our results can also clarify the light emission mechanism in QLEDs. In devices with ZnMgO ETL, the emission is dominated by the direct charge recombination, whereas in devices with TPBi ETL, the emission is contributed by both FRET and direct charge recombination. Our studies suggest that fluorescent probe can be a powerful tool for investigating the exciton recombination zone, light emission mechanism, and other fundamental processes in QLEDs.

Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster

PubMed Central

Singh, Nadia D.; Aquadro, Charles F.; Clark, Andrew G.

2009-01-01

Accurate assessment of local recombination rate variation is crucial for understanding the recombination process and for determining the impact of natural selection on linked sites. In Drosophila, local recombination intensity has been estimated primarily by statistical approaches, estimating the local slope of the relationship between the physical and genetic maps. However, these estimates are limited in resolution, and as a result, the physical scale at which recombination intensity varies in Drosophila is largely unknown. While there is some evidence suggesting as much as a 40-fold variation in crossover rate at a local scale in D. pseudoobscura, little is known about the fine-scale structure of recombination rate variation in D. melanogaster. Here, we experimentally examine the fine-scale distribution of crossover events in a 1.2 Mb region on the D. melanogaster X chromosome using a classic genetic mapping approach. Our results show that crossover frequency is significantly heterogeneous within this region, varying ~ 3.5 fold. Simulations suggest that this degree of heterogeneity is sufficient to affect levels of standing nucleotide diversity, although the magnitude of this effect is small. We recover no statistical association between empirical estimates of nucleotide diversity and recombination intensity, which is likely due to the limited number of loci sampled in our population genetic dataset. However, codon bias is significantly negatively correlated with fine-scale recombination intensity estimates, as expected. Our results shed light on the relevant physical scale to consider in evolutionary analyses relating to recombination rate, and highlight the motivations to increase the resolution of the recombination map in Drosophila. PMID:19504037

Strategies to Suspension Serum-Free Adaptation of Mammalian Cell Lines for Recombinant Glycoprotein Production.

PubMed

Caron, Angelo Luis; Biaggio, Rafael Tagé; Swiech, Kamilla

2018-01-01

Serum-free suspension cultures are preferably required for recombinant protein production due to its readiness in upstream/downstream processing and scale-up, therefore increasing process productivity and competitiveness. This type of culture replaces traditional cell culturing as the presence of animal-derived components may introduce lot-a-lot variability and adventitious pathogens to the process. However, adapting cells to serum-free conditions is challenging, time-consuming, and cell line and medium dependent. In this chapter, we present different approaches that can be used to adapt mammalian cell lines from an anchorage-dependent serum supplemented culture to a suspension serum-free culture.

Superacid Passivation of Crystalline Silicon Surfaces.

PubMed

Bullock, James; Kiriya, Daisuke; Grant, Nicholas; Azcatl, Angelica; Hettick, Mark; Kho, Teng; Phang, Pheng; Sio, Hang C; Yan, Di; Macdonald, Daniel; Quevedo-Lopez, Manuel A; Wallace, Robert M; Cuevas, Andres; Javey, Ali

2016-09-14

The reduction of parasitic recombination processes commonly occurring within the silicon crystal and at its surfaces is of primary importance in crystalline silicon devices, particularly in photovoltaics. Here we explore a simple, room temperature treatment, involving a nonaqueous solution of the superacid bis(trifluoromethane)sulfonimide, to temporarily deactivate recombination centers at the surface. We show that this treatment leads to a significant enhancement in optoelectronic properties of the silicon wafer, attaining a level of surface passivation in line with state-of-the-art dielectric passivation films. Finally, we demonstrate its advantage as a bulk lifetime and process cleanliness monitor, establishing its compatibility with large area photoluminescence imaging in the process.

Epistasis and the selective advantage of sex and recombination

NASA Astrophysics Data System (ADS)

de Oliveira, Viviane M.; da Silva, Juliana K.; Campos, Paulo R. A.

2008-09-01

The understanding of the central mechanisms favoring sex and recombination in real populations is one of the fundamental issues in evolutionary biology. Based on a previous stochastic formulation for the study of sex, here we aim to investigate the conditions under which epistasis favors the fixation of the sexual mode of reproduction in a given population. In addition, we try to identify the evolutionary forces which contribute to this process. One considers a finite population model which assumes the existence of a recombination modifier allele that can activate the recombination mechanism. We have found that sex is very little favored in a scenario of antagonistic epistasis, and this advantage only occurs in a narrow range of values of the selection coefficient sd . On the other hand, synergistic epistasis favors recombination in a very broad domain. However, the major mechanism contributing to the spreading of the modifier allele depends on the range of values of sd . At large sd , background selection favors recombination since it increases the efficacy of selection, while at low sd Muller’s ratchet is the leading mechanism.

Spatial heterogeneity and the evolution of sex in diploids.

PubMed

Agrawal, Aneil F

2009-07-01

Much of the theoretical work on the evolution of sex has focused on the effects of recombination. In diploids, segregation also occurs during sexual reproduction. Segregation breaks down some types of genetic associations that are not affected by recombination and thus influences the evolution of sex in ways that are not apparent from studying the evolution of recombination as a surrogate for sex. Here I examine the evolution of sex in diploids experiencing spatially heterogeneous selection. If divergent selection causes genetic differentiation, then migration can be a powerful force generating genetic associations that may not be favored by selection. An advantage to sex can arise from breaking down these associations. By examining modifiers of both sex and recombination, the model allows for a direct comparison of the forces acting on these related but different processes, illuminating the role of segregation. The model also includes inbreeding, which has been shown to be important for both segregation and recombination. I find that inbreeding affects the evolution of sex through segregation, not recombination. Several suggestions for empirical experiments are given.

Bloom syndrome helicase in meiosis: Pro-crossover functions of an anti-crossover protein.

PubMed

Hatkevich, Talia; Sekelsky, Jeff

2017-09-01

The functions of the Bloom syndrome helicase (BLM) and its orthologs are well characterized in mitotic DNA damage repair, but their roles within the context of meiotic recombination are less clear. In meiotic recombination, multiple repair pathways are used to repair meiotic DSBs, and current studies suggest that BLM may regulate the use of these pathways. Based on literature from Saccharomyces cerevisiae, Arabidopsis thaliana, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans, we present a unified model for a critical meiotic role of BLM and its orthologs. In this model, BLM and its orthologs utilize helicase activity to regulate the use of various pathways in meiotic recombination by continuously disassembling recombination intermediates. This unwinding activity provides the meiotic program with a steady pool of early recombination substrates, increasing the probability for a DSB to be processed by the appropriate pathway. As a result of BLM activity, crossovers are properly placed throughout the genome, promoting proper chromosomal disjunction at the end of meiosis. This unified model can be used to further refine the complex role of BLM and its orthologs in meiotic recombination. © 2017 WILEY Periodicals, Inc.

Corrected and Republished from: BCL11A Is a Critical Component of a Transcriptional Network That Activates Recombinase Activating Gene Expression and V(D)J Recombination

PubMed Central

Lee, Baeck-Seung; Lee, Bum-Kyu; Iyer, Vishwanath R.; Sleckman, Barry P.; Shaffer, Arthur L.; Ippolito, Gregory C.

2017-01-01

ABSTRACT Recombination activating gene 1 (RAG1) and RAG2 are critical enzymes for initiating variable-diversity-joining [V(D)J] segment recombination, an essential process for antigen receptor expression and lymphocyte development. The BCL11A transcription factor is required for B cell and plasmacytoid dendritic cell (pDC) development, but its molecular function(s) in early B cell fate specification and commitment is unknown. We show here that the major B cell isoform, BCL11A-XL, binds directly to the RAG1 promoter as well as directly to regulatory regions of transcription factors previously implicated in both B cell and pDC development to activate RAG1 and RAG2 gene transcription in pro- and pre-B cells. We employed BCL11A overexpression with recombination substrates to demonstrate direct consequences of BCL11A/RAG modulation on V(D)J recombination. We conclude that BCL11A is a critical component of a transcriptional network that regulates B cell fate by controlling V(D)J recombination. PMID:29038163

Transcending the slow bimolecular recombination in lead-halide perovskites for electroluminescence

PubMed Central

Xing, Guichuan; Wu, Bo; Wu, Xiangyang; Li, Mingjie; Du, Bin; Wei, Qi; Guo, Jia; Yeow, Edwin K. L.; Sum, Tze Chien; Huang, Wei

2017-01-01

The slow bimolecular recombination that drives three-dimensional lead-halide perovskites' outstanding photovoltaic performance is conversely a fundamental limitation for electroluminescence. Under electroluminescence working conditions with typical charge densities lower than 1015 cm−3, defect-states trapping in three-dimensional perovskites competes effectively with the bimolecular radiative recombination. Herein, we overcome this limitation using van-der-Waals-coupled Ruddlesden-Popper perovskite multi-quantum-wells. Injected charge carriers are rapidly localized from adjacent thin few layer (n≤4) multi-quantum-wells to the thick (n≥5) multi-quantum-wells with extremely high efficiency (over 85%) through quantum coupling. Light emission originates from excitonic recombination in the thick multi-quantum-wells at much higher decay rate and efficiency than bimolecular recombination in three-dimensional perovskites. These multi-quantum-wells retain the simple solution processability and high charge carrier mobility of two-dimensional lead-halide perovskites. Importantly, these Ruddlesden-Popper perovskites offer new functionalities unavailable in single phase constituents, permitting the transcendence of the slow bimolecular recombination bottleneck in lead-halide perovskites for efficient electroluminescence. PMID:28239146

Transcending the slow bimolecular recombination in lead-halide perovskites for electroluminescence.

PubMed

Xing, Guichuan; Wu, Bo; Wu, Xiangyang; Li, Mingjie; Du, Bin; Wei, Qi; Guo, Jia; Yeow, Edwin K L; Sum, Tze Chien; Huang, Wei

2017-02-27

The slow bimolecular recombination that drives three-dimensional lead-halide perovskites' outstanding photovoltaic performance is conversely a fundamental limitation for electroluminescence. Under electroluminescence working conditions with typical charge densities lower than 10 15  cm -3 , defect-states trapping in three-dimensional perovskites competes effectively with the bimolecular radiative recombination. Herein, we overcome this limitation using van-der-Waals-coupled Ruddlesden-Popper perovskite multi-quantum-wells. Injected charge carriers are rapidly localized from adjacent thin few layer (n≤4) multi-quantum-wells to the thick (n≥5) multi-quantum-wells with extremely high efficiency (over 85%) through quantum coupling. Light emission originates from excitonic recombination in the thick multi-quantum-wells at much higher decay rate and efficiency than bimolecular recombination in three-dimensional perovskites. These multi-quantum-wells retain the simple solution processability and high charge carrier mobility of two-dimensional lead-halide perovskites. Importantly, these Ruddlesden-Popper perovskites offer new functionalities unavailable in single phase constituents, permitting the transcendence of the slow bimolecular recombination bottleneck in lead-halide perovskites for efficient electroluminescence.

Biological and immunogenic properties of rabies virus glycoprotein expressed by canine herpesvirus vector.

PubMed

Xuan, X; Tuchiya, K; Sato, I; Nishikawa, Y; Onoderaz, Y; Takashima, Y; Yamamoto, A; Katsumata, A; Iwata, A; Ueda, S; Mikami, T; Otsuka, H

1998-01-01

In order to evaluate whether canine herpesvirus (CHV) could be used as a live vector for the expression of heterologous immunogenes, we constructed a recombinant canine herpesvirus (CHV) expressing glycoprotein (G protein) of rabies virus (RV). The gene of G protein was inserted within the thymidine kinase gene of CHV YP11mu strain under the control of the human cytomegalovirus immediate early promoter. The G protein expressed by the recombinant CHV was processed and transported to the cell surface as in RV infected cells, and showed the same biological activities such as low pH dependent cell fusion and hemadsorption. The antigenic authenticity of the recombinant G protein was confirmed by a panel of monoclonal antibodies specific for G protein. Dogs inoculated intransally with the recombinant CHV produced higher titres of virus neutralizing antibodies against RV than those inoculated with a commercial, inactivated rabies vaccine. These results suggest that the CHV recombinant expressing G protein can be used as a vaccine to control canine rabies and that CHV may be useful as a vector to develop live recombinant against other infectious diseases in dogs.

Accumulation of functional recombinant human coagulation factor IX in transgenic soybean seeds.

PubMed

Cunha, Nicolau B; Murad, André M; Ramos, Gustavo L; Maranhão, Andréia Q; Brígido, Marcelo M; Araújo, Ana Cláudia G; Lacorte, Cristiano; Aragão, Francisco J L; Covas, Dimas T; Fontes, Aparecida M; Souza, Gustavo H M F; Vianna, Giovanni R; Rech, Elíbio L

2011-08-01

The seed-based production of recombinant proteins is an efficient strategy to achieve the accumulation, correct folding, and increased stability of these recombinant proteins. Among potential plant molecular farming systems, soybean [Glycine max (L.) Merrill] is a viable option for the production of recombinant proteins due to its high protein content, known regulatory sequences, efficient gene transfer protocols, and a scalable production system under greenhouse conditions. We report here the expression and stable accumulation of human coagulation factor IX (hFIX) in transgenic soybean seeds. A biolistic process was utilised to co-introduce a plasmid carrying the hFIX gene under the transcriptional control of the α' subunit of a β-conglycinin seed-specific promoter and an α-Coixin signal peptide in soybean embryonic axes from mature seeds. The 56-kDa hFIX protein was expressed in the transgenic seeds at levels of up to 0.23% (0.8 g kg(-1) seed) of the total soluble seed protein as determined by an enzyme-linked immunosorbent assay (ELISA) and western blot. Ultrastructural immunocytochemistry assays indicated that the recombinant hFIX in seed cotyledonary cells was efficiently directed to protein storage vacuoles. Mass spectrometry characterisation confirmed the presence of the hFIX recombinant protein sequence. Protein extracts from transgenic seeds showed a blood-clotting activity of up to 1.4% of normal plasma. Our results demonstrate the correct processing and stable accumulation of functional hFIX in soybean seeds stored for 6 years under room temperature conditions (22 ± 2°C).

Recombination rate plasticity: revealing mechanisms by design

PubMed Central

Sefick, Stephen; Rushton, Chase

2017-01-01

For over a century, scientists have known that meiotic recombination rates can vary considerably among individuals, and that environmental conditions can modify recombination rates relative to the background. A variety of external and intrinsic factors such as temperature, age, sex and starvation can elicit ‘plastic’ responses in recombination rate. The influence of recombination rate plasticity on genetic diversity of the next generation has interesting and important implications for how populations evolve. Further, many questions remain regarding the mechanisms and molecular processes that contribute to recombination rate plasticity. Here, we review 100 years of experimental work on recombination rate plasticity conducted in Drosophila melanogaster. We categorize this work into four major classes of experimental designs, which we describe via classic studies in D. melanogaster. Based on these studies, we highlight molecular mechanisms that are supported by experimental results and relate these findings to studies in other systems. We synthesize lessons learned from this model system into experimental guidelines for using recent advances in genotyping technologies, to study recombination rate plasticity in non-model organisms. Specifically, we recommend (1) using fine-scale genome-wide markers, (2) collecting time-course data, (3) including crossover distribution measurements, and (4) using mixed effects models to analyse results. To illustrate this approach, we present an application adhering to these guidelines from empirical work we conducted in Drosophila pseudoobscura. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109222

Photovoltaic Devices: Opto-Electro-Thermal Physics and Modeling.

PubMed

Shang, Aixue; Li, Xiaofeng

2017-02-01

An opto-electro-thermal simulation of solar cells (SCs) is presented by addressing optoelectronic and thermodynamic responses simultaneously. The photocurrent losses due to carrier recombinations and the intrinsic heat generation (thermalization/Joule/Peltier/recombination heat) and dissipation (convective/radiative cooling) processes in the SCs are investigated quantitatively. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recombination of mitochondrial DNA without selection pressure among compatible strains of the Aspergillus niger species aggregate.

PubMed

Tóth, B; Hamari, Z; Ferenczy, L; Varga, J; Kevei, F

1998-03-01

Previous mitochondrial transmission experiments between oligomycin-resistant and oligomycin-sensitive incompatible strains of the A. niger aggregate bearing various mtDNA RFLP profiles resulted in a great variety of mitochondrial recombinants under selection pressure. Apart from the recombinant mtDNAs, resistant clones harbouring unchanged RFLP profiles of resistant donor mtDNAs with the recipient nuclear backgrounds were rarely isolated. These strains were anastomosed with nuclearly isogenic oligomycin-sensitive recipient partners and the mitochondria of the resulting progeny were examined under non-selective conditions. These experiments provide insights into events which are possibly similar to those occurring in nature. The heterokaryons obtained formed both oligomycin-resistant and -sensitive sectors, most of which were found to be homoplasmons. Progenies harbouring oligomycin-resistant and -sensitive mtDNAs may originate either from individual recombination events or be due to parental segregation. MtDNA recombination might take place in the heterokaryons without selection by oligomycin. The most frequent recombinant types of mtDNA RFLP profiles were indistinguishable from those recombinant mtDNAs which were frequently obtained under selection pressure from directed transfer experiments between incompatible strains. We present evidence that mixed mitochondrial populations may influence the compatibility reactions in the presence of an isogenic nuclear background, that recombination may take place without selection pressure, and that the process does not require specific nuclear sequences of both parental strains.

The consequences of sequence erosion in the evolution of recombination hotspots.

PubMed

Tiemann-Boege, Irene; Schwarz, Theresa; Striedner, Yasmin; Heissl, Angelika

2017-12-19

Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans -acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'. © 2017 The Authors.

The consequences of sequence erosion in the evolution of recombination hotspots

PubMed Central

Schwarz, Theresa; Heissl, Angelika

2017-01-01

Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans-acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro. Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109225

Replicative age induces mitotic recombination in the ribosomal RNA gene cluster of Saccharomyces cerevisiae.

PubMed

Lindstrom, Derek L; Leverich, Christina K; Henderson, Kiersten A; Gottschling, Daniel E

2011-03-01

Somatic mutations contribute to the development of age-associated disease. In earlier work, we found that, at high frequency, aging Saccharomyces cerevisiae diploid cells produce daughters without mitochondrial DNA, leading to loss of respiration competence and increased loss of heterozygosity (LOH) in the nuclear genome. Here we used the recently developed Mother Enrichment Program to ask whether aging cells that maintain the ability to produce respiration-competent daughters also experience increased genomic instability. We discovered that this population exhibits a distinct genomic instability phenotype that primarily affects the repeated ribosomal RNA gene array (rDNA array). As diploid cells passed their median replicative life span, recombination rates between rDNA arrays on homologous chromosomes progressively increased, resulting in mutational events that generated LOH at >300 contiguous open reading frames on the right arm of chromosome XII. We show that, while these recombination events were dependent on the replication fork block protein Fob1, the aging process that underlies this phenotype is Fob1-independent. Furthermore, we provide evidence that this aging process is not driven by mechanisms that modulate rDNA recombination in young cells, including loss of cohesion within the rDNA array or loss of Sir2 function. Instead, we suggest that the age-associated increase in rDNA recombination is a response to increasing DNA replication stress generated in aging cells.

N-terminal processing of affinity-tagged recombinant proteins purified by IMAC procedures.

PubMed

Mooney, Jane T; Fredericks, Dale P; Christensen, Thorkild; Bruun Schiødt, Christine; Hearn, Milton T W

2015-07-01

The ability of a new class of metal binding tags to facilitate the purification of recombinant proteins, exemplified by the tagged glutathione S-transferase and human growth hormone, from Escherichia coli fermentation broths and lysates has been further investigated. These histidine-containing tags exhibit high affinity for borderline metal ions chelated to the immobilised ligand, 1,4,7-triazacyclononane (tacn). The use of this tag-tacn immobilised metal ion affinity chromatography (IMAC) system engenders high selectivity with regard to host cell protein removal and permits facile tag removal from the E. coli-expressed recombinant protein. In particular, these tags were specifically designed to enable their efficient removal by the dipeptidyl aminopeptidase 1 (DAP-1), thus capturing the advantages of high substrate specificity and rates of cleavage. MALDI-TOF MS analysis of the cleaved products from the DAP-1 digestion of the recombinant N-terminally tagged proteins confirmed the complete removal of the tag within 4-12 h under mild experimental conditions. Overall, this study demonstrates that the use of tags specifically designed to target tacn-based IMAC resins offers a comprehensive and flexible approach for the purification of E. coli-expressed recombinant proteins, where complete removal of the tag is an essential prerequisite for subsequent application of the purified native proteins in studies aimed at delineating the molecular and cellular basis of specific biological processes. Copyright © 2015 John Wiley & Sons, Ltd.

Nanobodies and recombinant binders in cell biology.

PubMed

Helma, Jonas; Cardoso, M Cristina; Muyldermans, Serge; Leonhardt, Heinrich

2015-06-08

Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes. © 2015 Helma et al.

Precursors of Androctonus australis Scorpion Neurotoxins. Structures of Precursors, Processing Outcomes, and Expression of a Functional Recombinant Toxin II

DTIC Science & Technology

1989-05-24

29. Proudfoot, N. J., and Brownlee, G. G. (1976) NatUlgL263, 211-214 30. Detima, M. E ., Martin, M. F., Diniz , C. R., and Rochat, H. (1986) Biochem...Neurotoxins 7 12. PERSONAL AUTHOR(S) Drs. Pierre E . Bougis, Herve Rochat and Leonard A. Smith 13a. TYPE OF REPORT 13b. TIME COVERED 114. DATE OF REPORT...PRECURSORS, PROCESSING OUTCOMES, AND EXPRESSION OF A FUNCTIONAL RECOMBINANT TOXIN II Pierre E . Bougis, Herve Rochat1 and Leonard A. Smith from the

Use of a small molecule cell cycle inhibitor to control cell growth and improve specific productivity and product quality of recombinant proteins in CHO cell cultures.

PubMed

Du, Zhimei; Treiber, David; McCarter, John D; Fomina-Yadlin, Dina; Saleem, Ramsey A; McCoy, Rebecca E; Zhang, Yuling; Tharmalingam, Tharmala; Leith, Matthew; Follstad, Brian D; Dell, Brad; Grisim, Brent; Zupke, Craig; Heath, Carole; Morris, Arvia E; Reddy, Pranhitha

2015-01-01

The continued need to improve therapeutic recombinant protein productivity has led to ongoing assessment of appropriate strategies in the biopharmaceutical industry to establish robust processes with optimized critical variables, that is, viable cell density (VCD) and specific productivity (product per cell, qP). Even though high VCD is a positive factor for titer, uncontrolled proliferation beyond a certain cell mass is also undesirable. To enable efficient process development to achieve consistent and predictable growth arrest while maintaining VCD, as well as improving qP, without negative impacts on product quality from clone to clone, we identified an approach that directly targets the cell cycle G1-checkpoint by selectively inhibiting the function of cyclin dependent kinases (CDK) 4/6 with a small molecule compound. Results from studies on multiple recombinant Chinese hamster ovary (CHO) cell lines demonstrate that the selective inhibitor can mediate a complete and sustained G0/G1 arrest without impacting G2/M phase. Cell proliferation is consistently and rapidly controlled in all recombinant cell lines at one concentration of this inhibitor throughout the production processes with specific productivities increased up to 110 pg/cell/day. Additionally, the product quality attributes of the mAb, with regard to high molecular weight (HMW) and glycan profile, are not negatively impacted. In fact, high mannose is decreased after treatment, which is in contrast to other established growth control methods such as reducing culture temperature. Microarray analysis showed major differences in expression of regulatory genes of the glycosylation and cell cycle signaling pathways between these different growth control methods. Overall, our observations showed that cell cycle arrest by directly targeting CDK4/6 using selective inhibitor compound can be utilized consistently and rapidly to optimize process parameters, such as cell growth, qP, and glycosylation profile in recombinant antibody production cultures. © 2014 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

Carrier dynamics and surface vibration-assisted Auger recombination in porous silicon

NASA Astrophysics Data System (ADS)

Zakar, Ammar; Wu, Rihan; Chekulaev, Dimitri; Zerova, Vera; He, Wei; Canham, Leigh; Kaplan, Andrey

2018-04-01

Excitation and recombination dynamics of the photoexcited charge carriers in porous silicon membranes were studied using a femtosecond pump-probe technique. Near-infrared pulses (800 nm, 60 fs) were used for the pump while, for the probe, we employed different wavelengths in the range between 3.4 and 5 μ m covering the medium wavelength infrared range. The data acquired in these experiments consist of simultaneous measurements of the transmittance and reflectance as a function of the delay time between the pump and probe for different pump fluences and probe wavelengths. To evaluate the results, we developed an optical model based on the two-dimensional Maxwell-Garnett formula, incorporating the free-carrier Drude contribution and nonuniformity of the excitation by the Wentzel-Kramers-Brillouin model. This model allowed the retrieval of information about the carrier density as a function of the pump fluence, time, and wavelength. The carrier density data were analyzed to reveal that the recombination dynamics is governed by Shockley-Read-Hall and Auger processes, whereas the diffusion has an insignificant contribution. We show that, in porous silicon samples, the Auger recombination process is greatly enhanced at the wavelength corresponding to the infrared-active vibrational modes of the molecular impurities on the surface of the pores. This observation of surface-vibration-assisted Auger recombination is not only for porous silicon in particular, but for low-dimension and bulk semiconductors in general. We estimate the time constants of Shockley-Read-Hall and Auger processes, and demonstrate their wavelength dependence for the excited carrier density in the range of 1018-10191 /cm3 . We demonstrate that both processes are enhanced by up to three orders of magnitude with respect to the bulk counterpart. In addition, we provide a plethora of the physical parameters evaluated from the experimental data, such as the dielectric function and its dependence on the injection level of the free carriers, charge-carrier scattering time related high-frequency conductivity, and the free-carrier absorption at the midwave infrared range.

Seed-based expression systems for plant molecular farming.

PubMed

Boothe, Joseph; Nykiforuk, Cory; Shen, Yin; Zaplachinski, Steven; Szarka, Steven; Kuhlman, Philip; Murray, Elizabeth; Morck, Douglas; Moloney, Maurice M

2010-06-01

The evolution of the seed system provides enormous adaptability to the gymnosperms and angiosperms, because of the properties of dormancy, nutrient storage and seedling vigour. Many of the unique properties of seeds can be exploited in molecular farming applications, particularly where it is desirable to produce large quantities of a recombinant protein. Seeds of transgenic plants have been widely used to generate a raw material for the extraction and isolation of proteins and polypeptides, which can be processed into valuable biopharmaceuticals. The factors that control high-level accumulation of recombinant proteins in seed are reviewed in the following paragraphs. These include promoters and enhancers, which regulate transcript abundance. However, it is shown that subcellular trafficking and targeting of the desired polypeptides or proteins play a crucial role in their accumulation at economically useful levels. Seeds have proven to be versatile hosts for recombinant proteins of all types, including peptides or short and long polypeptides as well as complex, noncontiguous proteins like antibodies and other immunoglobulins. The extraction and recovery of recombinant proteins from seeds is greatly assisted by their dormancy properties, because this allows for long-term stability of stored products including recombinant proteins and a decoupling of processing from the growth and harvest cycles. Furthermore, the low water content and relatively low bioload of seeds help greatly in designing cost-effective manufacturing processes for the desired active pharmaceutical ingredient. The development of cGMP processes based on seed-derived materials has only been attempted by a few groups to date, but we provide a review of the key issues and criteria based on interactions with Food and Drug Administration and European Medicines Agency. This article uses 'case studies' to highlight the utility of seeds as vehicles for pharmaceutical production including: insulin, human growth hormone, lysozyme and lactoferrin. These examples serve to illustrate the preclinical and, in one case, clinical information required to move these plant-derived molecules through the research phase and into the regulatory pathway en route to eventual approval.

Laser-Matter Interaction in Dielectrics: Insight from Picosecond-Pulsed Second-Harmonic Generation in Periodically Poled LiTaO3

NASA Astrophysics Data System (ADS)

Louchev, Oleg A.; Wada, Satoshi; Panchenko, Vladislav Ya.

2017-08-01

We develop a modified two-temperature (2T) model of laser-matter interaction in dielectrics based on experimental insight from picosecond-pulsed high-frequency temperature-controlled second-harmonic (515 nm) generation in periodically poled stoichiometric LiTaO3 crystal and required for computational treatment of short-pulsed nonlinear optics and materials processing applications. We show that the incorporation of an extended set of recombination-kinetics-related energy-release and heat-exchange processes following short-pulsed photoionization by two-photon absorption of the second harmonic allows accurate simulation of the electron-lattice relaxation dynamics and electron-lattice temperature evolution in LiTaO3 crystal in nonlinear laser-frequency conversion. Our experimentally confirmed model and detailed simulation study show that two-photon ionization with the recombination mechanism via ion-electron-lattice interaction followed by a direct transfer of the recombination energy to the lattice is the main laser-matter energy-transfer pathway responsible for the majority of the crystal lattice heating (approximately 90%) continuing for approximately 50 ps after laser-pulse termination and competing with effect of electron-phonon energy transfer from the free electrons. This time delay is due to a recombination bottleneck which hinders faster relaxation to thermal equilibrium in photoionized dielectric crystal. Generally, our study suggests that in dielectrics photoionized by short-pulsed radiation with intensity range used in nonlinear laser-frequency conversion, the electron-lattice relaxation period is defined by the recombination-stage bottleneck of a few tens of picoseconds and not by the time of the electron-phonon energy transfer. This modification of the 2T model can be applied to a broad range of processes involving laser-matter interactions in dielectrics and semiconductors for charge density reaching the range of 1021- 1022 cm-3 .

Techno-economic analysis of the industrial production of a low-cost enzyme using E. coli: the case of recombinant β-glucosidase.

PubMed

Ferreira, Rafael da Gama; Azzoni, Adriano Rodrigues; Freitas, Sindelia

2018-01-01

The enzymatic conversion of lignocellulosic biomass into fermentable sugars is a promising approach for producing renewable fuels and chemicals. However, the cost and efficiency of the fungal enzyme cocktails that are normally employed in these processes remain a significant bottleneck. A potential route to increase hydrolysis yields and thereby reduce the hydrolysis costs would be to supplement the fungal enzymes with their lacking enzymatic activities, such as β-glucosidase. In this context, it is not clear from the literature whether recombinant E. coli could be a cost-effective platform for the production of some of these low-value enzymes, especially in the case of on-site production. Here, we present a conceptual design and techno-economic evaluation of the production of a low-cost industrial enzyme using recombinant E. coli . In a simulated baseline scenario for β-glucosidase demand in a hypothetical second-generation ethanol (2G) plant in Brazil, we found that the production cost (316 US$/kg) was higher than what is commonly assumed in the literature for fungal enzymes, owing especially to the facility-dependent costs (45%) and to consumables (23%) and raw materials (25%). Sensitivity analyses of process scale, inoculation volume, and volumetric productivity indicated that optimized conditions may promote a dramatic reduction in enzyme cost and also revealed the most relevant factors affecting production costs. Despite the considerable technical and economic uncertainties that surround 2G ethanol and the large-scale production of low-cost recombinant enzymes, this work sheds light on some relevant questions and supports future studies in this field. In particular, we conclude that process optimization, on many fronts, may strongly reduce the costs of E. coli recombinant enzymes, in the context of tailor-made enzymatic cocktails for 2G ethanol production.

Microwave plasma generation of hydrogen atoms for rocket propulsion

NASA Technical Reports Server (NTRS)

Chapman, R.; Filpus, J.; Morin, T.; Snellenberger, R.; Asmussen, J.; Hawley, M.; Kerber, R.

1981-01-01

A flow microwave plasma reaction system is used to study the conversion of hydrogen to hydrogen atoms as a function of pressure, power density, cavity tuning, cavity mode, and time in the plasma zone. Hydrogen atom concentration is measured down-stream from the plasma by NOCl titration. Extensive modeling of the plasma and recombination zones is performed with the plasma zone treated as a backmix reaction system and the recombination zone treated as a plug flow. The thermodynamics and kinetics of the recombination process are examined in detail to provide an understanding of the conversion of recombination energy to gas kinetic energy. It is found that cavity tuning, discharge stability, and optimum power coupling are critically dependent on the system pressure, but nearly independent of the flow rate.

V(D)J recombination process and the Pre-B to immature B-cells transition are altered in Fanca−/− mice

PubMed Central

Nguyen, Thuy Vy; Pawlikowska, Patrycja; Firlej, Virginie; Rosselli, Filippo; Aoufouchi, Saïd

2016-01-01

B-lymphocytes in the bone marrow (BM) must generate a functional B-cell receptor and overcome the negative selection induced by reactivity with autoantigens. Two rounds of DNA recombination are required for the production of functional immunoglobulin heavy (Ig-HCs) and light (LCs) chains necessary for the continuation of B-lymphocyte development in the BM. Both rounds depend on the joint action of recombination activating gene-1 (RAG-1) and RAG-2 endonucleases with the DNA non-homologous end-joining pathway. Loss of the FANC gene leads to the chromosome breakage and cancer predisposition syndrome Fanconi anemia. Because the FANC proteins are involved in certain aspects of the recombination process, we sought to determine the impact of the FANC pathway on the Ig diversification process using Fanca−/− mice. In this work we demonstrated that Fanca−/− animals have a mild B-cell differentiation defect characterized by a specific alteration of the IgM− to IgM+ transition of the B220low B-cell population. Pre-B cells from Fanca−/− mice show evidence of impaired kLC rearrangement at the level of the Vk-Jk junction. Furthermore, Fanca−/− mice showed a skewed Vκ gene usage during formation of the LCs Vk-Jk junctions. Therefore, the Fanca protein appears as a yet unidentified factor involved in the primary diversification of Ig. PMID:27883081

V(D)J recombination process and the Pre-B to immature B-cells transition are altered in Fanca-/- mice.

PubMed

Nguyen, Thuy Vy; Pawlikowska, Patrycja; Firlej, Virginie; Rosselli, Filippo; Aoufouchi, Saïd

2016-11-24

B-lymphocytes in the bone marrow (BM) must generate a functional B-cell receptor and overcome the negative selection induced by reactivity with autoantigens. Two rounds of DNA recombination are required for the production of functional immunoglobulin heavy (Ig-HCs) and light (LCs) chains necessary for the continuation of B-lymphocyte development in the BM. Both rounds depend on the joint action of recombination activating gene-1 (RAG-1) and RAG-2 endonucleases with the DNA non-homologous end-joining pathway. Loss of the FANC gene leads to the chromosome breakage and cancer predisposition syndrome Fanconi anemia. Because the FANC proteins are involved in certain aspects of the recombination process, we sought to determine the impact of the FANC pathway on the Ig diversification process using Fanca -/- mice. In this work we demonstrated that Fanca -/- animals have a mild B-cell differentiation defect characterized by a specific alteration of the IgM - to IgM + transition of the B220 low B-cell population. Pre-B cells from Fanca -/- mice show evidence of impaired kLC rearrangement at the level of the Vk-Jk junction. Furthermore, Fanca -/- mice showed a skewed Vκ gene usage during formation of the LCs Vk-Jk junctions. Therefore, the Fanca protein appears as a yet unidentified factor involved in the primary diversification of Ig.

Maltose-Binding Protein Enhances Secretion of Recombinant Human Granzyme B Accompanied by In Vivo Processing of a Precursor MBP Fusion Protein

PubMed Central

Dälken, Benjamin; Jabulowsky, Robert A.; Oberoi, Pranav; Benhar, Itai; Wels, Winfried S.

2010-01-01

Background The apoptosis-inducing serine protease granzyme B (GrB) is an important factor contributing to lysis of target cells by cytotoxic lymphocytes. Expression of enzymatically active GrB in recombinant form is a prerequisite for functional analysis and application of GrB for therapeutic purposes. Methods and Findings We investigated the influence of bacterial maltose-binding protein (MBP) fused to GrB via a synthetic furin recognition motif on the expression of the MBP fusion protein also containing an N-terminal α-factor signal peptide in the yeast Pichia pastoris. MBP markedly enhanced the amount of GrB secreted into culture supernatant, which was not the case when GrB was fused to GST. MBP-GrB fusion protein was cleaved during secretion by an endogenous furin-like proteolytic activity in vivo, liberating enzymatically active GrB without the need of subsequent in vitro processing. Similar results were obtained upon expression of a recombinant fragment of the ErbB2/HER2 receptor protein or GST as MBP fusions. Conclusions Our results demonstrate that combination of MBP as a solubility enhancer with specific in vivo cleavage augments secretion of processed and functionally active proteins from yeast. This strategy may be generally applicable to improve folding and increase yields of recombinant proteins. PMID:21203542

Carrier recombination dynamics in anatase TiO 2 nanoparticles

NASA Astrophysics Data System (ADS)

Cavigli, Lucia; Bogani, Franco; Vinattieri, Anna; Cortese, Lorenzo; Colocci, Marcello; Faso, Valentina; Baldi, Giovanni

2010-11-01

We present an experimental study of the radiative recombination dynamics in size-controlled TiO 2 nanoparticles in the range 20-130 nm. Time-integrated photoluminescence spectra clearly show a dominance of self-trapped exciton (STE) emission, with main features not dependent on the nanoparticle size and on its environment. From picosecond time-resolved experiments as a function of the excitation density and the nanoparticle size we address the STE recombination dynamics as the result of two main processes related to the direct STE formation and to the indirect STE formation mediated by non-radiative surface states.

Kinetics of DSB rejoining and formation of simple chromosome exchange aberrations

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Nikjoo, H.; O'Neill, P.; Goodhead, D. T.

2000-01-01

PURPOSE: To investigate the role of kinetics in the processing of DNA double strand breaks (DSB), and the formation of simple chromosome exchange aberrations following X-ray exposures to mammalian cells based on an enzymatic approach. METHODS: Using computer simulations based on a biochemical approach, rate-equations that describe the processing of DSB through the formation of a DNA-enzyme complex were formulated. A second model that allows for competition between two processing pathways was also formulated. The formation of simple exchange aberrations was modelled as misrepair during the recombination of single DSB with undamaged DNA. Non-linear coupled differential equations corresponding to biochemical pathways were solved numerically by fitting to experimental data. RESULTS: When mediated by a DSB repair enzyme complex, the processing of single DSB showed a complex behaviour that gives the appearance of fast and slow components of rejoining. This is due to the time-delay caused by the action time of enzymes in biomolecular reactions. It is shown that the kinetic- and dose-responses of simple chromosome exchange aberrations are well described by a recombination model of DSB interacting with undamaged DNA when aberration formation increases with linear dose-dependence. Competition between two or more recombination processes is shown to lead to the formation of simple exchange aberrations with a dose-dependence similar to that of a linear quadratic model. CONCLUSIONS: Using a minimal number of assumptions, the kinetics and dose response observed experimentally for DSB rejoining and the formation of simple chromosome exchange aberrations are shown to be consistent with kinetic models based on enzymatic reaction approaches. A non-linear dose response for simple exchange aberrations is possible in a model of recombination of DNA containing a DSB with undamaged DNA when two or more pathways compete for DSB repair.

Bioeconomy Initiative at MBI International

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kleff, Susanne, Ph.D.

Di-carboxylic acids have the potential to replace petrochemicals used in the polymer industry (Werpy and Petersen, 2004). MBI developed a process for the production of succinic acid using a proprietary organism. During this work MBI assessed the feasibility to produce other carboxylic acids either using A. succinogenes or other organisms. The development of recombinant A. succinogenes strain derivatives for a mono-carboxylic acid through over-expression of enzymatic activities was successful. Fermentations achieved titers of 58 g/L for this organic acid. Recombinant strains that produced the same acid, but a different stereoisomer, reached titers of 10 g/L. Attempts to increase the titersmore » for this isomer as well as other organic acids were unsuccessful. MBI is looking for commercial partners to pursue the development of recombinant A. succinogenes strains for the production of other organic acids. Attempts to develop recombinant strains of A. succinogenes for fumaric acid production through introduction of various antisense RNA constructs were unsuccessful. Alternative suitable organisms were evaluated and Rhizopus oryzae, a natural fumaric acid producer with potential for process improvements, was selected. A novel fermentation and one-step recovery process was developed that allowed capture of IP, produced titers of >80 g/L with a productivity of 1.8 g/L-h and 57% (g/g glucose) yield. The process was scaled to 2000 L pilot scale. The economic analysis projected a production cost of 72 c/lb. Recycling and re-use of the base was demonstrated and incorporated into the process. The ability of the organism to produce fumaric acid from other carbon sources and biomass hydrolysate was demonstrated. The production of other organic acids was evaluated and techno-economic de-risking roadmap documents were prepared.« less

Distribution of recombination hotspots in the human genome--a comparison of computer simulations with real data.

PubMed

Mackiewicz, Dorota; de Oliveira, Paulo Murilo Castro; Moss de Oliveira, Suzana; Cebrat, Stanisław

2013-01-01

Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar.

Distribution of Recombination Hotspots in the Human Genome – A Comparison of Computer Simulations with Real Data

PubMed Central

Mackiewicz, Dorota; de Oliveira, Paulo Murilo Castro; Moss de Oliveira, Suzana; Cebrat, Stanisław

2013-01-01

Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar. PMID:23776462

Atomic oxygen recombination on quartz at high temperature: experiments and molecular dynamics simulation.

PubMed

Bedra, L; Rutigliano, M; Balat-Pichelin, M; Cacciatore, M

2006-08-15

A joint experimental and theoretical approach has been developed to study oxygen atom recombination on a beta-quartz surface. The experimental MESOX setup has been applied for the direct measurement of the atomic oxygen recombination coefficient gamma at T(S) = 1000 K. The time evolution of the relative atomic oxygen concentration in the cell is described by the diffusion equation because the mean free path of the atoms is less than the characteristic dimension of the reactor. The recombination coefficient gamma is then calculated from the concentration profile obtained by visible spectroscopy. We get an experimental value of gamma = 0.008, which is a factor of about 3 less than the gamma value reported for O recombination over beta-cristobalite. The experimental results are discussed and compared with the semiclassical collision dynamics calculations performed on the same catalytic system aimed at determining the basic features of the surface catalytic activity. Agreement, both qualitative and quantitative, between the experimental and the theoretical recombination coefficients has been found that supports the Eley-Rideal recombination mechanism and gives more evidence of the impact that surface crystallographic variation has on catalytic activity. Also, several interesting aspects concerning the energetics and the mechanism of the surface processes involving the oxygen atoms are pointed out and discussed.

GATA3 Abundance Is a Critical Determinant of T Cell Receptor β Allelic Exclusion

PubMed Central

Ku, Chia-Jui; Sekiguchi, JoAnn M.; Panwar, Bharat; Guan, Yuanfang; Takahashi, Satoru; Yoh, Keigyou; Maillard, Ivan; Hosoya, Tomonori

2017-01-01

ABSTRACT Allelic exclusion describes the essential immunological process by which feedback repression of sequential DNA rearrangements ensures that only one autosome expresses a functional T or B cell receptor. In wild-type mammals, approximately 60% of cells have recombined the DNA of one T cell receptor β (TCRβ) V-to-DJ-joined allele in a functional configuration, while the second allele has recombined only the DJ sequences; the other 40% of cells have recombined the V to the DJ segments on both alleles, with only one of the two alleles predicting a functional TCRβ protein. Here we report that the transgenic overexpression of GATA3 leads predominantly to biallelic TCRβ gene (Tcrb) recombination. We also found that wild-type immature thymocytes can be separated into distinct populations based on intracellular GATA3 expression and that GATA3LO cells had almost exclusively recombined only one Tcrb locus (that predicted a functional receptor sequence), while GATA3HI cells had uniformly recombined both Tcrb alleles (one predicting a functional and the other predicting a nonfunctional rearrangement). These data show that GATA3 abundance regulates the recombination propensity at the Tcrb locus and provide new mechanistic insight into the historic immunological conundrum for how Tcrb allelic exclusion is mediated. PMID:28320875

The 3'-to-5' exonuclease activity of vaccinia virus DNA polymerase is essential and plays a role in promoting virus genetic recombination.

PubMed

Gammon, Don B; Evans, David H

2009-05-01

Poxviruses are subjected to extraordinarily high levels of genetic recombination during infection, although the enzymes catalyzing these reactions have never been identified. However, it is clear that virus-encoded DNA polymerases play some unknown yet critical role in virus recombination. Using a novel, antiviral-drug-based strategy to dissect recombination and replication reactions, we now show that the 3'-to-5' proofreading exonuclease activity of the viral DNA polymerase plays a key role in promoting recombination reactions. Linear DNA substrates were prepared containing the dCMP analog cidofovir (CDV) incorporated into the 3' ends of the molecules. The drug blocked the formation of concatemeric recombinant molecules in vitro in a process that was catalyzed by the proofreading activity of vaccinia virus DNA polymerase. Recombinant formation was also blocked when CDV-containing recombination substrates were transfected into cells infected with wild-type vaccinia virus. These inhibitory effects could be overcome if CDV-containing substrates were transfected into cells infected with CDV-resistant (CDV(r)) viruses, but only when resistance was linked to an A314T substitution mutation mapping within the 3'-to-5' exonuclease domain of the viral polymerase. Viruses encoding a CDV(r) mutation in the polymerase domain still exhibited a CDV-induced recombination deficiency. The A314T substitution also enhanced the enzyme's capacity to excise CDV molecules from the 3' ends of duplex DNA and to recombine these DNAs in vitro, as judged from experiments using purified mutant DNA polymerase. The 3'-to-5' exonuclease activity appears to be an essential virus function, and our results suggest that this might be because poxviruses use it to promote genetic exchange.

Simplified model to describe the dissociative recombination of linear polyatomic ions of astrophysical interest

NASA Astrophysics Data System (ADS)

Fonseca Dos Santos, Samantha; Douguet, Nicolas; Kokoouline, Viatcheslav; Orel, Ann

2013-05-01

We will present theoretical results on the dissociative recombination (DR) of the linear polyatomic ions HCNH+, HCO+ and N2H+. Besides their astrophysical importance, they also share the characteristic that at low electronic impact energies their DR process happens via the indirect DR mechanism. We apply a general simplified model successfully implemented to treat the DR process of the highly symmetric non-linear molecules H3+, CH3+, H3O+ and NH4+ to calculated cross sections and DR rates for these ions. The model is based on multichannel quantum defect theory and accounts for all the main ingredients of indirect DR. New perspectives on dissociative recombination of HCO+ will also be discussed, including the possible role of HOC+ in storage ring experimental results. This work is supported by the DOE Office of Basic Energy Science and the National Science Foundation, Grant No's PHY-11-60611 and PHY-10-68785.

Integrating metabolic modeling and population heterogeneity analysis into optimizing recombinant protein production by Komagataella (Pichia) pastoris.

PubMed

Theron, Chrispian W; Berrios, Julio; Delvigne, Frank; Fickers, Patrick

2018-01-01

The methylotrophic yeast Komagataella (Pichia) pastoris has become one of the most utilized cell factories for the production of recombinant proteins over the last three decades. This success story is linked to its specific physiological traits, i.e., the ability to grow at high cell density in inexpensive culture medium and to secrete proteins at high yield. Exploiting methanol metabolism is at the core of most P. pastoris-based processes but comes with its own challenges. Co-feeding cultures with glycerol/sorbitol and methanol is a promising approach, which can benefit from improved understanding and prediction of metabolic response. The development of profitable processes relies on the construction and selection of efficient producing strains from less efficient ones but also depends on the ability to master the bioreactor process itself. More specifically, how a bioreactor processes could be monitored and controlled to obtain high yield of production. In this review, new perspectives are detailed regarding a multi-faceted approach to recombinant protein production processes by P. pastoris; including gaining improved understanding of the metabolic pathways involved, accounting for variations in transcriptional and translational efficiency at the single cell level and efficient monitoring and control of methanol levels at the bioreactor level.

Effects of recombinant protein misfolding and aggregation on bacterial membranes.

PubMed

Ami, D; Natalello, A; Schultz, T; Gatti-Lafranconi, P; Lotti, M; Doglia, S M; de Marco, A

2009-02-01

The expression of recombinant proteins is known to induce a metabolic rearrangement in the host cell. We used aggregation-sensitive model systems to study the effects elicited in Escherichia coli cells by the aggregation of recombinant glutathione-S-transferase and its fusion with the green fluorescent protein that, according to the expression conditions, accumulate intracellularly as soluble protein, or soluble and insoluble aggregates. We show that the folding state of the recombinant protein and the complexity of the intracellular aggregates critically affect the cell response. Specifically, protein misfolding and aggregation induce changes in specific host proteins involved in lipid metabolism and oxidative stress, a reduction in the membrane permeability, as well as a rearrangement of its lipid composition. The temporal evolution of the host cell response and that of the aggregation process pointed out that the misfolded protein and soluble aggregates are responsible for the membrane modifications and the changes in the host protein levels. Interestingly, native recombinant protein and large insoluble aggregates do not seem to activate stress markers and membrane rearrangements.

Knowledge-based probabilistic representations of branching ratios in chemical networks: The case of dissociative recombinations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plessis, Sylvain; Carrasco, Nathalie; Pernot, Pascal

Experimental data about branching ratios for the products of dissociative recombination of polyatomic ions are presently the unique information source available to modelers of natural or laboratory chemical plasmas. Yet, because of limitations in the measurement techniques, data for many ions are incomplete. In particular, the repartition of hydrogen atoms among the fragments of hydrocarbons ions is often not available. A consequence is that proper implementation of dissociative recombination processes in chemical models is difficult, and many models ignore invaluable data. We propose a novel probabilistic approach based on Dirichlet-type distributions, enabling modelers to fully account for the available information.more » As an application, we consider the production rate of radicals through dissociative recombination in an ionospheric chemistry model of Titan, the largest moon of Saturn. We show how the complete scheme of dissociative recombination products derived with our method dramatically affects these rates in comparison with the simplistic H-loss mechanism implemented by default in all recent models.« less

Optimization of culturing conditions of recombined Escherichia coli to produce umami octopeptide-containing protein.

PubMed

Zhang, Yin; Wei, Xiong; Lu, Zhou; Pan, Zhongli; Gou, Xinhua; Venkitasamy, Chandrasekar; Guo, Siya; Zhao, Liming

2017-07-15

Using synthesized peptides to verify the taste of natural peptides was probably the leading cause for tasting disputes regarding umami peptides. A novel method was developed to prepare the natural peptide which could be used to verify the taste of umami peptide. A controversial octopeptide was selected and gene engineering was used to structure its Escherichia coli. expressing vector. A response surface method was adopted to optimize the expression conditions of the recombinant protein. The results of SDS-PAGE for the recombinant protein indicated that the recombinant expression system was successfully structured. The fitting results of the response surface experiment showed that the OD 600 value was the key factor which influenced the expression of the recombinant protein. The optimal culturing process conditions predicted with the fitting model were an OD 600 value of 0.5, an IPTG concentration of 0.6mM, a culturing temperature of 28.75°C and a culturing time of 5h. Copyright © 2017 Elsevier Ltd. All rights reserved.

Purification and characterization of recombinant supersweet protein thaumatin II from tomato fruit.

PubMed

Firsov, Aleksey; Shaloiko, Lyubov; Kozlov, Oleg; Vinokurov, Leonid; Vainstein, Alexander; Dolgov, Sergey

2016-07-01

Thaumatin, a supersweet protein from the African plant katemfe (Thaumatococcus daniellii Benth.), is a promising zero-calorie sweetener for use in the food and pharmaceutical industries. Due to limited natural sources of thaumatin, its production using transgenic plants is an advantageous alternative. We report a simple protocol for purification of recombinant thaumatin II from transgenic tomato. Thaumatin was extracted from ripe tomato fruit in a low-salt buffer and purified on an SP-Sephacryl column. Recombinant thaumatin yield averaged 50 mg/kg fresh fruit. MALDI-MS analysis showed correct processing of thaumatin in tomato plants. The recombinant thaumatin was indistinguishable from the native protein in a taste test. The purified tomato-derived thaumatin had an intrinsic sweetness with a threshold value in taste tests of around 50 nM. These results demonstrate the potential of an expression system based on transgenic tomato plants for production of recombinant thaumatin for the food and pharmaceutical industries. Copyright © 2016 Elsevier Inc. All rights reserved.

Knowledge-based probabilistic representations of branching ratios in chemical networks: the case of dissociative recombinations.

PubMed

Plessis, Sylvain; Carrasco, Nathalie; Pernot, Pascal

2010-10-07

Experimental data about branching ratios for the products of dissociative recombination of polyatomic ions are presently the unique information source available to modelers of natural or laboratory chemical plasmas. Yet, because of limitations in the measurement techniques, data for many ions are incomplete. In particular, the repartition of hydrogen atoms among the fragments of hydrocarbons ions is often not available. A consequence is that proper implementation of dissociative recombination processes in chemical models is difficult, and many models ignore invaluable data. We propose a novel probabilistic approach based on Dirichlet-type distributions, enabling modelers to fully account for the available information. As an application, we consider the production rate of radicals through dissociative recombination in an ionospheric chemistry model of Titan, the largest moon of Saturn. We show how the complete scheme of dissociative recombination products derived with our method dramatically affects these rates in comparison with the simplistic H-loss mechanism implemented by default in all recent models.

Do grain boundaries dominate non-radiative recombination in CH 3NH 3PbI 3 perovskite thin films?

DOE PAGES

Yang, Mengjin; Zeng, Yining; Li, Zhen; ...

2017-01-13

Here, we examine GBs with respect to non-GB regions (grain surfaces (GSs) and grain interiors (GIs)) in high-quality micrometer-sized perovskite CH 3NH 3PbI 3 (or MAPbI 3) thin films using high-resolution confocal fluorescence-lifetime imaging microscopy in conjunction with kinetic modeling of charge-transport and recombination processes. We show that, contrary to previous studies, GBs in our perovskite MAPbI3 thin films do not lead to increased recombination but that recombination in these films happens primarily in the non-GB regions (i.e., GSs or GIs). We also find that GBs in these films are not transparent to photogenerated carriers, which is likely associated withmore » a potential barrier at GBs. Lastly, even though GBs generally display lower luminescence intensities than GSs/GIs, the lifetimes at GBs are no worse than those at GSs/GIs, further suggesting that GBs do not dominate non-radiative recombination in MAPbI 3 thin films.« less

Unisexual Reproduction Drives Meiotic Recombination and Phenotypic and Karyotypic Plasticity in Cryptococcus neoformans

PubMed Central

Sun, Sheng; Billmyre, R. Blake; Mieczkowski, Piotr A.; Heitman, Joseph

2014-01-01

In fungi, unisexual reproduction, where sexual development is initiated without the presence of two compatible mating type alleles, has been observed in several species that can also undergo traditional bisexual reproduction, including the important human fungal pathogens Cryptococcus neoformans and Candida albicans. While unisexual reproduction has been well characterized qualitatively, detailed quantifications are still lacking for aspects of this process, such as the frequency of recombination during unisexual reproduction, and how this compares with bisexual reproduction. Here, we analyzed meiotic recombination during α-α unisexual and a-α bisexual reproduction of C. neoformans. We found that meiotic recombination operates in a similar fashion during both modes of sexual reproduction. Specifically, we observed that in α-α unisexual reproduction, the numbers of crossovers along the chromosomes during meiosis, recombination frequencies at specific chromosomal regions, as well as meiotic recombination hot and cold spots, are all similar to those observed during a-α bisexual reproduction. The similarity in meiosis is also reflected by the fact that phenotypic segregation among progeny collected from the two modes of sexual reproduction is also similar, with transgressive segregation being observed in both. Additionally, we found diploid meiotic progeny were also produced at similar frequencies in the two modes of sexual reproduction, and transient chromosomal loss and duplication likely occurs frequently and results in aneuploidy and loss of heterozygosity that can span entire chromosomes. Furthermore, in both α-α unisexual and a-α bisexual reproduction, we observed biased allele inheritance in regions on chromosome 4, suggesting the presence of fragile chromosomal regions that might be vulnerable to mitotic recombination. Interestingly, we also observed a crossover event that occurred within the MAT locus during α-α unisexual reproduction. Our results provide definitive evidence that α-α unisexual reproduction is a meiotic process similar to a-α bisexual reproduction. PMID:25503976

Unisexual reproduction drives meiotic recombination and phenotypic and karyotypic plasticity in Cryptococcus neoformans.

PubMed

Sun, Sheng; Billmyre, R Blake; Mieczkowski, Piotr A; Heitman, Joseph

2014-12-01

In fungi, unisexual reproduction, where sexual development is initiated without the presence of two compatible mating type alleles, has been observed in several species that can also undergo traditional bisexual reproduction, including the important human fungal pathogens Cryptococcus neoformans and Candida albicans. While unisexual reproduction has been well characterized qualitatively, detailed quantifications are still lacking for aspects of this process, such as the frequency of recombination during unisexual reproduction, and how this compares with bisexual reproduction. Here, we analyzed meiotic recombination during α-α unisexual and a-α bisexual reproduction of C. neoformans. We found that meiotic recombination operates in a similar fashion during both modes of sexual reproduction. Specifically, we observed that in α-α unisexual reproduction, the numbers of crossovers along the chromosomes during meiosis, recombination frequencies at specific chromosomal regions, as well as meiotic recombination hot and cold spots, are all similar to those observed during a-α bisexual reproduction. The similarity in meiosis is also reflected by the fact that phenotypic segregation among progeny collected from the two modes of sexual reproduction is also similar, with transgressive segregation being observed in both. Additionally, we found diploid meiotic progeny were also produced at similar frequencies in the two modes of sexual reproduction, and transient chromosomal loss and duplication likely occurs frequently and results in aneuploidy and loss of heterozygosity that can span entire chromosomes. Furthermore, in both α-α unisexual and a-α bisexual reproduction, we observed biased allele inheritance in regions on chromosome 4, suggesting the presence of fragile chromosomal regions that might be vulnerable to mitotic recombination. Interestingly, we also observed a crossover event that occurred within the MAT locus during α-α unisexual reproduction. Our results provide definitive evidence that α-α unisexual reproduction is a meiotic process similar to a-α bisexual reproduction.

On the mutagenicity of homologous recombination and double-strand break repair in bacteriophage.

PubMed

Shcherbakov, Victor P; Plugina, Lidiya; Shcherbakova, Tamara; Sizova, Svetlana; Kudryashova, Elena

2011-01-02

The double-strand break (DSB) repair via homologous recombination is generally construed as a high-fidelity process. However, some molecular genetic observations show that the recombination and the recombinational DSB repair may be mutagenic and even highly mutagenic. Here we developed an effective and precise method for studying the fidelity of DSB repair in vivo by combining DSBs produced site-specifically by the SegC endonuclease with the famous advantages of the recombination analysis of bacteriophage T4 rII mutants. The method is based on the comparison of the rate of reversion of rII mutation in the presence and in the absence of a DSB repair event initiated in the proximity of the mutation. We observed that DSB repair may moderately (up to 6-fold) increase the apparent reversion frequency, the effect of being dependent on the mutation structure. We also studied the effect of the T4 recombinase deficiency (amber mutation in the uvsX gene) on the fidelity of DSB repair. We observed that DSBs are still repaired via homologous recombination in the uvsX mutants, and the apparent fidelity of this repair is higher than that seen in the wild-type background. The mutator effect of the DSB repair may look unexpected given that most of the normal DNA synthesis in bacteriophage T4 is performed via a recombination-dependent replication (RDR) pathway, which is thought to be indistinguishable from DSB repair. There are three possible explanations for the observed mutagenicity of DSB repair: (1) the origin-dependent (early) DNA replication may be more accurate than the RDR; (2) the step of replication initiation may be more mutagenic than the process of elongation; and (3) the apparent mutagenicity may just reflect some non-randomness in the pool of replicating DNA, i.e., preferential replication of the sequences already involved in replication. We discuss the DSB repair pathway in the absence of UvsX recombinase. Copyright © 2010 Elsevier B.V. All rights reserved.

Performance assessment of low pressure nuclear thermal propulsion

NASA Technical Reports Server (NTRS)

Gerrish, Harrold P., Jr.; Doughty, Glen E.

1993-01-01

An increase in Isp for nuclear thermal propulsion systems is desirable for reducing the propellant requirements and cost of future applications, such as the Mars Transfer Vehicle. Several previous design studies have suggested that the Isp could be increased substantially with hydrogen dissociation/recombination. Hydrogen molecules (H2), at high temperatures and low pressures, will dissociate to monatomic hydrogen (H). The reverse process (i.e., formation of H2 from H) is exothermic. The exothermic energy in a nozzle increases the kinetic energy and therefore, increases the Isp. The low pressure nuclear thermal propulsion system (LPNTP) system is expected to maximize the hydrogen dissociation/recombination and Isp by operating at high chamber temperatures and low chamber pressures. The process involves hydrogen flow through a high temperature, low pressure fission reactor, and out a nozzle. The high temperature (approximately 3000 K) of the hydrogen in the reactor is limited by the temperature limits of the reactor material. The minimum chamber pressure is about 1 atm because lower pressures decrease the engines thrust to weight ratio below acceptable limits. This study assumes that hydrogen leaves the reactor and enters the nozzle at the 3000 K equilibrium dissociation level. Hydrogen dissociation in the reactor does not affect LPNTP performance like dissociation in traditional chemical propulsion systems, because energy from the reactor resupplies energy lost due to hydrogen dissociation. Recombination takes place in the nozzle due primarily to a drop in temperature as the Mach number increases. However, as the Mach number increases beyond the nozzle throat, the static pressure and density of the flow decreases and minimizes the recombination. The ideal LPNTP Isp at 3000 K and 10 psia is 1160 seconds due to the added energy from fast recombination rates. The actual Isp depends on the finite kinetic reaction rates which affect the amount of monatomic hydrogen recombination before the flow exits the nozzle. A LPNTP system has other technical issues (e.g. flow instability and two-phase flow) besides hydrogen dissociation/recombination which affect the systems practicality. In this study, only the effects of hydrogen dissociation/recombination are examined.

Analysis of Dibenzothiophene Desulfurization in a Recombinant Pseudomonas putida Strain▿

PubMed Central

Calzada, Javier; Zamarro, María T.; Alcón, Almudena; Santos, Victoria E.; Díaz, Eduardo; García, José L.; Garcia-Ochoa, Felix

2009-01-01

Biodesulfurization was monitored in a recombinant Pseudomonas putida CECT5279 strain. DszB desulfinase activity reached a sharp maximum at the early exponential phase, but it rapidly decreased at later growth phases. A model two-step resting-cell process combining sequentially P. putida cells from the late and early exponential growth phases was designed to significantly increase biodesulfurization. PMID:19047400

Human parainfluenza virus type 3 (HPIV-3); Construction and rescue of an infectious, recombinant virus expressing the enhanced green fluorescent protein (EGFP).

USDA-ARS?s Scientific Manuscript database

The ability to rescue an infectious, recombinant, RNA virus from a cDNA clone, has led to new opportunities for measuring viral replication from a viral expressed reporter gene. In this protocol, the process of inserting enhanced green fluorescent protein (EGFP) gene into the human parainfluenza vi...

Preparation of umami octopeptide with recombined Escherichia coli: Feasibility and challenges.

PubMed

Zhao, Liming; Zhang, Yin; Venkitasamy, Chandrasekar; Pan, Zhongli; Zhang, Longyi; Guo, Siya; Xiong, Wei; Xia, Hu; Wenlong, Liu; Xinhua, Gou

2018-01-01

The taste of umami peptide H-Lys-Gly-Asp-Glu-Glu-Ser-Leu-Ala-OH (LGAGGSLA) is controversial. One possible reason for this controversy is the use of chemically synthesized LGAGGSLA to confirm its taste. To explore other ways to further confirm the flavor of LGAGGSLA, we developed a new strategy to prepare a bio-source peptide by adopting a gene engineering method to express LGAGGSLA in recombinant Escherichia coli. In our previous work, we structured the LGAGGSLA recombinant expression system and optimized the culturing conditions for preparing a fusion protein. However, the fusion protein was not cleaved by enterokinase to obtain LGAGGSLA. Because the cleavage conditions of commercial enterokinase were not specific and recombinant engineered bacteria had the potential to be used in industrial processes, in this addendum, we calculated the mass and volume yields of key processing steps in the preparation of LGAGGSLA, and established a model of cleavage conditions with the cleavage ratio of LGAGGSLA. When the LGAGGSLA was confirmed to show umami taste, it is considered as a new umami or umami enhancer. The gene information of LGAGGSLA should have a great potential in the development of new flavor product and food product containing high umami flavor.

Proton-hydrogen collisions for Rydberg n,l-changing transitions in the early Universe

NASA Astrophysics Data System (ADS)

Vrinceanu, Daniel

2013-05-01

Cosmic Microwave Background (CMB) is a vestige radiation generated during the Recombination era, some 390,000 years after the Big Bang, when the Universe had become transparent for the first time. Initial observations of CMB made by the Wilkinson Microwave Anisotropy Probe (WMAP) led to determining the age of the Universe. The mechanisms that drove the recombination have been discovered by using modeling of the primordial plasma and seeking agreement with the observations. The new Plank Surveyor Instrument launched in 2009 is expected to produce data about the recombination era of an unprecedented accuracy, that require including better information regarding the basic atomic physics processes into the present models. In this talk, I will review the results for various Rydberg atom - charge particle collisions and establish their relative importance during the stages of recombination era, with respect to each other and to radiative processes. Energy changing and angular momentum changing collisions with electrons and ions are considered. This work has been supported by NSF through grants to the Institute for Theoretical Atomic and Molecular Physics at Harvard Smithsonian Center for Astrophysics and to the Center for Research on Complex Networks at Texas Southern University.

Reduced Carrier Recombination in PbS - CuInS2 Quantum Dot Solar Cells

PubMed Central

Sun, Zhenhua; Sitbon, Gary; Pons, Thomas; Bakulin, Artem A.; Chen, Zhuoying

2015-01-01

Energy loss due to carrier recombination is among the major factors limiting the performance of TiO2/PbS colloidal quantum dot (QD) heterojunction solar cells. In this work, enhanced photocurrent is achieved by incorporating another type of hole-transporting QDs, Zn-doped CuInS2 (Zn-CIS) QDs into the PbS QD matrix. Binary QD solar cells exhibit a reduced charge recombination associated with the spatial charge separation between these two types of QDs. A ~30% increase in short-circuit current density and a ~20% increase in power conversion efficiency are observed in binary QD solar cells compared to cells built from PbS QDs only. In agreement with the charge transfer process identified through ultrafast pump/probe spectroscopy between these two QD components, transient photovoltage characteristics of single-component and binary QDs solar cells reveal longer carrier recombination time constants associated with the incorporation of Zn-CIS QDs. This work presents a straightforward, solution-processed method based on the incorporation of another QDs in the PbS QD matrix to control the carrier dynamics in colloidal QD materials and enhance solar cell performance. PMID:26024021

Study of recombination characteristics in MOCVD grown GaN epi-layers on Si

NASA Astrophysics Data System (ADS)

Gaubas, E.; Ceponis, T.; Dobrovolskas, D.; Malinauskas, T.; Meskauskaite, D.; Miasojedovas, S.; Mickevicius, J.; Pavlov, J.; Rumbauskas, V.; Simoen, E.; Zhao, M.

2017-12-01

The radiative and non-radiative recombination carrier decay lifetimes in GaN epi-layers grown by metal-organic chemical vapour deposition technology on Si substrates were measured by contactless techniques of time-resolved photoluminescence and microwave-probed transients of photoconductivity. The lifetime variations were obtained to be dependent on growth regimes. These variations have been related to varied densities of edge dislocations associated with growth temperature. It has been also revealed that the lateral carrier lifetime and photoluminescence intensity distribution is determined by the formation of dislocation clusters dependent on the growth conditions. For low excitation level, the asymptotic component within the excess carrier decay transients is attributed to carrier trapping and anomalous diffusion through random-walk processes within dislocation cluster regions and barriers at dislocation cores. The two-componential decay process at high excitation conditions, where excess carriers may suppress barriers, proceeds through a nonlinear recombination, where band-to-band transitions determine the nonlinearity of the process, while the asymptotic component is ascribed to the impact of D-A pair PL within the long-wavelength wing of the UV-PL band.

Application of recombinant hemagglutinin proteins as alternative antigen standards for pandemic influenza vaccines.

PubMed

Choi, Yejin; Kwon, Seong Yi; Oh, Ho Jung; Shim, Sunbo; Chang, Seokkee; Chung, Hye Joo; Kim, Do Keun; Park, Younsang; Lee, Younghee

2017-09-01

The single radial immunodiffusion (SRID) assay, used to quantify hemagglutinin (HA) in influenza vaccines, requires reference reagents; however, because centralized production of reference reagents may slow the emergency deployment of vaccines, alternatives are needed. We investigated the production of HA proteins using recombinant DNA technology, rather than a traditional egg-based production process. The HA proteins were then used in an SRID assay as a reference antigen. We found that HA can be quantified in both egg-based and cell-based influenza vaccines when recombinant HAs (rHAs) are used as the reference antigen. Furthermore, we confirmed that rHAs obtained from strains with pandemic potential, such as H5N1, H7N3, H7N9, and H9N2 strains, can be utilized in the SRID assay. The rHA production process takes just one month, in contrast to the traditional process that takes three to four months. The use of rHAs may reduce the time required to produce reference reagents and facilitate timely introduction of vaccines during emergencies.

Frenkel pair recombinations in UO2: Importance of explicit description of polarizability in core-shell molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Devynck, Fabien; Iannuzzi, Marcella; Krack, Matthias

2012-05-01

The oxygen and uranium Frenkel pair (FP) recombination mechanisms are studied in UO2 using an empirical interatomic potential accounting for the polarizability of the ions, namely a dynamical core-shell model. The results are compared to a more conventional rigid-ion model. Both model types have been implemented into the cp2k program package and thoroughly validated. The overall picture indicates that the FP recombination mechanism is a complex process involving several phenomena. The FP recombination can happen instantaneously when the distance between the interstitial and the vacancy is small or can be thermally activated at larger separation distances. However, other criteria can prevail over the interstitial-vacancy distance. The surrounding environment of the FP defect, the mechanical stiffness of the matrix, and the orientation of the migration path are shown to be major factors acting on the FP lifetime. The core-shell and rigid-ion models provide a similar qualitative description of the FP recombination mechanism. However, the FP stabilities determined by both models significantly differ in the lower temperature range considered. Indeed, the recombination time of the oxygen and uranium FPs can be up to an order of magnitude lower in the core-shell model at T=600 K and T=1800 K, respectively. These differences highlight the importance of the explicit description of polarizability on some crucial properties such as the resistance to amorphization. This refined description of the interatomic interactions would certainly affect the description of the recrystallization process following a displacement cascade. In turn, the self-healing phase would be better accounted for in the core-shell model and the misestimate inherent to the lack of polarizability in the rigid-ion model corrected.

A tetO Toolkit To Alter Expression of Genes in Saccharomyces cerevisiae.

PubMed

Cuperus, Josh T; Lo, Russell S; Shumaker, Lucia; Proctor, Julia; Fields, Stanley

2015-07-17

Strategies to optimize a metabolic pathway often involve building a large collection of strains, each containing different versions of sequences that regulate the expression of pathway genes. Here, we develop reagents and methods to carry out this process at high efficiency in the yeast Saccharomyces cerevisiae. We identify variants of the Escherichia coli tet operator (tetO) sequence that bind a TetR-VP16 activator with differential affinity and therefore result in different TetR-VP16 activator-driven expression. By recombining these variants upstream of the genes of a pathway, we generate unique combinations of expression levels. Here, we built a tetO toolkit, which includes the I-OnuI homing endonuclease to create double-strand breaks, which increases homologous recombination by 10(5); a plasmid carrying six variant tetO sequences flanked by I-OnuI sites, uncoupling transformation and recombination steps; an S. cerevisiae-optimized TetR-VP16 activator; and a vector to integrate constructs into the yeast genome. We introduce into the S. cerevisiae genome the three crt genes from Erwinia herbicola required for yeast to synthesize lycopene and carry out the recombination process to produce a population of cells with permutations of tetO variants regulating the three genes. We identify 0.7% of this population as making detectable lycopene, of which the vast majority have undergone recombination at all three crt genes. We estimate a rate of ∼20% recombination per targeted site, much higher than that obtained in other studies. Application of this toolkit to medically or industrially important end products could reduce the time and labor required to optimize the expression of a set of metabolic genes.

Coinfection with recombinant vaccinia viruses expressing poliovirus P1 and P3 proteins results in polyprotein processing and formation of empty capsid structures.

PubMed

Ansardi, D C; Porter, D C; Morrow, C D

1991-04-01

The assembly process of poliovirus occurs via an ordered proteolytic processing of the capsid precursor protein, P1, by the virus-encoded proteinase 3CD. To further delineate this process, we have isolated a recombinant vaccinia virus which expresses, upon infection, the poliovirus P1 capsid precursor polyprotein with an authentic carboxy terminus. Coinfection of HeLa cells with the P1-expressing vaccinia virus and with a second recombinant vaccinia virus which expresses the poliovirus proteinase 3CD resulted in the correct processing of P1 to yield the three individual capsid proteins VP0, VP3, and VP1. When extracts from coinfected cells were fractionated on sucrose density gradients, the VP0, VP3, and VP1 capsid proteins were immunoprecipitated with type 1 poliovirus antisera from fractions corresponding to a sedimentation consistent for poliovirus 75S procapsids. Examination of these fractions by electron microscopy revealed structures which lacked electron-dense cores and which corresponded in size and shape to those expected for poliovirus empty capsids. We conclude that the expression of the two poliovirus proteins P1 and 3CD in coinfected cells is sufficient for the correct processing of the capsid precursor to VP0, VP3, and VP1 as well as for the assembly of poliovirus empty capsid-like structures.

J/ψ polarization in p + p collisions at √s = 200 GeV in STAR

DOE PAGES

Adamczyk, L.

2014-10-30

The study report on a polarization measurement of inclusive J/ψ mesons in the di-electron decay channel at mid-rapidity at 2T<6 GeV/c in p+p collisions at √s = 200 GeV. Data were taken with the STAR detector at RHIC. The J/ψ polarization measurement should help to distinguish between different models of the J/ψ production mechanism since they predict different p T dependences of the J/ψ polarization. In this analysis, J/ψ polarization is studied in the helicity frame. The polarization parameter λ θ measured at RHIC becomes smaller towards high p T, indicating more longitudinal J/ψ polarization as p T increases. Themore » result is compared with predictions of presently available models.« less

Measurement of Z boson production in Pb-Pb collisions at sqrt[s(NN)]=2.76  TeV with the ATLAS detector.

PubMed

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Sankey, D P C; Sansoni, A; Santamarina Rios, C; Santoni, C; Santonico, R; Santos, H; Saraiva, J G; Sarangi, T; Sarkisyan-Grinbaum, E; Sarri, F; Sartisohn, G; Sasaki, O; Sasaki, Y; Sasao, N; Satsounkevitch, I; Sauvage, G; Sauvan, E; Sauvan, J B; Savard, P; Savinov, V; Savu, D O; Sawyer, L; Saxon, D H; Saxon, J; Sbarra, C; Sbrizzi, A; Scannicchio, D A; Scarcella, M; Schaarschmidt, J; Schacht, P; Schaefer, D; Schäfer, U; Schaelicke, A; Schaepe, S; Schaetzel, S; Schaffer, A C; Schaile, D; Schamberger, R D; Schamov, A G; Scharf, V; Schegelsky, V A; Scheirich, D; Schernau, M; Scherzer, M I; Schiavi, C; Schieck, J; Schioppa, M; Schlenker, S; Schmidt, E; Schmieden, K; Schmitt, C; Schmitt, S; Schmitz, M; Schneider, B; Schnoor, U; Schoeffel, L; Schoening, A; Schorlemmer, A L S; Schott, M; Schouten, D; Schovancova, J; Schram, M; Schroeder, C; Schroer, N; Schultens, M J; Schultes, J; Schultz-Coulon, H-C; Schulz, H; Schumacher, M; Schumm, B A; Schune, Ph; Schwanenberger, C; Schwartzman, A; Schwegler, Ph; 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Slavicek, T; Sliwa, K; Smakhtin, V; Smart, B H; Smestad, L; Smirnov, S Yu; Smirnov, Y; Smirnova, L N; Smirnova, O; Smith, B C; Smith, D; Smith, K M; Smizanska, M; Smolek, K; Snesarev, A A; Snow, S W; Snow, J; Snyder, S; Sobie, R; Sodomka, J; Soffer, A; Solans, C A; Solar, M; Solc, J; Soldatov, E Yu; Soldevila, U; Solfaroli Camillocci, E; Solodkov, A A; Solovyanov, O V; Solovyev, V; Soni, N; Sopko, V; Sopko, B; Sosebee, M; Soualah, R; Soukharev, A; Spagnolo, S; Spanò, F; Spighi, R; Spigo, G; Spiwoks, R; Spousta, M; Spreitzer, T; Spurlock, B; St Denis, R D; Stahlman, J; Stamen, R; Stanecka, E; Stanek, R W; Stanescu, C; Stanescu-Bellu, M; Stanitzki, M M; Stapnes, S; Starchenko, E A; Stark, J; Staroba, P; Starovoitov, P; Staszewski, R; Staude, A; Stavina, P; Steele, G; Steinbach, P; Steinberg, P; Stekl, I; Stelzer, B; Stelzer, H J; Stelzer-Chilton, O; Stenzel, H; Stern, S; Stewart, G A; Stillings, J A; Stockton, M C; Stoerig, K; Stoicea, G; Stonjek, S; Strachota, P; Stradling, A R; Straessner, A; Strandberg, J; Strandberg, S; Strandlie, A; Strang, M; Strauss, E; Strauss, M; Strizenec, P; Ströhmer, R; Strom, D M; Strong, J A; Stroynowski, R; Stugu, B; Stumer, I; Stupak, J; Sturm, P; Styles, N A; Soh, D A; Su, D; Subramania, Hs; Subramaniam, R; Succurro, A; Sugaya, Y; Suhr, C; Suk, M; Sulin, V V; Sultansoy, S; Sumida, T; Sun, X; Sundermann, J E; Suruliz, K; Susinno, G; Sutton, M R; Suzuki, Y; Suzuki, Y; Svatos, M; Swedish, S; Sykora, I; Sykora, T; Sánchez, J; Ta, D; Tackmann, K; Taffard, A; Tafirout, R; Taiblum, N; Takahashi, Y; Takai, H; Takashima, R; Takeda, H; Takeshita, T; Takubo, Y; Talby, M; Talyshev, A; Tamsett, M C; Tanaka, J; Tanaka, R; Tanaka, S; Tanaka, S; Tanasijczuk, A J; Tani, K; Tannoury, N; Tapprogge, S; Tardif, D; Tarem, S; Tarrade, F; Tartarelli, G F; Tas, P; Tasevsky, M; Tassi, E; Tatarkhanov, M; Tayalati, Y; Taylor, C; Taylor, F E; Taylor, G N; Taylor, W; Teinturier, M; Teischinger, F A; Teixeira Dias Castanheira, M; Teixeira-Dias, P; Temming, K K; Ten Kate, H; Teng, P K; Terada, S; Terashi, K; Terron, J; Testa, M; Teuscher, R J; Therhaag, J; Theveneaux-Pelzer, T; Thoma, S; Thomas, J P; Thompson, E N; Thompson, P D; Thompson, P D; Thompson, A S; Thomsen, L A; Thomson, E; Thomson, M; Thong, W M; Thun, R P; Tian, F; Tibbetts, M J; Tic, T; Tikhomirov, V O; Tikhonov, Y A; Timoshenko, S; Tiouchichine, E; Tipton, P; Tisserant, S; Todorov, T; Todorova-Nova, S; Toggerson, B; Tojo, J; Tokár, S; Tokushuku, K; Tollefson, K; Tomoto, M; Tompkins, L; Toms, K; Tonoyan, A; Topfel, C; Topilin, N D; Torchiani, I; Torrence, E; Torres, H; Torró Pastor, E; Toth, J; Touchard, F; Tovey, D R; Trefzger, T; Tremblet, L; Tricoli, A; Trigger, I M; Trincaz-Duvoid, S; Tripiana, M F; Triplett, N; Trischuk, W; Trocmé, B; Troncon, C; Trottier-McDonald, M; Trzebinski, M; Trzupek, A; Tsarouchas, C; Tseng, J C-L; Tsiakiris, M; Tsiareshka, P V; Tsionou, D; Tsipolitis, G; Tsiskaridze, S; Tsiskaridze, V; Tskhadadze, E G; Tsukerman, I I; Tsulaia, V; Tsung, J-W; Tsuno, S; Tsybychev, D; Tua, A; Tudorache, A; Tudorache, V; Tuggle, J M; Turala, M; Turecek, D; Turk Cakir, I; Turlay, E; Turra, R; Tuts, P M; Tykhonov, A; Tylmad, M; Tyndel, M; Tzanakos, G; Uchida, K; Ueda, I; Ueno, R; Ugland, M; Uhlenbrock, M; Uhrmacher, M; Ukegawa, F; Unal, G; Undrus, A; Unel, G; Unno, Y; Urbaniec, D; Urquijo, P; Usai, G; Uslenghi, M; Vacavant, L; Vacek, V; Vachon, B; Vahsen, S; Valenta, J; Valentinetti, S; Valero, A; Valkar, S; Valladolid Gallego, E; Vallecorsa, S; Valls Ferrer, J A; Van Berg, R; Van Der Deijl, P C; van der Geer, R; van der Graaf, H; Van Der Leeuw, R; van der Poel, E; van der Ster, D; van Eldik, N; van Gemmeren, P; van Vulpen, I; Vanadia, M; Vandelli, W; Vaniachine, A; Vankov, P; Vannucci, F; Vari, R; Varol, T; Varouchas, D; Vartapetian, A; Varvell, K E; Vassilakopoulos, V I; Vazeille, F; Vazquez Schroeder, T; Vegni, G; Veillet, J J; Veloso, F; Veness, R; Veneziano, S; Ventura, A; Ventura, D; Venturi, M; Venturi, N; Vercesi, V; Verducci, M; Verkerke, W; Vermeulen, J C; Vest, A; Vetterli, M C; Vichou, I; Vickey, T; Vickey Boeriu, O E; Viehhauser, G H A; Viel, S; Villa, M; Villaplana Perez, M; Vilucchi, E; Vincter, M G; Vinek, E; Vinogradov, V B; Virchaux, M; Virzi, J; Vitells, O; Viti, M; Vivarelli, I; Vives Vaque, F; Vlachos, S; Vladoiu, D; Vlasak, M; Vogel, A; Vokac, P; Volpi, G; Volpi, M; Volpini, G; von der Schmitt, H; von Radziewski, H; von Toerne, E; Vorobel, V; Vorwerk, V; Vos, M; Voss, R; Voss, T T; Vossebeld, J H; Vranjes, N; Vranjes Milosavljevic, M; Vrba, V; Vreeswijk, M; Vu Anh, T; Vuillermet, R; Vukotic, I; Wagner, W; Wagner, P; Wahlen, H; Wahrmund, S; Wakabayashi, J; Walch, S; Walder, J; Walker, R; Walkowiak, W; Wall, R; Waller, P; Walsh, B; Wang, C; Wang, H; Wang, H; Wang, J; Wang, J; Wang, R; Wang, S M; Wang, T; Warburton, A; Ward, C P; Warsinsky, M; Washbrook, A; Wasicki, C; Watanabe, I; Watkins, P M; Watson, A T; Watson, I J; Watson, M F; Watts, G; Watts, S; Waugh, A T; Waugh, B M; Weber, M S; Weber, P; Webster, J S; Weidberg, A R; Weigell, P; Weingarten, J; Weiser, C; Wells, P S; Wenaus, T; Wendland, D; Weng, Z; Wengler, T; Wenig, S; Wermes, N; Werner, M; Werner, P; Werth, M; Wessels, M; Wetter, J; Weydert, C; Whalen, K; Wheeler-Ellis, S J; White, A; White, M J; White, S; Whitehead, S R; Whiteson, D; Whittington, D; Wicek, F; Wicke, D; Wickens, F J; Wiedenmann, W; Wielers, M; Wienemann, P; Wiglesworth, C; Wiik-Fuchs, L A M; Wijeratne, P A; Wildauer, A; Wildt, M A; Wilhelm, I; Wilkens, H G; Will, J Z; Williams, E; Williams, H H; Willis, W; Willocq, S; Wilson, J A; Wilson, M G; Wilson, A; Wingerter-Seez, I; Winkelmann, S; Winklmeier, F; Wittgen, M; Wollstadt, S J; Wolter, M W; Wolters, H; Wong, W C; Wooden, G; Wosiek, B K; Wotschack, J; Woudstra, M J; Wozniak, K W; Wraight, K; Wright, M; Wrona, B; Wu, S L; Wu, X; Wu, Y; Wulf, E; Wynne, B M; Xella, S; Xiao, M; Xie, S; Xu, C; Xu, D; Yabsley, B; Yacoob, S; Yamada, M; Yamaguchi, H; Yamamoto, A; Yamamoto, K; Yamamoto, S; Yamamura, T; Yamanaka, T; Yamazaki, T; Yamazaki, Y; Yan, Z; Yang, H; Yang, U K; Yang, Y; Yang, Z; Yanush, S; Yao, L; Yao, Y; Yasu, Y; Ybeles Smit, G V; Ye, J; Ye, S; Yilmaz, M; Yoosoofmiya, R; Yorita, K; Yoshida, R; Yoshihara, K; Young, C; Young, C J; Youssef, S; Yu, D; Yu, J; Yu, J; Yuan, L; Yurkewicz, A; Zabinski, B; Zaidan, R; Zaitsev, A M; Zajacova, Z; Zanello, L; Zanzi, D; Zaytsev, A; Zeitnitz, C; Zeman, M; Zemla, A; Zendler, C; Zenin, O; Ženiš, T; Zinonos, Z; Zenz, S; Zerwas, D; Zevi della Porta, G; Zhang, D; Zhang, H; Zhang, J; Zhang, X; Zhang, Z; Zhao, L; Zhao, Z; Zhemchugov, A; Zhong, J; Zhou, B; Zhou, N; Zhou, Y; Zhu, C G; Zhu, H; Zhu, J; Zhu, Y; Zhuang, X; Zhuravlov, V; Zieminska, D; Zimin, N I; Zimmermann, R; Zimmermann, S; Zimmermann, S; Ziolkowski, M; Zitoun, R; Živković, L; Zmouchko, V V; Zobernig, G; Zoccoli, A; zur Nedden, M; Zutshi, V; Zwalinski, L

2013-01-11

The ATLAS experiment has observed 1995 Z boson candidates in data corresponding to 0.15  nb(-1) of integrated luminosity obtained in the 2011 LHC Pb+Pb run at sqrt[s(NN)]=2.76  TeV. The Z bosons are reconstructed via dielectron and dimuon decay channels, with a background contamination of less than 3%. Results from the two channels are consistent and are combined. Within the statistical and systematic uncertainties, the per-event Z boson yield is proportional to the number of binary collisions estimated by the Glauber model. The elliptic anisotropy of the azimuthal distribution of the Z boson with respect to the event plane is found to be consistent with zero.

Study of high resolution x-ray spectrometer concepts for NIF experiments

NASA Astrophysics Data System (ADS)

Hill, K. W.; Bitter, M.; Delgado-Aparicio, L.; Efthimion, P.; Gao, L.; Maddox, J.; Pablant, N. A.; Beiersdorfer, P.; Chen, H.; Coppari, F.; Ma, T.; Nora, R.; Scott, H.; Schneider, M.; Mancini, R.

2015-11-01

Options have been investigated for DIM-insertable (Diagnostic Instrument Manipulator) high resolution (E/ ΔE ~ 3000 - 5000) Bragg crystal x-ray spectrometers for experiments on the NIF. Of interest are time integrated Cu K- and Ta L-edge absorption spectra and time resolved Kr He- β emission from compressed symcaps for inference of electron temperature from dielectronic satellites and electron density from Stark broadening. Cylindrical and conical von Hamos, Johann, and advanced high throughput designs have been studied. Predicted x-ray intensities, spectrometer throughputs, spectral resolution, and spatial focusing properties, as well as lab evaluations of some spectrometer candidates will be presented. Performed under the auspices of the US DOE by PPPL under contract DE-AC02-09CH11466 and by LLNL under contract DE-AC52-07NA27344.

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

PubMed

Lopes, J S; Arenas, M; Posada, D; Beaumont, M A

2014-03-01

The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

Impact of karyotype organization on interlocus recombination between T cell receptor genes in Equidae.

PubMed

Drbalova, Jitka; Musilova, Petra; Kubickova, Svatava; Sebestova, Hana; Vahala, Jiri; Rubes, Jiri

2014-01-01

The T cell receptor (TCR) genes (TRA, TRB, TRD and TRG) reside in 3 different chromosomal regions. During the maturation of T lymphocytes, the TCR genes are rearranged by site-specific recombination, a process that also predisposes T cells to aberrant rearrangements. Illegitimate recombination between the TCR genes occurs at a low level in healthy individuals, but this frequency may correlate with the risk of lymphoma. The aim of this work was to investigate interlocus recombination in equids. Illegitimate rearrangements were studied in peripheral blood lymphocytes by FISH with painting and BAC probes and by sequencing of PCR products, and the frequencies of recombination were assessed in horses and 4 other equids. The presence of several trans-rearrangement products between the TRA and TRG genes was verified by PCR in all investigated equids. Frequencies of trans-rearrangements in horses are higher than in humans, and colocalization of the TCR genes on the same chromosome increases the incidence of trans-rearrangements between them. The orientation of the TCR genes does not impact interlocus recombination itself but does affect the viability of cells carrying its products and consequently the number of trans-rearrangements observed in lymphocytes.

Termini of human chromosomes display elevated rates of mitotic recombination.

PubMed

Cornforth, M N; Eberle, R L

2001-01-01

The strand-specific in situ hybridization technique of CO-FISH was used to probe telomeres of human mitotic cells in order to determine the spontaneous frequency of crossover. This approach allowed the detection of recombinational crossovers occurring anywhere along the length of individual chromosomes, including reciprocal events taking place between sister chromatids. Although the process of sister chromatid exchange (SCE) is the most prominent type of recombination in somatic mammalian cells, our results show that SCEs accounted for less than a third of the recombinational events revealed by CO-FISH. It is concluded that chromosomal regions near the termini of chromosome arms undergo extraordinarily high rates of spontaneous recombination, producing terminal crossovers whose small size precludes detection by standard cytogenetic methods. That similar results were observed for transformed epithelial cells, as well as primary fibroblasts, suggests that the phenomenon is a common characteristic of human cells. These findings are noteworthy because, although telomeric and subtelomeric DNA is known to be preferentially involved in certain types of recombination, the tips of somatic mammalian chromosomes have not previously been identified as preferred sites for crossover. Implications of these results are discussed in terms of limitations imposed on CO-FISH for its proposed use in directional hybridization mapping.

V(D)J recombination on minichromosomes is not affected by transcription.

PubMed

Hsieh, C L; McCloskey, R P; Lieber, M R

1992-08-05

It has been shown previously by others that transcription is temporally correlated with the onset of V(D)J recombination at the endogenous antigen receptor loci. We have been interested in determining whether this temporal correlation indicates a causal connection between these two processes. We have compared V(D)J recombination minichromosome substrates that have transcripts running through the recombination zone with substrates that do not in a transient transfection assay. In this system, the substrates acquire a minichromosome conformation within the first several hours after transfection. We find that the substrates recombine equally well over a 100-fold range in transcriptional variation. In additional studies, we have taken substrates that have low levels of transcription and inhibited transcription further by methylating the substrate DNA or by treating the cells with a general transcription inhibitor (alpha-amanitin). Although these treatments decrease the level of expression an additional 10-100-fold, there is still no observable effect on V(D)J recombination. Based on these results, we conclude that transcription is not necessary for the V(D)J reaction mechanism and does not alter substrate structure at the DNA level or at the simplest levels of chromatin structure in a way that affects the reaction.

Crossovers are associated with mutation and biased gene conversion at recombination hotspots.

PubMed

Arbeithuber, Barbara; Betancourt, Andrea J; Ebner, Thomas; Tiemann-Boege, Irene

2015-02-17

Meiosis is a potentially important source of germline mutations, as sites of meiotic recombination experience recurrent double-strand breaks (DSBs). However, evidence for a local mutagenic effect of recombination from population sequence data has been equivocal, likely because mutation is only one of several forces shaping sequence variation. By sequencing large numbers of single crossover molecules obtained from human sperm for two recombination hotspots, we find direct evidence that recombination is mutagenic: Crossovers carry more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The observed mutations were primarily CG to TA transitions, with a higher frequency of transitions at CpG than non-CpGs sites. This enrichment of mutations at CpG sites at hotspots could predominate in methylated regions involving frequent single-stranded DNA processing as part of DSB repair. In addition, our data set provides evidence that GC alleles are preferentially transmitted during crossing over, opposing mutation, and shows that GC-biased gene conversion (gBGC) predominates over mutation in the sequence evolution of hotspots. These findings are consistent with the idea that gBGC could be an adaptation to counteract the mutational load of recombination.

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

PubMed Central

Arbeithuber, Barbara; Betancourt, Andrea J.; Ebner, Thomas; Tiemann-Boege, Irene

2015-01-01

Meiosis is a potentially important source of germline mutations, as sites of meiotic recombination experience recurrent double-strand breaks (DSBs). However, evidence for a local mutagenic effect of recombination from population sequence data has been equivocal, likely because mutation is only one of several forces shaping sequence variation. By sequencing large numbers of single crossover molecules obtained from human sperm for two recombination hotspots, we find direct evidence that recombination is mutagenic: Crossovers carry more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The observed mutations were primarily CG to TA transitions, with a higher frequency of transitions at CpG than non-CpGs sites. This enrichment of mutations at CpG sites at hotspots could predominate in methylated regions involving frequent single-stranded DNA processing as part of DSB repair. In addition, our data set provides evidence that GC alleles are preferentially transmitted during crossing over, opposing mutation, and shows that GC-biased gene conversion (gBGC) predominates over mutation in the sequence evolution of hotspots. These findings are consistent with the idea that gBGC could be an adaptation to counteract the mutational load of recombination. PMID:25646453

Switch junction sequences in PMS2-deficient mice reveal a microhomology-mediated mechanism of Ig class switch recombination

PubMed Central

Ehrenstein, Michael R.; Rada, Cristina; Jones, Anne-Marie; Milstein, César; Neuberger, Michael S.

2001-01-01

Isotype switching involves a region-specific, nonhomologous recombinational deletion that has been suggested to occur by nonhomologous joining of broken DNA ends. Here, we find increased donor/acceptor homology at switch junctions from PMS2-deficient mice and propose that class switching can occur by microhomology-mediated end-joining. Interestingly, although isotype switching and somatic hypermutation show many parallels, we confirm that PMS2 deficiency has no major effect on the pattern of nucleotide substitutions generated during somatic hypermutation. This finding is in contrast to MSH2 deficiency. With MSH2, the altered pattern of switch recombination and hypermutation suggests parallels in the mechanics of the two processes, whereas the fact that PMS2 deficiency affects only switch recombination may reflect differences in the pathways of break resolution. PMID:11717399

On the role of electron-driven processes in planetary atmospheres and comets

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.

2009-11-01

After the presence of ionized layers in the Earth's atmosphere was inferred, it took 50 years to quantitatively understand them. The electron density could not be accounted for until Sir David Bates first suggested (along with Sir Harrie Massey) that the main electron-loss process was dissociative recombination with molecular ions, and he and colleagues then developed a theory to predict those rates of dissociative recombination. However, electron impact processes, particularly excitation, have been considered insignificant in most situations, in both planetary and cometary atmospheres. Here we describe cases where recent calculations have shown that electron impact excitation of molecules is important, suggesting that, just as in the time of Sir David Bates, electron-driven processes remain fundamental to our quantitative understanding of atmospheric and cometary phenomena.

Recombination processes in quantum well lasers with superlattice barriers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blood, P.; Fletcher, E.D.; Foxon, C.T.

1989-12-04

Spontaneous emission spectra from GaAs quantum well lasers grown by molecular beam epitaxy show that the radiative recombination rate in (AlAs)(GaAs) superlattice barriers is greater than in alloy barriers of the same average composition ({ital x}=0.25) due to reduction in effective gap by superlattice effects. Measurements of emission spectra as functions of temperature show that these radiative processes account for a significant part of the temperature variation of the threshold current and we estimate that the nonradiative lifetime in the superlattice barriers is an order of magnitude longer than in alloy barriers grown under similar conditions.

Isolation, characterization and recombinant protein expression in Veggie-CHO: A serum-free CHO host cell line.

PubMed

Rasmussen, B; Davis, R; Thomas, J; Reddy, P

1998-11-01

The dihydrofolate reductase-deficient Chinese hamster ovary cell line, DXB11-CHO, commonly used as a host cell for the production of recombinant proteins requires 7.5% serum-supplementation for optimal growth. Regulatory issues surrounding the use of serum in clinical production processes and the direct and indirect costs of using serum in large-scale production and recovery processes have triggered efforts to derive serum-independent host cell lines. We have successfully isolated a serum-free host that we named Veggie- CHO. Veggie-CHO was generated by adapting DXB11-CHO cells to growth in serum-free media in the absence of exogenous growth factors such as Transferrin and Insulin-like growth factor, which we have previously shown to be essential for growth and viability of DXB11- CHO cells. Veggie-CHO cells have been shown to maintain an average doubling time of 22 hr in continuous growth cultures over a period of three months and have retained the dihydrofolate reductase -deficient phenotype of their parental DXB11-CHO cells. These properties and the stability of its serum-free phenotype have allowed the use of Veggie- CHO as host cells for transfection and amplified expression of recombinant proteins. We describe the derivation a serum-free recombinant cell line with an average doubling time of 20 hr and specific productivity of 2.5 Units recombinant Flt-3L protein per 10e6 cells per day.

Ultracold Heteronuclear Three-Body Systems: How Diabaticity Limits the Universality of Recombination into Shallow Dimers

NASA Astrophysics Data System (ADS)

Giannakeas, P.; Greene, Chris H.

2018-01-01

The mass-imbalanced three-body recombination process that forms a shallow dimer is shown to possess a rich Efimov-Stückelberg landscape, with corresponding spectra that differ fundamentally from the homonuclear case. A semianalytical treatment of the three-body recombination predicts unusual spectra with intertwined resonance peaks and minima and yields in-depth insight into the behavior of the corresponding Efimov spectra. In particular, the patterns of the Efimov-Stückelberg landscape are shown to depend inherently on the degree of diabaticity of the three-body collisions, which strongly affects the universality of the heteronuclear Efimov states.

Dependence of the quasiparticle recombination rate on the superconducting gap and TC

NASA Astrophysics Data System (ADS)

Carr, G. L.; Xi, Xiaoxiang; Hwang, J.; Tashiro, H.; Reitze, D. H.; Tanner, D. B.

2010-03-01

The relaxation of excess quasiparticles in a BCS superconductor is known to depend on quantities such as the quasiparticle & phonon density of states, and their coupling (Kaplan et al, Phys. Rev. B 14 4854, 1976). Disorder or an applied field can disrupt superconductivity, as evidenced by a reduced TC. We consider some simple modifications to the quasiparticle density of states consistent with a suppressed energy gap and TC, leading to changes in the intrinsic and effective (measured) rates for excess quasiparticles to recombine into pairs. We review some results for disordered MoGe and discuss the magnetic-field dependence of the recombination process.

Meiotic Crossover Control by Concerted Action of Rad51-Dmc1 in Homolog Template Bias and Robust Homeostatic Regulation

PubMed Central

Huang, Chu-Chun; Grubb, Jennifer; Thacker, Drew; Lee, Chih-Ying; Dresser, Michael E.; Hunter, Neil; Bishop, Douglas K.

2013-01-01

During meiosis, repair of programmed DNA double-strand breaks (DSBs) by recombination promotes pairing of homologous chromosomes and their connection by crossovers. Two DNA strand-exchange proteins, Rad51 and Dmc1, are required for meiotic recombination in many organisms. Studies in budding yeast imply that Rad51 acts to regulate Dmc1's strand exchange activity, while its own exchange activity is inhibited. However, in a dmc1 mutant, elimination of inhibitory factor, Hed1, activates Rad51's strand exchange activity and results in high levels of recombination without participation of Dmc1. Here we show that Rad51-mediated meiotic recombination is not subject to regulatory processes associated with high-fidelity chromosome segregation. These include homolog bias, a process that directs strand exchange between homologs rather than sister chromatids. Furthermore, activation of Rad51 does not effectively substitute for Dmc1's chromosome pairing activity, nor does it ensure formation of the obligate crossovers required for accurate homolog segregation. We further show that Dmc1's dominance in promoting strand exchange between homologs involves repression of Rad51's strand-exchange activity. This function of Dmc1 is independent of Hed1, but requires the meiotic kinase, Mek1. Hed1 makes a relatively minor contribution to homolog bias, but nonetheless this is important for normal morphogenesis of synaptonemal complexes and efficient crossing-over especially when DSB numbers are decreased. Super-resolution microscopy shows that Dmc1 also acts to organize discrete complexes of a Mek1 partner protein, Red1, into clusters along lateral elements of synaptonemal complexes; this activity may also contribute to homolog bias. Finally, we show that when interhomolog bias is defective, recombination is buffered by two feedback processes, one that increases the fraction of events that yields crossovers, and a second that we propose involves additional DSB formation in response to defective homolog interactions. Thus, robust crossover homeostasis is conferred by integrated regulation at initiation, strand-exchange and maturation steps of meiotic recombination. PMID:24367271

Production of tag-free recombinant fusion protein encompassing promiscuous T cell epitope of tetanus toxoid and dog zona pellucida glycoprotein-3 for contraceptive vaccine development.

PubMed

Gupta, Neha; Shrestha, Abhinav; Panda, Amulya Kumar; Gupta, Satish Kumar

2013-07-01

Affinity tags can interfere in various physicochemical properties and immunogenicity of the recombinant proteins. In the present study, tag-free recombinant fusion protein encompassing promiscuous T cell epitope of tetanus toxoid [TT; amino acid (aa) residues 830-844] followed by dilysine linker and dog zona pellucida glycoprotein-3 (ZP3; aa residues 23-348) (TT-KK-ZP3) was expressed in Escherichia coli. The recombinant protein, expressed as inclusion bodies (IBs), was purified by isolation of IBs, processed to remove host cell proteins, followed by solubilization and refolding. A specific 39 kDa protein including ZP3 was identified by SDS-PAGE. CD spectra showed the presence of α-helices and β-sheets, and fluorescent spectroscopy revealed emission maxima of 265 A.U. at 339 nm for refolded protein and showed red shift in the presence of 6 M guanidine hydrochloride. Immunization of inbred FvB/J female mice with purified recombinant TT-KK-ZP3 (25 μg/animal) led to generation of high antibody titers against the recombinant protein. The antibodies reacted specifically with ZP matrix surrounding mouse oocytes. Immunized mice showed significant reduction in fertility as compared to the control group. The studies described herein provide a simple method to produce and purify tag-free recombinant protein for the development of a contraceptive vaccine.

Direct conversion of starch to ethanol using recombınant Saccharomyces cerevisiae containing glucoamylase gene

NASA Astrophysics Data System (ADS)

Purkan, P.; Baktir, A.; Puspaningsih, N. N. T.; Ni'mah, M.

2017-09-01

Saccharomyces cerevisiae is known for its high fermentative capacity, high ethanol yield and its high ethanol tolerance. The yeast is inability converting starch (relatively inexpensive substrate) into biofuel ethanol. Insertion of glucoamylase gene in yeast cell of Saccharomyces cerevisiae had been done to increase the yeast function in ethanol fermentation from starch. Transformation of yeast of S. cerevisiae with recombinant plasmid yEP-GLO1 carrying gene encoding glucoamylase (GLO1) produced the recombinant yeast which enable to degrade starch. Optimizing of bioconversion process of starch into ethanol by the yeast of recombinant Saccharomyces cerevisiae [yEP-GLO1] had been also done. Starch concentration which could be digested by recombinant yeast of S. cerevisiae [yEP-GLO1] was 10% (w/v). Bioconversion of starch having concentration 10% (b/v) using recombinant yeast of S. cerevisiae BY5207 [yEP-GLO1] could result ethanol as 20% (v/v) to alcoholmeter and 19,5% (v/v) to gas of chromatography. Otherwise, using recombinant yeast S. cerevisiae S. cerevisiae AS3324 [yEP-GLO1] resulted ethanol as 17% (v/v) to alcoholmeter and 17,5% (v/v) to gas of chromatography. The highest ethanol in starch bioconversion using both recombinant yeasts BY5207 and AS3324 could be resulted on 144 hours of fermentation time as well as in pH 5.

Polarity of recombination in transformation of Streptococcus pneumoniae

PubMed Central

Pasta, Franck; Sicard, Michel A.

1999-01-01

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5′- and 3′-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami− transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5′ to the deletion, showing that, in vivo, the 5′ side is strongly favored by recombination. Further results suggest that exchanges occurring from 5′ to 3′ relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5′ preference. PMID:10077616

Polarity of recombination in transformation of Streptococcus pneumoniae.

PubMed

Pasta, F; Sicard, M A

1999-03-16

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5'- and 3'-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami- transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5' to the deletion, showing that, in vivo, the 5' side is strongly favored by recombination. Further results suggest that exchanges occurring from 5' to 3' relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5' preference.

[Improvement of thermal adaptability and fermentation of industrial ethanologenic yeast by genomic DNA mutagenesis-based genetic recombination].

PubMed

Liu, Xiuying; He, Xiuping; Lu, Ying; Zhang, Borun

2011-07-01

Ethanol is an attractive alternative to fossil fuels. Saccharomyces cerevisiae is the most important ethanol producer. However, in the process of industrial production of ethanol, both cell growth and fermentation of ethanologenic S. cerevisiae are dramatically affected by environmental stresses, such as thermal stress. In this study, we improved both the thermotolerance and fermentation performance of industrial ethanologenic S. cerevisiae by combined usage of chemical mutagenesis and genomic DNA mutagenesis-based genetic recombination method. The recombinant S. cerevisiae strain T44-2 could grow at 44 degrees C, 3 degrees C higher than that of the original strain CE6. The survival rate of T44-2 was 1.84 and 1.87-fold of that of CE6 when heat shock at 48 degrees C and 52 degrees C for 1 h respectively. At temperature higher than 37 degrees C, recombinant strain T44-2 always gave higher cell growth and ethanol production than those of strain CE6. Meanwhile, from 30 degrees C to 40 degrees C, recombinant strain T44-2 produces 91.2-83.8 g/L of ethanol from 200 g/L of glucose, which indicated that the recombinant strain T44-2 had both thermotolerance and broad thermal adaptability. The work offers a novel method, called genomic DNA mutagenesis-based genetic recombination, to improve the physiological functions of S. cerevisiae.

MSH6- or PMS2-deficiency causes re-replication in DT40 B cells, but it has little effect on immunoglobulin gene conversion or on repair of AID-generated uracils

PubMed Central

Campo, Vanina A.; Patenaude, Anne-Marie; Kaden, Svenja; Horb, Lori; Firka, Daniel; Jiricny, Josef; Di Noia, Javier M.

2013-01-01

The mammalian antibody repertoire is shaped by somatic hypermutation (SHM) and class switch recombination (CSR) of the immunoglobulin (Ig) loci of B lymphocytes. SHM and CSR are triggered by non-canonical, error-prone processing of G/U mismatches generated by activation-induced deaminase (AID). In birds, AID does not trigger SHM, but it triggers Ig gene conversion (GC), a ‘homeologous’ recombination process involving the Ig variable region and proximal pseudogenes. Because recombination fidelity is controlled by the mismatch repair (MMR) system, we investigated whether MMR affects GC in the chicken B cell line DT40. We show here that Msh6−/− and Pms2−/− DT40 cells display cell cycle defects, including genomic re-replication. However, although IgVλ GC tracts in MMR-deficient cells were slightly longer than in normal cells, Ig GC frequency, donor choice or the number of mutations per sequence remained unaltered. The finding that the avian MMR system, unlike that of mammals, does not seem to contribute towards the processing of G/U mismatches in vitro could explain why MMR is unable to initiate Ig GC in this species, despite initiating SHM and CSR in mammalian cells. Moreover, as MMR does not counteract or govern Ig GC, we report a rare example of ‘homeologous’ recombination insensitive to MMR. PMID:23314153

rhEGF-containing thermosensitive and mucoadhesive polymeric sol-gel for endoscopic treatment of gastric ulcer and bleeding.

PubMed

Maeng, Jin Hee; So, Jung Won; Kim, Jungju; Kim, In Ae; Jung, Ji Hoon; Min, Kyunghyun; Lee, Don Haeng; Yang, Su-Geun

2014-03-01

Gastrointestinal endoscopy is a standard diagnostic tool for gastrointestinal ulcers and cancer. In this study, we have developed recombinant human epidermal growth factor-containing ulcer-coating polymeric sol-gel for endoscopic application. Chitosan and pluronic F127 were employed for their thermoresponsive and bioadhesive properties. At temperatures below 21, polymeric sol-gel remains liquid during endoscopic application and transforms to gel at body temperature after application on ulcers. In an in vitro cellular wounding assay, recombinant human epidermal growth factor sol-gel significantly enhanced the cell migration and decreased the wounding area (68%) compared to nontreated, recombinant human epidermal growth factor solution, and sol-gel without recombinant human epidermal growth factor (42, 49, and 32 % decreased at day 1). The in vivo ulcer-healing study was performed in an acetic acid-induced gastric ulcer rat model and proved that our recombinant human epidermal growth factor endoscopic sol-gel facilitated the ulcer-healing process more efficiently than the other treatments. Ulcer sizes in the recombinant human epidermal growth factor sol-gel group were decreased 2.9- and 2.1-fold compared with those in the nontreated group on days 1 and 3 after ulceration, respectively. The mucosal thickness in the recombinant human epidermal growth factor sol-gel group was significantly increased compared to that in the nontreated group (3.2- and 6.9-fold on days 1 and 3 after ulceration, respectively). In a gastric retention study, recombinant human epidermal growth factor sol-gel stayed on the gastric mucosa more than 2 h after application. The present study suggests that recombinant human epidermal growth factor sol-gel is a prospective candidate for treating gastric ulcers via endoscopic application.

Genome-wide variation in recombination rate in Eucalyptus.

PubMed

Gion, Jean-Marc; Hudson, Corey J; Lesur, Isabelle; Vaillancourt, René E; Potts, Brad M; Freeman, Jules S

2016-08-09

Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = -0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = -0.75). The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.

Discrimination between spin-dependent charge transport and spin-dependent recombination in π-conjugated polymers by correlated current and electroluminescence-detected magnetic resonance

NASA Astrophysics Data System (ADS)

Kavand, Marzieh; Baird, Douglas; van Schooten, Kipp; Malissa, Hans; Lupton, John M.; Boehme, Christoph

2016-08-01

Spin-dependent processes play a crucial role in organic electronic devices. Spin coherence can give rise to spin mixing due to a number of processes such as hyperfine coupling, and leads to a range of magnetic field effects. However, it is not straightforward to differentiate between pure single-carrier spin-dependent transport processes which control the current and therefore the electroluminescence, and spin-dependent electron-hole recombination which determines the electroluminescence yield and in turn modulates the current. We therefore investigate the correlation between the dynamics of spin-dependent electric current and spin-dependent electroluminescence in two derivatives of the conjugated polymer poly(phenylene-vinylene) using simultaneously measured pulsed electrically detected (pEDMR) and optically detected (pODMR) magnetic resonance spectroscopy. This experimental approach requires careful analysis of the transient response functions under optical and electrical detection. At room temperature and under bipolar charge-carrier injection conditions, a correlation of the pEDMR and the pODMR signals is observed, consistent with the hypothesis that the recombination currents involve spin-dependent electronic transitions. This observation is inconsistent with the hypothesis that these signals are caused by spin-dependent charge-carrier transport. These results therefore provide no evidence that supports earlier claims that spin-dependent transport plays a role for room-temperature magnetoresistance effects. At low temperatures, however, the correlation between pEDMR and pODMR is weakened, demonstrating that more than one spin-dependent process influences the optoelectronic materials' properties. This conclusion is consistent with prior studies of half-field resonances that were attributed to spin-dependent triplet exciton recombination, which becomes significant at low temperatures when the triplet lifetime increases.

Temperature and doping dependent changes in surface recombination during UV illumination of (Al)GaN bulk layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Netzel, Carsten; Jeschke, Jörg; Brunner, Frank

2016-09-07

We have studied the effect of continuous illumination with above band gap energy on the emission intensity of polar (Al)GaN bulk layers during the photoluminescence experiments. A temporal change in emission intensity on time scales from seconds to hours is based on the modification of the semiconductor surface states and the surface recombination by the incident light. The temporal behavior of the photoluminescence intensity varies with the parameters such as ambient atmosphere, pretreatment of the surface, doping density, threading dislocation density, excitation power density, and sample temperature. By means of temperature-dependent photoluminescence measurements, we observed that at least two differentmore » processes at the semiconductor surface affect the non-radiative surface recombination during illumination. The first process leads to an irreversible decrease in photoluminescence intensity and is dominant around room temperature, and the second process leads to a delayed increase in intensity and becomes dominant around T = 150–200 K. Both processes become slower when the sample temperature decreases from room temperature. They cease for T < 150 K. Stable photoluminescence intensity at arbitrary sample temperature was obtained by passivating the analyzed layer with an epitaxially grown AlN cap layer.« less

Electronic perturbation investigations into excitation and ionization in the millisecond pulsed glow discharge plasma

NASA Astrophysics Data System (ADS)

Li, Lei; Robertson-Honecker, Jennifer; Vaghela, Vishal; King, Fred L.

2006-06-01

This study employed a power perturbation method to examine the energy transfer processes at different locations within the afterpeak regime of a millisecond pulsed glow discharge plasma. Brief power perturbation pulses were applied during the afterpeak regime altering the environment of the collapsing plasma. Responses of several transitions to the power perturbations were measured via atomic emission and absorption spectroscopic methods at various distances from the surface of the cathode. The experimental data provide further insight into the energy transfer processes that occur at different spatial locations and in different temporal regimes of these pulsed glow discharge plasmas. Although the enhancement of the large population of metastable argon atoms is again confirmed, the mechanism responsible for this enhancement remains unclear. The most likely possibility involves some form of ion-electron recombination followed by radiative relaxation of the resulting species. The metastable argon atoms subsequently Penning ionize sputtered copper atoms which then appear to undergo a similar ion-electron recombination process yielding variable degrees of observable afterpeak emission for copper atom transitions. The kinetic information of these processes was approximated from the corresponding relaxation time. The electron thermalization time allowing for recombination with ions was found to be ˜25 μs after the discharge power termination.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Mengjin; Zeng, Yining; Li, Zhen

Here, we examine GBs with respect to non-GB regions (grain surfaces (GSs) and grain interiors (GIs)) in high-quality micrometer-sized perovskite CH 3NH 3PbI 3 (or MAPbI 3) thin films using high-resolution confocal fluorescence-lifetime imaging microscopy in conjunction with kinetic modeling of charge-transport and recombination processes. We show that, contrary to previous studies, GBs in our perovskite MAPbI3 thin films do not lead to increased recombination but that recombination in these films happens primarily in the non-GB regions (i.e., GSs or GIs). We also find that GBs in these films are not transparent to photogenerated carriers, which is likely associated withmore » a potential barrier at GBs. Lastly, even though GBs generally display lower luminescence intensities than GSs/GIs, the lifetimes at GBs are no worse than those at GSs/GIs, further suggesting that GBs do not dominate non-radiative recombination in MAPbI 3 thin films.« less

Recombination-enhanced surface expansion of clusters in intense soft x-ray laser pulses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rupp, Daniela; Flückiger, Leonie; Adolph, Marcus

Here, we studied the nanoplasma formation and explosion dynamics of single large xenon clusters in ultrashort, intense x-ray free-electron laser pulses via ion spectroscopy. The simultaneous measurement of single-shot diffraction images enabled a single-cluster analysis that is free from any averaging over the cluster size and laser intensity distributions. The measured charge state-resolved ion energy spectra show narrow distributions with peak positions that scale linearly with final ion charge state. These two distinct signatures are attributed to highly efficient recombination that eventually leads to the dominant formation of neutral atoms in the cluster. The measured mean ion energies exceed themore » value expected without recombination by more than an order of magnitude, indicating that the energy release resulting from electron-ion recombination constitutes a previously unnoticed nanoplasma heating process. This conclusion is supported by results from semiclassical molecular dynamics simulations.« less

An Overview of the Molecular Mechanisms of Recombinational DNA Repair

PubMed Central

Kowalczykowski, Stephen C.

2015-01-01

Recombinational DNA repair is a universal aspect of DNA metabolism and is essential for genomic integrity. It is a template-directed process that uses a second chromosomal copy (sister, daughter, or homolog) to ensure proper repair of broken chromosomes. The key steps of recombination are conserved from phage through human, and an overview of those steps is provided in this review. The first step is resection by helicases and nucleases to produce single-stranded DNA (ssDNA) that defines the homologous locus. The ssDNA is a scaffold for assembly of the RecA/RAD51 filament, which promotes the homology search. On finding homology, the nucleoprotein filament catalyzes exchange of DNA strands to form a joint molecule. Recombination is controlled by regulating the fate of both RecA/RAD51 filaments and DNA pairing intermediates. Finally, intermediates that mature into Holliday structures are disjoined by either nucleolytic resolution or topological dissolution. PMID:26525148

Mobile DNA in the pathogenic Neisseria

PubMed Central

Obergfell, Kyle P.; Seifert, H. Steven

2015-01-01

The genus Neisseria contains two pathogenic species of notable public health concern: Neisseria gonorrhoeae and Neisseria meningitidis. These pathogens display a notable ability to undergo frequent programmed recombination events. The recombination mediated pathways of transformation and pilin antigenic variation in the Neisseria are well studied systems that are critical for pathogenesis. Here we will detail the conserved and unique aspects of transformation and antigenic variation in the Neisseria. Transformation will be followed from initial DNA binding through recombination into the genome with consideration to the factors necessary at each step. Additional focus is paid to the unique type IV secretion system that mediates donation of transforming DNA in the pathogenic Neisseria. The pilin antigenic variation system uses programed recombinations to alter a major surface determinant which allows immune avoidance and promotes infection. We discuss the trans- and cis- acting factors which facilitate pilin antigenic variation and present the current understanding of the mechanisms involved in the process. PMID:25866700

Recombination-enhanced surface expansion of clusters in intense soft x-ray laser pulses

DOE PAGES

Rupp, Daniela; Flückiger, Leonie; Adolph, Marcus; ...

2016-10-07

Here, we studied the nanoplasma formation and explosion dynamics of single large xenon clusters in ultrashort, intense x-ray free-electron laser pulses via ion spectroscopy. The simultaneous measurement of single-shot diffraction images enabled a single-cluster analysis that is free from any averaging over the cluster size and laser intensity distributions. The measured charge state-resolved ion energy spectra show narrow distributions with peak positions that scale linearly with final ion charge state. These two distinct signatures are attributed to highly efficient recombination that eventually leads to the dominant formation of neutral atoms in the cluster. The measured mean ion energies exceed themore » value expected without recombination by more than an order of magnitude, indicating that the energy release resulting from electron-ion recombination constitutes a previously unnoticed nanoplasma heating process. This conclusion is supported by results from semiclassical molecular dynamics simulations.« less

Dissociative recombination by frame transformation to Siegert pseudostates: A comparison with a numerically solvable model

NASA Astrophysics Data System (ADS)

Hvizdoš, Dávid; Váňa, Martin; Houfek, Karel; Greene, Chris H.; Rescigno, Thomas N.; McCurdy, C. William; Čurík, Roman

2018-02-01

We present a simple two-dimensional model of the indirect dissociative recombination process. The model has one electronic and one nuclear degree of freedom and it can be solved to high precision, without making any physically motivated approximations, by employing the exterior complex scaling method together with the finite-elements method and discrete variable representation. The approach is applied to solve a model for dissociative recombination of H2 + in the singlet ungerade channels, and the results serve as a benchmark to test validity of several physical approximations commonly used in the computational modeling of dissociative recombination for real molecular targets. The second, approximate, set of calculations employs a combination of multichannel quantum defect theory and frame transformation into a basis of Siegert pseudostates. The cross sections computed with the two methods are compared in detail for collision energies from 0 to 2 eV.

Auger recombination in Dirac materials: A tangle of many-body effects

NASA Astrophysics Data System (ADS)

Alymov, Georgy; Vyurkov, Vladimir; Ryzhii, Victor; Satou, Akira; Svintsov, Dmitry

2018-05-01

The peculiar electron dispersion in Dirac materials makes lowest-order Auger processes prohibited or marginally prohibited by energy and momentum conservation laws. Thus, Auger recombination (AR) in these materials is very sensitive to many-body effects. We incorporate them at the level of the G W approximation into the nonequilibrium Green's functions approach to AR and study the role of dynamic screening, spectrum broadening, and renormalization in the case of weakly pumped undoped graphene. We find that incorrect treatment of many-body effects can lead to an order-of-magnitude error in the recombination rate. We show that the AR time depends weakly (sublinearly) on the background dielectric constant, which limits the possibility to control recombination by the choice of substrate. However, the AR time can be considerably prolonged by placing graphene under a metal gate or by introducing a band gap. With carrier cooling taken into account, our results comply with experiments on photoexcited graphene.

The use of dissolved oxygen-controlled, fed-batch aerobic cultivation for recombinant protein subunit vaccine manufacturing.

PubMed

Farrell, Patrick; Sun, Jacob; Champagne, Paul-Philippe; Lau, Heron; Gao, Meg; Sun, Hong; Zeiser, Arno; D'Amore, Tony

2015-11-27

A simple "off-the-shelf" fed-batch approach to aerobic bacterial cultivation for recombinant protein subunit vaccine manufacturing is presented. In this approach, changes in the dissolved oxygen levels are used to adjust the nutrient feed rate (DO-stat), so that the desired dissolved oxygen level is maintained throughout cultivation. This enables high Escherichia coli cell densities and recombinant protein titers. When coupled to a kLa-matched scale-down model, process performance is shown to be consistent at the 2L, 20L, and 200L scales for two recombinant E. coli strains expressing different protein subunit vaccine candidates. Additionally, by mining historical DO-stat nutrient feeding data, a method to transition from DO-stat to a pre-determined feeding profile suitable for larger manufacturing scales without using feedback control is demonstrated at the 2L, 20L, and 200L scales. Copyright © 2015 Elsevier Ltd. All rights reserved.

Band-Edge Exciton Fine Structure and Recombination Dynamics in InP/ZnS Colloidal Nanocrystals.

PubMed

Biadala, Louis; Siebers, Benjamin; Beyazit, Yasin; Tessier, Mickaël D; Dupont, Dorian; Hens, Zeger; Yakovlev, Dmitri R; Bayer, Manfred

2016-03-22

We report on a temperature-, time-, and spectrally resolved study of the photoluminescence of type-I InP/ZnS colloidal nanocrystals with varying core size. By studying the exciton recombination dynamics we assess the exciton fine structure in these systems. In addition to the typical bright-dark doublet, the photoluminescence stems from an upper bright state in spite of its large energy splitting (∼100 meV). This striking observation results from dramatically lengthened thermalization processes among the fine structure levels and points to optical-phonon bottleneck effects in InP/ZnS nanocrystals. Furthermore, our data show that the radiative recombination of the dark exciton scales linearly with the bright-dark energy splitting for CdSe and InP nanocrystals. This finding strongly suggests a universal dangling bonds-assisted recombination of the dark exciton in colloidal nanostructures.

RAP80, ubiquitin and SUMO in the DNA damage response.

PubMed

Lombardi, Patrick M; Matunis, Michael J; Wolberger, Cynthia

2017-08-01

A decade has passed since the first reported connection between RAP80 and BRCA1 in DNA double-strand break repair. Despite the initial identification of RAP80 as a factor localizing BRCA1 to DNA double-strand breaks and potentially promoting homologous recombination, there is increasing evidence that RAP80 instead suppresses homologous recombination to fine-tune the balance of competing DNA repair processes during the S/G 2 phase of the cell cycle. RAP80 opposes homologous recombination by inhibiting DNA end-resection and sequestering BRCA1 into the BRCA1-A complex. Ubiquitin and SUMO modifications of chromatin at DNA double-strand breaks recruit RAP80, which contains distinct sequence motifs that recognize ubiquitin and SUMO. Here, we review RAP80's role in repressing homologous recombination at DNA double-strand breaks and how this role is facilitated by its ability to bind ubiquitin and SUMO modifications.

Heterologous expression of Oenococcus oeni malolactic enzyme in Lactobacillus plantarum for improved malolactic fermentation

PubMed Central

2012-01-01

Lactobacillus plantarum is involved in a multitude of food related industrial fermentation processes including the malolactic fermentation (MLF) of wine. This work is the first report on a recombinant L. plantarum strain successfully conducting MLF. The malolactic enzyme (MLE) from Oenococcus oeni was cloned into the lactobacillal expression vector pSIP409 which is based on the sakacin P operon of Lactobacillus sakei and expressed in the host strain L. plantarum WCFS1. Both recombinant and wild-type L. plantarum strains were tested for MLF using a buffered malic acid solution in absence of glucose. Under the conditions with L-malic acid as the only energy source and in presence of Mn2+ and NAD+, the recombinant L. plantarum and the wild-type strain converted 85% (2.5 g/l) and 51% (1.5 g/l), respectively, of L-malic acid in 3.5 days. Furthermore, the recombinant L. plantarum cells converted in a modified wine 15% (0.4 g/l) of initial L-malic acid concentration in 2 days. In conclusion, recombinant L. plantarum cells expressing MLE accelerate the malolactic fermentation. PMID:22452826

Mus81 and Yen1 promote reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast

PubMed Central

Ho, Chu Kwen; Mazón, Gerard; Lam, Alicia F.; Symington, Lorraine S.

2010-01-01

Holliday junction (HJ) resolution is required for segregation of chromosomes and for formation of crossovers during homologous recombination. The identity of the resolvase(s) that functions in vivo has yet to be established, although several proteins able to cut HJs in vitro have been identified as candidates in yeasts and mammals. Using an assay to detect unselected products of mitotic recombination we found a significant decrease in crossovers in the Saccharomyces cerevisiae mus81Δ mutant. Yen1 serves a back-up function responsible for resolving intermediates in mus81Δ mutants, or when conversion tracts are short. In the absence of both Mus81 and Yen1 intermediates are not channeled exclusively to non-crossover recombinants, but instead are processed by Pol32-dependent break-induced replication (BIR). The channeling of recombination from reciprocal exchange to BIR results in greatly increased spontaneous loss of heterozygosity (LOH) and chromosome mis-segregation in the mus81Δ yen1Δ mutant, typical of the genomic instability found in tumor cells. PMID:21172663

Tab2, a novel recombinant polypeptide tag offering sensitive and specific protein detection and reliable affinity purification.

PubMed

Crusius, Kerstin; Finster, Silke; McClary, John; Xia, Wei; Larsen, Brent; Schneider, Douglas; Lu, Hong-Tao; Biancalana, Sara; Xuan, Jian-Ai; Newton, Alicia; Allen, Debbie; Bringmann, Peter; Cobb, Ronald R

2006-10-01

The detection and purification of proteins are often time-consuming and frequently involve complicated protocols. The addition of a peptide tag to recombinant proteins can make this process more efficient. Many of the commonly used tags, such as Flagtrade mark, Myc, HA and V5 are recognized by specific monoclonal antibodies and therefore, allow immunoaffinity-based purification. Enhancing the current scope of flexibility in using diverse peptide tags, we report here the development of a novel, short polypeptide tag (Tab2) for detection and purification of recombinant proteins. The Tab2 epitope corresponds to the NH2-terminal seven amino acid residues of human TGFalpha. A monoclonal anti-Tab2 antibody was raised and characterized. To investigate the potential of this peptide sequence as a novel tag for recombinant proteins, we expressed several different recombinant proteins containing this tag in E. coli, baculovirus, and mammalian cells. The data presented demonstrates the Tab2 tag-anti-Tab2 antibody combination is a reliable tool enabling specific Western blot detection, FACS analysis, and immunoprecipitation as well as non-denaturing protein affinity purification.

Ultrafast Recombination Dynamics in Dye-Sensitized SnO2/TiO2 Core/Shell Films.

PubMed

Gish, Melissa K; Lapides, Alexander M; Brennaman, M Kyle; Templeton, Joseph L; Meyer, Thomas J; Papanikolas, John M

2016-12-15

Interfacial dynamics are investigated in SnO 2 /TiO 2 core/shell films derivatized with a Ru(II)-polypyridyl chromophore ([Ru II (bpy) 2 (4,4'-(PO 3 H 2 ) 2 bpy)] 2+ , RuP) using transient absorption methods. Electron injection from the chromophore into the TiO 2 shell occurs within a few picoseconds after photoexcitation. Loss of the oxidized dye through recombination occurs across time scales spanning 10 orders of magnitude. The majority (60%) of charge recombination events occur shortly after injection (τ = 220 ps), while a small fraction (≤20%) of the oxidized chromophores persists for milliseconds. The lifetime of long-lived charge-separated states (CSS) depends exponentially on shell thickness, suggesting that the injected electrons reside in the SnO 2 core and must tunnel through the TiO 2 shell to recombine with oxidized dyes. While the core/shell architecture extends the lifetime in a small fraction of the CSS, making water oxidation possible, the subnanosecond recombination process has profound implications for the overall efficiencies of dye-sensitized photoelectrosynthesis cells (DSPECs).

Meiotic recombination hotspots - a comparative view.

PubMed

Choi, Kyuha; Henderson, Ian R

2015-07-01

During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Genome engineering for improved recombinant protein expression in Escherichia coli.

PubMed

Mahalik, Shubhashree; Sharma, Ashish K; Mukherjee, Krishna J

2014-12-19

A metabolic engineering perspective which views recombinant protein expression as a multistep pathway allows us to move beyond vector design and identify the downstream rate limiting steps in expression. In E.coli these are typically at the translational level and the supply of precursors in the form of energy, amino acids and nucleotides. Further recombinant protein production triggers a global cellular stress response which feedback inhibits both growth and product formation. Countering this requires a system level analysis followed by a rational host cell engineering to sustain expression for longer time periods. Another strategy to increase protein yields could be to divert the metabolic flux away from biomass formation and towards recombinant protein production. This would require a growth stoppage mechanism which does not affect the metabolic activity of the cell or the transcriptional or translational efficiencies. Finally cells have to be designed for efficient export to prevent buildup of proteins inside the cytoplasm and also simplify downstream processing. The rational and the high throughput strategies that can be used for the construction of such improved host cell platforms for recombinant protein expression is the focus of this review.

Yeast Srs2 Helicase Promotes Redistribution of Single-Stranded DNA-Bound RPA and Rad52 in Homologous Recombination Regulation.

PubMed

De Tullio, Luisina; Kaniecki, Kyle; Kwon, Youngho; Crickard, J Brooks; Sung, Patrick; Greene, Eric C

2017-10-17

Srs2 is a super-family 1 helicase that promotes genome stability by dismantling toxic DNA recombination intermediates. However, the mechanisms by which Srs2 remodels or resolves recombination intermediates remain poorly understood. Here, single-molecule imaging is used to visualize Srs2 in real time as it acts on single-stranded DNA (ssDNA) bound by protein factors that function in recombination. We demonstrate that Srs2 is highly processive and translocates rapidly (∼170 nt per second) in the 3'→5' direction along ssDNA saturated with replication protein A (RPA). We show that RPA is evicted from DNA during the passage of Srs2. Remarkably, Srs2 also readily removes the recombination mediator Rad52 from RPA-ssDNA and, in doing so, promotes rapid redistribution of both Rad52 and RPA. These findings have important mechanistic implications for understanding how Srs2 and related nucleic acid motor proteins resolve potentially pathogenic nucleoprotein intermediates. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Photodetector having high speed and sensitivity

DOEpatents

Morse, Jeffrey D.; Mariella, Jr., Raymond P.

1991-01-01

The present invention provides a photodetector having an advantageous combination of sensitivity and speed; it has a high sensitivity while retaining high speed. In a preferred embodiment, visible light is detected, but in some embodiments, x-rays can be detected, and in other embodiments infrared can be detected. The present invention comprises a photodetector having an active layer, and a recombination layer. The active layer has a surface exposed to light to be detected, and comprises a semiconductor, having a bandgap graded so that carriers formed due to interaction of the active layer with the incident radiation tend to be swept away from the exposed surface. The graded semiconductor material in the active layer preferably comprises Al.sub.1-x Ga.sub.x As. An additional sub-layer of graded In.sub.1-y Ga.sub.y As may be included between the Al.sub.1-x Ga.sub.x As layer and the recombination layer. The recombination layer comprises a semiconductor material having a short recombination time such as a defective GaAs layer grown in a low temperature process. The recombination layer is positioned adjacent to the active layer so that carriers from the active layer tend to be swept into the recombination layer. In an embodiment, the photodetector may comprise one or more additional layers stacked below the active and recombination layers. These additional layers may include another active layer and another recombination layer to absorb radiation not absorbed while passing through the first layers. A photodetector having a stacked configuration may have enhanced sensitivity and responsiveness at selected wavelengths such as infrared.

Microscopic dynamics research on the "mature" process of dye-sensitized solar cells after injection of highly concentrated electrolyte.

PubMed

Liang, Zhongguan; Liu, Weiqing; Chen, Jun; Hu, Linhua; Dai, Songyuan

2015-01-21

After injection of electrolyte, the internal three-dimensional solid-liquid penetration system of dye-sensitized solar cells (DSCs) can take a period of time to reach "mature" state. This paper studies the changes of microscopic processes of DSCs including TiO2 energy-level movement, localized state distribution, charge accumulation, electron transport, and recombination dynamics, from the beginning of electrolyte injection to the time of reached mature state. The results show that the microscopic dynamics process of DSCs exhibited a time-dependent behavior and achieved maturity ∼12 h after injecting the electrolyte into DSCs. Within 0-12 h, several results were observed: (1) the conduction band edge of TiO2 moved slightly toward negative potential direction; (2) the localized states in the band gap of TiO2 was reduced according to the same distribution law; (3) the transport resistance in TiO2 film increased, and electron transport time was prolonged as the time of maturity went on, which indicated that the electron transport process is impeded gradually; (4) the recombination resistance at the TiO2/electrolyte (EL) interface increases, and electron lifetime gradually extends, therefore, the recombination process is continuously suppressed. Furthermore, results suggest that the parameters of EL/Pt-transparent conductive oxide (TCO) interface including the interfacial capacitance, electron-transfer resistance, and transfer time constant would change with time of maturity, indicating that the EL/Pt-TCO interface is a potential factor affecting the mature process of DSCs.

Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly

PubMed Central

Meirovitch, Sigal; Shtein, Zvi; Ben-Shalom, Tal; Lapidot, Shaul; Tamburu, Carmen; Hu, Xiao; Kluge, Jonathan A.; Raviv, Uri; Kaplan, David L.; Shoseyov, Oded

2016-01-01

The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs) and recombinant spider silk protein fused to a cellulose binding domain (CBD) is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg) of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (TEM) indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites. PMID:27649169

Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly.

PubMed

Meirovitch, Sigal; Shtein, Zvi; Ben-Shalom, Tal; Lapidot, Shaul; Tamburu, Carmen; Hu, Xiao; Kluge, Jonathan A; Raviv, Uri; Kaplan, David L; Shoseyov, Oded

2016-09-18

The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs) and recombinant spider silk protein fused to a cellulose binding domain (CBD) is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg) of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (TEM) indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites.

Advanced technologies for improved expression of recombinant proteins in bacteria: perspectives and applications.

PubMed

Gupta, Sanjeev K; Shukla, Pratyoosh

2016-12-01

Prokaryotic expression systems are superior in producing valuable recombinant proteins, enzymes and therapeutic products. Conventional microbial technology is evolving gradually and amalgamated with advanced technologies in order to give rise to improved processes for the production of metabolites, recombinant biopharmaceuticals and industrial enzymes. Recently, several novel approaches have been employed in a bacterial expression platform to improve recombinant protein expression. These approaches involve metabolic engineering, use of strong promoters, novel vector elements such as inducers and enhancers, protein tags, secretion signals, high-throughput devices for cloning and process screening as well as fermentation technologies. Advancement of the novel technologies in E. coli systems led to the production of "difficult to express" complex products including small peptides, antibody fragments, few proteins and full-length aglycosylated monoclonal antibodies in considerable large quantity. Wacker's secretion technologies, Pfenex system, inducers, cell-free systems, strain engineering for post-translational modification, such as disulfide bridging and bacterial N-glycosylation, are still under evaluation for the production of complex proteins and peptides in E. coli in an efficient manner. This appraisal provides an impression of expression technologies developed in recent times for enhanced production of heterologous proteins in E. coli which are of foremost importance for diverse applications in microbiology and biopharmaceutical production.

Reduction in Recombination Current Density in Boron Doped Silicon Using Atomic Hydrogen

NASA Astrophysics Data System (ADS)

Young, Matthew Garett

The solar industry has grown immensely in recent years and has reached a point where solar energy has now become inexpensive enough that it is starting to emerge as a mainstream electrical generation source. However, recent economic analysis has suggested that for solar to become a truly wide spread source of electricity, the costs still need to plummet by a factor of 8x. This demands new and innovative concepts to help lower such cost. In pursuit of this goal, this dissertation examines the use of atomic hydrogen to lessen the recombination current density in the boron doped region of n-type silicon solar cells. This required the development of a boron diffusion process that maintained the bulk lifetime of n-type silicon such that the recombination current density could be extracted by photoconductance spectroscopy. It is demonstrated that by hydrogenating boron diffusions, the majority carrier concentration can be controlled. By using symmetrically diffused test structures with quinhydrone-methanol surface passivation the recombination current density of a hydrogenated boron profile is shown to be less than that of a standard boron profile, by as much as 30%. This is then applied to a modified industrial silicon solar cell process to demonstrate an efficiency enhancement of 0.4%.

Reduced interface recombination in Cu{sub 2}ZnSnS{sub 4} solar cells with atomic layer deposition Zn{sub 1−x}Sn{sub x}O{sub y} buffer layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Platzer-Björkman, C.; Frisk, C.; Larsen, J. K.

2015-12-14

Cu{sub 2}ZnSnS{sub 4} (CZTS) solar cells typically include a CdS buffer layer in between the CZTS and ZnO front contact. For sulfide CZTS, with a bandgap around 1.5 eV, the band alignment between CZTS and CdS is not ideal (“cliff-like”), which enhances interface recombination. In this work, we show how a Zn{sub 1−x}Sn{sub x}O{sub y} (ZTO) buffer layer can replace CdS, resulting in improved open circuit voltages (V{sub oc}) for CZTS devices. The ZTO is deposited by atomic layer deposition (ALD), with a process previously developed for Cu(In,Ga)Se{sub 2} solar cells. By varying the ALD process temperature, the position of themore » conduction band minimum of the ZTO is varied in relation to that of CZTS. A ZTO process at 95 °C is found to give higher V{sub oc} and efficiency as compared with the CdS reference devices. For a ZTO process at 120 °C, where the conduction band alignment is expected to be the same as for CdS, the V{sub oc} and efficiency is similar to the CdS reference. Further increase in conduction band minimum by lowering the deposition temperature to 80 °C shows blocking of forward current and reduced fill factor, consistent with barrier formation at the junction. Temperature-dependent current voltage analysis gives an activation energy for recombination of 1.36 eV for the best ZTO device compared with 0.98 eV for CdS. We argue that the V{sub oc} of the best ZTO devices is limited by bulk recombination, in agreement with a room temperature photoluminescence peak at around 1.3 eV for both devices, while the CdS device is limited by interface recombination.« less

Engineering Saccharomyces cerevisiae for direct conversion of raw, uncooked or granular starch to ethanol.

PubMed

Görgens, Johann F; Bressler, David C; van Rensburg, Eugéne

2015-01-01

The production of raw starch-degrading amylases by recombinant Saccharomyces cerevisiae provides opportunities for the direct hydrolysis and fermentation of raw starch to ethanol without cooking or exogenous enzyme addition. Such a consolidated bioprocess (CBP) for raw starch fermentation will substantially reduce costs associated with energy usage and commercial granular starch hydrolyzing (GSH) enzymes. The core purpose of this review is to provide comprehensive insight into the physiological impact of recombinant amylase production on the ethanol-producing yeast. Key production parameters, based on outcomes from modifications to the yeast genome and levels of amylase production, were compared to key benchmark data. In turn, these outcomes are of significance from a process point of view to highlight shortcomings in the current state of the art of raw starch fermentation yeast compared to a set of industrial standards. Therefore, this study provides an integrated critical assessment of physiology, genetics and process aspects of recombinant raw starch fermenting yeast in relation to presently used technology. Various approaches to strain development were compared on a common basis of quantitative performance measures, including the extent of hydrolysis, fermentation-hydrolysis yield and productivity. Key findings showed that levels of α-amylase required for raw starch hydrolysis far exceeded enzyme levels for soluble starch hydrolysis, pointing to a pre-requisite for excess α-amylase compared to glucoamylase for efficient raw starch hydrolysis. However, the physiological limitations of amylase production by yeast, requiring high biomass concentrations and long cultivation periods for sufficient enzyme accumulation under anaerobic conditions, remained a substantial challenge. Accordingly, the fermentation performance of the recombinant S. cerevisiae strains reviewed in this study could not match the performance of conventional starch fermentation processes, based either on starch cooking and/or exogenous amylase enzyme addition. As an alternative strategy, the addition of exogenous GSH enzymes during early stages of raw starch fermentation may prove to be a viable approach for industrial application of recombinant S. cerevisiae, with the process still benefitting from amylase production by CBP yeast during later stages of cultivation.

Conditions for diffusion-limited and reaction-limited recombination in nanostructured solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ansari-Rad, Mehdi, E-mail: ansari.rad@ut.ac.ir; Department of Physics, University of Shahrood, Shahrood; Anta, Juan A., E-mail: anta@upo.es

2014-04-07

The performance of Dye-sensitized solar cells (DSC) and related devices made of nanostructured semiconductors relies on a good charge separation, which in turn is achieved by favoring charge transport against recombination. Although both processes occur at very different time scales, hence ensuring good charge separation, in certain cases the kinetics of transport and recombination can be connected, either in a direct or an indirect way. In this work, the connection between electron transport and recombination in nanostructured solar cells is studied both theoretically and by Monte Carlo simulation. Calculations using the Multiple-Trapping model and a realistic trap distribution for nanostructuredmore » TiO{sub 2} show that for attempt-to-jump frequencies higher than 10{sup 11}–10{sup 13} Hz, the system adopts a reaction limited (RL) regime, with a lifetime which is effectively independent from the speed of the electrons in the transport level. For frequencies lower than those, and depending on the concentration of recombination centers in the material, the system enters a diffusion-limited regime (DL), where the lifetime increases if the speed of free electrons decreases. In general, the conditions for RL or DL recombination depend critically on the time scale difference between recombination kinetics and free-electron transport. Hence, if the former is too rapid with respect to the latter, the system is in the DL regime and total thermalization of carriers is not possible. In the opposite situation, a RL regime arises. Numerical data available in the literature, and the behavior of the lifetime with respect to (1) density of recombination centers and (2) probability of recombination at a given center, suggest that a typical DSC in operation stays in the RL regime with complete thermalization, although a transition to the DL regime may occur for electrolytes or hole conductors where recombination is especially rapid or where there is a larger dispersion of energies of electron acceptors.« less

Dissociative recombination of HCl+

NASA Astrophysics Data System (ADS)

Larson, Åsa; Fonseca dos Santos, Samantha; E. Orel, Ann

2017-08-01

The dissociative recombination of HCl+, including both the direct and indirect mechanisms, is studied. For the direct process, the relevant electronic states are calculated ab initio by combining electron scattering calculations to obtain resonance positions and autoionization widths with multi-reference configuration interaction calculations of the ion and Rydberg states. The cross section for the direct dissociation along electronic resonant states is computed by solution of the time-dependent Schrödinger equation. For the indirect process, an upper bound value for the cross section is obtained using a vibrational frame transformation of the elements of the scattering matrix at energies just above the ionization threshold. Vibrational excitations of the ionic core from the ground vibrational state, v = 0 , to the first three excited vibrational states, v = 1 , v = 2 , and v = 3 , are considered. Autoionization is neglected and the effect of the spin-orbit splitting of the ionic potential energy upon the indirect dissociative recombination cross section is considered. The calculated cross sections are compared to measurements.

Progress and obstacles in the production and application of recombinant lignin-degrading peroxidases

PubMed Central

Lambertz, Camilla; Ece, Selin; Fischer, Rainer; Commandeur, Ulrich

2016-01-01

ABSTRACT Lignin is 1 of the 3 major components of lignocellulose. Its polymeric structure includes aromatic subunits that can be converted into high-value-added products, but this potential cannot yet been fully exploited because lignin is highly recalcitrant to degradation. Different approaches for the depolymerization of lignin have been tested, including pyrolysis, chemical oxidation, and hydrolysis under supercritical conditions. An additional strategy is the use of lignin-degrading enzymes, which imitates the natural degradation process. A versatile set of enzymes for lignin degradation has been identified, and research has focused on the production of recombinant enzymes in sufficient amounts to characterize their structure and reaction mechanisms. Enzymes have been analyzed individually and in combinations using artificial substrates, lignin model compounds, lignin and lignocellulose. Here we consider progress in the production of recombinant lignin-degrading peroxidases, the advantages and disadvantages of different expression hosts, and obstacles that must be overcome before such enzymes can be characterized and used for the industrial processing of lignin. PMID:27295524

Reproduction in Leishmania: A focus on genetic exchange.

PubMed

Rougeron, V; De Meeûs, T; Bañuls, A-L

2017-06-01

One key process of the life cycle of pathogens is their mode of reproduction. Indeed, this fundamental biological process conditions the multiplication and the transmission of genes and thus the propagation of diseases in the environment. Reproductive strategies of protozoan parasites have been a subject of debate for many years, principally due to the difficulty in making direct observations of sexual reproduction (i.e. genetic recombination). Traditionally, these parasites were considered as characterized by a preeminent clonal structure. Nevertheless, with the development of elaborate culture experiments, population genetics and evolutionary and population genomics, several studies suggested that most of these pathogens were also characterized by constitutive genetic recombination events. In this opinion, we focused on Leishmania parasites, pathogens responsible of leishmaniases, a major public health issue. We first discuss the evolutionary advantages of a mixed mating reproductive strategy, then we review the evidence of genetic exchange, and finally we detail available tools to detect naturally occurring genetic recombination in Leishmania parasites and more generally in protozoan parasites. Copyright © 2016. Published by Elsevier B.V.

Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies.

PubMed

Yamaguchi, Hiroshi; Miyazaki, Masaya

2014-02-20

Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. As inclusion bodies contain relatively pure and intact proteins, protein refolding is an important process to obtain active recombinant proteins from inclusion bodies. However, conventional refolding methods, such as dialysis and dilution, are time consuming and, often, recovered yields of active proteins are low, and a trial-and-error process is required to achieve success. Recently, several approaches have been reported to refold these aggregated proteins into an active form. The strategies largely aim at reducing protein aggregation during the refolding procedure. This review focuses on protein refolding techniques using chemical additives and laminar flow in microfluidic chips for the efficient recovery of active proteins from inclusion bodies.

HELIUM EFFECTS ON DISPLACEMENT CASCADE IN TUNGSTEN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.

2013-09-30

Molecular dynamics (MD) simulations were performed to investigate He effects on displacement cascades in W. Helium content, proportion of interstitial and substitutional He and temperature were varied to reveal the various effects. The effect of interstitial He on the number of self-interstitial atoms (SIAs) produced during cascade damage appears to be insignificant. However, interstitial He tends to fill a vacancy (V). Nevertheless, this process is less favorable than SIA-V recombination particularly when excess SIAs are present before a cascade. The efficiency of He filling and SIA-V recombination increases as temperature increases due to increased point defect mobility. Likewise, substitutional Hemore » is more susceptible to displacement during a collision cascade than W. This susceptibility increases towards higher temperatures. Consequently, the number of surviving V is governed by the interplay between displaced substitutional He and SIA-V recombination. The temperature dependence of these processes results in a minimum number of V reached at an intermediate temperature.« less

Dissociative recombination of HCl.

PubMed

Larson, Åsa; Fonseca Dos Santos, Samantha; E Orel, Ann

2017-08-28

The dissociative recombination of HCl + , including both the direct and indirect mechanisms, is studied. For the direct process, the relevant electronic states are calculated ab initio by combining electron scattering calculations to obtain resonance positions and autoionization widths with multi-reference configuration interaction calculations of the ion and Rydberg states. The cross section for the direct dissociation along electronic resonant states is computed by solution of the time-dependent Schrödinger equation. For the indirect process, an upper bound value for the cross section is obtained using a vibrational frame transformation of the elements of the scattering matrix at energies just above the ionization threshold. Vibrational excitations of the ionic core from the ground vibrational state, v = 0, to the first three excited vibrational states, v = 1, v = 2, and  v = 3, are considered. Autoionization is neglected and the effect of the spin-orbit splitting of the ionic potential energy upon the indirect dissociative recombination cross section is considered. The calculated cross sections are compared to measurements.

Bioethanol production from the dry powder of Jerusalem artichoke tubers by recombinant Saccharomyces cerevisiae in simultaneous saccharification and fermentation.

PubMed

Wang, Yi-Zhou; Zou, Shan-Mei; He, Mei-Lin; Wang, Chang-Hai

2015-04-01

It has been found that recombinant Saccharomyces cerevisiae 6525 can produce high concentration of ethanol in one-step fermentation from the extract of Jerusalem artichoke tubers or inulin. However, the utilization rate of raw materials was low and the fermentation process was costly and complicated. Therefore, in this study, after the optimum processing conditions for ethanol production in fed-batch fermentation were determined in flask, the recombinant S. cerevisiae 6525 was first used to produce ethanol from the dry powder of Jerusalem artichoke tubers in 5-L agitating fermentor. After 72 h of fermentation, around 84.3 g/L ethanol was produced in the fermentation liquids, and the conversion efficiency of inulin-type sugars to ethanol was 0.453, or 88.6 % of the theoretical value of 0.511. This study showed high feasibility of bioethanol industrial production from the Jerusalem artichoke tubers and provided a basis for it in the future.

Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background.

PubMed

Capilla, Laia; Medarde, Nuria; Alemany-Schmidt, Alexandra; Oliver-Bonet, Maria; Ventura, Jacint; Ruiz-Herrera, Aurora

2014-07-07

Despite the existence of formal models to explain how chromosomal rearrangements can be fixed in a population in the presence of gene flow, few empirical data are available regarding the mechanisms by which genome shuffling contributes to speciation, especially in mammals. In order to shed light on this intriguing evolutionary process, here we present a detailed empirical study that shows how Robertsonian (Rb) fusions alter the chromosomal distribution of recombination events during the formation of the germline in a Rb system of the western house mouse (Mus musculus domesticus). Our results indicate that both the total number of meiotic crossovers and the chromosomal distribution of recombination events are reduced in mice with Rb fusions and that this can be related to alterations in epigenetic signatures for heterochromatinization. Furthermore, we detected novel house mouse Prdm9 allelic variants in the Rb system. Remarkably, mean recombination rates were positively correlated with a decrease in the number of ZnF domains in the Prdm9 gene. The suggestion that recombination can be modulated by both chromosomal reorganizations and genetic determinants that control the formation of double-stranded breaks during meiosis opens new avenues for understanding the role of recombination in chromosomal speciation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

The RECG1 DNA Translocase Is a Key Factor in Recombination Surveillance, Repair, and Segregation of the Mitochondrial DNA in Arabidopsis[OPEN

PubMed Central

Le Ret, Monique; Bergdoll, Marc; Bichara, Marc; Dietrich, André

2015-01-01

The mitochondria of flowering plants have considerably larger and more complex genomes than the mitochondria of animals or fungi, mostly due to recombination activities that modulate their genomic structures. These activities most probably participate in the repair of mitochondrial DNA (mtDNA) lesions by recombination-dependent processes. Rare ectopic recombination across short repeats generates new genomic configurations that contribute to mtDNA heteroplasmy, which drives rapid evolution of the sequence organization of plant mtDNAs. We found that Arabidopsis thaliana RECG1, an ortholog of the bacterial RecG translocase, is an organellar protein with multiple roles in mtDNA maintenance. RECG1 targets to mitochondria and plastids and can complement a bacterial recG mutant that shows defects in repair and replication control. Characterization of Arabidopsis recG1 mutants showed that RECG1 is required for recombination-dependent repair and for suppression of ectopic recombination in mitochondria, most likely because of its role in recovery of stalled replication forks. The analysis of alternative mitotypes present in a recG1 line and of their segregation following backcross allowed us to build a model to explain how a new stable mtDNA configuration, compatible with normal plant development, can be generated by stoichiometric shift. PMID:26462909

Method for producing electrodes using microscale or nanoscale materials obtained from hydrogendriven metallurgical reactions

DOEpatents

Reilly, James J.; Adzic, Gordana D.; Johnson, John R.; Vogt, Thomas; McBreen, James

2003-09-02

A method is provided for producing electrodes using microscale and nanoscale metal materials formed from hydrogen driven metallurgical processes; such a the HD (hydriding, dehydriding) process, the HDDR (hydriding, dehydriding, disproportionation, and recombination) process, and variants thereof.

Effect of Dangling Bond Spins on the Dark Exciton Recombination and Spin Polarization in CdSe Colloidal Nanostructures

NASA Astrophysics Data System (ADS)

Rodina, A. V.; Golovatenko, A. A.; Shornikova, E. V.; Yakovlev, D. R.; Efros, Al. L.

2018-04-01

We present theoretical aspects of the exchange interaction between the ground optically-forbidden "dark" exciton state and surface dangling bonds in colloidal CdSe spherical nanocrystals and nanoplatelets. The influence of the dangling bond spins on the radiative recombination and spin splitting of the dark exciton is shown. Processes of optically-driven and external magnetic field-driven formation of the dangling bond magnetic polaron (DBMP) are considered. Thermodynamic and dynamic polarization mechanisms of the DBMP formation within these two processes and corresponding critical temperatures are compared. Experimental manifestations of the DBMP formation in CdSe nanocrystals and nanoplatelets are discussed.

[Advances in microbial production of alkaline polygalacturonate lyase and its application in clean production of textile industry].

PubMed

Liu, Long; Wang, Zhihao; Zhang, Dongxu; Li, Jianghua; Du, Guocheng; Chen, Jian

2009-12-01

We reviewed the microbial production of alkaline polygalacturonate lyase (PGL) and its application in the clean production of textile industry. Currently PGL is mainly produced by microbial fermentation and Bacillus sp. is an ideal wild strain for PGL production. Microbial PGL production was affected by many factors including the concentration and feeding mode of substrate, cell concentration, agitation speed, aeration rate, pH and temperature. Constructing the recombinant strain provided an effective alternative for PGL production, and the concentration of PGL produced by the recombinant Pichia pastoris reached 1305 U/mL in 10 m3 fermentor. The recombinant Pichia pastoris had the potential to reach the industrial production of PGL. PGL can be applied in bio-scouring process in the pre-treatment of cotton. Compared with the traditional alkaline cooking process, the application of PGL can protect fiber, improve the bio-scouring efficiency, decrease energy consumption and alleviate the environmental pollution. The future research focus will be the molecular directed evolution of PGL to make PGL more suitable for the application of PGL in bio-scouring process to realize the clean production of textile industry.

Caenorhabditis elegans HIM-18/SLX-4 interacts with SLX-1 and XPF-1 and maintains genomic integrity in the germline by processing recombination intermediates.

PubMed

Saito, Takamune T; Youds, Jillian L; Boulton, Simon J; Colaiácovo, Monica P

2009-11-01

Homologous recombination (HR) is essential for the repair of blocked or collapsed replication forks and for the production of crossovers between homologs that promote accurate meiotic chromosome segregation. Here, we identify HIM-18, an ortholog of MUS312/Slx4, as a critical player required in vivo for processing late HR intermediates in Caenorhabditis elegans. DNA damage sensitivity and an accumulation of HR intermediates (RAD-51 foci) during premeiotic entry suggest that HIM-18 is required for HR-mediated repair at stalled replication forks. A reduction in crossover recombination frequencies-accompanied by an increase in HR intermediates during meiosis, germ cell apoptosis, unstable bivalent attachments, and subsequent chromosome nondisjunction-support a role for HIM-18 in converting HR intermediates into crossover products. Such a role is suggested by physical interaction of HIM-18 with the nucleases SLX-1 and XPF-1 and by the synthetic lethality of him-18 with him-6, the C. elegans BLM homolog. We propose that HIM-18 facilitates processing of HR intermediates resulting from replication fork collapse and programmed meiotic DSBs in the C. elegans germline.

Caenorhabditis elegans HIM-18/SLX-4 Interacts with SLX-1 and XPF-1 and Maintains Genomic Integrity in the Germline by Processing Recombination Intermediates

PubMed Central

Saito, Takamune T.; Youds, Jillian L.; Boulton, Simon J.; Colaiácovo, Monica P.

2009-01-01

Homologous recombination (HR) is essential for the repair of blocked or collapsed replication forks and for the production of crossovers between homologs that promote accurate meiotic chromosome segregation. Here, we identify HIM-18, an ortholog of MUS312/Slx4, as a critical player required in vivo for processing late HR intermediates in Caenorhabditis elegans. DNA damage sensitivity and an accumulation of HR intermediates (RAD-51 foci) during premeiotic entry suggest that HIM-18 is required for HR–mediated repair at stalled replication forks. A reduction in crossover recombination frequencies—accompanied by an increase in HR intermediates during meiosis, germ cell apoptosis, unstable bivalent attachments, and subsequent chromosome nondisjunction—support a role for HIM-18 in converting HR intermediates into crossover products. Such a role is suggested by physical interaction of HIM-18 with the nucleases SLX-1 and XPF-1 and by the synthetic lethality of him-18 with him-6, the C. elegans BLM homolog. We propose that HIM-18 facilitates processing of HR intermediates resulting from replication fork collapse and programmed meiotic DSBs in the C. elegans germline. PMID:19936019

Dynamic measurement of fluorescent proteins spectral distribution on virus infected cells

NASA Astrophysics Data System (ADS)

Lee, Ja-Yun; Wu, Ming-Xiu; Kao, Chia-Yun; Wu, Tzong-Yuan; Hsu, I.-Jen

2006-09-01

We constructed a dynamic spectroscopy system that can simultaneously measure the intensity and spectral distributions of samples with multi-fluorophores in a single scan. The system was used to monitor the fluorescence distribution of cells infected by the virus, which is constructed by a recombinant baculoviruses, vAcD-Rhir-E, containing the red and green fluorescent protein gene that can simultaneously produce dual fluorescence in recombinant virus-infected Spodoptera frugiperda 21 cells (Sf21) under the control of a polyhedrin promoter. The system was composed of an excitation light source, a scanning system and a spectrometer. We also developed an algorithm and fitting process to analyze the pattern of fluorescence distribution of the dual fluorescence produced in the recombinant virus-infected cells. All the algorithm and calculation are automatically processed in a visualized scanning program and can monitor the specific region of sample by calculating its intensity distribution. The spectral measurement of each pixel was performed at millisecond range and the two dimensional distribution of full spectrum was recorded within several seconds. We have constructed a dynamic spectroscopy system to monitor the process of virus-infection of cells. The distributions of the dual fluorescence were simultaneously measured at micrometer resolution.

Genetic recombination induced by DNA double-strand break in bacteriophage T4: nature of the left/right bias.

PubMed

Shcherbakov, Victor P; Shcherbakova, Tamara; Plugina, Lidiya; Sizova, Svetlana; Kudryashova, Elena; Granovsky, Igor

2008-06-01

The experimental system combining double-strand breaks (DSBs), produced site-specifically by SegC endonuclease, with the famous advantages of the bacteriophage T4 rII mutant recombination analysis was used here to elucidate the origin of the recombination bias on two sides of the DSB, especially pronounced in gene 39 (topoisomerase II) and gene 59 (41-helicase loader) mutants. Three sources were found to contribute to the bias: (1) the SegC endonuclease may remain bound to the end of the broken DNA and thus protect it from exonuclease degradation; (2) in heteroduplex heterozygotes (HHs), arising as the recombinant products in the left-hand crosses, the transcribed strands are of rII mutant phenotype, so they, in contrast to the right-hand HHs, do not produce plaques on the lawn of the lambda-lysogenic host; and (3) the intrinsic polarity of T4 chromosome, reflected in transcription, may be a cause for discrimination of promoter-proximal and promoter-distal DNA sequences. It is shown that the apparent recombination bias does not imply one-sidedness of the DSB repair but just reflects a different depth of the end processing. It is inferred that the cause, underlying the "intrinsic" bias, might be interference between strand exchange and transcription. Topoisomerase and helicase functions are necessary to turn the process in favor of strand exchange. The idea is substantiated that the double-stranded to single-stranded DNA transition edge (not ss-DNA tip) serves as an actual recombinogenic element.

Coordination of Recombination with Meiotic Progression in the Caenorhabditis elegans Germline by KIN-18, a TAO Kinase That Regulates the Timing of MPK-1 Signaling

PubMed Central

Yin, Yizhi; Donlevy, Sean; Smolikove, Sarit

2016-01-01

Meiosis is a tightly regulated process requiring coordination of diverse events. A conserved ERK/MAPK-signaling cascade plays an essential role in the regulation of meiotic progression. The Thousand And One kinase (TAO) kinase is a MAPK kinase kinase, the meiotic role of which is unknown. We have analyzed the meiotic functions of KIN-18, the homolog of mammalian TAO kinases, in Caenorhabditis elegans. We found that KIN-18 is essential for normal meiotic progression; mutants exhibit accelerated meiotic recombination as detected both by analysis of recombination intermediates and by crossover outcome. In addition, ectopic germ-cell differentiation and enhanced levels of apoptosis were observed in kin-18 mutants. These defects correlate with ectopic activation of MPK-1 that includes premature, missing, and reoccurring MPK-1 activation. Late progression defects in kin-18 mutants are suppressed by inhibiting an upstream activator of MPK-1 signaling, KSR-2. However, the acceleration of recombination events observed in kin-18 mutants is largely MPK-1-independent. Our data suggest that KIN-18 coordinates meiotic progression by modulating the timing of MPK-1 activation and the progression of recombination events. The regulation of the timing of MPK-1 activation ensures the proper timing of apoptosis and is required for the formation of functional oocytes. Meiosis is a conserved process; thus, revealing that KIN-18 is a novel regulator of meiotic progression in C. elegans would help to elucidate TAO kinase’s role in germline development in higher eukaryotes. PMID:26510792

Hybrid Perovskites for Photovoltaics: Charge-Carrier Recombination, Diffusion, and Radiative Efficiencies.

PubMed

Johnston, Michael B; Herz, Laura M

2016-01-19

Photovoltaic (PV) devices that harvest the energy provided by the sun have great potential as renewable energy sources, yet uptake has been hampered by the increased cost of solar electricity compared with fossil fuels. Hybrid metal halide perovskites have recently emerged as low-cost active materials in PV cells with power conversion efficiencies now exceeding 20%. Rapid progress has been achieved over only a few years through improvements in materials processing and device design. In addition, hybrid perovskites appear to be good light emitters under certain conditions, raising the prospect of applications in low-cost light-emitting diodes and lasers. Further optimization of such hybrid perovskite devices now needs to be supported by a better understanding of how light is converted into electrical currents and vice versa. This Account provides an overview of charge-carrier recombination and mobility mechanisms encountered in such materials. Optical-pump-terahertz-probe (OPTP) photoconductivity spectroscopy is an ideal tool here, because it allows the dynamics of mobile charge carriers inside the perovskite to be monitored following excitation with a short laser pulse whose photon energy falls into the range of the solar spectrum. We first review our insights gained from transient OPTP and photoluminescence spectroscopy on the mechanisms dominating charge-carrier recombination in these materials. We discuss that mono-molecular charge-recombination predominantly originates from trapping of charges, with trap depths being relatively shallow (tens of millielectronvolts) for hybrid lead iodide perovskites. Bimolecular recombination arises from direct band-to-band electron-hole recombination and is found to be in significant violation of the simple Langevin model. Auger recombination exhibits links with electronic band structure, in accordance with its requirement for energy and momentum conservation for all charges involved. We further discuss charge-carrier mobility values extracted from OPTP measurements and their dependence on perovskite composition and morphology. The significance of the reviewed charge-carrier recombination and mobility parameters is subsequently evaluated in terms of the charge-carrier diffusion lengths and radiative efficiencies that may be obtained for such hybrid perovskites. We particularly focus on calculating such quantities in the limit of ultra-low trap-related recombination, which has not yet been demonstrated but could be reached through further advances in material processing. We find that for thin films of hybrid lead iodide perovskites with typical charge-carrier mobilities of ∼30cm(2)/(V s), charge-carrier diffusion lengths at solar (AM1.5) irradiation are unlikely to exceed ∼10 μm even if all trap-related recombination is eliminated. We further examine the radiative efficiency for hybrid lead halide perovskite films and show that if high efficiencies are to be obtained for intermediate charge-carrier densities (n ≈ 10(14) cm(-3)) trap-related recombination lifetimes will have to be enhanced well into the microsecond range.

Surface modifications of photoanodes in dye sensitized solar cells: enhanced light harvesting and reduced recombination

NASA Astrophysics Data System (ADS)

Saxena, Vibha; Aswal, D. K.

2015-06-01

In a quest to harvest solar power, dye-sensitized solar cells (DSSCs) have potential for low-cost eco-friendly photovoltaic devices. The major processes which govern the efficiency of a DSSC are photoelectron generation, injection of photo-generated electrons to the conduction band (CB) of the mesoporous nanocrystalline semiconductor (nc-SC); transport of CB electrons through nc-SC and subsequent collection of CB electrons at the counter electrode (CE) through the external circuit; and dye regeneration by redox couple or hole transport layer (HTL). Most of these processes occur at various interfaces of the photoanode. In addition, recombination losses of photo-generated electrons with either dye or redox molecules take place at the interfaces. Therefore, one of the key requirements for high efficiency is to improve light harvesting of the photoanode and to reduce the recombination losses at various interfaces. In this direction, surface modification of the photoanode is the simplest method among the various other approaches available in the literature. In this review, we present a comprehensive discussion on surface modification of the photoanode, which has been adopted in the literature for not only enhancing light harvesting but also reducing recombination. Various approaches towards surface modification of the photoanode discussed are (i) fluorine-doped tin oxide (FTO)/nc-SC interface modified via a compact layer of semiconductor material which blocks exposed sites of FTO to electrolyte (or HTL), (ii) nc-SC/dye interface modification either through acid treatment resulting in enhanced dye loading due to a positively charged surface or by depositing insulating/semiconducting blocking layer on the nc-SC surface, which acts as a tunneling barrier for recombination, (iii) nc-SC/dye interface modified by employing co-adsorbents which helps in reducing the dye aggregation and thereby recombination, and (iv) dye/electrolyte (or dye/HTL) interface modification using additives which provides surface passivation as well as positive movement of the nc-SC Fermi level owing to negative charge at the surface and hence improves light harvesting and reduced recombination. Finally, we discuss the advantages and disadvantages of various approaches towards high-efficiency DSSCs.

Soluble expression of an amebic cysteine protease in the cytoplasm of Escherichia coli SHuffle Express cells and purification of active enzyme.

PubMed

Jalomo-Khayrova, Ekaterina; Mares, Rosa E; Muñoz, Patricia L A; Meléndez-López, Samuel G; Rivero, Ignacio A; Ramos, Marco A

2018-04-03

Recombinant production of amebic cysteine proteases using Escherichia coli cells as the bacterial system has become a challenging effort, with protein insolubility being the most common issue. Since many of these enzymes need a native conformation stabilized by disulfide bonds, an elaborate process of oxidative folding is usually demanded to get a functional protein. The cytoplasm of E. coli SHuffle Express cells owns an enhanced ability to properly fold proteins with disulfide bonds. Because of this cellular feature, it was possible to assume that this strain represents a reliable expression system and worthwhile been considered as an efficient bacterial host for the recombinant production of amebic cysteine proteases. Using E. coli SHuffle Express cells as the bacterial system, we efficiently produce soluble recombinant EhCP1protein. Enzymatic and inhibition analyses revealed that it exhibits proper catalytic abilities, proceeds effectively over the substrate (following an apparent Michaelis-Menten kinetics), and displays a typical inhibition profile. We report the first feasibility study of the recombinant production of amebic cysteine proteases using E. coli SHuffle Express as the bacterial host. We present a simple protocol for the recombinant expression and purification of fully soluble and active EhCP1 enzyme. We confirm the suitability of recombinant EhCP1 as a therapeutic target. We propose an approachable bacterial system for the recombinant production of amebic proteins, particularly for those with a need for proper oxidative folding.

Mitochondrial Recombination and Introgression during Speciation by Hybridization.

PubMed

Leducq, Jean-Baptiste; Henault, Mathieu; Charron, Guillaume; Nielly-Thibault, Lou; Terrat, Yves; Fiumera, Heather L; Shapiro, B Jesse; Landry, Christian R

2017-08-01

Genome recombination is a major source of genotypic diversity and contributes to adaptation and speciation following interspecies hybridization. The contribution of recombination in these processes has been thought to be largely limited to the nuclear genome because organelles are mostly uniparentally inherited in animals and plants, which prevents recombination. Unicellular eukaryotes such as budding yeasts do, however, transmit mitochondria biparentally, suggesting that during hybridization, both parents could provide alleles that contribute to mitochondrial functions such as respiration and metabolism in hybrid populations or hybrid species. We examined the dynamics of mitochondrial genome transmission and evolution during speciation by hybridization in the natural budding yeast Saccharomyces paradoxus. Using population-scale mitochondrial genome sequencing in two endemic North American incipient species SpB and SpC and their hybrid species SpC*, we found that both parental species contributed to the hybrid mitochondrial genome through recombination. We support our findings by showing that mitochondrial recombination between parental types is frequent in experimental crosses that recreate the early step of this speciation event. In these artificial hybrids, we observed that mitochondrial genome recombination enhances phenotypic variation among diploid hybrids, suggesting that it could play a role in the phenotypic differentiation of hybrid species. Like the nuclear genome, the mitochondrial genome can, therefore, also play a role in hybrid speciation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Implication of RuvABC and RecG in homologous recombination in Streptomyces ambofaciens.

PubMed

Hoff, Grégory; Bertrand, Claire; Piotrowski, Emilie; Thibessard, Annabelle; Leblond, Pierre

2017-01-01

Most bacterial organisms rely on homologous recombination to repair DNA double-strand breaks and for the post-replicative repair of DNA single-strand gaps. Homologous recombination can be divided into three steps: (i) a pre-synaptic step in which the DNA 3'-OH ends are processed, (ii) a recA-dependent synaptic step allowing the invasion of an intact copy and the formation of Holliday junctions, and (iii) a post-synaptic step consisting of migration and resolution of these junctions. Currently, little is known about factors involved in homologous recombination, especially for the post-synaptic step. In Escherichia coli, branch migration and resolution are performed by the RuvABC complex, but could also rely on the RecG helicase in a redundant manner. In this study, we show that recG and ruvABC are well-conserved among Streptomyces. ΔruvABC, ΔrecG and ΔruvABC ΔrecG mutant strains were constructed. ΔruvABC ΔrecG is only slightly affected by exposure to DNA damage (UV). We also show that conjugational recombination decreases in the absence of RuvABC and RecG, but that intra-chromosomal recombination is not affected. These data suggest that RuvABC and RecG are indeed involved in homologous recombination in Streptomyces ambofaciens and that alternative factors are able to take over Holliday junction in Streptomyces. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Collective flow measurements with HADES in Au+Au collisions at 1.23A GeV

NASA Astrophysics Data System (ADS)

Kardan, Behruz; Hades Collaboration

2017-11-01

HADES has a large acceptance combined with a good mass-resolution and therefore allows the study of dielectron and hadron production in heavy-ion collisions with unprecedented precision. With the statistics of seven billion Au-Au collisions at 1.23A GeV recorded in 2012, the investigation of higher-order flow harmonics is possible. At the BEVALAC and SIS18 directed and elliptic flow has been measured for pions, charged kaons, protons, neutrons and fragments, but higher-order harmonics have not yet been studied. They provide additional important information on the properties of the dense hadronic medium produced in heavy-ion collisions. We present here a high-statistics, multidifferential measurement of v1 and v2 for protons in Au+Au collisions at 1.23A GeV.

Direct virtual photon production in Au+Au collisions at √{sNN} = 200 GeV

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Ajitanand, N. N.; Alekseev, I.; Anderson, D. M.; Aoyama, R.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Ashraf, M. U.; Attri, A.; Averichev, G. S.; Bai, X.; Bairathi, V.; Behera, A.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandenburg, J. D.; Brandin, A. V.; Brown, D.; Bunzarov, I.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Campbell, J. M.; Cebra, D.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chankova-Bunzarova, N.; Chatterjee, A.; Chattopadhyay, S.; Chen, X.; Chen, X.; Chen, J. H.; Cheng, J.; Cherney, M.; Christie, W.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Elsey, N.; Engelage, J.; Eppley, G.; Esha, R.; Esumi, S.; Evdokimov, O.; Ewigleben, J.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Federicova, P.; Fedorisin, J.; Feng, Z.; Filip, P.; Finch, E.; Fisyak, Y.; Flores, C. E.; Fujita, J.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, A.; Gupta, S.; Guryn, W.; Hamad, A. I.; Hamed, A.; Harlenderova, A.; Harris, J. W.; He, L.; Heppelmann, S.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Horvat, S.; Huang, B.; Huang, T.; Huang, H. Z.; Huang, X.; Humanic, T. J.; Huo, P.; Igo, G.; Jacobs, W. W.; Jentsch, A.; Jia, J.; Jiang, K.; Jowzaee, S.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z.; Kikoła, D. P.; Kisel, I.; Kisiel, A.; Kochenda, L.; Kocmanek, M.; Kollegger, T.; Kosarzewski, L. K.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kulathunga, N.; Kumar, L.; Kvapil, J.; Kwasizur, J. H.; Lacey, R.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, W.; Li, X.; Li, C.; Li, Y.; Lidrych, J.; Lin, T.; Lisa, M. A.; Liu, Y.; Liu, F.; Liu, H.; Liu, P.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, S.; Luo, X.; Ma, G. L.; Ma, Y. G.; Ma, L.; Ma, R.; Magdy, N.; Majka, R.; Mallick, D.; Margetis, S.; Markert, C.; Matis, H. S.; Meehan, K.; Mei, J. C.; Miller, Z. W.; Minaev, N. G.; Mioduszewski, S.; Mishra, D.; Mizuno, S.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Mustafa, M. K.; Nasim, Md.; Nayak, T. K.; Nelson, J. M.; Nie, M.; Nigmatkulov, G.; Niida, T.; Nogach, L. V.; Nonaka, T.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V. A.; Olvitt, D.; Page, B. S.; Pak, R.; Pandit, Y.; Panebratsev, Y.; Pawlik, B.; Pei, H.; Perkins, C.; Pile, P.; Pluta, J.; Poniatowska, K.; Porter, J.; Posik, M.; Poskanzer, A. M.; Pruthi, N. K.; Przybycien, M.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Ray, R. L.; Reed, R.; Rehbein, M. J.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Roth, J. D.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Salur, S.; Sandweiss, J.; Saur, M.; Schambach, J.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Schweid, B. R.; Seger, J.; Sergeeva, M.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, A.; Sharma, M. K.; Shen, W. Q.; Shi, Z.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Singha, S.; Skoby, M. J.; Smirnov, N.; Smirnov, D.; Solyst, W.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Strikhanov, M.; Stringfellow, B.; Sugiura, T.; Sumbera, M.; Summa, B.; Sun, Y.; Sun, X. M.; Sun, X.; Surrow, B.; Svirida, D. N.; Tang, A. H.; Tang, Z.; Taranenko, A.; Tarnowsky, T.; Tawfik, A.; Thäder, J.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Todoroki, T.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Trzeciak, B. A.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vasiliev, A. N.; Videbæk, F.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, G.; Wang, Y.; Wang, F.; Wang, Y.; Webb, J. C.; Webb, G.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y.; Xiao, Z. G.; Xie, W.; Xie, G.; Xu, J.; Xu, N.; Xu, Q. H.; Xu, Y. F.; Xu, Z.; Yang, Y.; Yang, Q.; Yang, C.; Yang, S.; Ye, Z.; Ye, Z.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, Z.; Zhang, X. P.; Zhang, J. B.; Zhang, S.; Zhang, J.; Zhang, Y.; Zhang, J.; Zhang, S.; Zhao, J.; Zhong, C.; Zhou, L.; Zhou, C.; Zhu, X.; Zhu, Z.; Zyzak, M.

2017-07-01

We report the direct virtual photon invariant yields in the transverse momentum ranges 1 6 GeV / c the production follows TAA scaling. Model calculations with contributions from thermal radiation and initial hard parton scattering are consistent within uncertainties with the direct virtual photon invariant yield.

The Differential cross section distribution of Drell-Yan dielectron pairs in the z boson mass region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Jiyeon

We report on a measurement of the rapidity distribution, dσ/dy, for Z=Drell-Yan → ee events produced in pmore » $$\\bar{p}$$ collisions at √s = 1.96 TeV. The data sample consists of 2.13 fb -1 corresponding to about 160,000 Z/Drell-Yan → ee candidates in the Z boson mass region collected by the Collider Detector at Fermilab. The dσ/dy distribution, which is measured over the full kinematic range for e +e - pairs in the invariant mass range 66 < M ee < 116 GeV/c 2, is compared with theory predictions. There is good agreement between the data and predictions of Quantum Chromodynamics in Next to Leading Order with the CTEQ6.1M Parton Distribution Functions.« less

Studying Strangeness Production with HADES

NASA Astrophysics Data System (ADS)

Schuldes, Heidi

2018-02-01

The High-Acceptance DiElectron Spectrometer (HADES) operates in the 1 - 2A GeV energy regime in fixed target experiments to explore baryon-rich strongly interacting matter in heavy-ion collisions at moderate temperatures with rare and penetrating probes. We present results on the production of strange hadrons below their respective NN threshold energy in Au+Au collisions at 1.23A GeV ( = 2.4 GeV). Special emphasis is put on the enhanced feed-down contribution of ϕ mesons to the inclusive yield of K- and its implication on the measured spectral shape of K-. Furthermore, we investigate global properties of the system, confronting the measured hadron yields and transverse mass spectra with a Statistical Hadronization Model (SHM) and a blastwave parameterization, respectively. These supplement the world data of the chemical and kinetic freeze-out temperatures.

The dissociation and recombination rates of CH4 through the Ni(111) surface: The effect of lattice motion

NASA Astrophysics Data System (ADS)

Wang, Wenji; Zhao, Yi

2017-07-01

Methane dissociation is a prototypical system for the study of surface reaction dynamics. The dissociation and recombination rates of CH4 through the Ni(111) surface are calculated by using the quantum instanton method with an analytical potential energy surface. The Ni(111) lattice is treated rigidly, classically, and quantum mechanically so as to reveal the effect of lattice motion. The results demonstrate that it is the lateral displacements rather than the upward and downward movements of the surface nickel atoms that affect the rates a lot. Compared with the rigid lattice, the classical relaxation of the lattice can increase the rates by lowering the free energy barriers. For instance, at 300 K, the dissociation and recombination rates with the classical lattice exceed the ones with the rigid lattice by 6 and 10 orders of magnitude, respectively. Compared with the classical lattice, the quantum delocalization rather than the zero-point energy of the Ni atoms further enhances the rates by widening the reaction path. For instance, the dissociation rate with the quantum lattice is about 10 times larger than that with the classical lattice at 300 K. On the rigid lattice, due to the zero-point energy difference between CH4 and CD4, the kinetic isotope effects are larger than 1 for the dissociation process, while they are smaller than 1 for the recombination process. The increasing kinetic isotope effect with decreasing temperature demonstrates that the quantum tunneling effect is remarkable for the dissociation process.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaera, Francisco; Bardeen, Christopher J.; Yin, Yadong

The overall goal of this project has been to develop new a new and novel class of well-characterized nanostructured Metal@TiO 2 core-shell and yolk-shell photocatalysts to address two fundamental issues presently limiting this field: (1) the fast recombination of electron-hole pairs once generated by light absorption, and (2) the recombination of H 2 and O 2 on the metal surface once produced. These model samples are also used to study the fundamentals of the photocatalytic processes.

Resonant recombination and autoionization in electron-ion collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mueller, A.

1990-06-01

The occurence of resonances in elastic and inelastic electron-ion collisions is discussed. Resonant processes involve excitation of the ion with simultaneous capture of the initially free electron. The decay mechanism subsequent to the formation of the intermediate multiply excited state determines whether a resonance is found in recombination, excitation, elastic scattering, in single or even in multiple ionization. This review concentrates on resonances in the ionization channel. Correlated two-electron transitions are considered.

n-B-pi-p Superlattice Infrared Detector

NASA Technical Reports Server (NTRS)

Ting, David Z.; Bandara, Sumith V.; Hill, Cory J.; Gunapala, Sarath D.

2011-01-01

A specially designed barrier (B) is inserted at the n-pi junction [where most GR (generation-recombination) processes take place] in the standard n-pi-p structure to substantially reduce generation-recombination dark currents. The resulting n-Bpi- p structure also has reduced tunneling dark currents, thereby solving some of the limitations to which current type II strained layer superlattice infrared detectors are prone. This innovation is compatible with common read-out integrated circuits (ROICs).

pLS010 plasmid vector

DOEpatents

Lacks, Sanford A.; Balganesh, Tanjore S.

1988-01-01

Disclosed is recombinant plasmid pLS101, consisting essentially of a 2.0 Kb malM gene fragment ligated to a 4.4 Kb T.sub.c r DNA fragment, which is particularly useful for transforming Gram-positive bacteria. This plasmid contains at least four restriction sites suitable for inserting exogeneous gene sequences. Also disclosed is a method for plasmid isolation by penicillin selection, as well as processes for enrichment of recombinant plasmids in Gram-positive bacterial systems.

Achieving 14.4% Alcohol-Based Solution-Processed Cu(In,Ga)(S,Se)2 Thin Film Solar Cell through Interface Engineering.

PubMed

Park, Gi Soon; Chu, Van Ben; Kim, Byoung Woo; Kim, Dong-Wook; Oh, Hyung-Suk; Hwang, Yun Jeong; Min, Byoung Koun

2018-03-28

An optimization of band alignment at the p-n junction interface is realized on alcohol-based solution-processed Cu(In,Ga)(S,Se) 2 (CIGS) thin film solar cells, achieving a power-conversion-efficiency (PCE) of 14.4%. To obtain a CIGS thin film suitable for interface engineering, we designed a novel "3-step chalcogenization process" for Cu 2- x Se-derived grain growth and a double band gap grading structure. Considering S-rich surface of the CIGS thin film, an alternative ternary (Cd,Zn)S buffer layer is adopted to build favorable "spike" type conduction band alignment instead of "cliff" type. Suppression of interface recombination is elucidated by comparing recombination activation energies using a dark J- V- T analysis.

Construction and characterization of recombinant flaviviruses bearing insertions between E and NS1 genes

PubMed Central

Bonaldo, Myrna C; Mello, Samanta M; Trindade, Gisela F; Rangel, Aymara A; Duarte, Adriana S; Oliveira, Prisciliana J; Freire, Marcos S; Kubelka, Claire F; Galler, Ricardo

2007-01-01

Background The yellow fever virus, a member of the genus Flavivirus, is an arthropod-borne pathogen causing severe disease in humans. The attenuated yellow fever 17D virus strain has been used for human vaccination for 70 years and has several characteristics that are desirable for the development of new, live attenuated vaccines. We described here a methodology to construct a viable, and immunogenic recombinant yellow fever 17D virus expressing a green fluorescent protein variant (EGFP). This approach took into account the presence of functional motifs and amino acid sequence conservation flanking the E and NS1 intergenic region to duplicate and fuse them to the exogenous gene and thereby allow the correct processing of the viral polyprotein precursor. Results YF 17D EGFP recombinant virus was grew in Vero cells and reached a peak titer of approximately 6.45 ± 0.4 log10 PFU/mL at 96 hours post-infection. Immunoprecipitation and confocal laser scanning microscopy demonstrated the expression of the EGFP, which was retained in the endoplasmic reticulum and not secreted from infected cells. The association with the ER compartment did not interfere with YF assembly, since the recombinant virus was fully competent to replicate and exit the cell. This virus was genetically stable up to the tenth serial passage in Vero cells. The recombinant virus was capable to elicit a neutralizing antibody response to YF and antibodies to EGFP as evidenced by an ELISA test. The applicability of this cloning strategy to clone gene foreign sequences in other flavivirus genomes was demonstrated by the construction of a chimeric recombinant YF 17D/DEN4 virus. Conclusion This system is likely to be useful for a broader live attenuated YF 17D virus-based vaccine development for human diseases. Moreover, insertion of foreign genes into the flavivirus genome may also allow in vivo studies on flavivirus cell and tissue tropism as well as cellular processes related to flavivirus infection. PMID:17971212

RICO: A NEW APPROACH FOR FAST AND ACCURATE REPRESENTATION OF THE COSMOLOGICAL RECOMBINATION HISTORY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fendt, W. A.; Wandelt, B. D.; Chluba, J.

2009-04-15

We present RICO, a code designed to compute the ionization fraction of the universe during the epoch of hydrogen and helium recombination with an unprecedented combination of speed and accuracy. This is accomplished by training the machine learning code PICO on the calculations of a multilevel cosmological recombination code which self-consistently includes several physical processes that were neglected previously. After training, RICO is used to fit the free electron fraction as a function of the cosmological parameters. While, for example, at low redshifts (z {approx}< 900), much of the net change in the ionization fraction can be captured by loweringmore » the hydrogen fudge factor in RECFAST by about 3%, RICO provides a means of effectively using the accurate ionization history of the full recombination code in the standard cosmological parameter estimation framework without the need to add new or refined fudge factors or functions to a simple recombination model. Within the new approach presented here, it is easy to update RICO whenever a more accurate full recombination code becomes available. Once trained, RICO computes the cosmological ionization history with negligible fitting error in {approx}10 ms, a speedup of at least 10{sup 6} over the full recombination code that was used here. Also RICO is able to reproduce the ionization history of the full code to a level well below 0.1%, thereby ensuring that the theoretical power spectra of cosmic microwave background (CMB) fluctuations can be computed to sufficient accuracy and speed for analysis from upcoming CMB experiments like Planck. Furthermore, it will enable cross-checking different recombination codes across cosmological parameter space, a comparison that will be very important in order to assure the accurate interpretation of future CMB data.« less

Meiotic recombination modulates the structure and dynamics of the synaptonemal complex during C. elegans meiosis

PubMed Central

2017-01-01

During meiotic prophase, a structure called the synaptonemal complex (SC) assembles at the interface between aligned pairs of homologous chromosomes, and crossover recombination events occur between their DNA molecules. Here we investigate the inter-relationships between these two hallmark features of the meiotic program in the nematode C. elegans, revealing dynamic properties of the SC that are modulated by recombination. We demonstrate that the SC incorporates new subunits and switches from a more highly dynamic/labile state to a more stable state as germ cells progress through the pachytene stage of meiotic prophase. We further show that the more dynamic state of the SC is prolonged in mutants where meiotic recombination is impaired. Moreover, in meiotic mutants where recombination intermediates are present in limiting numbers, SC central region subunits become preferentially stabilized on the subset of chromosome pairs that harbor a site where pro-crossover factors COSA-1 and MutSγ are concentrated. Polo-like kinase PLK-2 becomes preferentially localized to the SCs of chromosome pairs harboring recombination sites prior to the enrichment of SC central region proteins on such chromosomes, and PLK-2 is required for this enrichment to occur. Further, late pachytene nuclei in a plk-2 mutant exhibit the more highly dynamic SC state. Together our data demonstrate that crossover recombination events elicit chromosome-autonomous stabilizing effects on the SC and implicate PLK-2 in this process. We discuss how this recombination-triggered modulation of SC state might contribute to regulatory mechanisms that operate during meiosis to ensure the formation of crossovers while at the same time limiting their numbers. PMID:28339470

Temperature dependent characteristics of a recombinant infectious hematopoietic necrosis virus glycoprotein produced in insect cells.

PubMed

Cain, K D; Byrne, K M; Brassfield, A L; LaPatra, S E; Ristow, S S

1999-04-15

A recombinant infectious hematopoietic necrosis virus (IHNV) glycoprotein (G protein) was produced in insect cells using a baculovirus vector (Autographa californica nuclear polyhedrosis virus). Characteristics of this protein were evaluated in relation to native viral G protein. A full-length (1.6 kb) cDNA copy of the glycoprotein gene of IHNV was inserted into the baculovirus vector under control of the polyhedrin promoter. High levels of G protein (approximately 0.5 microgram/1 x 10(5) cells) were produced in Spodoptera frugiperda (Sf9) cells following recombinant baculovirus infection. Analysis of cell lysates by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot revealed a recombinant IHNV G of slightly higher mobility on the gel than the viral G protein. Differences in mobility were abrogated by endoglycosidase treatment. When the recombinant G protein was produced in insect cells at 20 degrees C (RecGlow), immunostaining and cell fusion activity demonstrated surface localization of the protein. In contrast, when recombinant protein was produced at 27 degrees C (RecGhigh), G protein was sequestered within the cell, suggesting that at the 2 different temperatures processing differences may exist. Eleven monoclonal antibodies (MAbs) were tested by immunoblotting for reactivity to the recombinant G protein. All 11 MAbs reacted to the reduced proteins. Four MAbs recognized both RecGhigh and RecGlow under non-reducing conditions; however, 1 neutralizing MAb (92A) recognized RecGlow but failed to react to RecGhigh under non-reducing conditions. This suggests that differences exist between RecGlow and RecGhigh which may have implications in the development of a properly folded recombinant G protein with the ability to elicit protective immunity in fish.

Generation and CRISPR/Cas9 editing of transformed progenitor B cells as a pseudo-physiological system to study DNA repair gene function in V(D)J recombination.

PubMed

Lenden Hasse, Hélène; Lescale, Chloé; Bianchi, Joy J; Yu, Wei; Bedora-Faure, Marie; Deriano, Ludovic

2017-12-01

Antigen receptor gene assembly is accomplished in developing lymphocytes by the V(D)J recombination reaction, which can be separated into two steps: DNA cleavage by the recombination-activating gene (RAG) nuclease and joining of DNA double strand breaks (DSBs) by components of the nonhomologous end joining (NHEJ) pathway. Deficiencies for NHEJ factors can result in immunodeficiency and a propensity to accumulate genomic instability, thus highlighting the importance of identifying all players in this process and deciphering their functions. Bcl2 transgenic v-Abl kinase-transformed pro-B cells provide a pseudo-physiological cellular system to study V(D)J recombination. Treatment of v-Abl/Bcl2 pro-B cells with the Abl kinase inhibitor Imatinib leads to G1 cell cycle arrest, the rapid induction of Rag1/2 gene expression and V(D)J recombination. In this system, the Bcl2 transgene alleviates Imatinib-induced apoptosis enabling the analysis of induced V(D)J recombination. Although powerful, the use of mouse models carrying the Bcl2 transgene for the generation of v-Abl pro-B cell lines is time and money consuming. Here, we describe a method for generating v-Abl/Bcl2 pro-B cell lines from wild type mice and for performing gene knock-out using episomal CRISPR/Cas9 targeting vectors. Using this approach, we generated distinct NHEJ-deficient pro-B cell lines and quantified V(D)J recombination levels in these cells. Furthermore, this methodology can be adapted to generate pro-B cell lines deficient for any gene suspected to play a role in V(D)J recombination, and more generally DSB repair. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Recombination between vaccine and field strains of canine parvovirus is revealed by isolation of virus in canine and feline cell cultures.

PubMed

Mochizuki, Masami; Ohshima, Takahisa; Une, Yumi; Yachi, Akiko

2008-12-01

Canine parvovirus type 2 (CPV) is a pathogen that causes severe hemorrhagic gastroenteritis with a high fatality rate in pups worldwide. Since CPV emerged in the late 1970s, its origin has been explored with the conclusion that CPV originated from feline panleukopenia virus or a closely related virus. Both high mutation rate and recombination are assumed to be key factors in the evolution of parvoviruses. Here we provide evidence for natural recombination in CPV isolated from dogs in cell culture. Antigenic and genetic properties of isolates from 10 diseased pups were elucidated. Six pups had been vaccinated beforehand with live combined vaccine containing original antigenic type CPV (CPV-2). Six isolates recovered from 4 vaccinated pups in cell cultures were found to contain either CPV-2 or CPV-2-like viruses. The other isolates, including all those from non-vaccinated pups, were CPV-2b viruses. Antigenic typing of two CPV-2-like isolates, 03-029/M and 1887/f, with a monoclonal antibody panel suggested they were a mixture of CPV-2 and CPV-2a (03-029/M) and a recombinant of CPV-2 and CPV-2b (1887/f). Genetic analysis of the VP1 gene indicated that isolate 03-029/M was a mixture of CPV-2, CPV-2a and a recombinant of CPV-2 and CPV-2a viruses, while isolate 1887/f was composed of a recombinant of CPV-2 and CPV-2b viruses. This is the first demonstration of natural CPV recombination in the field and suggests that recombination in the evolution of CPV is a more frequent and important process than previously believed.

Continuous Manufacturing of Recombinant Therapeutic Proteins: Upstream and Downstream Technologies.

PubMed

Patil, Rohan; Walther, Jason

2017-03-07

Continuous biomanufacturing of recombinant therapeutic proteins offers several potential advantages over conventional batch processing, including reduced cost of goods, more flexible and responsive manufacturing facilities, and improved and consistent product quality. Although continuous approaches to various upstream and downstream unit operations have been considered and studied for decades, in recent years interest and application have accelerated. Researchers have achieved increasingly higher levels of process intensification, and have also begun to integrate different continuous unit operations into larger, holistically continuous processes. This review first discusses approaches for continuous cell culture, with a focus on perfusion-enabling cell separation technologies including gravitational, centrifugal, and acoustic settling, as well as filtration-based techniques. We follow with a review of various continuous downstream unit operations, covering categories such as clarification, chromatography, formulation, and viral inactivation and filtration. The review ends by summarizing case studies of integrated and continuous processing as reported in the literature.

High-performance recombinant protein production with Escherichia coli in continuously operated cascades of stirred-tank reactors.

PubMed

Schmideder, Andreas; Weuster-Botz, Dirk

2017-07-01

The microbial expression of intracellular, recombinant proteins in continuous bioprocesses suffers from low product concentrations. Hence, a process for the intracellular production of photoactivatable mCherry with Escherichia coli in a continuously operated cascade of two stirred-tank reactors was established to separate biomass formation (first reactor) and protein expression (second reactor) spatially. Cascades of miniaturized stirred-tank reactors were implemented, which enable the 24-fold parallel characterization of cascade processes and the direct scale-up of results to the liter scale. With PAmCherry concentrations of 1.15 g L -1 cascades of stirred-tank reactors improved the process performance significantly compared to production processes in chemostats. In addition, an optimized fed-batch process was outperformed regarding space-time yield (149 mg L -1  h -1 ). This study implicates continuous cascade processes to be a promising alternative to fed-batch processes for microbial protein production and demonstrates that miniaturized stirred-tank reactors can reduce the timeline and costs for cascade process characterization.

Fanca deficiency reduces A/T transitions in somatic hypermutation and alters class switch recombination junctions in mouse B cells

PubMed Central

Nguyen, Thuy Vy; Riou, Lydia

2014-01-01

Fanconi anemia is a rare genetic disorder that can lead to bone marrow failure, congenital abnormalities, and increased risk for leukemia and cancer. Cells with loss-of-function mutations in the FANC pathway are characterized by chromosome fragility, altered mutability, and abnormal regulation of the nonhomologous end-joining (NHEJ) pathway. Somatic hypermutation (SHM) and immunoglobulin (Ig) class switch recombination (CSR) enable B cells to produce high-affinity antibodies of various isotypes. Both processes are initiated after the generation of dG:dU mismatches by activation-induced cytidine deaminase. Whereas SHM involves an error-prone repair process that introduces novel point mutations into the Ig gene, the mismatches generated during CSR are processed to create double-stranded breaks (DSBs) in DNA, which are then repaired by the NHEJ pathway. As several lines of evidence suggest a possible role for the FANC pathway in SHM and CSR, we analyzed both processes in B cells derived from Fanca−/− mice. Here we show that Fanca is required for the induction of transition mutations at A/T residues during SHM and that despite globally normal CSR function in splenic B cells, Fanca is required during CSR to stabilize duplexes between pairs of short microhomology regions, thereby impeding short-range recombination downstream of DSB formation. PMID:24799500

Fanca deficiency reduces A/T transitions in somatic hypermutation and alters class switch recombination junctions in mouse B cells.

PubMed

Nguyen, Thuy Vy; Riou, Lydia; Aoufouchi, Saïd; Rosselli, Filippo

2014-06-02

Fanconi anemia is a rare genetic disorder that can lead to bone marrow failure, congenital abnormalities, and increased risk for leukemia and cancer. Cells with loss-of-function mutations in the FANC pathway are characterized by chromosome fragility, altered mutability, and abnormal regulation of the nonhomologous end-joining (NHEJ) pathway. Somatic hypermutation (SHM) and immunoglobulin (Ig) class switch recombination (CSR) enable B cells to produce high-affinity antibodies of various isotypes. Both processes are initiated after the generation of dG:dU mismatches by activation-induced cytidine deaminase. Whereas SHM involves an error-prone repair process that introduces novel point mutations into the Ig gene, the mismatches generated during CSR are processed to create double-stranded breaks (DSBs) in DNA, which are then repaired by the NHEJ pathway. As several lines of evidence suggest a possible role for the FANC pathway in SHM and CSR, we analyzed both processes in B cells derived from Fanca(-/-) mice. Here we show that Fanca is required for the induction of transition mutations at A/T residues during SHM and that despite globally normal CSR function in splenic B cells, Fanca is required during CSR to stabilize duplexes between pairs of short microhomology regions, thereby impeding short-range recombination downstream of DSB formation. © 2014 Nguyen et al.

The typical RB76 recombination breakpoint of the invasive recombinant tomato yellow leaf curl virus of Morocco can be generated experimentally but is not positively selected in tomato.

PubMed

Belabess, Z; Urbino, C; Granier, M; Tahiri, A; Blenzar, A; Peterschmitt, M

2018-01-02

TYLCV-IS76 is an unusual recombinant between the highly recombinogenic tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), two Mediterranean begomoviruses (Geminiviridae). In contrast with the previously reported TYLCV/TYLCSV recombinants, it has a TYLCSV derived fragment of only 76 nucleotides, and has replaced its parental viruses in natural conditions (Morocco, Souss region). The viral population shift coincided with the deployment of the popular Ty-1 resistant tomato cultivars, and according to experimental studies, has been driven by a strong positive selection in such resistant plants. However, although Ty-1 cultivars were extensively used in Mediterranean countries, TYLCV-IS76 was not reported outside Morocco. This, in combination with its unusual recombination pattern suggests that it was generated through a rare and possibly multistep process. The potential generation of a recombination breakpoint (RB) at locus 76 (RB76) was investigated over time in 10 Ty-1 resistant and 10 nearly isogenic susceptible tomato plants co-inoculated with TYLCV and TYLCSV clones. RB76 could not be detected in the recombinant progeny using the standard PCR/sequencing approach that was previously designed to monitor the emergence of TYLCV-IS76 in Morocco. Using a more sensitive PCR test, RB76 was detected in one resistant and five susceptible plants. The results are consistent with a very low intra-plant frequency of RB76 bearing recombinants throughout the test and support the hypothesis of a rare emergence of TYLCV-IS76. More generally, RBs were more scattered in resistant than in susceptible plants and an unusual RB at position 141 (RB141) was positively selected in the resistant cultivar; interestingly, RB141 bearing recombinants were detected in resistant tomato plants from the field. Scenarios of TYLCV-IS76 pre-emergence are proposed. Copyright © 2017 Elsevier B.V. All rights reserved.